WorldWideScience

Sample records for integrative multi-dimensional genetic

  1. An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

    Directory of Open Access Journals (Sweden)

    Lockwood William W

    2010-05-01

    Full Text Available Abstract Background Genomics has substantially changed our approach to cancer research. Gene expression profiling, for example, has been utilized to delineate subtypes of cancer, and facilitated derivation of predictive and prognostic signatures. The emergence of technologies for the high resolution and genome-wide description of genetic and epigenetic features has enabled the identification of a multitude of causal DNA events in tumors. This has afforded the potential for large scale integration of genome and transcriptome data generated from a variety of technology platforms to acquire a better understanding of cancer. Results Here we show how multi-dimensional genomics data analysis would enable the deciphering of mechanisms that disrupt regulatory/signaling cascades and downstream effects. Since not all gene expression changes observed in a tumor are causal to cancer development, we demonstrate an approach based on multiple concerted disruption (MCD analysis of genes that facilitates the rational deduction of aberrant genes and pathways, which otherwise would be overlooked in single genomic dimension investigations. Conclusions Notably, this is the first comprehensive study of breast cancer cells by parallel integrative genome wide analyses of DNA copy number, LOH, and DNA methylation status to interpret changes in gene expression pattern. Our findings demonstrate the power of a multi-dimensional approach to elucidate events which would escape conventional single dimensional analysis and as such, reduce the cohort sample size for cancer gene discovery.

  2. A Generic multi-dimensional feature extraction method using multiobjective genetic programming.

    Science.gov (United States)

    Zhang, Yang; Rockett, Peter I

    2009-01-01

    In this paper, we present a generic feature extraction method for pattern classification using multiobjective genetic programming. This not only evolves the (near-)optimal set of mappings from a pattern space to a multi-dimensional decision space, but also simultaneously optimizes the dimensionality of that decision space. The presented framework evolves vector-to-vector feature extractors that maximize class separability. We demonstrate the efficacy of our approach by making statistically-founded comparisons with a wide variety of established classifier paradigms over a range of datasets and find that for most of the pairwise comparisons, our evolutionary method delivers statistically smaller misclassification errors. At very worst, our method displays no statistical difference in a few pairwise comparisons with established classifier/dataset combinations; crucially, none of the misclassification results produced by our method is worse than any comparator classifier. Although principally focused on feature extraction, feature selection is also performed as an implicit side effect; we show that both feature extraction and selection are important to the success of our technique. The presented method has the practical consequence of obviating the need to exhaustively evaluate a large family of conventional classifiers when faced with a new pattern recognition problem in order to attain a good classification accuracy.

  3. Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data.

    Science.gov (United States)

    Gong, Wuming; Koyano-Nakagawa, Naoko; Li, Tongbin; Garry, Daniel J

    2015-03-07

    -CM transitions. We report a novel method to systematically integrate multi-dimensional -omics data and reconstruct the gene regulatory networks. This method will allow one to rapidly determine the cis-modules that regulate key genes during cardiac differentiation.

  4. On generalized de Rham-Hodge complexes, the related characteristic Chern classes and some applications to integrable multi-dimensional differential systems on Riemannian manifolds

    International Nuclear Information System (INIS)

    Bogolubov, Nikolai N. Jr.; Prykarpatsky, Anatoliy K.

    2006-12-01

    The differential-geometric aspects of generalized de Rham-Hodge complexes naturally related with integrable multi-dimensional differential systems of M. Gromov type, as well as the geometric structure of Chern characteristic classes are studied. Special differential invariants of the Chern type are constructed, their importance for the integrability of multi-dimensional nonlinear differential systems on Riemannian manifolds is discussed. An example of the three-dimensional Davey-Stewartson type nonlinear strongly integrable differential system is considered, its Cartan type connection mapping and related Chern type differential invariants are analyzed. (author)

  5. Multi-dimensional optimization of a terawatt seeded tapered Free Electron Laser with a Multi-Objective Genetic Algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Juhao, E-mail: jhwu@SLAC.Stanford.EDU [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Hu, Newman [Valley Christian High School, 100 Skyway Drive, San Jose, CA 95111 (United States); Setiawan, Hananiel [The Facility for Rare Isotope Beams, Michigan State University, East Lansing, MI 48824 (United States); Huang, Xiaobiao; Raubenheimer, Tor O. [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Jiao, Yi [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Yu, George [Columbia University, New York, NY 10027 (United States); Mandlekar, Ajay [California Institute of Technology, Pasadena, CA 91125 (United States); Spampinati, Simone [Sincrotrone Trieste S.C.p.A. di interesse nazionale, Strada Statale 14-km 163,5 in AREA Science Park, 34149 Basovizza, Trieste (Italy); Fang, Kun [SLAC National Accelerator Laboratory, Menlo Park, CA 94025 (United States); Chu, Chungming [The Facility for Rare Isotope Beams, Michigan State University, East Lansing, MI 48824 (United States); Qiang, Ji [Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720 (United States)

    2017-02-21

    There is a great interest in generating high-power hard X-ray Free Electron Laser (FEL) in the terawatt (TW) level that can enable coherent diffraction imaging of complex molecules like proteins and probe fundamental high-field physics. A feasibility study of producing such X-ray pulses was carried out employing a configuration beginning with a Self-Amplified Spontaneous Emission FEL, followed by a “self-seeding” crystal monochromator generating a fully coherent seed, and finishing with a long tapered undulator where the coherent seed recombines with the electron bunch and is amplified to high power. The undulator tapering profile, the phase advance in the undulator break sections, the quadrupole focusing strength, etc. are parameters to be optimized. A Genetic Algorithm (GA) is adopted for this multi-dimensional optimization. Concrete examples are given for LINAC Coherent Light Source (LCLS) and LCLS-II-type systems. Analytical estimate is also developed to cross check the simulation and optimization results as a quick and complimentary tool.

  6. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets.

    Science.gov (United States)

    Gosline, Sara J C; Spencer, Sarah J; Ursu, Oana; Fraenkel, Ernest

    2012-11-01

    The rapid development of high throughput biotechnologies has led to an onslaught of data describing genetic perturbations and changes in mRNA and protein levels in the cell. Because each assay provides a one-dimensional snapshot of active signaling pathways, it has become desirable to perform multiple assays (e.g. mRNA expression and phospho-proteomics) to measure a single condition. However, as experiments expand to accommodate various cellular conditions, proper analysis and interpretation of these data have become more challenging. Here we introduce a novel approach called SAMNet, for Simultaneous Analysis of Multiple Networks, that is able to interpret diverse assays over multiple perturbations. The algorithm uses a constrained optimization approach to integrate mRNA expression data with upstream genes, selecting edges in the protein-protein interaction network that best explain the changes across all perturbations. The result is a putative set of protein interactions that succinctly summarizes the results from all experiments, highlighting the network elements unique to each perturbation. We evaluated SAMNet in both yeast and human datasets. The yeast dataset measured the cellular response to seven different transition metals, and the human dataset measured cellular changes in four different lung cancer models of Epithelial-Mesenchymal Transition (EMT), a crucial process in tumor metastasis. SAMNet was able to identify canonical yeast metal-processing genes unique to each commodity in the yeast dataset, as well as human genes such as β-catenin and TCF7L2/TCF4 that are required for EMT signaling but escaped detection in the mRNA and phospho-proteomic data. Moreover, SAMNet also highlighted drugs likely to modulate EMT, identifying a series of less canonical genes known to be affected by the BCR-ABL inhibitor imatinib (Gleevec), suggesting a possible influence of this drug on EMT.

  7. An integrated approach for the knowledge discovery in computer simulation models with a multi-dimensional parameter space

    Energy Technology Data Exchange (ETDEWEB)

    Khawli, Toufik Al; Eppelt, Urs; Hermanns, Torsten [RWTH Aachen University, Chair for Nonlinear Dynamics, Steinbachstr. 15, 52047 Aachen (Germany); Gebhardt, Sascha [RWTH Aachen University, Virtual Reality Group, IT Center, Seffenter Weg 23, 52074 Aachen (Germany); Kuhlen, Torsten [Forschungszentrum Jülich GmbH, Institute for Advanced Simulation (IAS), Jülich Supercomputing Centre (JSC), Wilhelm-Johnen-Straße, 52425 Jülich (Germany); Schulz, Wolfgang [Fraunhofer, ILT Laser Technology, Steinbachstr. 15, 52047 Aachen (Germany)

    2016-06-08

    In production industries, parameter identification, sensitivity analysis and multi-dimensional visualization are vital steps in the planning process for achieving optimal designs and gaining valuable information. Sensitivity analysis and visualization can help in identifying the most-influential parameters and quantify their contribution to the model output, reduce the model complexity, and enhance the understanding of the model behavior. Typically, this requires a large number of simulations, which can be both very expensive and time consuming when the simulation models are numerically complex and the number of parameter inputs increases. There are three main constituent parts in this work. The first part is to substitute the numerical, physical model by an accurate surrogate model, the so-called metamodel. The second part includes a multi-dimensional visualization approach for the visual exploration of metamodels. In the third part, the metamodel is used to provide the two global sensitivity measures: i) the Elementary Effect for screening the parameters, and ii) the variance decomposition method for calculating the Sobol indices that quantify both the main and interaction effects. The application of the proposed approach is illustrated with an industrial application with the goal of optimizing a drilling process using a Gaussian laser beam.

  8. Multi-dimensional imaging

    CERN Document Server

    Javidi, Bahram; Andres, Pedro

    2014-01-01

    Provides a broad overview of advanced multidimensional imaging systems with contributions from leading researchers in the field Multi-dimensional Imaging takes the reader from the introductory concepts through to the latest applications of these techniques. Split into 3 parts covering 3D image capture, processing, visualization and display, using 1) a Multi-View Approach and 2.) a Holographic Approach, followed by a 3rd part addressing other 3D systems approaches, applications and signal processing for advanced 3D imaging. This book describes recent developments, as well as the prospects and

  9. Efficient Hybrid Genetic Based Multi Dimensional Host Load Aware Algorithm for Scheduling and Optimization of Virtual Machines

    OpenAIRE

    Thiruvenkadam, T; Karthikeyani, V

    2014-01-01

    Mapping the virtual machines to the physical machines cluster is called the VM placement. Placing the VM in the appropriate host is necessary for ensuring the effective resource utilization and minimizing the datacenter cost as well as power. Here we present an efficient hybrid genetic based host load aware algorithm for scheduling and optimization of virtual machines in a cluster of Physical hosts. We developed the algorithm based on two different methods, first initial VM packing is done by...

  10. Multi-Dimensional Path Queries

    DEFF Research Database (Denmark)

    Bækgaard, Lars

    1998-01-01

    to create nested path structures. We present an SQL-like query language that is based on path expressions and we show how to use it to express multi-dimensional path queries that are suited for advanced data analysis in decision support environments like data warehousing environments......We present the path-relationship model that supports multi-dimensional data modeling and querying. A path-relationship database is composed of sets of paths and sets of relationships. A path is a sequence of related elements (atoms, paths, and sets of paths). A relationship is a binary path...

  11. Collaborative Visualization and Analysis of Multi-dimensional, Time-dependent and Distributed Data in the Geosciences Using the Unidata Integrated Data Viewer

    Science.gov (United States)

    Meertens, C. M.; Murray, D.; McWhirter, J.

    2004-12-01

    Over the last five years, UNIDATA has developed an extensible and flexible software framework for analyzing and visualizing geoscience data and models. The Integrated Data Viewer (IDV), initially developed for visualization and analysis of atmospheric data, has broad interdisciplinary application across the geosciences including atmospheric, ocean, and most recently, earth sciences. As part of the NSF-funded GEON Information Technology Research project, UNAVCO has enhanced the IDV to display earthquakes, GPS velocity vectors, and plate boundary strain rates. These and other geophysical parameters can be viewed simultaneously with three-dimensional seismic tomography and mantle geodynamic model results. Disparate data sets of different formats, variables, geographical projections and scales can automatically be displayed in a common projection. The IDV is efficient and fully interactive allowing the user to create and vary 2D and 3D displays with contour plots, vertical and horizontal cross-sections, plan views, 3D isosurfaces, vector plots and streamlines, as well as point data symbols or numeric values. Data probes (values and graphs) can be used to explore the details of the data and models. The IDV is a freely available Java application using Java3D and VisAD and runs on most computers. UNIDATA provides easy-to-follow instructions for download, installation and operation of the IDV. The IDV primarily uses netCDF, a self-describing binary file format, to store multi-dimensional data, related metadata, and source information. The IDV is designed to work with OPeNDAP-equipped data servers that provide real-time observations and numerical models from distributed locations. Users can capture and share screens and animations, or exchange XML "bundles" that contain the state of the visualization and embedded links to remote data files. A real-time collaborative feature allows groups of users to remotely link IDV sessions via the Internet and simultaneously view and

  12. Multi-dimensional Laplace transforms and applications

    International Nuclear Information System (INIS)

    Mughrabi, T.A.

    1988-01-01

    In this dissertation we establish new theorems for computing certain types of multidimensional Laplace transform pairs from known one-dimensional Laplace transforms. The theorems are applied to the most commonly used special functions and so we obtain many two and three dimensional Laplace transform pairs. As applications, some boundary value problems involving linear partial differential equations are solved by the use of multi-dimensional Laplace transformation. Also we establish some relations between the Laplace transformation and other integral transformation in two variables

  13. Multi-dimensional Fuzzy Euler Approximation

    Directory of Open Access Journals (Sweden)

    Yangyang Hao

    2017-05-01

    Full Text Available Multi-dimensional Fuzzy differential equations driven by multi-dimen-sional Liu process, have been intensively applied in many fields. However, we can not obtain the analytic solution of every multi-dimensional fuzzy differential equation. Then, it is necessary for us to discuss the numerical results in most situations. This paper focuses on the numerical method of multi-dimensional fuzzy differential equations. The multi-dimensional fuzzy Taylor expansion is given, based on this expansion, a numerical method which is designed for giving the solution of multi-dimensional fuzzy differential equation via multi-dimensional Euler method will be presented, and its local convergence also will be discussed.

  14. Integrated genetic analysis microsystems

    International Nuclear Information System (INIS)

    Lagally, Eric T; Mathies, Richard A

    2004-01-01

    With the completion of the Human Genome Project and the ongoing DNA sequencing of the genomes of other animals, bacteria, plants and others, a wealth of new information about the genetic composition of organisms has become available. However, as the demand for sequence information grows, so does the workload required both to generate this sequence and to use it for targeted genetic analysis. Microfabricated genetic analysis systems are well poised to assist in the collection and use of these data through increased analysis speed, lower analysis cost and higher parallelism leading to increased assay throughput. In addition, such integrated microsystems may point the way to targeted genetic experiments on single cells and in other areas that are otherwise very difficult. Concomitant with these advantages, such systems, when fully integrated, should be capable of forming portable systems for high-speed in situ analyses, enabling a new standard in disciplines such as clinical chemistry, forensics, biowarfare detection and epidemiology. This review will discuss the various technologies available for genetic analysis on the microscale, and efforts to integrate them to form fully functional robust analysis devices. (topical review)

  15. Two multi-dimensional uncertainty relations

    International Nuclear Information System (INIS)

    Skala, L; Kapsa, V

    2008-01-01

    Two multi-dimensional uncertainty relations, one related to the probability density and the other one related to the probability density current, are derived and discussed. Both relations are stronger than the usual uncertainty relations for the coordinates and momentum

  16. NLSEmagic: Nonlinear Schrödinger equation multi-dimensional Matlab-based GPU-accelerated integrators using compact high-order schemes

    Science.gov (United States)

    Caplan, R. M.

    2013-04-01

    We present a simple to use, yet powerful code package called NLSEmagic to numerically integrate the nonlinear Schrödinger equation in one, two, and three dimensions. NLSEmagic is a high-order finite-difference code package which utilizes graphic processing unit (GPU) parallel architectures. The codes running on the GPU are many times faster than their serial counterparts, and are much cheaper to run than on standard parallel clusters. The codes are developed with usability and portability in mind, and therefore are written to interface with MATLAB utilizing custom GPU-enabled C codes with the MEX-compiler interface. The packages are freely distributed, including user manuals and set-up files. Catalogue identifier: AEOJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOJ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 124453 No. of bytes in distributed program, including test data, etc.: 4728604 Distribution format: tar.gz Programming language: C, CUDA, MATLAB. Computer: PC, MAC. Operating system: Windows, MacOS, Linux. Has the code been vectorized or parallelized?: Yes. Number of processors used: Single CPU, number of GPU processors dependent on chosen GPU card (max is currently 3072 cores on GeForce GTX 690). Supplementary material: Setup guide, Installation guide. RAM: Highly dependent on dimensionality and grid size. For typical medium-large problem size in three dimensions, 4GB is sufficient. Keywords: Nonlinear Schröodinger Equation, GPU, high-order finite difference, Bose-Einstien condensates. Classification: 4.3, 7.7. Nature of problem: Integrate solutions of the time-dependent one-, two-, and three-dimensional cubic nonlinear Schrödinger equation. Solution method: The integrators utilize a fully-explicit fourth-order Runge-Kutta scheme in time

  17. Multi-Dimensional Aggregation for Temporal Data

    DEFF Research Database (Denmark)

    Böhlen, M. H.; Gamper, J.; Jensen, Christian Søndergaard

    2006-01-01

    Business Intelligence solutions, encompassing technologies such as multi-dimensional data modeling and aggregate query processing, are being applied increasingly to non-traditional data. This paper extends multi-dimensional aggregation to apply to data with associated interval values that capture...... that the data holds for each point in the interval, as well as the case where the data holds only for the entire interval, but must be adjusted to apply to sub-intervals. The paper reports on an implementation of the new operator and on an empirical study that indicates that the operator scales to large data...

  18. Multi-dimensional quasitoeplitz Markov chains

    Directory of Open Access Journals (Sweden)

    Alexander N. Dudin

    1999-01-01

    Full Text Available This paper deals with multi-dimensional quasitoeplitz Markov chains. We establish a sufficient equilibrium condition and derive a functional matrix equation for the corresponding vector-generating function, whose solution is given algorithmically. The results are demonstrated in the form of examples and applications in queues with BMAP-input, which operate in synchronous random environment.

  19. Development and assessment of multi-dimensional flow model in MARS compared with the RPI air-water experiment

    International Nuclear Information System (INIS)

    Lee, Seok Min; Lee, Un Chul; Bae, Sung Won; Chung, Bub Dong

    2004-01-01

    The Multi-Dimensional flow models in system code have been developed during the past many years. RELAP5-3D, CATHARE and TRACE has its specific multi-dimensional flow models and successfully applied it to the system safety analysis. In KAERI, also, MARS(Multi-dimensional Analysis of Reactor Safety) code was developed by integrating RELAP5/MOD3 code and COBRA-TF code. Even though COBRA-TF module can analyze three-dimensional flow models, it has a limitation to apply 3D shear stress dominant phenomena or cylindrical geometry. Therefore, Multi-dimensional analysis models are newly developed by implementing three-dimensional momentum flux and diffusion terms. The multi-dimensional model has been assessed compared with multi-dimensional conceptual problems and CFD code results. Although the assessment results were reasonable, the multi-dimensional model has not been validated to two-phase flow using experimental data. In this paper, the multi-dimensional air-water two-phase flow experiment was simulated and analyzed

  20. Transport stochastic multi-dimensional media

    International Nuclear Information System (INIS)

    Haran, O.; Shvarts, D.

    1996-01-01

    Many physical phenomena evolve according to known deterministic rules, but in a stochastic media in which the composition changes in space and time. Examples to such phenomena are heat transfer in turbulent atmosphere with non uniform diffraction coefficients, neutron transfer in boiling coolant of a nuclear reactor and radiation transfer through concrete shields. The results of measurements conducted upon such a media are stochastic by nature, and depend on the specific realization of the media. In the last decade there has been a considerable efforts to describe linear particle transport in one dimensional stochastic media composed of several immiscible materials. However, transport in two or three dimensional stochastic media has been rarely addressed. The important effect in multi-dimensional transport that does not appear in one dimension is the ability to bypass obstacles. The current work is an attempt to quantify this effect. (authors)

  1. Transport stochastic multi-dimensional media

    Energy Technology Data Exchange (ETDEWEB)

    Haran, O; Shvarts, D [Israel Atomic Energy Commission, Beersheba (Israel). Nuclear Research Center-Negev; Thiberger, R [Ben-Gurion Univ. of the Negev, Beersheba (Israel)

    1996-12-01

    Many physical phenomena evolve according to known deterministic rules, but in a stochastic media in which the composition changes in space and time. Examples to such phenomena are heat transfer in turbulent atmosphere with non uniform diffraction coefficients, neutron transfer in boiling coolant of a nuclear reactor and radiation transfer through concrete shields. The results of measurements conducted upon such a media are stochastic by nature, and depend on the specific realization of the media. In the last decade there has been a considerable efforts to describe linear particle transport in one dimensional stochastic media composed of several immiscible materials. However, transport in two or three dimensional stochastic media has been rarely addressed. The important effect in multi-dimensional transport that does not appear in one dimension is the ability to bypass obstacles. The current work is an attempt to quantify this effect. (authors).

  2. The multi-dimensional roles of astrocytes in ALS.

    Science.gov (United States)

    Yamanaka, Koji; Komine, Okiru

    2018-01-01

    Despite significant progress in understanding the molecular and genetic aspects of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease characterized by the progressive loss of motor neurons, the precise and comprehensive pathomechanisms remain largely unknown. In addition to motor neuron involvement, recent studies using cellular and animal models of ALS indicate that there is a complex interplay between motor neurons and neighboring non-neuronal cells, such as astrocytes, in non-cell autonomous neurodegeneration. Astrocytes are key homeostatic cells that play numerous supportive roles in maintaining the brain environment. In neurodegenerative diseases such as ALS, astrocytes change their shape and molecular expression patterns and are referred to as reactive or activated astrocytes. Reactive astrocytes in ALS lose their beneficial functions and gain detrimental roles. In addition, interactions between motor neurons and astrocytes are impaired in ALS. In this review, we summarize growing evidence that astrocytes are critically involved in the survival and demise of motor neurons through several key molecules and cascades in astrocytes in both sporadic and inherited ALS. These observations strongly suggest that astrocytes have multi-dimensional roles in disease and are a viable therapeutic target for ALS. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Multi-dimensional analysis of the ECC behavior in the UPI plant Kori Unit 1

    International Nuclear Information System (INIS)

    Bae, Sungwon; Chung, Bub-Dong; Bang, Young Seok

    2008-01-01

    by the ratio of the integrated ECCS water flow to the integrated two hot leg flows. The peak cladding temperature is predicted as 1236.32 K and the location is 7 ft from the bottom of fuel at the inner radial region of reactor core nodalization. The peripheral location is the opposite against the active ECCS. It can be concluded that the multi-dimensional analysis about the ECCS behaviors in the upper plenum space during the LBLOCA of Kori Unit 1 shows a meaningful agreement in the phenomenological validity. (author)

  4. Multi-Dimensional Customer Data Analysis in Online Auctions

    Institute of Scientific and Technical Information of China (English)

    LAO Guoling; XIONG Kuan; QIN Zheng

    2007-01-01

    In this paper, we designed a customer-centered data warehouse system with five subjects: listing, bidding, transaction,accounts, and customer contact based on the business process of online auction companies. For each subject, we analyzed its fact indexes and dimensions. Then take transaction subject as example,analyzed the data warehouse model in detail, and got the multi-dimensional analysis structure of transaction subject. At last, using data mining to do customer segmentation, we divided customers into four types: impulse customer, prudent customer, potential customer, and ordinary customer. By the result of multi-dimensional customer data analysis, online auction companies can do more target marketing and increase customer loyalty.

  5. Multi-dimensional discovery of biomarker and phenotype complexes

    Directory of Open Access Journals (Sweden)

    Huang Kun

    2010-10-01

    Full Text Available Abstract Background Given the rapid growth of translational research and personalized healthcare paradigms, the ability to relate and reason upon networks of bio-molecular and phenotypic variables at various levels of granularity in order to diagnose, stage and plan treatments for disease states is highly desirable. Numerous techniques exist that can be used to develop networks of co-expressed or otherwise related genes and clinical features. Such techniques can also be used to create formalized knowledge collections based upon the information incumbent to ontologies and domain literature. However, reports of integrative approaches that bridge such networks to create systems-level models of disease or wellness are notably lacking in the contemporary literature. Results In response to the preceding gap in knowledge and practice, we report upon a prototypical series of experiments that utilize multi-modal approaches to network induction. These experiments are intended to elicit meaningful and significant biomarker-phenotype complexes spanning multiple levels of granularity. This work has been performed in the experimental context of a large-scale clinical and basic science data repository maintained by the National Cancer Institute (NCI funded Chronic Lymphocytic Leukemia Research Consortium. Conclusions Our results indicate that it is computationally tractable to link orthogonal networks of genes, clinical features, and conceptual knowledge to create multi-dimensional models of interrelated biomarkers and phenotypes. Further, our results indicate that such systems-level models contain interrelated bio-molecular and clinical markers capable of supporting hypothesis discovery and testing. Based on such findings, we propose a conceptual model intended to inform the cross-linkage of the results of such methods. This model has as its aim the identification of novel and knowledge-anchored biomarker-phenotype complexes.

  6. Decay rate in a multi-dimensional fission problem

    Energy Technology Data Exchange (ETDEWEB)

    Brink, D M; Canto, L F

    1986-06-01

    The multi-dimensional diffusion approach of Zhang Jing Shang and Weidenmueller (1983 Phys. Rev. C28, 2190) is used to study a simplified model for induced fission. In this model it is shown that the coupling of the fission coordinate to the intrinsic degrees of freedom is equivalent to an extra friction and a mass correction in the corresponding one-dimensional problem.

  7. Image matrix processor for fast multi-dimensional computations

    Science.gov (United States)

    Roberson, George P.; Skeate, Michael F.

    1996-01-01

    An apparatus for multi-dimensional computation which comprises a computation engine, including a plurality of processing modules. The processing modules are configured in parallel and compute respective contributions to a computed multi-dimensional image of respective two dimensional data sets. A high-speed, parallel access storage system is provided which stores the multi-dimensional data sets, and a switching circuit routes the data among the processing modules in the computation engine and the storage system. A data acquisition port receives the two dimensional data sets representing projections through an image, for reconstruction algorithms such as encountered in computerized tomography. The processing modules include a programmable local host, by which they may be configured to execute a plurality of different types of multi-dimensional algorithms. The processing modules thus include an image manipulation processor, which includes a source cache, a target cache, a coefficient table, and control software for executing image transformation routines using data in the source cache and the coefficient table and loading resulting data in the target cache. The local host processor operates to load the source cache with a two dimensional data set, loads the coefficient table, and transfers resulting data out of the target cache to the storage system, or to another destination.

  8. Development and Validation of Multi-Dimensional Personality ...

    African Journals Online (AJOL)

    This study was carried out to establish the scientific processes for the development and validation of Multi-dimensional Personality Inventory (MPI). The process of development and validation occurred in three phases with five components of Agreeableness, Conscientiousness, Emotional stability, Extroversion, and ...

  9. Integrated analysis of genetic data with R

    Directory of Open Access Journals (Sweden)

    Zhao Jing

    2006-01-01

    Full Text Available Abstract Genetic data are now widely available. There is, however, an apparent lack of concerted effort to produce software systems for statistical analysis of genetic data compared with other fields of statistics. It is often a tremendous task for end-users to tailor them for particular data, especially when genetic data are analysed in conjunction with a large number of covariates. Here, R http://www.r-project.org, a free, flexible and platform-independent environment for statistical modelling and graphics is explored as an integrated system for genetic data analysis. An overview of some packages currently available for analysis of genetic data is given. This is followed by examples of package development and practical applications. With clear advantages in data management, graphics, statistical analysis, programming, internet capability and use of available codes, it is a feasible, although challenging, task to develop it into an integrated platform for genetic analysis; this will require the joint efforts of many researchers.

  10. Balanced sensitivity functions for tuning multi-dimensional Bayesian network classifiers

    NARCIS (Netherlands)

    Bolt, J.H.; van der Gaag, L.C.

    Multi-dimensional Bayesian network classifiers are Bayesian networks of restricted topological structure, which are tailored to classifying data instances into multiple dimensions. Like more traditional classifiers, multi-dimensional classifiers are typically learned from data and may include

  11. An integrated system for genetic analysis

    Directory of Open Access Journals (Sweden)

    Duan Xiao

    2006-04-01

    Full Text Available Abstract Background Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. Description We have developed an Integrated Genotyping System (IGS to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. Conclusion IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

  12. Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-dimensional Scientific Data

    International Nuclear Information System (INIS)

    Rubel, Oliver; Ahern, Sean; Bethel, E. Wes; Biggin, Mark D.; Childs, Hank; Cormier-Michel, Estelle; DePace, Angela; Eisen, Michael B.; Fowlkes, Charless C.; Geddes, Cameron G.R.; Hagen, Hans; Hamann, Bernd; Huang, Min-Yu; Keranen, Soile V.E.; Knowles, David W.; Hendriks, Chris L. Luengo; Malik, Jitendra; Meredith, Jeremy; Messmer, Peter; Prabhat; Ushizima, Daniela; Weber, Gunther H.; Wu, Kesheng

    2010-01-01

    Knowledge discovery from large and complex scientific data is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the growing number of data dimensions and data objects presents tremendous challenges for effective data analysis and data exploration methods and tools. The combination and close integration of methods from scientific visualization, information visualization, automated data analysis, and other enabling technologies 'such as efficient data management' supports knowledge discovery from multi-dimensional scientific data. This paper surveys two distinct applications in developmental biology and accelerator physics, illustrating the effectiveness of the described approach.

  13. Multi-dimensional Bin Packing Problems with Guillotine Constraints

    DEFF Research Database (Denmark)

    Amossen, Rasmus Resen; Pisinger, David

    2010-01-01

    The problem addressed in this paper is the decision problem of determining if a set of multi-dimensional rectangular boxes can be orthogonally packed into a rectangular bin while satisfying the requirement that the packing should be guillotine cuttable. That is, there should exist a series of face...... parallel straight cuts that can recursively cut the bin into pieces so that each piece contains a box and no box has been intersected by a cut. The unrestricted problem is known to be NP-hard. In this paper we present a generalization of a constructive algorithm for the multi-dimensional bin packing...... problem, with and without the guillotine constraint, based on constraint programming....

  14. Multi-dimensional Code Development for Safety Analysis of LMR

    International Nuclear Information System (INIS)

    Ha, K. S.; Jeong, H. Y.; Kwon, Y. M.; Lee, Y. B.

    2006-08-01

    A liquid metal reactor loaded a metallic fuel has the inherent safety mechanism due to the several negative reactivity feedback. Although this feature demonstrated through experiments in the EBR-II, any of the computer programs until now did not exactly analyze it because of the complexity of the reactivity feedback mechanism. A multi-dimensional detail program was developed through the International Nuclear Energy Research Initiative(INERI) from 2003 to 2005. This report includes the numerical coupling the multi-dimensional program and SSC-K code which is used to the safety analysis of liquid metal reactors in KAERI. The coupled code has been proved by comparing the analysis results using the code with the results using SAS-SASSYS code of ANL for the UTOP, ULOF, and ULOHS applied to the safety analysis for KALIMER-150

  15. Peer Pressure in Multi-Dimensional Work Tasks

    OpenAIRE

    Felix Ebeling; Gerlinde Fellner; Johannes Wahlig

    2012-01-01

    We study the influence of peer pressure in multi-dimensional work tasks theoretically and in a controlled laboratory experiment. Thereby, workers face peer pressure in only one work dimension. We find that effort provision increases in the dimension where peer pressure is introduced. However, not all of this increase translates into a productivity gain, since the effect is partly offset by a decrease of effort in the work dimension without peer pressure. Furthermore, this tradeoff is stronger...

  16. Multi-dimensional virtual system introduced to enhance canonical sampling

    Science.gov (United States)

    Higo, Junichi; Kasahara, Kota; Nakamura, Haruki

    2017-10-01

    When an important process of a molecular system occurs via a combination of two or more rare events, which occur almost independently to one another, computational sampling for the important process is difficult. Here, to sample such a process effectively, we developed a new method, named the "multi-dimensional Virtual-system coupled Monte Carlo (multi-dimensional-VcMC)" method, where the system interacts with a virtual system expressed by two or more virtual coordinates. Each virtual coordinate controls sampling along a reaction coordinate. By setting multiple reaction coordinates to be related to the corresponding rare events, sampling of the important process can be enhanced. An advantage of multi-dimensional-VcMC is its simplicity: Namely, the conformation moves widely in the multi-dimensional reaction coordinate space without knowledge of canonical distribution functions of the system. To examine the effectiveness of the algorithm, we introduced a toy model where two molecules (receptor and its ligand) bind and unbind to each other. The receptor has a deep binding pocket, to which the ligand enters for binding. Furthermore, a gate is set at the entrance of the pocket, and the gate is usually closed. Thus, the molecular binding takes place via the two events: ligand approach to the pocket and gate opening. In two-dimensional (2D)-VcMC, the two molecules exhibited repeated binding and unbinding, and an equilibrated distribution was obtained as expected. A conventional canonical simulation, which was 200 times longer than 2D-VcMC, failed in sampling the binding/unbinding effectively. The current method is applicable to various biological systems.

  17. Code Coupling for Multi-Dimensional Core Transient Analysis

    International Nuclear Information System (INIS)

    Park, Jin-Woo; Park, Guen-Tae; Park, Min-Ho; Ryu, Seok-Hee; Um, Kil-Sup; Lee Jae-Il

    2015-01-01

    After the CEA ejection, the nuclear power of the reactor dramatically increases in an exponential behavior until the Doppler effect becomes important and turns the reactivity balance and power down to lower levels. Although this happens in a very short period of time, only few seconds, the energy generated can be very significant and cause fuel failures. The current safety analysis methodology which is based on overly conservative assumptions with the point kinetics model results in quite adverse consequences. Thus, KEPCO Nuclear Fuel(KNF) is developing the multi-dimensional safety analysis methodology to mitigate the consequences of the single CEA ejection accident. For this purpose, three-dimensional core neutron kinetics code ASTRA, sub-channel analysis code THALES, and fuel performance analysis code FROST, which have transient calculation performance, were coupled using message passing interface (MPI). This paper presents the methodology used for code coupling and the preliminary simulation results with the coupled code system (CHASER). Multi-dimensional core transient analysis code system, CHASER, has been developed and it was applied to simulate a single CEA ejection accident. CHASER gave a good prediction of multi-dimensional core transient behaviors during transient. In the near future, the multi-dimension CEA ejection analysis methodology using CHASER is planning to be developed. CHASER is expected to be a useful tool to gain safety margin for reactivity initiated accidents (RIAs), such as a single CEA ejection accident

  18. Code Coupling for Multi-Dimensional Core Transient Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jin-Woo; Park, Guen-Tae; Park, Min-Ho; Ryu, Seok-Hee; Um, Kil-Sup; Lee Jae-Il [KEPCO NF, Daejeon (Korea, Republic of)

    2015-05-15

    After the CEA ejection, the nuclear power of the reactor dramatically increases in an exponential behavior until the Doppler effect becomes important and turns the reactivity balance and power down to lower levels. Although this happens in a very short period of time, only few seconds, the energy generated can be very significant and cause fuel failures. The current safety analysis methodology which is based on overly conservative assumptions with the point kinetics model results in quite adverse consequences. Thus, KEPCO Nuclear Fuel(KNF) is developing the multi-dimensional safety analysis methodology to mitigate the consequences of the single CEA ejection accident. For this purpose, three-dimensional core neutron kinetics code ASTRA, sub-channel analysis code THALES, and fuel performance analysis code FROST, which have transient calculation performance, were coupled using message passing interface (MPI). This paper presents the methodology used for code coupling and the preliminary simulation results with the coupled code system (CHASER). Multi-dimensional core transient analysis code system, CHASER, has been developed and it was applied to simulate a single CEA ejection accident. CHASER gave a good prediction of multi-dimensional core transient behaviors during transient. In the near future, the multi-dimension CEA ejection analysis methodology using CHASER is planning to be developed. CHASER is expected to be a useful tool to gain safety margin for reactivity initiated accidents (RIAs), such as a single CEA ejection accident.

  19. The 'thousand words' problem: Summarizing multi-dimensional data

    International Nuclear Information System (INIS)

    Scott, David M.

    2011-01-01

    Research highlights: → Sophisticated process sensors produce large multi-dimensional data sets. → Plant control systems cannot handle images or large amounts of data. → Various techniques reduce the dimensionality, extracting information from raw data. → Simple 1D and 2D methods can often be extended to 3D and 4D applications. - Abstract: An inherent difficulty in the application of multi-dimensional sensing to process monitoring and control is the extraction and interpretation of useful information. Ultimately the measured data must be collapsed into a relatively small number of values that capture the salient characteristics of the process. Although multiple dimensions are frequently necessary to isolate a particular physical attribute (such as the distribution of a particular chemical species in a reactor), plant control systems are not equipped to use such data directly. The production of a multi-dimensional data set (often displayed as an image) is not the final step of the measurement process, because information must still be extracted from the raw data. In the metaphor of one picture being equal to a thousand words, the problem becomes one of paraphrasing a lengthy description of the image with one or two well-chosen words. Various approaches to solving this problem are discussed using examples from the fields of particle characterization, image processing, and process tomography.

  20. Assessing Extinction Risk: Integrating Genetic Information

    Directory of Open Access Journals (Sweden)

    Jason Dunham

    1999-06-01

    Full Text Available Risks of population extinction have been estimated using a variety of methods incorporating information from different spatial and temporal scales. We briefly consider how several broad classes of extinction risk assessments, including population viability analysis, incidence functions, and ranking methods integrate information on different temporal and spatial scales. In many circumstances, data from surveys of neutral genetic variability within, and among, populations can provide information useful for assessing extinction risk. Patterns of genetic variability resulting from past and present ecological and demographic events, can indicate risks of extinction that are otherwise difficult to infer from ecological and demographic analyses alone. We provide examples of how patterns of neutral genetic variability, both within, and among populations, can be used to corroborate and complement extinction risk assessments.

  1. A multi-dimensional sampling method for locating small scatterers

    International Nuclear Information System (INIS)

    Song, Rencheng; Zhong, Yu; Chen, Xudong

    2012-01-01

    A multiple signal classification (MUSIC)-like multi-dimensional sampling method (MDSM) is introduced to locate small three-dimensional scatterers using electromagnetic waves. The indicator is built with the most stable part of signal subspace of the multi-static response matrix on a set of combinatorial sampling nodes inside the domain of interest. It has two main advantages compared to the conventional MUSIC methods. First, the MDSM is more robust against noise. Second, it can work with a single incidence even for multi-scatterers. Numerical simulations are presented to show the good performance of the proposed method. (paper)

  2. Multi-dimensional cubic interpolation for ICF hydrodynamics simulation

    International Nuclear Information System (INIS)

    Aoki, Takayuki; Yabe, Takashi.

    1991-04-01

    A new interpolation method is proposed to solve the multi-dimensional hyperbolic equations which appear in describing the hydrodynamics of inertial confinement fusion (ICF) implosion. The advection phase of the cubic-interpolated pseudo-particle (CIP) is greatly improved, by assuming the continuities of the second and the third spatial derivatives in addition to the physical value and the first derivative. These derivatives are derived from the given physical equation. In order to evaluate the new method, Zalesak's example is tested, and we obtain successfully good results. (author)

  3. Multi-dimensional beam emittance and β-functions

    International Nuclear Information System (INIS)

    Buon, J.

    1993-05-01

    The concept of r.m.s. emittance is extended to the case of several degrees of freedom that are coupled. That multi-dimensional emittance is lower than the product of the emittances attached to each degree of freedom, but is conserved in a linear motion. An envelope-hyperellipsoid is introduced to define the β-functions of the beam envelope. On the contrary of an one-degree of freedom motion, it is emphasized that these envelope functions differ from the amplitude functions of the normal modes of motion as a result of the difference between the Liouville and Lagrange invariants. (author) 4 refs

  4. Multi-dimensional technology-enabled social learning approach

    DEFF Research Database (Denmark)

    Petreski, Hristijan; Tsekeridou, Sofia; Prasad, Neeli R.

    2013-01-01

    ’t respond to this systemic and structural changes and/or challenges and retains its status quo than it is jeopardizing its own existence or the existence of the education, as we know it. This paper aims to precede one step further by proposing a multi-dimensional approach for technology-enabled social...... in learning while socializing within their learning communities. However, their “educational” usage is still limited to facilitation of online learning communities and to collaborative authoring of learning material complementary to existing formal (e-) learning services. If the educational system doesn...

  5. Quantifying multi-dimensional attributes of human activities at various geographic scales based on smartphone tracking.

    Science.gov (United States)

    Zhou, Xiaolu; Li, Dongying

    2018-05-09

    Advancement in location-aware technologies, and information and communication technology in the past decades has furthered our knowledge of the interaction between human activities and the built environment. An increasing number of studies have collected data regarding individual activities to better understand how the environment shapes human behavior. Despite this growing interest, some challenges exist in collecting and processing individual's activity data, e.g., capturing people's precise environmental contexts and analyzing data at multiple spatial scales. In this study, we propose and implement an innovative system that integrates smartphone-based step tracking with an app and the sequential tile scan techniques to collect and process activity data. We apply the OpenStreetMap tile system to aggregate positioning points at various scales. We also propose duration, step and probability surfaces to quantify the multi-dimensional attributes of activities. Results show that, by running the app in the background, smartphones can measure multi-dimensional attributes of human activities, including space, duration, step, and location uncertainty at various spatial scales. By coordinating Global Positioning System (GPS) sensor with accelerometer sensor, this app can save battery which otherwise would be drained by GPS sensor quickly. Based on a test dataset, we were able to detect the recreational center and sports center as the space where the user was most active, among other places visited. The methods provide techniques to address key issues in analyzing human activity data. The system can support future studies on behavioral and health consequences related to individual's environmental exposure.

  6. Multi-Dimensional Damage Detection for Surfaces and Structures

    Science.gov (United States)

    Williams, Martha; Lewis, Mark; Roberson, Luke; Medelius, Pedro; Gibson, Tracy; Parks, Steen; Snyder, Sarah

    2013-01-01

    Current designs for inflatable or semi-rigidized structures for habitats and space applications use a multiple-layer construction, alternating thin layers with thicker, stronger layers, which produces a layered composite structure that is much better at resisting damage. Even though such composite structures or layered systems are robust, they can still be susceptible to penetration damage. The ability to detect damage to surfaces of inflatable or semi-rigid habitat structures is of great interest to NASA. Damage caused by impacts of foreign objects such as micrometeorites can rupture the shell of these structures, causing loss of critical hardware and/or the life of the crew. While not all impacts will have a catastrophic result, it will be very important to identify and locate areas of the exterior shell that have been damaged by impacts so that repairs (or other provisions) can be made to reduce the probability of shell wall rupture. This disclosure describes a system that will provide real-time data regarding the health of the inflatable shell or rigidized structures, and information related to the location and depth of impact damage. The innovation described here is a method of determining the size, location, and direction of damage in a multilayered structure. In the multi-dimensional damage detection system, layers of two-dimensional thin film detection layers are used to form a layered composite, with non-detection layers separating the detection layers. The non-detection layers may be either thicker or thinner than the detection layers. The thin-film damage detection layers are thin films of materials with a conductive grid or striped pattern. The conductive pattern may be applied by several methods, including printing, plating, sputtering, photolithography, and etching, and can include as many detection layers that are necessary for the structure construction or to afford the detection detail level required. The damage is detected using a detector or

  7. Analysis of multi-dimensional and countercurrent effects in a BWR loss-of-coolant accident

    International Nuclear Information System (INIS)

    Shiralkar, B.S.; Dix, G.E.; Alamgir, M.

    1989-01-01

    The presence of parallel enclosed channels in a BWR provides opportunities for multiple flow regimes in co-current and countercurrent flow under Loss-of-Coolant Accident (LOCA) conditions. To address and understand these phenomena, an integrated experimental and analytical study has been conducted. The primary experimental facility was the Steam Sector Test Facility (SSTF) which simulated a full scale 30deg sector of a BWR/6 reactor vessel. Both steady-state separate effects tests and integral transients with vessel blowdown and refill were performed. The present of multi-dimensional and parallel channel effects was found to be very beneficial to BWR LOCA performance. The best estimate TRAC-BWR computer code was extended as part of this study by incorporation of a phenomenological upper plenum mixing model. TRAC-BWR was applied to the analysis of these full scale experiments. Excellent predictions of phenomena and experimental trends were achieved. (orig.)

  8. Multi-dimensional diagnostics of high power ion beams by Arrayed Pinhole Camera System

    International Nuclear Information System (INIS)

    Yasuike, K.; Miyamoto, S.; Shirai, N.; Akiba, T.; Nakai, S.; Imasaki, K.; Yamanaka, C.

    1993-01-01

    The authors developed multi-dimensional beam diagnostics system (with spatially and time resolution). They used newly developed Arrayed Pinhole Camera (APC) for this diagnosis. The APC can get spatial distribution of divergence and flux density. They use two types of particle detectors in this study. The one is CR-39 can get time integrated images. The other one is gated Micro-Channel-Plate (MCP) with CCD camera. It enables time resolving diagnostics. The diagnostics systems have resolution better than 10mrad divergence, 0.5mm spatial resolution on the objects respectively. The time resolving system has 10ns time resolution. The experiments are performed on Reiden-IV and Reiden-SHVS induction linac. The authors get time integrated divergence distributions on Reiden-IV proton beam. They also get time resolved image on Reiden-SHVS

  9. Multi-dimensional medical images compressed and filtered with wavelets

    International Nuclear Information System (INIS)

    Boyen, H.; Reeth, F. van; Flerackers, E.

    2002-01-01

    Full text: Using the standard wavelet decomposition methods, multi-dimensional medical images can be compressed and filtered by repeating the wavelet-algorithm on 1D-signals in an extra loop per extra dimension. In the non-standard decomposition for multi-dimensional images the areas that must be zero-filled in case of band- or notch-filters are more complex than geometric areas such as rectangles or cubes. Adding an additional dimension in this algorithm until 4D (e.g. a 3D beating heart) increases the geometric complexity of those areas even more. The aim of our study was to calculate the boundaries of the formed complex geometric areas, so we can use the faster non-standard decomposition to compress and filter multi-dimensional medical images. Because a lot of 3D medical images taken by PET- or SPECT-cameras have only a few layers in the Z-dimension and compressing images in a dimension with a few voxels is usually not worthwhile, we provided a solution in which one can choose which dimensions will be compressed or filtered. With the proposal of non-standard decomposition on Daubechies' wavelets D2 to D20 by Steven Gollmer in 1992, 1D data can be compressed and filtered. Each additional level works only on the smoothed data, so the transformation-time halves per extra level. Zero-filling a well-defined area alter the wavelet-transform and then performing the inverse transform will do the filtering. To be capable to compress and filter up to 4D-Images with the faster non-standard wavelet decomposition method, we have investigated a new method for calculating the boundaries of the areas which must be zero-filled in case of filtering. This is especially true for band- and notch filtering. Contrary to the standard decomposition method, the areas are no longer rectangles in 2D or cubes in 3D or a row of cubes in 4D: they are rectangles expanded with a half-sized rectangle in the other direction for 2D, cubes expanded with half cubes in one and quarter cubes in the

  10. Device for multi-dimensional γ-γ-coincidence study

    International Nuclear Information System (INIS)

    Gruzinova, T.M.; Erokhina, K.I.; Kutuzov, V.I.; Lemberg, I.Kh.; Petrov, S.A.; Revenko, V.S.; Senin, A.T.; Chugunov, I.N.; Shishlinov, V.M.

    1977-01-01

    A device for studying multi-dimensional γ-γ coincidences is described which operates on-line with the BESM-4 computer. The device comprises Ge(Li) detectors, analog-to-digital converters, shaper discriminators and fast amplifiers. To control the device operation as a whole and to elaborate necessary commands, an information distributor has been developed. The following specific features of the device operation are noted: the device may operate both in the regime of recording spectra of direct γ radiation in the block memory of multi-channel analyzer, and in the regime of data transfer to the computer memory; the device performs registration of coincidences; it transfers information to the computer which has a channel of direct access to the memory. The procedure of data processing is considered, the data being recorded on a magnetic tape. Partial spectra obtained are in a good agreement with data obtained elsewhere

  11. Benchmarking multi-dimensional large strain consolidation analyses

    International Nuclear Information System (INIS)

    Priestley, D.; Fredlund, M.D.; Van Zyl, D.

    2010-01-01

    Analyzing the consolidation of tailings slurries and dredged fills requires a more extensive formulation than is used for common (small strain) consolidation problems. Large strain consolidation theories have traditionally been limited to 1-D formulations. SoilVision Systems has developed the capacity to analyze large strain consolidation problems in 2 and 3-D. The benchmarking of such formulations is not a trivial task. This paper presents several examples of modeling large strain consolidation in the beta versions of the new software. These examples were taken from the literature and were used to benchmark the large strain formulation used by the new software. The benchmarks reported here are: a comparison to the consolidation software application CONDES0, Townsend's Scenario B and a multi-dimensional analysis of long-term column tests performed on oil sands tailings. All three of these benchmarks were attained using the SVOffice suite. (author)

  12. A Multi-Dimensional Classification Model for Scientific Workflow Characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Lavanya; Plale, Beth

    2010-04-05

    Workflows have been used to model repeatable tasks or operations in manufacturing, business process, and software. In recent years, workflows are increasingly used for orchestration of science discovery tasks that use distributed resources and web services environments through resource models such as grid and cloud computing. Workflows have disparate re uirements and constraints that affects how they might be managed in distributed environments. In this paper, we present a multi-dimensional classification model illustrated by workflow examples obtained through a survey of scientists from different domains including bioinformatics and biomedical, weather and ocean modeling, astronomy detailing their data and computational requirements. The survey results and classification model contribute to the high level understandingof scientific workflows.

  13. Anonymous voting for multi-dimensional CV quantum system

    International Nuclear Information System (INIS)

    Shi Rong-Hua; Xiao Yi; Shi Jin-Jing; Guo Ying; Lee, Moon-Ho

    2016-01-01

    We investigate the design of anonymous voting protocols, CV-based binary-valued ballot and CV-based multi-valued ballot with continuous variables (CV) in a multi-dimensional quantum cryptosystem to ensure the security of voting procedure and data privacy. The quantum entangled states are employed in the continuous variable quantum system to carry the voting information and assist information transmission, which takes the advantage of the GHZ-like states in terms of improving the utilization of quantum states by decreasing the number of required quantum states. It provides a potential approach to achieve the efficient quantum anonymous voting with high transmission security, especially in large-scale votes. (paper)

  14. Fast multi-dimensional NMR by minimal sampling

    Science.gov (United States)

    Kupče, Ēriks; Freeman, Ray

    2008-03-01

    A new scheme is proposed for very fast acquisition of three-dimensional NMR spectra based on minimal sampling, instead of the customary step-wise exploration of all of evolution space. The method relies on prior experiments to determine accurate values for the evolving frequencies and intensities from the two-dimensional 'first planes' recorded by setting t1 = 0 or t2 = 0. With this prior knowledge, the entire three-dimensional spectrum can be reconstructed by an additional measurement of the response at a single location (t1∗,t2∗) where t1∗ and t2∗ are fixed values of the evolution times. A key feature is the ability to resolve problems of overlap in the acquisition dimension. Applied to a small protein, agitoxin, the three-dimensional HNCO spectrum is obtained 35 times faster than systematic Cartesian sampling of the evolution domain. The extension to multi-dimensional spectroscopy is outlined.

  15. Advanced concepts in multi-dimensional radiation detection and imaging

    International Nuclear Information System (INIS)

    Vetter, Kai; Barnowski, Ross; Pavlovsky, Ryan; Haefner, Andy; Torii, Tatsuo; Shikaze, Yoshiaki; Sanada, Yukihisa

    2016-01-01

    Recent developments in the detector fabrication, signal readout, and data processing enable new concepts in radiation detection that are relevant for applications ranging from fundamental physics to medicine as well as nuclear security and safety. We present recent progress in multi-dimensional radiation detection and imaging in the Berkeley Applied Nuclear Physics program. It is based on the ability to reconstruct scenes in three dimensions and fuse it with gamma-ray image information. We are using the High-Efficiency Multimode Imager HEMI in its Compton imaging mode and combining it with contextual sensors such as the Microsoft Kinect or visual cameras. This new concept of volumetric imaging or scene data fusion provides unprecedented capabilities in radiation detection and imaging relevant for the detection and mapping of radiological and nuclear materials. This concept brings us one step closer to the seeing the world with gamma-ray eyes. (author)

  16. MEASURING PERFORMANCE IN ORGANIZATIONS FROM MULTI-DIMENSIONAL PERSPECTIVE

    Directory of Open Access Journals (Sweden)

    ȘTEFĂNESCU CRISTIAN

    2017-08-01

    Full Text Available In turbulent financial and economic present conditions a major challenge for the general management of organizations and in particular for the strategic human resources management is to establish a clear, coherent and consistent framework in terms of measuring organizational performance and economic efficiency. This paper aims to conduct an exploratory research of literature concerning measuring organizational performance. Based on the results of research the paper proposes a multi-dimensional model for measuring organizational performance providing a mechanism that will allow quantification of performance based on selected criteria. The model will attempt to eliminate inconsistencies and incongruities of organizational effectiveness models developed by specialists from organization theory area, performance measurement models developed by specialists from accounting management area and models of measuring the efficiency and effectiveness developed by specialists from strategic management and entrepreneurship areas.

  17. Multi-dimensional knowledge translation: enabling health informatics capacity audits using patient journey models.

    Science.gov (United States)

    Catley, Christina; McGregor, Carolyn; Percival, Jennifer; Curry, Joanne; James, Andrew

    2008-01-01

    This paper presents a multi-dimensional approach to knowledge translation, enabling results obtained from a survey evaluating the uptake of Information Technology within Neonatal Intensive Care Units to be translated into knowledge, in the form of health informatics capacity audits. Survey data, having multiple roles, patient care scenarios, levels, and hospitals, is translated using a structured data modeling approach, into patient journey models. The data model is defined such that users can develop queries to generate patient journey models based on a pre-defined Patient Journey Model architecture (PaJMa). PaJMa models are then analyzed to build capacity audits. Capacity audits offer a sophisticated view of health informatics usage, providing not only details of what IT solutions a hospital utilizes, but also answering the questions: when, how and why, by determining when the IT solutions are integrated into the patient journey, how they support the patient information flow, and why they improve the patient journey.

  18. An exploration study to find important factors influencing on multi-dimensional organizational culture

    Directory of Open Access Journals (Sweden)

    Naser Azad

    2013-08-01

    Full Text Available This paper presents an empirical investigation to find important factors influencing multi-dimensional organizational culture. The proposed study designs a questionnaire in Likert scale consists of 21 questions, distributes it among 300 people who worked for different business units and collects 283 filled ones. Cronbach alpha is calculated as 0.799. In addition, Kaiser-Meyer-Olkin Measure of Sampling Adequacy and Approx. Chi-Square are 0.821 and 1395.74, respectively. The study has implemented principal component analysis and the results have indicated that there were four factors influencing organizational culture including, diversity in culture, connection based culture, integrated culture and structure of culture. In terms of diversity in culture, sensitivity to quality data and cultural flexibility are the most influential sub-factors while connection based marketing and relational satisfaction are two important sub-factors associated with diversity in culture. The study discusses other issues.

  19. Racial-ethnic self-schemas: Multi-dimensional identity-based motivation

    Science.gov (United States)

    Oyserman, Daphna

    2008-01-01

    Prior self-schema research focuses on benefits of being schematic vs. aschematic in stereotyped domains. The current studies build on this work, examining racial-ethnic self-schemas as multi-dimensional, containing multiple, conflicting, and non-integrated images. A multidimensional perspective captures complexity; examining net effects of dimensions predicts within-group differences in academic engagement and well-being. When racial-ethnicity self-schemas focus attention on membership in both in-group and broader society, engagement with school should increase since school is not seen as out-group defining. When racial-ethnicity self-schemas focus attention on inclusion (not obstacles to inclusion) in broader society, risk of depressive symptoms should decrease. Support for these hypotheses was found in two separate samples (8th graders, n = 213, 9th graders followed to 12th grade n = 141). PMID:19122837

  20. Scientific Visualization and Simulation for Multi-dimensional Marine Environment Data

    Science.gov (United States)

    Su, T.; Liu, H.; Wang, W.; Song, Z.; Jia, Z.

    2017-12-01

    As higher attention on the ocean and rapid development of marine detection, there are increasingly demands for realistic simulation and interactive visualization of marine environment in real time. Based on advanced technology such as GPU rendering, CUDA parallel computing and rapid grid oriented strategy, a series of efficient and high-quality visualization methods, which can deal with large-scale and multi-dimensional marine data in different environmental circumstances, has been proposed in this paper. Firstly, a high-quality seawater simulation is realized by FFT algorithm, bump mapping and texture animation technology. Secondly, large-scale multi-dimensional marine hydrological environmental data is virtualized by 3d interactive technologies and volume rendering techniques. Thirdly, seabed terrain data is simulated with improved Delaunay algorithm, surface reconstruction algorithm, dynamic LOD algorithm and GPU programming techniques. Fourthly, seamless modelling in real time for both ocean and land based on digital globe is achieved by the WebGL technique to meet the requirement of web-based application. The experiments suggest that these methods can not only have a satisfying marine environment simulation effect, but also meet the rendering requirements of global multi-dimension marine data. Additionally, a simulation system for underwater oil spill is established by OSG 3D-rendering engine. It is integrated with the marine visualization method mentioned above, which shows movement processes, physical parameters, current velocity and direction for different types of deep water oil spill particle (oil spill particles, hydrates particles, gas particles, etc.) dynamically and simultaneously in multi-dimension. With such application, valuable reference and decision-making information can be provided for understanding the progress of oil spill in deep water, which is helpful for ocean disaster forecasting, warning and emergency response.

  1. Advanced multi-dimensional imaging of gamma-ray radiation

    International Nuclear Information System (INIS)

    Woodring, Mitchell; Beddingfield, David; Souza, David; Entine, Gerald; Squillante, Michael; Christian, James; Kogan, Alex

    2003-01-01

    The tracking of radiation contamination and distribution has become a high-priority US DOE task. To support DOE needs, Radiation Monitoring Devices Inc. has been actively carrying out research and development on a gamma-radiation imager, RadCam 2000 TM . The imager is based upon a position-sensitive PMT coupled to a scintillator near a MURA coded aperture. The modulated gamma flux detected by the PSPMT is mathematically decoded to produce images that are computer displayed in near real time. Additionally, we have developed a data-manipulation scheme which allows a multi-dimensional data array, comprised of x position, y position, and energy, to be used in the imaging process. In the imager software a gate can be set on a specific isotope energy to reveal where in the field of view the gated data lies or, conversely, a gate can be set on an area in the field of view to examine what isotopes are present in that area. This process is complicated by the FFT decoding process used with the coded aperture; however, we have achieved excellent performance and results are presented here

  2. Secondary Channel Bifurcation Geometry: A Multi-dimensional Problem

    Science.gov (United States)

    Gaeuman, D.; Stewart, R. L.

    2017-12-01

    The construction of secondary channels (or side channels) is a popular strategy for increasing aquatic habitat complexity in managed rivers. Such channels, however, frequently experience aggradation that prevents surface water from entering the side channels near their bifurcation points during periods of relatively low discharge. This failure to maintain an uninterrupted surface water connection with the main channel can reduce the habitat value of side channels for fish species that prefer lotic conditions. Various factors have been proposed as potential controls on the fate of side channels, including water surface slope differences between the main and secondary channels, the presence of main channel secondary circulation, transverse bed slopes, and bifurcation angle. A quantitative assessment of more than 50 natural and constructed secondary channels in the Trinity River of northern California indicates that bifurcations can assume a variety of configurations that are formed by different processes and whose longevity is governed by different sets of factors. Moreover, factors such as bifurcation angle and water surface slope vary with discharge level and are continuously distributed in space, such that they must be viewed as a multi-dimensional field rather than a single-valued attribute that can be assigned to a particular bifurcation.

  3. MULTI-DIMENSIONAL PATTERN DISCOVERY OF TRAJECTORIES USING CONTEXTUAL INFORMATION

    Directory of Open Access Journals (Sweden)

    M. Sharif

    2017-10-01

    Full Text Available Movement of point objects are highly sensitive to the underlying situations and conditions during the movement, which are known as contexts. Analyzing movement patterns, while accounting the contextual information, helps to better understand how point objects behave in various contexts and how contexts affect their trajectories. One potential solution for discovering moving objects patterns is analyzing the similarities of their trajectories. This article, therefore, contextualizes the similarity measure of trajectories by not only their spatial footprints but also a notion of internal and external contexts. The dynamic time warping (DTW method is employed to assess the multi-dimensional similarities of trajectories. Then, the results of similarity searches are utilized in discovering the relative movement patterns of the moving point objects. Several experiments are conducted on real datasets that were obtained from commercial airplanes and the weather information during the flights. The results yielded the robustness of DTW method in quantifying the commonalities of trajectories and discovering movement patterns with 80 % accuracy. Moreover, the results revealed the importance of exploiting contextual information because it can enhance and restrict movements.

  4. The development of a multi-dimensional gambling accessibility scale.

    Science.gov (United States)

    Hing, Nerilee; Haw, John

    2009-12-01

    The aim of the current study was to develop a scale of gambling accessibility that would have theoretical significance to exposure theory and also serve to highlight the accessibility risk factors for problem gambling. Scale items were generated from the Productivity Commission's (Australia's Gambling Industries: Report No. 10. AusInfo, Canberra, 1999) recommendations and tested on a group with high exposure to the gambling environment. In total, 533 gaming venue employees (aged 18-70 years; 67% women) completed a questionnaire that included six 13-item scales measuring accessibility across a range of gambling forms (gaming machines, keno, casino table games, lotteries, horse and dog racing, sports betting). Also included in the questionnaire was the Problem Gambling Severity Index (PGSI) along with measures of gambling frequency and expenditure. Principal components analysis indicated that a common three factor structure existed across all forms of gambling and these were labelled social accessibility, physical accessibility and cognitive accessibility. However, convergent validity was not demonstrated with inconsistent correlations between each subscale and measures of gambling behaviour. These results are discussed in light of exposure theory and the further development of a multi-dimensional measure of gambling accessibility.

  5. Multi-Dimensional Pattern Discovery of Trajectories Using Contextual Information

    Science.gov (United States)

    Sharif, M.; Alesheikh, A. A.

    2017-10-01

    Movement of point objects are highly sensitive to the underlying situations and conditions during the movement, which are known as contexts. Analyzing movement patterns, while accounting the contextual information, helps to better understand how point objects behave in various contexts and how contexts affect their trajectories. One potential solution for discovering moving objects patterns is analyzing the similarities of their trajectories. This article, therefore, contextualizes the similarity measure of trajectories by not only their spatial footprints but also a notion of internal and external contexts. The dynamic time warping (DTW) method is employed to assess the multi-dimensional similarities of trajectories. Then, the results of similarity searches are utilized in discovering the relative movement patterns of the moving point objects. Several experiments are conducted on real datasets that were obtained from commercial airplanes and the weather information during the flights. The results yielded the robustness of DTW method in quantifying the commonalities of trajectories and discovering movement patterns with 80 % accuracy. Moreover, the results revealed the importance of exploiting contextual information because it can enhance and restrict movements.

  6. Multi-dimensional conversion to the ion-hybrid mode

    International Nuclear Information System (INIS)

    Tracy, E.R.; Kaufman, A.N.; Brizard, A.J.; Morehead, J.J.

    1996-01-01

    We first demonstrate that the dispersion matrix for linear conversion of a magnetosonic wave to an ion-hybrid wave (as in a D-T plasma) can be congruently transformed to Friedland's normal form. As a result, this conversion can be represented as a two-step process of successive linear conversions in phase space. We then proceed to study the multi-dimensional case of tokamak geometry. After fourier transforming the toroidal dependence, we deal with the two-dimensional poloidal xy-plane and the two-dimensional k x k y -plane, forming a four-dimensional phase space. The dispersion manifolds for the magnetosonic wave [D M (x, k) = 0] and the ion-hybrid wave [D H (x, k) = 0] are each three-dimensional. (Their intersection, on which mode conversion occurs, is two-dimensional.) The incident magnetosonic wave (radiated by an antenna) is a two-dimensional set of rays (a lagrangian manifold): k(x) = ∇θ(x), with θ(x) the phase of the magnetosonic wave. When these rays pierce the ion-hybrid dispersion manifold, they convert to a set of ion-hybrid rays. Then, when those rays intersect the magnetosonic dispersion manifold, they convert to a set of open-quotes reflectedclose quotes magnetosonic rays. This set of rays is distinct from the set of incident rays that have been reflected by the inner surface of the tokamak plasma. As a result, the total destructive interference that can occur in the one-dimensional case may become only partial. We explore the implications of this startling phenomenon both analytically and geometrically

  7. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease.

    Science.gov (United States)

    Yang, Hyun-Jin; Ratnapriya, Rinki; Cogliati, Tiziana; Kim, Jung-Woong; Swaroop, Anand

    2015-05-01

    Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases. Published by Elsevier Ltd.

  8. Hitchhiker's guide to multi-dimensional plant pathology.

    Science.gov (United States)

    Saunders, Diane G O

    2015-02-01

    Filamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next-generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.

  9. Analytic Approximations to the Free Boundary and Multi-dimensional Problems in Financial Derivatives Pricing

    Science.gov (United States)

    Lau, Chun Sing

    This thesis studies two types of problems in financial derivatives pricing. The first type is the free boundary problem, which can be formulated as a partial differential equation (PDE) subject to a set of free boundary condition. Although the functional form of the free boundary condition is given explicitly, the location of the free boundary is unknown and can only be determined implicitly by imposing continuity conditions on the solution. Two specific problems are studied in details, namely the valuation of fixed-rate mortgages and CEV American options. The second type is the multi-dimensional problem, which involves multiple correlated stochastic variables and their governing PDE. One typical problem we focus on is the valuation of basket-spread options, whose underlying asset prices are driven by correlated geometric Brownian motions (GBMs). Analytic approximate solutions are derived for each of these three problems. For each of the two free boundary problems, we propose a parametric moving boundary to approximate the unknown free boundary, so that the original problem transforms into a moving boundary problem which can be solved analytically. The governing parameter of the moving boundary is determined by imposing the first derivative continuity condition on the solution. The analytic form of the solution allows the price and the hedging parameters to be computed very efficiently. When compared against the benchmark finite-difference method, the computational time is significantly reduced without compromising the accuracy. The multi-stage scheme further allows the approximate results to systematically converge to the benchmark results as one recasts the moving boundary into a piecewise smooth continuous function. For the multi-dimensional problem, we generalize the Kirk (1995) approximate two-asset spread option formula to the case of multi-asset basket-spread option. Since the final formula is in closed form, all the hedging parameters can also be derived in

  10. Design of a Multi Dimensional Database for the Archimed DataWarehouse.

    Science.gov (United States)

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

    2005-01-01

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

  11. Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data.

    Science.gov (United States)

    Kehl, Catherine; Simms, Andrew M; Toofanny, Rudesh D; Daggett, Valerie

    2008-06-01

    The Dynameomics project is our effort to characterize the native-state dynamics and folding/unfolding pathways of representatives of all known protein folds by way of molecular dynamics simulations, as described by Beck et al. (in Protein Eng. Des. Select., the first paper in this series). The data produced by these simulations are highly multidimensional in structure and multi-terabytes in size. Both of these features present significant challenges for storage, retrieval and analysis. For optimal data modeling and flexibility, we needed a platform that supported both multidimensional indices and hierarchical relationships between related types of data and that could be integrated within our data warehouse, as described in the accompanying paper directly preceding this one. For these reasons, we have chosen On-line Analytical Processing (OLAP), a multi-dimensional analysis optimized database, as an analytical platform for these data. OLAP is a mature technology in the financial sector, but it has not been used extensively for scientific analysis. Our project is further more unusual for its focus on the multidimensional and analytical capabilities of OLAP rather than its aggregation capacities. The dimensional data model and hierarchies are very flexible. The query language is concise for complex analysis and rapid data retrieval. OLAP shows great promise for the dynamic protein analysis for bioengineering and biomedical applications. In addition, OLAP may have similar potential for other scientific and engineering applications involving large and complex datasets.

  12. Towards Semantic Web Services on Large, Multi-Dimensional Coverages

    Science.gov (United States)

    Baumann, P.

    2009-04-01

    Observed and simulated data in the Earth Sciences often come as coverages, the general term for space-time varying phenomena as set forth by standardization bodies like the Open GeoSpatial Consortium (OGC) and ISO. Among such data are 1-d time series, 2-D surface data, 3-D surface data time series as well as x/y/z geophysical and oceanographic data, and 4-D metocean simulation results. With increasing dimensionality the data sizes grow exponentially, up to Petabyte object sizes. Open standards for exploiting coverage archives over the Web are available to a varying extent. The OGC Web Coverage Service (WCS) standard defines basic extraction operations: spatio-temporal and band subsetting, scaling, reprojection, and data format encoding of the result - a simple interoperable interface for coverage access. More processing functionality is available with products like Matlab, Grid-type interfaces, and the OGC Web Processing Service (WPS). However, these often lack properties known as advantageous from databases: declarativeness (describe results rather than the algorithms), safe in evaluation (no request can keep a server busy infinitely), and optimizable (enable the server to rearrange the request so as to produce the same result faster). WPS defines a geo-enabled SOAP interface for remote procedure calls. This allows to webify any program, but does not allow for semantic interoperability: a function is identified only by its function name and parameters while the semantics is encoded in the (only human readable) title and abstract. Hence, another desirable property is missing, namely an explicit semantics which allows for machine-machine communication and reasoning a la Semantic Web. The OGC Web Coverage Processing Service (WCPS) language, which has been adopted as an international standard by OGC in December 2008, defines a flexible interface for the navigation, extraction, and ad-hoc analysis of large, multi-dimensional raster coverages. It is abstract in that it

  13. Multi-dimensional Analysis Method of Hydrogen Combustion in the Containment of a Nuclear Power Plant

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jongtae; Hong, Seongwan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Kim, Gun Hong [Kyungwon E and C Co., Seongnam (Korea, Republic of)

    2014-05-15

    The most severe case is the occurrence of detonation, which induces a few-fold greater pressure load on the containment wall than a deflagration flame. The occurrence of a containment-wise global detonation is prohibited by a national regulation. The compartments located in the flow path such as steam generator compartment, annular compartment, and dome region are likely to have highly-concentrated hydrogen. If it is found that hydrogen concentration in any compartment is far below a detonation criterion during an accident progression, it can be thought that the occurrence of a detonative explosion in a compartment is excluded. However, if it is not, it is necessary to evaluate the characteristics of flame acceleration in the containment. The possibility of a flame transition from a deflagration to a detonation (DDT) can be evaluated from a calculated hydrogen distribution in a compartment by using sigma-lambda criteria. However, this method can provide a very conservative result because the geometric characteristics of a real compartment are not considered well. In order to evaluate the containment integrity from a threat of a hydrogen explosion, it is necessary to establish an integrated evaluation system, which includes a lumped-parameter and detail analysis methods. In this study, a method for the multi-dimensional analysis of hydrogen combustion is proposed to mechanistically evaluate the flame acceleration characteristics with a geometric effect. The geometry of the containment is modeled 3-dimensionally using a CAD tool. To resolve a propagating flame front, an adaptive mesh refinement method is coupled with a combustion analysis solver.

  14. Oceans 2.0: Interactive tools for the Visualization of Multi-dimensional Ocean Sensor Data

    Science.gov (United States)

    Biffard, B.; Valenzuela, M.; Conley, P.; MacArthur, M.; Tredger, S.; Guillemot, E.; Pirenne, B.

    2016-12-01

    Ocean Networks Canada (ONC) operates ocean observatories on all three of Canada's coasts. The instruments produce 280 gigabytes of data per day with 1/2 petabyte archived so far. In 2015, 13 terabytes were downloaded by over 500 users from across the world. ONC's data management system is referred to as "Oceans 2.0" owing to its interactive, participative features. A key element of Oceans 2.0 is real time data acquisition and processing: custom device drivers implement the input-output protocol of each instrument. Automatic parsing and calibration takes place on the fly, followed by event detection and quality control. All raw data are stored in a file archive, while the processed data are copied to fast databases. Interactive access to processed data is provided through data download and visualization/quick look features that are adapted to diverse data types (scalar, acoustic, video, multi-dimensional, etc). Data may be post or re-processed to add features, analysis or correct errors, update calibrations, etc. A robust storage structure has been developed consisting of an extensive file system and a no-SQL database (Cassandra). Cassandra is a node-based open source distributed database management system. It is scalable and offers improved performance for big data. A key feature is data summarization. The system has also been integrated with web services and an ERDDAP OPeNDAP server, capable of serving scalar and multidimensional data from Cassandra for fixed or mobile devices.A complex data viewer has been developed making use of the big data capability to interactively display live or historic echo sounder and acoustic Doppler current profiler data, where users can scroll, apply processing filters and zoom through gigabytes of data with simple interactions. This new technology brings scientists one step closer to a comprehensive, web-based data analysis environment in which visual assessment, filtering, event detection and annotation can be integrated.

  15. Multi-dimensional simulations of core-collapse supernova explosions with CHIMERA

    Science.gov (United States)

    Messer, O. E. B.; Harris, J. A.; Hix, W. R.; Lentz, E. J.; Bruenn, S. W.; Mezzacappa, A.

    2018-04-01

    Unraveling the core-collapse supernova (CCSN) mechanism is a problem that remains essentially unsolved despite more than four decades of effort. Spherically symmetric models with otherwise high physical fidelity generally fail to produce explosions, and it is widely accepted that CCSNe are inherently multi-dimensional. Progress in realistic modeling has occurred recently through the availability of petascale platforms and the increasing sophistication of supernova codes. We will discuss our most recent work on understanding neutrino-driven CCSN explosions employing multi-dimensional neutrino-radiation hydrodynamics simulations with the Chimera code. We discuss the inputs and resulting outputs from these simulations, the role of neutrino radiation transport, and the importance of multi-dimensional fluid flows in shaping the explosions. We also highlight the production of 48Ca in long-running Chimera simulations.

  16. Towards Optimal Multi-Dimensional Query Processing with BitmapIndices

    Energy Technology Data Exchange (ETDEWEB)

    Rotem, Doron; Stockinger, Kurt; Wu, Kesheng

    2005-09-30

    Bitmap indices have been widely used in scientific applications and commercial systems for processing complex, multi-dimensional queries where traditional tree-based indices would not work efficiently. This paper studies strategies for minimizing the access costs for processing multi-dimensional queries using bitmap indices with binning. Innovative features of our algorithm include (a) optimally placing the bin boundaries and (b) dynamically reordering the evaluation of the query terms. In addition, we derive several analytical results concerning optimal bin allocation for a probabilistic query model. Our experimental evaluation with real life data shows an average I/O cost improvement of at least a factor of 10 for multi-dimensional queries on datasets from two different applications. Our experiments also indicate that the speedup increases with the number of query dimensions.

  17. Development of multi-dimensional body image scale for malaysian female adolescents.

    Science.gov (United States)

    Chin, Yit Siew; Taib, Mohd Nasir Mohd; Shariff, Zalilah Mohd; Khor, Geok Lin

    2008-01-01

    The present study was conducted to develop a Multi-dimensional Body Image Scale for Malaysian female adolescents. Data were collected among 328 female adolescents from a secondary school in Kuantan district, state of Pahang, Malaysia by using a self-administered questionnaire and anthropometric measurements. The self-administered questionnaire comprised multiple measures of body image, Eating Attitude Test (EAT-26; Garner & Garfinkel, 1979) and Rosenberg Self-esteem Inventory (Rosenberg, 1965). The 152 items from selected multiple measures of body image were examined through factor analysis and for internal consistency. Correlations between Multi-dimensional Body Image Scale and body mass index (BMI), risk of eating disorders and self-esteem were assessed for construct validity. A seven factor model of a 62-item Multi-dimensional Body Image Scale for Malaysian female adolescents with construct validity and good internal consistency was developed. The scale encompasses 1) preoccupation with thinness and dieting behavior, 2) appearance and body satisfaction, 3) body importance, 4) muscle increasing behavior, 5) extreme dieting behavior, 6) appearance importance, and 7) perception of size and shape dimensions. Besides, a multidimensional body image composite score was proposed to screen negative body image risk in female adolescents. The result found body image was correlated with BMI, risk of eating disorders and self-esteem in female adolescents. In short, the present study supports a multi-dimensional concept for body image and provides a new insight into its multi-dimensionality in Malaysian female adolescents with preliminary validity and reliability of the scale. The Multi-dimensional Body Image Scale can be used to identify female adolescents who are potentially at risk of developing body image disturbance through future intervention programs.

  18. Genetics of healthy aging in Europe: the EU-integrated project GEHA (GEnetics of Healthy Aging)

    DEFF Research Database (Denmark)

    Franceschi, Claudio; Bezrukov, Vladyslav; Blanché, Hélène

    2007-01-01

    The aim of the 5-year European Union (EU)-Integrated Project GEnetics of Healthy Aging (GEHA), constituted by 25 partners (24 from Europe plus the Beijing Genomics Institute from China), is to identify genes involved in healthy aging and longevity, which allow individuals to survive to advanced old......DNA). The genetic analysis will be performed by 9 high-throughput platforms, within the framework of centralized databases for phenotypic, genetic, and mtDNA data. Additional advanced approaches (bioinformatics, advanced statistics, mathematical modeling, functional genomics and proteomics, molecular biology...... age in good cognitive and physical function and in the absence of major age-related diseases. To achieve this aim a coherent, tightly integrated program of research that unites demographers, geriatricians, geneticists, genetic epidemiologists, molecular biologists, bioinfomaticians, and statisticians...

  19. Evaluating accessibility to Bangkok Metro Systems using multi-dimensional criteria across user groups

    Directory of Open Access Journals (Sweden)

    Duangporn Prasertsubpakij

    2012-07-01

    Full Text Available Metro systems act as fast and efficient transport systems for many modern metropolises; however, enhancing higher usage of such systems often conflicts with providing suitable accessibility options. The traditional approach of metro accessibility studies seems to be an ineffective measure to gage sustainable access in which the equal rights of all users are taken into account. Bangkok Metropolitan Region (BMR transportation has increasingly relied on the role of two mass rapid transport systems publicly called “BTS Skytrain” and “MRT Subway”, due to limited availability of land and massive road congestion; however, access to such transit arguably treats some vulnerable groups, especially women, the elderly and disabled people unfairly. This study constructs a multi-dimensional assessment of accessibility considerations to scrutinize how user groups access metro services based on BMR empirical case. 600 individual passengers at various stations were asked to rate the questionnaire that simultaneously considers accessibility aspects of spatial, feeder connectivity, temporal, comfort/safety, psychosocial and other dimensions. It was interestingly found by user disaggregated accessibility model that the lower the accessibility perceptions—related uncomfortable and unsafe environment conditions, the greater the equitable access to services, as illustrated by MRT — Hua Lumphong and MRT — Petchaburi stations. The study suggests that, to balance the access priorities of groups on services, policy actions should emphasize acceptably safe access for individuals, cost efficient feeder services connecting the metro lines, socioeconomic influences and time allocation. Insightful discussions on integrated approach balancing different dimensions of accessibility and recommendations would contribute to accessibility-based knowledge and potential propensity to use the public transits towards transport sustainability.

  20. Development and empirical validation of symmetric component measures of multi-dimensional constructs

    DEFF Research Database (Denmark)

    Sørensen, Hans Eibe; Slater, Stanley F.

    2008-01-01

    Atheoretical measure purification may lead to construct deficient measures. The purpose of this paper is to provide a theoretically driven procedure for the development and empirical validation of symmetric component measures of multi-dimensional constructs. We place particular emphasis on establ...

  1. Developing a Multi-Dimensional Evaluation Framework for Faculty Teaching and Service Performance

    Science.gov (United States)

    Baker, Diane F.; Neely, Walter P.; Prenshaw, Penelope J.; Taylor, Patrick A.

    2015-01-01

    A task force was created in a small, AACSB-accredited business school to develop a more comprehensive set of standards for faculty performance. The task force relied heavily on faculty input to identify and describe key dimensions that capture effective teaching and service performance. The result is a multi-dimensional framework that will be used…

  2. Developing Multi-Dimensional Evaluation Criteria for English Learning Websites with University Students and Professors

    Science.gov (United States)

    Liu, Gi-Zen; Liu, Zih-Hui; Hwang, Gwo-Jen

    2011-01-01

    Many English learning websites have been developed worldwide, but little research has been conducted concerning the development of comprehensive evaluation criteria. The main purpose of this study is thus to construct a multi-dimensional set of criteria to help learners and teachers evaluate the quality of English learning websites. These…

  3. A Replication Study on the Multi-Dimensionality of Online Social Presence

    Science.gov (United States)

    Mykota, David B.

    2015-01-01

    The purpose of the present study is to conduct an external replication into the multi-dimensionality of social presence as measured by the Computer-Mediated Communication Questionnaire (Tu, 2005). Online social presence is one of the more important constructs for determining the level of interaction and effectiveness of learning in an online…

  4. Multi-dimensional microanalysis of masklessly implanted atoms using focused heavy ion beam

    International Nuclear Information System (INIS)

    Mokuno, Yoshiaki; Iiorino, Yuji; Chayahara, Akiyoshi; Kiuchi, Masato; Fujii, Kanenaga; Satou, Mamoru

    1992-01-01

    Multi-dimensional structure fabricated by maskless MeV gold implantation in silicon wafer was analyzed by 3 MeV carbon ion microprobe using a microbeam line developed at GIRIO. The minimum line width of the implanted region was estimated to be about 5 μm. The advantages of heavy ions for microanalysis were demonstrated. (author)

  5. Multi-dimensional database design and implementation of dam safety monitoring system

    Directory of Open Access Journals (Sweden)

    Zhao Erfeng

    2008-09-01

    Full Text Available To improve the effectiveness of dam safety monitoring database systems, the development process of a multi-dimensional conceptual data model was analyzed and a logic design was achieved in multi-dimensional database mode. The optimal data model was confirmed by identifying data objects, defining relations and reviewing entities. The conversion of relations among entities to external keys and entities and physical attributes to tables and fields was interpreted completely. On this basis, a multi-dimensional database that reflects the management and analysis of a dam safety monitoring system on monitoring data information has been established, for which factual tables and dimensional tables have been designed. Finally, based on service design and user interface design, the dam safety monitoring system has been developed with Delphi as the development tool. This development project shows that the multi-dimensional database can simplify the development process and minimize hidden dangers in the database structure design. It is superior to other dam safety monitoring system development models and can provide a new research direction for system developers.

  6. Skip-webs: Efficient distributed data structures for multi-dimensional data sets

    DEFF Research Database (Denmark)

    Arge, Lars; Eppstein, David; Goodrich, Michael T.

    2005-01-01

    querying scenarios, which include linear (one-dimensional) data, such as sorted sets, as well as multi-dimensional data, such as d-dimensional octrees and digital tries of character strings defined over a fixed alphabet. We show how to perform a query over such a set of n items spread among n hosts using O...

  7. Uncertainty Evaluation with Multi-Dimensional Model of LBLOCA in OPR1000 Plant

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jieun; Oh, Deog Yeon; Seul, Kwang-Won; Lee, Jin Ho [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2016-10-15

    KINS has used KINS-REM (KINS-Realistic Evaluation Methodology) which developed for Best- Estimate (BE) calculation and uncertainty quantification for regulatory audit. This methodology has been improved continuously by numerous studies, such as uncertainty parameters and uncertainty ranges. In this study, to evaluate the applicability of improved KINS-REM for OPR1000 plant, uncertainty evaluation with multi-dimensional model for confirming multi-dimensional phenomena was conducted with MARS-KS code. In this study, the uncertainty evaluation with multi- dimensional model of OPR1000 plant was conducted for confirming the applicability of improved KINS- REM The reactor vessel modeled using MULTID component of MARS-KS code, and total 29 uncertainty parameters were considered by 124 sampled calculations. Through 124 calculations using Mosaique program with MARS-KS code, peak cladding temperature was calculated and final PCT was determined by the 3rd order Wilks' formula. The uncertainty parameters which has strong influence were investigated by Pearson coefficient analysis. They were mostly related with plant operation and fuel material properties. Evaluation results through the 124 calculations and sensitivity analysis show that improved KINS-REM could be reasonably applicable for uncertainty evaluation with multi-dimensional model calculations of OPR1000 plants.

  8. Multi-dimensional information diffusion and balancing market supply: an agent-based approach

    NARCIS (Netherlands)

    Osinga, S.A.; Kramer, M.R.; Hofstede, G.J.; Beulens, A.J.M.

    2013-01-01

    This agent-based information management model is designed to explore how multi-dimensional information, spreading through a population of agents (for example farmers) affects market supply. Farmers make quality decisions that must be aligned with available markets. Markets distinguish themselves by

  9. Exact asymptotic expansions for solutions of multi-dimensional renewal equations

    International Nuclear Information System (INIS)

    Sgibnev, M S

    2006-01-01

    We derive expansions with exact asymptotic expressions for the remainders for solutions of multi-dimensional renewal equations. The effect of the roots of the characteristic equation on the asymptotic representation of solutions is taken into account. The resulting formulae are used to investigate the asymptotic behaviour of the average number of particles in age-dependent branching processes having several types of particles

  10. Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

    NARCIS (Netherlands)

    Baak, M.; Gadatsch, S.; Harrington, R.; Verkerke, W.

    2015-01-01

    A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model׳s parameters and transformed according to a specific

  11. Effects of bathymetric lidar errors on flow properties predicted with a multi-dimensional hydraulic model

    Science.gov (United States)

    J. McKean; D. Tonina; C. Bohn; C. W. Wright

    2014-01-01

    New remote sensing technologies and improved computer performance now allow numerical flow modeling over large stream domains. However, there has been limited testing of whether channel topography can be remotely mapped with accuracy necessary for such modeling. We assessed the ability of the Experimental Advanced Airborne Research Lidar, to support a multi-dimensional...

  12. The application of a multi-dimensional assessment approach to talent identification in Australian football.

    Science.gov (United States)

    Woods, Carl T; Raynor, Annette J; Bruce, Lyndell; McDonald, Zane; Robertson, Sam

    2016-07-01

    This study investigated whether a multi-dimensional assessment could assist with talent identification in junior Australian football (AF). Participants were recruited from an elite under 18 (U18) AF competition and classified into two groups; talent identified (State U18 Academy representatives; n = 42; 17.6 ± 0.4 y) and non-talent identified (non-State U18 Academy representatives; n = 42; 17.4 ± 0.5 y). Both groups completed a multi-dimensional assessment, which consisted of physical (standing height, dynamic vertical jump height and 20 m multistage fitness test), technical (kicking and handballing tests) and perceptual-cognitive (video decision-making task) performance outcome tests. A multivariate analysis of variance tested the main effect of status on the test criterions, whilst a receiver operating characteristic curve assessed the discrimination provided from the full assessment. The talent identified players outperformed their non-talent identified peers in each test (P talent identified and non-talent identified participants, respectively. When compared to single assessment approaches, this multi-dimensional assessment reflects a more comprehensive means of talent identification in AF. This study further highlights the importance of assessing multi-dimensional performance qualities when identifying talented team sports.

  13. Low-diffusion rotated upwind schemes, multigrid and defect correction for steady, multi-dimensional Euler flows

    NARCIS (Netherlands)

    Koren, B.; Hackbusch, W.; Trottenberg, U.

    1991-01-01

    Two simple, multi-dimensional upwind discretizations for the steady Euler equations are derived, with the emphasis Iying on bath a good accuracy and a good solvability. The multi-dimensional upwinding consists of applying a one-dimensional Riemann solver with a locally rotated left and right state,

  14. Pedagogical Factors Stimulating the Self-Development of Students' Multi-Dimensional Thinking in Terms of Subject-Oriented Teaching

    Science.gov (United States)

    Andreev, Valentin I.

    2014-01-01

    The main aim of this research is to disclose the essence of students' multi-dimensional thinking, also to reveal the rating of factors which stimulate the raising of effectiveness of self-development of students' multi-dimensional thinking in terms of subject-oriented teaching. Subject-oriented learning is characterized as a type of learning where…

  15. Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.

    Directory of Open Access Journals (Sweden)

    Christopher G Bell

    2010-11-01

    Full Text Available Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D, focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip and absolute methylation values were estimated using a Bayesian algorithm (BATMAN. Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10(-4, permutation p = 1.0×10(-3. Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p = 1.13×10(-7. Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM, encapsulates a Highly Conserved Non-Coding Element (HCNE that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases.

  16. An Overview of Multi-Dimensional Models of the Sacramento–San Joaquin Delta

    Directory of Open Access Journals (Sweden)

    Michael L. MacWilliams

    2016-12-01

    Full Text Available doi: https://doi.org/10.15447/sfews.2016v14iss4art2Over the past 15 years, the development and application of multi-dimensional hydrodynamic models in San Francisco Bay and the Sacramento–San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system. Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta under future conditions. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship among X2, flow, fish abundance, and the low salinity zone. Through the coupling of multi-dimensional models with wind wave and sediment transport models, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms in the estuary, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta. This paper provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multi-dimensional models to predict how future Delta conditions will affect both fish and water supply.

  17. Multi-dimensional population balance models of crystallization processes

    DEFF Research Database (Denmark)

    Meisler, Kresten Troelstrup; von Solms, Nicolas

    A generic and model-based framework for batch cooling crystallization operations has been extended to incorporate continuous and fed-batch processes. Modules for the framework have been developed, including a module for reactions, allowing the study of reactive crystallization within the framework....... A kinetic model library together with an ontology for knowledge representation has been developed, in which kinetic models and relations from the literature are stored along with the references and data. The model library connects to the generic modelling framework as well, as models can be retrieved......, analyzed, used for simulation and stored again. The model library facilitates comparison of expressions for kinetic phenomena and is tightly integrated with the model analysis tools of the framework.Through the framework, a model for a crystallization operation may be systematically generated...

  18. Multi dimensional analysis of Design Basis Events using MARS-LMR

    International Nuclear Information System (INIS)

    Woo, Seung Min; Chang, Soon Heung

    2012-01-01

    Highlights: ► The one dimensional analyzed sodium hot pool is modified to a three dimensional node system, because the one dimensional analysis cannot represent the phenomena of the inside pool of a big size pool with many compositions. ► The results of the multi-dimensional analysis compared with the one dimensional analysis results in normal operation, TOP (Transient of Over Power), LOF (Loss of Flow), and LOHS (Loss of Heat Sink) conditions. ► The difference of the sodium flow pattern due to structure effect in the hot pool and mass flow rates in the core lead the different sodium temperature and temperature history under transient condition. - Abstract: KALIMER-600 (Korea Advanced Liquid Metal Reactor), which is a pool type SFR (Sodium-cooled Fast Reactor), was developed by KAERI (Korea Atomic Energy Research Institute). DBE (Design Basis Events) for KALIMER-600 has been analyzed in the one dimension. In this study, the one dimensional analyzed sodium hot pool is modified to a three dimensional node system, because the one dimensional analysis cannot represent the phenomena of the inside pool of a big size pool with many compositions, such as UIS (Upper Internal Structure), IHX (Intermediate Heat eXchanger), DHX (Decay Heat eXchanger), and pump. The results of the multi-dimensional analysis compared with the one dimensional analysis results in normal operation, TOP (Transient of Over Power), LOF (Loss of Flow), and LOHS (Loss of Heat Sink) conditions. First, the results in normal operation condition show the good agreement between the one and multi-dimensional analysis. However, according to the sodium temperatures of the core inlet, outlet, the fuel central line, cladding and PDRC (Passive Decay heat Removal Circuit), the temperatures of the one dimensional analysis are generally higher than the multi-dimensional analysis in conditions except the normal operation state, and the PDRC operation time in the one dimensional analysis is generally longer than

  19. Chemistry and Transport In a Multi-Dimensional Model

    Science.gov (United States)

    Yung, Yuk L.; Allen, M.; Zurek, R. W.; Salawitch, R. J.

    2002-01-01

    The focus of the work funded under this proposal is the exchange between the stratosphere and the troposphere, and between the troposphere and the blaspheme. These two interfaces represent the frontiers of atmospheric chemistry. It is the combination of exchange processes at both interfaces that ultimately controls how the blaspheme (including human activities) affects the ozone layer. The modeling work was motivated by and attempts to integrate information obtained by aircraft, spacecraft, shuttle and oceanic measurements. The model development and research activities accomplished in the past three years provide a technical and intellectual basis for the research in this group. The innovative part of our research program is related to the IAV of ozone and the hydrological cycle. Other related but independently supported work include the study of isotopic fractionation of atmospheric species, e.g., N2O and CO2. Our theory suggests that we now have the ability to probe the middle atmosphere at a level of sensitivity where subtle details such as the isotopic composition of simple molecules can yield measurable systematic effects. This creates the possibility for probing the chemistry and dynamics of the middle atmosphere using all of the N2O and CO2 isotopologues. In the following we will briefly describe the model development and review the highlights of recent accomplishments.

  20. Development of a multi-dimensional realistic thermal-hydraulic system analysis code, MARS 1.3 and its verification

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Won Jae; Chung, Bub Dong; Jeong, Jae Jun; Ha, Kwi Seok [Korea Atomic Energy Research Institute, Taejon (Korea)

    1998-06-01

    A multi-dimensional realistic thermal-hydraulic system analysis code, MARS version 1.3 has been developed. Main purpose of MARS 1.3 development is to have the realistic analysis capability of transient two-phase thermal-hydraulics of Pressurized Water Reactors (PWRs) especially during Large Break Loss of Coolant Accidents (LBLOCAs) where the multi-dimensional phenomena domain the transients. MARS code is a unified version of USNRC developed COBRA-TF, domain the transients. MARS code is a unified version of USNRC developed COBRA-TF, three-dimensional (3D) reactor vessel analysis code, and RELAP5/MOD3.2.1.2, one-dimensional (1D) reactor system analysis code., Developmental requirements for MARS are chosen not only to best utilize the existing capability of the codes but also to have the enhanced capability in code maintenance, user accessibility, user friendliness, code portability, code readability, and code flexibility. For the maintenance of existing codes capability and the enhancement of code maintenance capability, user accessibility and user friendliness, MARS has been unified to be a single code consisting of 1D module (RELAP5) and 3D module (COBRA-TF). This is realized by implicitly integrating the system pressure matrix equations of hydrodynamic models and solving them simultaneously, by modifying the 1D/3D calculation sequence operable under a single Central Processor Unit (CPU) and by unifying the input structure and the light water property routines of both modules. In addition, the code structure of 1D module is completely restructured using the modular data structure of standard FORTRAN 90, which greatly improves the code maintenance capability, readability and portability. For the code flexibility, a dynamic memory management scheme is applied in both modules. MARS 1.3 now runs on PC/Windows and HP/UNIX platforms having a single CPU, and users have the options to select the 3D module to model the 3D thermal-hydraulics in the reactor vessel or other

  1. A multi-dimensional assessment of urban vulnerability to climate change in Sub-Saharan Africa

    DEFF Research Database (Denmark)

    Herslund, Lise Byskov; Jalyer, Fatameh; Jean-Baptiste, Nathalie

    2016-01-01

    In this paper, we develop and apply a multi-dimensional vulnerability assessment framework for understanding the impacts of climate change-induced hazards in Sub- Saharan African cities. The research was carried out within the European/African FP7 project CLimate change and Urban Vulnerability...... in Africa, which investigated climate change-induced risks, assessed vulnerability and proposed policy initiatives in five African cities. Dar es Salaam (Tanzania) was used as a main case with a particular focus on urban flooding. The multi-dimensional assessment covered the physical, institutional...... encroachment on green and flood-prone land). Scenario modeling suggests that vulnerability will continue to increase strongly due to the expected loss of agricultural land at the urban fringes and loss of green space within the city. However, weak institutional commitment and capacity limit the potential...

  2. Multi-dimensional instability of electrostatic solitary structures in magnetized nonthermal dusty plasmas

    International Nuclear Information System (INIS)

    Mamun, A.A.; Russel, S.M.; Mendoza-Briceno, C.A.; Alam, M.N.; Datta, T.K.; Das, A.K.

    1999-05-01

    A rigorous theoretical investigation has been made of multi-dimensional instability of obliquely propagating electrostatic solitary structures in a hot magnetized nonthermal dusty plasma which consists of a negatively charged hot dust fluid, Boltzmann distributed electrons, and nonthermally distributed ions. The Zakharov-Kuznetsov equation for the electrostatic solitary structures that exist in such a dusty plasma system is derived by the reductive perturbation method. The multi-dimensional instability of these solitary waves is also studied by the small-k (long wavelength plane wave) perturbation expansion method. The nature of these solitary structures, the instability criterion, and their growth rate depending on dust-temperature, external magnetic field, and obliqueness are discussed. The implications of these results to some space and astrophysical dusty plasma situations are briefly mentioned. (author)

  3. A Shell Multi-dimensional Hierarchical Cubing Approach for High-Dimensional Cube

    Science.gov (United States)

    Zou, Shuzhi; Zhao, Li; Hu, Kongfa

    The pre-computation of data cubes is critical for improving the response time of OLAP systems and accelerating data mining tasks in large data warehouses. However, as the sizes of data warehouses grow, the time it takes to perform this pre-computation becomes a significant performance bottleneck. In a high dimensional data warehouse, it might not be practical to build all these cuboids and their indices. In this paper, we propose a shell multi-dimensional hierarchical cubing algorithm, based on an extension of the previous minimal cubing approach. This method partitions the high dimensional data cube into low multi-dimensional hierarchical cube. Experimental results show that the proposed method is significantly more efficient than other existing cubing methods.

  4. Finite element method for radiation heat transfer in multi-dimensional graded index medium

    International Nuclear Information System (INIS)

    Liu, L.H.; Zhang, L.; Tan, H.P.

    2006-01-01

    In graded index medium, ray goes along a curved path determined by Fermat principle, and curved ray-tracing is very difficult and complex. To avoid the complicated and time-consuming computation of curved ray trajectories, a finite element method based on discrete ordinate equation is developed to solve the radiative transfer problem in a multi-dimensional semitransparent graded index medium. Two particular test problems of radiative transfer are taken as examples to verify this finite element method. The predicted dimensionless net radiative heat fluxes are determined by the proposed method and compared with the results obtained by finite volume method. The results show that the finite element method presented in this paper has a good accuracy in solving the multi-dimensional radiative transfer problem in semitransparent graded index medium

  5. Rationale for an integrated approach to genetic epidemiology.

    Science.gov (United States)

    Laberge, Claude M; Knoppers, Bartha Maria

    1992-10-01

    Genetic knowledge is now in the public domain and its interpretation by the media and the citizens brings the issues into the public forum of discussion for the necessary ethical, legal and socio-cultural evaluation of its application. Science is being perceived by some as dangerous and as requiring international regulation. Others feel that genetic knowledge will be the breakthrough that will permit medical progress and individual autonomy with regards to personal health and lifestyle choices. The mapping of the human genome has already yielded valuable information on an increasing number of diseases and their variants. Prevailing popular and journalistic archetypes ("imaginaires") used in the media are perceived by the producers as slowing down the possible application of genetic knowledge. The answers to these dilemmas are not readily apparent nor are they prescribed by classical philosophy of medicine. Since genetic knowledge eventually resides with the individual who carries the genes of disease and/or susceptibility, a logical approach to integration of this knowledge at a societal level would seem to reside with individual education and decision-making. The politics of the ensuing social debate could transform the current social contract since an individual's interests need to be balanced against those of his or her immediate family in the sharing of information. The ethical foundations of such a contract requires the genetic education of "Everyone" as a matter of urgent priority. Genetic education should not serve ideological power struggles between the medical establishment and the ethical-legal alliance. Instead, it should ensure the transfer of knowledge to physicians, to patients, to users, to planners, to social science and humanities researchers and to politicians, so that they may make "informed" and free decisions....

  6. Genetic integration of molar cusp size variation in baboons.

    Science.gov (United States)

    Koh, Christina; Bates, Elizabeth; Broughton, Elizabeth; Do, Nicholas T; Fletcher, Zachary; Mahaney, Michael C; Hlusko, Leslea J

    2010-06-01

    Many studies of primate diversity and evolution rely on dental morphology for insight into diet, behavior, and phylogenetic relationships. Consequently, variation in molar cusp size has increasingly become a phenotype of interest. In 2007 we published a quantitative genetic analysis of mandibular molar cusp size variation in baboons. Those results provided more questions than answers, as the pattern of genetic integration did not fit predictions from odontogenesis. To follow up, we expanded our study to include data from the maxillary molar cusps. Here we report on these later analyses, as well as inter-arch comparisons with the mandibular data. We analyzed variation in two-dimensional maxillary molar cusp size using data collected from a captive pedigreed breeding colony of baboons, Papio hamadryas, housed at the Southwest National Primate Research Center. These analyses show that variation in maxillary molar cusp size is heritable and sexually dimorphic. We also estimated additive genetic correlations between cusps on the same crown, homologous cusps along the tooth row, and maxillary and mandibular cusps. The pattern for maxillary molars yields genetic correlations of one between the paracone-metacone and protocone-hypocone. Bivariate analyses of cuspal homologues on adjacent teeth yield correlations that are high or not significantly different from one. Between dental arcades, the nonoccluding cusps consistently yield high genetic correlations, especially the metaconid-paracone and metaconid-metacone. This pattern of genetic correlation does not immediately accord with the pattern of development and/or calcification, however these results do follow predictions that can be made from the evolutionary history of the tribosphenic molar. Copyright 2009 Wiley-Liss, Inc.

  7. towards a theory-based multi-dimensional framework for assessment in mathematics: The "SEA" framework

    Science.gov (United States)

    Anku, Sitsofe E.

    1997-09-01

    Using the reform documents of the National Council of Teachers of Mathematics (NCTM) (NCTM, 1989, 1991, 1995), a theory-based multi-dimensional assessment framework (the "SEA" framework) which should help expand the scope of assessment in mathematics is proposed. This framework uses a context based on mathematical reasoning and has components that comprise mathematical concepts, mathematical procedures, mathematical communication, mathematical problem solving, and mathematical disposition.

  8. Ionizing Shocks in Argon. Part 2: Transient and Multi-Dimensional Effects (Preprint)

    Science.gov (United States)

    2010-09-09

    stability in ionizing monatomic gases. Part 1. Argon ,” J. Fluid Mech., 84, 55 (1978). 2M. P. F. Bristow and I. I. Glass, “ Polarizability of singly...Article 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Ionizing Shocks in Argon . Part 2: Transient...Physics. 14. ABSTRACT We extend the computations of ionizing shocks in argon to unsteady and multi-dimensional, using a collisional-radiative

  9. Development of multi-dimensional body image scale for malaysian female adolescents

    OpenAIRE

    Chin, Yit Siew; Taib, Mohd Nasir Mohd; Shariff, Zalilah Mohd; Khor, Geok Lin

    2008-01-01

    The present study was conducted to develop a Multi-dimensional Body Image Scale for Malaysian female adolescents. Data were collected among 328 female adolescents from a secondary school in Kuantan district, state of Pahang, Malaysia by using a self-administered questionnaire and anthropometric measurements. The self-administered questionnaire comprised multiple measures of body image, Eating Attitude Test (EAT-26; Garner & Garfinkel, 1979) and Rosenberg Self-esteem Inventory (Rosenberg, 1965...

  10. Functional consequences of trust in the construction supply chain: a multi-dimensional view

    OpenAIRE

    Manu, E; Ankrah, N; Chinyio, EA; Proverbs, D

    2016-01-01

    Trust is often linked to the emergence of cooperative behaviours that contribute to successful project outcomes. However, some have questioned the functional relevance of trust in contractual relations, arguing that control-induced cooperation can emerge from enforcement of contracts. These mixed views are further complicated by the multi-dimensional nature of trust, as different trust dimensions could have varying functional consequences. The aim of this study was to provide some clarity on ...

  11. Development of MARS for multi-dimensional and multi-purpose thermal-hydraulic system analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Won Jae; Chung, Bub Dong; Kim, Kyung Doo; Hwang, Moon Kyu; Jeong, Jae Jun; Ha, Kwi Seok; Joo, Han Gyu [Korea Atomic Energy Research Institute, T/H Safety Research Team, Yusung, Daejeon (Korea)

    2000-10-01

    MARS (Multi-dimensional Analysis of Reactor Safety) code is being developed by KAERI for the realistic thermal-hydraulic simulation of light water reactor system transients. MARS 1.4 has been developed as a final version of basic code frame for the multi-dimensional analysis of system thermal-hydraulics. Since MARS 1.3, MARS 1.4 has been improved to have the enhanced code capability and user friendliness through the unification of input/output features, code models and code functions, and through the code modernization. Further improvements of thermal-hydraulic models, numerical method and user friendliness are being carried out for the enhanced code accuracy. As a multi-purpose safety analysis code system, a coupled analysis system, MARS/MASTER/CONTEMPT, has been developed using multiple DLL (Dynamic Link Library) techniques of Windows system. This code system enables the coupled, that is, more realistic analysis of multi-dimensional thermal-hydraulics (MARS 2.0), three-dimensional core kinetics (MASTER) and containment thermal-hydraulics (CONTEMPT). This paper discusses the MARS development program, and the developmental progress of the MARS 1.4 and the MARS/MASTER/CONTEMPT focusing on major features of the codes and their verification. It also discusses thermal hydraulic models and new code features under development. (author)

  12. Development of MARS for multi-dimensional and multi-purpose thermal-hydraulic system analysis

    International Nuclear Information System (INIS)

    Lee, Won Jae; Chung, Bub Dong; Kim, Kyung Doo; Hwang, Moon Kyu; Jeong, Jae Jun; Ha, Kwi Seok; Joo, Han Gyu

    2000-01-01

    MARS (Multi-dimensional Analysis of Reactor Safety) code is being developed by KAERI for the realistic thermal-hydraulic simulation of light water reactor system transients. MARS 1.4 has been developed as a final version of basic code frame for the multi-dimensional analysis of system thermal-hydraulics. Since MARS 1.3, MARS 1.4 has been improved to have the enhanced code capability and user friendliness through the unification of input/output features, code models and code functions, and through the code modernization. Further improvements of thermal-hydraulic models, numerical method and user friendliness are being carried out for the enhanced code accuracy. As a multi-purpose safety analysis code system, a coupled analysis system, MARS/MASTER/CONTEMPT, has been developed using multiple DLL (Dynamic Link Library) techniques of Windows system. This code system enables the coupled, that is, more realistic analysis of multi-dimensional thermal-hydraulics (MARS 2.0), three-dimensional core kinetics (MASTER) and containment thermal-hydraulics (CONTEMPT). This paper discusses the MARS development program, and the developmental progress of the MARS 1.4 and the MARS/MASTER/CONTEMPT focusing on major features of the codes and their verification. It also discusses thermal hydraulic models and new code features under development. (author)

  13. Study on the construction of multi-dimensional Remote Sensing feature space for hydrological drought

    International Nuclear Information System (INIS)

    Xiang, Daxiang; Tan, Debao; Wen, Xiongfei; Shen, Shaohong; Li, Zhe; Cui, Yuanlai

    2014-01-01

    Hydrological drought refers to an abnormal water shortage caused by precipitation and surface water shortages or a groundwater imbalance. Hydrological drought is reflected in a drop of surface water, decrease of vegetation productivity, increase of temperature difference between day and night and so on. Remote sensing permits the observation of surface water, vegetation, temperature and other information from a macro perspective. This paper analyzes the correlation relationship and differentiation of both remote sensing and surface measured indicators, after the selection and extraction a series of representative remote sensing characteristic parameters according to the spectral characterization of surface features in remote sensing imagery, such as vegetation index, surface temperature and surface water from HJ-1A/B CCD/IRS data. Finally, multi-dimensional remote sensing features such as hydrological drought are built on a intelligent collaborative model. Further, for the Dong-ting lake area, two drought events are analyzed for verification of multi-dimensional features using remote sensing data with different phases and field observation data. The experiments results proved that multi-dimensional features are a good method for hydrological drought

  14. Minimizing I/O Costs of Multi-Dimensional Queries with BitmapIndices

    Energy Technology Data Exchange (ETDEWEB)

    Rotem, Doron; Stockinger, Kurt; Wu, Kesheng

    2006-03-30

    Bitmap indices have been widely used in scientific applications and commercial systems for processing complex,multi-dimensional queries where traditional tree-based indices would not work efficiently. A common approach for reducing the size of a bitmap index for high cardinality attributes is to group ranges of values of an attribute into bins and then build a bitmap for each bin rather than a bitmap for each value of the attribute. Binning reduces storage costs,however, results of queries based on bins often require additional filtering for discarding it false positives, i.e., records in the result that do not satisfy the query constraints. This additional filtering,also known as ''candidate checking,'' requires access to the base data on disk and involves significant I/O costs. This paper studies strategies for minimizing the I/O costs for ''candidate checking'' for multi-dimensional queries. This is done by determining the number of bins allocated for each dimension and then placing bin boundaries in optimal locations. Our algorithms use knowledge of data distribution and query workload. We derive several analytical results concerning optimal bin allocation for a probabilistic query model. Our experimental evaluation with real life data shows an average I/O cost improvement of at least a factor of 10 for multi-dimensional queries on datasets from two different applications. Our experiments also indicate that the speedup increases with the number of query dimensions.

  15. Integrating economic parameters into genetic selection for Large White pigs.

    Science.gov (United States)

    Dube, Bekezela; Mulugeta, Sendros D; Dzama, Kennedy

    2013-08-01

    The objective of the study was to integrate economic parameters into genetic selection for sow productivity, growth performance and carcass characteristics in South African Large White pigs. Simulation models for sow productivity and terminal production systems were performed based on a hypothetical 100-sow herd, to derive economic values for the economically relevant traits. The traits included in the study were number born alive (NBA), 21-day litter size (D21LS), 21-day litter weight (D21LWT), average daily gain (ADG), feed conversion ratio (FCR), age at slaughter (AGES), dressing percentage (DRESS), lean content (LEAN) and backfat thickness (BFAT). Growth of a pig was described by the Gompertz growth function, while feed intake was derived from the nutrient requirements of pigs at the respective ages. Partial budgeting and partial differentiation of the profit function were used to derive economic values, which were defined as the change in profit per unit genetic change in a given trait. The respective economic values (ZAR) were: 61.26, 38.02, 210.15, 33.34, -21.81, -68.18, 5.78, 4.69 and -1.48. These economic values indicated the direction and emphases of selection, and were sensitive to changes in feed prices and marketing prices for carcasses and maiden gilts. Economic values for NBA, D21LS, DRESS and LEAN decreased with increasing feed prices, suggesting a point where genetic improvement would be a loss, if feed prices continued to increase. The economic values for DRESS and LEAN increased as the marketing prices for carcasses increased, while the economic value for BFAT was not sensitive to changes in all prices. Reductions in economic values can be counterbalanced by simultaneous increases in marketing prices of carcasses and maiden gilts. Economic values facilitate genetic improvement by translating it to proportionate profitability. Breeders should, however, continually recalculate economic values to place the most appropriate emphases on the respective

  16. A Systematic Bayesian Integration of Epidemiological and Genetic Data

    Science.gov (United States)

    Lau, Max S. Y.; Marion, Glenn; Streftaris, George; Gibson, Gavin

    2015-01-01

    Genetic sequence data on pathogens have great potential to inform inference of their transmission dynamics ultimately leading to better disease control. Where genetic change and disease transmission occur on comparable timescales additional information can be inferred via the joint analysis of such genetic sequence data and epidemiological observations based on clinical symptoms and diagnostic tests. Although recently introduced approaches represent substantial progress, for computational reasons they approximate genuine joint inference of disease dynamics and genetic change in the pathogen population, capturing partially the joint epidemiological-evolutionary dynamics. Improved methods are needed to fully integrate such genetic data with epidemiological observations, for achieving a more robust inference of the transmission tree and other key epidemiological parameters such as latent periods. Here, building on current literature, a novel Bayesian framework is proposed that infers simultaneously and explicitly the transmission tree and unobserved transmitted pathogen sequences. Our framework facilitates the use of realistic likelihood functions and enables systematic and genuine joint inference of the epidemiological-evolutionary process from partially observed outbreaks. Using simulated data it is shown that this approach is able to infer accurately joint epidemiological-evolutionary dynamics, even when pathogen sequences and epidemiological data are incomplete, and when sequences are available for only a fraction of exposures. These results also characterise and quantify the value of incomplete and partial sequence data, which has important implications for sampling design, and demonstrate the abilities of the introduced method to identify multiple clusters within an outbreak. The framework is used to analyse an outbreak of foot-and-mouth disease in the UK, enhancing current understanding of its transmission dynamics and evolutionary process. PMID:26599399

  17. The INTERGROWTH-21st Project Neurodevelopment Package: a novel method for the multi-dimensional assessment of neurodevelopment in pre-school age children.

    Directory of Open Access Journals (Sweden)

    Michelle Fernandes

    Full Text Available BACKGROUND: The International Fetal and Newborn Growth Consortium for the 21st Century (INTERGROWTH-21st Project is a population-based, longitudinal study describing early growth and development in an optimally healthy cohort of 4607 mothers and newborns. At 24 months, children are assessed for neurodevelopmental outcomes with the INTERGROWTH-21st Neurodevelopment Package. This paper describes neurodevelopment tools for preschoolers and the systematic approach leading to the development of the Package. METHODS: An advisory panel shortlisted project-specific criteria (such as multi-dimensional assessments and suitability for international populations to be fulfilled by a neurodevelopment instrument. A literature review of well-established tools for preschoolers revealed 47 candidates, none of which fulfilled all the project's criteria. A multi-dimensional assessment was, therefore, compiled using a package-based approach by: (i categorizing desired outcomes into domains, (ii devising domain-specific criteria for tool selection, and (iii selecting the most appropriate measure for each domain. RESULTS: The Package measures vision (Cardiff tests; cortical auditory processing (auditory evoked potentials to a novelty oddball paradigm; and cognition, language skills, behavior, motor skills and attention (the INTERGROWTH-21st Neurodevelopment Assessment in 35-45 minutes. Sleep-wake patterns (actigraphy are also assessed. Tablet-based applications with integrated quality checks and automated, wireless electroencephalography make the Package easy to administer in the field by non-specialist staff. The Package is in use in Brazil, India, Italy, Kenya and the United Kingdom. CONCLUSIONS: The INTERGROWTH-21st Neurodevelopment Package is a multi-dimensional instrument measuring early child development (ECD. Its developmental approach may be useful to those involved in large-scale ECD research and surveillance efforts.

  18. Multi-dimensional regulation of metabolic networks shaping plant development and performance

    NARCIS (Netherlands)

    Kooke, R.; Keurentjes, J.J.B.

    2012-01-01

    The metabolome is an integral part of a plant’s life cycle and determines for a large part its external phenotype. It is the final, internal product of chemical interactions, obtained through developmental, genetic, and environmental inputs, and as such, it defines the state of a plant in terms of

  19. An integrated genetic, physical, and transcriptional map of chromosome 13

    Energy Technology Data Exchange (ETDEWEB)

    Scheffer, H.; Kooy, R.F.; Wijngaard, A. [Univ. of Groningen (Netherlands)] [and others

    1994-09-01

    In this study a genetic map containing 20 markers and typed in 40 CEPH families is presented. It includes 7 thusfar untyped microsatellite markers, 7 that have previously been mapped on a subset of 8 CEPH families, one reference marker, D13S71, and three telomeric VNTR markers. Also, 4 intragenic RB1 markers were typed. The markers have an average heterozygosity of 73% (80%, excluding the three RFLPs). The total sex average length of the map is 140 cM. The mean female to male ratio is 1.54. For the non-telomeric part of the chromosome between the markers D13S221 in 13q12 and D13S173 in 13q33-q34, this ratio is 1.99. This ratio is reversed in the telomeric part of the chromosome between D13S173 and D13S234 in distal 13q34, where it is 0.47. A high new mutation frequency of 1% was detected in the (CTTT(T)){sub n} repeat in intron 20 of the RB1 gene. The map has been integrated with 7 microsatellite markers and 2 RFLP markers from CEPH database version 7.0, resulting in a map with 32 markers (28 loci) of chromosome 13q. In addition, a deletion hybrid breakpoint map ordering 50 markers in 18 intervals is constructed. It includes 32 microsatellite markers, 4 genes, 5 STSs, and 9 ESTs. Each of 18 intervals contains at least one microsatellite marker included in the extended genetic map. These data allow a correlation between the genetic and physical map of chromosome 13. New ESTs are currently being identified and localized at this integrated map.

  20. Confirmatory factor analysis of the Multi-dimensional Emotional Empathy Scale in the South African context

    Directory of Open Access Journals (Sweden)

    Chantal Olckers

    2010-11-01

    Full Text Available Orientation: Empathy is a core competency in aiding individuals to address the challenges of social living. An indicator of emotional intelligence, it is useful in a globalising and cosmopolitan world. Moreover, managing staff, stakeholders and conflict in many social settings relies on communicative skills, of which empathy forms a large part. Empathy plays a pivotal role in negotiating, persuading and influencing behaviour. The skill of being able to empathise thus enables the possessor to attune to the needs of clients and employees and provides opportunities to become responsive to these needs. Research purpose: This study attempted to determine the construct validity of the Multi-dimensional Emotional Empathy Scale within the South African context. Motivation for the study: In South Africa, a large number of psychometrical instruments have been adopted directly from abroad. Studies determining the construct validity of several of these imported instruments, however, have shown that these instruments are not suited for use in the South African context. Research design, approach and method: The study was based on a quantitative research method with a survey design. A convenience sample of 212 respondents completed the Multi-dimensional Emotional Empathy Scale. The constructs explored were Suffering, Positive Sharing, Responsive Crying, Emotional Attention, a Feel for Others and Emotional Contagion. The statistical procedure used was a confirmatory factor analysis. Main findings: The study showed that, from a South African perspective, the Multi-dimensional Emotional Empathy Scale lacks sufficient construct validity. Practical/managerial implications: Further refinement of the model would provide valuable information that would aid people to be more appreciative of individual contributions, to meet client needs and to understand the motivations of others. Contribution/value-add: From a South African perspective, the findings of this study are

  1. Structural diversity: a multi-dimensional approach to assess recreational services in urban parks.

    Science.gov (United States)

    Voigt, Annette; Kabisch, Nadja; Wurster, Daniel; Haase, Dagmar; Breuste, Jürgen

    2014-05-01

    Urban green spaces provide important recreational services for urban residents. In general, when park visitors enjoy "the green," they are in actuality appreciating a mix of biotic, abiotic, and man-made park infrastructure elements and qualities. We argue that these three dimensions of structural diversity have an influence on how people use and value urban parks. We present a straightforward approach for assessing urban parks that combines multi-dimensional landscape mapping and questionnaire surveys. We discuss the method as well the results from its application to differently sized parks in Berlin and Salzburg.

  2. MINIMUM ENTROPY DECONVOLUTION OF ONE-AND MULTI-DIMENSIONAL NON-GAUSSIAN LINEAR RANDOM PROCESSES

    Institute of Scientific and Technical Information of China (English)

    程乾生

    1990-01-01

    The minimum entropy deconvolution is considered as one of the methods for decomposing non-Gaussian linear processes. The concept of peakedness of a system response sequence is presented and its properties are studied. With the aid of the peakedness, the convergence theory of the minimum entropy deconvolution is established. The problem of the minimum entropy deconvolution of multi-dimensional non-Gaussian linear random processes is first investigated and the corresponding theory is given. In addition, the relation between the minimum entropy deconvolution and parameter method is discussed.

  3. On the use of multi-dimensional scaling and electromagnetic tracking in high dose rate brachytherapy

    Science.gov (United States)

    Götz, Th I.; Ermer, M.; Salas-González, D.; Kellermeier, M.; Strnad, V.; Bert, Ch; Hensel, B.; Tomé, A. M.; Lang, E. W.

    2017-10-01

    High dose rate brachytherapy affords a frequent reassurance of the precise dwell positions of the radiation source. The current investigation proposes a multi-dimensional scaling transformation of both data sets to estimate dwell positions without any external reference. Furthermore, the related distributions of dwell positions are characterized by uni—or bi—modal heavy—tailed distributions. The latter are well represented by α—stable distributions. The newly proposed data analysis provides dwell position deviations with high accuracy, and, furthermore, offers a convenient visualization of the actual shapes of the catheters which guide the radiation source during the treatment.

  4. Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

    Energy Technology Data Exchange (ETDEWEB)

    Baak, M., E-mail: max.baak@cern.ch [CERN, CH-1211 Geneva 23 (Switzerland); Gadatsch, S., E-mail: stefan.gadatsch@nikhef.nl [Nikhef, PO Box 41882, 1009 DB Amsterdam (Netherlands); Harrington, R. [School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, Scotland (United Kingdom); Verkerke, W. [Nikhef, PO Box 41882, 1009 DB Amsterdam (Netherlands)

    2015-01-21

    A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates are often required to model the impact of systematic uncertainties.

  5. Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

    International Nuclear Information System (INIS)

    Baak, M.; Gadatsch, S.; Harrington, R.; Verkerke, W.

    2015-01-01

    A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates are often required to model the impact of systematic uncertainties

  6. Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

    CERN Document Server

    Baak, Max; Harrington, Robert; Verkerke, Wouter

    2014-01-01

    A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates is often required to model the impact of systematic uncertainties.

  7. Interpolation between multi-dimensional histograms using a new non-linear moment morphing method

    CERN Document Server

    Baak, Max; Harrington, Robert; Verkerke, Wouter

    2015-01-01

    A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates is often required to model the impact of systematic uncertainties.

  8. MXA: a customizable HDF5-based data format for multi-dimensional data sets

    International Nuclear Information System (INIS)

    Jackson, M; Simmons, J P; De Graef, M

    2010-01-01

    A new digital file format is proposed for the long-term archival storage of experimental data sets generated by serial sectioning instruments. The format is known as the multi-dimensional eXtensible Archive (MXA) format and is based on the public domain Hierarchical Data Format (HDF5). The MXA data model, its description by means of an eXtensible Markup Language (XML) file with associated Document Type Definition (DTD) are described in detail. The public domain MXA package is available through a dedicated web site (mxa.web.cmu.edu), along with implementation details and example data files

  9. Portable laser synthesizer for high-speed multi-dimensional spectroscopy

    Science.gov (United States)

    Demos, Stavros G [Livermore, CA; Shverdin, Miroslav Y [Sunnyvale, CA; Shirk, Michael D [Brentwood, CA

    2012-05-29

    Portable, field-deployable laser synthesizer devices designed for multi-dimensional spectrometry and time-resolved and/or hyperspectral imaging include a coherent light source which simultaneously produces a very broad, energetic, discrete spectrum spanning through or within the ultraviolet, visible, and near infrared wavelengths. The light output is spectrally resolved and each wavelength is delayed with respect to each other. A probe enables light delivery to a target. For multidimensional spectroscopy applications, the probe can collect the resulting emission and deliver this radiation to a time gated spectrometer for temporal and spectral analysis.

  10. Investigation of multi-dimensional computational models for calculating pollutant transport

    International Nuclear Information System (INIS)

    Pepper, D.W.; Cooper, R.E.; Baker, A.J.

    1980-01-01

    A performance study of five numerical solution algorithms for multi-dimensional advection-diffusion prediction on mesoscale grids was made. Test problems include transport of point and distributed sources, and a simulation of a continuous source. In all cases, analytical solutions are available to assess relative accuracy. The particle-in-cell and second-moment algorithms, both of which employ sub-grid resolution coupled with Lagrangian advection, exhibit superior accuracy in modeling a point source release. For modeling of a distributed source, algorithms based upon the pseudospectral and finite element interpolation concepts, exhibit improved accuracy on practical discretizations

  11. Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface.

    Science.gov (United States)

    Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

    2015-06-05

    Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

  12. Development of an Output-based Adaptive Method for Multi-Dimensional Euler and Navier-Stokes Simulations

    Science.gov (United States)

    Darmofal, David L.

    2003-01-01

    The use of computational simulations in the prediction of complex aerodynamic flows is becoming increasingly prevalent in the design process within the aerospace industry. Continuing advancements in both computing technology and algorithmic development are ultimately leading to attempts at simulating ever-larger, more complex problems. However, by increasing the reliance on computational simulations in the design cycle, we must also increase the accuracy of these simulations in order to maintain or improve the reliability arid safety of the resulting aircraft. At the same time, large-scale computational simulations must be made more affordable so that their potential benefits can be fully realized within the design cycle. Thus, a continuing need exists for increasing the accuracy and efficiency of computational algorithms such that computational fluid dynamics can become a viable tool in the design of more reliable, safer aircraft. The objective of this research was the development of an error estimation and grid adaptive strategy for reducing simulation errors in integral outputs (functionals) such as lift or drag from from multi-dimensional Euler and Navier-Stokes simulations. In this final report, we summarize our work during this grant.

  13. Assessment of wall friction model in multi-dimensional component of MARS with air–water cross flow experiment

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jin-Hwa [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Choi, Chi-Jin [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Cho, Hyoung-Kyu, E-mail: chohk@snu.ac.kr [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Euh, Dong-Jin [Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Park, Goon-Cherl [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of)

    2017-02-15

    Recently, high precision and high accuracy analysis on multi-dimensional thermal hydraulic phenomena in a nuclear power plant has been considered as state-of-the-art issues. System analysis code, MARS, also adopted a multi-dimensional module to simulate them more accurately. Even though it was applied to represent the multi-dimensional phenomena, but implemented models and correlations in that are one-dimensional empirical ones based on one-dimensional pipe experimental results. Prior to the application of the multi-dimensional simulation tools, however, the constitutive models for a two-phase flow need to be carefully validated, such as the wall friction model. Especially, in a Direct Vessel Injection (DVI) system, the injected emergency core coolant (ECC) on the upper part of the downcomer interacts with the lateral steam flow during the reflood phase in the Large-Break Loss-Of-Coolant-Accident (LBLOCA). The interaction between the falling film and lateral steam flow induces a multi-dimensional two-phase flow. The prediction of ECC flow behavior plays a key role in determining the amount of coolant that can be used as core cooling. Therefore, the wall friction model which is implemented to simulate the multi-dimensional phenomena should be assessed by multidimensional experimental results. In this paper, the air–water cross film flow experiments simulating the multi-dimensional phenomenon in upper part of downcomer as a conceptual problem will be introduced. The two-dimensional local liquid film velocity and thickness data were used as benchmark data for code assessment. And then the previous wall friction model of the MARS-MultiD in the annular flow regime was modified. As a result, the modified MARS-MultiD produced improved calculation result than previous one.

  14. Introduction: integrating genetic and cultural evolutionary approaches to language.

    Science.gov (United States)

    Mesoudi, Alex; McElligott, Alan G; Adger, David

    2011-04-01

    The papers in this special issue of Human Biology address recent research in the field of language evolution, both the genetic evolution of the language faculty and the cultural evolution of specific languages. While both of these areas have received increasing interest in recent years, there is also a need to integrate these somewhat separate efforts and explore the relevant gene-culture coevolutionary interactions. Here we summarize the individual contributions, set them in the context of the wider literature, and identify outstanding future research questions. The first set of papers concerns the comparative study of nonhuman communication in primates and birds from both a behavioral and neurobiological perspective, revealing evidence for several common language-related traits in various nonhuman species and providing clues as to the evolutionary origin and function of the human language faculty. The second set of papers discusses the consequences of viewing language as a culturally evolving system in its own right, including claims that this removes the need for strong genetic biases for language acquisition, and that phylogenetic evolutionary methods can be used to reconstruct language histories. We conclude by highlighting outstanding areas for future research, including identifying the precise selection pressures that gave rise to the language faculty in ancestral hominin species, and determining the strength, domain specificity, and origin of the cultural transmission biases that shape languages as they pass along successive generations of language learners.

  15. Integrating common and rare genetic variation in diverse human populations.

    Science.gov (United States)

    Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Dermitzakis, Emmanouil; Schaffner, Stephen F; Yu, Fuli; Peltonen, Leena; Dermitzakis, Emmanouil; Bonnen, Penelope E; Altshuler, David M; Gibbs, Richard A; de Bakker, Paul I W; Deloukas, Panos; Gabriel, Stacey B; Gwilliam, Rhian; Hunt, Sarah; Inouye, Michael; Jia, Xiaoming; Palotie, Aarno; Parkin, Melissa; Whittaker, Pamela; Yu, Fuli; Chang, Kyle; Hawes, Alicia; Lewis, Lora R; Ren, Yanru; Wheeler, David; Gibbs, Richard A; Muzny, Donna Marie; Barnes, Chris; Darvishi, Katayoon; Hurles, Matthew; Korn, Joshua M; Kristiansson, Kati; Lee, Charles; McCarrol, Steven A; Nemesh, James; Dermitzakis, Emmanouil; Keinan, Alon; Montgomery, Stephen B; Pollack, Samuela; Price, Alkes L; Soranzo, Nicole; Bonnen, Penelope E; Gibbs, Richard A; Gonzaga-Jauregui, Claudia; Keinan, Alon; Price, Alkes L; Yu, Fuli; Anttila, Verneri; Brodeur, Wendy; Daly, Mark J; Leslie, Stephen; McVean, Gil; Moutsianas, Loukas; Nguyen, Huy; Schaffner, Stephen F; Zhang, Qingrun; Ghori, Mohammed J R; McGinnis, Ralph; McLaren, William; Pollack, Samuela; Price, Alkes L; Schaffner, Stephen F; Takeuchi, Fumihiko; Grossman, Sharon R; Shlyakhter, Ilya; Hostetter, Elizabeth B; Sabeti, Pardis C; Adebamowo, Clement A; Foster, Morris W; Gordon, Deborah R; Licinio, Julio; Manca, Maria Cristina; Marshall, Patricia A; Matsuda, Ichiro; Ngare, Duncan; Wang, Vivian Ota; Reddy, Deepa; Rotimi, Charles N; Royal, Charmaine D; Sharp, Richard R; Zeng, Changqing; Brooks, Lisa D; McEwen, Jean E

    2010-09-02

    Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of genetic variation.

  16. The conservation genetics juggling act: Integrating genetics and ecology, science and policy

    Science.gov (United States)

    Haig, Susan M.; Miller, Mark P.; Bellinger, Renee; Draheim, Hope M.; Mercer, Dacey; Mullins, Tom

    2016-01-01

    The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980’s following development of the polymerase chain reaction and now into the genomics era. Our lab has “grown up” with the field, having worked on these issues for over three decades. Our multi-disciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal lab, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de-list or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions. 

  17. Improvement of multi-dimensional realistic thermal-hydraulic system analysis code, MARS 1.3

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Won Jae; Chung, Bub Dong; Jeong, Jae Jun; Ha, Kwi Seok

    1998-09-01

    The MARS (Multi-dimensional Analysis of Reactor Safety) code is a multi-dimensional, best-estimate thermal-hydraulic system analysis code. This report describes the new features that have been improved in the MARS 1.3 code since the release of MARS 1.3 in July 1998. The new features include: - implementation of point kinetics model into the 3D module - unification of the heat structure model - extension of the control function to the 3D module variables - improvement of the 3D module input check function. Each of the items has been implemented in the developmental version of the MARS 1.3.1 code and, then, independently verified and assessed. The effectiveness of the new features is well verified and it is shown that these improvements greatly extend the code capability and enhance the user friendliness. Relevant input data changes are also described. In addition to the improvements, this report briefly summarizes the future code developmental activities that are being carried out or planned, such as coupling of MARS 1.3 with the containment code CONTEMPT and the three-dimensional reactor kinetics code MASTER 2.0. (author). 8 refs.

  18. ANALISIS POSITIONING KERIPIK KENTANG DENGAN PENDEKATAN METODE MULTI DIMENSIONAL SCALLING DI KOTA BATU

    Directory of Open Access Journals (Sweden)

    Siti Asmaul Mustaniroh

    2016-11-01

    Full Text Available Potato chips are one of the main products of Batu city. Based on data from Batu government’s  in 2002, there are only 2 selling units. In 2008, amount of potato chips   and another selling unit, so the research on positioning of potato chips in Batu city is important to do. The purpose of this research are to understand which attributes which influence custumer consideration to buy and to consume potato chips, and to analyze positioning which is formed between four potato chips brand (Cita Mandiri, Gizi Food, Leo, Rimbaku based on costumer perception in Batu city by using Multi Dimensional Scaling method. Attributes that influence costumer to buy and to consume potato chips are product (taste and crunchy level, price (product price compare with quality, and considerable price products, distribution (the local stock of the products or how strategic is the selling location, promotion (the using of advertising or promotion media (such as internet, radio, or brochure. Based on the Multi Dimensional Scaling Method, positioning follow this structure are Gizi Food as market leader, Leo as market challenger, and Rimbaku and Cita Mandiri as market follower.

  19. Multi-dimensional analysis of high resolution γ-ray data

    International Nuclear Information System (INIS)

    Flibotte, S.; Huttmeier, U.J.; France, G. de; Haas, B.; Romain, P.; Theisen, Ch.; Vivien, J.P.; Zen, J.; Bednarczyk, P.

    1992-01-01

    High resolution γ-ray multi-detectors capable of measuring high-fold coincidences with a large efficiency are presently under construction (EUROGAM, GASP, GAMMASPHERE). The future experimental progress in our understanding of nuclear structure at high spin critically depends on our ability to analyze the data in a multi-dimensional space and to resolve small photopeaks of interest from the generally large background. Development of programs to process such high-fold events is still in its infancy and only the 3-fold case has been treated so far. As a contribution to the software development associated with the EUROGAM spectrometer, we have written and tested the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases. The tests were performed on events generated with a Monte Carlo simulation and also on experimental data (triples) recorded with the 8π spectrometer and with a preliminary version of the EUROGAM array. (author). 7 refs., 3 tabs., 1 fig

  20. Continuous Energy, Multi-Dimensional Transport Calculations for Problem Dependent Resonance Self-Shielding

    International Nuclear Information System (INIS)

    Downar, T.

    2009-01-01

    The overall objective of the work here has been to eliminate the approximations used in current resonance treatments by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. The work here builds on the existing resonance treatment capabilities in the ORNL SCALE code system. The overall objective of the work here has been to eliminate the approximations used in current resonance treatments by developing continuous energy multidimensional transport calculations for problem dependent self-shielding calculations. The work here builds on the existing resonance treatment capabilities in the ORNL SCALE code system. Specifically, the methods here utilize the existing continuous energy SCALE5 module, CENTRM, and the multi-dimensional discrete ordinates solver, NEWT to develop a new code, CENTRM( ) NEWT. The work here addresses specific theoretical limitations in existing CENTRM resonance treatment, as well as investigates advanced numerical and parallel computing algorithms for CENTRM and NEWT in order to reduce the computational burden. The result of the work here will be a new computer code capable of performing problem dependent self-shielding analysis for both existing and proposed GENIV fuel designs. The objective of the work was to have an immediate impact on the safety analysis of existing reactors through improvements in the calculation of fuel temperature effects, as well as on the analysis of more sophisticated GENIV/NGNP systems through improvements in the depletion/transmutation of actinides for Advanced Fuel Cycle Initiatives.

  1. Estimate of pulse-sequence data acquisition system for multi-dimensional measurement

    International Nuclear Information System (INIS)

    Kitamura, Yasunori; Sakae, Takeji; Nohtomi, Akihiro; Matoba, Masaru; Matsumoto, Yuzuru.

    1996-01-01

    A pulse-sequence data acquisition system has been newly designed and estimated for the measurement of one- or multi-dimensional pulse train coming from radiation detectors. In this system, in order to realize the pulse-sequence data acquisition, the arrival time of each pulse is recorded to a memory of a personal computer (PC). For the multi-dimensional data acquisition with several input channels, each arrival-time data is tagged with a 'flag' which indicates the input channel of arriving pulse. Counting losses due to the existence of processing time of the PC are expected to be reduced by using a First-In-First-Out (FIFO) memory unit. In order to verify this system, a computer simulation was performed, Various sets of random pulse trains with different mean pulse rate (1-600 kcps) were generated by using Monte Carlo simulation technique. Those pulse trains were dealt with another code which simulates the newly-designed data acquisition system including a FIFO memory unit; the memory size was assumed to be 0-100 words. And the recorded pulse trains on the PC with the various FIFO memory sizes have been observed. From the result of the simulation, it appears that the system with 3 words FIFO memory unit works successfully up to the pulse rate of 10 kcps without any severe counting losses. (author)

  2. Improvement of multi-dimensional realistic thermal-hydraulic system analysis code, MARS 1.3

    International Nuclear Information System (INIS)

    Lee, Won Jae; Chung, Bub Dong; Jeong, Jae Jun; Ha, Kwi Seok

    1998-09-01

    The MARS (Multi-dimensional Analysis of Reactor Safety) code is a multi-dimensional, best-estimate thermal-hydraulic system analysis code. This report describes the new features that have been improved in the MARS 1.3 code since the release of MARS 1.3 in July 1998. The new features include: - implementation of point kinetics model into the 3D module - unification of the heat structure model - extension of the control function to the 3D module variables - improvement of the 3D module input check function. Each of the items has been implemented in the developmental version of the MARS 1.3.1 code and, then, independently verified and assessed. The effectiveness of the new features is well verified and it is shown that these improvements greatly extend the code capability and enhance the user friendliness. Relevant input data changes are also described. In addition to the improvements, this report briefly summarizes the future code developmental activities that are being carried out or planned, such as coupling of MARS 1.3 with the containment code CONTEMPT and the three-dimensional reactor kinetics code MASTER 2.0. (author). 8 refs

  3. Identifying associations between pig pathologies using a multi-dimensional machine learning methodology

    Directory of Open Access Journals (Sweden)

    Sanchez-Vazquez Manuel J

    2012-08-01

    Full Text Available Abstract Background Abattoir detected pathologies are of crucial importance to both pig production and food safety. Usually, more than one pathology coexist in a pig herd although it often remains unknown how these different pathologies interrelate to each other. Identification of the associations between different pathologies may facilitate an improved understanding of their underlying biological linkage, and support the veterinarians in encouraging control strategies aimed at reducing the prevalence of not just one, but two or more conditions simultaneously. Results Multi-dimensional machine learning methodology was used to identify associations between ten typical pathologies in 6485 batches of slaughtered finishing pigs, assisting the comprehension of their biological association. Pathologies potentially associated with septicaemia (e.g. pericarditis, peritonitis appear interrelated, suggesting on-going bacterial challenges by pathogens such as Haemophilus parasuis and Streptococcus suis. Furthermore, hepatic scarring appears interrelated with both milk spot livers (Ascaris suum and bacteria-related pathologies, suggesting a potential multi-pathogen nature for this pathology. Conclusions The application of novel multi-dimensional machine learning methodology provided new insights into how typical pig pathologies are potentially interrelated at batch level. The methodology presented is a powerful exploratory tool to generate hypotheses, applicable to a wide range of studies in veterinary research.

  4. Identifying associations between pig pathologies using a multi-dimensional machine learning methodology.

    Science.gov (United States)

    Sanchez-Vazquez, Manuel J; Nielen, Mirjam; Edwards, Sandra A; Gunn, George J; Lewis, Fraser I

    2012-08-31

    Abattoir detected pathologies are of crucial importance to both pig production and food safety. Usually, more than one pathology coexist in a pig herd although it often remains unknown how these different pathologies interrelate to each other. Identification of the associations between different pathologies may facilitate an improved understanding of their underlying biological linkage, and support the veterinarians in encouraging control strategies aimed at reducing the prevalence of not just one, but two or more conditions simultaneously. Multi-dimensional machine learning methodology was used to identify associations between ten typical pathologies in 6485 batches of slaughtered finishing pigs, assisting the comprehension of their biological association. Pathologies potentially associated with septicaemia (e.g. pericarditis, peritonitis) appear interrelated, suggesting on-going bacterial challenges by pathogens such as Haemophilus parasuis and Streptococcus suis. Furthermore, hepatic scarring appears interrelated with both milk spot livers (Ascaris suum) and bacteria-related pathologies, suggesting a potential multi-pathogen nature for this pathology. The application of novel multi-dimensional machine learning methodology provided new insights into how typical pig pathologies are potentially interrelated at batch level. The methodology presented is a powerful exploratory tool to generate hypotheses, applicable to a wide range of studies in veterinary research.

  5. High-frequency stock linkage and multi-dimensional stationary processes

    Science.gov (United States)

    Wang, Xi; Bao, Si; Chen, Jingchao

    2017-02-01

    In recent years, China's stock market has experienced dramatic fluctuations; in particular, in the second half of 2014 and 2015, the market rose sharply and fell quickly. Many classical financial phenomena, such as stock plate linkage, appeared repeatedly during this period. In general, these phenomena have usually been studied using daily-level data or minute-level data. Our paper focuses on the linkage phenomenon in Chinese stock 5-second-level data during this extremely volatile period. The method used to select the linkage points and the arbitrage strategy are both based on multi-dimensional stationary processes. A new program method for testing the multi-dimensional stationary process is proposed in our paper, and the detailed program is presented in the paper's appendix. Because of the existence of the stationary process, the strategy's logarithmic cumulative average return will converge under the condition of the strong ergodic theorem, and this ensures the effectiveness of the stocks' linkage points and the more stable statistical arbitrage strategy.

  6. Statistical Projections for Multi-resolution, Multi-dimensional Visual Data Exploration and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Hoa T. [Univ. of Utah, Salt Lake City, UT (United States); Stone, Daithi [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bethel, E. Wes [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2016-01-01

    An ongoing challenge in visual exploration and analysis of large, multi-dimensional datasets is how to present useful, concise information to a user for some specific visualization tasks. Typical approaches to this problem have proposed either reduced-resolution versions of data, or projections of data, or both. These approaches still have some limitations such as consuming high computation or suffering from errors. In this work, we explore the use of a statistical metric as the basis for both projections and reduced-resolution versions of data, with a particular focus on preserving one key trait in data, namely variation. We use two different case studies to explore this idea, one that uses a synthetic dataset, and another that uses a large ensemble collection produced by an atmospheric modeling code to study long-term changes in global precipitation. The primary findings of our work are that in terms of preserving the variation signal inherent in data, that using a statistical measure more faithfully preserves this key characteristic across both multi-dimensional projections and multi-resolution representations than a methodology based upon averaging.

  7. Estimate of pulse-sequence data acquisition system for multi-dimensional measurement

    Energy Technology Data Exchange (ETDEWEB)

    Kitamura, Yasunori; Sakae, Takeji; Nohtomi, Akihiro; Matoba, Masaru [Kyushu Univ., Fukuoka (Japan). Faculty of Engineering; Matsumoto, Yuzuru

    1996-07-01

    A pulse-sequence data acquisition system has been newly designed and estimated for the measurement of one- or multi-dimensional pulse train coming from radiation detectors. In this system, in order to realize the pulse-sequence data acquisition, the arrival time of each pulse is recorded to a memory of a personal computer (PC). For the multi-dimensional data acquisition with several input channels, each arrival-time data is tagged with a `flag` which indicates the input channel of arriving pulse. Counting losses due to the existence of processing time of the PC are expected to be reduced by using a First-In-First-Out (FIFO) memory unit. In order to verify this system, a computer simulation was performed, Various sets of random pulse trains with different mean pulse rate (1-600 kcps) were generated by using Monte Carlo simulation technique. Those pulse trains were dealt with another code which simulates the newly-designed data acquisition system including a FIFO memory unit; the memory size was assumed to be 0-100 words. And the recorded pulse trains on the PC with the various FIFO memory sizes have been observed. From the result of the simulation, it appears that the system with 3 words FIFO memory unit works successfully up to the pulse rate of 10 kcps without any severe counting losses. (author)

  8. Multi-dimensional analysis of high resolution {gamma}-ray data

    Energy Technology Data Exchange (ETDEWEB)

    Flibotte, S; Huttmeier, U J; France, G de; Haas, B; Romain, P; Theisen, Ch; Vivien, J P; Zen, J [Centre National de la Recherche Scientifique (CNRS), 67 - Strasbourg (France); Bednarczyk, P [Institute of Nuclear Physics, Cracow (Poland)

    1992-08-01

    High resolution {gamma}-ray multi-detectors capable of measuring high-fold coincidences with a large efficiency are presently under construction (EUROGAM, GASP, GAMMASPHERE). The future experimental progress in our understanding of nuclear structure at high spin critically depends on our ability to analyze the data in a multi-dimensional space and to resolve small photopeaks of interest from the generally large background. Development of programs to process such high-fold events is still in its infancy and only the 3-fold case has been treated so far. As a contribution to the software development associated with the EUROGAM spectrometer, we have written and tested the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases. The tests were performed on events generated with a Monte Carlo simulation and also on experimental data (triples) recorded with the 8{pi} spectrometer and with a preliminary version of the EUROGAM array. (author). 7 refs., 3 tabs., 1 fig.

  9. Meta-modelling, visualization and emulation of multi-dimensional data for virtual production intelligence

    Science.gov (United States)

    Schulz, Wolfgang; Hermanns, Torsten; Al Khawli, Toufik

    2017-07-01

    Decision making for competitive production in high-wage countries is a daily challenge where rational and irrational methods are used. The design of decision making processes is an intriguing, discipline spanning science. However, there are gaps in understanding the impact of the known mathematical and procedural methods on the usage of rational choice theory. Following Benjamin Franklin's rule for decision making formulated in London 1772, he called "Prudential Algebra" with the meaning of prudential reasons, one of the major ingredients of Meta-Modelling can be identified finally leading to one algebraic value labelling the results (criteria settings) of alternative decisions (parameter settings). This work describes the advances in Meta-Modelling techniques applied to multi-dimensional and multi-criterial optimization by identifying the persistence level of the corresponding Morse-Smale Complex. Implementations for laser cutting and laser drilling are presented, including the generation of fast and frugal Meta-Models with controlled error based on mathematical model reduction Reduced Models are derived to avoid any unnecessary complexity. Both, model reduction and analysis of multi-dimensional parameter space are used to enable interactive communication between Discovery Finders and Invention Makers. Emulators and visualizations of a metamodel are introduced as components of Virtual Production Intelligence making applicable the methods of Scientific Design Thinking and getting the developer as well as the operator more skilled.

  10. Goodness-of-fit tests for multi-dimensional copulas: Expanding application to historical drought data

    Directory of Open Access Journals (Sweden)

    Ming-wei Ma

    2013-01-01

    Full Text Available The question of how to choose a copula model that best fits a given dataset is a predominant limitation of the copula approach, and the present study aims to investigate the techniques of goodness-of-fit tests for multi-dimensional copulas. A goodness-of-fit test based on Rosenblatt's transformation was mathematically expanded from two dimensions to three dimensions and procedures of a bootstrap version of the test were provided. Through stochastic copula simulation, an empirical application of historical drought data at the Lintong Gauge Station shows that the goodness-of-fit tests perform well, revealing that both trivariate Gaussian and Student t copulas are acceptable for modeling the dependence structures of the observed drought duration, severity, and peak. The goodness-of-fit tests for multi-dimensional copulas can provide further support and help a lot in the potential applications of a wider range of copulas to describe the associations of correlated hydrological variables. However, for the application of copulas with the number of dimensions larger than three, more complicated computational efforts as well as exploration and parameterization of corresponding copulas are required.

  11. Adherence is a multi-dimensional construct in the POUNDS LOST trial

    Science.gov (United States)

    Williamson, Donald A.; Anton, Stephen D.; Han, Hongmei; Champagne, Catherine M.; Allen, Ray; LeBlanc, Eric; Ryan, Donna H.; McManus, Katherine; Laranjo, Nancy; Carey, Vincent J.; Loria, Catherine M.; Bray, George A.; Sacks, Frank M.

    2011-01-01

    Research on the conceptualization of adherence to treatment has not addressed a key question: Is adherence best defined as being a uni-dimensional or multi-dimensional behavioral construct? The primary aim of this study was to test which of these conceptual models best described adherence to a weight management program. This ancillary study was conducted as a part of the POUNDS LOST trial that tested the efficacy of four dietary macro-nutrient compositions for promoting weight loss. A sample of 811 overweight/obese adults was recruited across two clinical sites, and each participant was randomly assigned to one of four macronutrient prescriptions: (1) Low fat (20% of energy), average protein (15% of energy); (2) High fat (40%), average protein (15%); (3) Low fat (20%), high protein (25%); (4) High fat (40%), high protein (25%). Throughout the first 6 months of the study, a computer tracking system collected data on eight indicators of adherence. Computer tracking data from the initial 6 months of the intervention were analyzed using exploratory and confirmatory analyses. Two factors (accounting for 66% of the variance) were identified and confirmed: (1) behavioral adherence and (2) dietary adherence. Behavioral adherence did not differ across the four interventions, but prescription of a high fat diet (vs. a low fat diet) was found to be associated with higher levels of dietary adherence. The findings of this study indicated that adherence to a weight management program was best conceptualized as being multi-dimensional, with two dimensions: behavioral and dietary adherence. PMID:19856202

  12. Multi-dimensional self-esteem and magnitude of change in the treatment of anorexia nervosa.

    Science.gov (United States)

    Collin, Paula; Karatzias, Thanos; Power, Kevin; Howard, Ruth; Grierson, David; Yellowlees, Alex

    2016-03-30

    Self-esteem improvement is one of the main targets of inpatient eating disorder programmes. The present study sought to examine multi-dimensional self-esteem and magnitude of change in eating psychopathology among adults participating in a specialist inpatient treatment programme for anorexia nervosa. A standardised assessment battery, including multi-dimensional measures of eating psychopathology and self-esteem, was completed pre- and post-treatment for 60 participants (all white Scottish female, mean age=25.63 years). Statistical analyses indicated that self-esteem improved with eating psychopathology and weight over the course of treatment, but that improvements were domain-specific and small in size. Global self-esteem was not predictive of treatment outcome. Dimensions of self-esteem at baseline (Lovability and Moral Self-approval), however, were predictive of magnitude of change in dimensions of eating psychopathology (Shape and Weight Concern). Magnitude of change in Self-Control and Lovability dimensions were predictive of magnitude of change in eating psychopathology (Global, Dietary Restraint, and Shape Concern). The results of this study demonstrate that the relationship between self-esteem and eating disorder is far from straightforward, and suggest that future research and interventions should focus less exclusively on self-esteem as a uni-dimensional psychological construct. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. Multi-dimensional design window search system using neural networks in reactor core design

    International Nuclear Information System (INIS)

    Kugo, Teruhiko; Nakagawa, Masayuki

    2000-02-01

    In the reactor core design, many parametric survey calculations should be carried out to decide an optimal set of basic design parameter values. They consume a large amount of computation time and labor in the conventional way. To support directly design work, we investigate a procedure to search efficiently a design window, which is defined as feasible design parameter ranges satisfying design criteria and requirements, in a multi-dimensional space composed of several basic design parameters. We apply the present method to the neutronics and thermal hydraulics fields and develop the multi-dimensional design window search system using it. The principle of the present method is to construct the multilayer neural network to simulate quickly a response of an analysis code through a training process, and to reduce computation time using the neural network without parametric study using analysis codes. The system works on an engineering workstation (EWS) with efficient man-machine interface for pre- and post-processing. This report describes the principle of the present method, the structure of the system, the guidance of the usages of the system, the guideline for the efficient training of neural networks, the instructions of the input data for analysis calculation and so on. (author)

  14. Experimental observation of a multi-dimensional mixing behavior of steam-water flow in the MIDAS test facility

    International Nuclear Information System (INIS)

    Kweon, T. S.; Yun, B. J.; Ah, D. J.; Ju, I. C.; Song, C. H.; Park, J. K.

    2001-01-01

    Multi-dimensional thermal-hydraulic hehavior, such as ECC (Emergency Core Cooling) bypass, ECC penetration, steam-water condensation and accumulated water level, in an annular downcomer of a PWR (Pressurized Water Reactor) reactor vessel with a DVI(Direct Vessel Injection) injection mode is presented based on the experimental observations in the MIDAS (Multi-dimensional Investigation in Downcomer Annulus Simulation) steam-water facility. From the steady-state tests to similate a late reflood phase of LBLOCA (Large Break Loss-of-Coolant Accidents), major thermal-hydraulic phenomena in the downcomer are quantified under a wide range of test conditions. Especially, isothermal lines show well multi-dimensional phenomena of phase interaction between steam and water in the annulus downcomer. Overall test results show that multi-dimensional thermal-hydraulic behaviors occur in the downcomer annulus region as expected. The MIDAS test facility is a steam-water separate effect test facility, which is 1/4.93 linearly scaled-down of a 1400 MWe PWR type of nuclear reactor, with focusing on understanding multi-dimensional thermal-hydraulic phenomena in annulus downcomer with various types of safety injection location during refill or reflood phase of a LBLOCA in PWR

  15. Integration of Generic Multi-dimensional Model and Operational Policies for Batch Cooling Crystallization

    DEFF Research Database (Denmark)

    Abdul Samad, Noor Asma Fazli; Singh, Ravendra; Sin, Gürkan

    2011-01-01

    Crystallization processes form an important class of separation methods that are frequently used in the chemical, the pharmaceutical and the food industry. The specifications of the crystal product are usually given in terms of crystal size, shape and purity. In order to predict the desired cryst...

  16. Adaptive method for multi-dimensional integration and selection of a base of chaos polynomials

    International Nuclear Information System (INIS)

    Crestaux, T.

    2011-01-01

    This research thesis addresses the propagation of uncertainty in numerical simulations and its processing within a probabilistic framework by a functional approach based on random variable functions. The author reports the use of the spectral method to represent random variables by development in polynomial chaos. More precisely, the author uses the method of non-intrusive projection which uses the orthogonality of Chaos Polynomials to compute the development coefficients by approximation of scalar products. The approach is applied to a cavity and to waste storage [fr

  17. Development and assessment of Multi-dimensional flow models in the thermal-hydraulic system analysis code MARS

    Energy Technology Data Exchange (ETDEWEB)

    Chung, B. D.; Bae, S. W.; Jeong, J. J.; Lee, S. M

    2005-04-15

    A new multi-dimensional component has been developed to allow for more flexible 3D capabilities in the system code, MARS. This component can be applied in the Cartesian and cylindrical coordinates. For the development of this model, the 3D convection and diffusion terms are implemented in the momentum and energy equation. And a simple Prandtl's mixing length model is applied for the turbulent viscosity. The developed multi-dimensional component was assessed against five conceptual problems with analytic solution. And some SETs are calculated and compared with experimental data. With this newly developed multi-dimensional flow module, the MARS code can realistic calculate the flow fields in pools such as those occurring in the core, steam generators and IRWST.

  18. Development and assessment of Multi-dimensional flow models in the thermal-hydraulic system analysis code MARS

    International Nuclear Information System (INIS)

    Chung, B. D.; Bae, S. W.; Jeong, J. J.; Lee, S. M.

    2005-04-01

    A new multi-dimensional component has been developed to allow for more flexible 3D capabilities in the system code, MARS. This component can be applied in the Cartesian and cylindrical coordinates. For the development of this model, the 3D convection and diffusion terms are implemented in the momentum and energy equation. And a simple Prandtl's mixing length model is applied for the turbulent viscosity. The developed multi-dimensional component was assessed against five conceptual problems with analytic solution. And some SETs are calculated and compared with experimental data. With this newly developed multi-dimensional flow module, the MARS code can realistic calculate the flow fields in pools such as those occurring in the core, steam generators and IRWST

  19. Best-estimated multi-dimensional calculation during LB LOCA for APR1400

    International Nuclear Information System (INIS)

    Oh, D. Y.; Bang, Y. S.; Cheong, A. J.; Woong, S.; Korea, W.

    2010-01-01

    Best-estimated (BE) calculation with uncertainty quantification for the emergency core cooling system (ECCS) performance analysis during Loss of Coolant Accident (LOCA) is more broadly used in nuclear industries and regulations. In Korea, demand on regulatory audit calculation is continuously increasing to support the safety review for life extension, power up-rating and advanced nuclear reactor design. The thermal-hydraulic system code, MARS (Multi-dimensional Analysis of Reactor Safety), with multi-dimensional capability is used for audit calculation. It achieves to describe the complicated phenomena in reactor coolant system by very effectively consolidating the one dimensional RELAP5/MOD3 with the multidimensional COBRA-TF codes. The advanced power reactors (APR1400) to be evaluated has four separated hydraulic trains of the high pressure injection system (HPSI) with direct vessel injection (DVI) which is different from the existing commercial PWRs. Also, the therma-hydraulic behavior of DVI plant would be considerably different from that of a cold-leg safety injection since the low pressure safety injection system are eliminated and the high pressure safety flow are injected into the specific elevation of reactor vessel downcomer. The ECCS bypass induced by the downcomer boiling due to hot wall heating of reactor vessel during reflooding phase is one of the important phenomena which should be considered in DVI plants. Therefore, in this study, BE calculation with one-dimensional (1-D) and multi-dimensional (multi-D) MARS models during LBLOCA are performed for APR1400 plant. In the multi-D evaluation, the reactor vessel is modeled by multi-D components and the specific treatment of flow path inside reactor vessel, e.g., upper guide structure, is essential. The concept of hot zone is adopted to simulate the limiting thermal-hydraulic conditions surrounding hot rod, which is similar to hot channel in 1-D. Also, alternative treatment of the hot rods in multi-D is

  20. Approximate series solution of multi-dimensional, time fractional-order (heat-like) diffusion equations using FRDTM.

    Science.gov (United States)

    Singh, Brajesh K; Srivastava, Vineet K

    2015-04-01

    The main goal of this paper is to present a new approximate series solution of the multi-dimensional (heat-like) diffusion equation with time-fractional derivative in Caputo form using a semi-analytical approach: fractional-order reduced differential transform method (FRDTM). The efficiency of FRDTM is confirmed by considering four test problems of the multi-dimensional time fractional-order diffusion equation. FRDTM is a very efficient, effective and powerful mathematical tool which provides exact or very close approximate solutions for a wide range of real-world problems arising in engineering and natural sciences, modelled in terms of differential equations.

  1. Rarefaction and shock waves for multi-dimensional hyperbolic conservation laws

    International Nuclear Information System (INIS)

    Dening, Li

    1991-01-01

    In this paper, the author wants to show the local existence of a solution of combination of shock and rarefaction waves for the multi-dimensional hyperbolic system of conservation laws. The typical example he has in mind is the Euler equations for compressible fluid. More generally, he studies the hyperbolic system of conservation laws ∂ t F 0 (u) + Σ j=1 n ∂ x j F j (u)=0 where u=(u 1 ....,u m ) and F j (u), j=0,...,n are m-dimensional vector-valued functions. He'll impose some conditions in the following on the systems (1.2). All these conditions are satisfied by the Euler equations

  2. A new analytical method to solve the heat equation for a multi-dimensional composite slab

    International Nuclear Information System (INIS)

    Lu, X; Tervola, P; Viljanen, M

    2005-01-01

    A novel analytical approach has been developed for heat conduction in a multi-dimensional composite slab subject to time-dependent boundary changes of the first kind. Boundary temperatures are represented as Fourier series. Taking advantage of the periodic properties of boundary changes, the analytical solution is obtained and expressed explicitly. Nearly all the published works necessitate searching for associated eigenvalues in solving such a problem even for a one-dimensional composite slab. In this paper, the proposed method involves no iterative computation such as numerically searching for eigenvalues and no residue evaluation. The adopted method is simple which represents an extension of the novel analytical approach derived for the one-dimensional composite slab. Moreover, the method of 'separation of variables' employed in this paper is new. The mathematical formula for solutions is concise and straightforward. The physical parameters are clearly shown in the formula. Further comparison with numerical calculations is presented

  3. Extending the Implicit Association Test (IAT): assessing consumer attitudes based on multi-dimensional implicit associations.

    Science.gov (United States)

    Gattol, Valentin; Sääksjärvi, Maria; Carbon, Claus-Christian

    2011-01-05

    The authors present a procedural extension of the popular Implicit Association Test (IAT) that allows for indirect measurement of attitudes on multiple dimensions (e.g., safe-unsafe; young-old; innovative-conventional, etc.) rather than on a single evaluative dimension only (e.g., good-bad). In two within-subjects studies, attitudes toward three automobile brands were measured on six attribute dimensions. Emphasis was placed on evaluating the methodological appropriateness of the new procedure, providing strong evidence for its reliability, validity, and sensitivity. This new procedure yields detailed information on the multifaceted nature of brand associations that can add up to a more abstract overall attitude. Just as the IAT, its multi-dimensional extension/application (dubbed md-IAT) is suited for reliably measuring attitudes consumers may not be consciously aware of, able to express, or willing to share with the researcher.

  4. Single-phase multi-dimensional thermohydraulics direct numerical simulation code DINUS-3. Input data description

    Energy Technology Data Exchange (ETDEWEB)

    Muramatsu, Toshiharu [Power Reactor and Nuclear Fuel Development Corp., Oarai, Ibaraki (Japan). Oarai Engineering Center

    1998-08-01

    This report explains the numerical methods and the set-up method of input data for a single-phase multi-dimensional thermohydraulics direct numerical simulation code DINUS-3 (Direct Numerical Simulation using a 3rd-order upwind scheme). The code was developed to simulate non-stationary temperature fluctuation phenomena related to thermal striping phenomena, developed at Power Reactor and Nuclear Fuel Development Corporation (PNC). The DINUS-3 code was characterized by the use of a third-order upwind scheme for convection terms in instantaneous Navier-Stokes and energy equations, and an adaptive control system based on the Fuzzy theory to control time step sizes. Author expect this report is very useful to utilize the DINUS-3 code for the evaluation of various non-stationary thermohydraulic phenomena in reactor applications. (author)

  5. Application of neural network to multi-dimensional design window search

    International Nuclear Information System (INIS)

    Kugo, T.; Nakagawa, M.

    1996-01-01

    In the reactor core design, many parametric survey calculations should be carried out to decide an optimal set of basic design parameter values. They consume a large amount of computation time and labor in the conventional way. To support directly such a work, we investigate a procedure to search efficiently a design window, which is defined as feasible design parameter ranges satisfying design criteria and requirements, in a multi-dimensional space composed of several basic design parameters. A principle of the present method is to construct the multilayer neural network to simulate quickly a response of an analysis code through a training process, and to reduce computation time using the neural network as a substitute of an analysis code. We apply the present method to a fuel pin design of high conversion light water reactors for the neutronics and thermal hydraulics fields to demonstrate performances of the method. (author)

  6. Multi-dimensional analysis of high resolution {gamma}-ray data

    Energy Technology Data Exchange (ETDEWEB)

    Flibotte, S.; Huettmeier, U.J.; France, G. de; Haas, B.; Romain, P.; Theisen, Ch.; Vivien, J.P.; Zen, J. [Strasbourg-1 Univ., 67 (France). Centre de Recherches Nucleaires

    1992-12-31

    A new generation of high resolution {gamma}-ray spectrometers capable of recording high-fold coincidence events with a large efficiency will soon be available. Algorithms are developed to analyze high-fold {gamma}-ray coincidences. As a contribution to the software development associated with the EUROGAM spectrometer, the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases were tested. The tests were performed on events generated with a Monte Carlo simulation and also on real experimental triple data recorded with the 8{pi} spectrometer and with a preliminary version of the EUROGAM array. (R.P.) 14 refs.; 3 figs.; 3 tabs.

  7. A Complete Video Coding Chain Based on Multi-Dimensional Discrete Cosine Transform

    Directory of Open Access Journals (Sweden)

    T. Fryza

    2010-09-01

    Full Text Available The paper deals with a video compression method based on the multi-dimensional discrete cosine transform. In the text, the encoder and decoder architectures including the definitions of all mathematical operations like the forward and inverse 3-D DCT, quantization and thresholding are presented. According to the particular number of currently processed pictures, the new quantization tables and entropy code dictionaries are proposed in the paper. The practical properties of the 3-D DCT coding chain compared with the modern video compression methods (such as H.264 and WebM and the computing complexity are presented as well. It will be proved the best compress properties could be achieved by complex H.264 codec. On the other hand the computing complexity - especially on the encoding side - is lower for the 3-D DCT method.

  8. Multi-dimensional analysis of high resolution γ-ray data

    International Nuclear Information System (INIS)

    Flibotte, S.; Huettmeier, U.J.; France, G. de; Haas, B.; Romain, P.; Theisen, Ch.; Vivien, J.P.; Zen, J.

    1992-01-01

    A new generation of high resolution γ-ray spectrometers capable of recording high-fold coincidence events with a large efficiency will soon be available. Algorithms are developed to analyze high-fold γ-ray coincidences. As a contribution to the software development associated with the EUROGAM spectrometer, the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases were tested. The tests were performed on events generated with a Monte Carlo simulation and also on real experimental triple data recorded with the 8π spectrometer and with a preliminary version of the EUROGAM array. (R.P.) 14 refs.; 3 figs.; 3 tabs

  9. MULTI-DIMENSIONAL MASS SPECTROMETRY-BASED SHOTGUN LIPIDOMICS AND NOVEL STRATEGIES FOR LIPIDOMIC ANALYSES

    Science.gov (United States)

    Han, Xianlin; Yang, Kui; Gross, Richard W.

    2011-01-01

    Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell’s lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems. PMID:21755525

  10. Challenges in Constructing a Multi-dimensional European Job Quality Index

    DEFF Research Database (Denmark)

    Leschke, Janine; Watt, Andrew

    2014-01-01

    quality performances and the outcomes in six sub-dimensions of job quality and compare them with each other, across gender and over time. At the same time, the limitations of such a composite index need to be borne in mind. The most important challenges are the availability (over time), timeliness......There are few attempts to benchmark job quality in a multi-dimensional perspective across Europe. Against this background, we have created a synthetic job quality index (JQI) for the EU27 countries in an attempt to shed light on the question of how European countries compare with each other and how...... they are developing over time in terms of job quality. Taking account of the multi-faceted nature of job quality, the JQI is compiled on the basis of six sub-indices which cover the most important dimensions of job quality as identified in the literature. The paper addresses the methods used to construct the JQI...

  11. Energy method for multi-dimensional balance laws with non-local dissipation

    KAUST Repository

    Duan, Renjun

    2010-06-01

    In this paper, we are concerned with a class of multi-dimensional balance laws with a non-local dissipative source which arise as simplified models for the hydrodynamics of radiating gases. At first we introduce the energy method in the setting of smooth perturbations and study the stability of constants states. Precisely, we use Fourier space analysis to quantify the energy dissipation rate and recover the optimal time-decay estimates for perturbed solutions via an interpolation inequality in Fourier space. As application, the developed energy method is used to prove stability of smooth planar waves in all dimensions n2, and also to show existence and stability of time-periodic solutions in the presence of the time-periodic source. Optimal rates of convergence of solutions towards the planar waves or time-periodic states are also shown provided initially L1-perturbations. © 2009 Elsevier Masson SAS.

  12. Multi-dimensional fiber-optic radiation sensor for ocular proton therapy dosimetry

    International Nuclear Information System (INIS)

    Jang, K.W.; Yoo, W.J.; Moon, J.; Han, K.T.; Park, B.G.; Shin, D.; Park, S-Y.; Lee, B.

    2012-01-01

    In this study, we fabricated a multi-dimensional fiber-optic radiation sensor, which consists of organic scintillators, plastic optical fibers and a water phantom with a polymethyl methacrylate structure for the ocular proton therapy dosimetry. For the purpose of sensor characterization, we measured the spread out Bragg-peak of 120 MeV proton beam using a one-dimensional sensor array, which has 30 fiber-optic radiation sensors with a 1.5 mm interval. A uniform region of spread out Bragg-peak using the one-dimensional fiber-optic radiation sensor was obtained from 20 to 25 mm depth of a phantom. In addition, the Bragg-peak of 109 MeV proton beam was measured at the depth of 11.5 mm of a phantom using a two-dimensional sensor array, which has 10×3 sensor array with a 0.5 mm interval.

  13. Multi-dimensional relativistic simulations of core-collapse supernovae with energy-dependent neutrino transport

    International Nuclear Information System (INIS)

    Mueller, Bernhard

    2009-01-01

    In this thesis, we have presented the first multi-dimensional models of core-collapse supernovae that combine a detailed, up-to-date treatment of neutrino transport, the equation of state, and - in particular - general relativistic gravity. Building on the well-tested neutrino transport code VERTEX and the GR hydrodynamics code CoCoNuT, we developed and implemented a relativistic generalization of a ray-by-ray-plus method for energy-dependent neutrino transport. The result of these effort, the VERTEX-CoCoNuT code, also incorporates a number of improved numerical techniques that have not been used in the code components VERTEX and CoCoNuT before. In order to validate the VERTEX-CoCoNuT code, we conducted several test simulations in spherical symmetry, most notably a comparison with the one-dimensional relativistic supernova code AGILE-BOLTZTRAN and the Newtonian PROMETHEUSVERTEX code. (orig.)

  14. Multi-dimensional single-spin nano-optomechanics with a levitated nanodiamond

    Science.gov (United States)

    Neukirch, Levi P.; von Haartman, Eva; Rosenholm, Jessica M.; Nick Vamivakas, A.

    2015-10-01

    Considerable advances made in the development of nanomechanical and nano-optomechanical devices have enabled the observation of quantum effects, improved sensitivity to minute forces, and provided avenues to probe fundamental physics at the nanoscale. Concurrently, solid-state quantum emitters with optically accessible spin degrees of freedom have been pursued in applications ranging from quantum information science to nanoscale sensing. Here, we demonstrate a hybrid nano-optomechanical system composed of a nanodiamond (containing a single nitrogen-vacancy centre) that is levitated in an optical dipole trap. The mechanical state of the diamond is controlled by modulation of the optical trapping potential. We demonstrate the ability to imprint the multi-dimensional mechanical motion of the cavity-free mechanical oscillator into the nitrogen-vacancy centre fluorescence and manipulate the mechanical system's intrinsic spin. This result represents the first step towards a hybrid quantum system based on levitating nanoparticles that simultaneously engages optical, phononic and spin degrees of freedom.

  15. CANDU safety analysis system establishment; development of trip coverage and multi-dimensional hydrogen analysis methodology

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jong Ho; Ohn, M. Y.; Cho, C. H. [KOPEC, Taejon (Korea)

    2002-03-01

    The trip coverage analysis model requires the geometry network for primary and secondary circuit as well as the plant control system to simulate all the possible plant operating conditions throughout the plant life. The model was validated for the power maneuvering and the Wolsong 4 commissioning test. The trip coverage map was produced for the large break loss of coolant accident and the complete loss of class IV power event. The reliable multi-dimensional hydrogen analysis requires the high capability for thermal hydraulic modelling. To acquire such a basic capability and verify the applicability of GOTHIC code, the assessment of heat transfer model, hydrogen mixing and combustion model was performed. Also, the assessment methodology for flame acceleration and deflagration-to-detonation transition is established. 22 refs., 120 figs., 31 tabs. (Author)

  16. Development of Multi-Dimensional RELAP5 with Conservative Momentum Flux

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Hyung Wook; Lee, Sang Yong [KINGS, Ulsan (Korea, Republic of)

    2016-10-15

    The non-conservative form of the momentum equations are used in many codes. It tells us that using the non-conservative form in the non-porous or open body problem may not be good. In this paper, two aspects concerning the multi-dimensional codes will be discussed. Once the validity of the modified code is confirmed, it is applied to the analysis of the large break LOCA for APR-1400. One of them is the properness of the type of the momentum equations. The other discussion will be the implementation of the conservative momentum flux term in RELAP5. From the present study and former, it is shown that the RELAP5 Multi-D with conservative convective terms is applicable to LOCA analysis. And the implementation of the conservative convective terms in RELAP5 seems to be successful. Further efforts have to be made on making it more robust.

  17. A nodal collocation approximation for the multi-dimensional PL equations - 2D applications

    International Nuclear Information System (INIS)

    Capilla, M.; Talavera, C.F.; Ginestar, D.; Verdu, G.

    2008-01-01

    A classical approach to solve the neutron transport equation is to apply the spherical harmonics method obtaining a finite approximation known as the P L equations. In this work, the derivation of the P L equations for multi-dimensional geometries is reviewed and a nodal collocation method is developed to discretize these equations on a rectangular mesh based on the expansion of the neutronic fluxes in terms of orthogonal Legendre polynomials. The performance of the method and the dominant transport Lambda Modes are obtained for a homogeneous 2D problem, a heterogeneous 2D anisotropic scattering problem, a heterogeneous 2D problem and a benchmark problem corresponding to a MOX fuel reactor core

  18. Fuzzy Regression Prediction and Application Based on Multi-Dimensional Factors of Freight Volume

    Science.gov (United States)

    Xiao, Mengting; Li, Cheng

    2018-01-01

    Based on the reality of the development of air cargo, the multi-dimensional fuzzy regression method is used to determine the influencing factors, and the three most important influencing factors of GDP, total fixed assets investment and regular flight route mileage are determined. The system’s viewpoints and analogy methods, the use of fuzzy numbers and multiple regression methods to predict the civil aviation cargo volume. In comparison with the 13th Five-Year Plan for China’s Civil Aviation Development (2016-2020), it is proved that this method can effectively improve the accuracy of forecasting and reduce the risk of forecasting. It is proved that this model predicts civil aviation freight volume of the feasibility, has a high practical significance and practical operation.

  19. Multi Dimensional Honey Bee Foraging Algorithm Based on Optimal Energy Consumption

    Science.gov (United States)

    Saritha, R.; Vinod Chandra, S. S.

    2017-10-01

    In this paper a new nature inspired algorithm is proposed based on natural foraging behavior of multi-dimensional honey bee colonies. This method handles issues that arise when food is shared from multiple sources by multiple swarms at multiple destinations. The self organizing nature of natural honey bee swarms in multiple colonies is based on the principle of energy consumption. Swarms of multiple colonies select a food source to optimally fulfill the requirements of its colonies. This is based on the energy requirement for transporting food between a source and destination. Minimum use of energy leads to maximizing profit in each colony. The mathematical model proposed here is based on this principle. This has been successfully evaluated by applying it on multi-objective transportation problem for optimizing cost and time. The algorithm optimizes the needs at each destination in linear time.

  20. Energy method for multi-dimensional balance laws with non-local dissipation

    KAUST Repository

    Duan, Renjun; Fellner, Klemens; Zhu, Changjiang

    2010-01-01

    In this paper, we are concerned with a class of multi-dimensional balance laws with a non-local dissipative source which arise as simplified models for the hydrodynamics of radiating gases. At first we introduce the energy method in the setting of smooth perturbations and study the stability of constants states. Precisely, we use Fourier space analysis to quantify the energy dissipation rate and recover the optimal time-decay estimates for perturbed solutions via an interpolation inequality in Fourier space. As application, the developed energy method is used to prove stability of smooth planar waves in all dimensions n2, and also to show existence and stability of time-periodic solutions in the presence of the time-periodic source. Optimal rates of convergence of solutions towards the planar waves or time-periodic states are also shown provided initially L1-perturbations. © 2009 Elsevier Masson SAS.

  1. Multi-dimensional relativistic simulations of core-collapse supernovae with energy-dependent neutrino transport

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Bernhard

    2009-05-07

    In this thesis, we have presented the first multi-dimensional models of core-collapse supernovae that combine a detailed, up-to-date treatment of neutrino transport, the equation of state, and - in particular - general relativistic gravity. Building on the well-tested neutrino transport code VERTEX and the GR hydrodynamics code CoCoNuT, we developed and implemented a relativistic generalization of a ray-by-ray-plus method for energy-dependent neutrino transport. The result of these effort, the VERTEX-CoCoNuT code, also incorporates a number of improved numerical techniques that have not been used in the code components VERTEX and CoCoNuT before. In order to validate the VERTEX-CoCoNuT code, we conducted several test simulations in spherical symmetry, most notably a comparison with the one-dimensional relativistic supernova code AGILE-BOLTZTRAN and the Newtonian PROMETHEUSVERTEX code. (orig.)

  2. Multi-Dimensional Bitmap Indices for Optimising Data Access within Object Oriented Databases at CERN

    CERN Document Server

    Stockinger, K

    2001-01-01

    Efficient query processing in high-dimensional search spaces is an important requirement for many analysis tools. In the literature on index data structures one can find a wide range of methods for optimising database access. In particular, bitmap indices have recently gained substantial popularity in data warehouse applications with large amounts of read mostly data. Bitmap indices are implemented in various commercial database products and are used for querying typical business applications. However, scientific data that is mostly characterised by non-discrete attribute values cannot be queried efficiently by the techniques currently supported. In this thesis we propose a novel access method based on bitmap indices that efficiently handles multi-dimensional queries against typical scientific data. The algorithm is called GenericRangeEval and is an extension of a bitmap index for discrete attribute values. By means of a cost model we study the performance of queries with various selectivities against uniform...

  3. Analytical modeling for fractional multi-dimensional diffusion equations by using Laplace transform

    Directory of Open Access Journals (Sweden)

    Devendra Kumar

    2015-01-01

    Full Text Available In this paper, we propose a simple numerical algorithm for solving multi-dimensional diffusion equations of fractional order which describes density dynamics in a material undergoing diffusion by using homotopy analysis transform method. The fractional derivative is described in the Caputo sense. This homotopy analysis transform method is an innovative adjustment in Laplace transform method and makes the calculation much simpler. The technique is not limited to the small parameter, such as in the classical perturbation method. The scheme gives an analytical solution in the form of a convergent series with easily computable components, requiring no linearization or small perturbation. The numerical solutions obtained by the proposed method indicate that the approach is easy to implement and computationally very attractive.

  4. A multi-dimensional framework to assist in the design of successful shared services centres

    Directory of Open Access Journals (Sweden)

    Mark Borman

    2012-04-01

    Full Text Available Organisations are increasingly looking to realise the benefits of shared services yet there is little guidance available as to the best way to proceed. A multi-dimensional framework is presented that considers the service provided, the design of the shared services centre and the organisational context it sits within. Case studies are then used to determine what specific attributes from each dimension are associated with success and how they should be aligned. It is concluded that there appears to be a single, broadly standard pattern of attributes for successful Shared Services Centres (SSCs across the proposed dimensions of Activity, Environment, History, Resources, Strategy, Structure, Management, Technology and Individual Skills. It should also be noted though that some deviation from the identified standard along some dimensions is possible without adverse effect – ie that the alignment identified appears to be relatively soft.

  5. TWO-DIMENSIONAL CORE-COLLAPSE SUPERNOVA MODELS WITH MULTI-DIMENSIONAL TRANSPORT

    International Nuclear Information System (INIS)

    Dolence, Joshua C.; Burrows, Adam; Zhang, Weiqun

    2015-01-01

    We present new two-dimensional (2D) axisymmetric neutrino radiation/hydrodynamic models of core-collapse supernova (CCSN) cores. We use the CASTRO code, which incorporates truly multi-dimensional, multi-group, flux-limited diffusion (MGFLD) neutrino transport, including all relevant O(v/c) terms. Our main motivation for carrying out this study is to compare with recent 2D models produced by other groups who have obtained explosions for some progenitor stars and with recent 2D VULCAN results that did not incorporate O(v/c) terms. We follow the evolution of 12, 15, 20, and 25 solar-mass progenitors to approximately 600 ms after bounce and do not obtain an explosion in any of these models. Though the reason for the qualitative disagreement among the groups engaged in CCSN modeling remains unclear, we speculate that the simplifying ''ray-by-ray'' approach employed by all other groups may be compromising their results. We show that ''ray-by-ray'' calculations greatly exaggerate the angular and temporal variations of the neutrino fluxes, which we argue are better captured by our multi-dimensional MGFLD approach. On the other hand, our 2D models also make approximations, making it difficult to draw definitive conclusions concerning the root of the differences between groups. We discuss some of the diagnostics often employed in the analyses of CCSN simulations and highlight the intimate relationship between the various explosion conditions that have been proposed. Finally, we explore the ingredients that may be missing in current calculations that may be important in reproducing the properties of the average CCSNe, should the delayed neutrino-heating mechanism be the correct mechanism of explosion

  6. Calculation of multi-dimensional dose distribution in medium due to proton beam incidence

    International Nuclear Information System (INIS)

    Kawachi, Kiyomitsu; Inada, Tetsuo

    1978-01-01

    The method of analyzing the multi-dimensional dose distribution in a medium due to proton beam incidence is presented to obtain the reliable and simplified method from clinical viewpoint, especially for the medical treatment of cancer. The heavy ion beam being taken out of an accelerator has to be adjusted to fit cancer location and size, utilizing a modified range modulator, a ridge filter, a bolus and a special scanning apparatus. The precise calculation of multi-dimensional dose distribution of proton beam is needed to fit treatment to a limit part. The analytical formulas consist of those for the fluence distribution in a medium, the divergence of flying range, the energy distribution itself, the dose distribution in side direction and the two-dimensional dose distribution. The fluence distribution in polystyrene in case of the protons with incident energy of 40 and 60 MeV, the energy distribution of protons at the position of a Bragg peak for various values of incident energy, the depth dose distribution in polystyrene in case of the protons with incident energy of 40 and 60 MeV and average energy of 100 MeV, the proton fluence and dose distribution as functions of depth for the incident average energy of 250 MeV, the statistically estimated percentage errors in the proton fluence and dose distribution, the estimated minimum detectable tumor thickness as a function of the number of incident protons for the different incident spectra with average energy of 250 MeV, the isodose distribution in a plane containing the central axis in case of the incident proton beam of 3 mm diameter and 40 MeV and so on are presented as the analytical results, and they are evaluated. (Nakai, Y.)

  7. Predicting respiratory tumor motion with multi-dimensional adaptive filters and support vector regression

    International Nuclear Information System (INIS)

    Riaz, Nadeem; Wiersma, Rodney; Mao Weihua; Xing Lei; Shanker, Piyush; Gudmundsson, Olafur; Widrow, Bernard

    2009-01-01

    Intra-fraction tumor tracking methods can improve radiation delivery during radiotherapy sessions. Image acquisition for tumor tracking and subsequent adjustment of the treatment beam with gating or beam tracking introduces time latency and necessitates predicting the future position of the tumor. This study evaluates the use of multi-dimensional linear adaptive filters and support vector regression to predict the motion of lung tumors tracked at 30 Hz. We expand on the prior work of other groups who have looked at adaptive filters by using a general framework of a multiple-input single-output (MISO) adaptive system that uses multiple correlated signals to predict the motion of a tumor. We compare the performance of these two novel methods to conventional methods like linear regression and single-input, single-output adaptive filters. At 400 ms latency the average root-mean-square-errors (RMSEs) for the 14 treatment sessions studied using no prediction, linear regression, single-output adaptive filter, MISO and support vector regression are 2.58, 1.60, 1.58, 1.71 and 1.26 mm, respectively. At 1 s, the RMSEs are 4.40, 2.61, 3.34, 2.66 and 1.93 mm, respectively. We find that support vector regression most accurately predicts the future tumor position of the methods studied and can provide a RMSE of less than 2 mm at 1 s latency. Also, a multi-dimensional adaptive filter framework provides improved performance over single-dimension adaptive filters. Work is underway to combine these two frameworks to improve performance.

  8. Optimal sensor configuration for flexible structures with multi-dimensional mode shapes

    International Nuclear Information System (INIS)

    Chang, Minwoo; Pakzad, Shamim N

    2015-01-01

    A framework for deciding the optimal sensor configuration is implemented for civil structures with multi-dimensional mode shapes, which enhances the applicability of structural health monitoring for existing structures. Optimal sensor placement (OSP) algorithms are used to determine the best sensor configuration for structures with a priori knowledge of modal information. The signal strength at each node is evaluated by effective independence and modified variance methods. Euclidean norm of signal strength indices associated with each node is used to expand OSP applicability into flexible structures. The number of sensors for each method is determined using the threshold for modal assurance criterion (MAC) between estimated (from a set of observations) and target mode shapes. Kriging is utilized to infer the modal estimates for unobserved locations with a weighted sum of known neighbors. A Kriging model can be expressed as a sum of linear regression and random error which is assumed as the realization of a stochastic process. This study presents the effects of Kriging parameters for the accurate estimation of mode shapes and the minimum number of sensors. The feasible ranges to satisfy MAC criteria are investigated and used to suggest the adequate searching bounds for associated parameters. The finite element model of a tall building is used to demonstrate the application of optimal sensor configuration. The dynamic modes of flexible structure at centroid are appropriately interpreted into the outermost sensor locations when OSP methods are implemented. Kriging is successfully used to interpolate the mode shapes from a set of sensors and to monitor structures associated with multi-dimensional mode shapes. (paper)

  9. On Some New Properties of the Fundamental Solution to the Multi-Dimensional Space- and Time-Fractional Diffusion-Wave Equation

    Directory of Open Access Journals (Sweden)

    Yuri Luchko

    2017-12-01

    Full Text Available In this paper, some new properties of the fundamental solution to the multi-dimensional space- and time-fractional diffusion-wave equation are deduced. We start with the Mellin-Barnes representation of the fundamental solution that was derived in the previous publications of the author. The Mellin-Barnes integral is used to obtain two new representations of the fundamental solution in the form of the Mellin convolution of the special functions of the Wright type. Moreover, some new closed-form formulas for particular cases of the fundamental solution are derived. In particular, we solve the open problem of the representation of the fundamental solution to the two-dimensional neutral-fractional diffusion-wave equation in terms of the known special functions.

  10. Development and validation of the Bullying and Cyberbullying Scale for Adolescents: A multi-dimensional measurement model.

    Science.gov (United States)

    Thomas, Hannah J; Scott, James G; Coates, Jason M; Connor, Jason P

    2018-05-03

    Intervention on adolescent bullying is reliant on valid and reliable measurement of victimization and perpetration experiences across different behavioural expressions. This study developed and validated a survey tool that integrates measurement of both traditional and cyber bullying to test a theoretically driven multi-dimensional model. Adolescents from 10 mainstream secondary schools completed a baseline and follow-up survey (N = 1,217; M age  = 14 years; 66.2% male). The Bullying and cyberbullying Scale for Adolescents (BCS-A) developed for this study comprised parallel victimization and perpetration subscales, each with 20 items. Additional measures of bullying (Olweus Global Bullying and the Forms of Bullying Scale [FBS]), as well as measures of internalizing and externalizing problems, school connectedness, social support, and personality, were used to further assess validity. Factor structure was determined, and then, the suitability of items was assessed according to the following criteria: (1) factor interpretability, (2) item correlations, (3) model parsimony, and (4) measurement equivalence across victimization and perpetration experiences. The final models comprised four factors: physical, verbal, relational, and cyber. The final scale was revised to two 13-item subscales. The BCS-A demonstrated acceptable concurrent and convergent validity (internalizing and externalizing problems, school connectedness, social support, and personality), as well as predictive validity over 6 months. The BCS-A has sound psychometric properties. This tool establishes measurement equivalence across types of involvement and behavioural forms common among adolescents. An improved measurement method could add greater rigour to the evaluation of intervention programmes and also enable interventions to be tailored to subscale profiles. © 2018 The British Psychological Society.

  11. Ethnicity, work-related stress and subjective reports of health by migrant workers: a multi-dimensional model.

    Science.gov (United States)

    Capasso, Roberto; Zurlo, Maria Clelia; Smith, Andrew P

    2018-02-01

    This study integrates different aspects of ethnicity and work-related stress dimensions (based on the Demands-Resources-Individual-Effects model, DRIVE [Mark, G. M., and A. P. Smith. 2008. "Stress Models: A Review and Suggested New Direction." In Occupational Health Psychology, edited by J. Houdmont and S. Leka, 111-144. Nottingham: Nottingham University Press]) and aims to test a multi-dimensional model that combines individual differences, ethnicity dimensions, work characteristics, and perceived job satisfaction/stress as independent variables in the prediction of subjectives reports of health by workers differing in ethnicity. A questionnaire consisting of the following sections was submitted to 900 workers in Southern Italy: for individual and cultural characteristics, coping strategies, personality behaviours, and acculturation strategies; for work characteristics, perceived job demands and job resources/rewards; for appraisals, perceived job stress/satisfaction and racial discrimination; for subjective reports of health, psychological disorders and general health. To test the reliability and construct validity of the extracted factors referred to all dimensions involved in the proposed model and logistic regression analyses to evaluate the main effects of the independent variables on the health outcomes were conducted. Principal component analysis (PCA) yielded seven factors for individual and cultural characteristics (emotional/relational coping, objective coping, Type A behaviour, negative affectivity, social inhibition, affirmation/maintenance culture, and search identity/adoption of the host culture); three factors for work characteristics (work demands, intrinsic/extrinsic rewards, and work resources); three factors for appraisals (perceived job satisfaction, perceived job stress, perceived racial discrimination) and three factors for subjective reports of health (interpersonal disorders, anxious-depressive disorders, and general health). Logistic

  12. The Multi-Dimensional Blood/Injury Phobia Inventory : Its psychometric properties and relationship with disgust propensity and disgust sensitivity

    NARCIS (Netherlands)

    van Overveld, Mark; de Jong, Peter J.; Peters, Madelon L.

    The Multi-Dimensional Blood Phobia Inventory (MBPI: Wenzel & Holt, 2003) is the only instrument available that assesses both disgust and anxiety for blood-phobic stimuli. As inflated levels of disgust propensity (i.e., tendency to experience disgust more readily) are often observed in blood phobia,

  13. A multi-dimensional approach to talent: An empirical analysis of the definition of talent in Dutch academia

    NARCIS (Netherlands)

    Thunissen, M.; Arensbergen, P. van

    2015-01-01

    - Purpose – The purpose of this paper is to contribute to the development of a broader, multi-dimensional approach to talent that helps scholars and practitioners to fully understand the nuances and complexity of talent in the organizational context. - Design/methodology/approach – The data were

  14. Integration of georeferencing, habitat, sampling, and genetic data for documentation of wild plant genetic resources

    Science.gov (United States)

    Plant genetic resource collections provide novel materials to the breeding and research communities. Availability of detailed documentation of passport, phenotypic, and genetic data increases the value of the genebank accessions. Inclusion of georeferenced sources, habitats, and sampling data in co...

  15. An Integrated Genetic and Cytogenetic Map of the Cucumber Genome

    Science.gov (United States)

    The Cucurbitaceae includes important crops as cucumber, melon, watermelon, and squash and pumpkin. However, few genetic and genomic resources are available for plant improvement. Some cucurbit species such as cucumber have a narrow genetic base, which impedes construction of saturated molecular li...

  16. An overview of posttraumatic stress disorder genetic studies by analyzing and integrating genetic data into genetic database PTSDgene

    NARCIS (Netherlands)

    Zhang, Kunlin; Qu, Susu; Chang, Suhua; Li, Gen; Cao, Chengqi; Fang, Kechi; Olff, Miranda; Wang, Li; Wang, Jing

    2017-01-01

    Posttraumatic stress disorder (PTSD) is a debilitating psychiatric syndrome with complex etiology. Studies aiming to explore genetic susceptibility and environmental triggers of PTSD have been increasing. However, the results are limited and highly heterogeneous. To understand the genetic study

  17. Multi-dimensional Analysis for SLB Transient in ATLAS Facility as Activity of DSP (Domestic Standard Problem)

    International Nuclear Information System (INIS)

    Bae, B. U.; Park, Y. S.; Kim, J. R.; Kang, K. H.; Choi, K. Y.; Sung, H. J.; Hwang, M. J.; Kang, D. H.; Lim, S. G.; Jun, S. S.

    2015-01-01

    Participants of DSP-03 were divided in three groups and each group has focused on the specific subject related to the enhancement of the code analysis. The group A tried to investigate scaling capability of ATLAS test data by comparing to the code analysis for a prototype, and the group C studied to investigate effect of various models in the one-dimensional codes. This paper briefly summarizes the code analysis result from the group B participants in the DSP-03 of the ATLAS test facility. The code analysis by Group B focuses highly on investigating the multi-dimensional thermal hydraulic phenomena in the ATLAS facility during the SLB transient. Even though the one-dimensional system analysis code cannot simulate the whole system of the ATLAS facility with a nodalization of the CFD (Computational Fluid Dynamics) scale, a reactor pressure vessel can be considered with multi-dimensional components to reflect the thermal mixing phenomena inside a downcomer and a core. Also, the CFD could give useful information for understanding complex phenomena in specific components such as the reactor pressure vessel. From the analysis activity of Group B in ATLAS DSP-03, participants adopted a multi-dimensional approach to the code analysis for the SLB transient in the ATLAS test facility. The main purpose of the analysis was to investigate prediction capability of multi-dimensional analysis tools for the SLB experiment result. In particular, the asymmetric cooling and thermal mixing phenomena in the reactor pressure vessel could be significantly focused for modeling the multi-dimensional components

  18. Shroud leakage flow models and a multi-dimensional coupling CFD (computational fluid dynamics) method for shrouded turbines

    International Nuclear Information System (INIS)

    Zou, Zhengping; Liu, Jingyuan; Zhang, Weihao; Wang, Peng

    2016-01-01

    Multi-dimensional coupling simulation is an effective approach for evaluating the flow and aero-thermal performance of shrouded turbines, which can balance the simulation accuracy and computing cost effectively. In this paper, 1D leakage models are proposed based on classical jet theories and dynamics equations, which can be used to evaluate most of the main features of shroud leakage flow, including the mass flow rate, radial and circumferential momentum, temperature and the jet width. Then, the 1D models are expanded to 2D distributions on the interface by using a multi-dimensional scaling method. Based on the models and multi-dimensional scaling, a multi-dimensional coupling simulation method for shrouded turbines is developed, in which, some boundary source and sink are set on the interface between the shroud and the main flow passage. To verify the precision, some simulations on the design point and off design points of a 1.5 stage turbine are conducted. It is indicated that the models and methods can give predictions with sufficient accuracy for most of the flow field features and will contribute to pursue deeper understanding and better design methods of shrouded axial turbines, which are the important devices in energy engineering. - Highlights: • Free and wall attached jet theories are used to model the leakage flow in shrouds. • Leakage flow rate is modeled by virtual labyrinth number and residual-energy factor. • A scaling method is applied to 1D model to obtain 2D distributions on interfaces. • A multi-dimensional coupling CFD method for shrouded turbines is proposed. • The proposed coupling method can give accurate predictions with low computing cost.

  19. Analysis of Phenix End-of-Life asymmetry test with multi-dimensional pool modeling of MARS-LMR code

    International Nuclear Information System (INIS)

    Jeong, H.-Y.; Ha, K.-S.; Choi, C.-W.; Park, M.-G.

    2015-01-01

    Highlights: • Pool behaviors under asymmetrical condition in an SFR were evaluated with MARS-LMR. • The Phenix asymmetry test was analyzed one-dimensionally and multi-dimensionally. • One-dimensional modeling has limitation to predict the cold pool temperature. • Multi-dimensional modeling shows improved prediction of stratification and mixing. - Abstract: The understanding of complicated pool behaviors and its modeling is essential for the design and safety analysis of a pool-type Sodium-cooled Fast Reactor. One of the remarkable recent efforts on the study of pool thermal–hydraulic behaviors is the asymmetrical test performed as a part of Phenix End-of-Life tests by the CEA. To evaluate the performance of MARS-LMR code, which is a key system analysis tool for the design of an SFR in Korea, in the prediction of thermal hydraulic behaviors during an asymmetrical condition, the Phenix asymmetry test is analyzed with MARS-LMR in the present study. Pool regions are modeled with two different approaches, one-dimensional modeling and multi-dimensional one, and the prediction results are analyzed to identify the appropriateness of each modeling method. The prediction with one-dimensional pool modeling shows a large deviation from the measured data at the early stage of the test, which suggests limitations to describe the complicated thermal–hydraulic phenomena. When the pool regions are modeled multi-dimensionally, the prediction gives improved results quite a bit. This improvement is explained by the enhanced modeling of pool mixing with the multi-dimensional modeling. On the basis of the results from the present study, it is concluded that an accurate modeling of pool thermal–hydraulics is a prerequisite for the evaluation of design performance and safety margin quantification in the future SFR developments

  20. Software Defined Networking (SDN) controlled all optical switching networks with multi-dimensional switching architecture

    Science.gov (United States)

    Zhao, Yongli; Ji, Yuefeng; Zhang, Jie; Li, Hui; Xiong, Qianjin; Qiu, Shaofeng

    2014-08-01

    Ultrahigh throughout capacity requirement is challenging the current optical switching nodes with the fast development of data center networks. Pbit/s level all optical switching networks need to be deployed soon, which will cause the high complexity of node architecture. How to control the future network and node equipment together will become a new problem. An enhanced Software Defined Networking (eSDN) control architecture is proposed in the paper, which consists of Provider NOX (P-NOX) and Node NOX (N-NOX). With the cooperation of P-NOX and N-NOX, the flexible control of the entire network can be achieved. All optical switching network testbed has been experimentally demonstrated with efficient control of enhanced Software Defined Networking (eSDN). Pbit/s level all optical switching nodes in the testbed are implemented based on multi-dimensional switching architecture, i.e. multi-level and multi-planar. Due to the space and cost limitation, each optical switching node is only equipped with four input line boxes and four output line boxes respectively. Experimental results are given to verify the performance of our proposed control and switching architecture.

  1. Effect of a Multi-Dimensional Intervention Programme on the Motivation of Physical Education Students

    Science.gov (United States)

    Amado, Diana; Del Villar, Fernando; Leo, Francisco Miguel; Sánchez-Oliva, David; Sánchez-Miguel, Pedro Antonio; García-Calvo, Tomás

    2014-01-01

    This research study purports to verify the effect produced on the motivation of physical education students of a multi-dimensional programme in dance teaching sessions. This programme incorporates the application of teaching skills directed towards supporting the needs of autonomy, competence and relatedness. A quasi-experimental design was carried out with two natural groups of 4th year Secondary Education students - control and experimental -, delivering 12 dance teaching sessions. A prior training programme was carried out with the teacher in the experimental group to support these needs. An initial and final measurement was taken in both groups and the results revealed that the students from the experimental group showed an increase of the perception of autonomy and, in general, of the level of self-determination towards the curricular content of corporal expression focused on dance in physical education. To this end, we highlight the programme's usefulness in increasing the students' motivation towards this content, which is so complicated for teachers of this area to develop. PMID:24454831

  2. Wind Farm Power Forecasting for Less Than an Hour Using Multi Dimensional Models

    DEFF Research Database (Denmark)

    Knudsen, Torben; Bak, Thomas; Jensen, Tom Nørgaard

    2018-01-01

    The paper focus on prediction of wind farm power for horizons of 0-10 minutes and not more than one hour using statistical methods. These short term predictions are relevant for both transmission system operators, wind farm operators and traders. Previous research indicates that for short time ho...... the prediction error variance estimate compared to the persistence method. We also present convincing examples showing that the predictions follow the wind farm power over a window of an hour.......The paper focus on prediction of wind farm power for horizons of 0-10 minutes and not more than one hour using statistical methods. These short term predictions are relevant for both transmission system operators, wind farm operators and traders. Previous research indicates that for short time...... horizons the persistence method performs as well as more complex methods. However, these results are based on accumulated power for an entire wind farm. The contribution in this paper is to develop multi-dimensional linear methods based on measurements of power or wind speed from individual wind turbine...

  3. Stochastic volatility and multi-dimensional modeling in the European energy market

    Energy Technology Data Exchange (ETDEWEB)

    Vos, Linda

    2012-07-01

    In energy prices there is evidence for stochastic volatility. Stochastic volatility has effect on the price of path-dependent options and therefore has to be modeled properly. We introduced a multi-dimensional non-Gaussian stochastic volatility model with leverage which can be used in energy pricing. It captures special features of energy prices like price spikes, mean-reversion, stochastic volatility and inverse leverage. Moreover it allows modeling dependencies between different commodities.The derived forward price dynamics based on this multi-variate spot price model, provides a very flexible structure. It includes cotango, backwardation and hump shape forward curves.Alternatively energy prices could be modeled by a 2-factor model consisting of a non-Gaussian stable CARMA process and a non-stationary trend models by a Levy process. Also this model is able to capture special features like price spikes, mean reversion and the low frequency dynamics in the market. An robust L1-filter is introduced to filter out the states of the CARMA process. When applying to German electricity EEX exchange data an overall negative risk-premium is found. However close to delivery a positive risk-premium is observed.(Author)

  4. A Simple Free Surface Tracking Model for Multi-dimensional Two-Fluid Approaches

    International Nuclear Information System (INIS)

    Lee, Seungjun; Yoon, Han Young

    2014-01-01

    The development in two-phase experiments devoted to find unknown phenomenological relationships modified conventional flow pattern maps into a sophisticated one and even extended to the multi-dimensional usage. However, for a system including a large void fraction gradient, such as a pool with the free surface, the flow patterns varies spatially throughout small number of cells and sometimes results in an unstable and unrealistic prediction of flows at the large gradient void fraction cells. Then, the numerical stability problem arising from the free surface is the major interest in the analyses of a passive cooling pool convecting the decay heat naturally, which has become a design issue to increase the safety level of nuclear reactors recently. In this research, a new and simple free surface tracking method combined with a simplified topology map is presented. The method modified the interfacial drag coefficient only for the cells defined as the free surface. The performance is shown by comparing the natural convection analysis of a small scale pool with respect to single- and two-phase condition. A simple free surface tracking model with a simplified topology map is developed

  5. Application of neural network to multi-dimensional design window search in reactor core design

    International Nuclear Information System (INIS)

    Kugo, Teruhiko; Nakagawa, Masayuki

    1999-01-01

    In the reactor core design, many parametric survey calculations should be carried out to decide an optimal set of basic design parameter values. They consume a large amount of computation time and labor in the conventional way. To support design work, we investigate a procedure to search efficiently a design window, which is defined as feasible design parameter ranges satisfying design criteria and requirements, in a multi-dimensional space composed of several basic design parameters. The present method is applied to the neutronics and thermal hydraulics fields. The principle of the present method is to construct the multilayer neural network to simulate quickly a response of an analysis code through a training process, and to reduce computation time using the neural network without parametric study using analysis codes. To verify the applicability of the present method to the neutronics and the thermal hydraulics design, we have applied it to high conversion water reactors and examined effects of the structure of the neural network and the number of teaching patterns on the accuracy of the design window estimated by the neural network. From the results of the applications, a guideline to apply the present method is proposed and the present method can predict an appropriate design window in a reasonable computation time by following the guideline. (author)

  6. Psychometric evaluation of a multi-dimensional measure of satisfaction with behavioral interventions.

    Science.gov (United States)

    Sidani, Souraya; Epstein, Dana R; Fox, Mary

    2017-10-01

    Treatment satisfaction is recognized as an essential aspect in the evaluation of an intervention's effectiveness, but there is no measure that provides for its comprehensive assessment with regard to behavioral interventions. Informed by a conceptualization generated from a literature review, we developed a measure that covers several domains of satisfaction with behavioral interventions. In this paper, we briefly review its conceptualization and describe the Multi-Dimensional Treatment Satisfaction Measure (MDTSM) subscales. Satisfaction refers to the appraisal of the treatment's process and outcome attributes. The MDTSM has 11 subscales assessing treatment process and outcome attributes: treatment components' suitability and utility, attitude toward treatment, desire for continued treatment use, therapist competence and interpersonal style, format and dose, perceived benefits of the health problem and everyday functioning, discomfort, and attribution of outcomes to treatment. The MDTSM was completed by persons (N = 213) in the intervention group in a large trial of a multi-component behavioral intervention for insomnia within 1 week following treatment completion. The MDTSM's subscales demonstrated internal consistency reliability (α: .65 - .93) and validity (correlated with self-reported adherence and perceived insomnia severity at post-test). The MDTSM subscales can be used to assess satisfaction with behavioral interventions and point to aspects of treatments that are viewed favorably or unfavorably. © 2017 Wiley Periodicals, Inc.

  7. Development of a multi-dimensional measure of resilience in adolescents: the Adolescent Resilience Questionnaire

    Directory of Open Access Journals (Sweden)

    Buzwell Simone

    2011-10-01

    Full Text Available Abstract Background The concept of resilience has captured the imagination of researchers and policy makers over the past two decades. However, despite the ever growing body of resilience research, there is a paucity of relevant, comprehensive measurement tools. In this article, the development of a theoretically based, comprehensive multi-dimensional measure of resilience in adolescents is described. Methods Extensive literature review and focus groups with young people living with chronic illness informed the conceptual development of scales and items. Two sequential rounds of factor and scale analyses were undertaken to revise the conceptually developed scales using data collected from young people living with a chronic illness and a general population sample. Results The revised Adolescent Resilience Questionnaire comprises 93 items and 12 scales measuring resilience factors in the domains of self, family, peer, school and community. All scales have acceptable alpha coefficients. Revised scales closely reflect conceptually developed scales. Conclusions It is proposed that, with further psychometric testing, this new measure of resilience will provide researchers and clinicians with a comprehensive and developmentally appropriate instrument to measure a young person's capacity to achieve positive outcomes despite life stressors.

  8. Fluorescence Intrinsic Characterization of Excitation-Emission Matrix Using Multi-Dimensional Ensemble Empirical Mode Decomposition

    Directory of Open Access Journals (Sweden)

    Tzu-Chien Hsiao

    2013-11-01

    Full Text Available Excitation-emission matrix (EEM fluorescence spectroscopy is a noninvasive method for tissue diagnosis and has become important in clinical use. However, the intrinsic characterization of EEM fluorescence remains unclear. Photobleaching and the complexity of the chemical compounds make it difficult to distinguish individual compounds due to overlapping features. Conventional studies use principal component analysis (PCA for EEM fluorescence analysis, and the relationship between the EEM features extracted by PCA and diseases has been examined. The spectral features of different tissue constituents are not fully separable or clearly defined. Recently, a non-stationary method called multi-dimensional ensemble empirical mode decomposition (MEEMD was introduced; this method can extract the intrinsic oscillations on multiple spatial scales without loss of information. The aim of this study was to propose a fluorescence spectroscopy system for EEM measurements and to describe a method for extracting the intrinsic characteristics of EEM by MEEMD. The results indicate that, although PCA provides the principal factor for the spectral features associated with chemical compounds, MEEMD can provide additional intrinsic features with more reliable mapping of the chemical compounds. MEEMD has the potential to extract intrinsic fluorescence features and improve the detection of biochemical changes.

  9. Effect of a multi-dimensional intervention programme on the motivation of physical education students.

    Science.gov (United States)

    Amado, Diana; Del Villar, Fernando; Leo, Francisco Miguel; Sánchez-Oliva, David; Sánchez-Miguel, Pedro Antonio; García-Calvo, Tomás

    2014-01-01

    This research study purports to verify the effect produced on the motivation of physical education students of a multi-dimensional programme in dance teaching sessions. This programme incorporates the application of teaching skills directed towards supporting the needs of autonomy, competence and relatedness. A quasi-experimental design was carried out with two natural groups of 4(th) year Secondary Education students--control and experimental -, delivering 12 dance teaching sessions. A prior training programme was carried out with the teacher in the experimental group to support these needs. An initial and final measurement was taken in both groups and the results revealed that the students from the experimental group showed an increase of the perception of autonomy and, in general, of the level of self-determination towards the curricular content of corporal expression focused on dance in physical education. To this end, we highlight the programme's usefulness in increasing the students' motivation towards this content, which is so complicated for teachers of this area to develop.

  10. Multi-dimensional SAR tomography for monitoring the deformation of newly built concrete buildings

    Science.gov (United States)

    Ma, Peifeng; Lin, Hui; Lan, Hengxing; Chen, Fulong

    2015-08-01

    Deformation often occurs in buildings at early ages, and the constant inspection of deformation is of significant importance to discover possible cracking and avoid wall failure. This paper exploits the multi-dimensional SAR tomography technique to monitor the deformation performances of two newly built buildings (B1 and B2) with a special focus on the effects of concrete creep and shrinkage. To separate the nonlinear thermal expansion from total deformations, the extended 4-D SAR technique is exploited. The thermal map estimated from 44 TerraSAR-X images demonstrates that the derived thermal amplitude is highly related to the building height due to the upward accumulative effect of thermal expansion. The linear deformation velocity map reveals that B1 is subject to settlement during the construction period, in addition, the creep and shrinkage of B1 lead to wall shortening that is a height-dependent movement in the downward direction, and the asymmetrical creep of B2 triggers wall deflection that is a height-dependent movement in the deflection direction. It is also validated that the extended 4-D SAR can rectify the bias of estimated wall shortening and wall deflection by 4-D SAR.

  11. Spectral analysis of multi-dimensional self-similar Markov processes

    International Nuclear Information System (INIS)

    Modarresi, N; Rezakhah, S

    2010-01-01

    In this paper we consider a discrete scale invariant (DSI) process {X(t), t in R + } with scale l > 1. We consider a fixed number of observations in every scale, say T, and acquire our samples at discrete points α k , k in W, where α is obtained by the equality l = α T and W = {0, 1, ...}. We thus provide a discrete time scale invariant (DT-SI) process X(.) with the parameter space {α k , k in W}. We find the spectral representation of the covariance function of such a DT-SI process. By providing the harmonic-like representation of multi-dimensional self-similar processes, spectral density functions of them are presented. We assume that the process {X(t), t in R + } is also Markov in the wide sense and provide a discrete time scale invariant Markov (DT-SIM) process with the above scheme of sampling. We present an example of the DT-SIM process, simple Brownian motion, by the above sampling scheme and verify our results. Finally, we find the spectral density matrix of such a DT-SIM process and show that its associated T-dimensional self-similar Markov process is fully specified by {R H j (1), R j H (0), j = 0, 1, ..., T - 1}, where R H j (τ) is the covariance function of jth and (j + τ)th observations of the process.

  12. Measurement of multi-dimensional flow structure for flow boiling in a tube

    International Nuclear Information System (INIS)

    Adachi, Yu; Ito, Daisuke; Saito, Yasushi

    2014-01-01

    With an aim of the measurement of multi-dimensional flow structure of in-tube boiling two-phase flow, the authors built their own wire mesh measurement system based on electrical conductivity measurement, and examined the relationship between the electrical conductivity obtained by the wire mesh sensor and the void fraction. In addition, the authors measured the void fraction using neutron radiography, and compared the result with the measured value using the wire mesh sensor. From the comparison with neutron radiography, it was found that the new method underestimated the void fraction in the flow in the vicinity of the void fraction of 0.2-0.5, similarly to the conventional result. In addition, since the wire mesh sensor cannot measure dispersed droplets, it tends to overestimate the void fraction in the high void fraction region, such as churn flow accompanied by droplet generation. In the electrical conductivity wire-mesh sensor method, it is necessary to correctly take into account the effect of liquid film or droplets. The authors also built a measurement system based on the capacitance wire mesh sensor method using the difference in dielectric constant, performed the confirmation of transmission and reception signals using deionized water as a medium, and showed the validity of the system. As for the dispersed droplets, the capacitance method has a potential to be able to measure them. (A.O.)

  13. Operationalising the Sustainable Knowledge Society Concept through a Multi-dimensional Scorecard

    Science.gov (United States)

    Dragomirescu, Horatiu; Sharma, Ravi S.

    Since the early 21st Century, building a Knowledge Society represents an aspiration not only for the developed countries, but for the developing ones too. There is an increasing concern worldwide for rendering this process manageable towards a sustainable, equitable and ethically sound societal system. As proper management, including at the societal level, requires both wisdom and measurement, the operationalisation of the Knowledge Society concept encompasses a qualitative side, related to vision-building, and a quantitative one, pertaining to designing and using dedicated metrics. The endeavour of enabling policy-makers mapping, steering and monitoring the sustainable development of the Knowledge Society at national level, in a world increasingly based on creativity, learning and open communication, led researchers to devising a wide range of composite indexes. However, as such indexes are generated through weighting and aggregation, their usefulness is limited to retrospectively assessing and comparing levels and states already attained; therefore, to better serve policy-making purposes, composite indexes should be complemented by other instruments. Complexification, inspired by the systemic paradigm, allows obtaining "rich pictures" of the Knowledge Society; to this end, a multi-dimensional scorecard of the Knowledge Society development is hereby suggested, that seeks a more contextual orientation towards sustainability. It is assumed that, in the case of the Knowledge Society, the sustainability condition goes well beyond the "greening" desideratum and should be of a higher order, relying upon the conversion of natural and productive life-cycles into virtuous circles of self-sustainability.

  14. Moving toward multi-dimensional radiotherapy and the role of radiobiology

    International Nuclear Information System (INIS)

    Oita, Masataka; Uto, Yoshihiro; Aoyama, Hideki

    2014-01-01

    Recent radiotherapy for cancer treatment enable the high-precision irradiation to the target under the computed image guidance. Developments of such radiotherapy has played large role in the improved strategy of cancer treatments. In addition, the molecular mechanistic studies related to proliferations of cancer cell contribute the multidisciplinary fields of clinical radiotherapies. Therefore, the combination of the image guidance and molecular targeting of cancer cells make it possible for individualized cancer treatment. Especially, the use of particle beam or boron neutron capture therapy (BNCT) has been spotlighted, and installations of such devices are planned widely. As the progress and collaborations of radiation biology and engineering physics, establishment of a new style of radiotherapy becomes available in post-genome era. In 2010s, the hi-tech machines controlling the spaciotemporal radiotherapy become in practice. Although, there still remains to be improved, e.g., more precise prediction of radiosensitivity or growth of individual tumors, and adverse outcomes after treatments, multi-dimensional optimizations of the individualized irradiations based on the molecular radiation biologies and medical physics are important for further development of radiotherapy. (author)

  15. Analysis of UPTF downcomer tests with the Cathare multi-dimensional model

    International Nuclear Information System (INIS)

    Dor, I.

    1993-01-01

    This paper presents the analysis and the modelling - with the system code CATHARE - of UPTF downcomer refill tests simulating the refill phase of a large break LOCA. The modelling approach in a system code is discussed. First the reasons why in this particular case available flooding correlations are difficult to use in system code are developed. Then the use of a 1 - D modelling of the downcomer with specific closure relations for the annular geometry is examined. But UPTF 1:1 scale tests and CREARE reduced scale tests point out some weaknesses of this modelling due to the particular multi-dimensional nature of the flow in the upper part of the downcomer. Thus a 2-D model is elaborated and implemented into CATHARE version 1.3e code. The assessment of the model is based on UPTF 1:1 scale tests (saturated and subcooled conditions). Discretization and meshing influence are investigated. On the basis of saturated tests a new discretization is proposed for different terms of the momentum balance equations (interfacial friction, momentum transport terms) which results in a significant improvement. Sensitivity studies performed on subcooled tests show that the water downflow predictions are improved by increasing the condensation in the downcomer. (author). 8 figs., 5 tabs., 9 refs., 2 appendix

  16. Multi-dimensional self-esteem and substance use among Chinese adolescents.

    Science.gov (United States)

    Wu, Cynthia S T; Wong, Ho Ting; Shek, Carmen H M; Loke, Alice Yuen

    2014-10-01

    Substance use among adolescents has caused worldwide public health concern in recent years. Overseas studies have demonstrated an association between adolescent self-esteem and substance use, but studies within a Chinese context are limited. A study was therefore initiated to: (1) explore the 30 days prevalence of substance use (smoking, drinking, and drugs) among male and female adolescents in Hong Kong; (2) identify the significant associations between multidimensional self-esteem and gender; and (3) examine the relationship between multi-dimensional self-esteem and substance use. A self-esteem scale and the Chinese version of the global school-based student health survey were adopted. A total of 1,223 students were recruited from two mixed-gender schools and one boys' school. Among females, there was a lower 30-day prevalence of cigarette, alcohol, and drug use. They also had significantly higher peer and family self-esteem but lower sport-related self-esteem. Body image self-esteem was a predictor of alcohol use among females, while peer and school self-esteem were predictors of drug use among males. In summary, the findings demonstrated the influence of self-esteem to the overall well-being of adolescents. Schools could play a role in promoting physical fitness and positive relationships between adolescents and their peers, family, and schools to fulfill their physical and psychological self-esteem needs.

  17. The knock study of methanol fuel based on multi-dimensional simulation analysis

    International Nuclear Information System (INIS)

    Zhen, Xudong; Liu, Daming; Wang, Yang

    2017-01-01

    Methanol is an alternative fuel, and considered to be one of the most favorable fuels for engines. In this study, knocking combustion in a developed ORCEM (optical rapid compression and expansion machine) is studied based on the multi-dimensional simulation analysis. The LES (large-eddy simulation) models coupled with methanol chemical reaction kinetics (contains 21-species and 84-elementary reactions) is adopted to study knocking combustion. The results showed that the end-gas auto-ignition first occurred in the position near the chamber wall because of the higher temperature and pressure. The H_2O_2 species could be a good flame front indicator. OH radicals played the major role, and the HCO radicals almost could be ignored during knocking combustion. The HCO radicals generated little, so its concentration during knocking combustion almost may be ignored. The mean reaction intensity results of CH_2O, OH, H_2O_2, and CO were higher than others during knocking combustion. Finally, this paper put forward some new suggestions on the weakness in the knocking combustion researches of methanol fuel. - Highlights: • Knocking combustion of methanol was studied in a developed ORCEM. • The LES coupled with detailed chemical kinetics was adopted to simulation study. • The end-gas auto-ignition first occurred in the place near the chamber wall. • OH radical was the predominant species during knocking combustion. • The H_2O_2 species could be a good flame front indicator.

  18. Democracy and genetic privacy: the value of bodily integrity.

    Science.gov (United States)

    Beckman, Ludvig

    2005-01-01

    The right to genetic privacy is presently being incorporated in legal systems all over the world. It remains largely unclear however what interests and values this right serves to protect. There are many different arguments made in the literature, yet none takes into account the problem of how particular values can be justified given the plurality of moral and religious doctrines in our societies. In this article theories of public reason are used in order to explore how genetic privacy could be justified in a way that is sensitive to the "fact of pluralism". The idea of public reason is specified as the idea that governments should appeal only to values and beliefs that are acceptable to all reasonable citizens in the justification of rights. In examining prevalent arguments for genetic privacy--based on the value of autonomy or on the value of intimacy--it is concluded that they do not meet this requirement. In dealing with this deficiency in the literature, an argument is developed that genetic privacy is fundamental to the democratic participation of all citizens. By referring to the preconditions of democratic citizenship, genetic privacy can be justified in a way that respects the plurality of comprehensive doctrines of morality and religion in contemporary societies.

  19. Genetic regulation of immunoglobulin E level in different pathological states: integration of mouse and human genetics

    Czech Academy of Sciences Publication Activity Database

    Gusareva, Elena; Kurey, Irina; Grekov, Igor; Lipoldová, Marie

    2014-01-01

    Roč. 89, č. 2 (2014), s. 375-405 ISSN 1464-7931 R&D Projects: GA ČR GA310/08/1697; GA MŠk LH12049 Institutional support: RVO:68378050 Keywords : Genetic control of complex diseases * Immunoglobulin E * Epistasis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.670, year: 2014

  20. Rethinking dog domestication by integrating genetics, archeology, and biogeography

    DEFF Research Database (Denmark)

    Larson, Greger; Karlsson, Elinor K.; Perri, Angela

    2012-01-01

    The dog was the first domesticated animal but it remains uncertain when the domestication process began and whether it occurred just once or multiple times across the Northern Hemisphere. To ascertain the value of modern genetic data to elucidate the origins of dog domestication, we analyzed 49......,024 autosomal SNPs in 1,375 dogs (representing 35 breeds) and 19 wolves. After combining our data with previously published data, we contrasted the genetic signatures of 121 breeds with a worldwide archeological assessment of the earliest dog remains. Correlating the earliest archeological dogs......, and New Guinea Singing Dogs) come from regions outside the natural range of Canis lupus (the dog's wild ancestor) and where dogs were introduced more than 10,000 y after domestication. These results demonstrate that the unifying characteristic among all genetically distinct so-called ancient breeds...

  1. Community standards for genomic resources, genetic conservation, and data integration

    Science.gov (United States)

    Jill Wegrzyn; Meg Staton; Emily Grau; Richard Cronn; C. Dana Nelson

    2017-01-01

    Genetics and genomics are increasingly important in forestry management and conservation. Next generation sequencing can increase analytical power, but still relies on building on the structure of previously acquired data. Data standards and data sharing allow the community to maximize the analytical power of high throughput genomics data. The landscape of incomplete...

  2. A Distributed Multi-dimensional SOLAP Model of Remote Sensing Data and Its Application in Drought Analysis

    Directory of Open Access Journals (Sweden)

    LI Jiyuan

    2014-06-01

    Full Text Available SOLAP (Spatial On-Line Analytical Processing has been applied to multi-dimensional analysis of remote sensing data recently. However, its computation performance faces a considerable challenge from the large-scale dataset. A geo-raster cube model extended by Map-Reduce is proposed, which refers to the application of Map-Reduce (a data-intensive computing paradigm in the OLAP field. In this model, the existing methods are modified to adapt to distributed environment based on the multi-level raster tiles. Then the multi-dimensional map algebra is introduced to decompose the SOLAP computation into multiple distributed parallel map algebra functions on tiles under the support of Map-Reduce. The drought monitoring by remote sensing data is employed as a case study to illustrate the model construction and application. The prototype is also implemented, and the performance testing shows the efficiency and scalability of this model.

  3. Effect of a Multi-Dimensional and Inter-Sectoral Intervention on the Adherence of Psychiatric Patients.

    Directory of Open Access Journals (Sweden)

    Anne Pauly

    Full Text Available In psychiatry, hospital stays and transitions to the ambulatory sector are susceptible to major changes in drug therapy that lead to complex medication regimens and common non-adherence among psychiatric patients. A multi-dimensional and inter-sectoral intervention is hypothesized to improve the adherence of psychiatric patients to their pharmacotherapy.269 patients from a German university hospital were included in a prospective, open, clinical trial with consecutive control and intervention groups. Control patients (09/2012-03/2013 received usual care, whereas intervention patients (05/2013-12/2013 underwent a program to enhance adherence during their stay and up to three months after discharge. The program consisted of therapy simplification and individualized patient education (multi-dimensional component during the stay and at discharge, as well as subsequent phone calls after discharge (inter-sectoral component. Adherence was measured by the "Medication Adherence Report Scale" (MARS and the "Drug Attitude Inventory" (DAI.The improvement in the MARS score between admission and three months after discharge was 1.33 points (95% CI: 0.73-1.93 higher in the intervention group compared to controls. In addition, the DAI score improved 1.93 points (95% CI: 1.15-2.72 more for intervention patients.These two findings indicate significantly higher medication adherence following the investigated multi-dimensional and inter-sectoral program.German Clinical Trials Register DRKS00006358.

  4. Comparative study of the two-fluid momentum equations for multi-dimensional bubbly flows: Modification of Reynolds stress

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung Jun; Park, Ik Kyu; Yoon, Han Young [Thermal-Hydraulic Safety Research Division, Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Jae, Byoung [School of Mechanical Engineering, Chungnam National University, Daejeon (Korea, Republic of)

    2017-01-15

    Two-fluid equations are widely used to obtain averaged behaviors of two-phase flows. This study addresses a problem that may arise when the two-fluid equations are used for multi-dimensional bubbly flows. If steady drag is the only accounted force for the interfacial momentum transfer, the disperse-phase velocity would be the same as the continuous-phase velocity when the flow is fully developed without gravity. However, existing momentum equations may show unphysical results in estimating the relative velocity of the disperse phase against the continuous-phase. First, we examine two types of existing momentum equations. One is the standard two-fluid momentum equation in which the disperse-phase is treated as a continuum. The other is the averaged momentum equation derived from a solid/ fluid particle motion. We show that the existing equations are not proper for multi-dimensional bubbly flows. To resolve the problem mentioned above, we modify the form of the Reynolds stress terms in the averaged momentum equation based on the solid/fluid particle motion. The proposed equation shows physically correct results for both multi-dimensional laminar and turbulent flows.

  5. Multi-dimensional two-phase flow measurements in a large-diameter pipe using wire-mesh sensor

    International Nuclear Information System (INIS)

    Kanai, Taizo; Furuya, Masahiro; Arai, Takahiro; Shirakawa, Kenetsu; Nishi, Yoshihisa; Ueda, Nobuyuki

    2011-01-01

    The authors developed a method of measurement to determine the multi-dimensionality of two phase flow. A wire-mesh sensor (WMS) can acquire a void fraction distribution at a high temporal and spatial resolution and also estimate the velocity of a vertical rising flow by investigating the signal time-delay of the upstream WMS relative to downstream. Previously, one-dimensional velocity was estimated by using the same point of each WMS at a temporal resolution of 1.0 - 5.0 s. The authors propose to extend this time series analysis to estimate the multi-dimensional velocity profile via cross-correlation analysis between a point of upstream WMS and multiple points downstream. Bubbles behave in various ways according to size, which is used to classify them into certain groups via wavelet analysis before cross-correlation analysis. This method was verified by air-water straight and swirl flows within a large-diameter vertical pipe. A high-speed camera is used to set the parameter of cross-correlation analysis. The results revealed that for the rising straight and swirl flows, large scale bubbles tend to move to the center, while the small bubble is pushed to the outside or sucked into the space where the large bubbles existed. Moreover, it is found that this method can estimate the rotational component of velocity of the swirl flow as well as measuring the multi-dimensional velocity vector at high temporal resolutions of 0.2 s. (author)

  6. Integrating population genetics and conservation biology in the era of genomics.

    Science.gov (United States)

    Ouborg, N Joop

    2010-02-23

    As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled 'Integrating Population Genetics and Conservation Biology' was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

  7. Consumer preference of fertilizer in West Java using multi-dimensional scaling approach

    Science.gov (United States)

    Utami, Hesty Nurul; Sadeli, Agriani Hermita; Perdana, Tomy; Renaldy, Eddy; Mahra Arari, H.; Ajeng Sesy N., P.; Fernianda Rahayu, H.; Ginanjar, Tetep; Sanjaya, Sonny

    2018-02-01

    There are various fertilizer products in the markets for farmers to be used for farming activities. Fertilizers are a supplements supply to soil nutrients, build up soil fertility in order to support plant nutrients and increase plants productivity. Fertilizers consists of nitrogen, phosphorous, potassium, micro vitamins and other complex nutrient in farming systems that commonly used in agricultural activities to improve quantity and quality of harvest. Recently, market demand for fertilizer has been increased dramatically; furthermore, fertilizer companies are required to develop strategies to know about consumer preferences towards several issues. Consumer preference depends on consumer needs selected by subject (individual) that is measured by utilization from several things that market offered and as final decision on purchase process. West Java is one of province as the main producer of agricultural products and automatically is one of the potential consumer's fertilizers on farming activities. This research is a case study in nine districts in West Java province, i.e., Bandung, West Bandung, Bogor, Depok, Garut, Indramayu, Majalengka, Cirebon and Cianjur. The purpose of this research is to describe the attributes on consumer preference for fertilizers. The multi-dimensional scaling method is used as quantitative method to help visualize the level of similarity of individual cases on a dataset, to describe and mapping the information system and to accept the goal. The attributes in this research are availability, nutrients content, price, form of fertilizer, decomposition speed, easy to use, label, packaging type, color, design and size of packaging, hardening process and promotion. There are tendency towards two fertilizer brand have similarity on availability of products, price, speed of decomposition and hardening process.

  8. POLARIZED LINE FORMATION IN MULTI-DIMENSIONAL MEDIA. III. HANLE EFFECT WITH PARTIAL FREQUENCY REDISTRIBUTION

    International Nuclear Information System (INIS)

    Anusha, L. S.; Nagendra, K. N.

    2011-01-01

    In two previous papers, we solved the polarized radiative transfer (RT) equation in multi-dimensional (multi-D) geometries with partial frequency redistribution as the scattering mechanism. We assumed Rayleigh scattering as the only source of linear polarization (Q/I, U/I) in both these papers. In this paper, we extend these previous works to include the effect of weak oriented magnetic fields (Hanle effect) on line scattering. We generalize the technique of Stokes vector decomposition in terms of the irreducible spherical tensors T K Q , developed by Anusha and Nagendra, to the case of RT with Hanle effect. A fast iterative method of solution (based on the Stabilized Preconditioned Bi-Conjugate-Gradient technique), developed by Anusha et al., is now generalized to the case of RT in magnetized three-dimensional media. We use the efficient short-characteristics formal solution method for multi-D media, generalized appropriately to the present context. The main results of this paper are the following: (1) a comparison of emergent (I, Q/I, U/I) profiles formed in one-dimensional (1D) media, with the corresponding emergent, spatially averaged profiles formed in multi-D media, shows that in the spatially resolved structures, the assumption of 1D may lead to large errors in linear polarization, especially in the line wings. (2) The multi-D RT in semi-infinite non-magnetic media causes a strong spatial variation of the emergent (Q/I, U/I) profiles, which is more pronounced in the line wings. (3) The presence of a weak magnetic field modifies the spatial variation of the emergent (Q/I, U/I) profiles in the line core, by producing significant changes in their magnitudes.

  9. Magnetic quantum tunneling: key insights from multi-dimensional high-field EPR.

    Science.gov (United States)

    Lawrence, J; Yang, E-C; Hendrickson, D N; Hill, S

    2009-08-21

    Multi-dimensional high-field/frequency electron paramagnetic resonance (HFEPR) spectroscopy is performed on single-crystals of the high-symmetry spin S = 4 tetranuclear single-molecule magnet (SMM) [Ni(hmp)(dmb)Cl](4), where hmp(-) is the anion of 2-hydroxymethylpyridine and dmb is 3,3-dimethyl-1-butanol. Measurements performed as a function of the applied magnetic field strength and its orientation within the hard-plane reveal the four-fold behavior associated with the fourth order transverse zero-field splitting (ZFS) interaction, (1/2)B(S + S), within the framework of a rigid spin approximation (with S = 4). This ZFS interaction mixes the m(s) = +/-4 ground states in second order of perturbation, generating a sizeable (12 MHz) tunnel splitting, which explains the fast magnetic quantum tunneling in this SMM. Meanwhile, multi-frequency measurements performed with the field parallel to the easy-axis reveal HFEPR transitions associated with excited spin multiplets (S spin s = 1 Ni(II) ions within the cluster, as well as a characterization of the ZFS within excited states. The combined experimental studies support recent work indicating that the fourth order anisotropy associated with the S = 4 state originates from second order ZFS interactions associated with the individual Ni(II) centers, but only as a result of higher-order processes that occur via S-mixing between the ground state and higher-lying (S spin multiplets. We argue that this S-mixing plays an important role in the low-temperature quantum dynamics associated with many other well known SMMs.

  10. Installation of aerosol behavior model into multi-dimensional thermal hydraulic analysis code AQUA

    International Nuclear Information System (INIS)

    Kisohara, Naoyuki; Yamaguchi, Akira

    1997-12-01

    The safety analysis of FBR plant system for sodium leak phenomena needs to evaluate the deposition of the aerosol particle to the components in the plant, the chemical reaction of aerosol to humidity in the air and the effect of the combustion heat through aerosol to the structural component. For this purpose, ABC-INTG (Aerosol Behavior in Containment-INTeGrated Version) code has been developed and used until now. This code calculates aerosol behavior in the gas area of uniform temperature and pressure by 1 cell-model. Later, however, more detailed calculation of aerosol behavior requires the installation of aerosol model into multi-cell thermal hydraulic analysis code AQUA. AQUA can calculate the carrier gas flow, temperature and the distribution of the aerosol spatial concentration. On the other hand, ABC-INTG can calculate the generation, deposition to the wall and flower, agglomeration of aerosol particle and figure out the distribution of the aerosol particle size. Thus, the combination of these two codes enables to deal with aerosol model coupling the distribution of the aerosol spatial concentration and that of the aerosol particle size. This report describes aerosol behavior model, how to install the aerosol model to AQUA and new subroutine equipped to the code. Furthermore, the test calculations of the simple structural model were executed by this code, appropriate results were obtained. Thus, this code has prospect to predict aerosol behavior by the introduction of coupling analysis with multi-dimensional gas thermo-dynamics for sodium combustion evaluation. (J.P.N.)

  11. A revised Thai Multi-Dimensional Scale of Perceived Social Support.

    Science.gov (United States)

    Wongpakaran, Nahathai; Wongpakaran, Tinakon

    2012-11-01

    In order to ensure the construct validity of the three-factor model of the Multi-dimensional Scale of Perceived Social Support (MSPSS), and based on the assumption that it helps users differentiate between sources of social support, in this study a revised version was created and tested. The aim was to compare the level of model fit of the original version of the MSPSS against the revised version--which contains a minor change from the original. The study was conducted on 486 medical students who completed the original and revised versions of the MSPSS, as well as the Rosenberg Self-Esteem Scale (Rosenberg, 1965) and Beck Depression Inventory II (Beck, Steer, & Brown, 1996). Confirmatory factor analysis was performed to compare the results, showing that the revised version of MSPSS demonstrated a good internal consistency--with a Cronbach's alpha of .92 for the MSPSS questionnaire, and a significant correlation with the other scales, as predicted. The revised version provided better internal consistency, increasing the Cronbach's alpha for the Significant Others sub-scale from 0.86 to 0.92. Confirmatory factor analysis revealed an acceptable model fit: chi2 128.11, df 51, p < .001; TLI 0.94; CFI 0.95; GFI 0.90; PNFI 0.71; AGFI 0.85; RMSEA 0.093 (0.073-0.113) and SRMR 0.042, which is better than the original version. The tendency of the new version was to display a better level of fit with a larger sample size. The limitations of the study are discussed, as well as recommendations for further study.

  12. Studying Operation Rules of Cascade Reservoirs Based on Multi-Dimensional Dynamics Programming

    Directory of Open Access Journals (Sweden)

    Zhiqiang Jiang

    2017-12-01

    Full Text Available Although many optimization models and methods are applied to the optimization of reservoir operation at present, the optimal operation decision that is made through these models and methods is just a retrospective review. Due to the limitation of hydrological prediction accuracy, it is practical and feasible to obtain the suboptimal or satisfactory solution by the established operation rules in the actual reservoir operation, especially for the mid- and long-term operation. In order to obtain the optimized sample data with global optimality; and make the extracted operation rules more reasonable and reliable, this paper presents the multi-dimensional dynamic programming model of the optimal joint operation of cascade reservoirs and provides the corresponding recursive equation and the specific solving steps. Taking Li Xianjiang cascade reservoirs as a case study, seven uncertain problems in the whole operation period of the cascade reservoirs are summarized after a detailed analysis to the obtained optimal sample data, and two sub-models are put forward to solve these uncertain problems. Finally, by dividing the whole operation period into four characteristic sections, this paper extracts the operation rules of each reservoir for each section respectively. When compared the simulation results of the extracted operation rules with the conventional joint operation method; the result indicates that the power generation of the obtained rules has a certain degree of improvement both in inspection years and typical years (i.e., wet year; normal year and dry year. So, the rationality and effectiveness of the extracted operation rules are verified by the comparative analysis.

  13. The use of multi-dimensional flow and morphodynamic models for restoration design analysis

    Science.gov (United States)

    McDonald, R.; Nelson, J. M.

    2013-12-01

    River restoration projects with the goal of restoring a wide range of morphologic and ecologic channel processes and functions have become common. The complex interactions between flow and sediment-transport make it challenging to design river channels that are both self-sustaining and improve ecosystem function. The relative immaturity of the field of river restoration and shortcomings in existing methodologies for evaluating channel designs contribute to this problem, often leading to project failures. The call for increased monitoring of constructed channels to evaluate which restoration techniques do and do not work is ubiquitous and may lead to improved channel restoration projects. However, an alternative approach is to detect project flaws before the channels are built by using numerical models to simulate hydraulic and sediment-transport processes and habitat in the proposed channel (Restoration Design Analysis). Multi-dimensional models provide spatially distributed quantities throughout the project domain that may be used to quantitatively evaluate restoration designs for such important metrics as (1) the change in water-surface elevation which can affect the extent and duration of floodplain reconnection, (2) sediment-transport and morphologic change which can affect the channel stability and long-term maintenance of the design; and (3) habitat changes. These models also provide an efficient way to evaluate such quantities over a range of appropriate discharges including low-probability events which often prove the greatest risk to the long-term stability of restored channels. Currently there are many free and open-source modeling frameworks available for such analysis including iRIC, Delft3D, and TELEMAC. In this presentation we give examples of Restoration Design Analysis for each of the metrics above from projects on the Russian River, CA and the Kootenai River, ID. These examples demonstrate how detailed Restoration Design Analysis can be used to

  14. Construction of an integrated genetic map for Capsicum baccatum L.

    Science.gov (United States)

    Moulin, M M; Rodrigues, R; Ramos, H C C; Bento, C S; Sudré, C P; Gonçalves, L S A; Viana, A P

    2015-06-18

    Capsicum baccatum L. is one of the five Capsicum domesticated species and has multiple uses in the food, pharmaceutical and cosmetic industries. This species is also a valuable source of genes for chili pepper breeding, especially genes for disease resistance and fruit quality. However, knowledge of the genetic structure of C. baccatum is limited. A reference map for C. baccatum (2n = 2x = 24) based on 42 microsatellite, 85 inter-simple sequence repeat, and 56 random amplified polymorphic DNA markers was constructed using an F2 population consisting of 203 individuals. The map was generated using the JoinMap software (version 4.0) and the linkage groups were formed and ordered using a LOD score of 3.0 and maximum of 40% recombination. The genetic map consisted of 12 major and four minor linkage groups covering a total genome distance of 2547.5 cM with an average distance of 14.25 cM between markers. Of the 152 pairs of microsatellite markers available for Capsicum annuum, 62 were successfully transferred to C. baccatum, generating polymorphism. Forty-two of these markers were mapped, allowing the introduction of C. baccatum in synteny studies with other species of the genus Capsicum.

  15. Quantifying multi-dimensional functional trait spaces of trees: empirical versus theoretical approaches

    Science.gov (United States)

    Ogle, K.; Fell, M.; Barber, J. J.

    2016-12-01

    Empirical, field studies of plant functional traits have revealed important trade-offs among pairs or triplets of traits, such as the leaf (LES) and wood (WES) economics spectra. Trade-offs include correlations between leaf longevity (LL) vs specific leaf area (SLA), LL vs mass-specific leaf respiration rate (RmL), SLA vs RmL, and resistance to breakage vs wood density. Ordination analyses (e.g., PCA) show groupings of traits that tend to align with different life-history strategies or taxonomic groups. It is unclear, however, what underlies such trade-offs and emergent spectra. Do they arise from inherent physiological constraints on growth, or are they more reflective of environmental filtering? The relative importance of these mechanisms has implications for predicting biogeochemical cycling, which is influenced by trait distributions of the plant community. We address this question using an individual-based model of tree growth (ACGCA) to quantify the theoretical trait space of trees that emerges from physiological constraints. ACGCA's inputs include 32 physiological, anatomical, and allometric traits, many of which are related to the LES and WES. We fit ACGCA to 1.6 million USFS FIA observations of tree diameters and heights to obtain vectors of trait values that produce realistic growth, and we explored the structure of this trait space. No notable correlations emerged among the 496 trait pairs, but stepwise regressions revealed complicated multi-variate structure: e.g., relationships between pairs of traits (e.g., RmL and SLA) are governed by other traits (e.g., LL, radiation-use efficiency [RUE]). We also simulated growth under various canopy gap scenarios that impose varying degrees of environmental filtering to explore the multi-dimensional trait space (hypervolume) of trees that died vs survived. The centroid and volume of the hypervolumes differed among dead and live trees, especially under gap conditions leading to low mortality. Traits most predictive

  16. Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer

    DEFF Research Database (Denmark)

    Thingholm, Louise B; Andersen, Lars; Makalic, Enes

    2016-01-01

    The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis...... to integration strategies used for analyzing genetic risk factors for cancer. We critically examine the ability of these strategies to handle the complexity of the human genome and also accommodate information about the biological and functional interactions between the elements that have been measured...

  17. Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges

    DEFF Research Database (Denmark)

    Thingholm, Louise Bruun; Andersen, Lars; Makalic, Enes

    2016-01-01

    to integration strategies used for analyzing genetic risk factors for cancer. We critically examine the ability of these strategies to handle the complexity of the human genome and also accommodate information about the biological and functional interactions between the elements that have been measured......The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis...

  18. INTEGRATING NEW TESTS OF SPERM GENETIC INTEGRITY INTO SEMEN ANALYSIS: BREAKOUT GROUP DISCUSSION

    Science.gov (United States)

    The First International Conference on Male-Mediated Developmental Toxicity, held in September 1992, reported that the spermatozoon can bring genetic damage into the oocyte at fertilization and thereby contribute to subsequent abnormal pregnancy outcomes. At that time, laboratory ...

  19. GDR (Genome Database for Rosaceae: integrated web resources for Rosaceae genomics and genetics research

    Directory of Open Access Journals (Sweden)

    Ficklin Stephen

    2004-09-01

    Full Text Available Abstract Background Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. Description The Genome Database for Rosaceae (GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. Conclusions The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

  20. GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research.

    Science.gov (United States)

    Jung, Sook; Jesudurai, Christopher; Staton, Margaret; Du, Zhidian; Ficklin, Stephen; Cho, Ilhyung; Abbott, Albert; Tomkins, Jeffrey; Main, Dorrie

    2004-09-09

    Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

  1. Devaney chaos, Li-Yorke chaos, and multi-dimensional Li-Yorke chaos for topological dynamics

    Science.gov (United States)

    Dai, Xiongping; Tang, Xinjia

    2017-11-01

    Let π : T × X → X, written T↷π X, be a topological semiflow/flow on a uniform space X with T a multiplicative topological semigroup/group not necessarily discrete. We then prove: If T↷π X is non-minimal topologically transitive with dense almost periodic points, then it is sensitive to initial conditions. As a result of this, Devaney chaos ⇒ Sensitivity to initial conditions, for this very general setting. Let R+↷π X be a C0-semiflow on a Polish space; then we show: If R+↷π X is topologically transitive with at least one periodic point p and there is a dense orbit with no nonempty interior, then it is multi-dimensional Li-Yorke chaotic; that is, there is a uncountable set Θ ⊆ X such that for any k ≥ 2 and any distinct points x1 , … ,xk ∈ Θ, one can find two time sequences sn → ∞ ,tn → ∞ with Moreover, let X be a non-singleton Polish space; then we prove: Any weakly-mixing C0-semiflow R+↷π X is densely multi-dimensional Li-Yorke chaotic. Any minimal weakly-mixing topological flow T↷π X with T abelian is densely multi-dimensional Li-Yorke chaotic. Any weakly-mixing topological flow T↷π X is densely Li-Yorke chaotic. We in addition construct a completely Li-Yorke chaotic minimal SL (2 , R)-acting flow on the compact metric space R ∪ { ∞ }. Our various chaotic dynamics are sensitive to the choices of the topology of the phase semigroup/group T.

  2. A Two-Temperature Open-Source CFD Model for Hypersonic Reacting Flows, Part Two: Multi-Dimensional Analysis †

    OpenAIRE

    Vincent Casseau; Daniel E. R. Espinoza; Thomas J. Scanlon; Richard E. Brown

    2016-01-01

    hy2Foam is a newly-coded open-source two-temperature computational fluid dynamics (CFD) solver that has previously been validated for zero-dimensional test cases. It aims at (1) giving open-source access to a state-of-the-art hypersonic CFD solver to students and researchers; and (2) providing a foundation for a future hybrid CFD-DSMC (direct simulation Monte Carlo) code within the OpenFOAM framework. This paper focuses on the multi-dimensional verification of hy2Foam and firstly describes th...

  3. Theoretical background and implementation of the finite element method for multi-dimensional Fokker-Planck equation analysis

    Czech Academy of Sciences Publication Activity Database

    Král, Radomil; Náprstek, Jiří

    2017-01-01

    Roč. 113, November (2017), s. 54-75 ISSN 0965-9978 R&D Projects: GA ČR(CZ) GP14-34467P; GA ČR(CZ) GA15-01035S Institutional support: RVO:68378297 Keywords : Fokker-Planck equation * finite element method * simplex element * multi-dimensional problem * non-symmetric operator Subject RIV: JM - Building Engineering OBOR OECD: Mechanical engineering Impact factor: 3.000, year: 2016 https://www.sciencedirect.com/science/ article /pii/S0965997817301904

  4. Algorithm for locating the extremum of a multi-dimensional constrained function and its application to the PPPL Hybrid Study

    International Nuclear Information System (INIS)

    Bathke, C.

    1978-03-01

    A description is presented of a general algorithm for locating the extremum of a multi-dimensional constrained function. The algorithm employs a series of techniques dominated by random shrinkage, steepest descent, and adaptive creeping. A discussion follows of the algorithm's application to a ''real world'' problem, namely the optimization of the price of electricity, P/sub eh/, from a hybrid fusion-fission reactor. Upon the basis of comparisons with other optimization schemes of a survey nature, the algorithm is concluded to yield a good approximation to the location of a function's optimum

  5. Comparison and improvements of different Bayesian procedures to integrate external information into genetic evaluations

    NARCIS (Netherlands)

    Vandenplas, J.; Gengler, N.

    2012-01-01

    The aim of this research was to compare different Bayesian procedures to integrate information from outside a given evaluation system, hereafter called external information, and in this context estimated breeding values (EBV), into this genetic evaluation, hereafter called internal evaluation, and

  6. Integrating population and genetic monitoring to understand changes in the abundance of a threatened seabird

    Science.gov (United States)

    Catalina Vásquez-Carrillo; R. William Henry; Laird Henkel; M. Zachariah. Peery

    2013-01-01

    Population monitoring programs for threatened species are rarely designed to disentangle the effects of movements from changes in birth and death rates on estimated trends in abundance. Here, we illustrate how population and genetic monitoring can be integrated to understand the cause of large changes in the abundance of a threatened species of seabird, the Marbled...

  7. Filling the knowledge gap: Integrating quantitative genetics and genomics in graduate education and outreach

    Science.gov (United States)

    The genomics revolution provides vital tools to address global food security. Yet to be incorporated into livestock breeding, molecular techniques need to be integrated into a quantitative genetics framework. Within the U.S., with shrinking faculty numbers with the requisite skills, the capacity to ...

  8. Integrated screening concept in women with genetic predisposition for breast cancer

    International Nuclear Information System (INIS)

    Bick, U.

    1997-01-01

    Breast cancer is in 5% of cases due to a genetic disposition. BRCA1 and BRCA2 are by far the most common breast cancer susceptibility genes. For a woman with a genetic predisposition, the individual risk of developing breast cancer sometime in her life is between 70 and 90%. Compared to the spontaneous forms of breast cancer, woman with a genetic predisposition often develop breast cancer at a much younger age. This is why conventional screening programs on the basis of mammography alone cannot be applied without modification to this high-risk group. In this article, an integrated screening concept for women with genetic prodisposition for breast cancer using breast self-examination, clinical examination, ultrasound, mammography and magnetic resonance imaging is introduced. (orig.) [de

  9. [Dignity or integrity - does the genetic modification of animals require new concepts in animal ethics?].

    Science.gov (United States)

    Schmidt, Kirsten

    2008-01-01

    Animal genetic engineering seems to point at a normative gap beyond pathocentric welfare theories in animal ethics. Recently developed approaches aim to bridge this gap by means of new normative criteria such as animal dignity and animal integrity. The following comparison of dignity and integrity in the context of animal ethics shows that the dignity concept faces serious problems because of its necessarily anthroporelational character and the different functions of contingent and inherent dignity within ethical reasoning. Unlike animal dignity the concept of animal integrity could prove to be a useful enhancement for pathocentric approaches.

  10. Assessment of multi-dimensional analysis cacpacity of the MARS using the OECD-SETH PANDA tests

    International Nuclear Information System (INIS)

    Bae, S. W.; Jung, J. J.; Jung, B. D.

    2004-01-01

    The objectives of OECD/NEA-PANDA tests are to validate and assess computer codes that analyze the non-condensable gas concentrations and mixing phenomena in a reactor containment building. Especially, the main issue is multi-dimensional analysis capability which is involved in the mixing of non-condensable gases, i. e. hydrogen. The main tests consist of a superheated steam flow injection into a large vessel initially filled with air or air/helium mixtures. Then the temperature and concentration of noncondensable gases are measured. A pre-calculation has been performed with the MARS about PANDA Tests even though MARS is not a containment analysis code. Three cases among 25 PANDA Tests are selected and are modeled to simulate the jet plumes and air mixing in a large vessel. The dimensions of large vessel are 4 m diameter and 8 m height. For the conclusion of calculation, the cylindrical vessel which dimensions are 4 m diameter and 8 m height was simplified as rectangular geometry. It is revealed that the MARS code has the capability to distinguish the multi-dimensional distribution of the velocity and the temperature fields

  11. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data.

    Science.gov (United States)

    Jung, Sook; Staton, Margaret; Lee, Taein; Blenda, Anna; Svancara, Randall; Abbott, Albert; Main, Dorrie

    2008-01-01

    The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

  12. Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.

    Science.gov (United States)

    Leo, Sarah S T; Gonzalez, Andrew; Millien, Virginie

    2016-05-01

    Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies.

  13. Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data.

    Science.gov (United States)

    Fu, Changhe; Deng, Su; Jin, Guangxu; Wang, Xinxin; Yu, Zu-Guo

    2017-09-21

    Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despite advances in inferring biological pathways using genetic interaction data, there still exists weakness in developed models, such as, activity pathway networks (APN), when integrating the data from proteomic and genetic levels. It is necessary to develop new methods to infer pathway structure by both of interaction data. We utilized probabilistic graphical model to develop a new method that integrates genetic interaction and protein interaction data and infers exquisitely detailed pathway structure. We modeled the pathway network as Bayesian network and applied this model to infer pathways for the coherent subsets of the global genetic interaction profiles, and the available data set of endoplasmic reticulum genes. The protein interaction data were derived from the BioGRID database. Our method can accurately reconstruct known cellular pathway structures, including SWR complex, ER-Associated Degradation (ERAD) pathway, N-Glycan biosynthesis pathway, Elongator complex, Retromer complex, and Urmylation pathway. By comparing N-Glycan biosynthesis pathway and Urmylation pathway identified from our approach with that from APN, we found that our method is able to overcome its weakness (certain edges are inexplicable). According to underlying protein interaction network, we defined a simple scoring function that only adopts genetic interaction information to avoid the balance difficulty in the APN. Using the effective stochastic simulation algorithm, the performance of our proposed method is significantly high. We developed a new method based on Bayesian network to infer detailed pathway structures from interaction data at proteomic and genetic levels. The results indicate that the developed method performs better in predicting signaling pathways than previously

  14. Inferring genetic architecture of complex traits using Bayesian integrative analysis of genome and transcriptiome data

    DEFF Research Database (Denmark)

    Ehsani, Alireza; Sørensen, Peter; Pomp, Daniel

    2012-01-01

    Background To understand the genetic architecture of complex traits and bridge the genotype-phenotype gap, it is useful to study intermediate -omics data, e.g. the transcriptome. The present study introduces a method for simultaneous quantification of the contributions from single nucleotide......-modal distribution of genomic values collapses, when gene expressions are added to the model Conclusions With increased availability of various -omics data, integrative approaches are promising tools for understanding the genetic architecture of complex traits. Partitioning of explained variances at the chromosome...

  15. Urban agriculture: multi-dimensional tools for social development in poor neighbourhoods

    Directory of Open Access Journals (Sweden)

    E. Duchemin

    2009-01-01

    Full Text Available For over 30 years, different urban agriculture (UA experiments have been undertaken in Montreal (Quebec, Canada. The Community Gardening Program, managed by the City, and 6 collective gardens, managed by community organizations, are discussed in this article. These experiments have different objectives, including food security, socialization and education. Although these have changed over time, they have also differed depending on geographic location (neighbourhood. The UA initiatives in Montreal have resulted in the development of a centre with a significant vegetable production and a socialization and education environment that fosters individual and collective social development in districts with a significant economically disadvantaged population. The various approaches attain the established objectives and these are multi-dimensional tools used for the social development of disadvantaged populations.Depuis plus de 30 ans, différentes expériences d’AU ont été tentée à Montréal (Québec, Canada. Le programme des jardins communautaires, géré par la Ville, et 6 jardins collectifs, gérés par des organisations communautaires, sont examinés dans le cadre de cet article.  Ces expériences visent différents objectifs : accroître la sécurité alimentaire, sociabiliser, éduquer, etc. Les objectifs évoluent dans le temps mais aussi selon les quartiers. Notre étude révèle que les initiatives en AU à Montréal sont un lieu de production de légumes non négligeable, un espace pour sociabiliser et un lieu d’éducation favorisant un développement social individuel et collectif des quartiers ayant une forte présence de population économique défavorisée. Les différentes approches atteignent les objectifs identifiés et permettent le développement d’outils multi-facettes favorisant le développement social des populations défavorisées.Durante más de 30 años se han realizado diversos experimentos relacionados con la

  16. Synthesis of Joint Volumes, Visualization of Paths, and Revision of Viewing Sequences in a Multi-dimensional Seismic Data Viewer

    Science.gov (United States)

    Chen, D. M.; Clapp, R. G.; Biondi, B.

    2006-12-01

    Ricksep is a freely-available interactive viewer for multi-dimensional data sets. The viewer is very useful for simultaneous display of multiple data sets from different viewing angles, animation of movement along a path through the data space, and selection of local regions for data processing and information extraction. Several new viewing features are added to enhance the program's functionality in the following three aspects. First, two new data synthesis algorithms are created to adaptively combine information from a data set with mostly high-frequency content, such as seismic data, and another data set with mainly low-frequency content, such as velocity data. Using the algorithms, these two data sets can be synthesized into a single data set which resembles the high-frequency data set on a local scale and at the same time resembles the low- frequency data set on a larger scale. As a result, the originally separated high and low-frequency details can now be more accurately and conveniently studied together. Second, a projection algorithm is developed to display paths through the data space. Paths are geophysically important because they represent wells into the ground. Two difficulties often associated with tracking paths are that they normally cannot be seen clearly inside multi-dimensional spaces and depth information is lost along the direction of projection when ordinary projection techniques are used. The new algorithm projects samples along the path in three orthogonal directions and effectively restores important depth information by using variable projection parameters which are functions of the distance away from the path. Multiple paths in the data space can be generated using different character symbols as positional markers, and users can easily create, modify, and view paths in real time. Third, a viewing history list is implemented which enables Ricksep's users to create, edit and save a recipe for the sequence of viewing states. Then, the recipe

  17. An Extended Genetic Algorithm for Distributed Integration of Fuzzy Process Planning and Scheduling

    Directory of Open Access Journals (Sweden)

    Shuai Zhang

    2016-01-01

    Full Text Available The distributed integration of process planning and scheduling (DIPPS aims to simultaneously arrange the two most important manufacturing stages, process planning and scheduling, in a distributed manufacturing environment. Meanwhile, considering its advantage corresponding to actual situation, the triangle fuzzy number (TFN is adopted in DIPPS to represent the machine processing and transportation time. In order to solve this problem and obtain the optimal or near-optimal solution, an extended genetic algorithm (EGA with innovative three-class encoding method, improved crossover, and mutation strategies is proposed. Furthermore, a local enhancement strategy featuring machine replacement and order exchange is also added to strengthen the local search capability on the basic process of genetic algorithm. Through the verification of experiment, EGA achieves satisfactory results all in a very short period of time and demonstrates its powerful performance in dealing with the distributed integration of fuzzy process planning and scheduling (DIFPPS.

  18. Integrating genetic and toxicogenomic information for determining underlying susceptibility to developmental disorders.

    Science.gov (United States)

    Robinson, Joshua F; Port, Jesse A; Yu, Xiaozhong; Faustman, Elaine M

    2010-10-01

    To understand the complex etiology of developmental disorders, an understanding of both genetic and environmental risk factors is needed. Human and rodent genetic studies have identified a multitude of gene candidates for specific developmental disorders such as neural tube defects (NTDs). With the emergence of toxicogenomic-based assessments, scientists now also have the ability to compare and understand the expression of thousands of genes simultaneously across strain, time, and exposure in developmental models. Using a systems-based approach in which we are able to evaluate information from various parts and levels of the developing organism, we propose a framework for integrating genetic information with toxicogenomic-based studies to better understand gene-environmental interactions critical for developmental disorders. This approach has allowed us to characterize candidate genes in the context of variables critical for determining susceptibility such as strain, time, and exposure. Using a combination of toxicogenomic studies and complementary bioinformatic tools, we characterize NTD candidate genes during normal development by function (gene ontology), linked phenotype (disease outcome), location, and expression (temporally and strain-dependent). In addition, we show how environmental exposures (cadmium, methylmercury) can influence expression of these genes in a strain-dependent manner. Using NTDs as an example of developmental disorder, we show how simple integration of genetic information from previous studies into the standard microarray design can enhance analysis of gene-environment interactions to better define environmental exposure-disease pathways in sensitive and resistant mouse strains. © Wiley-Liss, Inc.

  19. Reclassification of Mixed Oligoastrocytic Tumors Using a Genetically Integrated Diagnostic Approach

    Directory of Open Access Journals (Sweden)

    Seong-Ik Kim

    2018-01-01

    Full Text Available Background Mixed gliomas, such as oligoastrocytomas (OA, anaplastic oligoastrocytomas, and glioblastomas (GBMs with an oligodendroglial component (GBMO are defined as tumors composed of a mixture of two distinct neoplastic cell types, astrocytic and oligodendroglial. Recently, mutations ATRX and TP53, and codeletion of 1p/19q are shown to be genetic hallmarks of astrocytic and oligodendroglial tumors, respectively. Subsequent molecular analyses of mixed gliomas preferred the reclassification to either oligodendroglioma or astrocytoma. This study was designed to apply genetically integrated diagnostic criteria to mixed gliomas and determine usefulness and prognostic value of new classification in Korean patients. Methods Fifty-eight cases of mixed OAs and GBMOs were retrieved from the pathology archives of Seoul National University Hospital from 2004 to 2015. Reclassification was performed according to genetic and immunohistochemical properties. Clinicopathological characteristics of each subgroup were evaluated. Overall survival was assessed and compared between subgroups. Results We could reclassify all mixed OAs and GBMOs into either astrocytic or oligodendroglial tumors. Notably, 29 GBMOs could be reclassified into 11 cases of GBM, IDH-mutant, 16 cases of GBM, IDH-wildtype, and two cases of anaplastic oligodendroglioma, IDH mutant. Overall survival was significantly different among these new groups (p<.001. Overall survival and progression-free survival were statistically better in gliomas with IDH mutation, ATRX mutation, no microscopic necrosis, and young patient age (cut off, 45 years old. Conclusions Our results strongly suggest that a genetically integrated diagnosis of glioma better reflects prognosis than former morphology-based methods.

  20. Metabologenomics of Phaeochromocytoma and Paraganglioma: An Integrated Approach for Personalised Biochemical and Genetic Testing.

    Science.gov (United States)

    Eisenhofer, Graeme; Klink, Barbara; Richter, Susan; Lenders, Jacques Wm; Robledo, Mercedes

    2017-04-01

    The tremendous advances over the past two decades in both clinical genetics and biochemical testing of chromaffin cell tumours have led to new considerations about how these aspects of laboratory medicine can be integrated to improve diagnosis and management of affected patients. With germline mutations in 15 genes now identified to be responsible for over a third of all cases of phaeochromocytomas and paragangliomas, these tumours are recognised to have one of the richest hereditary backgrounds among all neoplasms. Depending on the mutation, tumours show distinct differences in metabolic pathways that relate to or even directly impact clinical presentation. At the same time, there has been improved understanding about how catecholamines are synthesised, stored, secreted and metabolised by chromaffin cell tumours. Although the tumours may not always secrete catecholamines it has become clear that almost all continuously produce and metabolise catecholamines. This has not only fuelled changes in laboratory medicine, but has also assisted in recognition of genotype-biochemical phenotype relationships important for diagnostics and clinical care. In particular, differences in catecholamine and energy pathway metabolomes can guide genetic testing, assist with test interpretation and provide predictions about the nature, behaviour and imaging characteristics of the tumours. Conversely, results of genetic testing are important for guiding how routine biochemical testing should be employed and interpreted in surveillance programmes for at-risk patients. In these ways there are emerging needs for modern laboratory medicine to seamlessly integrate biochemical and genetic testing into the diagnosis and management of patients with chromaffin cell tumours.

  1. Safe genetic modification of cardiac stem cells using a site-specific integration technique.

    Science.gov (United States)

    Lan, Feng; Liu, Junwei; Narsinh, Kazim H; Hu, Shijun; Han, Leng; Lee, Andrew S; Karow, Marisa; Nguyen, Patricia K; Nag, Divya; Calos, Michele P; Robbins, Robert C; Wu, Joseph C

    2012-09-11

    Human cardiac progenitor cells (hCPCs) are a promising cell source for regenerative repair after myocardial infarction. Exploitation of their full therapeutic potential may require stable genetic modification of the cells ex vivo. Safe genetic engineering of stem cells, using facile methods for site-specific integration of transgenes into known genomic contexts, would significantly enhance the overall safety and efficacy of cellular therapy in a variety of clinical contexts. We used the phiC31 site-specific recombinase to achieve targeted integration of a triple fusion reporter gene into a known chromosomal context in hCPCs and human endothelial cells. Stable expression of the reporter gene from its unique chromosomal integration site resulted in no discernible genomic instability or adverse changes in cell phenotype. Namely, phiC31-modified hCPCs were unchanged in their differentiation propensity, cellular proliferative rate, and global gene expression profile when compared with unaltered control hCPCs. Expression of the triple fusion reporter gene enabled multimodal assessment of cell fate in vitro and in vivo using fluorescence microscopy, bioluminescence imaging, and positron emission tomography. Intramyocardial transplantation of genetically modified hCPCs resulted in significant improvement in myocardial function 2 weeks after cell delivery, as assessed by echocardiography (P=0.002) and MRI (P=0.001). We also demonstrated the feasibility and therapeutic efficacy of genetically modifying differentiated human endothelial cells, which enhanced hind limb perfusion (Pmodification system is a safe, efficient tool to enable site-specific integration of reporter transgenes in progenitor and differentiated cell types.

  2. Ruminant Nutrition Symposium: a systems approach to integrating genetics, nutrition, and metabolic efficiency in dairy cattle.

    Science.gov (United States)

    McNamara, J P

    2012-06-01

    The role of the dairy cow is to help provide high-quality protein and other nutrients for humans. We must select and manage cows with the goal of reaching the greatest possible efficiency for any given environment. We have increased efficiency tremendously over the years, yet the variation in productive and reproductive efficiency among animals is still quite large. In part this is because of a lack of full integration of genetic, nutritional, and reproductive biology into management decisions. However, integration across these disciplines is increasing as biological research findings show more specific control points at which genetics, nutrition, and reproduction interact. An ordered systems biology approach that focuses on why and how cells regulate energy and N use and on how and why organs interact by endocrine and neurocrine mechanisms will speed improvements in efficiency. More sophisticated dairy managers will demand better information to improve the efficiency of their animals. Using genetic improvement and proper animal management to improve milk productive and reproductive efficiency requires a deeper understanding of metabolic processes during the transition period. Using existing metabolic models, we can design experiments specifically to integrate new data from transcriptional arrays into models that describe nutrient use in farm animals. A systems modeling approach can help focus our research to make faster and large advances in efficiency and show directly how this can be applied on the farms.

  3. Integrating environmental and genetic effects to predict responses of tree populations to climate.

    Science.gov (United States)

    Wang, Tongli; O'Neill, Gregory A; Aitken, Sally N

    2010-01-01

    Climate is a major environmental factor affecting the phenotype of trees and is also a critical agent of natural selection that has molded among-population genetic variation. Population response functions describe the environmental effect of planting site climates on the performance of a single population, whereas transfer functions describe among-population genetic variation molded by natural selection for climate. Although these approaches are widely used to predict the responses of trees to climate change, both have limitations. We present a novel approach that integrates both genetic and environmental effects into a single "universal response function" (URF) to better predict the influence of climate on phenotypes. Using a large lodgepole pine (Pinus contorta Dougl. ex Loud.) field transplant experiment composed of 140 populations planted on 62 sites to demonstrate the methodology, we show that the URF makes full use of data from provenance trials to: (1) improve predictions of climate change impacts on phenotypes; (2) reduce the size and cost of future provenance trials without compromising predictive power; (3) more fully exploit existing, less comprehensive provenance tests; (4) quantify and compare environmental and genetic effects of climate on population performance; and (5) predict the performance of any population growing in any climate. Finally, we discuss how the last attribute allows the URF to be used as a mechanistic model to predict population and species ranges for the future and to guide assisted migration of seed for reforestation, restoration, or afforestation and genetic conservation in a changing climate.

  4. A novel and efficient analytical method for calculation of the transient temperature field in a multi-dimensional composite slab

    International Nuclear Information System (INIS)

    Lu, X; Tervola, P; Viljanen, M

    2005-01-01

    This paper provides an efficient analytical tool for solving the heat conduction equation in a multi-dimensional composite slab subject to generally time-dependent boundary conditions. A temporal Laplace transformation and novel separation of variables are applied to the heat equation. The time-dependent boundary conditions are approximated with Fourier series. Taking advantage of the periodic properties of Fourier series, the corresponding analytical solution is obtained and expressed explicitly through employing variable transformations. For such conduction problems, nearly all the published works necessitate numerical work such as computing residues or searching for eigenvalues even for a one-dimensional composite slab. In this paper, the proposed method involves no numerical iteration. The final closed form solution is straightforward; hence, the physical parameters are clearly shown in the formula. The accuracy of the developed analytical method is demonstrated by comparison with numerical calculations

  5. Numerical solution to a multi-dimensional linear inverse heat conduction problem by a splitting-based conjugate gradient method

    International Nuclear Information System (INIS)

    Dinh Nho Hao; Nguyen Trung Thanh; Sahli, Hichem

    2008-01-01

    In this paper we consider a multi-dimensional inverse heat conduction problem with time-dependent coefficients in a box, which is well-known to be severely ill-posed, by a variational method. The gradient of the functional to be minimized is obtained by aids of an adjoint problem and the conjugate gradient method with a stopping rule is then applied to this ill-posed optimization problem. To enhance the stability and the accuracy of the numerical solution to the problem we apply this scheme to the discretized inverse problem rather than to the continuous one. The difficulties with large dimensions of discretized problems are overcome by a splitting method which only requires the solution of easy-to-solve one-dimensional problems. The numerical results provided by our method are very good and the techniques seem to be very promising.

  6. Assessment of the RELAP5 multi-dimensional component model using data from LOFT test L2-5

    International Nuclear Information System (INIS)

    Davis, C.B.

    1998-01-01

    The capability of the RELAP5-3D computer code to perform multi-dimensional analysis of a pressurized water reactor (PWR) was assessed using data from the LOFT L2-5 experiment. The LOFT facility was a 50 MW PWR that was designed to simulate the response of a commercial PWR during a loss-of-coolant accident. Test L2-5 simulated a 200% double-ended cold leg break with an immediate primary coolant pump trip. A three-dimensional model of the LOFT reactor vessel was developed. Calculations of the LOFT L2-5 experiment were performed using the RELAP5-3D Version BF02 computer code. The calculated thermal-hydraulic responses of the LOFT primary and secondary coolant systems were generally in reasonable agreement with the test. The calculated results were also generally as good as or better than those obtained previously with RELAP/MOD3

  7. Chemical shift-dependent apparent scalar couplings: An alternative concept of chemical shift monitoring in multi-dimensional NMR experiments

    International Nuclear Information System (INIS)

    Kwiatkowski, Witek; Riek, Roland

    2003-01-01

    The paper presents an alternative technique for chemical shift monitoring in a multi-dimensional NMR experiment. The monitored chemical shift is coded in the line-shape of a cross-peak through an apparent residual scalar coupling active during an established evolution period or acquisition. The size of the apparent scalar coupling is manipulated with an off-resonance radio-frequency pulse in order to correlate the size of the coupling with the position of the additional chemical shift. The strength of this concept is that chemical shift information is added without an additional evolution period and accompanying polarization transfer periods. This concept was incorporated into the three-dimensional triple-resonance experiment HNCA, adding the information of 1 H α chemical shifts. The experiment is called HNCA coded HA, since the chemical shift of 1 H α is coded in the line-shape of the cross-peak along the 13 C α dimension

  8. Lithium Depletion in Solar-like Stars: Effect of Overshooting Based on Realistic Multi-dimensional Simulations

    Science.gov (United States)

    Baraffe, I.; Pratt, J.; Goffrey, T.; Constantino, T.; Folini, D.; Popov, M. V.; Walder, R.; Viallet, M.

    2017-08-01

    We study lithium depletion in low-mass and solar-like stars as a function of time, using a new diffusion coefficient describing extra-mixing taking place at the bottom of a convective envelope. This new form is motivated by multi-dimensional fully compressible, time-implicit hydrodynamic simulations performed with the MUSIC code. Intermittent convective mixing at the convective boundary in a star can be modeled using extreme value theory, a statistical analysis frequently used for finance, meteorology, and environmental science. In this Letter, we implement this statistical diffusion coefficient in a one-dimensional stellar evolution code, using parameters calibrated from multi-dimensional hydrodynamic simulations of a young low-mass star. We propose a new scenario that can explain observations of the surface abundance of lithium in the Sun and in clusters covering a wide range of ages, from ˜50 Myr to ˜4 Gyr. Because it relies on our physical model of convective penetration, this scenario has a limited number of assumptions. It can explain the observed trend between rotation and depletion, based on a single additional assumption, namely, that rotation affects the mixing efficiency at the convective boundary. We suggest the existence of a threshold in stellar rotation rate above which rotation strongly prevents the vertical penetration of plumes and below which rotation has small effects. In addition to providing a possible explanation for the long-standing problem of lithium depletion in pre-main-sequence and main-sequence stars, the strength of our scenario is that its basic assumptions can be tested by future hydrodynamic simulations.

  9. A new improvement on a chemical kinetic model of primary reference fuel for multi-dimensional CFD simulation

    International Nuclear Information System (INIS)

    Zhen, Xudong; Wang, Yang; Liu, Daming

    2016-01-01

    Highlights: • A new optimized chemical kinetic mechanism for PRF is developed. • New mechanism optimization is performed based on the CHEMKIN simulations. • More reactions of C_0–C_1 oxidation are added in the present mechanism. • Good performance is achieved of mechanism by validating various reactors and operating conditions. - Abstract: In the present study, for the multi-dimensional CFD (computational fluid dynamics) combustion simulations of internal combustion engines, a new optimized chemical kinetic reaction mechanism for the oxidation of PRF (primary reference fuel) instead of gasoline has been developed. In order to carry out the in-depth research for combustion phenomenon of internal combustion engines, an optimized reduced PRF mechanism including more intermediate species and radicals was developed. The developed mechanism contains of iso-octane (C_8H_1_8) and n-heptane (C_7H_1_6) surrogates, which contains of 51-species and 193 reactions. Compared with many other mechanisms of PRF, more reactions of C_0–C_1 oxidation (100 reactions) are added in the present mechanism. In order to improve the performances of the model, the developed mechanism focused on the improvement through the prediction of the ignition delay time. The developed mechanism has been validated against various experimental and simulation data including shock tube data, laminar flame speed data and HCCI (homogeneous charge compression ignition) engine data. The results showed that the developed PRF mechanism was agreements with the experimental data and other approved reduced mechanisms, and it could be applied to the multi-dimensional CFD simulations for internal combustion engines.

  10. Lithium Depletion in Solar-like Stars: Effect of Overshooting Based on Realistic Multi-dimensional Simulations

    International Nuclear Information System (INIS)

    Baraffe, I.; Pratt, J.; Goffrey, T.; Constantino, T.; Viallet, M.; Folini, D.; Popov, M. V.; Walder, R.

    2017-01-01

    We study lithium depletion in low-mass and solar-like stars as a function of time, using a new diffusion coefficient describing extra-mixing taking place at the bottom of a convective envelope. This new form is motivated by multi-dimensional fully compressible, time-implicit hydrodynamic simulations performed with the MUSIC code. Intermittent convective mixing at the convective boundary in a star can be modeled using extreme value theory, a statistical analysis frequently used for finance, meteorology, and environmental science. In this Letter, we implement this statistical diffusion coefficient in a one-dimensional stellar evolution code, using parameters calibrated from multi-dimensional hydrodynamic simulations of a young low-mass star. We propose a new scenario that can explain observations of the surface abundance of lithium in the Sun and in clusters covering a wide range of ages, from ∼50 Myr to ∼4 Gyr. Because it relies on our physical model of convective penetration, this scenario has a limited number of assumptions. It can explain the observed trend between rotation and depletion, based on a single additional assumption, namely, that rotation affects the mixing efficiency at the convective boundary. We suggest the existence of a threshold in stellar rotation rate above which rotation strongly prevents the vertical penetration of plumes and below which rotation has small effects. In addition to providing a possible explanation for the long-standing problem of lithium depletion in pre-main-sequence and main-sequence stars, the strength of our scenario is that its basic assumptions can be tested by future hydrodynamic simulations.

  11. Lithium Depletion in Solar-like Stars: Effect of Overshooting Based on Realistic Multi-dimensional Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Baraffe, I.; Pratt, J.; Goffrey, T.; Constantino, T.; Viallet, M. [Astrophysics Group, University of Exeter, Exeter EX4 4QL (United Kingdom); Folini, D.; Popov, M. V.; Walder, R., E-mail: i.baraffe@ex.ac.uk [Ecole Normale Supérieure de Lyon, CRAL, UMR CNRS 5574, F-69364 Lyon Cedex 07 (France)

    2017-08-10

    We study lithium depletion in low-mass and solar-like stars as a function of time, using a new diffusion coefficient describing extra-mixing taking place at the bottom of a convective envelope. This new form is motivated by multi-dimensional fully compressible, time-implicit hydrodynamic simulations performed with the MUSIC code. Intermittent convective mixing at the convective boundary in a star can be modeled using extreme value theory, a statistical analysis frequently used for finance, meteorology, and environmental science. In this Letter, we implement this statistical diffusion coefficient in a one-dimensional stellar evolution code, using parameters calibrated from multi-dimensional hydrodynamic simulations of a young low-mass star. We propose a new scenario that can explain observations of the surface abundance of lithium in the Sun and in clusters covering a wide range of ages, from ∼50 Myr to ∼4 Gyr. Because it relies on our physical model of convective penetration, this scenario has a limited number of assumptions. It can explain the observed trend between rotation and depletion, based on a single additional assumption, namely, that rotation affects the mixing efficiency at the convective boundary. We suggest the existence of a threshold in stellar rotation rate above which rotation strongly prevents the vertical penetration of plumes and below which rotation has small effects. In addition to providing a possible explanation for the long-standing problem of lithium depletion in pre-main-sequence and main-sequence stars, the strength of our scenario is that its basic assumptions can be tested by future hydrodynamic simulations.

  12. Genetic counselors' views and experiences with the clinical integration of genome sequencing.

    Science.gov (United States)

    Machini, Kalotina; Douglas, Jessica; Braxton, Alicia; Tsipis, Judith; Kramer, Kate

    2014-08-01

    In recent years, new sequencing technologies known as next generation sequencing (NGS) have provided scientists the ability to rapidly sequence all known coding as well as non-coding sequences in the human genome. As the two emerging approaches, whole exome (WES) and whole genome (WGS) sequencing, have started to be integrated in the clinical arena, we sought to survey health care professionals who are likely to be involved in the implementation process now and/or in the future (e.g., genetic counselors, geneticists and nurse practitioners). Two hundred twenty-one genetic counselors- one third of whom currently offer WES/WGS-participated in an anonymous online survey. The aims of the survey were first, to identify barriers to the implementation of WES/WGS, as perceived by survey participants; second, to provide the first systematic report of current practices regarding the integration of WES/WGS in clinic and/or research across the US and Canada and to illuminate the roles and challenges of genetic counselors participating in this process; and third to evaluate the impact of WES/WGS on patient care. Our results showed that genetic counseling practices with respect to WES/WGS are consistent with the criteria set forth in the ACMG 2012 policy statement, which highlights indications for testing, reporting, and pre/post test considerations. Our respondents described challenges related to offering WES/WGS, which included billing issues, the duration and content of the consent process, result interpretation and disclosure of incidental findings and variants of unknown significance. In addition, respondents indicated that specialty area (i.e., prenatal and cancer), lack of clinical utility of WES/WGS and concerns about interpretation of test results were factors that prevented them from offering this technology to patients. Finally, study participants identified the aspects of their professional training which have been most beneficial in aiding with the integration of

  13. Unified method to integrate and blend several, potentially related, sources of information for genetic evaluation.

    Science.gov (United States)

    Vandenplas, Jérémie; Colinet, Frederic G; Gengler, Nicolas

    2014-09-30

    A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For example, in dairy cattle, internal (i.e. local) populations lead to evaluations based only on internal records while widely used foreign sires have been selected using internally unavailable external records. In such cases, internal genetic evaluations may be less accurate and biased. Because external records are unavailable, methods were developed to combine external information that summarizes these records, i.e. external estimated breeding values and associated reliabilities, with internal records to improve accuracy of internal genetic evaluations. Two issues of these methods concern double-counting of contributions due to relationships and due to records. These issues could be worse if external information came from several evaluations, at least partially based on the same records, and combined into a single internal evaluation. Based on a Bayesian approach, the aim of this research was to develop a unified method to integrate and blend simultaneously several sources of information into an internal genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. This research resulted in equations that integrate and blend simultaneously several sources of information and avoid double-counting of contributions due to relationships and due to records. The performance of the developed equations was evaluated using simulated and real datasets. The results showed that the developed equations integrated and blended several sources of information well into a genetic evaluation. The developed equations also avoided double-counting of contributions due to relationships and due to records. Furthermore, because all available external sources of information were correctly propagated, relatives of external animals benefited from the integrated

  14. BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple.

    Science.gov (United States)

    Han, Yuepeng; Chagné, David; Gasic, Ksenija; Rikkerink, Erik H A; Beever, Jonathan E; Gardiner, Susan E; Korban, Schuyler S

    2009-03-01

    A genome-wide BAC physical map of the apple, Malus x domestica Borkh., has been recently developed. Here, we report on integrating the physical and genetic maps of the apple using a SNP-based approach in conjunction with bin mapping. Briefly, BAC clones located at ends of BAC contigs were selected, and sequenced at both ends. The BAC end sequences (BESs) were used to identify candidate SNPs. Subsequently, these candidate SNPs were genetically mapped using a bin mapping strategy for the purpose of mapping the physical onto the genetic map. Using this approach, 52 (23%) out of 228 BESs tested were successfully exploited to develop SNPs. These SNPs anchored 51 contigs, spanning approximately 37 Mb in cumulative physical length, onto 14 linkage groups. The reliability of the integration of the physical and genetic maps using this SNP-based strategy is described, and the results confirm the feasibility of this approach to construct an integrated physical and genetic maps for apple.

  15. Automated multi-dimensional liquid chromatography : sample preparation and identification of peptides from human blood filtrate

    NARCIS (Netherlands)

    Machtejevas, Egidijus; John, Harald; Wagner, Knut; Standker, Ludger; Marko-Varga, Gyorgy; Georg Forssmann, Wolf; Bischoff, Rainer; K. Unger, Klaus

    2004-01-01

    A comprehensive on-line sample clean-up with an integrated two-dimensional HPLC system was developed for the analysis of natural peptides. Samples comprised of endogenous peptides with molecular weights up to 20 kDa were generated from human hemofiltrate (HF) obtained from patients with chronic

  16. Integrated genetic and epigenetic prediction of coronary heart disease in the Framingham Heart Study.

    Directory of Open Access Journals (Sweden)

    Meeshanthini V Dogan

    Full Text Available An improved method for detecting coronary heart disease (CHD could have substantial clinical impact. Building on the idea that systemic effects of CHD risk factors are a conglomeration of genetic and environmental factors, we use machine learning techniques and integrate genetic, epigenetic and phenotype data from the Framingham Heart Study to build and test a Random Forest classification model for symptomatic CHD. Our classifier was trained on n = 1,545 individuals and consisted of four DNA methylation sites, two SNPs, age and gender. The methylation sites and SNPs were selected during the training phase. The final trained model was then tested on n = 142 individuals. The test data comprised of individuals removed based on relatedness to those in the training dataset. This integrated classifier was capable of classifying symptomatic CHD status of those in the test set with an accuracy, sensitivity and specificity of 78%, 0.75 and 0.80, respectively. In contrast, a model using only conventional CHD risk factors as predictors had an accuracy and sensitivity of only 65% and 0.42, respectively, but with a specificity of 0.89 in the test set. Regression analyses of the methylation signatures illustrate our ability to map these signatures to known risk factors in CHD pathogenesis. These results demonstrate the capability of an integrated approach to effectively model symptomatic CHD status. These results also suggest that future studies of biomaterial collected from longitudinally informative cohorts that are specifically characterized for cardiac disease at follow-up could lead to the introduction of sensitive, readily employable integrated genetic-epigenetic algorithms for predicting onset of future symptomatic CHD.

  17. Integrative Functional Genomics for Systems Genetics in GeneWeaver.org.

    Science.gov (United States)

    Bubier, Jason A; Langston, Michael A; Baker, Erich J; Chesler, Elissa J

    2017-01-01

    The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

  18. Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data.

    Science.gov (United States)

    Gu, Deqing; Jian, Xingxing; Zhang, Cheng; Hua, Qiang

    2017-01-01

    Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.

  19. Strategies for integrated analysis of genetic, epigenetic and gene expression variation in cancer: addressing the challenges

    Directory of Open Access Journals (Sweden)

    Louise Bruun Thingholm

    2016-02-01

    Full Text Available The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis. However, integration of heterogeneous measurements of biological variation is a non-trivial exercise due to the diversity of the human genome and the variety of output data formats and genome coverage obtained from the commonly used molecular platforms. This review article will provide an introduction to integration strategies used for analyzing genetic risk factors for cancer. We critically examine the ability of these strategies to handle the complexity of the human genome and also accommodate information about the biological and functional interactions between the elements that have been measured – making the assessment of disease risk against a composite genomic factor possible. The focus of this review is to provide an overview and introduction to the main strategies and to discuss where there is a need for further development.

  20. The Visual Geophysical Exploration Environment: A Multi-dimensional Scientific Visualization

    Science.gov (United States)

    Pandya, R. E.; Domenico, B.; Murray, D.; Marlino, M. R.

    2003-12-01

    The Visual Geophysical Exploration Environment (VGEE) is an online learning environment designed to help undergraduate students understand fundamental Earth system science concepts. The guiding principle of the VGEE is the importance of hands-on interaction with scientific visualization and data. The VGEE consists of four elements: 1) an online, inquiry-based curriculum for guiding student exploration; 2) a suite of El Nino-related data sets adapted for student use; 3) a learner-centered interface to a scientific visualization tool; and 4) a set of concept models (interactive tools that help students understand fundamental scientific concepts). There are two key innovations featured in this interactive poster session. One is the integration of concept models and the visualization tool. Concept models are simple, interactive, Java-based illustrations of fundamental physical principles. We developed eight concept models and integrated them into the visualization tool to enable students to probe data. The ability to probe data using a concept model addresses the common problem of transfer: the difficulty students have in applying theoretical knowledge to everyday phenomenon. The other innovation is a visualization environment and data that are discoverable in digital libraries, and installed, configured, and used for investigations over the web. By collaborating with the Integrated Data Viewer developers, we were able to embed a web-launchable visualization tool and access to distributed data sets into the online curricula. The Thematic Real-time Environmental Data Distributed Services (THREDDS) project is working to provide catalogs of datasets that can be used in new VGEE curricula under development. By cataloging this curricula in the Digital Library for Earth System Education (DLESE), learners and educators can discover the data and visualization tool within a framework that guides their use.

  1. Simple one-dimensional finite element algorithm with multi-dimensional capabilities

    International Nuclear Information System (INIS)

    Pepper, D.W.; Baker, A.J.

    1978-01-01

    The application of the finite element procedure for the solution of partial differential equations is gaining widespread acceptance. The ability of the finite element procedure to solve problems which are arbitrarily shaped as well as the alleviation of boundary condition problems is well known. By using local interpolation functionals over each subdomain, or element, a set of linearized algebraic equations are obtained which can be solved using any direct, iterative, or inverse numerical technique. Subsequent use of an explicit or implicit integration procedure permits closure of the solution over the global domain

  2. Integration of genetic and demographic data to assess population risk in a continuously distributed species

    Science.gov (United States)

    Fedy, Bradley C.; Row, Jeffery R.; Oyler-McCance, Sara J.

    2017-01-01

    The identification and demographic assessment of biologically meaningful populations is fundamental to species’ ecology and management. Although genetic tools are used frequently to identify populations, studies often do not incorporate demographic data to understand their respective population trends. We used genetic data to define subpopulations in a continuously distributed species. We assessed demographic independence and variation in population trends across the distribution. Additionally, we identified potential barriers to gene flow among subpopulations. We sampled greater sage-grouse (Centrocercus urophasianus) leks from across their range (≈175,000 Km2) in Wyoming and amplified DNA at 14 microsatellite loci for 1761 samples. Subsequently, we assessed population structure in unrelated individuals (n = 872) by integrating results from multiple Bayesian clustering approaches and used the boundaries to inform our assessment of long-term population trends and lek activity over the period of 1995–2013. We identified four genetic clusters of which two northern ones showed demographic independence from the others. Trends in population size for the northwest subpopulation were statistically different from the other three genetic clusters and the northeast and southwest subpopulations demonstrated a general trend of increasing proportion of inactive leks over time. Population change from 1996 to 2012 suggested population growth in the southern subpopulations and decline, or neutral, change in the northern subpopulations. We suggest that sage-grouse subpopulations in northern Wyoming are at greater risk of extirpation than the southern subpopulations due to smaller census and effective population sizes and higher variability within subpopulations. Our research is an example of incorporating genetic and demographic data and provides guidance on the identification of subpopulations of conservation concern.

  3. Pedagogic discourse in introductory classes: Multi-dimensional analysis of textbooks and lectures in biology and macroeconomics

    Science.gov (United States)

    Carkin, Susan

    The broad goal of this study is to represent the linguistic variation of textbooks and lectures, the primary input for student learning---and sometimes the sole input in the large introductory classes which characterize General Education at many state universities. Computer techniques are used to analyze a corpus of textbooks and lectures from first-year university classes in macroeconomics and biology. These spoken and written variants are compared to each other as well as to benchmark texts from other multi-dimensional studies in order to examine their patterns, relations, and functions. A corpus consisting of 147,000 words was created from macroeconomics and biology lectures at a medium-large state university and from a set of nationally "best-selling" textbooks used in these same introductory survey courses. The corpus was analyzed using multi-dimensional methodology (Biber, 1988). The analysis consists of both empirical and qualitative phases. Quantitative analyses are undertaken on the linguistic features, their patterns of co-occurrence, and on the contextual elements of classrooms and textbooks. The contextual analysis is used to functionally interpret the statistical patterns of co-occurrence along five dimensions of textual variation, demonstrating patterns of difference and similarity with reference to text excerpts. Results of the analysis suggest that academic discourse is far from monolithic. Pedagogic discourse in introductory classes varies by modality and discipline, but not always in the directions expected. In the present study the most abstract texts were biology lectures---more abstract than written genres of academic prose and more abstract than introductory textbooks. Academic lectures in both disciplines, monologues which carry a heavy informational load, were extremely interactive, more like conversation than academic prose. A third finding suggests that introductory survey textbooks differ from those used in upper division classes by being

  4. A multi-dimensional Smolyak collocation method in curvilinear coordinates for computing vibrational spectra

    International Nuclear Information System (INIS)

    Avila, Gustavo; Carrington, Tucker

    2015-01-01

    In this paper, we improve the collocation method for computing vibrational spectra that was presented in Avila and Carrington, Jr. [J. Chem. Phys. 139, 134114 (2013)]. Using an iterative eigensolver, energy levels and wavefunctions are determined from values of the potential on a Smolyak grid. The kinetic energy matrix-vector product is evaluated by transforming a vector labelled with (nondirect product) grid indices to a vector labelled by (nondirect product) basis indices. Both the transformation and application of the kinetic energy operator (KEO) scale favorably. Collocation facilitates dealing with complicated KEOs because it obviates the need to calculate integrals of coordinate dependent coefficients of differential operators. The ideas are tested by computing energy levels of HONO using a KEO in bond coordinates

  5. Multi-dimensional modeling of CO poisoning effects on proton exchange membrane fuel cells (PEMFCs)

    International Nuclear Information System (INIS)

    Ju, Hyun Chul; Lee, Kwan Soo; Um, Suk Kee

    2008-01-01

    Carbon monoxide (CO), which is preferentially absorbed on the platinum catalyst layer of a proton exchange membrane fuel cell (PEMFC), is extremely detrimental to cell performance. Essentially, the carbon monoxide absorption diminishes the cell's performance by blocking and reducing the number of catalyst sites available for the hydrogen oxidation reaction. In order to obtain a full understanding of CO poisoning characteristics and remediate CO-poisoned PEMFCs, a CO poisoning numerical model is developed and incorporated into a fully three-dimensional electrochemical and transport coupled PEMFC model. By performing CFD numerical simulations, this paper clearly demonstrates the CO poisoning mechanisms and characteristics of PEMFCs. The predictive capability for CO poisoning effects enables us to find major contributors to CO tolerance in a PEMFC and thus successfully integrate CO-resistant fuel cell systems

  6. Multi-dimensional spectrum analysis for 2-D vector velocity estimation

    DEFF Research Database (Denmark)

    Oddershede, Niels; Løvstakken, Lasse; Torp, Hans

    2007-01-01

    Fourier space, which is found through the 3-D Fourier transform of the data matrix, and that the plane is tilted according to the axial and lateral velocity components. Two estimators are derived for finding the plane in the 3-D Fourier space, where the integrated power spectrum is largest. The first uses...... the 3-D Fourier transform to find the power spectrum, while the second uses a minimum variance approach. Based on this plane, the axial and lateral velocity components are estimated. A number of phantom How measurements, for flow-to-beam angles of 60, 75, and 90 degrees, were performed to test...... the estimator. The data were collected using our RASMUS experimental ultrasound scanner and a 128 element commercial linear array transducer. The receive apodization function was manipulated, creating an oscillation in the lateral direction, and multiple parallel lines were beamformed simultaneously. The two...

  7. GO(vis), a gene ontology visualization tool based on multi-dimensional values.

    Science.gov (United States)

    Ning, Zi; Jiang, Zhenran

    2010-05-01

    Most of gene product similarity measurements concentrate on the information content of Gene Ontology (GO) terms or use a path-based similarity between GO terms, which may ignore other important information contained in the structure of the ontology. In our study, we integrate different GO similarity measure approaches to analyze the functional relationship of genes and gene products with a new triangle-based visualization tool called GO(Vis). The purpose of this tool is to demonstrate the effect of three important information factors when measuring the similarity between gene products. One advantage of this tool is that its important ratio can be adjusted to meet different measuring requirements according to the biological knowledge of each factor. The experimental results demonstrate that GO(Vis) can display diagrams of the functional relationship for gene products effectively.

  8. Optimization of Grillages Using Genetic Algorithms for Integrating Matlab and Fortran Environments

    Directory of Open Access Journals (Sweden)

    Darius Mačiūnas

    2012-12-01

    Full Text Available The purpose of the paper is to present technology applied for the global optimization of grillage-type pile foundations (further grillages. The goal of optimization is to obtain the optimal layout of pile placement in the grillages. The problem can be categorized as a topology optimization problem. The objective function is comprised of maximum reactive force emerging in a pile. The reactive force is minimized during the procedure of optimization during which variables enclose the positions of piles beneath connecting beams. Reactive forces in all piles are computed utilizing an original algorithm implemented in the Fortran programming language. The algorithm is integrated into the MatLab environment where the optimization procedure is executed utilizing a genetic algorithm. The article also describes technology enabling the integration of MatLab and Fortran environments. The authors seek to evaluate the quality of a solution to the problem analyzing experimental results obtained applying the proposed technology.

  9. Optimization of Grillages Using Genetic Algorithms for Integrating Matlab and Fortran Environments

    Directory of Open Access Journals (Sweden)

    Darius Mačiūnas

    2013-02-01

    Full Text Available The purpose of the paper is to present technology applied for the global optimization of grillage-type pile foundations (further grillages. The goal of optimization is to obtain the optimal layout of pile placement in the grillages. The problem can be categorized as a topology optimization problem. The objective function is comprised of maximum reactive force emerging in a pile. The reactive force is minimized during the procedure of optimization during which variables enclose the positions of piles beneath connecting beams. Reactive forces in all piles are computed utilizing an original algorithm implemented in the Fortran programming language. The algorithm is integrated into the MatLab environment where the optimization procedure is executed utilizing a genetic algorithm. The article also describes technology enabling the integration of MatLab and Fortran environments. The authors seek to evaluate the quality of a solution to the problem analyzing experimental results obtained applying the proposed technology.

  10. magHD: a new approach to multi-dimensional data storage, analysis, display and exploitation

    International Nuclear Information System (INIS)

    Angleraud, Christophe

    2014-01-01

    The ever increasing amount of data and processing capabilities – following the well- known Moore's law – is challenging the way scientists and engineers are currently exploiting large datasets. The scientific visualization tools, although quite powerful, are often too generic and provide abstract views of phenomena, thus preventing cross disciplines fertilization. On the other end, Geographic information Systems allow nice and visually appealing maps to be built but they often get very confused as more layers are added. Moreover, the introduction of time as a fourth analysis dimension to allow analysis of time dependent phenomena such as meteorological or climate models, is encouraging real-time data exploration techniques that allow spatial-temporal points of interests to be detected by integration of moving images by the human brain. Magellium is involved in high performance image processing chains for satellite image processing as well as scientific signal analysis and geographic information management since its creation (2003). We believe that recent work on big data, GPU and peer-to-peer collaborative processing can open a new breakthrough in data analysis and display that will serve many new applications in collaborative scientific computing, environment mapping and understanding. The magHD (for Magellium Hyper-Dimension) project aims at developing software solutions that will bring highly interactive tools for complex datasets analysis and exploration commodity hardware, targeting small to medium scale clusters with expansion capabilities to large cloud based clusters

  11. An efficient multi-dimensional implementation of VSIAM3 and its applications to free surface flows

    Science.gov (United States)

    Yokoi, Kensuke; Furuichi, Mikito; Sakai, Mikio

    2017-12-01

    We propose an efficient multidimensional implementation of VSIAM3 (volume/surface integrated average-based multi-moment method). Although VSIAM3 is a highly capable fluid solver based on a multi-moment concept and has been used for a wide variety of fluid problems, VSIAM3 could not simulate some simple benchmark problems well (for instance, lid-driven cavity flows) due to relatively high numerical viscosity. In this paper, we resolve the issue by using the efficient multidimensional approach. The proposed VSIAM3 is shown to capture lid-driven cavity flows of the Reynolds number up to Re = 7500 with a Cartesian grid of 128 × 128, which was not capable for the original VSIAM3. We also tested the proposed framework in free surface flow problems (droplet collision and separation of We = 40 and droplet splashing on a superhydrophobic substrate). The numerical results by the proposed VSIAM3 showed reasonable agreements with these experiments. The proposed VSIAM3 could capture droplet collision and separation of We = 40 with a low numerical resolution (8 meshes for the initial diameter of droplets). We also simulated free surface flows including particles toward non-Newtonian flow applications. These numerical results have showed that the proposed VSIAM3 can robustly simulate interactions among air, particles (solid), and liquid.

  12. A Parallel Compact Multi-Dimensional Numerical Algorithm with Aeroacoustics Applications

    Science.gov (United States)

    Povitsky, Alex; Morris, Philip J.

    1999-01-01

    In this study we propose a novel method to parallelize high-order compact numerical algorithms for the solution of three-dimensional PDEs (Partial Differential Equations) in a space-time domain. For this numerical integration most of the computer time is spent in computation of spatial derivatives at each stage of the Runge-Kutta temporal update. The most efficient direct method to compute spatial derivatives on a serial computer is a version of Gaussian elimination for narrow linear banded systems known as the Thomas algorithm. In a straightforward pipelined implementation of the Thomas algorithm processors are idle due to the forward and backward recurrences of the Thomas algorithm. To utilize processors during this time, we propose to use them for either non-local data independent computations, solving lines in the next spatial direction, or local data-dependent computations by the Runge-Kutta method. To achieve this goal, control of processor communication and computations by a static schedule is adopted. Thus, our parallel code is driven by a communication and computation schedule instead of the usual "creative, programming" approach. The obtained parallelization speed-up of the novel algorithm is about twice as much as that for the standard pipelined algorithm and close to that for the explicit DRP algorithm.

  13. A Generic Framework for Using Multi-Dimensional Earth Observation Data in GIS

    Directory of Open Access Journals (Sweden)

    Yunfeng Jiang

    2016-05-01

    Full Text Available Earth Observation (EO data are critical for many Geographic Information System (GIS-based decision support systems to provide factual information. However, it is challenging for GIS to understand traditional EO data formats (e.g., Hierarchical Data Format (HDF given the different contents and formats in the two domains. To address this gap between EO data and GIS, the barriers and strategies of integrating various types of EO data with GIS are explored, especially with the popular Geospatial Data Abstraction Library (GDAL that is used by many GISs to access EO data. The research investigates four key technical aspects: (i designing a generic plug-in framework for consuming different types of EO data; (ii implementing the framework to fix the errors in GIS when using GDAL to understand EO data; and (iii developing extension for commercial and open source GIS (i.e., ArcGIS and QGIS to demonstrate the usability of the proposed framework and its implementation in GDAL. A series of EO data products collected from NASA’s Atmospheric Scientific Data Center (ASDC are used in the tests and the results prove the proposed framework is efficient to solve different problems in interpreting EO data without compromising their original content.

  14. Epigenome-wide association study of DNA methylation in narcolepsy: an integrated genetic and epigenetic approach.

    Science.gov (United States)

    Shimada, Mihoko; Miyagawa, Taku; Toyoda, Hiromi; Tokunaga, Katsushi; Honda, Makoto

    2018-04-01

    Narcolepsy with cataplexy, which is a hypersomnia characterized by excessive daytime sleepiness and cataplexy, is a multifactorial disease caused by both genetic and environmental factors. Several genetic factors including HLA-DQB1*06:02 have been identified; however, the disease etiology is still unclear. Epigenetic modifications, such as DNA methylation, have been suggested to play an important role in the pathogenesis of complex diseases. Here, we examined DNA methylation profiles of blood samples from narcolepsy and healthy control individuals and performed an epigenome-wide association study (EWAS) to investigate methylation loci associated with narcolepsy. Moreover, data from the EWAS and a previously performed narcolepsy genome-wide association study were integrated to search for methylation loci with causal links to the disease. We found that (1) genes annotated to the top-ranked differentially methylated positions (DMPs) in narcolepsy were associated with pathways of hormone secretion and monocarboxylic acid metabolism. (2) Top-ranked narcolepsy-associated DMPs were significantly more abundant in non-CpG island regions and more than 95 per cent of such sites were hypomethylated in narcolepsy patients. (3) The integrative analysis identified the CCR3 region where both a single methylation site and multiple single-nucleotide polymorphisms were found to be associated with the disease as a candidate region responsible for narcolepsy. The findings of this study suggest the importance of future replication studies, using methylation technologies with wider genome coverage and/or larger number of samples, to confirm and expand on these results.

  15. A study on the multi-dimensional spectral analysis for response of a piping model with two-seismic inputs

    International Nuclear Information System (INIS)

    Suzuki, K.; Sato, H.

    1975-01-01

    The power and the cross power spectrum analysis by which the vibration characteristic of structures, such as natural frequency, mode of vibration and damping ratio, can be identified would be effective for the confirmation of the characteristics after the construction is completed by using the response for small earthquakes or the micro-tremor under the operating condition. This method of analysis previously utilized only from the view point of systems with single input so far, is extensively applied for the analysis of a medium scale model of a piping system subjected to two seismic inputs. The piping system attached to a three storied concrete structure model which is constructed on a shaking table was excited due to earthquake motions. The inputs to the piping system were recorded at the second floor and the ceiling of the third floor where the system was attached to. The output, the response of the piping system, was instrumented at a middle point on the system. As a result, the multi-dimensional power spectrum analysis is effective for a more reliable identification of the vibration characteristics of the multi-input structure system

  16. A multi-dimensional quasi-discrete model for the analysis of Diesel fuel droplet heating and evaporation

    KAUST Repository

    Sazhin, Sergei S.

    2014-08-01

    A new multi-dimensional quasi-discrete model is suggested and tested for the analysis of heating and evaporation of Diesel fuel droplets. As in the original quasi-discrete model suggested earlier, the components of Diesel fuel with close thermodynamic and transport properties are grouped together to form quasi-components. In contrast to the original quasi-discrete model, the new model takes into account the contribution of not only alkanes, but also various other groups of hydrocarbons in Diesel fuels; quasi-components are formed within individual groups. Also, in contrast to the original quasi-discrete model, the contributions of individual components are not approximated by the distribution function of carbon numbers. The formation of quasi-components is based on taking into account the contributions of individual components without any approximations. Groups contributing small molar fractions to the composition of Diesel fuel (less than about 1.5%) are replaced with characteristic components. The actual Diesel fuel is simplified to form six groups: alkanes, cycloalkanes, bicycloalkanes, alkylbenzenes, indanes & tetralines, and naphthalenes, and 3 components C19H34 (tricycloalkane), C13H 12 (diaromatic), and C14H10 (phenanthrene). It is shown that the approximation of Diesel fuel by 15 quasi-components and components, leads to errors in estimated temperatures and evaporation times in typical Diesel engine conditions not exceeding about 3.7% and 2.5% respectively, which is acceptable for most engineering applications. © 2014 Published by Elsevier Ltd. All rights reserved.

  17. The multi-dimensional model of Māori identity and cultural engagement: item response theory analysis of scale properties.

    Science.gov (United States)

    Sibley, Chris G; Houkamau, Carla A

    2013-01-01

    We argue that there is a need for culture-specific measures of identity that delineate the factors that most make sense for specific cultural groups. One such measure, recently developed specifically for Māori peoples, is the Multi-Dimensional Model of Māori Identity and Cultural Engagement (MMM-ICE). Māori are the indigenous peoples of New Zealand. The MMM-ICE is a 6-factor measure that assesses the following aspects of identity and cultural engagement as Māori: (a) group membership evaluation, (b) socio-political consciousness, (c) cultural efficacy and active identity engagement, (d) spirituality, (e) interdependent self-concept, and (f) authenticity beliefs. This article examines the scale properties of the MMM-ICE using item response theory (IRT) analysis in a sample of 492 Māori. The MMM-ICE subscales showed reasonably even levels of measurement precision across the latent trait range. Analysis of age (cohort) effects further indicated that most aspects of Māori identification tended to be higher among older Māori, and these cohort effects were similar for both men and women. This study provides novel support for the reliability and measurement precision of the MMM-ICE. The study also provides a first step in exploring change and stability in Māori identity across the life span. A copy of the scale, along with recommendations for scale scoring, is included.

  18. Parallel Implementation of the Multi-Dimensional Spectral Code SPECT3D on large 3D grids.

    Science.gov (United States)

    Golovkin, Igor E.; Macfarlane, Joseph J.; Woodruff, Pamela R.; Pereyra, Nicolas A.

    2006-10-01

    The multi-dimensional collisional-radiative, spectral analysis code SPECT3D can be used to study radiation from complex plasmas. SPECT3D can generate instantaneous and time-gated images and spectra, space-resolved and streaked spectra, which makes it a valuable tool for post-processing hydrodynamics calculations and direct comparison between simulations and experimental data. On large three dimensional grids, transporting radiation along lines of sight (LOS) requires substantial memory and CPU resources. Currently, the parallel option in SPECT3D is based on parallelization over photon frequencies and allows for a nearly linear speed-up for a variety of problems. In addition, we are introducing a new parallel mechanism that will greatly reduce memory requirements. In the new implementation, spatial domain decomposition will be utilized allowing transport along a LOS to be performed only on the mesh cells the LOS crosses. The ability to operate on a fraction of the grid is crucial for post-processing the results of large-scale three-dimensional hydrodynamics simulations. We will present a parallel implementation of the code and provide a scalability study performed on a Linux cluster.

  19. 640-slice DVCT multi-dimensionally and dynamically presents changes in bladder volume and urine flow rate

    Science.gov (United States)

    Su, Yunshan; Fang, Kewei; Mao, Chongwen; Xiang, Shutian; Wang, Jin; Li, Yingwen

    2018-01-01

    The present study aimed to explore the application of 640-slice dynamic volume computed tomography (DVCT) to excretory cystography and urethrography. A total of 70 healthy subjects were included in the study. Excretory cystography and urethrography using 640-slice DVCT was conducted to continuously record the motions of the bladder and the proximal female and male urethra. The patients' voiding process was divided into early, early to middle, middle, middle to late, and late voiding phases. The subjects were analyzed using DVCT and conventional CT. The cross-sectional areas of various sections of the male and female urethra were evaluated, and the average urine flow rate was calculated. The 640-slice DVCT technique was used to dynamically observe the urine flow rate and changes in bladder volume at all voiding phases. The urine volume detected by 640-slice DVCT exhibited no significant difference compared with the actual volume, and no significant difference compared with that determined using conventional CT. Furthermore, no significant difference in the volume of the bladder at each phase of the voiding process was detected between 640-slice DVCT and conventional CT. The results indicate that 640-slice DVCT can accurately evaluate the status of the male posterior urethra and female urethra. In conclusion, 640-slice DVCT is able to multi-dimensionally and dynamically present changes in bladder volume and urine flow rate, and could obtain similar results to conventional CT in detecting urine volume, as well as the status of the male posterior urethra and female urethra. PMID:29467853

  20. A Two-Temperature Open-Source CFD Model for Hypersonic Reacting Flows, Part Two: Multi-Dimensional Analysis †

    Directory of Open Access Journals (Sweden)

    Vincent Casseau

    2016-12-01

    Full Text Available hy2Foam is a newly-coded open-source two-temperature computational fluid dynamics (CFD solver that has previously been validated for zero-dimensional test cases. It aims at (1 giving open-source access to a state-of-the-art hypersonic CFD solver to students and researchers; and (2 providing a foundation for a future hybrid CFD-DSMC (direct simulation Monte Carlo code within the OpenFOAM framework. This paper focuses on the multi-dimensional verification of hy2Foam and firstly describes the different models implemented. In conjunction with employing the coupled vibration-dissociation-vibration (CVDV chemistry–vibration model, novel use is made of the quantum-kinetic (QK rates in a CFD solver. hy2Foam has been shown to produce results in good agreement with previously published data for a Mach 11 nitrogen flow over a blunted cone and with the dsmcFoam code for a Mach 20 cylinder flow for a binary reacting mixture. This latter case scenario provides a useful basis for other codes to compare against.

  1. Multi-dimensional approach of MARS-LMR for the analysis of Phenix End-of-Life natural circulation test

    International Nuclear Information System (INIS)

    Jeong, Hae Yong; Ha, Kwi Seok; Chang, Won Pyo; Lee, Kwi Lim

    2012-01-01

    Phenix is one of the important prototype sodium-cooled fast reactors (SFR) in nuclear reactor development history. It had been operated successfully for 35 years by the French Commissariat a l'energie atomique (CEA) and the Electricite de France (EdF) achieving its original objectives of demonstrating a fast breeder reactor technology and of playing the role of irradiation facility for innovative fuels and materials. After its final shutdown in 2009, CEA launched the Phenix End-of-life (EOL) test program. It provided a unique opportunity to generate reliable test data which is inevitable in the validation and verification of a SFR system analysis code. KAERI joined this international collaboration program of IAEA CRP and has performed the pretest analysis and post-test analysis utilizing the one-dimensional modeling of the MARS-LMR code, which had been developed by KAERI for the transient analysis of SFR systems. Through the previous studies, it has been identified that there are some limitations in the modeling of complicated thermal-hydraulic behaviors in the large pool volumes with the one-dimensional modeling. Recently, KAERI performed the analysis of Phenix EOL natural circulation test with multi-dimensional pool modeling, which is detailed below

  2. Optimization of an Electromagnetics Code with Multicore Wavefront Diamond Blocking and Multi-dimensional Intra-Tile Parallelization

    KAUST Repository

    Malas, Tareq M.

    2016-07-21

    Understanding and optimizing the properties of solar cells is becoming a key issue in the search for alternatives to nuclear and fossil energy sources. A theoretical analysis via numerical simulations involves solving Maxwell\\'s Equations in discretized form and typically requires substantial computing effort. We start from a hybrid-parallel (MPI+OpenMP) production code that implements the Time Harmonic Inverse Iteration Method (THIIM) with Finite-Difference Frequency Domain (FDFD) discretization. Although this algorithm has the characteristics of a strongly bandwidth-bound stencil update scheme, it is significantly different from the popular stencil types that have been exhaustively studied in the high performance computing literature to date. We apply a recently developed stencil optimization technique, multicore wavefront diamond tiling with multi-dimensional cache block sharing, and describe in detail the peculiarities that need to be considered due to the special stencil structure. Concurrency in updating the components of the electric and magnetic fields provides an additional level of parallelism. The dependence of the cache size requirement of the optimized code on the blocking parameters is modeled accurately, and an auto-tuner searches for optimal configurations in the remaining parameter space. We were able to completely decouple the execution from the memory bandwidth bottleneck, accelerating the implementation by a factor of three to four compared to an optimal implementation with pure spatial blocking on an 18-core Intel Haswell CPU.

  3. Assessment of the physico-chemical behavior of titanium dioxide nanoparticles in aquatic environments using multi-dimensional parameter testing

    International Nuclear Information System (INIS)

    Kammer, Frank von der; Ottofuelling, Stephanie; Hofmann, Thilo

    2010-01-01

    Assessment of the behavior and fate of engineered nanoparticles (ENPs) in natural aquatic media is crucial for the identification of environmentally critical properties of the ENPs. Here we present a methodology for testing the dispersion stability, ζ-potential and particle size of engineered nanoparticles as a function of pH and water composition. The results obtained from already widely used titanium dioxide nanoparticles (Evonik P25 and Hombikat UV-100) serve as a proof-of-concept for the proposed testing scheme. In most cases the behavior of the particles in the tested settings follows the expectations derived from classical DLVO theory for metal oxide particles with variable charge and an isoelectric point at around pH 5, but deviations also occur. Regardless of a 5-fold difference in BET specific surface area particles composed of the same core material behave in an overall comparable manner. The presented methodology can act as a basis for the development of standardised methods for comparing the behavior of different nanoparticles within aquatic systems. - The behavior of engineered nanoparticles in the aquatic environment can be elucidated using a multi-dimensional parameter set acquired by a semi automated experimental set-up.

  4. Psychometric Properties of Multi-Dimensional Scale of Perceived Social Support in Chinese Parents of Children with Cerebral Palsy

    Directory of Open Access Journals (Sweden)

    Yongli Wang

    2017-11-01

    Full Text Available The Multi-dimensional Scale of Perceived Social Support (MSPSS is one of the most extensively used instruments to assess social support. The purpose of this research was to test the reliability, factorial validity, concurrent validity and measurement invariance across gender groups of the MSPSS in Chinese parents of children with cerebral palsy. A total of 487 participants aged 21–55 years were recruited to complete the Chinese MSPSS and Parenting Stress Index-Short Form (PSI-SF. Composite reliability was calculated as the internal consistency of the Chinese MSPSS and a (multi-group confirmatory factor analysis (CFA was conducted to test the factorial validity and measurement invariance across gender. And Pearson correlations were calculated to test the relationships between MSPSS and PSI-SF. The Chinese MSPSS had satisfactory internal reliability with composite reliability values of more than 0.7. The CFA indicated that the original three-factor model was replicated in this specific population. Importantly, the results of the multi-group CFA demonstrated that configural, metric, and scalar invariance across gender groups was supported. In addition, all the three subscales of MSPSS were significant related with PSI-SF. These findings suggest that the Chinese MSPSS is a reliable and valid tool for assessing social support and can generally be utilized across sex in the parents of children with cerebral palsy.

  5. Multi-dimensional approach of MARS-LMR for the analysis of Phenix End-of-Life natural circulation test

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Hae Yong; Ha, Kwi Seok; Chang, Won Pyo; Lee, Kwi Lim [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-05-15

    Phenix is one of the important prototype sodium-cooled fast reactors (SFR) in nuclear reactor development history. It had been operated successfully for 35 years by the French Commissariat a l'energie atomique (CEA) and the Electricite de France (EdF) achieving its original objectives of demonstrating a fast breeder reactor technology and of playing the role of irradiation facility for innovative fuels and materials. After its final shutdown in 2009, CEA launched the Phenix End-of-life (EOL) test program. It provided a unique opportunity to generate reliable test data which is inevitable in the validation and verification of a SFR system analysis code. KAERI joined this international collaboration program of IAEA CRP and has performed the pretest analysis and post-test analysis utilizing the one-dimensional modeling of the MARS-LMR code, which had been developed by KAERI for the transient analysis of SFR systems. Through the previous studies, it has been identified that there are some limitations in the modeling of complicated thermal-hydraulic behaviors in the large pool volumes with the one-dimensional modeling. Recently, KAERI performed the analysis of Phenix EOL natural circulation test with multi-dimensional pool modeling, which is detailed below

  6. Induction machine bearing faults detection based on a multi-dimensional MUSIC algorithm and maximum likelihood estimation.

    Science.gov (United States)

    Elbouchikhi, Elhoussin; Choqueuse, Vincent; Benbouzid, Mohamed

    2016-07-01

    Condition monitoring of electric drives is of paramount importance since it contributes to enhance the system reliability and availability. Moreover, the knowledge about the fault mode behavior is extremely important in order to improve system protection and fault-tolerant control. Fault detection and diagnosis in squirrel cage induction machines based on motor current signature analysis (MCSA) has been widely investigated. Several high resolution spectral estimation techniques have been developed and used to detect induction machine abnormal operating conditions. This paper focuses on the application of MCSA for the detection of abnormal mechanical conditions that may lead to induction machines failure. In fact, this paper is devoted to the detection of single-point defects in bearings based on parametric spectral estimation. A multi-dimensional MUSIC (MD MUSIC) algorithm has been developed for bearing faults detection based on bearing faults characteristic frequencies. This method has been used to estimate the fundamental frequency and the fault related frequency. Then, an amplitude estimator of the fault characteristic frequencies has been proposed and fault indicator has been derived for fault severity measurement. The proposed bearing faults detection approach is assessed using simulated stator currents data, issued from a coupled electromagnetic circuits approach for air-gap eccentricity emulating bearing faults. Then, experimental data are used for validation purposes. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

  7. Multi-dimensional fission-barrier calculations from Se to the SHE; from the proton to the neutron drip lines

    International Nuclear Information System (INIS)

    Moeller, Peter; Sierk, Arnold J.; Bengtsson, Ragnar; Iwamoto, Akira

    2003-01-01

    We present fission-barrier-height calculations for nuclei throughout the periodic system based on a realistic theoretical model of the multi-dimensional potential-energy surface of a fissioning nucleus. This surface guides the nuclear shape evolution from the ground state, over inner and outer saddle points, to the final configurations of separated fission fragments. We have previously shown that our macroscopic-microscopic nuclear potential-energy model yields calculated 'outer' fission-barrier heights (E B ) for even-even nuclei throughout the periodic system that agree with experimental data to within about 1.0 MeV. We present final results of this work. Just recently we have enhanced our macroscopic-microscopic nuclear potential-energy model to also allow the consideration of axially asymmetric shapes. This shape degree of freedom has a substantial effect on the calculated height (E A ) of the inner peak of some actinide fission barriers. We present examples of fission-barrier calculations by use of this model with its redetermined constants. Finally we discuss what the model now tells us about fission barriers at the end of the r-process nucleosynthesis path. (author)

  8. A demonstration of adjoint methods for multi-dimensional remote sensing of the atmosphere and surface

    Science.gov (United States)

    Martin, William G. K.; Hasekamp, Otto P.

    2018-01-01

    In previous work, we derived the adjoint method as a computationally efficient path to three-dimensional (3D) retrievals of clouds and aerosols. In this paper we will demonstrate the use of adjoint methods for retrieving two-dimensional (2D) fields of cloud extinction. The demonstration uses a new 2D radiative transfer solver (FSDOM). This radiation code was augmented with adjoint methods to allow efficient derivative calculations needed to retrieve cloud and surface properties from multi-angle reflectance measurements. The code was then used in three synthetic retrieval studies. Our retrieval algorithm adjusts the cloud extinction field and surface albedo to minimize the measurement misfit function with a gradient-based, quasi-Newton approach. At each step we compute the value of the misfit function and its gradient with two calls to the solver FSDOM. First we solve the forward radiative transfer equation to compute the residual misfit with measurements, and second we solve the adjoint radiative transfer equation to compute the gradient of the misfit function with respect to all unknowns. The synthetic retrieval studies verify that adjoint methods are scalable to retrieval problems with many measurements and unknowns. We can retrieve the vertically-integrated optical depth of moderately thick clouds as a function of the horizontal coordinate. It is also possible to retrieve the vertical profile of clouds that are separated by clear regions. The vertical profile retrievals improve for smaller cloud fractions. This leads to the conclusion that cloud edges actually increase the amount of information that is available for retrieving the vertical profile of clouds. However, to exploit this information one must retrieve the horizontally heterogeneous cloud properties with a 2D (or 3D) model. This prototype shows that adjoint methods can efficiently compute the gradient of the misfit function. This work paves the way for the application of similar methods to 3D remote

  9. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

    Directory of Open Access Journals (Sweden)

    Daniel P Riordan

    Full Text Available Characterization of the molecular attributes and spatial arrangements of cells and features within complex human tissues provides a critical basis for understanding processes involved in development and disease. Moreover, the ability to automate steps in the analysis and interpretation of histological images that currently require manual inspection by pathologists could revolutionize medical diagnostics. Toward this end, we developed a new imaging approach called multidimensional microscopic molecular profiling (MMMP that can measure several independent molecular properties in situ at subcellular resolution for the same tissue specimen. MMMP involves repeated cycles of antibody or histochemical staining, imaging, and signal removal, which ultimately can generate information analogous to a multidimensional flow cytometry analysis on intact tissue sections. We performed a MMMP analysis on a tissue microarray containing a diverse set of 102 human tissues using a panel of 15 informative antibody and 5 histochemical stains plus DAPI. Large-scale unsupervised analysis of MMMP data, and visualization of the resulting classifications, identified molecular profiles that were associated with functional tissue features. We then directly annotated H&E images from this MMMP series such that canonical histological features of interest (e.g. blood vessels, epithelium, red blood cells were individually labeled. By integrating image annotation data, we identified molecular signatures that were associated with specific histological annotations and we developed statistical models for automatically classifying these features. The classification accuracy for automated histology labeling was objectively evaluated using a cross-validation strategy, and significant accuracy (with a median per-pixel rate of 77% per feature from 15 annotated samples for de novo feature prediction was obtained. These results suggest that high-dimensional profiling may advance the

  10. A demonstration of adjoint methods for multi-dimensional remote sensing of the atmosphere and surface

    International Nuclear Information System (INIS)

    Martin, William G.K.; Hasekamp, Otto P.

    2018-01-01

    Highlights: • We demonstrate adjoint methods for atmospheric remote sensing in a two-dimensional setting. • Searchlight functions are used to handle the singularity of measurement response functions. • Adjoint methods require two radiative transfer calculations to evaluate the measurement misfit function and its derivatives with respect to all unknown parameters. • Synthetic retrieval studies show the scalability of adjoint methods to problems with thousands of measurements and unknown parameters. • Adjoint methods and the searchlight function technique are generalizable to 3D remote sensing. - Abstract: In previous work, we derived the adjoint method as a computationally efficient path to three-dimensional (3D) retrievals of clouds and aerosols. In this paper we will demonstrate the use of adjoint methods for retrieving two-dimensional (2D) fields of cloud extinction. The demonstration uses a new 2D radiative transfer solver (FSDOM). This radiation code was augmented with adjoint methods to allow efficient derivative calculations needed to retrieve cloud and surface properties from multi-angle reflectance measurements. The code was then used in three synthetic retrieval studies. Our retrieval algorithm adjusts the cloud extinction field and surface albedo to minimize the measurement misfit function with a gradient-based, quasi-Newton approach. At each step we compute the value of the misfit function and its gradient with two calls to the solver FSDOM. First we solve the forward radiative transfer equation to compute the residual misfit with measurements, and second we solve the adjoint radiative transfer equation to compute the gradient of the misfit function with respect to all unknowns. The synthetic retrieval studies verify that adjoint methods are scalable to retrieval problems with many measurements and unknowns. We can retrieve the vertically-integrated optical depth of moderately thick clouds as a function of the horizontal coordinate. It is also

  11. Low child survival index in a multi-dimensionally poor Amerindian population in Venezuela.

    Directory of Open Access Journals (Sweden)

    Julian A Villalba

    Full Text Available Warao Amerindians, who inhabit the Orinoco Delta, are the second largest indigenous group in Venezuela.  High Warao general mortality rates were mentioned in a limited study 21 years ago. However, there have been no comprehensive studies addressing child survival across the entire population.To determine the Child Survival-Index (CSI (ratio: still-living children/total-live births in the Warao population, the principal causes of childhood death and the socio-demographic factors associated with childhood deaths.We conducted a cross-sectional epidemiological survey of 688 women from 97 communities in 7 different subregions of the Orinoco Delta. Data collected included socio-demographic characteristics and the reproductive history of each woman surveyed. The multidimensional poverty index (MPI was used to classify the households as deprived across the three dimensions of the Human Development Index. Multivariable linear regression and Generalized Linear Model Procedures were used to identify socioeconomic and environmental characteristics statistically associated with the CSI.The average CSI was 73.8% ±26. The two most common causes of death were gastroenteritis/diarrhea (63% and acute respiratory tract Infection/pneumonia (18%.  Deaths in children under five years accounted for 97.3% of childhood deaths, with 54% occurring in the neonatal period or first year of life.  Most of the women (95.5% were classified as multidimensionally poor.  The general MPI in the sample was 0.56.   CSI was negatively correlated with MPI, maternal age, residence in a traditional dwelling and profession of the head of household other than nurse or teacher.The Warao have a low CSI which is correlated with MPI and maternal age.  Infectious diseases are responsible for 85% of childhood deaths.  The low socioeconomic development, lack of infrastructure and geographic and cultural isolation suggest that an integrated approach is urgently needed to

  12. Low child survival index in a multi-dimensionally poor Amerindian population in Venezuela.

    Science.gov (United States)

    Villalba, Julian A; Liu, Yushi; Alvarez, Mauyuri K; Calderon, Luisana; Canache, Merari; Cardenas, Gaudymar; Del Nogal, Berenice; Takiff, Howard E; De Waard, Jacobus H

    2013-01-01

    Warao Amerindians, who inhabit the Orinoco Delta, are the second largest indigenous group in Venezuela.  High Warao general mortality rates were mentioned in a limited study 21 years ago. However, there have been no comprehensive studies addressing child survival across the entire population. To determine the Child Survival-Index (CSI) (ratio: still-living children/total-live births) in the Warao population, the principal causes of childhood death and the socio-demographic factors associated with childhood deaths. We conducted a cross-sectional epidemiological survey of 688 women from 97 communities in 7 different subregions of the Orinoco Delta. Data collected included socio-demographic characteristics and the reproductive history of each woman surveyed. The multidimensional poverty index (MPI) was used to classify the households as deprived across the three dimensions of the Human Development Index. Multivariable linear regression and Generalized Linear Model Procedures were used to identify socioeconomic and environmental characteristics statistically associated with the CSI. The average CSI was 73.8% ±26. The two most common causes of death were gastroenteritis/diarrhea (63%) and acute respiratory tract Infection/pneumonia (18%).  Deaths in children under five years accounted for 97.3% of childhood deaths, with 54% occurring in the neonatal period or first year of life.  Most of the women (95.5%) were classified as multidimensionally poor.  The general MPI in the sample was 0.56.   CSI was negatively correlated with MPI, maternal age, residence in a traditional dwelling and profession of the head of household other than nurse or teacher. The Warao have a low CSI which is correlated with MPI and maternal age.  Infectious diseases are responsible for 85% of childhood deaths.  The low socioeconomic development, lack of infrastructure and geographic and cultural isolation suggest that an integrated approach is urgently needed to improve the

  13. Genetic algorithms and their applications in accelerator physics

    Energy Technology Data Exchange (ETDEWEB)

    Hofler, Alicia S. [JLAB

    2013-12-01

    Multi-objective optimization techniques are widely used in an extremely broad range of fields. Genetic optimization for multi-objective optimization was introduced in the accelerator community in relatively recent times and quickly spread becoming a fundamental tool in multi-dimensional optimization problems. This discussion introduces the basics of the technique and reviews applications in accelerator problems.

  14. The Effects of Meiosis/Genetics Integration and Instructional Sequence on College Biology Student Achievement in Genetics.

    Science.gov (United States)

    Browning, Mark

    The purpose of the research was to manipulate two aspects of genetics instruction in order to measure their effects on college, introductory biology students' achievement in genetics. One instructional sequence that was used dealt first with monohybrid autosomal inheritance patterns, then sex-linkage. The alternate sequence was the reverse.…

  15. Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats

    Science.gov (United States)

    Bryce A. Richardson; Marcus V. Warwell; Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald

    2010-01-01

    To assess threats or predict responses to disturbances, or both, it is essential to recognize and characterize the population structures of forest species in relation to changing environments. Appropriate management of these genetic resources in the future will require (1) understanding the existing genetic diversity/variation and population structure of forest trees...

  16. Operational Excellence through Schedule Optimization and Production Simulation of Application Specific Integrated Circuits.

    Energy Technology Data Exchange (ETDEWEB)

    Flory, John Andrew [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Padilla, Denise D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gauthier, John H. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Zwerneman, April Marie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Miller, Steven P [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2016-05-01

    Upcoming weapon programs require an aggressive increase in Application Specific Integrated Circuit (ASIC) production at Sandia National Laboratories (SNL). SNL has developed unique modeling and optimization tools that have been instrumental in improving ASIC production productivity and efficiency, identifying optimal operational and tactical execution plans under resource constraints, and providing confidence in successful mission execution. With ten products and unprecedented levels of demand, a single set of shared resources, highly variable processes, and the need for external supplier task synchronization, scheduling is an integral part of successful manufacturing. The scheduler uses an iterative multi-objective genetic algorithm and a multi-dimensional performance evaluator. Schedule feasibility is assessed using a discrete event simulation (DES) that incorporates operational uncertainty, variability, and resource availability. The tools provide rapid scenario assessments and responses to variances in the operational environment, and have been used to inform major equipment investments and workforce planning decisions in multiple SNL facilities.

  17. The development of a collapsing method for the mixed group and point cross sections and its application on multi-dimensional deep penetration calculations

    International Nuclear Information System (INIS)

    Bor-Jing Chang; Yen-Wan H. Liu

    1992-01-01

    The HYBRID, or mixed group and point, method was developed to solve the neutron transport equation deterministically using detailed treatment at cross section minima for deep penetration calculations. Its application so far is limited to one-dimensional calculations due to the enormous computing time involved in multi-dimensional calculations. In this article, a collapsing method is developed for the mixed group and point cross section sets to provide a more direct and practical way of using the HYBRID method in the multi-dimensional calculations. A testing problem is run. The method is then applied to the calculation of a deep penetration benchmark experiment. It is observed that half of the window effect is smeared in the collapsing treatment, but it still provide a better cross section set than the VITAMIN-C cross sections for the deep penetrating calculations

  18. The method of separation for evolutionary spectral density estimation of multi-variate and multi-dimensional non-stationary stochastic processes

    KAUST Repository

    Schillinger, Dominik

    2013-07-01

    The method of separation can be used as a non-parametric estimation technique, especially suitable for evolutionary spectral density functions of uniformly modulated and strongly narrow-band stochastic processes. The paper at hand provides a consistent derivation of method of separation based spectrum estimation for the general multi-variate and multi-dimensional case. The validity of the method is demonstrated by benchmark tests with uniformly modulated spectra, for which convergence to the analytical solution is demonstrated. The key advantage of the method of separation is the minimization of spectral dispersion due to optimum time- or space-frequency localization. This is illustrated by the calibration of multi-dimensional and multi-variate geometric imperfection models from strongly narrow-band measurements in I-beams and cylindrical shells. Finally, the application of the method of separation based estimates for the stochastic buckling analysis of the example structures is briefly discussed. © 2013 Elsevier Ltd.

  19. Effect of multi-dimensional ultraviolet light exposure on the growth of pentacene film and application to organic field-effect transistors.

    Science.gov (United States)

    Bae, Jin-Hyuk; Lee, Sin-Doo; Choi, Jong Sun; Park, Jaehoon

    2012-05-01

    We report on the multi-dimensional alignment of pentacene molecules on a poly(methyl methacrylate)-based photosensitive polymer (PMMA-polymer) and its effect on the electrical performance of the pentacene-based field-effect transistor (FET). Pentacene molecules are shown to be preferentially aligned on the linearly polarized ultraviolet (LPUV)-exposed PMMA-polymer layer, which is contrast to an isotropic alignment on the bare PMMA-polymer layer. Multi-dimensional alignment of pentacene molecules in the film could be achieved by adjusting the direction of LPUV exposed to the PMMA-polymer. The control of pentacene molecular alignment is found to be promising for the field-effect mobility enhancement in the pentacene FET.

  20. SPECT3D - A multi-dimensional collisional-radiative code for generating diagnostic signatures based on hydrodynamics and PIC simulation output

    Science.gov (United States)

    MacFarlane, J. J.; Golovkin, I. E.; Wang, P.; Woodruff, P. R.; Pereyra, N. A.

    2007-05-01

    SPECT3D is a multi-dimensional collisional-radiative code used to post-process the output from radiation-hydrodynamics (RH) and particle-in-cell (PIC) codes to generate diagnostic signatures (e.g. images, spectra) that can be compared directly with experimental measurements. This ability to post-process simulation code output plays a pivotal role in assessing the reliability of RH and PIC simulation codes and their physics models. SPECT3D has the capability to operate on plasmas in 1D, 2D, and 3D geometries. It computes a variety of diagnostic signatures that can be compared with experimental measurements, including: time-resolved and time-integrated spectra, space-resolved spectra and streaked spectra; filtered and monochromatic images; and X-ray diode signals. Simulated images and spectra can include the effects of backlighters, as well as the effects of instrumental broadening and time-gating. SPECT3D also includes a drilldown capability that shows where frequency-dependent radiation is emitted and absorbed as it propagates through the plasma towards the detector, thereby providing insights on where the radiation seen by a detector originates within the plasma. SPECT3D has the capability to model a variety of complex atomic and radiative processes that affect the radiation seen by imaging and spectral detectors in high energy density physics (HEDP) experiments. LTE (local thermodynamic equilibrium) or non-LTE atomic level populations can be computed for plasmas. Photoabsorption rates can be computed using either escape probability models or, for selected 1D and 2D geometries, multi-angle radiative transfer models. The effects of non-thermal (i.e. non-Maxwellian) electron distributions can also be included. To study the influence of energetic particles on spectra and images recorded in intense short-pulse laser experiments, the effects of both relativistic electrons and energetic proton beams can be simulated. SPECT3D is a user-friendly software package that runs

  1. Large Break LOCA Analysis with New downcomer Nodalizaion and Multi-Dimensional Model and Effect of Cross flow option in MARS code

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Hyung-wook; Lee, Sang-yong; Oh, Seung-jong; Kim, Woong-bae [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

    2016-10-15

    The phenomena of LOCA have been investigated for long time. The most extensive research project for LOCA was the 2D/3D program experiments. The results of the 2D/3D experiments show flow conditions in the downcomer during end-of-blowdown were highly multi-dimensional at full-scale. In this paper, the authors modified the nodalization of MARS code LBLOCA input deck and performed LBLOCA analysis with new input deck. An LBLOCA analysis for APR1400 with new downcomer input deck was conducted using KREM with MARS-KS 1.4 Version code. Analysis was processed under LBCOCA of 100% break size of cold leg case. The authors developed input deck with new downcomer nodalizaion and Multi-Dimensional downcomer model, then implemented LOCA analysis with new input decks and compared with existing analysis results. PCT from new input and multi-dimensional input deck shows similar PCT trend from original input deck. There occurred more rapid drop of PCT from new and multidimensional input deck than original input deck. PCT from new and multidimensional input deck are satisfied with PCT design limit. It can be concluded that there occurs no acceptance criteria issue even though new and multidimensional input deck are applied to LBLOCA analysis. In future study, comparative analysis with experiment results will be implemented.

  2. Multi-dimensional Mixing Behavior of Steam-Water Flow in a Downcomer Annulus during LBLOCA Reflood Phase with a DVI Injection Mode

    International Nuclear Information System (INIS)

    Kwon, T.S.; Yun, B.J.; Euh, D.J.; Chu, I.C.; Song, C.H.

    2002-01-01

    Multi-dimensional thermal-hydraulic behavior in the downcomer annulus of a pressurized water reactor vessel with a Direct Vessel Injection (DVI) mode is presented based on the experimental observation in the MIDAS (Multi-dimensional Investigation in Downcomer Annulus Simulation) steam-water test facility. From the steady-state test results to simulate the late reflood phase of a Large Break Loss-of-Coolant Accidents(LBLOCA), isothermal lines show the multidimensional phenomena of a phasic interaction between steam and water in the downcomer annulus very well. MIDAS is a steam-water separate effect test facility, which is 1/4.93 linearly scaled-down of 1400 MWe PWR type of a nuclear reactor, focused on understanding multi-dimensional thermalhydraulic phenomena in downcomer annulus with various types of safety injection during the refill or reflood phase of a LBLOCA. The initial and the boundary conditions are scaled from the pre-test analysis based on the preliminary calculation using the TRAC code. The superheated steam with a superheating degree of 80 K at a given downcomer pressure of 180 kPa is injected equally through three intact cold legs into the downcomer. (authors)

  3. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

    DEFF Research Database (Denmark)

    Olsen, Morten Tange; Andersen, Liselotte Wesley; Dietz, Rune

    2014-01-01

    present a novel approach, integrating genetic, life-history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic...... structure in harbour seals. Second, we used harbour seal demographic and life-history data to conduct population viability analyses (PVAs) in the VORTEX simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (2010......, and that the combined use of genetic data and PVAs constitute a promising approach for delineating populations and management units. This article is protected by copyright. All rights reserved....

  4. SU-F-T-312: Identifying Distinct Radiation Therapy Plan Classes Through Multi-Dimensional Analysis of Plan Complexity Metrics

    Energy Technology Data Exchange (ETDEWEB)

    Desai, V; Labby, Z; Culberson, W [University of Wisc Madison, Madison, WI (United States)

    2016-06-15

    Purpose: To determine whether body site-specific treatment plans form unique “plan class” clusters in a multi-dimensional analysis of plan complexity metrics such that a single beam quality correction determined for a representative plan could be universally applied within the “plan class”, thereby increasing the dosimetric accuracy of a detector’s response within a subset of similarly modulated nonstandard deliveries. Methods: We collected 95 clinical volumetric modulated arc therapy (VMAT) plans from four body sites (brain, lung, prostate, and spine). The lung data was further subdivided into SBRT and non-SBRT data for a total of five plan classes. For each control point in each plan, a variety of aperture-based complexity metrics were calculated and stored as unique characteristics of each patient plan. A multiple comparison of means analysis was performed such that every plan class was compared to every other plan class for every complexity metric in order to determine which groups could be considered different from one another. Statistical significance was assessed after correcting for multiple hypothesis testing. Results: Six out of a possible 10 pairwise plan class comparisons were uniquely distinguished based on at least nine out of 14 of the proposed metrics (Brain/Lung, Brain/SBRT lung, Lung/Prostate, Lung/SBRT Lung, Lung/Spine, Prostate/SBRT Lung). Eight out of 14 of the complexity metrics could distinguish at least six out of the possible 10 pairwise plan class comparisons. Conclusion: Aperture-based complexity metrics could prove to be useful tools to quantitatively describe a distinct class of treatment plans. Certain plan-averaged complexity metrics could be considered unique characteristics of a particular plan. A new approach to generating plan-class specific reference (pcsr) fields could be established through a targeted preservation of select complexity metrics or a clustering algorithm that identifies plans exhibiting similar

  5. [Multi-dimensional exploration of the characteristics of emotional regulation in children with attention-deficit/hyperactivity disorder].

    Science.gov (United States)

    Yu, Xiaoyan; Liu, Lu; Sun, Li; Qian, Ying; Qian, Qiujin; Wu, Zhaomin; Cao, Qingjiu; Wang, Yufeng

    2015-10-20

    To explore the characteristics of emotional regulation in children with attention-deficit/hyperactivity disorder (ADHD). Two hundred and eighty-two children who were diagnosed as ADHD according to the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) were recruited from the child psychiatric clinic of Peking University Sixth Hospital/Institute of Mental Health from August 2012 to April 2014. And 260 normal children from the local primary schools were selected as the healthy control group. The emotional factors or items of Conners' Parent Rating Scale, Behavior Rating Inventory of Executive Function (BRIEF), Achenbach's Child Behavior Checklist (CBCL) and Rutter Children Behavior Questionnaire were used to assess the characteristics of emotional regulation multi-dimensionally. After controlling for the effects of age, sex and intelligence quotient (IQ), in Conner scale, the emotional lability (EL) scores of ADHD group were significantly higher than that of healthy control group [(4.3±2.6) vs (1.4±1.5), Pemotional control (ECTRL) scores of ADHD group were significantly higher than that of control group [(16.1±4.4) vs (12.0±2.5), Pemotional self-regulation (DESR) scores of ADHD group were significantly higher than that of control group [(26.8±11.0) vs (6.6±6.8), Pemotional symptoms (ES) scores of ADHD group were significantly higher than that of control group [(2.7±2.0) vs (1.7±1.5), Pemotional regulation.

  6. Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder.

    Science.gov (United States)

    Andrews, Shan V; Ellis, Shannon E; Bakulski, Kelly M; Sheppard, Brooke; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Feinberg, Andrew P; Arking, Dan E; Ladd-Acosta, Christine; Fallin, M Daniele

    2017-10-24

    Integration of emerging epigenetic information with autism spectrum disorder (ASD) genetic results may elucidate functional insights not possible via either type of information in isolation. Here we use the genotype and DNA methylation (DNAm) data from cord blood and peripheral blood to identify SNPs associated with DNA methylation (meQTL lists). Additionally, we use publicly available fetal brain and lung meQTL lists to assess enrichment of ASD GWAS results for tissue-specific meQTLs. ASD-associated SNPs are enriched for fetal brain (OR = 3.55; P < 0.001) and peripheral blood meQTLs (OR = 1.58; P < 0.001). The CpG targets of ASD meQTLs across cord, blood, and brain tissues are enriched for immune-related pathways, consistent with other expression and DNAm results in ASD, and reveal pathways not implicated by genetic findings. This joint analysis of genotype and DNAm demonstrates the potential of both brain and blood-based DNAm for insights into ASD and psychiatric phenotypes more broadly.

  7. Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments.

    Science.gov (United States)

    McNamara, John M; Dall, Sasha R X; Hammerstein, Peter; Leimar, Olof

    2016-10-01

    There are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist. © 2016 John Wiley & Sons Ltd/CNRS.

  8. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

    Directory of Open Access Journals (Sweden)

    Page Michel

    2009-12-01

    Full Text Available Abstract Background The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level. Results We have developed a generic and modular web service, based on a service-oriented architecture, for integrating the modeling and formal verification of genetic regulatory networks. The architecture has been implemented in the context of the qualitative modeling and simulation tool GNA and the model checkers NUSMV and CADP. GNA has been extended with a verification module for the specification and checking of biological properties. The verification module also allows the display and visual inspection of the verification results. Conclusions The practical use of the proposed web service is illustrated by means of a scenario involving the analysis of a qualitative model of the carbon starvation response in E. coli. The service-oriented architecture allows modelers to define the model and proceed with the specification and formal verification of the biological properties by means of a unified graphical user interface. This guarantees a transparent access to formal verification technology for modelers of genetic regulatory networks.

  9. Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling.

    Directory of Open Access Journals (Sweden)

    Christine T Ferrara

    2008-03-01

    Full Text Available Although numerous quantitative trait loci (QTL influencing disease-related phenotypes have been detected through gene mapping and positional cloning, identification of the individual gene(s and molecular pathways leading to those phenotypes is often elusive. One way to improve understanding of genetic architecture is to classify phenotypes in greater depth by including transcriptional and metabolic profiling. In the current study, we have generated and analyzed mRNA expression and metabolic profiles in liver samples obtained in an F2 intercross between the diabetes-resistant C57BL/6 leptin(ob/ob and the diabetes-susceptible BTBR leptin(ob/ob mouse strains. This cross, which segregates for genotype and physiological traits, was previously used to identify several diabetes-related QTL. Our current investigation includes microarray analysis of over 40,000 probe sets, plus quantitative mass spectrometry-based measurements of sixty-seven intermediary metabolites in three different classes (amino acids, organic acids, and acyl-carnitines. We show that liver metabolites map to distinct genetic regions, thereby indicating that tissue metabolites are heritable. We also demonstrate that genomic analysis can be integrated with liver mRNA expression and metabolite profiling data to construct causal networks for control of specific metabolic processes in liver. As a proof of principle of the practical significance of this integrative approach, we illustrate the construction of a specific causal network that links gene expression and metabolic changes in the context of glutamate metabolism, and demonstrate its validity by showing that genes in the network respond to changes in glutamine and glutamate availability. Thus, the methods described here have the potential to reveal regulatory networks that contribute to chronic, complex, and highly prevalent diseases and conditions such as obesity and diabetes.

  10. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  11. Improved Genetic Algorithm-Based Unit Commitment Considering Uncertainty Integration Method

    Directory of Open Access Journals (Sweden)

    Kyu-Hyung Jo

    2018-05-01

    Full Text Available In light of the dissemination of renewable energy connected to the power grid, it has become necessary to consider the uncertainty in the generation of renewable energy as a unit commitment (UC problem. A methodology for solving the UC problem is presented by considering various uncertainties, which are assumed to have a normal distribution, by using a Monte Carlo simulation. Based on the constructed scenarios for load, wind, solar, and generator outages, a combination of scenarios is found that meets the reserve requirement to secure the power balance of the power grid. In those scenarios, the uncertainty integration method (UIM identifies the best combination by minimizing the additional reserve requirements caused by the uncertainty of power sources. An integration process for uncertainties is formulated for stochastic unit commitment (SUC problems and optimized by the improved genetic algorithm (IGA. The IGA is composed of five procedures and finds the optimal combination of unit status at the scheduled time, based on the determined source data. According to the number of unit systems, the IGA demonstrates better performance than the other optimization methods by applying reserve repairing and an approximation process. To account for the result of the proposed method, various UC strategies are tested with a modified 24-h UC test system and compared.

  12. Integrated genetic linkage map of cultivated peanut by three RIL populations

    Institute of Scientific and Technical Information of China (English)

    Yanbin Song; Huifang Jiang; Huaiyong Luo; Li Huang; Yuning Chen; Weigang Chen; Nian Liu; Xiaoping Ren; Bolun Yu; Jianbin Guo

    2017-01-01

    High-density and precise genetic linkage map is fundamental to detect quanti-tative trait locus (QTL) of agronomic and quality related traits in cultivated peanut (Arachis hypogaea L.). In this study, three linkage maps from three RIL (recombinant inbred line) populations were used to construct an integrated map. A total of 2,069 SSR and transposon markers were anchored on the high-density integrated map which covered 2,231.53 cM with 20 linkage groups. Totally, 92 QTLs correlating with pod length (PL), pod width (PW), hun-dred pods weight (HPW) and plant height (PH) from above RIL populations were mapped on it. Seven intervals were found to harbor QTLs controlling the same traits in different pop-ulations, including one for PL, three for PW, two for HPW, and one for PH. Besides, QTLs controlling different traits in different populations were found to be overlapped in four inter-vals. Interval on A05 contains 17 QTLs for different traits from two RIL populations. New markers were added to these intervals to detect QTLs with narrow confidential intervals. Results obtained in this study may facilitate future genomic researches such as QTL study, fine mapping, positional cloning and marker-assisted selection (MAS) in peanut.

  13. Genetic evidence for role of integration of fast and slow neurotransmission in schizophrenia.

    Science.gov (United States)

    Devor, A; Andreassen, O A; Wang, Y; Mäki-Marttunen, T; Smeland, O B; Fan, C-C; Schork, A J; Holland, D; Thompson, W K; Witoelar, A; Chen, C-H; Desikan, R S; McEvoy, L K; Djurovic, S; Greengard, P; Svenningsson, P; Einevoll, G T; Dale, A M

    2017-06-01

    The most recent genome-wide association studies (GWAS) of schizophrenia (SCZ) identified hundreds of risk variants potentially implicated in the disease. Further, novel statistical methodology designed for polygenic architecture revealed more potential risk variants. This can provide a link between individual genetic factors and the mechanistic underpinnings of SCZ. Intriguingly, a large number of genes coding for ionotropic and metabotropic receptors for various neurotransmitters-glutamate, γ-aminobutyric acid (GABA), dopamine, serotonin, acetylcholine and opioids-and numerous ion channels were associated with SCZ. Here, we review these findings from the standpoint of classical neurobiological knowledge of neuronal synaptic transmission and regulation of electrical excitability. We show that a substantial proportion of the identified genes are involved in intracellular cascades known to integrate 'slow' (G-protein-coupled receptors) and 'fast' (ionotropic receptors) neurotransmission converging on the protein DARPP-32. Inspection of the Human Brain Transcriptome Project database confirms that that these genes are indeed expressed in the brain, with the expression profile following specific developmental trajectories, underscoring their relevance to brain organization and function. These findings extend the existing pathophysiology hypothesis by suggesting a unifying role of dysregulation in neuronal excitability and synaptic integration in SCZ. This emergent model supports the concept of SCZ as an 'associative' disorder-a breakdown in the communication across different slow and fast neurotransmitter systems through intracellular signaling pathways-and may unify a number of currently competing hypotheses of SCZ pathophysiology.

  14. Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma.

    Directory of Open Access Journals (Sweden)

    Stine H Kresse

    Full Text Available BACKGROUND: Osteosarcomas are the most common non-haematological primary malignant tumours of bone, and all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. PRINCIPAL FINDINGS: The cell lines showed complex patterns of DNA copy number changes, where genomic copy number gains were significantly associated with gene-rich regions and losses with gene-poor regions. By integrating the datasets, 350 genes were identified as having two types of aberrations (gain/over-expression, hypo-methylation/over-expression, loss/under-expression or hyper-methylation/under-expression using a recurrence threshold of 6/19 (>30% cell lines. The genes showed in general alterations in either DNA copy number or DNA methylation, both within individual samples and across the sample panel. These 350 genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. The aberrations of three selected genes, CXCL5, DLX5 and RUNX2, were validated in five cell lines and five tumour samples using PCR techniques. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2'-deoxycytidine treatment for four genes tested; AKAP12, CXCL5, EFEMP1 and IL11RA. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for detrimental genes. CONCLUSIONS: Integrative analysis of genome-wide genetic and epigenetic alterations identified dependencies and relationships between

  15. Integrating social science and behavioral genetics: testing the origin of socioeconomic disparities in depression using a genetically informed design.

    Science.gov (United States)

    Mezuk, Briana; Myers, John M; Kendler, Kenneth S

    2013-10-01

    We tested 3 hypotheses-social causation, social drift, and common cause-regarding the origin of socioeconomic disparities in major depression and determined whether the relationship between socioeconomic status (SES) and major depression varied by genetic liability for major depression. Data were from a sample of female twins in the baseline Virginia Adult Twin Study of Psychiatric and Substance Use Disorders interviewed between 1987 and 1989 (n = 2153). We used logistic regression and structural equation twin models to evaluate these 3 hypotheses. Consistent with the social causation hypothesis, education (odds ratio [OR] = 0.78; 95% confidence interval [CI] = 0.66, 0.93; P social mobility was associated with lower risk of depression. There was no evidence that childhood SES was related to development of major depression (OR = 0.98; 95% CI = 0.89, 1.09; P > .1). Consistent with a common genetic cause, there was a negative correlation between the genetic components of major depression and education (r(2) = -0.22). Co-twin control analyses indicated a protective effect of education and income on major depression even after accounting for genetic liability. This study utilized a genetically informed design to address how social position relates to major depression. Results generally supported the social causation model.

  16. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  17. Hybridization Leads to Loss of Genetic Integrity in Shortleaf Pine: Unexpected Consequences of Pine Management and Fire Suppression

    Science.gov (United States)

    Charles G. Tauer; John F. Stewart; Rodney E. Will; Curtis J. Lilly; James M. Guldin; C. Dana Nelson

    2012-01-01

    Hybridization between shortleaf pine and loblolly pine is causing loss of genetic integrity (the tendency of a population to maintain its genotypes over generations) in shortleaf pine, a species already exhibiting dramatic declines due to land-use changes. Recent findings indicate hybridization has increased in shortleaf pine stands from 3% during the 1950s to 45% for...

  18. Recovery patterns, histological observations and genetic integrity in Malus shoot tips cryopreserved using droplet vitrification and encapsulation-dehydration procedures

    Science.gov (United States)

    A droplet-vitrification procedure is described for cryopreservation of Malus shoot tips. Survival patterns, recovery types, histological observations, and genetic integrity were compared for Malus shoot tips cryopreserved using this droplet-vitrification procedure and an encapsulation-dehydration pr...

  19. Application of the multi-dimensional surface water modeling system at Bridge 339, Copper River Highway, Alaska

    Science.gov (United States)

    Brabets, Timothy P.; Conaway, Jeffrey S.

    2009-01-01

    The Copper River Basin, the sixth largest watershed in Alaska, drains an area of 24,200 square miles. This large, glacier-fed river flows across a wide alluvial fan before it enters the Gulf of Alaska. Bridges along the Copper River Highway, which traverses the alluvial fan, have been impacted by channel migration. Due to a major channel change in 2001, Bridge 339 at Mile 36 of the highway has undergone excessive scour, resulting in damage to its abutments and approaches. During the snow- and ice-melt runoff season, which typically extends from mid-May to September, the design discharge for the bridge often is exceeded. The approach channel shifts continuously, and during our study it has shifted back and forth from the left bank to a course along the right bank nearly parallel to the road.Maintenance at Bridge 339 has been costly and will continue to be so if no action is taken. Possible solutions to the scour and erosion problem include (1) constructing a guide bank to redirect flow, (2) dredging approximately 1,000 feet of channel above the bridge to align flow perpendicular to the bridge, and (3) extending the bridge. The USGS Multi-Dimensional Surface Water Modeling System (MD_SWMS) was used to assess these possible solutions. The major limitation of modeling these scenarios was the inability to predict ongoing channel migration. We used a hybrid dataset of surveyed and synthetic bathymetry in the approach channel, which provided the best approximation of this dynamic system. Under existing conditions and at the highest measured discharge and stage of 32,500 ft3/s and 51.08 ft, respectively, the velocities and shear stresses simulated by MD_SWMS indicate scour and erosion will continue. Construction of a 250-foot-long guide bank would not improve conditions because it is not long enough. Dredging a channel upstream of Bridge 339 would help align the flow perpendicular to Bridge 339, but because of the mobility of the channel bed, the dredged channel would

  20. Multi-Dimensional Spectrum-Effect Relationship of the Impact of Chinese Herbal Formula Lichong Shengsui Yin on Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Yanhong Wang

    2017-06-01

    Full Text Available Lichong Shengsui Yin (LCSSY is an effective and classic compound prescription of Traditional Chinese Medicines (TCMs used for the treatment of ovarian cancer. To investigate its pharmacodynamic basis for treating ovarian cancer, the multi-dimensional spectrum-effect relationship was determined. Four compositions (I to IV were obtained by extracting LCSSY successively with supercritical CO2 fluid extraction, 75% ethanol reflux extraction, and the water extraction-ethanol precipitation method. Nine samples for pharmacological evaluation and fingerprint analysis were prepared by changing the content of the four compositions. The specific proportions of the four compositions were designed according to a four-factor, three-level L9(34 orthogonal test. The pharmacological evaluation included in vitro tumor inhibition experiments and the survival extension rate in tumor-bearing nude mice. The fingerprint analyzed by chromatographic condition I (high-performance liquid chromatography-photodiode array detec tor,HPLC-PDA identified 19 common peaks. High-performance liquid chromatography-photodiode array detector-Evaporative Light-scattering Detector (HPLC-PDA-ELSD hyphenated techniques were used to compensate for the use of a single detector, and the fingerprint analyzed by chromatographic condition II identified 28 common peaks in PDA and 23 common peaks in ELSD. Furthermore, multiple statistical analyses were utilized to calculate the relationships between the peaks and the pharmacological results. The union of the regression and the correlation analysis results were the peaks of X5, X9, X11, X12, X16, X18, Y5, Y8, Y12, Y14, Y20, Z4, Z5, Z6, and Z8. The intersection of the regression and the correlation analysis results were the peaks of X11, X12, X16, X18, Y5, Y12, and Z5. The correlated peaks were assigned by comparing the fingerprints with the negative control samples and reference standard samples, and identifying the structure using high

  1. Perceived Changes to Obstetric Care and the Integration of Personal and Professional Life as a Pregnant Prenatal Genetic Counselor.

    Science.gov (United States)

    Rietzler, Jennifer L; Birkeland, Laura E; Petty, Elizabeth M

    2018-02-08

    The impact of practicing as a prenatal genetic counselor while pregnant is unclear given the limited amount of published literature on this issue. To address this gap in knowledge, a total of 215 current and past prenatal genetic counselors provided insights regarding this personal yet professional juncture through completion of an online survey that allowed for both close-ended and open-ended responses. While participants agreed that experiencing pregnancy affected their perspectives and counseling in several ways, this paper focuses on one particular finding-that of the changes in their own obstetric care perceived by genetic counselors while working within the prenatal setting and being pregnant themselves. As a result of these changes, considerations about when to disclose a pregnancy to colleagues along with how to integrate personal and professional needs as a pregnant prenatal genetic counselor surfaced. Additional findings, practice implications, and research recommendations are discussed.

  2. metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.

    Science.gov (United States)

    Lyne, Mike; Smith, Richard N; Lyne, Rachel; Aleksic, Jelena; Hu, Fengyuan; Kalderimis, Alex; Stepan, Radek; Micklem, Gos

    2013-01-01

    Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first

  3. Computational Integration of Human Genetic Data to Evaluate AOP-Specific Susceptibility

    Science.gov (United States)

    There is a need for approaches to efficiently evaluate human genetic variability and susceptibility related to environmental chemical exposure. Direct estimation of the genetic contribution to variability in susceptibility to environmental chemicals is only possible in special ca...

  4. Computational Integration of Human Genetic and Toxicological Data to Evaluate AOP-Specific Susceptibility

    Science.gov (United States)

    Susceptibility to environmental chemicals can be modulated by genetic differences. Direct estimation of the genetic contribution to variability in susceptibility to environmental chemicals is only possible in special cases where there is an observed association between exposure a...

  5. Integration of genetic algorithm, computer simulation and design of experiments for forecasting electrical energy consumption

    International Nuclear Information System (INIS)

    Azadeh, A.; Tarverdian, S.

    2007-01-01

    This study presents an integrated algorithm for forecasting monthly electrical energy consumption based on genetic algorithm (GA), computer simulation and design of experiments using stochastic procedures. First, time-series model is developed as a benchmark for GA and simulation. Computer simulation is developed to generate random variables for monthly electricity consumption. This is achieved to foresee the effects of probabilistic distribution on monthly electricity consumption. The GA and simulated-based GA models are then developed by the selected time-series model. Therefore, there are four treatments to be considered in analysis of variance (ANOVA) which are actual data, time series, GA and simulated-based GA. Furthermore, ANOVA is used to test the null hypothesis of the above four alternatives being equal. If the null hypothesis is accepted, then the lowest mean absolute percentage error (MAPE) value is used to select the best model, otherwise the Duncan Multiple Range Test (DMRT) method of paired comparison is used to select the optimum model, which could be time series, GA or simulated-based GA. In case of ties the lowest MAPE value is considered as the benchmark. The integrated algorithm has several unique features. First, it is flexible and identifies the best model based on the results of ANOVA and MAPE, whereas previous studies consider the best-fit GA model based on MAPE or relative error results. Second, the proposed algorithm may identify conventional time series as the best model for future electricity consumption forecasting because of its dynamic structure, whereas previous studies assume that GA always provide the best solutions and estimation. To show the applicability and superiority of the proposed algorithm, the monthly electricity consumption in Iran from March 1994 to February 2005 (131 months) is used and applied to the proposed algorithm

  6. Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

    Science.gov (United States)

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

  7. Integrating text mining, data mining, and network analysis for identifying genetic breast cancer trends.

    Science.gov (United States)

    Jurca, Gabriela; Addam, Omar; Aksac, Alper; Gao, Shang; Özyer, Tansel; Demetrick, Douglas; Alhajj, Reda

    2016-04-26

    Breast cancer is a serious disease which affects many women and may lead to death. It has received considerable attention from the research community. Thus, biomedical researchers aim to find genetic biomarkers indicative of the disease. Novel biomarkers can be elucidated from the existing literature. However, the vast amount of scientific publications on breast cancer make this a daunting task. This paper presents a framework which investigates existing literature data for informative discoveries. It integrates text mining and social network analysis in order to identify new potential biomarkers for breast cancer. We utilized PubMed for the testing. We investigated gene-gene interactions, as well as novel interactions such as gene-year, gene-country, and abstract-country to find out how the discoveries varied over time and how overlapping/diverse are the discoveries and the interest of various research groups in different countries. Interesting trends have been identified and discussed, e.g., different genes are highlighted in relationship to different countries though the various genes were found to share functionality. Some text analysis based results have been validated against results from other tools that predict gene-gene relations and gene functions.

  8. Genetic integrity of the human Y chromosome exposed to groundwater arsenic

    Directory of Open Access Journals (Sweden)

    Ali Sher

    2010-08-01

    Full Text Available Abstract Background Arsenic is a known human carcinogen reported to cause chromosomal deletions and genetic anomalies in cultured cells. The vast human population inhabiting the Ganges delta in West Bengal, India and Bangladesh is exposed to critical levels of arsenic present in the groundwater. The genetic and physiological mechanism of arsenic toxicity in the human body is yet to be fully established. In addition, lack of animal models has made work on this line even more challenging. Methods Human male blood samples were collected with their informed consent from 5 districts in West Bengal having groundwater arsenic level more than 50 μg/L. Isolation of genomic DNA and preparation of metaphase chromosomes was done using standard protocols. End point PCR was performed for established sequence tagged sites to ascertain the status of recombination events. Single nucleotide variants of candidate genes and amplicons were carried out using appropriate restriction enzymes. The copy number of DYZ1 array per haploid genome was calculated using real time PCR and its chromosomal localization was done by fluorescence in-situ hybridization (FISH. Results We studied effects of arsenic exposure on the human Y chromosome in males from different areas of West Bengal focusing on known recombination events (P5-P1 proximal; P5-P1 distal; gr/gr; TSPY-TSPY, b1/b3 and b2/b3, single nucleotide variants (SNVs of a few candidate Y-linked genes (DAZ, TTY4, BPY2, GOLGA2LY and the amplicons of AZFc region. Also, possible chromosomal reorganization of DYZ1 repeat arrays was analyzed. Barring a few microdeletions, no major changes were detected in blood DNA samples. SNV analysis showed a difference in some alleles. Similarly, DYZ1 arrays signals detected by FISH were found to be affected in some males. Conclusions Our Y chromosome analysis suggests that the same is protected from the effects of arsenic by some unknown mechanisms maintaining its structural and functional

  9. THEORY OF CREATION AND THE GENETIC INTEGRITY OF THE WORLD – THE FUTURE OF HUMANITY BASIS OF IDEOLOGY

    Directory of Open Access Journals (Sweden)

    B. A. Astafyev

    2013-01-01

    Full Text Available Article describes one of the most difficult problems – the Theory of genetic energy-information unity of the World, according to which the World is the single entity hierarchically organized and directed by the World Creator, appearance of the Creator and creation by Him the Basic Genome of the World (BGW. The integral-dynamic formula of the BGW is described. The World Genome manifests the basic idea of the evolution: it is the code for structural and functional organization and evolution of all entities. The World Genome forms the General Laws of the World. The Theory of genetic energy-information unity of the World is proved the general idea – modern crisis can be transformed by realization of genetic energyinformation unity of the World-Natura-Man.

  10. Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports.

    Science.gov (United States)

    Kothari, Cartik; Wack, Maxime; Hassen-Khodja, Claire; Finan, Sean; Savova, Guergana; O'Boyle, Megan; Bliss, Geraldine; Cornell, Andria; Horn, Elizabeth J; Davis, Rebecca; Jacobs, Jacquelyn; Kohane, Isaac; Avillach, Paul

    2017-09-01

    The heterogeneity of patient phenotype data are an impediment to the research into the origins and progression of neuropsychiatric disorders. This difficulty is compounded in the case of rare disorders such as Phelan-McDermid Syndrome (PMS) by the paucity of patient clinical data. PMS is a rare syndromic genetic cause of autism and intellectual deficiency. In this paper, we describe the Phelan-McDermid Syndrome Data Network (PMS_DN), a platform that facilitates research into phenotype-genotype correlation and progression of PMS by: a) integrating knowledge of patient phenotypes extracted from Patient Reported Outcomes (PRO) data and clinical notes-two heterogeneous, underutilized sources of knowledge about patient phenotypes-with curated genetic information from the same patient cohort and b) making this integrated knowledge, along with a suite of statistical tools, available free of charge to authorized investigators on a Web portal https://pmsdn.hms.harvard.edu. PMS_DN is a Patient Centric Outcomes Research Initiative (PCORI) where patients and their families are involved in all aspects of the management of patient data in driving research into PMS. To foster collaborative research, PMS_DN also makes patient aggregates from this knowledge available to authorized investigators using distributed research networks such as the PCORnet PopMedNet. PMS_DN is hosted on a scalable cloud based environment and complies with all patient data privacy regulations. As of October 31, 2016, PMS_DN integrates high-quality knowledge extracted from the clinical notes of 112 patients and curated genetic reports of 176 patients with preprocessed PRO data from 415 patients. © 2017 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc.

  11. A comparative map viewer integrating genetic maps for Brassica and Arabidopsis

    Directory of Open Access Journals (Sweden)

    Erwin Timothy A

    2007-07-01

    Full Text Available Abstract Background Molecular genetic maps provide a means to link heritable traits with underlying genome sequence variation. Several genetic maps have been constructed for Brassica species, yet to date, there has been no simple means to compare this information or to associate mapped traits with the genome sequence of the related model plant, Arabidopsis. Description We have developed a comparative genetic map database for the viewing, comparison and analysis of Brassica and Arabidopsis genetic, physical and trait map information. This web-based tool allows users to view and compare genetic and physical maps, search for traits and markers, and compare genetic linkage groups within and between the amphidiploid and diploid Brassica genomes. The inclusion of Arabidopsis data enables comparison between Brassica maps that share no common markers. Analysis of conserved syntenic blocks between Arabidopsis and collated Brassica genetic maps validates the application of this system. This tool is freely available over the internet on http://bioinformatics.pbcbasc.latrobe.edu.au/cmap. Conclusion This database enables users to interrogate the relationship between Brassica genetic maps and the sequenced genome of A. thaliana, permitting the comparison of genetic linkage groups and mapped traits and the rapid identification of candidate genes.

  12. Assessment of MARS for downcomer multi-dimensional thermal hydraulics during LBLOCA reflood using KAERI air-water direct vessel injection tests

    Energy Technology Data Exchange (ETDEWEB)

    Won-Jae, Lee; Kwi-Seok, Ha; Chul-Hwa, Song [Korea Atomic Energy Research Inst., Daejeon (Korea, Republic of)

    2001-07-01

    The MARS code has been assessed for the downcomer multi-dimensional thermal hydraulics during a large break loss-of-coolant accident (LBLOCA) reflood of Korean Next Generation Reactor (KNGR) that adopted an upper direct vessel injection (DVI) design. Direct DVI bypass and downcomer level sweep-out tests carried out at 1/50-scale air-water DVI test facility are simulated to examine the capability of MARS. Test conditions are selected such that they represent typical reflood conditions of KNGR, that is, DVI injection velocities of 1.0 {approx} 1.6 m/sec and air injection velocities of 18.0 {approx} 35.0 m/sec, for single and double DVI configurations. MARS calculation is first adjusted to the experimental DVI film distribution that largely affects air-water interaction in a scaled-down downcomer, then, the code is assessed for the selected test matrix. With some improvements of MARS thermal-hydraulic (T/H) models, it has been demonstrated that the MARS code is capable of simulating the direct DVI bypass and downcomer level sweep-out as well as the multi-dimensional thermal hydraulics in downcomer, where condensation effect is excluded. (authors)

  13. Urban air quality forecasting based on multi-dimensional collaborative Support Vector Regression (SVR): A case study of Beijing-Tianjin-Shijiazhuang.

    Science.gov (United States)

    Liu, Bing-Chun; Binaykia, Arihant; Chang, Pei-Chann; Tiwari, Manoj Kumar; Tsao, Cheng-Chin

    2017-01-01

    Today, China is facing a very serious issue of Air Pollution due to its dreadful impact on the human health as well as the environment. The urban cities in China are the most affected due to their rapid industrial and economic growth. Therefore, it is of extreme importance to come up with new, better and more reliable forecasting models to accurately predict the air quality. This paper selected Beijing, Tianjin and Shijiazhuang as three cities from the Jingjinji Region for the study to come up with a new model of collaborative forecasting using Support Vector Regression (SVR) for Urban Air Quality Index (AQI) prediction in China. The present study is aimed to improve the forecasting results by minimizing the prediction error of present machine learning algorithms by taking into account multiple city multi-dimensional air quality information and weather conditions as input. The results show that there is a decrease in MAPE in case of multiple city multi-dimensional regression when there is a strong interaction and correlation of the air quality characteristic attributes with AQI. Also, the geographical location is found to play a significant role in Beijing, Tianjin and Shijiazhuang AQI prediction.

  14. Development of multi-dimensional analysis method for porous blockage in fuel subassembly. Numerical simulation for 4 subchannel geometry water test

    International Nuclear Information System (INIS)

    Tanaka, Masa-aki; Kamide, Hideki

    2001-02-01

    This investigation deals with the porous blockage in a wire spacer type fuel subassembly in Fast Breeder Reactors (FBR's). Multi-dimensional analysis method for a porous blockage in a fuel subassembly is developed using the standard k-ε turbulence model with the typical correlations in handbooks. The purpose of this analysis method is to evaluate the position and the magnitude of the maximum temperature, and to investigate the thermo-hydraulic phenomena in the porous blockage. Verification of this analysis method was conducted based on the results of 4-subchannel geometry water test. It was revealed that the evaluation of the porosity distribution and the particle diameter in a porous blockage was important to predict the temperature distribution. This analysis method could simulate the spatial characteristic of velocity and temperature distributions in the blockage and evaluate the pin surface temperature inside the porous blockage. Through the verification of this analysis method, it is shown that this multi-dimensional analysis method is useful to predict the thermo-hydraulic field and the highest temperature in a porous blockage. (author)

  15. Genetic regulation of colony social organization in fire ants: an integrative overview.

    Science.gov (United States)

    Gotzek, Dietrich; Ross, Kenneth G

    2007-09-01

    Expression of colony social organization in fire ants appears to be under the control of a single Mendelian factor of large effect. Variation in colony queen number in Solenopsis invicta and its relatives is associated with allelic variation at the gene Gp-9, but not with variation at other unlinked genes; workers regulate queen identity and number on the basis of Gp-9 genotypic compatibility. Nongenetic factors, such as prior social experience, queen reproductive status, and local environment, have negligible effects on queen numbers which illustrates the nearly complete penetrance of Gp-9. As predicted, queen number can be manipulated experimentally by altering worker Gp-9 genotype frequencies. The Gp-9 allele lineage associated with polygyny in South American fire ants has been retained across multiple speciation events, which may signal the action of balancing selection to maintain social polymorphism in these species. Moreover, positive selection is implicated in driving the molecular evolution of Gp-9 in association with the origin of polygyny. The identity of the product of Gp-9 as an odorant-binding protein suggests plausible scenarios for its direct involvement in the regulation of queen number via a role in chemical communication. While these and other lines of evidence show that Gp-9 represents a legitimate candidate gene of major effect, studies aimed at determining (i) the biochemical pathways in which GP-9 functions; (ii) the phenotypic effects of molecular variation at Gp-9 and other pathway genes; and (iii) the potential involvement of genes in linkage disequilibrium with Gp-9 are needed to elucidate the genetic architecture underlying social organization in fire ants. Information that reveals the links between molecular variation, individual phenotype, and colony-level behaviors, combined with behavioral models that incorporate details of the chemical communication involved in regulating queen number, will yield a novel integrated view of the

  16. Development of an integrated genome informatics, data management and workflow infrastructure: A toolbox for the study of complex disease genetics

    Directory of Open Access Journals (Sweden)

    Burren Oliver S

    2004-01-01

    Full Text Available Abstract The genetic dissection of complex disease remains a significant challenge. Sample-tracking and the recording, processing and storage of high-throughput laboratory data with public domain data, require integration of databases, genome informatics and genetic analyses in an easily updated and scaleable format. To find genes involved in multifactorial diseases such as type 1 diabetes (T1D, chromosome regions are defined based on functional candidate gene content, linkage information from humans and animal model mapping information. For each region, genomic information is extracted from Ensembl, converted and loaded into ACeDB for manual gene annotation. Homology information is examined using ACeDB tools and the gene structure verified. Manually curated genes are extracted from ACeDB and read into the feature database, which holds relevant local genomic feature data and an audit trail of laboratory investigations. Public domain information, manually curated genes, polymorphisms, primers, linkage and association analyses, with links to our genotyping database, are shown in Gbrowse. This system scales to include genetic, statistical, quality control (QC and biological data such as expression analyses of RNA or protein, all linked from a genomics integrative display. Our system is applicable to any genetic study of complex disease, of either large or small scale.

  17. Genetic tests in major psychiatric disorders-integrating molecular medicine with clinical psychiatry-why is it so difficult?

    Science.gov (United States)

    Demkow, U; Wolańczyk, T

    2017-06-13

    With the advent of post-genomic era, new technologies create extraordinary possibilities for diagnostics and personalized therapy, transforming todays' medicine. Rooted in both medical genetics and clinical psychiatry, the paper is designed as an integrated source of information of the current and potential future application of emerging genomic technologies as diagnostic tools in psychiatry, moving beyond the classical concept of patient approach. Selected approaches are presented, starting from currently used technologies (next-generation sequencing (NGS) and microarrays), followed by newer options (reverse phenotyping). Next, we describe an old concept in a new light (endophenotypes), subsequently coming up with a sophisticated and complex approach (gene networks) ending by a nascent field (computational psychiatry). The challenges and barriers that exist to translate genomic research to real-world patient assessment are further discussed. We emphasize the view that only a paradigm shift can bring a fundamental change in psychiatric practice, allowing to disentangle the intricacies of mental diseases. All the diagnostic methods, as described, are directed at uncovering the integrity of the system including many types of relations within a complex structure. The integrative system approach offers new opportunity to connect genetic background with specific diseases entities, or concurrently, with symptoms regardless of a diagnosis. To advance the field, we propose concerted cross-disciplinary effort to provide a diagnostic platform operating at the general level of genetic pathogenesis of complex-trait psychiatric disorders rather than at the individual level of a specific disease.

  18. Accelerating Genetic Gains in Legumes for the Development of Prosperous Smallholder Agriculture: Integrating Genomics, Phenotyping, Systems Modelling and Agronomy.

    Science.gov (United States)

    Varshney, Rajeev K; Thudi, Mahendar; Pandey, Manish K; Tardieu, Francois; Ojiewo, Chris; Vadez, Vincent; Whitbread, Anthony M; Siddique, Kadambot H M; Nguyen, Henry T; Carberry, Peter S; Bergvinson, David

    2018-03-05

    Grain legumes form an important component of the human diet, feed for livestock and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress that is posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the last half century. For achieving faster genetic gains in legumes in rainfed conditions, this review article proposes the integration of modern genomics approaches, high throughput phenomics and simulation modelling as support for crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experiment plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains including not only productivity but also nutritional and market traits will increase the profitability of farmers and the availability of affordable nutritious food especially in developing countries.

  19. Missing Links in Genes to Traits: Toward Teaching for an Integrated Framework of Genetics

    Science.gov (United States)

    Pavlova, Iglika V.; Kreher, Scott A.

    2013-01-01

    Genetics, one of the most influential fields, underlies all of biology and produces discoveries that are in the news daily. However, many students leave introductory biology and genetics courses lacking a coherent framework of knowledge to use in their daily lives. We identify substantial "missing links" in the teaching of foundational…

  20. An integrated map of genetic variation from 1.092 human genomes

    DEFF Research Database (Denmark)

    Abecasis, Goncalo R.; Auton, Adam; Brooks, Lisa D.

    2012-01-01

    By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination ...

  1. Transverse Position Reconstruction in a Liquid Argon Time Projection Chamber using Principal Component Analysis and Multi-Dimensional Fitting

    Science.gov (United States)

    Watson, Andrew William

    2017-08-01

    pocket above the liquid region, respectively. One of the lingering challenges in this experiment, however, is the determination of an event's position along the other two spatial dimensions, that is, its transverse or "xy" position. Some liquid noble element TPCs have achieved remarkably accurate event position reconstructions, typically using the relative amounts of S2 light collected by Photo-Multiplier Tubes ("PMTs") as the input data to their reconstruction algorithms. This approach has been partic- ularly challenging in DarkSide-50, partly due to unexpected asymmetries in the detector, and partly due to the design of the detector itself. A variety of xy-Reconstruction methods ("xy methods" for short) have come and gone in DS- 50, with only a few of them providing useful results. The xy method described in this dissertation is a two-step Principal Component Analysis / Multi-Dimensional Fit (PCAMDF) reconstruction. In a nutshell, this method develops a functional mapping from the 19-dimensional space of the signal received by the PMTs at the "top" (or the "anode" end) of the DarkSide-50 TPC to each of the transverse coordinates, x and y. PCAMDF is a low-level "machine learning" algorithm, and as such, needs to be "trained" with a sample of representative events; in this case, these are provided by the DarkSide geant4-based Monte Carlo, g4ds. In this work, a thorough description of the PCAMDF xy-Reconstruction method is provided along with an analysis of its performance on MC events and data. The method is applied to several classes of data events, including coincident decays, external gamma rays from calibration sources, and both atmospheric argon "AAr" and underground argon "UAr". Discrepancies between the MC and data are explored, and fiducial volume cuts are calculated. Finally, a novel method is proposed for finding the accuracy of the PCAMDF reconstruction on data by using the asymmetry of the S2 light collected on the anode and cathode PMT arrays as a function

  2. TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae

    Directory of Open Access Journals (Sweden)

    Yoshida Takuhiro

    2008-06-01

    Full Text Available Abstract Background The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species. Description The Triticeae mapped expressed sequence tag (EST database (TriMEDB provides information, along with various annotations, regarding mapped cDNA markers that are related to barley and their homologues in wheat. The current version of TriMEDB provides map-location data for barley and wheat ESTs that were retrieved from 3 published barley linkage maps (the barley single nucleotide polymorphism database of the Scottish Crop Research Institute, the barley transcript map of Leibniz Institute of Plant Genetics and Crop Plant Research, and HarvEST barley ver. 1.63 and 1 diploid wheat map. These data were imported to CMap to allow the visualization of the map positions of the ESTs and interrelationships of these ESTs with public gene models and representative cDNA sequences. The retrieved cDNA sequences corresponding to each EST marker were assigned to the rice genome to predict an exon-intron structure. Furthermore, to generate a unique set of EST markers in Triticeae plants among the public domain, 3472 markers were

  3. Integrating Nonadditive Genomic Relationship Matrices into the Study of Genetic Architecture of Complex Traits.

    Science.gov (United States)

    Nazarian, Alireza; Gezan, Salvador A

    2016-03-01

    The study of genetic architecture of complex traits has been dramatically influenced by implementing genome-wide analytical approaches during recent years. Of particular interest are genomic prediction strategies which make use of genomic information for predicting phenotypic responses instead of detecting trait-associated loci. In this work, we present the results of a simulation study to improve our understanding of the statistical properties of estimation of genetic variance components of complex traits, and of additive, dominance, and genetic effects through best linear unbiased prediction methodology. Simulated dense marker information was used to construct genomic additive and dominance matrices, and multiple alternative pedigree- and marker-based models were compared to determine if including a dominance term into the analysis may improve the genetic analysis of complex traits. Our results showed that a model containing a pedigree- or marker-based additive relationship matrix along with a pedigree-based dominance matrix provided the best partitioning of genetic variance into its components, especially when some degree of true dominance effects was expected to exist. Also, we noted that the use of a marker-based additive relationship matrix along with a pedigree-based dominance matrix had the best performance in terms of accuracy of correlations between true and estimated additive, dominance, and genetic effects. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Mayo Alliance Prognostic Model for Myelodysplastic Syndromes: Integration of Genetic and Clinical Information.

    Science.gov (United States)

    Tefferi, Ayalew; Gangat, Naseema; Mudireddy, Mythri; Lasho, Terra L; Finke, Christy; Begna, Kebede H; Elliott, Michelle A; Al-Kali, Aref; Litzow, Mark R; Hook, C Christopher; Wolanskyj, Alexandra P; Hogan, William J; Patnaik, Mrinal M; Pardanani, Animesh; Zblewski, Darci L; He, Rong; Viswanatha, David; Hanson, Curtis A; Ketterling, Rhett P; Tang, Jih-Luh; Chou, Wen-Chien; Lin, Chien-Chin; Tsai, Cheng-Hong; Tien, Hwei-Fang; Hou, Hsin-An

    2018-06-01

    To develop a new risk model for primary myelodysplastic syndromes (MDS) that integrates information on mutations, karyotype, and clinical variables. Patients with World Health Organization-defined primary MDS seen at Mayo Clinic (MC) from December 28, 1994, through December 19, 2017, constituted the core study group. The National Taiwan University Hospital (NTUH) provided the validation cohort. Model performance, compared with the revised International Prognostic Scoring System, was assessed by Akaike information criterion and area under the curve estimates. The study group consisted of 685 molecularly annotated patients from MC (357) and NTUH (328). Multivariate analysis of the MC cohort identified monosomal karyotype (hazard ratio [HR], 5.2; 95% CI, 3.1-8.6), "non-MK abnormalities other than single/double del(5q)" (HR, 1.8; 95% CI, 1.3-2.6), RUNX1 (HR, 2.0; 95% CI, 1.2-3.1) and ASXL1 (HR, 1.7; 95% CI, 1.2-2.3) mutations, absence of SF3B1 mutations (HR, 1.6; 95% CI, 1.1-2.4), age greater than 70 years (HR, 2.2; 95% CI, 1.6-3.1), hemoglobin level less than 8 g/dL in women or less than 9 g/dL in men (HR, 2.3; 95% CI, 1.7-3.1), platelet count less than 75 × 10 9 /L (HR, 1.5; 95% CI, 1.1-2.1), and 10% or more bone marrow blasts (HR, 1.7; 95% CI, 1.1-2.8) as predictors of inferior overall survival. Based on HR-weighted risk scores, a 4-tiered Mayo alliance prognostic model for MDS was devised: low (89 patients), intermediate-1 (104), intermediate-2 (95), and high (69); respective median survivals (5-year overall survival rates) were 85 (73%), 42 (34%), 22 (7%), and 9 months (0%). The Mayo alliance model was subsequently validated by using the external NTUH cohort and, compared with the revised International Prognostic Scoring System, displayed favorable Akaike information criterion (1865 vs 1943) and area under the curve (0.87 vs 0.76) values. We propose a simple and contemporary risk model for MDS that is based on a limited set of genetic and clinical variables

  5. Genetic and epigenetic alterations induced by different levels of rye genome integration in wheat recipient.

    Science.gov (United States)

    Zheng, X L; Zhou, J P; Zang, L L; Tang, A T; Liu, D Q; Deng, K J; Zhang, Y

    2016-06-17

    The narrow genetic variation present in common wheat (Triticum aestivum) varieties has greatly restricted the improvement of crop yield in modern breeding systems. Alien addition lines have proven to be an effective means to broaden the genetic diversity of common wheat. Wheat-rye addition lines, which are the direct bridge materials for wheat improvement, have been wildly used to produce new wheat cultivars carrying alien rye germplasm. In this study, we investigated the genetic and epigenetic alterations in two sets of wheat-rye disomic addition lines (1R-7R) and the corresponding triticales. We used expressed sequence tag-simple sequence repeat, amplified fragment length polymorphism, and methylation-sensitive amplification polymorphism analyses to analyze the effects of the introduction of alien chromosomes (either the entire genome or sub-genome) to wheat genetic background. We found obvious and diversiform variations in the genomic primary structure, as well as alterations in the extent and pattern of the genomic DNA methylation of the recipient. Meanwhile, these results also showed that introduction of different rye chromosomes could induce different genetic and epigenetic alterations in its recipient, and the genetic background of the parents is an important factor for genomic and epigenetic variation induced by alien chromosome addition.

  6. Toward an integrated genetic model for vent-distal SEDEX deposits

    Science.gov (United States)

    Sangster, D. F.

    2018-04-01

    Although genetic models have been proposed for vent-proximal SEDEX deposits, an equivalent model for vent-distal deposits has not yet appeared. In view of this, it is the object of this paper to present a preliminary integrated vent-distal genetic model through exploration of four major components: (i) nature of the ore-forming fluid, (ii) role of density of the unconsolidated host sediments, (iii) dynamics of sulfate reduction and (iv) depositional environment. Two sub-groups of SEDEX Pb-Zn deposits, vent-proximal and vent-distal, are widely recognized today. Of the two, the latter is by far the largest in terms of metal content with each of the 13 largest containing in excess of 7.5 M (Zn+Pb) metal. In contrast, only one vent-proximal deposit (Sullivan) falls within this size range. Vent-proximal deposits are characteristically underlain by local networks of sulfide-filled veins (commonly regarded as feeder veins) surrounded by a discordant complex of host rock alteration. These attributes are missing in vent-distal deposits, which has led to the widespread view that vent-distal ore-forming fluids have migrated unknown distances away from their vent sites. Because of the characteristic fine grain size of ore minerals, critical fluid inclusion data are lacking for vent-distal ore-stage sulfides. Consequently, hypothetical fluids such as those which formed MVT deposits (120 °C, 20% NaCl equiv.) are considered to represent vent-distal fluids as well. Such high-salinity fluids are capable of carrying significant concentrations of Pb and Zn as chloride complexes while the relatively low temperatures preclude high Cu contents. Densities of such metalliferous brines result in bottom-hugging fluids that collect in shallow saucer-shaped depressions (collector basins). Lateral metal zoning in several deposits reveals the direction from which the brines came. Relative densities of the ore-forming fluid and sediment determine whether the ore-forming fluid stabilizes on top

  7. Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century

    International Nuclear Information System (INIS)

    Mortensen, Holly M.; Euling, Susan Y.

    2013-01-01

    Response to environmental chemicals can vary widely among individuals and between population groups. In human health risk assessment, data on susceptibility can be utilized by deriving risk levels based on a study of a susceptible population and/or an uncertainty factor may be applied to account for the lack of information about susceptibility. Defining genetic susceptibility in response to environmental chemicals across human populations is an area of interest in the NAS' new paradigm of toxicity pathway-based risk assessment. Data from high-throughput/high content (HT/HC), including -omics (e.g., genomics, transcriptomics, proteomics, metabolomics) technologies, have been integral to the identification and characterization of drug target and disease loci, and have been successfully utilized to inform the mechanism of action for numerous environmental chemicals. Large-scale population genotyping studies may help to characterize levels of variability across human populations at identified target loci implicated in response to environmental chemicals. By combining mechanistic data for a given environmental chemical with next generation sequencing data that provides human population variation information, one can begin to characterize differential susceptibility due to genetic variability to environmental chemicals within and across genetically heterogeneous human populations. The integration of such data sources will be informative to human health risk assessment

  8. Optimism and well-being: a prospective multi-method and multi-dimensional examination of optimism as a resilience factor following the occurrence of stressful life events.

    Science.gov (United States)

    Kleiman, Evan M; Chiara, Alexandra M; Liu, Richard T; Jager-Hyman, Shari G; Choi, Jimmy Y; Alloy, Lauren B

    2017-02-01

    Optimism has been conceptualised variously as positive expectations (PE) for the future , optimistic attributions , illusion of control , and self-enhancing biases. Relatively little research has examined these multiple dimensions of optimism in relation to psychological and physical health. The current study assessed the multi-dimensional nature of optimism within a prospective vulnerability-stress framework. Initial principal component analyses revealed the following dimensions: PEs, Inferential Style (IS), Sense of Invulnerability (SI), and Overconfidence (O). Prospective follow-up analyses demonstrated that PE was associated with fewer depressive episodes and moderated the effect of stressful life events on depressive symptoms. SI also moderated the effect of life stress on anxiety symptoms. Generally, our findings indicated that optimism is a multifaceted construct and not all forms of optimism have the same effects on well-being. Specifically, our findings indicted that PE may be the most relevant to depression, whereas SI may be the most relevant to anxiety.

  9. The discharge behavior of lithium-ion batteries using the Dual-Potential Multi-Scale Multi-Dimensional (MSMD) Battery Model

    DEFF Research Database (Denmark)

    Saeed Madani, Seyed; Swierczynski, Maciej Jozef; Kær, Søren Knudsen

    2017-01-01

    This paper gives insight into the discharge behavior of lithium-ion batteries based on the investigations, which have been done by the researchers [1– 19]. In this article, the battery's discharge behaviour at various discharge rates is studied and surface monitor, discharge curve, volume monitor...... to analysis the discharge behaviour of lithium-ion batteries. The results show that surface monitor plot of discharge curve at 1 C has a decreasing trend and volume monitor plot of maximum temperature in the domain has slightly increasing pattern over the simulation time. For the curves of discharge...... plot of maximum temperature in the domain and maximum temperature in the area are illustrated. Additionally, an external and internal short-circuit treatment for three cases have been studied. The Dual-Potential Multi-Scale Multi-Dimensional (MSMD) Battery Model (BM) was used by ANSYS FLUENT software...

  10. The multi-dimensional talent support tool (mBET – a systemic approach towards individualized support of the gifted and talented in Austria

    Directory of Open Access Journals (Sweden)

    Johanna Stahl

    2015-03-01

    Full Text Available Providing gifted students with personalized talent development programs is a challenge for teachers and educators alike. The multi-dimensional talent development tool (mBET guides teachers on their way to individualized gifted programs. Within a holistic and systemic concept of giftedness, the mBET brings together the perspectives of teachers, parents and the individual student in assessing talents as well as relevant personality characteristics and environment factors. By facilitating support-oriented round-table talks, the mBET helps teachers, parents and students to develop individually tailored talent development programs, taking into consideration both talents and other factors relevant for successful gifted education (i.e. non-cognitive personality characteristics and environmental factors.

  11. Critical Need for Family-Based, Quasi-Experimental Designs in Integrating Genetic and Social Science Research

    Science.gov (United States)

    Lahey, Benjamin B.; Turkheimer, Eric; Lichtenstein, Paul

    2013-01-01

    Researchers have identified environmental risks that predict subsequent psychological and medical problems. Based on these correlational findings, researchers have developed and tested complex developmental models and have examined biological moderating factors (e.g., gene–environment interactions). In this context, we stress the critical need for researchers to use family-based, quasi-experimental designs when trying to integrate genetic and social science research involving environmental variables because these designs rigorously examine causal inferences by testing competing hypotheses. We argue that sibling comparison, offspring of twins or siblings, in vitro fertilization designs, and other genetically informed approaches play a unique role in bridging gaps between basic biological and social science research. We use studies on maternal smoking during pregnancy to exemplify these principles. PMID:23927516

  12. Disentangling the health benefits of walking from increased exposure to falls in older people using remote gait monitoring and multi-dimensional analysis.

    Science.gov (United States)

    Brodie, Matthew A; Okubo, Yoshiro; Annegarn, Janneke; Wieching, Rainer; Lord, Stephen R; Delbaere, Kim

    2017-01-01

    Falls and physical deconditioning are two major health problems for older people. Recent advances in remote physiological monitoring provide new opportunities to investigate why walking exercise, with its many health benefits, can both increase and decrease fall rates in older people. In this paper we combine remote wearable device monitoring of daily gait with non-linear multi-dimensional pattern recognition analysis; to disentangle the complex associations between walking, health and fall rates. One week of activities of daily living (ADL) were recorded with a wearable device in 96 independent living older people prior to completing 6 months of exergaming interventions. Using the wearable device data; the quantity, intensity, variability and distribution of daily walking patterns were assessed. At baseline, clinical assessments of health, falls, sensorimotor and physiological fall risks were completed. At 6 months, fall rates, sensorimotor and physiological fall risks were re-assessed. A non-linear multi-dimensional analysis was conducted to identify risk-groups according to their daily walking patterns. Four distinct risk-groups were identified: The Impaired (93% fallers), Restrained (8% fallers), Active (50% fallers) and Athletic (4% fallers). Walking was strongly associated with multiple health benefits and protective of falls for the top performing Athletic risk-group. However, in the middle of the spectrum, the Active risk-group, who were more active, younger and healthier were 6.25 times more likely to be fallers than their Restrained counterparts. Remote monitoring of daily walking patterns may provide a new way to distinguish Impaired people at risk of falling because of frailty from Active people at risk of falling from greater exposure to situations were falls could occur, but further validation is required. Wearable device risk-profiling could help in developing more personalised interventions for older people seeking the health benefits of walking

  13. MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.

    Science.gov (United States)

    Wang, Julia; Al-Ouran, Rami; Hu, Yanhui; Kim, Seon-Young; Wan, Ying-Wooi; Wangler, Michael F; Yamamoto, Shinya; Chao, Hsiao-Tuan; Comjean, Aram; Mohr, Stephanie E; Perrimon, Norbert; Liu, Zhandong; Bellen, Hugo J

    2017-06-01

    One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  14. Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA Genes in Flax (Linum usitatissimum L.

    Directory of Open Access Journals (Sweden)

    Olga Y. Yurkevich

    2017-08-01

    Full Text Available Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH-based chromosomal localization of the CesA conserved fragment (KF011584.1, 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

  15. Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.).

    Science.gov (United States)

    Yurkevich, Olga Y; Kirov, Ilya V; Bolsheva, Nadezhda L; Rachinskaya, Olga A; Grushetskaya, Zoya E; Zoschuk, Svyatoslav A; Samatadze, Tatiana E; Bogdanova, Marina V; Lemesh, Valentina A; Amosova, Alexandra V; Muravenko, Olga V

    2017-01-01

    Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase ( CesA ) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum . Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

  16. Energetic integration of discontinuous processes by means of genetic algorithms, GABSOBHIN; Integration energetique de procedes discontinus a l'aide d'algorithmes genetiques, GABSOBHIN

    Energy Technology Data Exchange (ETDEWEB)

    Krummenacher, P.; Renaud, B.; Marechal, F.; Favrat, D.

    2001-07-01

    This report presents a new methodological approach for the optimal design of energy-integrated batch processes. The main emphasis is put on indirect and, to some extend, on direct heat exchange networks with the possibility of introducing closed or open storage systems. The study demonstrates the feasibility of optimising with genetic algorithms while highlighting the pros and cons of this type of approach. The study shows that the resolution of such problems should preferably be done in several steps to better target the expected solutions. Demonstration is made that in spite of relatively large computer times (on PCs) the use of genetic algorithm allows the consideration of both continuous decision variables (size, operational rating of equipment, etc.) and integer variables (related to the structure at design and during operation). Comparison of two optimisation strategies is shown with a preference for a two-steps optimisation scheme. One of the strengths of genetic algorithms is the capacity to accommodate heuristic rules, which can be introduced in the model. However, a rigorous modelling strategy is advocated to improve robustness and adequate coding of the decision variables. The practical aspects of the research work are converted into a software developed with MATLAB to solve the energy integration of batch processes with a reasonable number of closed or open stores. This software includes the model of superstructures, including the heat exchangers and the storage alternatives, as well as the link to the Struggle algorithm developed at MIT via a dedicated new interface. The package also includes a user-friendly pre-processing using EXCEL, which is to facilitate to application to other similar industrial problems. These software developments have been validated both on an academic and on an industrial type of problems. (author)

  17. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

    Directory of Open Access Journals (Sweden)

    Druka Arnis

    2008-11-01

    Full Text Available Abstract Background A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community. Description Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits. Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them. Conclusion By

  18. Integrating paleoecology and genetics of bird populations in two sky island archipelagos.

    Science.gov (United States)

    McCormack, John E; Bowen, Bonnie S; Smith, Thomas B

    2008-06-27

    Genetic tests of paleoecological hypotheses have been rare, partly because recent genetic divergence is difficult to detect and time. According to fossil plant data, continuous woodland in the southwestern USA and northern Mexico became fragmented during the last 10,000 years, as warming caused cool-adapted species to retreat to high elevations. Most genetic studies of resulting 'sky islands' have either failed to detect recent divergence or have found discordant evidence for ancient divergence. We test this paleoecological hypothesis for the region with intraspecific mitochondrial DNA and microsatellite data from sky-island populations of a sedentary bird, the Mexican jay (Aphelocoma ultramarina). We predicted that populations on different sky islands would share common, ancestral alleles that existed during the last glaciation, but that populations on each sky island, owing to their isolation, would contain unique variants of postglacial origin. We also predicted that divergence times estimated from corrected genetic distance and a coalescence model would post-date the last glacial maximum. Our results provide multiple independent lines of support for postglacial divergence, with the predicted pattern of shared and unique mitochondrial DNA haplotypes appearing in two independent sky-island archipelagos, and most estimates of divergence time based on corrected genetic distance post-dating the last glacial maximum. Likewise, an isolation model based on multilocus gene coalescence indicated postglacial divergence of five pairs of sky islands. In contrast to their similar recent histories, the two archipelagos had dissimilar historical patterns in that sky islands in Arizona showed evidence for older divergence, suggesting different responses to the last glaciation. This study is one of the first to provide explicit support from genetic data for a postglacial divergence scenario predicted by one of the best paleoecological records in the world. Our results

  19. A System-level Infrastructure for Multi-dimensional MP-SoC Design Space Co-exploration

    NARCIS (Netherlands)

    Jia, Z.J.; Bautista, T.; Nunez, A.; Pimentel, A.D.; Thompson, M.

    2013-01-01

    In this article, we present a flexible and extensible system-level MP-SoC design space exploration (DSE) infrastructure, called NASA. This highly modular framework uses well-defined interfaces to easily integrate different system-level simulation tools as well as different combinations of search

  20. An integrated biochemistry and genetics outreach program designed for elementary school students.

    Science.gov (United States)

    Ross, Eric D; Lee, Sarah K; Radebaugh, Catherine A; Stargell, Laurie A

    2012-02-01

    Exposure to genetic and biochemical experiments typically occurs late in one's academic career. By the time students have the opportunity to select specialized courses in these areas, many have already developed negative attitudes toward the sciences. Given little or no direct experience with the fields of genetics and biochemistry, it is likely that many young people rule these out as potential areas of study or career path. To address this problem, we developed a 7-week (~1 hr/week) hands-on course to introduce fifth grade students to basic concepts in genetics and biochemistry. These young students performed a series of investigations (ranging from examining phenotypic variation, in vitro enzymatic assays, and yeast genetic experiments) to explore scientific reasoning through direct experimentation. Despite the challenging material, the vast majority of students successfully completed each experiment, and most students reported that the experience increased their interest in science. Additionally, the experiments within the 7-week program are easily performed by instructors with basic skills in biological sciences. As such, this program can be implemented by others motivated to achieve a broader impact by increasing the accessibility of their university and communicating to a young audience a positive impression of the sciences and the potential for science as a career.

  1. Genetic evidence and integration of various data sources for classifying uncertain variants into a single model.

    NARCIS (Netherlands)

    Goldgar, D.E.; Easton, D.F.; Byrnes, G.B.; Spurdle, A.B.; Iversen, E.S.; Greenblatt, M.S.; Boffetta, P.; Couch, F.J.; Wind, N. de; Eccles, D.; Foulkes, W.D.; Genuardi, M.; Hofstra, R.M.; Hogervorst, F.; Hoogerbrugge-van der Linden, N.; Plon, S.E.; Radice, P.; Rasmussen, L.; Sinilnikova, O.M.; Tavtigian, S.V.

    2008-01-01

    Genetic testing often results in the finding of a variant whose clinical significance is unknown. A number of different approaches have been employed in the attempt to classify such variants. For some variants, case-control, segregation, family history, or other statistical studies can provide

  2. Grand challenges in evolutionary and population genetics: The importance of integrating epigenetics, genomics, modeling, and experimentation

    Science.gov (United States)

    Samuel A. Cushman

    2014-01-01

    This is a time of explosive growth in the fields of evolutionary and population genetics, with whole genome sequencing and bioinformatics driving a transformative paradigm shift (Morozova and Marra, 2008). At the same time, advances in epigenetics are thoroughly transforming our understanding of evolutionary processes and their implications for populations, species and...

  3. Towards an integrated ecosystem of R packages for the analysis of population genetic data

    Science.gov (United States)

    Computer programs have early on taken a central place in the analysis of population genetic data. The continuous increase in amount and diversity of data, together with the emergence of new pressing questions related to the adaptation of populations of plants and animals in the face of global change...

  4. Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

    Science.gov (United States)

    MacMillan, Don

    2010-01-01

    This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

  5. Integrating genetic, transcriptional, and functional analyses to identify 5 novel genes for atrial fibrillation

    DEFF Research Database (Denmark)

    Sinner, Moritz F; Tucker, Nathan R; Lunetta, Kathryn L

    2014-01-01

    BACKGROUND: Atrial fibrillation (AF) affects >30 million individuals worldwide and is associated with an increased risk of stroke, heart failure, and death. AF is highly heritable, yet the genetic basis for the arrhythmia remains incompletely understood. METHODS AND RESULTS: To identify new AF-re...

  6. How to measure genetic heterogeneity

    International Nuclear Information System (INIS)

    Yamada, Ryo

    2009-01-01

    Genetic information of organisms is coded as a string of four letters, A, T, G and C, a sequence in macromolecules called deoxyribonucleic acid (DNA). DNA sequence offers blueprint of organisms and its heterogeneity determines identity and variation of species. The quantitation of this genetic heterogeneity is fundamental to understand biology. We compared previously-reported three measures, covariance matrix expression of list of loci (pair-wise r 2 ), the most popular index in genetics, and its multi-dimensional form, Ψ, and entropy-based index, ε. Thereafter we proposed two methods so that we could handle the diplotypic heterogeneity and quantitate the conditions where the number of DNA sequence samples is much smaller than the number of possible variants.

  7. Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment

    Science.gov (United States)

    Gonçalves, Juliana; Moreira, Elsa; Sequeira, Inês J.; Rodrigues, António S.; Rueff, José; Brás, Aldina

    2016-01-01

    Chromosomal fragile sites (FSs) are loci where gaps and breaks may occur and are preferential integration targets for some viruses, for example, Hepatitis B, Epstein-Barr virus, HPV16, HPV18, and MLV vectors. However, the integration of the human immunodeficiency virus (HIV) in Giemsa bands and in FSs is not yet completely clear. This study aimed to assess the integration preferences of HIV in FSs and in Giemsa bands using an in silico study. HIV integration positions from Jurkat cells were used and two nonparametric tests were applied to compare HIV integration in dark versus light bands and in FS versus non-FS (NFSs). The results show that light bands are preferential targets for integration of HIV-1 in Jurkat cells and also that it integrates with equal intensity in FSs and in NFSs. The data indicates that HIV displays different preferences for FSs compared to other viruses. The aim was to develop and apply an approach to predict the conditions and constraints of HIV insertion in the human genome which seems to adequately complement empirical data. PMID:27294106

  8. Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

    Science.gov (United States)

    Sharma, Sanjeev Kumar; Bolser, Daniel; de Boer, Jan; Sønderkær, Mads; Amoros, Walter; Carboni, Martin Federico; D'Ambrosio, Juan Martín; de la Cruz, German; Di Genova, Alex; Douches, David S; Eguiluz, Maria; Guo, Xiao; Guzman, Frank; Hackett, Christine A; Hamilton, John P; Li, Guangcun; Li, Ying; Lozano, Roberto; Maass, Alejandro; Marshall, David; Martinez, Diana; McLean, Karen; Mejía, Nilo; Milne, Linda; Munive, Susan; Nagy, Istvan; Ponce, Olga; Ramirez, Manuel; Simon, Reinhard; Thomson, Susan J; Torres, Yerisf; Waugh, Robbie; Zhang, Zhonghua; Huang, Sanwen; Visser, Richard G F; Bachem, Christian W B; Sagredo, Boris; Feingold, Sergio E; Orjeda, Gisella; Veilleux, Richard E; Bonierbale, Merideth; Jacobs, Jeanne M E; Milbourne, Dan; Martin, David Michael Alan; Bryan, Glenn J

    2013-11-06

    The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

  9. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

    Science.gov (United States)

    Edwards, J D; Baldo, A M; Mueller, L A

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

  10. Intra-Day Trading System Design Based on the Integrated Model of Wavelet De-Noise and Genetic Programming

    Directory of Open Access Journals (Sweden)

    Hongguang Liu

    2016-12-01

    Full Text Available Technical analysis has been proved to be capable of exploiting short-term fluctuations in financial markets. Recent results indicate that the market timing approach beats many traditional buy-and-hold approaches in most of the short-term trading periods. Genetic programming (GP was used to generate short-term trade rules on the stock markets during the last few decades. However, few of the related studies on the analysis of financial time series with genetic programming considered the non-stationary and noisy characteristics of the time series. In this paper, to de-noise the original financial time series and to search profitable trading rules, an integrated method is proposed based on the Wavelet Threshold (WT method and GP. Since relevant information that affects the movement of the time series is assumed to be fully digested during the market closed periods, to avoid the jumping points of the daily or monthly data, in this paper, intra-day high-frequency time series are used to fully exploit the short-term forecasting advantage of technical analysis. To validate the proposed integrated approach, an empirical study is conducted based on the China Securities Index (CSI 300 futures in the emerging China Financial Futures Exchange (CFFEX market. The analysis outcomes show that the wavelet de-noise approach outperforms many comparative models.

  11. Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization.

    Directory of Open Access Journals (Sweden)

    Xiaoquan Wen

    2017-03-01

    Full Text Available We propose a novel statistical framework for integrating the result from molecular quantitative trait loci (QTL mapping into genome-wide genetic association analysis of complex traits, with the primary objectives of quantitatively assessing the enrichment of the molecular QTLs in complex trait-associated genetic variants and the colocalizations of the two types of association signals. We introduce a natural Bayesian hierarchical model that treats the latent association status of molecular QTLs as SNP-level annotations for candidate SNPs of complex traits. We detail a computational procedure to seamlessly perform enrichment, fine-mapping and colocalization analyses, which is a distinct feature compared to the existing colocalization analysis procedures in the literature. The proposed approach is computationally efficient and requires only summary-level statistics. We evaluate and demonstrate the proposed computational approach through extensive simulation studies and analyses of blood lipid data and the whole blood eQTL data from the GTEx project. In addition, a useful utility from our proposed method enables the computation of expected colocalization signals using simple characteristics of the association data. Using this utility, we further illustrate the importance of enrichment analysis on the ability to discover colocalized signals and the potential limitations of currently available molecular QTL data. The software pipeline that implements the proposed computation procedures, enloc, is freely available at https://github.com/xqwen/integrative.

  12. Integrated Analysis of Genetic and Proteomic Data Identifies Biomarkers Associated with Adverse Events Following Smallpox Vaccination

    Science.gov (United States)

    Complex clinical outcomes, such as adverse reaction to vaccination, arise from the concerted interactions among the myriad components of a biological system. Therefore, comprehensive etiological models can be developed only through the integrated study of multiple types of experi...

  13. Network-assisted crop systems genetics: network inference and integrative analysis.

    Science.gov (United States)

    Lee, Tak; Kim, Hyojin; Lee, Insuk

    2015-04-01

    Although next-generation sequencing (NGS) technology has enabled the decoding of many crop species genomes, most of the underlying genetic components for economically important crop traits remain to be determined. Network approaches have proven useful for the study of the reference plant, Arabidopsis thaliana, and the success of network-based crop genetics will also require the availability of a genome-scale functional networks for crop species. In this review, we discuss how to construct functional networks and elucidate the holistic view of a crop system. The crop gene network then can be used for gene prioritization and the analysis of resequencing-based genome-wide association study (GWAS) data, the amount of which will rapidly grow in the field of crop science in the coming years. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Elucidating novel dysfunctional pathways in Alzheimer's disease by integrating loci identified in genetic and epigenetic studies

    Directory of Open Access Journals (Sweden)

    Adam R. Smith

    2016-06-01

    Full Text Available Alzheimer's disease is a complex neurodegenerative disorder. A large number of genome-wide association studies have been performed, which have been supplemented more recently by the first epigenome-wide association studies, leading to the identification of a number of novel loci altered in disease. Twin studies have shown monozygotic twin discordance for Alzheimer's disease (Gatz et al., 2006, leading to the conclusion that a combination of genetic and epigenetic mechanisms is likely to be involved in disease etiology (Lunnon & Mill, 2013. This review focuses on identifying overlapping pathways between published genome-wide association studies and epigenome-wide association studies, highlighting dysfunctional synaptic, lipid metabolism, plasma membrane/cytoskeleton, mitochondrial, and immune cell activation pathways. Identifying common pathways altered in genetic and epigenetic studies will aid our understanding of disease mechanisms and identify potential novel targets for pharmacological intervention.

  15. A hybrid approach to device integration on a genetic analysis platform

    International Nuclear Information System (INIS)

    Brennan, Des; Justice, John; Aherne, Margaret; Galvin, Paul; Jary, Dorothee; Kurg, Ants; Berik, Evgeny; Macek, Milan

    2012-01-01

    Point-of-care (POC) systems require significant component integration to implement biochemical protocols associated with molecular diagnostic assays. Hybrid platforms where discrete components are combined in a single platform are a suitable approach to integration, where combining multiple device fabrication steps on a single substrate is not possible due to incompatible or costly fabrication steps. We integrate three devices each with a specific system functionality: (i) a silicon electro-wetting-on-dielectric (EWOD) device to move and mix sample and reagent droplets in an oil phase, (ii) a polymer microfluidic chip containing channels and reservoirs and (iii) an aqueous phase glass microarray for fluorescence microarray hybridization detection. The EWOD device offers the possibility of fully integrating on-chip sample preparation using nanolitre sample and reagent volumes. A key challenge is sample transfer from the oil phase EWOD device to the aqueous phase microarray for hybridization detection. The EWOD device, waveguide performance and functionality are maintained during the integration process. An on-chip biochemical protocol for arrayed primer extension (APEX) was implemented for single nucleotide polymorphism (SNiP) analysis. The prepared sample is aspirated from the EWOD oil phase to the aqueous phase microarray for hybridization. A bench-top instrumentation system was also developed around the integrated platform to drive the EWOD electrodes, implement APEX sample heating and image the microarray after hybridization. (paper)

  16. Integrated biochemical, molecular genetic, and bioacoustical analysis of mesoscale variability of the euphausiid Nematoscelis difficilis in the California Current

    Science.gov (United States)

    Bucklin, Ann; Wiebe, Peter H.; Smolenack, Sara B.; Copley, Nancy J.; Clarke, M. Elizabeth

    2002-03-01

    Integrated assessment of the euphausiid Nematoscelis difficilis (Crustacea; Euphausiacea) and the zooplankton assemblage of the California Current was designed to investigate individual, population, and community responses to mesoscale variability in biological and physical characters of the ocean. Zooplankton samples and observational data were collected along a cross-shelf transect of the California Current in association with the California Cooperative Fisheries Investigations (CalCOFI) Survey during October 1996. The transect crossed three domains defined by temperature and salinity: nearshore, mid-Current, and offshore. Individual N. difficilis differed in physiological condition along the transect, with higher size-corrected concentrations of four central metabolic enzymes (citrate synthetase, hexokinase, lactate dehydrogenase (LDH), and phosphoglucose isomerase (PGI)) for euphausiids collected in nearshore waters than in mid-Current and offshore waters. There was little variation in the DNA sequences of the genes encoding PGI and LDH (all DNA changes were either silent or heterozygous base substitutions), suggesting that differences in enzyme concentration did not result from underlying molecular genetic variation. The population genetic makeup of N. difficilis varied from sample to sample based on haplotype frequencies of mitochondrial cytochrome oxidase I (mtCOI; P=0.029). There were significant differences between pooled nearshore and offshore samples, based on allele frequencies at two sites of common substitutions in the mtCOI sequence ( P=0.020 and 0.026). Silhouette and bioacoustical backscattering measurements of the zooplankton assemblage of the top 100 m showed marked diel vertical migration of the scattering layer, of which euphausiids were a small but significant fraction. The biochemical and molecular assays are used as indices of complex physiological (i.e., growth and condition) and genetic (i.e., mortality) processes; the bioacoustical

  17. Integration of Multilocus Genetic Risk into the Default Mode Network Longitudinal Trajectory during the Alzheimer's Disease Process.

    Science.gov (United States)

    Su, Fan; Shu, Hao; Ye, Qing; Xie, Chunming; Yuan, Baoyu; Zhang, Zhijun; Bai, Feng

    2017-01-01

    The aim of the study was to investigate the cognitive significance of the changes in default mode network (DMN) during the process of Alzheimer's disease (AD) and the genetic basis that drives the alteration. Eighty-seven subjects with mild cognitive impairment (MCI) and 131 healthy controls (HC) were employed at baseline, and they had the genetic risk scores (GRS) based on the GWAS-validated AD-related top loci. Eleven MCIs who converted to AD (c-MCIs), 32 subjects who remained stable (nc-MCIs), and 56 HCs participated in the follow-up analyses after an average of 35 months. Decreased functional connectivity (FC) within temporal cortex was identified for MCIs at baseline, which was partially determined by the GRS; moreover, compensations may occur within the frontal-parietal brain to maintain relatively intact cognition. During the follow-ups, c-MCIs exhibited more FC declines within the prefrontal-parietal lobes and parahippocampal gyrus/hippocampus than the HCs and nc-MCIs. The GRS did not significantly vary among the three groups, whereas associations were identified at risky alleles and FC declines in all AD spectra. Interestingly, the influence of APOEɛ4 varied as the disease progressed; APOEɛ4 was associated with longitudinal FC decreases only for HCs in the single variance-based analyses and deteriorated DMN integration in nc-MCIs by combining the effects of other loci. However, the GRS without APOEɛ4 predicted FC decline for converters. It is suggested that the integration of multilocus genetic risk predicted the longitudinal trajectory of DMN and may be used as a clinical strategy to track AD progression.

  18. Integrating the landscape epidemiology and genetics of RNA viruses: rabies in domestic dogs as a model.

    Science.gov (United States)

    Brunker, K; Hampson, K; Horton, D L; Biek, R

    2012-12-01

    Landscape epidemiology and landscape genetics combine advances in molecular techniques, spatial analyses and epidemiological models to generate a more real-world understanding of infectious disease dynamics and provide powerful new tools for the study of RNA viruses. Using dog rabies as a model we have identified how key questions regarding viral spread and persistence can be addressed using a combination of these techniques. In contrast to wildlife rabies, investigations into the landscape epidemiology of domestic dog rabies requires more detailed assessment of the role of humans in disease spread, including the incorporation of anthropogenic landscape features, human movements and socio-cultural factors into spatial models. In particular, identifying and quantifying the influence of anthropogenic features on pathogen spread and measuring the permeability of dispersal barriers are important considerations for planning control strategies, and may differ according to cultural, social and geographical variation across countries or continents. Challenges for dog rabies research include the development of metapopulation models and transmission networks using genetic information to uncover potential source/sink dynamics and identify the main routes of viral dissemination. Information generated from a landscape genetics approach will facilitate spatially strategic control programmes that accommodate for heterogeneities in the landscape and therefore utilise resources in the most cost-effective way. This can include the efficient placement of vaccine barriers, surveillance points and adaptive management for large-scale control programmes.

  19. Genetics and crime: Integrating new genomic discoveries into psychological research about antisocial behavior

    Science.gov (United States)

    Wertz, J.; Caspi, A.; Belsky, D. W.; Beckley, A. L.; Arseneault, L.; Barnes, J. C.; Corcoran, D. L.; Hogan, S.; Houts, R. M.; Morgan, N.; Odgers, C. L.; Prinz, J. A.; Sugden, K.; Williams, B. S.; Poulton, R.; Moffitt, T. E.

    2018-01-01

    Drawing on psychological and sociological theories of crime causation, we tested the hypothesis that genetic risk for low educational attainment (assessed via a genome-wide polygenic score) is associated with offending. We further tested hypotheses of how polygenic risk relates to the development of antisocial behavior from childhood through adulthood. Across the Dunedin and E-Risk birth cohorts of individuals growing up 20 years and 20,000 kilometres apart, education polygenic scores predicted risk of a criminal record, with modest effects. Polygenic risk manifested during primary schooling, in lower cognitive abilities, lower self-control, academic difficulties, and truancy, and predicted a life-course persistent pattern of antisocial behavior that onsets in childhood and persists into adulthood. Crime is central in the nature/nurture debate, and findings reported here demonstrate how molecular-genetic discoveries can be incorporated into established theories of antisocial behavior. They also suggest the hypothesis that improving school experiences might prevent genetic influences on crime from unfolding. PMID:29513605

  20. Genetics and Crime: Integrating New Genomic Discoveries Into Psychological Research About Antisocial Behavior.

    Science.gov (United States)

    Wertz, J; Caspi, A; Belsky, D W; Beckley, A L; Arseneault, L; Barnes, J C; Corcoran, D L; Hogan, S; Houts, R M; Morgan, N; Odgers, C L; Prinz, J A; Sugden, K; Williams, B S; Poulton, R; Moffitt, T E

    2018-05-01

    Drawing on psychological and sociological theories of crime causation, we tested the hypothesis that genetic risk for low educational attainment (assessed via a genome-wide polygenic score) is associated with criminal offending. We further tested hypotheses of how polygenic risk relates to the development of antisocial behavior from childhood through adulthood. Across the Dunedin and Environmental Risk (E-Risk) birth cohorts of individuals growing up 20 years and 20,000 kilometers apart, education polygenic scores predicted risk of a criminal record with modest effects. Polygenic risk manifested during primary schooling in lower cognitive abilities, lower self-control, academic difficulties, and truancy, and it was associated with a life-course-persistent pattern of antisocial behavior that onsets in childhood and persists into adulthood. Crime is central in the nature-nurture debate, and findings reported here demonstrate how molecular-genetic discoveries can be incorporated into established theories of antisocial behavior. They also suggest that improving school experiences might prevent genetic influences on crime from unfolding.

  1. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

    Science.gov (United States)

    2014-01-01

    Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over

  2. An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).

    Science.gov (United States)

    Ren, Yi; McGregor, Cecilia; Zhang, Yan; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Sun, Honghe; Cai, Wantao; Zhang, Jie; Xu, Yong

    2014-01-20

    Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A

  3. PV-PCM integration in glazed building. Co-simulation and genetic optimization study

    DEFF Research Database (Denmark)

    Elarga, Hagar; Dal Monte, Andrea; Andersen, Rune Korsholm

    2017-01-01

    . An exploratory step has also been considered prior to the optimization algorithm: it evaluates the energy profiles before and after the application of PCM to PV module integrated in glazed building. The optimization analysis investigate parameters such as ventilation flow rates and time schedule to obtain......The study describes a multi-objective optimization algorithm for an innovative integration of forced ventilated PV-PCM modules in glazed façade buildings: the aim is to identify and optimize the parameters that most affect thermal and energy performances. 1-D model, finite difference method FDM...

  4. Development and application of a living probabilistic safety assessment tool: Multi-objective multi-dimensional optimization of surveillance requirements in NPPs considering their ageing

    International Nuclear Information System (INIS)

    Kančev, Duško; Čepin, Marko; Gjorgiev, Blaže

    2014-01-01

    The benefits of utilizing the probabilistic safety assessment towards improvement of nuclear power plant safety are presented in this paper. Namely, a nuclear power plant risk reduction can be achieved by risk-informed optimization of the deterministically-determined surveillance requirements. A living probabilistic safety assessment tool for time-dependent risk analysis on component, system and plant level is developed. The study herein focuses on the application of this living probabilistic safety assessment tool as a computer platform for multi-objective multi-dimensional optimization of the surveillance requirements of selected safety equipment seen from the aspect of the risk-informed reasoning. The living probabilistic safety assessment tool is based on a newly developed model for calculating time-dependent unavailability of ageing safety equipment within nuclear power plants. By coupling the time-dependent unavailability model with a commercial software used for probabilistic safety assessment modelling on plant level, the frames of the new platform i.e. the living probabilistic safety assessment tool are established. In such way, the time-dependent core damage frequency is obtained and is further on utilized as first objective function within a multi-objective multi-dimensional optimization case study presented within this paper. The test and maintenance costs are designated as the second and the incurred dose due to performing the test and maintenance activities as the third objective function. The obtained results underline, in general, the usefulness and importance of a living probabilistic safety assessment, seen as a dynamic probabilistic safety assessment tool opposing the conventional, time-averaged unavailability-based, probabilistic safety assessment. The results of the optimization, in particular, indicate that test intervals derived as optimal differ from the deterministically-determined ones defined within the existing technical specifications

  5. Controllable preparation of multi-dimensional hybrid materials of nickel-cobalt layered double hydroxide nanorods/nanosheets on electrospun carbon nanofibers for high-performance supercapacitors

    International Nuclear Information System (INIS)

    Lai, Feili; Huang, Yunpeng; Miao, Yue-E; Liu, Tianxi

    2015-01-01

    Graphical Abstract: Multi-dimensional hybrid materials of nickel-cobalt layered double hydroxide nanorods/nanosheets grown on electrospun carbon nanofiber membranes were prepared via electrospinning combined with solution co-deposition for high-performance supercapacitor electrodes. - Highlights: • Ni-Co LDH@CNFhybridswerepreparedbyelectrospinningandsolutionco-deposition. • Ni-Co LDH@CNF hybrids show high electrochemical performance for supercapacitors. • This method can be extended to other bimetallic@CNF hybrids for electrode materials. - Abstract: Hybrid nanomaterials with hierarchical structures have been considered as one kind of the most promising electrode materials for high-performance supercapacitors with high capacity and long cycle lifetime. In this work, multi-dimensional hybrid materials of nickel-cobalt layered double hydroxide (Ni-Co LDH) nanorods/nanosheets on carbon nanofibers (CNFs) were prepared by electrospinning technique combined with one-step solution co-deposition method. Carbon nanofiber membranes were obtained by electrospinning of polyacrylonitrile (PAN) followed by pre-oxidation and carbonization. The successful growth of Ni-Co LDH with different morphologies on CNF membrane by using two kinds of auxiliary agents reveals the simplicity and universality of this method. The uniform and immense growth of Ni-Co LDH on CNFs significantly improves its dispersion and distribution. Meanwhile the hierarchical structure of carbon nanofiber@nickel-cobalt layered double hydroxide nanorods/nanosheets (CNF@Ni-Co LDH NR/NS) hybrid membranes provide not only more active sites for electrochemical reaction but also more efficient pathways for electron transport. Galvanostatic charge-discharge measurements reveal high specific capacitances of 1378.2 F g −1 and 1195.4 F g −1 (based on Ni-Co LDH mass) at 1 A g −1 for CNF@Ni-Co LDH NR and CNF@Ni-Co LDH NS hybrid membranes, respectively. Moreover, cycling stabilities for both hybrid membranes are

  6. Numerical solutions of multi-dimensional solidification/melting problems by the dual reciprocity boundary element method

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Jong Chull; Shin, Won Ky [Korea Institute of Nuclear Safety, Taejon (Korea, Republic of)

    1997-12-31

    This paper presents an effective and simple procedure for the simulation of the motion of the solid-liquid interfacial boundary and the transient temperature field during phase change process. To accomplish this purpose, an iterative implicit solution algorithm has been developed by employing the dual reciprocity boundary element method. The dual reciprocity boundary element approach provided in this paper is much simpler than the usual boundary element method applying a reciprocity principle and an available technique for dealing with domain integral of boundary element formulation simultaneously. The effectiveness of the present analysis method have been illustrated through comparisons of the calculation results of an example with its semi-analytical or other numerical solutions where available. 22 refs., 3 figs. (Author)

  7. Numerical solutions of multi-dimensional solidification/melting problems by the dual reciprocity boundary element method

    International Nuclear Information System (INIS)

    Jo, Jong Chull; Shin, Won Ky

    1997-01-01

    This paper presents an effective and simple procedure for the simulation of the motion of the solid-liquid interfacial boundary and the transient temperature field during phase change process. To accomplish this purpose, an iterative implicit solution algorithm has been developed by employing the dual reciprocity boundary element method. The dual reciprocity boundary element approach provided in this paper is much simpler than the usual boundary element method applying a reciprocity principle and an available technique for dealing with domain integral of boundary element formulation simultaneously. The effectiveness of the present analysis method have been illustrated through comparisons of the calculation results of an example with its semi-analytical or other numerical solutions where available

  8. Numerical solutions of multi-dimensional solidification/melting problems by the dual reciprocity boundary element method

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Jong Chull; Shin, Won Ky [Korea Institute of Nuclear Safety, Taejon (Korea, Republic of)

    1998-12-31

    This paper presents an effective and simple procedure for the simulation of the motion of the solid-liquid interfacial boundary and the transient temperature field during phase change process. To accomplish this purpose, an iterative implicit solution algorithm has been developed by employing the dual reciprocity boundary element method. The dual reciprocity boundary element approach provided in this paper is much simpler than the usual boundary element method applying a reciprocity principle and an available technique for dealing with domain integral of boundary element formulation simultaneously. The effectiveness of the present analysis method have been illustrated through comparisons of the calculation results of an example with its semi-analytical or other numerical solutions where available. 22 refs., 3 figs. (Author)

  9. Multi-Dimensional Evaluation of Simulated Small-Scale Irrigation Intervention: A Case Study in Dimbasinia Watershed, Ghana

    Directory of Open Access Journals (Sweden)

    Abeyou W. Worqlul

    2018-05-01

    Full Text Available This paper studied the impacts of small-scale irrigation (SSI interventions on environmental sustainability, agricultural production, and socio-economics using an Integrated Decision Support System (IDSS. The IDSS is comprised of a suite of models, namely the Soil and Water Assessment Tool (SWAT, Agricultural Policy/Environmental eXtender (APEX, and Farm Income and Nutrition Simulator (FARMSIM. The IDSS was applied in Dimbasinia watershed in northern Ghana using irrigation water from shallow groundwater. The watershed has a modest amount of shallow groundwater resources. However, the average annual irrigation water requirement exceeded the average annual shallow groundwater recharge. It was found that the current crop yield in Dimbasinia watershed was only ~40% of the potential crop production. This is mainly related to climate variability, low soil fertility, and land-management practices. For example, application of 50 kg/ha urea and 50 kg/ha DAP doubled maize and sorghum yield from the current farmers’ practices. Better income was obtained when irrigated vegetables/fodder were cultivated in rotation with sorghum as compared to in rotation with maize. Investment in solar pumps paid better dividends and also supplied clean energy. The socio-economic analysis indicated that having irrigated dry season vegetables will improve household nutrition. Since shallow groundwater recharge alone may not provide sufficient water for irrigation in a sustainable manner, surface water may be stored using water-harvesting structures to supplement the groundwater for irrigation. Integrated use of the water resources will also reduce depletion of the shallow groundwater aquifer. We conclude that IDSS is a promising tool to study gaps and constraints as well as upscaling of SSI.

  10. Integrating a Genetic Algorithm Into a Knowledge-Based System for Ordering Complex Design Processes

    Science.gov (United States)

    Rogers, James L.; McCulley, Collin M.; Bloebaum, Christina L.

    1996-01-01

    The design cycle associated with large engineering systems requires an initial decomposition of the complex system into design processes which are coupled through the transference of output data. Some of these design processes may be grouped into iterative subcycles. In analyzing or optimizing such a coupled system, it is essential to be able to determine the best ordering of the processes within these subcycles to reduce design cycle time and cost. Many decomposition approaches assume the capability is available to determine what design processes and couplings exist and what order of execution will be imposed during the design cycle. Unfortunately, this is often a complex problem and beyond the capabilities of a human design manager. A new feature, a genetic algorithm, has been added to DeMAID (Design Manager's Aid for Intelligent Decomposition) to allow the design manager to rapidly examine many different combinations of ordering processes in an iterative subcycle and to optimize the ordering based on cost, time, and iteration requirements. Two sample test cases are presented to show the effects of optimizing the ordering with a genetic algorithm.

  11. Genetics of borderline personality disorder: systematic review and proposal of an integrative model.

    Science.gov (United States)

    Amad, Ali; Ramoz, Nicolas; Thomas, Pierre; Jardri, Renaud; Gorwood, Philip

    2014-03-01

    Borderline personality disorder (BPD) is one of the most common mental disorders and is characterized by a pervasive pattern of emotional lability, impulsivity, interpersonal difficulties, identity disturbances, and disturbed cognition. Here, we performed a systematic review of the literature concerning the genetics of BPD, including familial and twin studies, association studies, and gene-environment interaction studies. Moreover, meta-analyses were performed when at least two case-control studies testing the same polymorphism were available. For each gene variant, a pooled odds ratio (OR) was calculated using fixed or random effects models. Familial and twin studies largely support the potential role of a genetic vulnerability at the root of BPD, with an estimated heritability of approximately 40%. Moreover, there is evidence for both gene-environment interactions and correlations. However, association studies for BPD are sparse, making it difficult to draw clear conclusions. According to our meta-analysis, no significant associations were found for the serotonin transporter gene, the tryptophan hydroxylase 1 gene, or the serotonin 1B receptor gene. We hypothesize that such a discrepancy (negative association studies but high heritability of the disorder) could be understandable through a paradigm shift, in which "plasticity" genes (rather than "vulnerability" genes) would be involved. Such a framework postulates a balance between positive and negative events, which interact with plasticity genes in the genesis of BPD. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. OPTIMIZATION OF LAND USE SUITABILITY FOR AGRICULTURE USING INTEGRATED GEOSPATIAL MODEL AND GENETIC ALGORITHMS

    Directory of Open Access Journals (Sweden)

    S. B. Mansor

    2012-08-01

    Full Text Available In this study, a geospatial model for land use allocation was developed from the view of simulating the biological autonomous adaptability to environment and the infrastructural preference. The model was developed based on multi-agent genetic algorithm. The model was customized to accommodate the constraint set for the study area, namely the resource saving and environmental-friendly. The model was then applied to solve the practical multi-objective spatial optimization allocation problems of land use in the core region of Menderjan Basin in Iran. The first task was to study the dominant crops and economic suitability evaluation of land. Second task was to determine the fitness function for the genetic algorithms. The third objective was to optimize the land use map using economical benefits. The results has indicated that the proposed model has much better performance for solving complex multi-objective spatial optimization allocation problems and it is a promising method for generating land use alternatives for further consideration in spatial decision-making.

  13. Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R21 | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

  14. Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R01 | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

  15. Fracture Network and Fluid Flow Imaging for Enhanced Geothermal Systems Applications from Multi-Dimensional Electrical Resistivity Structure

    Energy Technology Data Exchange (ETDEWEB)

    Wannamaker, Philip E. [Univ. of Utah, Salt Lake City, UT (United States)

    2016-03-26

    We have developed an algorithm for the inversion of magnetotelluric (MT) data to a 3D earth resistivity model based upon the finite element method. Hexahedral edge finite elements are implemented to accommodate discontinuities in the electric field across resistivity boundaries, and to accurately simulate topographic variations. All matrices are reduced and solved using direct solution modules which avoids ill-conditioning endemic to iterative solvers such as conjugate gradients, principally PARDISO for the finite element system and PLASMA for the parameter step estimate. Large model parameterizations can be handled by transforming the Gauss-Newton estimator to data-space form. Accuracy of the forward problem and jacobians has been checked by comparison to integral equations results and by limiting asymptotes. Inverse accuracy and performance has been verified against the public Dublin Secret Test Model 2 and the well-known Mount St Helens 3D MT data set. This algorithm we believe is the most capable yet for forming 3D images of earth resistivity structure and their implications for geothermal fluids and pathways.

  16. A Cross-Cultural Comparison of Singaporean and Taiwanese Eighth Graders' Science Learning Self-Efficacy from a Multi-Dimensional Perspective

    Science.gov (United States)

    Lin, Tzung-Jin; Tan, Aik Ling; Tsai, Chin-Chung

    2013-05-01

    Due to the scarcity of cross-cultural comparative studies in exploring students' self-efficacy in science learning, this study attempted to develop a multi-dimensional science learning self-efficacy (SLSE) instrument to measure 316 Singaporean and 303 Taiwanese eighth graders' SLSE and further to examine the differences between the two student groups. Moreover, within-culture comparisons were made in terms of gender. The results showed that, first, the SLSE instrument was valid and reliable for measuring the Singaporean and Taiwanese students' SLSE. Second, through a two-way multivariate analysis of variance analysis (nationality by gender), the main result indicated that the SLSE held by the Singaporean eighth graders was significantly higher than that of their Taiwanese counterparts in all dimensions, including 'conceptual understanding and higher-order cognitive skills', 'practical work (PW)', 'everyday application', and 'science communication'. In addition, the within-culture gender comparisons indicated that the male Singaporean students tended to possess higher SLSE than the female students did in all SLSE dimensions except for the 'PW' dimension. However, no gender differences were found in the Taiwanese sample. The findings unraveled in this study were interpreted from a socio-cultural perspective in terms of the curriculum differences, societal expectations of science education, and educational policies in Singapore and Taiwan.

  17. Multi-dimensional, fully-implicit, spectral method for the Vlasov-Maxwell equations with exact conservation laws in discrete form

    Science.gov (United States)

    Delzanno, G. L.

    2015-11-01

    A spectral method for the numerical solution of the multi-dimensional Vlasov-Maxwell equations is presented. The plasma distribution function is expanded in Fourier (for the spatial part) and Hermite (for the velocity part) basis functions, leading to a truncated system of ordinary differential equations for the expansion coefficients (moments) that is discretized with an implicit, second order accurate Crank-Nicolson time discretization. The discrete non-linear system is solved with a preconditioned Jacobian-Free Newton-Krylov method. It is shown analytically that the Fourier-Hermite method features exact conservation laws for total mass, momentum and energy in discrete form. Standard tests involving plasma waves and the whistler instability confirm the validity of the conservation laws numerically. The whistler instability test also shows that we can step over the fastest time scale in the system without incurring in numerical instabilities. Some preconditioning strategies are presented, showing that the number of linear iterations of the Krylov solver can be drastically reduced and a significant gain in performance can be obtained.

  18. Performance of Edmonton Frail Scale on frailty assessment: its association with multi-dimensional geriatric conditions assessed with specific screening tools.

    Science.gov (United States)

    Perna, Simone; Francis, Matthew D'Arcy; Bologna, Chiara; Moncaglieri, Francesca; Riva, Antonella; Morazzoni, Paolo; Allegrini, Pietro; Isu, Antonio; Vigo, Beatrice; Guerriero, Fabio; Rondanelli, Mariangela

    2017-01-04

    The aim of this study was to evaluate the performance of Edmonton Frail Scale (EFS) on frailty assessment in association with multi-dimensional conditions assessed with specific screening tools and to explore the prevalence of frailty by gender. We enrolled 366 hospitalised patients (women\\men: 251\\115), mean age 81.5 years. The EFS was given to the patients to evaluate their frailty. Then we collected data concerning cognitive status through Mini-Mental State Examination (MMSE), health status (evaluated with the number of diseases), functional independence (Barthel Index and Activities Daily Living; BI, ADL, IADL), use of drugs (counting of drugs taken every day), Mini Nutritional Assessment (MNA), Geriatric Depression Scale (GDS), Skeletal Muscle Index of sarcopenia (SMI), osteoporosis and functionality (Handgrip strength). According with the EFS, the 19.7% of subjects were classified as non frail, 66.4% as apparently vulnerable and 13.9% with severe frailty. The EFS scores were associated with cognition (MMSE: β = 0.980; p nutrition (MNA: β = -0.413; p performance (Handgrip: β = -0.114, p performance tool for stratifying the state of fragility in a group of institutionalized elderly. As matter of facts the EFS has been shown to be associated with several geriatric conditions such independence, drugs assumption, mood, mental, functional and nutritional status.

  19. AdS and stabilized extra dimensions in multi-dimensional gravitational models with nonlinear scalar curvature terms R-1 and R4

    International Nuclear Information System (INIS)

    Guenther, Uwe; Zhuk, Alexander; Bezerra, Valdir B; Romero, Carlos

    2005-01-01

    We study multi-dimensional gravitational models with scalar curvature nonlinearities of types R -1 and R 4 . It is assumed that the corresponding higher dimensional spacetime manifolds undergo a spontaneous compactification to manifolds with a warped product structure. Special attention has been paid to the stability of the extra-dimensional factor spaces. It is shown that for certain parameter regions the systems allow for a freezing stabilization of these spaces. In particular, we find for the R -1 model that configurations with stabilized extra dimensions do not provide a late-time acceleration (they are AdS), whereas the solution branch which allows for accelerated expansion (the dS branch) is incompatible with stabilized factor spaces. In the case of the R 4 model, we obtain that the stability region in parameter space depends on the total dimension D = dim(M) of the higher dimensional spacetime M. For D > 8 the stability region consists of a single (absolutely stable) sector which is shielded from a conformal singularity (and an antigravity sector beyond it) by a potential barrier of infinite height and width. This sector is smoothly connected with the stability region of a curvature-linear model. For D 4 model

  20. Examining the evolution towards turbulence through spatio-temporal analysis of multi-dimensional structures formed by instability growth along a shear layer

    Science.gov (United States)

    Merritt, Elizabeth; Doss, Forrest; Loomis, Eric; Flippo, Kirk; Devolder, Barbara; Welser-Sherrill, Leslie; Fincke, James; Kline, John

    2014-10-01

    The counter-propagating shear campaign is examining instability growth and its transition to turbulence relevant to mix in ICF capsules. Experimental platforms on both OMEGA and NIF use anti-symmetric flows about a shear interface to examine isolated Kelvin-Helmholtz instability growth. Measurements of interface (an Al or Ti tracer layer) dynamics are used to benchmark the LANL RAGE hydrocode with BHR turbulence model. The tracer layer does not expand uniformly, but breaks up into multi-dimensional structures that are initially quasi-2D due to the target geometry. We are developing techniques to analyze the multi-D structure growth along the tracer surface with a focus on characterizing the time-dependent structures' spectrum of scales in order to appraise a transition to turbulence in the system and potentially provide tighter constraints on initialization schemes for the BHR model. To this end, we use a wavelet based analysis to diagnose single-time radiographs of the tracer layer surface (w/low and amplified roughness for random noise seeding) with observed spatially non-repetitive features, in order to identify spatial and temporal trends in radiographs taken at different times across several experimental shots. This work conducted under the auspices of the U.S. Department of Energy by LANL under Contract DE-AC52-06NA25396.

  1. Enhanced hexose fermentation by Saccharomyces cerevisiae through integration of stoichiometric modeling and genetic screening.

    Science.gov (United States)

    Quarterman, Josh; Kim, Soo Rin; Kim, Pan-Jun; Jin, Yong-Su

    2015-01-20

    In order to determine beneficial gene deletions for ethanol production by the yeast Saccharomyces cerevisiae, we performed an in silico gene deletion experiment based on a genome-scale metabolic model. Genes coding for two oxidative phosphorylation reactions (cytochrome c oxidase and ubiquinol cytochrome c reductase) were identified by the model-based simulation as potential deletion targets for enhancing ethanol production and maintaining acceptable overall growth rate in oxygen-limited conditions. Since the two target enzymes are composed of multiple subunits, we conducted a genetic screening study to evaluate the in silico results and compare the effect of deleting various portions of the respiratory enzyme complexes. Over two-thirds of the knockout mutants identified by the in silico study did exhibit experimental behavior in qualitative agreement with model predictions, but the exceptions illustrate the limitation of using a purely stoichiometric model-based approach. Furthermore, there was a substantial quantitative variation in phenotype among the various respiration-deficient mutants that were screened in this study, and three genes encoding respiratory enzyme subunits were identified as the best knockout targets for improving hexose fermentation in microaerobic conditions. Specifically, deletion of either COX9 or QCR9 resulted in higher ethanol production rates than the parental strain by 37% and 27%, respectively, with slight growth disadvantages. Also, deletion of QCR6 led to improved ethanol production rate by 24% with no growth disadvantage. The beneficial effects of these gene deletions were consistently demonstrated in different strain backgrounds and with four common hexoses. The combination of stoichiometric modeling and genetic screening using a systematic knockout collection was useful for narrowing a large set of gene targets and identifying targets of interest. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Multi-dimensional perspectives of flood risk - using a participatory framework to develop new approaches to flood risk communication

    Science.gov (United States)

    Rollason, Edward; Bracken, Louise; Hardy, Richard; Large, Andy

    2017-04-01

    Flooding is a major hazard across Europe which, since, 1998 has caused over €52 million in damages and displaced over half a million people. Climate change is predicted to increase the risks posed by flooding in the future. The 2007 EU Flood Directive cemented the use of flood risk maps as a central tool in understanding and communicating flood risk. Following recent flooding in England, an urgent need to integrate people living at risk from flooding into flood management approaches, encouraging flood resilience and the up-take of resilient activities has been acknowledged. The effective communication of flood risk information plays a major role in allowing those at risk to make effective decisions about flood risk and increase their resilience, however, there are emerging concerns over the effectiveness of current approaches. The research presented explores current approaches to flood risk communication in England and the effectiveness of these methods in encouraging resilient actions before and during flooding events. The research also investigates how flood risk communications could be undertaken more effectively, using a novel participatory framework to integrate the perspectives of those living at risk. The research uses co-production between local communities and researchers in the environmental sciences, using a participatory framework to bring together local knowledge of flood risk and flood communications. Using a local competency group, the research explores what those living at risk from flooding want from flood communications in order to develop new approaches to help those at risk understand and respond to floods. Suggestions for practice are refined by the communities to co-produce recommendations. The research finds that current approaches to real-time flood risk communication fail to forecast the significance of predicted floods, whilst flood maps lack detailed information about how floods occur, or use scientific terminology which people at risk

  3. An 'integrative neuroscience' perspective on ADHD: linking cognition, emotion, brain and genetic measures with implications for clinical support.

    Science.gov (United States)

    Williams, Leanne M; Tsang, Tracey W; Clarke, Simon; Kohn, Michael

    2010-10-01

    There remains a translational gap between research findings and their implementation in clinical practice that applies to attention-deficit/hyperactivity disorder (ADHD), as well as to other major disorders of brain health in childhood, adolescence and adulthood. Research studies have identified potential 'markers' to support diagnostic, functional assessment and treatment decisions, but there is little consensus about these markers. Of these potential markers, cognitive measures of thinking functions, such as sustaining attention and associated electrical brain activity, show promise in complementing the clinical management process. Emerging evidence highlights the relevance of emotional, as well as thinking, functions to ADHD. Here, we outline an integrative neuroscience framework for ADHD that offers one means to bring together cognitive measures of thinking functions with measures of emotion, and their brain and genetic correlates. Understanding these measures and the relationships between them is a first step towards the development of tools that will help to assess the heterogeneity of ADHD, and aid in tailoring treatment choices.

  4. al mena: a comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and North African populations.

    Science.gov (United States)

    Koshy, Remya; Ranawat, Anop; Scaria, Vinod

    2017-10-01

    Middle East and North Africa (MENA) encompass very unique populations, with a rich history and encompasses characteristic ethnic, linguistic and genetic diversity. The genetic diversity of MENA region has been largely unknown. The recent availability of whole-exome and whole-genome sequences from the region has made it possible to collect population-specific allele frequencies. The integration of data sets from this region would provide insights into the landscape of genetic variants in this region. We integrated genetic variants from multiple data sets systematically, available from this region to create a compendium of over 26 million genetic variations. The variants were systematically annotated and their allele frequencies in the data sets were computed and available as a web interface which enables quick query. As a proof of principle for application of the compendium for genetic epidemiology, we analyzed the allele frequencies for variants in transglutaminase 1 (TGM1) gene, associated with autosomal recessive lamellar ichthyosis. Our analysis revealed that the carrier frequency of selected variants differed widely with significant interethnic differences. To the best of our knowledge, al mena is the first and most comprehensive repertoire of genetic variations from the Arab, Middle Eastern and North African region. We hope al mena would accelerate Precision Medicine in the region.

  5. Quantum integrals from coalgebra structure

    International Nuclear Information System (INIS)

    Post, S; Riglioni, D

    2015-01-01

    Quantum versions of the hydrogen atom and the harmonic oscillator are studied on non Euclidean spaces of dimension N. 2N−1 integrals, of arbitrary order, are constructed via a multi-dimensional version of the factorization method, thus confirming the conjecture of Riglioni (2013 J. Phys. A: Math. Theor. 46 265207). The systems are extended via coalgebra extension of sl(2) representations, although not all integrals are expressible in these generators. As an example, dimensional reduction is applied to four-dimensional systems to obtain extension and new proofs of the superintegrability of known families of Hamiltonians. (paper)

  6. Assuring the safety of genetically modified (GM) foods: the importance of an holistic, integrative approach.

    Science.gov (United States)

    Cockburn, Andrew

    2002-09-11

    Genes change continuously by natural mutation and recombination enabling man to select and breed crops having the most desirable traits such as yield or flavour. Genetic modification (GM) is a recent development which allows specific genes to be identified, isolated, copied and inserted into other plants with a high level of specificity. The food safety considerations for GM crops are basically the same as those arising from conventionally bred crops, very few of which have been subject to any testing yet are generally regarded as being safe to eat. In contrast a rigorous safety testing paradigm has been developed for GM crops, which utilises a systematic, stepwise and holistic approach. The resultant science based process, focuses on a classical evaluation of the toxic potential of the introduced novel trait and the wholesomeness of the transformed crop. In addition, detailed consideration is given to the history and safe use of the parent crop as well as that of the gene donor. The overall safety evaluation is conducted under the concept known as substantial equivalence which is enshrined in all international crop biotechnology guidelines. This provides the framework for a comparative approach to identify the similarities and differences between the GM product and its comparator which has a known history of safe use. By building a detailed profile on each step in the transformation process, from parent to new crop, and by thoroughly evaluating the significance from a safety perspective, of any differences that may be detected, a very comprehensive matrix of information is constructed which enables the conclusion as to whether the GM crop, derived food or feed is as safe as its traditional counterpart. Using this approach in the evaluation of more than 50 GM crops which have been approved worldwide, the conclusion has been that foods and feeds derived from genetically modified crops are as safe and nutritious as those derived from traditional crops. The lack of

  7. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  8. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.).

    Science.gov (United States)

    Cloutier, Sylvie; Ragupathy, Raja; Miranda, Evelyn; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Ward, Kerry; Rowland, Gordon; Duguid, Scott; Banik, Mitali

    2012-12-01

    Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.

  9. Integrative Genetic and Epigenetic Analysis Uncovers Regulatory Mechanisms of Autoimmune Disease.

    Science.gov (United States)

    Shooshtari, Parisa; Huang, Hailiang; Cotsapas, Chris

    2017-07-06

    Genome-wide association studies in autoimmune and inflammatory diseases (AID) have uncovered hundreds of loci mediating risk. These associations are preferentially located in non-coding DNA regions and in particular in tissue-specific DNase I hypersensitivity sites (DHSs). While these analyses clearly demonstrate the overall enrichment of disease risk alleles on gene regulatory regions, they are not designed to identify individual regulatory regions mediating risk or the genes under their control, and thus uncover the specific molecular events driving disease risk. To do so we have departed from standard practice by identifying regulatory regions which replicate across samples and connect them to the genes they control through robust re-analysis of public data. We find significant evidence of regulatory potential in 78/301 (26%) risk loci across nine autoimmune and inflammatory diseases, and we find that individual genes are targeted by these effects in 53/78 (68%) of these. Thus, we are able to generate testable mechanistic hypotheses of the molecular changes that drive disease risk. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  10. Placebo analgesia and reward processing: integrating genetics, personality, and intrinsic brain activity.

    Science.gov (United States)

    Yu, Rongjun; Gollub, Randy L; Vangel, Mark; Kaptchuk, Ted; Smoller, Jordan W; Kong, Jian

    2014-09-01

    Our expectations about an event can strongly shape our subjective evaluation and actual experience of events. This ability, applied to the modulation of pain, has the potential to affect therapeutic analgesia substantially and constitutes a foundation for non-pharmacological pain relief. A typical example of such modulation is the placebo effect. Studies indicate that placebo may be regarded as a reward, and brain activity in the reward system is involved in this modulation process. In the present study, we combined resting-state functional magnetic resonance imaging (rs-fMRI) measures, genotype at a functional COMT polymorphism (Val158Met), and personality measures in a model to predict the magnitude of placebo conditioning effect indicated by subjective pain rating reduction to calibrated noxious stimuli. We found that the regional homogeneity (ReHo), an index of local neural coherence, in the ventral striatum, was significantly associated with conditioning effects on pain rating changes. We also found that the number of Met alleles at the COMT polymorphism was linearly correlated to the suppression of pain. In a fitted regression model, we found the ReHo in the ventral striatum, COMT genotype, and Openness scores accounted for 59% of the variance in the change in pain ratings. The model was further tested using a separate data set from the same study. Our findings demonstrate the potential of combining resting-state connectivity, genetic information, and personality to predict placebo effect. Copyright © 2014 Wiley Periodicals, Inc.

  11. Design of a novel integration-deficient lentivector technology that incorporates genetic and posttranslational elements to target human dendritic cells.

    Science.gov (United States)

    Tareen, Semih U; Kelley-Clarke, Brenna; Nicolai, Christopher J; Cassiano, Linda A; Nelson, Lisa T; Slough, Megan M; Vin, Chintan D; Odegard, Jared M; Sloan, Derek D; Van Hoeven, Neal; Allen, James M; Dubensky, Thomas W; Robbins, Scott H

    2014-03-01

    As sentinels of the immune system, dendritic cells (DCs) play an essential role in regulating cellular immune responses. One of the main challenges of developing DC-targeted therapies includes the delivery of antigen to DCs in order to promote the activation of antigen-specific effector CD8 T cells. With the goal of creating antigen-directed immunotherapeutics that can be safely administered directly to patients, Immune Design has developed a platform of novel integration-deficient lentiviral vectors that target and deliver antigen-encoding nucleic acids to human DCs. This platform, termed ID-VP02, utilizes a novel genetic variant of a Sindbis virus envelope glycoprotein with posttranslational carbohydrate modifications in combination with Vpx, a SIVmac viral accessory protein, to achieve efficient targeting and transduction of human DCs. In addition, ID-VP02 incorporates safety features in its design that include two redundant mechanisms to render ID-VP02 integration-deficient. Here, we describe the characteristics that allow ID-VP02 to specifically transduce human DCs, and the advances that ID-VP02 brings to conventional third-generation lentiviral vector design as well as demonstrate upstream production yields that will enable manufacturing feasibility studies to be conducted.

  12. Functional properties and synaptic integration of genetically labelled dopaminergic neurons in intrastriatal grafts

    DEFF Research Database (Denmark)

    Sørensen, Andreas Toft; Thompson, Lachlan; Kirik, Deniz

    2005-01-01

    in the dopamine-depleted striatum than of those in the intact striatum. Our findings define specific electrophysiological characteristics of transplanted fetal dopaminergic neurons, and we provide the first direct evidence of functional synaptic integration of these neurons into host neural circuitries......., the electrophysiological properties grafted cells need to have in order to induce substantial functional recovery are poorly defined. It has not been possible to prospectively identify and record from dopaminergic neurons in fetal transplants. Here we used transgenic mice expressing green fluorescent protein under control...... of the rat tyrosine hydroxylase promoter for whole-cell patch-clamp recordings of endogenous and grafted dopaminergic neurons. We transplanted ventral mesencephalic tissue from E12.5 transgenic mice into striatum of neonatal rats with or without lesions of the nigrostriatal dopamine system. The transplanted...

  13. A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus

    DEFF Research Database (Denmark)

    Wang, Ying; Duan, Zhenhong; Zhu, Haojun

    2007-01-01

    An integrative non-conjugative extrachromosomal genetic element, denoted as pSSVi, has been isolated from a Sulfolobus solfataricus P2 strain and was characterized. This genetic element is a double-stranded DNA of 5740 bp in size and contains eight open reading frames (ORFs). It resembles members....... Interestingly, pSSVi encodes an SSV-type integrase which probably catalyzes the integration of its genome into a specific site (a tRNA(Arg) gene) in the S. solfataricus P2 genome. Like pSSVx, pSSVi can be packaged into a spindle-like viral particle and spread with the help of SSV1 or SSV2. In addition, both SSV......1 and SSV2 appeared to replicate more efficiently in the presence of pSSVi. Given the versatile genetic abilities, pSSVi appears to be well suited for a role in horizontal gene transfer....

  14. Sensitivity improvement for correlations involving arginine side-chain Nε/Hε resonances in multi-dimensional NMR experiments using broadband 15N 180o pulses

    International Nuclear Information System (INIS)

    Iwahara, Junji; Clore, G. Marius

    2006-01-01

    Due to practical limitations in available 15 N rf field strength, imperfections in 15 N 180 o pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amide groups, cross-peaks arising from the Arg guanidino 15 Nε (∼85 ppm) are highly attenuated by the presence of multiple INEPT transfer steps. To improve the sensitivity for correlations involving Arg Nε-Hε groups, we have incorporated 15 N broadband 180 deg. pulses into 3D 15 N-separated NOE-HSQC and HNCACB experiments. Two 15 N-WURST pulses incorporated at the INEPT transfer steps of the 3D 15 N-separated NOE-HSQC pulse sequence resulted in a ∼1.5-fold increase in sensitivity for the Arg Nε-Hε signals at 800 MHz. For the 3D HNCACB experiment, five 15 N Abramovich-Vega pulses were incorporated for broadband inversion and refocusing, and the sensitivity of Arg 1 Hε- 15 Nε- 13 Cγ/ 13 Cδ correlation peaks was enhanced by a factor of ∼1.7 at 500 MHz. These experiments eliminate the necessity for additional experiments to assign Arg 1 Hε and 15 Nε resonances. In addition, the increased sensitivity afforded for the detection of NOE cross-peaks involving correlations with the 15 Nε/ 1 Hε of Arg in 3D 15 N-separated NOE experiments should prove to be very useful for structural analysis of interactions involving Arg side-chains

  15. Generalized multi-dimensional adaptive filtering for conventional and spiral single-slice, multi-slice, and cone-beam CT

    International Nuclear Information System (INIS)

    Kachelriess, Marc; Watzke, Oliver; Kalender, Willi A.

    2001-01-01

    In modern computed tomography (CT) there is a strong desire to reduce patient dose and/or to improve image quality by increasing spatial resolution and decreasing image noise. These are conflicting demands since increasing resolution at a constant noise level or decreasing noise at a constant resolution level implies a higher demand on x-ray power and an increase of patient dose. X-ray tube power is limited due to technical reasons. We therefore developed a generalized multi-dimensional adaptive filtering approach that applies nonlinear filters in up to three dimensions in the raw data domain. This new method differs from approaches in the literature since our nonlinear filters are applied not only in the detector row direction but also in the view and in the z-direction. This true three-dimensional filtering improves the quantum statistics of a measured projection value proportional to the third power of the filter size. Resolution tradeoffs are shared among these three dimensions and thus are considerably smaller as compared to one-dimensional smoothing approaches. Patient data of spiral and sequential single- and multi-slice CT scans as well as simulated spiral cone-beam data were processed to evaluate these new approaches. Image quality was assessed by evaluation of difference images, by measuring the image noise and the noise reduction, and by calculating the image resolution using point spread functions. The use of generalized adaptive filters helps to reduce image noise or, alternatively, patient dose. Image noise structures, typically along the direction of the highest attenuation, are effectively reduced. Noise reduction values of typically 30%-60% can be achieved in noncylindrical body regions like the shoulder. The loss in image resolution remains below 5% for all cases. In addition, the new method has a great potential to reduce metal artifacts, e.g., in the hip region

  16. AdS and stabilized extra dimensions in multi-dimensional gravitational models with nonlinear scalar curvature terms R{sup -1} and R{sup 4}

    Energy Technology Data Exchange (ETDEWEB)

    Guenther, Uwe [Gravitationsprojekt, Mathematische Physik I, Institut fuer Mathematik, Universitaet Potsdam, Am Neuen Palais 10, PF 601553, D-14415 Potsdam (Germany); Zhuk, Alexander [Department of Physics, University of Odessa, 2 Dvoryanskaya St, Odessa 65100 (Ukraine); Bezerra, Valdir B [Departamento de Fisica, Universidade Federal de ParaIba C Postal 5008, Joao Pessoa, PB, 58059-970 (Brazil); Romero, Carlos [Departamento de Fisica, Universidade Federal de ParaIba C Postal 5008, Joao Pessoa, PB, 58059-970 (Brazil)

    2005-08-21

    We study multi-dimensional gravitational models with scalar curvature nonlinearities of types R{sup -1} and R{sup 4}. It is assumed that the corresponding higher dimensional spacetime manifolds undergo a spontaneous compactification to manifolds with a warped product structure. Special attention has been paid to the stability of the extra-dimensional factor spaces. It is shown that for certain parameter regions the systems allow for a freezing stabilization of these spaces. In particular, we find for the R{sup -1} model that configurations with stabilized extra dimensions do not provide a late-time acceleration (they are AdS), whereas the solution branch which allows for accelerated expansion (the dS branch) is incompatible with stabilized factor spaces. In the case of the R{sup 4} model, we obtain that the stability region in parameter space depends on the total dimension D = dim(M) of the higher dimensional spacetime M. For D > 8 the stability region consists of a single (absolutely stable) sector which is shielded from a conformal singularity (and an antigravity sector beyond it) by a potential barrier of infinite height and width. This sector is smoothly connected with the stability region of a curvature-linear model. For D < 8 an additional (metastable) sector exists which is separated from the conformal singularity by a potential barrier of finite height and width so that systems in this sector are prone to collapse into the conformal singularity. This second sector is not smoothly connected with the first (absolutely stable) one. Several limiting cases and the possibility of inflation are discussed for the R{sup 4} model.

  17. A NEW MULTI-DIMENSIONAL GENERAL RELATIVISTIC NEUTRINO HYDRODYNAMICS CODE FOR CORE-COLLAPSE SUPERNOVAE. II. RELATIVISTIC EXPLOSION MODELS OF CORE-COLLAPSE SUPERNOVAE

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Bernhard; Janka, Hans-Thomas; Marek, Andreas, E-mail: bjmuellr@mpa-garching.mpg.de, E-mail: thj@mpa-garching.mpg.de [Max-Planck-Institut fuer Astrophysik, Karl-Schwarzschild-Str. 1, D-85748 Garching (Germany)

    2012-09-01

    We present the first two-dimensional general relativistic (GR) simulations of stellar core collapse and explosion with the COCONUT hydrodynamics code in combination with the VERTEX solver for energy-dependent, three-flavor neutrino transport, using the extended conformal flatness condition for approximating the space-time metric and a ray-by-ray-plus ansatz to tackle the multi-dimensionality of the transport. For both of the investigated 11.2 and 15 M{sub Sun} progenitors we obtain successful, though seemingly marginal, neutrino-driven supernova explosions. This outcome and the time evolution of the models basically agree with results previously obtained with the PROMETHEUS hydro solver including an approximative treatment of relativistic effects by a modified Newtonian potential. However, GR models exhibit subtle differences in the neutrinospheric conditions compared with Newtonian and pseudo-Newtonian simulations. These differences lead to significantly higher luminosities and mean energies of the radiated electron neutrinos and antineutrinos and therefore to larger energy-deposition rates and heating efficiencies in the gain layer with favorable consequences for strong nonradial mass motions and ultimately for an explosion. Moreover, energy transfer to the stellar medium around the neutrinospheres through nucleon recoil in scattering reactions of heavy-lepton neutrinos also enhances the mentioned effects. Together with previous pseudo-Newtonian models, the presented relativistic calculations suggest that the treatment of gravity and energy-exchanging neutrino interactions can make differences of even 50%-100% in some quantities and is likely to contribute to a finally successful explosion mechanism on no minor level than hydrodynamical differences between different dimensions.

  18. Preliminary H{sub 2} Combustion Analysis in the Containment of APR1400 for SBLOCA Accident using a Multi-Dimensional H{sub 2} Analysis System

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Hyung Seok; Kim, Jongtae; Kim, Sang-Baik; Hong, Seong-Wan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-10-15

    The COM3D analyze an overpressure buildup resulting from a propagation of hydrogen flame along the structure and wall in the containment using the hydrogen distribution result calculated by the GASFLOW. The MAAP evaluates a hydrogen source during a severe accident and transfer it to the GASFLOW. We performed a hydrogen combustion analysis using the multidimensional hydrogen analysis system for a station blackout (SBO) accident under the assumption of 100% metal-water reaction in the reactor vessel. The COM3D results showed that the pressure buildup was about 250 kPa because the flame speed was not increased above 300 m/s and the pressure wave passed through the open spaces in the large containment. To increase the reliability of the COM3D calculation, it is necessary to perform the hydrogen combustion analysis for another accident such as a small break loss of coolant (SBLOCA). KAERI performed a hydrogen combustion analysis for a SBLOCA accident using the multi-dimensional hydrogen analysis system under the assumption of 100% metal-water reaction in the reactor vessel. From the COM3D results, we can know that the pressure buildup was approximately 310 kPa because the flame speed was not increased above 100 m/s owing to the high steam concentration and low oxygen concentration in the hydrogen distributed region of the containment. The predicted maximum overpressure in the SBLOCA accident is similar to that of the COM3D results for the SBO accident. Thus, we found that the maximum overpressure due to the hydrogen combustion in the containment may depend on the amount of hydrogen mass released from the reactor vessel.

  19. IMPROVEMENT OF ACCURACY OF RADIATIVE HEAT TRANSFER DIFFERENTIAL APPROXIMATION METHOD FOR MULTI DIMENSIONAL SYSTEMS BY MEANS OF AUTO-ADAPTABLE BOUNDARY CONDITIONS

    Directory of Open Access Journals (Sweden)

    K. V. Dobrego

    2015-01-01

    Full Text Available Differential approximation is derived from radiation transfer equation by averaging over the solid angle. It is one of the more effective methods for engineering calculations of radia- tive heat transfer in complex three-dimensional thermal power systems with selective and scattering media. The new method for improvement of accuracy of the differential approximation based on using of auto-adaptable boundary conditions is introduced in the paper. The  efficiency  of  the  named  method  is  proved  for  the  test  2D-systems.  Self-consistent auto-adaptable boundary conditions taking into consideration the nonorthogonal component of the incident to the boundary radiation flux are formulated. It is demonstrated that taking in- to consideration of the non- orthogonal incident flux in multi-dimensional systems, such as furnaces, boilers, combustion chambers improves the accuracy of the radiant flux simulations and to more extend in the zones adjacent to the edges of the chamber.Test simulations utilizing the differential approximation method with traditional boundary conditions, new self-consistent boundary conditions and “precise” discrete ordinates method were performed. The mean square errors of the resulting radiative fluxes calculated along the boundary of rectangular and triangular test areas were decreased 1.5–2 times by using auto- adaptable boundary conditions. Radiation flux gaps in the corner points of non-symmetric sys- tems are revealed by using auto-adaptable boundary conditions which can not be obtained by using the conventional boundary conditions.

  20. Distribution and Genetic Characteristics of SXT/R391 Integrative Conjugative Elements in Shewanella spp. From China

    Directory of Open Access Journals (Sweden)

    Yujie Fang

    2018-05-01

    Full Text Available The genus Shewanella consists of facultatively anaerobic Gram-negative bacteria, which are regarded as potential agents of food contamination and opportunistic human pathogens. Information about the distribution and genetic characteristics of SXT/R391 integrative conjugative elements (ICEs in Shewanella species is limited. Here, 91 Shewanella strains collected from diverse samples in China were studied for the presence of SXT/R391 ICEs. Three positive strains, classified as Shewanella upenei, were obtained from patients and water from a local mill. In light of their close clonal relationships and high sequence similarity, a representative ICE was selected and designated ICESupCHN110003. The BLASTn searches against GenBank showed that ICEVchBan5 was most closely related to ICESupCHN110003, with the coverage of 76% and identity of 99%. The phylogenetic tree of concatenated core genes demonstrated that ICESupCHN110003 formed a distinct branch outside the cluster comprising ICEValA056-1, ICEPmiCHN2410, and ICEPmiChn1. Comparison of the genetic structures revealed that ICESupCHN110003 encoded uncommon genes in hotspots, such as specific type III restriction-modification system, conferring adaptive functions to the host. Based on the low coverage in the sequence analysis, independent clade in the phylogenetic tree, and unique inserted fragments in hotspots, ICESupCHN110003 represented a novel SXT/R391 element, which widened the list of ICEs. Furthermore, the antibiotic resistance genes floR, strA, strB, and sul2 in ICESupCHN110003 and resistance to multiple drugs of the positive isolates were detected. A cross-species transfer capability of the SXT/R391 ICEs was also discovered. In summary, it is necessary to reinforce continuous surveillance of SXT/R391 ICEs in the genus Shewanella.

  1. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses.

    Science.gov (United States)

    Luo, Jie; Xu, Pei; Cao, Peijian; Wan, Hongjian; Lv, Xiaonan; Xu, Shengchun; Wang, Gangjun; Cook, Melloni N; Jones, Byron C; Lu, Lu; Wang, Xusheng

    2018-01-01

    Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (RSS) and NOE, and further amplification in RSE (pattern 3), and up-regulation in RSS but reduction in both NOE and RSE (pattern 4). We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs) to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA) signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

  2. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses

    Directory of Open Access Journals (Sweden)

    Jie Luo

    2018-04-01

    Full Text Available Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1, down-regulation in NOE but rescue in RSE (pattern 2, up-regulation in both restraint stress followed by a saline injection (RSS and NOE, and further amplification in RSE (pattern 3, and up-regulation in RSS but reduction in both NOE and RSE (pattern 4. We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

  3. Sound is Multi-Dimensional

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2006-01-01

    First part of this work examines the concept of musical parameter theory and discusses its methodical use. Second part is an annotated catalogue of 33 different students' compositions, presented in their totality with English translations, created between 1985 and 2006 as part of the subject...... Intuitive Music at Music Therapy, AAU. 20 of these have sound files as well. The work thus serves as an anthology of this form of composition. All the compositions are systematically presented according to parameters: pitch, duration, dynamics, timbre, density, pulse-no pulse, tempo, stylistic...

  4. Integration

    DEFF Research Database (Denmark)

    Emerek, Ruth

    2004-01-01

    Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration......Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration...

  5. Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis.

    Science.gov (United States)

    Shchetynsky, Klementy; Diaz-Gallo, Lina-Marcella; Folkersen, Lasse; Hensvold, Aase Haj; Catrina, Anca Irinel; Berg, Louise; Klareskog, Lars; Padyukov, Leonid

    2017-02-02

    Here we integrate verified signals from previous genetic association studies with gene expression and pathway analysis for discovery of new candidate genes and signaling networks, relevant for rheumatoid arthritis (RA). RNA-sequencing-(RNA-seq)-based expression analysis of 377 genes from previously verified RA-associated loci was performed in blood cells from 5 newly diagnosed, non-treated patients with RA, 7 patients with treated RA and 12 healthy controls. Differentially expressed genes sharing a similar expression pattern in treated and untreated RA sub-groups were selected for pathway analysis. A set of "connector" genes derived from pathway analysis was tested for differential expression in the initial discovery cohort and validated in blood cells from 73 patients with RA and in 35 healthy controls. There were 11 qualifying genes selected for pathway analysis and these were grouped into two evidence-based functional networks, containing 29 and 27 additional connector molecules. The expression of genes, corresponding to connector molecules was then tested in the initial RNA-seq data. Differences in the expression of ERBB2, TP53 and THOP1 were similar in both treated and non-treated patients with RA and an additional nine genes were differentially expressed in at least one group of patients compared to healthy controls. The ERBB2, TP53. THOP1 expression profile was successfully replicated in RNA-seq data from peripheral blood mononuclear cells from healthy controls and non-treated patients with RA, in an independent collection of samples. Integration of RNA-seq data with findings from association studies, and consequent pathway analysis implicate new candidate genes, ERBB2, TP53 and THOP1 in the pathogenesis of RA.

  6. Exact series expansions, recurrence relations, properties and integrals of the generalized exponential integral functions

    International Nuclear Information System (INIS)

    Altac, Zekeriya

    2007-01-01

    Generalized exponential integral functions (GEIF) are encountered in multi-dimensional thermal radiative transfer problems in the integral equation kernels. Several series expansions for the first-order generalized exponential integral function, along with a series expansion for the general nth order GEIF, are derived. The convergence issues of these series expansions are investigated numerically as well as theoretically, and a recurrence relation which does not require derivatives of the GEIF is developed. The exact series expansions of the two dimensional cylindrical and/or two-dimensional planar integral kernels as well as their spatial moments have been explicitly derived and compared with numerical values

  7. An integrated portfolio optimisation procedure based on data envelopment analysis, artificial bee colony algorithm and genetic programming

    Science.gov (United States)

    Hsu, Chih-Ming

    2014-12-01

    Portfolio optimisation is an important issue in the field of investment/financial decision-making and has received considerable attention from both researchers and practitioners. However, besides portfolio optimisation, a complete investment procedure should also include the selection of profitable investment targets and determine the optimal timing for buying/selling the investment targets. In this study, an integrated procedure using data envelopment analysis (DEA), artificial bee colony (ABC) and genetic programming (GP) is proposed to resolve a portfolio optimisation problem. The proposed procedure is evaluated through a case study on investing in stocks in the semiconductor sub-section of the Taiwan stock market for 4 years. The potential average 6-month return on investment of 9.31% from 1 November 2007 to 31 October 2011 indicates that the proposed procedure can be considered a feasible and effective tool for making outstanding investment plans, and thus making profits in the Taiwan stock market. Moreover, it is a strategy that can help investors to make profits even when the overall stock market suffers a loss.

  8. A Novel Multiscale Ensemble Carbon Price Prediction Model Integrating Empirical Mode Decomposition, Genetic Algorithm and Artificial Neural Network

    Directory of Open Access Journals (Sweden)

    Bangzhu Zhu

    2012-02-01

    Full Text Available Due to the movement and complexity of the carbon market, traditional monoscale forecasting approaches often fail to capture its nonstationary and nonlinear properties and accurately describe its moving tendencies. In this study, a multiscale ensemble forecasting model integrating empirical mode decomposition (EMD, genetic algorithm (GA and artificial neural network (ANN is proposed to forecast carbon price. Firstly, the proposed model uses EMD to decompose carbon price data into several intrinsic mode functions (IMFs and one residue. Then, the IMFs and residue are composed into a high frequency component, a low frequency component and a trend component which have similar frequency characteristics, simple components and strong regularity using the fine-to-coarse reconstruction algorithm. Finally, those three components are predicted using an ANN trained by GA, i.e., a GAANN model, and the final forecasting results can be obtained by the sum of these three forecasting results. For verification and testing, two main carbon future prices with different maturity in the European Climate Exchange (ECX are used to test the effectiveness of the proposed multiscale ensemble forecasting model. Empirical results obtained demonstrate that the proposed multiscale ensemble forecasting model can outperform the single random walk (RW, ARIMA, ANN and GAANN models without EMD preprocessing and the ensemble ARIMA model with EMD preprocessing.

  9. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.

    Science.gov (United States)

    Bajaj, Deepak; Saxena, Maneesha S; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-03-01

    Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  10. [Integrity].

    Science.gov (United States)

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  11. Horizontal integration of OMIM across the medical school preclinical curriculum for early reinforcement of clinical genetics principles.

    Science.gov (United States)

    Diehl, Adam C; Reader, Lauren; Hamosh, Ada; Bodurtha, Joann N

    2015-02-01

    With the relentless expansion of genetics into every field of medicine, stronger preclinical and clinical medical student education in genetics is needed. The explosion of genetic information cannot be addressed by simply adding content hours. We proposed that students be provided a tool to access accurate clinical information on genetic conditions and, through this tool, build life-long learning habits to carry them through their medical careers. Surveys conducted at the Johns Hopkins University School of Medicine revealed that medical students in all years lacked confidence when approaching genetic conditions and lacked a reliable resource for accurate genetic information. In response, the school created a horizontal thread that stretches across the first-year curriculum and is devoted to teaching students how to use Online Mendelian Inheritance in Man (OMIM) (http://omim.org) and the databases to which it links as a starting point for approaching genetic conditions. The thread improved the first-year students' confidence in clinical genetics concepts and encouraged use of OMIM as a primary source for genetic information. Most students showed confidence in OMIM as a learning tool and wanted to see the thread repeated in subsequent years. Incorporating OMIM into the preclinical curriculum improved students' confidence in clinical genetics concepts.

  12. Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data

    OpenAIRE

    Pinto, M. Alice; Henriques, Dora; Chavez-Galarza, Julio; Kryger, Per; Garnery, Lionel; Zee, Romée van der; Dahle, Bjørn; Soland-Reckeweg, Gabriele; De la Rúa, Pilar; Dall’ Olio, Raffaele; Carreck, Norman L.; Johnston, J. Spencer

    2014-01-01

    The recognition that the Dark European honey bee, Apis mellifera mellifera, is increasingly threatened in its native range has led to the establishment of conservation programmes and protected areas throughout western Europe. Previous molecular surveys showed that, despite management strategies to preserve the genetic integrity of A. m. mellifera, protected populations had a measurable component of their gene pool derived from commercial C-lineage honey bees. Here we used both sequence data f...

  13. Integration of genetic and clinical risk factors improves prognostication in relapsed childhood B-cell precursor acute lymphoblastic leukemia

    NARCIS (Netherlands)

    Irving, J.A.; Enshaei, A.; Parker, C.A.; Sutton, R.; Kuiper, R.P.; Erhorn, A.; Minto, L.; Venn, N.C.; Law, T.; Yu, J.; Schwab, C.; Davies, R.; Matheson, E.; Davies, A.; Sonneveld, E.; Boer, M.L. Den; Love, S.B.; Harrison, C.J.; Hoogerbrugge, P.M.; Revesz, T.; Saha, V.; Moorman, A.V.

    2016-01-01

    Somatic genetic abnormalities are initiators and drivers of disease and have proven clinical utility at initial diagnosis. However, the genetic landscape and its clinical utility at relapse are less well understood and have not been studied comprehensively. We analyzed cytogenetic data from 427

  14. Integration of genetic and clinical risk factors improves prognostication in relapsed childhood B-cell precursor acute lymphoblastic leukemia

    NARCIS (Netherlands)

    J. Irving (Julie); A. Enshaei; Parker, C.A. (Catriona A.); R. Sutton; R. Kuiper (Ruud); Erhorn, A. (Amy); L. Minto (L.); N. Venn; T. Law (T.); Yu, J. (Jiangyan); C. Schwab (Claire); Davies, R. (Rosanna); Matheson, E. (Elizabeth); Davies, A. (Alysia); E. Sonneveld (Edwin); M.L. den Boer (Monique); Love, S.B. (Sharon B.); C.J. Harrison (Christine); P.M. Hoogerbrugge (Peter); T. Revesz (Tamas); V. Saha (Vaskar); A.V. Moorman (Anthony)

    2016-01-01

    textabstractSomatic genetic abnormalities are initiators and drivers of disease and have proven clinical utility at initial diagnosis. However, the genetic landscape and its clinical utility at relapse are less well understood and have not been studied comprehensively. We analyzed cytogenetic data

  15. Characterization of dissolved organic matter in a coral reef ecosystem subjected to anthropogenic pressures (La Réunion Island, Indian Ocean) using multi-dimensional fluorescence spectroscopy.

    Science.gov (United States)

    Tedetti, Marc; Cuet, Pascale; Guigue, Catherine; Goutx, Madeleine

    2011-05-01

    highly impacted by sewage effluents, numerous in this coastal area of La Réunion Island. We conclude that multi-dimensional fluorescence spectroscopy (EEM) coupled to the determination of HIX and BIX is a good tool for assessing the origin and distribution of DOM in the coral reef ecosystems submitted to anthropogenic impacts. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. Integrative Analysis of Genetic, Genomic, and Phenotypic Data for Ethanol Behaviors: A Network-Based Pipeline for Identifying Mechanisms and Potential Drug Targets.

    Science.gov (United States)

    Bogenpohl, James W; Mignogna, Kristin M; Smith, Maren L; Miles, Michael F

    2017-01-01

    Complex behavioral traits, such as alcohol abuse, are caused by an interplay of genetic and environmental factors, producing deleterious functional adaptations in the central nervous system. The long-term behavioral consequences of such changes are of substantial cost to both the individual and society. Substantial progress has been made in the last two decades in understanding elements of brain mechanisms underlying responses to ethanol in animal models and risk factors for alcohol use disorder (AUD) in humans. However, treatments for AUD remain largely ineffective and few medications for this disease state have been licensed. Genome-wide genetic polymorphism analysis (GWAS) in humans, behavioral genetic studies in animal models and brain gene expression studies produced by microarrays or RNA-seq have the potential to produce nonbiased and novel insight into the underlying neurobiology of AUD. However, the complexity of such information, both statistical and informational, has slowed progress toward identifying new targets for intervention in AUD. This chapter describes one approach for integrating behavioral, genetic, and genomic information across animal model and human studies. The goal of this approach is to identify networks of genes functioning in the brain that are most relevant to the underlying mechanisms of a complex disease such as AUD. We illustrate an example of how genomic studies in animal models can be used to produce robust gene networks that have functional implications, and to integrate such animal model genomic data with human genetic studies such as GWAS for AUD. We describe several useful analysis tools for such studies: ComBAT, WGCNA, and EW_dmGWAS. The end result of this analysis is a ranking of gene networks and identification of their cognate hub genes, which might provide eventual targets for future therapeutic development. Furthermore, this combined approach may also improve our understanding of basic mechanisms underlying gene x

  17. INTEGRATING GENETIC AND STRUCTURAL DATA ON HUMAN PROTEIN KINOME IN NETWORK-BASED MODELING OF KINASE SENSITIVITIES AND RESISTANCE TO TARGETED AND PERSONALIZED ANTICANCER DRUGS.

    Science.gov (United States)

    Verkhivker, Gennady M

    2016-01-01

    The human protein kinome presents one of the largest protein families that orchestrate functional processes in complex cellular networks, and when perturbed, can cause various cancers. The abundance and diversity of genetic, structural, and biochemical data underlies the complexity of mechanisms by which targeted and personalized drugs can combat mutational profiles in protein kinases. Coupled with the evolution of system biology approaches, genomic and proteomic technologies are rapidly identifying and charactering novel resistance mechanisms with the goal to inform rationale design of personalized kinase drugs. Integration of experimental and computational approaches can help to bring these data into a unified conceptual framework and develop robust models for predicting the clinical drug resistance. In the current study, we employ a battery of synergistic computational approaches that integrate genetic, evolutionary, biochemical, and structural data to characterize the effect of cancer mutations in protein kinases. We provide a detailed structural classification and analysis of genetic signatures associated with oncogenic mutations. By integrating genetic and structural data, we employ network modeling to dissect mechanisms of kinase drug sensitivities to oncogenic EGFR mutations. Using biophysical simulations and analysis of protein structure networks, we show that conformational-specific drug binding of Lapatinib may elicit resistant mutations in the EGFR kinase that are linked with the ligand-mediated changes in the residue interaction networks and global network properties of key residues that are responsible for structural stability of specific functional states. A strong network dependency on high centrality residues in the conformation-specific Lapatinib-EGFR complex may explain vulnerability of drug binding to a broad spectrum of mutations and the emergence of drug resistance. Our study offers a systems-based perspective on drug design by unravelling

  18. Integrating Fisheries Dependent and Independent Approaches to assess Fisheries, Abundance, Diversity, Distribution and Genetic Connectivity of Red Sea Elasmobranch Populations

    KAUST Repository

    Spaet, Julia L.

    2014-05-01

    The Red Sea has long been recognized as a global hotspot of marine biodiversity. Ongoing overfishing, however, is threatening this unique ecosystem, recently leading to the identification of the Red Sea as one of three major hotspots of extinction risk for sharks and rays worldwide. Elasmobranch catches in Saudi Arabian Red Sea waters are unregulated, often misidentified and unrecorded, resulting in a lack of species-specific landings information, which would be vital for the formulation of effective management strategies. Here we employed an integrated approach of fisheries dependent and independent survey methods combined with molecular tools to provide biological, ecological and fisheries data to aid in the assessment of the status of elasmobranch populations in the Red Sea. Over the course of two years, we conducted market surveys at the biggest Saudi Arabian fish market in Jeddah. Market landings were dominated by, mostly immature individuals - implying both recruitment and growth overfishing. Additionally, we employed baited remote underwater video (BRUVS) and longline surveys along almost the entire length of the Red Sea coast of Saudi Arabia as well as at selected reef systems in Sudan. The comparison of catch per unit effort (CPUE) data for Saudi Arabian Red Sea BRUVS and longline surveys to published data originating from non-Red Sea ocean systems revealed CPUE values several orders of magnitude lower for both survey methods in the Red Sea compared to other locations around the world. Finally, we infered the regional population structure of four commercially important shark species between the Red Sea and the Western Indian Ocean.We genotyped nearly 2000 individuals at the mitochondrial control region as well as a total of 20 microsatellite loci. Genetic homogeneity could not be rejected for any of the four species across the spatial comparison. Based on high levels of region-wide exploitation, we suggest that, for management purposes, the population

  19. f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome

    OpenAIRE

    Tang, Shaojun; Hemberg, Martin; Cansizoglu, Ertugrul; Belin, Stephane; Kosik, Kenneth; Kreiman, Gabriel; Steen, Hanno; Steen, Judith

    2016-01-01

    The ability to integrate 'omics' (i.e., transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs)across different 'omics'data types or multi-dimensional data including time courses. We present a model capable of simultaneously identifying DEGs from continuous and discrete transcriptomic, proteomic and integrated proteogenomic data. We show that...

  20. Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans

    NARCIS (Netherlands)

    Hernandez, W.; Gamazon, E. R.; Aquino-Michaels, K.; Smithberger, E.; O'Brien, T. J.; Harralson, A. F.; Tuck, M.; Barbour, A.; Cavallari, L. H.; Perera, M. A.

    2017-01-01

    Essentials Genetic variants controlling gene regulation have not been explored in pharmacogenomics. We tested liver expression quantitative trait loci for association with warfarin dose response. A novel predictor for increased warfarin dose response in African Americans was identified. Precision

  1. PhenomeCentral: An Integrated Portal for Sharing and Searching Patient Phenotype Data for Rare Genetic Disorders.

    OpenAIRE

    Brudno, Michael; Girdea, Marta; Dumitriu, Sergiu; Buske, Orion; Köhler, Sebastian; Robinson, Peter N.; Brookes, Andrew J.; Boycott, Kym; Boerkoel, Cornelius F.; Gahl, William A.; CARE RARE, Canadian for Consortium; NIH, Undiagnosed Diseases Program

    2014-01-01

    The availability of low-cost genome sequencing has allowed for the identification of the molecular cause of hundreds of rare genetic disorders. Solved disorders, however, only represent the “tip of the iceberg”. Because the discovery of disease-causing variants typically requires confirmation of the mutation or gene in multiple unrelated individuals, an even larger number of genetic disorders remain unsolved due to difficulty identifying second families. With many groups now tackling these re...

  2. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    Directory of Open Access Journals (Sweden)

    King Graham J

    2010-10-01

    Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

  3. Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity

    Science.gov (United States)

    Anterola, Aldwin M.; Lewis, Norman G.

    2002-01-01

    A comprehensive assessment of lignin configuration in transgenic and mutant plants is long overdue. This review thus undertook the systematic analysis of trends manifested through genetic and mutational manipulations of the various steps associated with monolignol biosynthesis; this included consideration of the downstream effects on organized lignin assembly in the various cell types, on vascular function/integrity, and on plant growth and development. As previously noted for dirigent protein (homologs), distinct and sophisticated monolignol forming metabolic networks were operative in various cell types, tissues and organs, and form the cell-specific guaiacyl (G) and guaiacyl-syringyl (G-S) enriched lignin biopolymers, respectively. Regardless of cell type undergoing lignification, carbon allocation to the different monolignol pools is apparently determined by a combination of phenylalanine availability and cinnamate-4-hydroxylase/"p-coumarate-3-hydroxylase" (C4H/C3H) activities, as revealed by transcriptional and metabolic profiling. Downregulation of either phenylalanine ammonia lyase or cinnamate-4-hydroxylase thus predictably results in reduced lignin levels and impaired vascular integrity, as well as affecting related (phenylpropanoid-dependent) metabolism. Depletion of C3H activity also results in reduced lignin deposition, albeit with the latter being derived only from hydroxyphenyl (H) units, due to both the guaiacyl (G) and syringyl (S) pathways being blocked. Apparently the cells affected are unable to compensate for reduced G/S levels by increasing the amounts of H-components. The downstream metabolic networks for G-lignin enriched formation in both angiosperms and gymnosperms utilize specific cinnamoyl CoA O-methyltransferase (CCOMT), 4-coumarate:CoA ligase (4CL), cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) isoforms: however, these steps neither affect carbon allocation nor H/G designations, this being determined by C4H/C3H

  4. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    Directory of Open Access Journals (Sweden)

    Yash Paul Khajuria

    Full Text Available The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777 of an inter-specific reference mapping population. High amplification efficiency (87%, experimental validation success rate (81% and polymorphic potential (55% of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48% detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%. An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777 having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped

  5. Obsessive-compulsive disorder, which genes? Which functions? Which pathways? An integrated holistic view regarding OCD and its complex genetic etiology.

    Science.gov (United States)

    Bozorgmehr, Ali; Ghadirivasfi, Mohammad; Shahsavand Ananloo, Esmaeil

    2017-09-01

    Obsessive-compulsive disorder (OCD) is characterized by recurrent obtrusive and repetitive acts typically occurred following anxiety. In the last two decades, studies done on the gene sequences, large-scale and point mutations and gene-gene, gene-environment and gene-drug interactions have led to the discovery of hundreds of genes associated with OCD. Although each gene in turn is a part of the etiology of this disorder; however, OCD, like other mental disorders is complex and a comprehensive and integrated view is necessary to understand its genetic basis. In this study, through an extensive review of existing published studies, all genes associated with OCD were found. Then, in order to integrate the results, all the interactions between these genes were explored and the achievement was represented as an interactive genetic network. Furthermore, the reconstructed network was analyzed. It was found that GRIN2A, GRIN2B and GRIA2 are the most central nodes in the network. Functional and pathway enrichment analysis showed that glutamate-related pathways are the main deficient systems in patients with OCD. By studying genes shared between OCD and other diseases, it was cleared that OCD, epilepsy and some types of cancer have the most number of shared genes. The results of this study, in addition to reviewing the available results as a comprehensive and integrated manner, provide new hypotheses for future studies.

  6. 'Integration'

    DEFF Research Database (Denmark)

    Olwig, Karen Fog

    2011-01-01

    , while the countries have adopted disparate policies and ideologies, differences in the actual treatment and attitudes towards immigrants and refugees in everyday life are less clear, due to parallel integration programmes based on strong similarities in the welfare systems and in cultural notions...... of equality in the three societies. Finally, it shows that family relations play a central role in immigrants’ and refugees’ establishment of a new life in the receiving societies, even though the welfare society takes on many of the social and economic functions of the family....

  7. Genetic engineering in Actinoplanes sp. SE50/110 - development of an intergeneric conjugation system for the introduction of actinophage-based integrative vectors.

    Science.gov (United States)

    Gren, Tetiana; Ortseifen, Vera; Wibberg, Daniel; Schneiker-Bekel, Susanne; Bednarz, Hanna; Niehaus, Karsten; Zemke, Till; Persicke, Marcus; Pühler, Alfred; Kalinowski, Jörn

    2016-08-20

    The α-glucosidase inhibitor acarbose is used for treatment of diabetes mellitus type II, and is manufactured industrially with overproducing derivatives of Actinoplanes sp. SE50/110, reportedly obtained by conventional mutagenesis. Despite of high industrial significance, only limited information exists regarding acarbose metabolism, function and regulation of these processes, due to the absence of proper genetic engineering methods and tools developed for this strain. Here, a basic toolkit for genetic engineering of Actinoplanes sp. SE50/110 was developed, comprising a standardized protocol for a DNA transfer through Escherichia coli-Actinoplanes intergeneric conjugation and applied for the transfer of ϕC31, ϕBT1 and VWB actinophage-based integrative vectors. Integration sites, occurring once per genome for all vectors, were sequenced and characterized for the first time in Actinoplanes sp. SE50/110. Notably, in case of ϕC31 based vector pSET152, the integration site is highly conserved, while for ϕBT1 and the VWB based vectors pRT801 and pSOK804, respectively, no sequence similarities to those in other bacteria were detected. The studied plasmids were proven to be stable and neutral with respect to strain morphology and acarbose production, enabling future use for genetic manipulations of Actinoplanes sp. SE50/110. To further broaden the spectrum of available tools, a GUS reporter system, based on the pSET152 derived vector, was also established in Actinoplanes sp. SE50/110. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide.

    Science.gov (United States)

    Baeza, J Antonio; Behringer, Donald C

    2017-01-01

    The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi , an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni . Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across  550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.

  9. Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics.

    Science.gov (United States)

    Bubier, Jason A; Jay, Jeremy J; Baker, Christopher L; Bergeson, Susan E; Ohno, Hiroshi; Metten, Pamela; Crabbe, John C; Chesler, Elissa J

    2014-08-01

    Extensive genetic and genomic studies of the relationship between alcohol drinking preference and withdrawal severity have been performed using animal models. Data from multiple such publications and public data resources have been incorporated in the GeneWeaver database with >60,000 gene sets including 285 alcohol withdrawal and preference-related gene sets. Among these are evidence for positional candidates regulating these behaviors in overlapping quantitative trait loci (QTL) mapped in distinct mouse populations. Combinatorial integration of functional genomics experimental results revealed a single QTL positional candidate gene in one of the loci common to both preference and withdrawal. Functional validation studies in Ap3m2 knockout mice confirmed these relationships. Genetic validation involves confirming the existence of segregating polymorphisms that could account for the phenotypic effect. By exploiting recent advances in mouse genotyping, sequence, epigenetics, and phylogeny resources, we confirmed that Ap3m2 resides in an appropriately segregating genomic region. We have demonstrated genetic and alcohol-induced regulation of Ap3m2 expression. Although sequence analysis revealed no polymorphisms in the Ap3m2-coding region that could account for all phenotypic differences, there are several upstream SNPs that could. We have identified one of these to be an H3K4me3 site that exhibits strain differences in methylation. Thus, by making cross-species functional genomics readily computable we identified a common QTL candidate for two related bio-behavioral processes via functional evidence and demonstrate sufficiency of the genetic locus as a source of variation underlying two traits. Copyright © 2014 by the Genetics Society of America.

  10. An integrated epigenetic and genetic analysis of DNA methyltransferase genes (DNMTs) in tumor resistant and susceptible chicken lines

    Science.gov (United States)

    Both epigenetic alterations and genetic variations play essential roles in tumorigenesis. The epigenetic modification of DNA methylation is catalyzed and maintained by the DNA methyltransferases (DNMT3a, DNMT3b and DNMT1). DNA mutations and DNA methylation profiles of DNMTs themselves and their rela...

  11. Systems genetics of metabolism: the use of the BXD murine reference panel for multiscalar integration of traits

    NARCIS (Netherlands)

    Andreux, Pénélope A.; Williams, Evan G.; Koutnikova, Hana; Houtkooper, Riekelt H.; Champy, Marie-France; Henry, Hugues; Schoonjans, Kristina; Williams, Robert W.; Auwerx, Johan

    2012-01-01

    Metabolic homeostasis is achieved by complex molecular and cellular networks that differ significantly among individuals and are difficult to model with genetically engineered lines of mice optimized to study single gene function. Here, we systematically acquired metabolic phenotypes by using the

  12. Integrating Genetic Studies of Nicotine Addiction into Public Health Practice: Stakeholder Views on Challenges, Barriers and Opportunities

    Science.gov (United States)

    Dingel, M.J.; Hicks, A.D.; Robinson, M.E.; Koenig, B.A.

    2011-01-01

    Objective: Will emerging genetic research strengthen tobacco control programs? In this empirical study, we interview stakeholders in tobacco control to illuminate debates about the role of genomics in public health. Methods: The authors performed open-ended interviews with 86 stakeholders from 5 areas of tobacco control: basic scientists, clinicians, tobacco prevention specialists, health payers, and pharmaceutical industry employees. Interviews were qualitatively analyzed using standard techniques. Results: The central tension is between the hope that an expanding genomic knowledge base will improve prevention and smoking cessation therapies and the fear that genetic research might siphon resources away from traditional and proven public health programs. While showing strong support for traditional public health approaches to tobacco control, stakeholders recognize weaknesses, specifically the difficulty of countering the powerful voice of the tobacco industry when mounting public campaigns and the problem of individuals who are resistant to treatment and continue smoking. Conclusions: In order for genetic research to be effectively translated into efforts to minimize the harm of smoking-related disease, the views of key stakeholders must be voiced and disagreements reconciled. Effective translation requires honest evaluation of both the strengths and limitations of genetic approaches. PMID:21757875

  13. Gene-Culture Coevolution in a Social Cetacean: Integrating Acoustic and Genetic Data to Understand Population Structure in the Short-Finned Pilot Whale (Globicephala macrorhynchus)

    Science.gov (United States)

    Van Cise, Amy

    The evolutionary ecology of a species is driven by a combination of random events, ecological and environmental mechanisms, and social behavior. Gene-culture coevolutionary theory attempts to understand the evolutionary trajectory of a species by examining the interactions between these potential drivers. Further, our choice of data type will affect the patterns we observe, therefore by integrating several types of data we achieve a holistic understanding of the various aspects of evolutionary ecology within a species. In order to understand population structure in short-finned pilot whales, I use a combination of genetic and acoustic data to examine structure on evolutionary (genetic) and cultural (acoustic) timescales. I first examine structure among geographic populations in the Pacific Ocean. Using genetic sequences from the mitochondrial control region, I show that two genetically and morphologically distinct types of short-finned pilot whale, described off the coast of Japan, have non-overlapping distributions throughout their range in the Pacific Ocean. Analysis of the acoustic features of their social calls indicates that they are acoustically differentiated, possibly due to limited communication between the two types. This evidence supports the hypothesis that the two types may be separate species or subspecies. Next, I examine structure among island communities and social groups within the Hawaiian Island population of short-finned pilot whales. Using a combination of mitochondrial and nuclear DNA, I showed that the hierarchical social structure in Hawaiian pilot whales is driven by genetic relatedness; individuals remain in groups with their immediate family members, and preferentially associate with relatives. Similarly, social structure affects genetic differentiation, likely by restricting access to mates. Acoustic differentiation among social groups indicates that social structure may also restrict the flow of cultural information, such as vocal

  14. Research on uranium resource models. Part IV. Logic: a computer graphics program to construct integrated logic circuits for genetic-geologic models. Progress report

    International Nuclear Information System (INIS)

    Scott, W.A.; Turner, R.M.; McCammon, R.B.

    1981-01-01

    Integrated logic circuits were described as a means of formally representing genetic-geologic models for estimating undiscovered uranium resources. The logic circuits are logical combinations of selected geologic characteristics judged to be associated with particular types of uranium deposits. Each combination takes on a value which corresponds to the combined presence, absence, or don't know states of the selected characteristic within a specified geographic cell. Within each cell, the output of the logic circuit is taken as a measure of the favorability of occurrence of an undiscovered deposit of the type being considered. In this way, geological, geochemical, and geophysical data are incorporated explicitly into potential uranium resource estimates. The present report describes how integrated logic circuits are constructed by use of a computer graphics program. A user's guide is also included

  15. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in Brassica rapa Fast Plants

    Science.gov (United States)

    Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dósa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question “What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev),” we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students’ cognitive structures before and after the unit and explanations in students’ final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on “variation” as a proposed threshold concept and primary goal for students’ explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from “plug and play,” this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics. PMID:25185225

  16. Solving a mathematical model integrating unequal-area facilities layout and part scheduling in a cellular manufacturing system by a genetic algorithm.

    Science.gov (United States)

    Ebrahimi, Ahmad; Kia, Reza; Komijan, Alireza Rashidi

    2016-01-01

    In this article, a novel integrated mixed-integer nonlinear programming model is presented for designing a cellular manufacturing system (CMS) considering machine layout and part scheduling problems simultaneously as interrelated decisions. The integrated CMS model is formulated to incorporate several design features including part due date, material handling time, operation sequence, processing time, an intra-cell layout of unequal-area facilities, and part scheduling. The objective function is to minimize makespan, tardiness penalties, and material handling costs of inter-cell and intra-cell movements. Two numerical examples are solved by the Lingo software to illustrate the results obtained by the incorporated features. In order to assess the effects and importance of integration of machine layout and part scheduling in designing a CMS, two approaches, sequentially and concurrent are investigated and the improvement resulted from a concurrent approach is revealed. Also, due to the NP-hardness of the integrated model, an efficient genetic algorithm is designed. As a consequence, computational results of this study indicate that the best solutions found by GA are better than the solutions found by B&B in much less time for both sequential and concurrent approaches. Moreover, the comparisons between the objective function values (OFVs) obtained by sequential and concurrent approaches demonstrate that the OFV improvement is averagely around 17 % by GA and 14 % by B&B.

  17. Fault Diagnosis Method of Rolling Bearings Based on Multi-dimensional Vibration Features%基于多维振动特征的滚动轴承故障诊断方法

    Institute of Scientific and Technical Information of China (English)

    付云骁; 贾利民; 季常煦; 姚德臣; 李文球

    2014-01-01

    单独提取滚动轴承振动信号的时域或频域特征进行故障诊断,是目前常用的轴承诊断方法,诊断精度有待提高。以时域和频域的多维振动特征参量为指标,以历史诊断正确率作为特征参量权值,分别对滚动轴承的无故障和经常出现的滚珠故障、内环故障和外环故障工况进行特征提取和故障识别。多维时频域振动特征是单维特征依据诊断精度权重的集合。运用BP神经网络分别对信号的时域特征(TDF)、IMF能量矩(IEM)、小波包能量矩(WPEM),以及多维时频域特征进行智能故障判别。实验验证用多维时频域振动特征参量综合诊断的方法进行滚动轴承故障诊断,比单维特征的诊断结果精确且效率较高,该方法可以在滚动轴承故障诊断领域展开应用。%Extracting the time-domain or the frequency-domain features of vibration signals for analysis is a conventional method for rolling bearings fault diagnosis. But the effects of this diagnosis method need to be improved. In this paper, taking the multi-dimensional vibration characteristic parameters in time-domain and frequency-domain as the indexes and the correctness rate of historical diagnosis as the parametric weight, the features of fault-free rolling bearings and the features of rolling bearings with ball fault, inner and outer race faults are extracted and the faults are identified. It shows that the multi-dimensional vibration characteristic in time-frequency domains is the assemblage of single features. BP neural network is used for intelligent fault classification of signals according to the time-domain feature (TDF) parameters, IMF energy moment (IEM), wavelet package energy moment (WPEM) and multi-dimensional features respectively. Results of the diagnoses are compared one another. The experiment results verify that using the multi-dimensional feature in time and frequency domains to evaluate the rolling bearing faults is

  18. An investment plan for preventing child injuries using risk priority number of failure mode and effects analysis methodology and a multi-objective, multi-dimensional mixed 0-1 knapsack model

    International Nuclear Information System (INIS)

    Bas, Esra

    2011-01-01

    In this paper, a general framework for child injury prevention and a multi-objective, multi-dimensional mixed 0-1 knapsack model were developed to determine the optimal time to introduce preventive measures against child injuries. Furthermore, the model maximises the prevention of injuries with the highest risks for each age period by combining preventive measures and supervision as well as satisfying budget limits and supervision time constraints. The risk factors for each injury, variable, and time period were based on risk priority numbers (RPNs) obtained from failure mode and effects analysis (FMEA) methodology, and these risk factors were incorporated into the model as objective function parameters. A numerical experiment based on several different situations was conducted, revealing that the model provided optimal timing of preventive measures for child injuries based on variables considered.

  19. Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene.

    Directory of Open Access Journals (Sweden)

    Yukinori Okada

    Full Text Available Integrating genetic data from families with highly penetrant forms of disease together with genetic data from outbred populations represents a promising strategy to uncover the complete frequency spectrum of risk alleles for complex traits such as rheumatoid arthritis (RA. Here, we demonstrate that rare, low-frequency and common alleles at one gene locus, phospholipase B1 (PLB1, might contribute to risk of RA in a 4-generation consanguineous pedigree (Middle Eastern ancestry and also in unrelated individuals from the general population (European ancestry. Through identity-by-descent (IBD mapping and whole-exome sequencing, we identified a non-synonymous c.2263G>C (p.G755R mutation at the PLB1 gene on 2q23, which significantly co-segregated with RA in family members with a dominant mode of inheritance (P = 0.009. We further evaluated PLB1 variants and risk of RA using a GWAS meta-analysis of 8,875 RA cases and 29,367 controls of European ancestry. We identified significant contributions of two independent non-coding variants near PLB1 with risk of RA (rs116018341 [MAF = 0.042] and rs116541814 [MAF = 0.021], combined P = 3.2 × 10(-6. Finally, we performed deep exon sequencing of PLB1 in 1,088 RA cases and 1,088 controls (European ancestry, and identified suggestive dispersion of rare protein-coding variant frequencies between cases and controls (P = 0.049 for C-alpha test and P = 0.055 for SKAT. Together, these data suggest that PLB1 is a candidate risk gene for RA. Future studies to characterize the full spectrum of genetic risk in the PLB1 genetic locus are warranted.

  20. Autism genetic database (AGD: a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites

    Directory of Open Access Journals (Sweden)

    Talebizadeh Zohreh

    2009-09-01

    community to evaluate genetic findings for this complex multifactorial disorder in an integrated format. AGD provides a genome browser and a web based query client for conveniently selecting features of interest. Access to AGD is freely available at http://wren.bcf.ku.edu/.

  1. Genetic integrity of European grayling (Thymallus thymallus L. 1758 within the Vienne River drainage basin after five decades of stockings

    Directory of Open Access Journals (Sweden)

    Henri Persat

    2015-11-01

    Full Text Available European grayling of the upper Vienne River drainage basin represent the westernmost populations inside the natural distribution of the species. Since the 19th century, their extension across this sub-basin has been dramatically reduced by the harnessing of the river network for dams, initially serving mills but then hydroelectric power generation. Since the 1960s, local fishing authorities have attempted to compensate for these declines with stocking programs, but the efficiency of these efforts have never been accurately monitored. We aim to evaluate the genetic imprints of these stocking programs and thus provide an indirect measure of the long-term survival of stocked fish. Three target populations were analyzed at both mtDNA (Control Region and nDNA levels (12 µSats, and compared to populations representative of surrounding drainage basins or fish farm facilities. Among 37 "wild" fish sequenced, only three control region haplotypes were identified, all belonging to the highly divergent Loire basin lineage. Two were specific to the Upper Vienne area, and one was observed in some individuals of the most downstream location, but previously described from the upper Allier sub-drainage. Microsatellite analysis of 87 "wild" fish also demonstrated a rather low diversity within each population (but typical for the Loire drainage with all Upper Vienne individuals belonging to a single diagnosable unit. This genetic cluster was clearly distinct from all other samples including hatchery strains, which strongly supports its native origin. The only piece of evidence of a possible stocking contribution was the occurrence of the Allier haplotype, but it cannot be excluded that this haplotype was also native to this reach of river. The total lack of genetic impact of five decades of stocking deeply questions the efficacy of this management approach, at least in a regional context.

  2. The genetic interaction network of CCW12, a Saccharomyces cerevisiae gene required for cell wall integrity during budding and formation of mating projections

    Science.gov (United States)

    2011-01-01

    Background Mannoproteins construct the outer cover of the fungal cell wall. The covalently linked cell wall protein Ccw12p is an abundant mannoprotein. It is considered as crucial structural cell wall component since in baker's yeast the lack of CCW12 results in severe cell wall damage and reduced mating efficiency. Results In order to explore the function of CCW12, we performed a Synthetic Genetic Analysis (SGA) and identified genes that are essential in the absence of CCW12. The resulting interaction network identified 21 genes involved in cell wall integrity, chitin synthesis, cell polarity, vesicular transport and endocytosis. Among those are PFD1, WHI3, SRN2, PAC10, FEN1 and YDR417C, which have not been related to cell wall integrity before. We correlated our results with genetic interaction networks of genes involved in glucan and chitin synthesis. A core of genes essential to maintain cell integrity in response to cell wall stress was identified. In addition, we performed a large-scale transcriptional analysis and compared the transcriptional changes observed in mutant ccw12Δ with transcriptomes from studies investigating responses to constitutive or acute cell wall damage. We identified a set of genes that are highly induced in the majority of the mutants/conditions and are directly related to the cell wall integrity pathway and cell wall compensatory responses. Among those are BCK1, CHS3, EDE1, PFD1, SLT2 and SLA1 that were also identified in the SGA. In contrast, a specific feature of mutant ccw12Δ is the transcriptional repression of genes involved in mating. Physiological experiments substantiate this finding. Further, we demonstrate that Ccw12p is present at the cell periphery and highly concentrated at the presumptive budding site, around the bud, at the septum and at the tip of the mating projection. Conclusions The combination of high throughput screenings, phenotypic analyses and localization studies provides new insight into the function of Ccw

  3. Performance-Oriented Design of Large Passive Solar Roofs : A method for the integration of parametric modelling and genetic algorithms

    NARCIS (Netherlands)

    Turrin, M.; Von Buelow, P.; Stouffs, R.M.F.; Kilian, A.

    2010-01-01

    The paper addresses the design of large roof structures for semi outdoor spaces through an investigation of a type of performance-oriented design, which aims at integrating performance evaluations in the early stages of the design process. Particularly, aiming at improving daylight and thermal

  4. Soft sensor development and optimization of the commercial petrochemical plant integrating support vector regression and genetic algorithm

    Directory of Open Access Journals (Sweden)

    S.K. Lahiri

    2009-09-01

    Full Text Available Soft sensors have been widely used in the industrial process control to improve the quality of the product and assure safety in the production. The core of a soft sensor is to construct a soft sensing model. This paper introduces support vector regression (SVR, a new powerful machine learning methodbased on a statistical learning theory (SLT into soft sensor modeling and proposes a new soft sensing modeling method based on SVR. This paper presents an artificial intelligence based hybrid soft sensormodeling and optimization strategies, namely support vector regression – genetic algorithm (SVR-GA for modeling and optimization of mono ethylene glycol (MEG quality variable in a commercial glycol plant. In the SVR-GA approach, a support vector regression model is constructed for correlating the process data comprising values of operating and performance variables. Next, model inputs describing the process operating variables are optimized using genetic algorithm with a view to maximize the process performance. The SVR-GA is a new strategy for soft sensor modeling and optimization. The major advantage of the strategies is that modeling and optimization can be conducted exclusively from the historic process data wherein the detailed knowledge of process phenomenology (reaction mechanism, kinetics etc. is not required. Using SVR-GA strategy, a number of sets of optimized operating conditions were found. The optimized solutions, when verified in an actual plant, resulted in a significant improvement in the quality.

  5. An integration of historical records and genetic data to the assessment of global distribution and population structure in Octopus vulgaris

    Directory of Open Access Journals (Sweden)

    Daniele eDe Luca

    2014-09-01

    Full Text Available The common octopus (Octopus vulgaris Cuvier, 1797 is one of the most widely distributed species belonging to the genus Octopus as well as an important commercially harvested species and a model organism for behavioral biology of invertebrates. It has been described for the first time in the Mediterranean Sea but it is considered a cosmopolitan species inhabiting the temperate and tropical sea of the northern and southern hemispheres. In the last few years, several species previously considered as O. vulgaris have been recognized as new species, limiting the distributional range of vulgaris and reinforcing the thesis of a species complex. Where it is an important fishery resource, numerous studies have been conducted in order to define its genetic structure with the purpose of managing different stocks. However, many locations are still poorly investigated from this point of view and others are under taxonomic revision to exclude or confirm its occurrence. Here we provide a summary of the current status of knowledge on distribution and genetic structure in this species in the different oceanic regions.

  6. Deciphering the genomes of 16 Acanthamoeba species does not provide evidence of integration of known giant virus-associated mobile genetic elements.

    Science.gov (United States)

    Chelkha, Nisrine; Colson, Philippe; Levasseur, Anthony; La Scola, Bernard

    2018-06-02

    Giant viruses infect protozoa, especially amoebae of the genus Acanthamoeba. These viruses possess genetic elements named Mobilome. So far, this mobilome comprises provirophages which are integrated into the genome of their hosts, transpovirons, and Maverick/Polintons. Virophages replicate inside virus factories within Acanthamoeba and can decrease the infectivity of giant viruses. The virophage infecting CroV was found to be integrated in the host of CroV, Cafeteria roenbergensis, thus protecting C. roenbergensis by reduction of CroV multiplication. Because of this unique property, assessment of the mechanisms of replication of virophages and their relationship with giant viruses is a key element of this investigation. This work aimed at evaluating the presence and the dynamic of these mobile elements in sixteen Acanthamoeba genomes. No significant traces of the integration of genomes or sequences from known virophages were identified in all the available Acanthamoeba genomes. These results brought us to hypothesize that the interactions between mimiviruses and their virophages might occur through different mechanisms, or at low frequency. An additional explanation could be that our knowledge of the diversity of virophages is still very limited. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Genetic effect of MTHFR C677T polymorphism on the structural covariance network and white-matter integrity in Alzheimer's disease.

    Science.gov (United States)

    Chang, Yu-Tzu; Hsu, Shih-Wei; Tsai, Shih-Jen; Chang, Ya-Ting; Huang, Chi-Wei; Liu, Mu-En; Chen, Nai-Ching; Chang, Wen-Neng; Hsu, Jung-Lung; Lee, Chen-Chang; Chang, Chiung-Chih

    2017-06-01

    The 677 C to T transition in the MTHFR gene is a genetic determinant for hyperhomocysteinemia. We investigated whether this polymorphism modulates gray matter (GM) structural covariance networks independently of white-matter integrity in patients with Alzheimer's disease (AD). GM structural covariance networks were constructed by 3D T1-magnetic resonance imaging and seed-based analysis. The patients were divided into two genotype groups: C homozygotes (n = 73) and T carriers (n = 62). Using diffusion tensor imaging and white-matter parcellation, 11 fiber bundle integrities were compared between the two genotype groups. Cognitive test scores were the major outcome factors. The T carriers had higher homocysteine levels, lower posterior cingulate cortex GM volume, and more clusters in the dorsal medial lobe subsystem showing stronger covariance strength. Both posterior cingulate cortex seed and interconnected peak cluster volumes predicted cognitive test scores, especially in the T carriers. There were no between-group differences in fiber tract diffusion parameters. The MTHFR 677T polymorphism modulates posterior cingulate cortex-anchored structural covariance strength independently of white matter integrities. Hum Brain Mapp 38:3039-3051, 2017. © 2017 The Authors Human Brain Mapping Published Wiley by Periodicals, Inc. © 2017 The Authors Human Brain Mapping Published Wiley by Periodicals, Inc.

  8. Genetic modification of Lactobacillus plantarum by heterologous gene integration in a not functional region of the chromosome.

    Science.gov (United States)

    Rossi, Franca; Capodaglio, Alessandro; Dellaglio, Franco

    2008-08-01

    This report describes the vector-free engineering of Lactobacillus plantarum by chromosomal integration of an exogenous gene without inactivation of physiological traits. The integrative plasmid vector pP7B6 was derived from pGIP73 by replacing the cbh site, encoding the L. plantarum conjugated bile salt hydrolase, with the prophage fragment P7B6, from L. plantarum Lp80 (DSM 4229). Plasmid pP7B6NI was obtained by inserting the nisin immunity gene nisI of Lactococcus lactis subsp. lactis DSM 20729, preceded by the constitutive promoter P32 from the same strain, in a unique XbaI site of fragment P7B6 and was used to electrotransform L. plantarum Lp80. A food grade recombinant L. plantarum Lp80NI, with 480-fold higher immunity to nisin than the wild type, was derived by integration of pP7B6NI followed by the excision of pP7B6. Polymerase chain reaction tests demonstrated that the integration of nisI in the prophage region had occurred and that the erythromycin resistance marker from pP7B6 was lost. Fifteen among 31 L. plantarum strains tested hybridized with P7B6, indicating that the integration of pP7B6-derived vectors might occur in some other L. plantarum strains. This was experimentally confirmed by constructing the recombinant strain L. plantarum LZNI from the dairy isolate L. plantarum LZ (LMG 24600).

  9. CRISPR-Cas9 mediated genetic engineering for the purification of the endogenous integrator complex from mammalian cells.

    Science.gov (United States)

    Baillat, David; Russell, William K; Wagner, Eric J

    2016-12-01

    The Integrator Complex (INT) is a large multi-subunit protein complex, containing at least 14 subunits and a host of associated factors. These protein components have been established through pulldowns of overexpressed epitope tagged subunits or by using antibodies raised against specific subunits. Here, we utilize CRISPR/Cas9 gene editing technology to introduce N-terminal FLAG epitope tags into the endogenous genes that encode Integrator subunit 4 and 11 within HEK293T cells. We provide specific details regarding design, approaches for facile screening, and our observed frequency of successful recombination. Finally, using silver staining, Western blotting and LC-MS/MS we compare the components of INT of purifications from CRISPR derived lines to 293T cells overexpressing FLAG-INTS11 to define a highly resolved constituency of mammalian INT. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

    OpenAIRE

    Willnow, TE; Antignac, C; Brändli, AW; Christensen, EI; Cox, RD; Davidson, D; Davies, JA; Devuyst, O; Eichele, G; Hastie, ND; Verroust, PJ; Schedl, A; Meij, IC

    2005-01-01

    Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a thr...

  11. Toward a Predictive Framework for Convergent Evolution: Integrating Natural History, Genetic Mechanisms, and Consequences for the Diversity of Life.

    Science.gov (United States)

    Agrawal, Anurag A

    2017-08-01

    A charm of biology as a scientific discipline is the diversity of life. Although this diversity can make laws of biology challenging to discover, several repeated patterns and general principles govern evolutionary diversification. Convergent evolution, the independent evolution of similar phenotypes, has been at the heart of one approach to understand generality in the evolutionary process. Yet understanding when and why organismal traits and strategies repeatedly evolve has been a central challenge. These issues were the focus of the American Society of Naturalists Vice Presidential Symposium in 2016 and are the subject of this collection of articles. Although naturalists have long made inferences about convergent evolution and its importance, there has been confusion in the interpretation of the pattern of convergence. Does convergence primarily indicate adaptation or constraint? How often should convergence be expected? Are there general principles that would allow us to predict where and when and by what mechanisms convergent evolution should occur? What role does natural history play in advancing our understanding of general evolutionary principles? In this introductory article, I address these questions, review several generalizations about convergent evolution that have emerged over the past 15 years, and present a framework for advancing the study and interpretation of convergence. Perhaps the most important emerging conclusion is that the genetic mechanisms of convergent evolution are phylogenetically conserved; that is, more closely related species tend to share the same genetic basis of traits, even when independently evolved. Finally, I highlight how the articles in this special issue further develop concepts, methodologies, and case studies at the frontier of our understanding of the causes and consequences of convergent evolution.

  12. Practical animal breeding as the key to an integrated view of genetics, eugenics and evolutionary theory: Arend L. Hagedoorn (1885-1953).

    Science.gov (United States)

    Theunissen, Bert

    2014-06-01

    In the history of genetics Arend Hagedoorn (1885-1953) is mainly known for the 'Hagedoorn effect', which states that part of the changes in variability that populations undergo over time are due to chance effects. Leaving this contribution aside, Hagedoorn's work has received scarcely any attention from historians. This is mainly due to the fact that Hagedoorn was an expert in animal breeding, a field that historians have only recently begun to explore. His work provides an example of how a prominent geneticist envisaged animal breeding to be reformed by the new science of heredity. Hagedoorn, a pupil of Hugo de Vries, tried to integrate his insights as a Mendelian geneticist and an animal breeding expert in a unified view of heredity, eugenics and evolution. In this paper I aim to elucidate how these fields were connected in Hagedoorn's work. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. A Pseudo-Parallel Genetic Algorithm Integrating Simulated Annealing for Stochastic Location-Inventory-Routing Problem with Consideration of Returns in E-Commerce

    Directory of Open Access Journals (Sweden)

    Bailing Liu

    2015-01-01

    Full Text Available Facility location, inventory control, and vehicle routes scheduling are three key issues to be settled in the design of logistics system for e-commerce. Due to the online shopping features of e-commerce, customer returns are becoming much more than traditional commerce. This paper studies a three-phase supply chain distribution system consisting of one supplier, a set of retailers, and a single type of product with continuous review (Q, r inventory policy. We formulate a stochastic location-inventory-routing problem (LIRP model with no quality defects returns. To solve the NP-hand problem, a pseudo-parallel genetic algorithm integrating simulated annealing (PPGASA is proposed. The computational results show that PPGASA outperforms GA on optimal solution, computing time, and computing stability.

  14. Beyond Punnett squares: Student word association and explanations of phenotypic variation through an integrative quantitative genetics unit investigating anthocyanin inheritance and expression in Brassica rapa Fast plants.

    Science.gov (United States)

    Batzli, Janet M; Smith, Amber R; Williams, Paul H; McGee, Seth A; Dósa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students' cognitive structures before and after the unit and explanations in students' final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on "variation" as a proposed threshold concept and primary goal for students' explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from "plug and play," this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics. © 2014 J. M. Batzli et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  15. A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

    Directory of Open Access Journals (Sweden)

    Eleonora Barilli

    2018-02-01

    Full Text Available Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM−1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%. QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2 was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.

  16. Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice

    Directory of Open Access Journals (Sweden)

    Rosemary eShrestha

    2012-08-01

    Full Text Available The Crop Ontology (CO of the Generation Challenge Program (GCP (http://cropontology.org/ is developed for the Integrated Breeding Platform (https://www.integratedbreeding.net/ by several centers of The Consultative Group on International Agricultural Research (CGIAR: Bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The Crop Ontology provides validated trait names used by the crop communities of practice for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB fieldbooks are synchronized with the Crop Ontology terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum and wheat. Online curation and annotation tools facilitate (http://cropontology.org direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology and Trait Ontology. Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS. Cross-referencing and annotation will be further applied in the Integrated Breeding Platform.

  17. Integral and discrete inequalities and their applications

    CERN Document Server

    Qin, Yuming

    2016-01-01

    This book focuses on one- and multi-dimensional linear integral and discrete Gronwall-Bellman type inequalities. It provides a useful collection and systematic presentation of known and new results, as well as many applications to differential (ODE and PDE), difference, and integral equations. With this work the author fills a gap in the literature on inequalities, offering an ideal source for researchers in these topics. The present volume is part 1 of the author’s two-volume work on inequalities. Integral and discrete inequalities are a very important tool in classical analysis and play a crucial role in establishing the well-posedness of the related equations, i.e., differential, difference and integral equations.

  18. IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome.

    Science.gov (United States)

    Wang, Jun; Dayem Ullah, Abu Z; Chelala, Claude

    2018-01-30

    The vast majority of germline and somatic variations occur in the noncoding part of the genome, only a small fraction of which are believed to be functional. From the tens of thousands of noncoding variations detectable in each genome, identifying and prioritizing driver candidates with putative functional significance is challenging. To address this, we implemented IW-Scoring, a new Integrative Weighted Scoring model to annotate and prioritise functionally relevant noncoding variations. We evaluate 11 scoring methods, and apply an unsupervised spectral approach for subsequent selective integration into two linear weighted functional scoring schemas for known and novel variations. IW-Scoring produces stable high-quality performance as the best predictors for three independent data sets. We demonstrate the robustness of IW-Scoring in identifying recurrent functional mutations in the TERT promoter, as well as disease SNPs in proximity to consensus motifs and with gene regulatory effects. Using follicular lymphoma as a paradigmatic cancer model, we apply IW-Scoring to locate 11 recurrently mutated noncoding regions in 14 follicular lymphoma genomes, and validate 9 of these regions in an extension cohort, including the promoter and enhancer regions of PAX5. Overall, IW-Scoring demonstrates greater versatility in identifying trait- and disease-associated noncoding variants. Scores from IW-Scoring as well as other methods are freely available from http://www.snp-nexus.org/IW-Scoring/. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. An Integrated Multi-Echelon Supply Chain Network Design Considering Stochastic Demand: A Genetic Algorithm Based Solution

    Directory of Open Access Journals (Sweden)

    Sara Nakhjirkan

    2017-09-01

    in green supply chain. Vehicle routing between distribution centres and customers has been considered in the model. Establishment place of distribution centres among potential places is determined by the model. The distributors use continuous review policy (r, Q to control the inventory. The proposed model object is to find an optimal supply chain with minimum costs. To validate the proposed model and measure its compliance with real world problems, GAMS IDE/Cplex has been used. In order to measure the efficiency of the proposed model in large scale problems, a genetic algorithm has been used. The results confirm the efficiency of the proposed model as a practical tool for decision makers to solve location-inventory-routing problems in green supply chain. The proposed GA could reduce the solving time by 85% while reaching on the average 97% of optimal solution compared with exact method.

  20. Lab-on-capillary: a rapid, simple and quantitative genetic analysis platform integrating nucleic acid extraction, amplification and detection.

    Science.gov (United States)

    Fu, Yu; Zhou, Xiaoming; Xing, Da

    2017-12-05

    In this work, we describe for the first time a genetic diagnosis platform employing a polydiallyldimethylammonium chloride (PDDA)-modified capillary and a liquid-based thermalization system for rapid, simple and quantitative DNA analysis with minimal user interaction. Positively charged PDDA is modified on the inner surface of the silicon dioxide capillary by using an electrostatic self-assembly approach that allows the negatively charged DNA to be separated from the lysate in less than 20 seconds. The capillary loaded with the PCR mix is incorporated in the thermalization system, which can achieve on-site real-time PCR. This system is based on the circulation of pre-heated liquids in the chamber, allowing for high-speed thermalization of the capillary and fast amplification. Multiple targets can be simultaneously analysed with multiplex spatial melting. Starting with live Escherichia coli (E. coli) cells in milk, as a realistic sample, the current method can achieve DNA extraction, amplification, and detection within 40 min.