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Sample records for modeling toolbox nft

  1. Towards a binaural modelling toolbox

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Culling, John F.; Dau, Torsten

    2011-01-01

    The Auditory Modelling Toolbox (AMToolbox) is a new Matlab / Octave toolbox for developing and applying auditory perceptual models and in particular binaural models. The philosophy behind the project is that the models should be implemented in a consistent manner, well documented and user...

  2. EEGLAB, SIFT, NFT, BCILAB, and ERICA: new tools for advanced EEG processing.

    Science.gov (United States)

    Delorme, Arnaud; Mullen, Tim; Kothe, Christian; Akalin Acar, Zeynep; Bigdely-Shamlo, Nima; Vankov, Andrey; Makeig, Scott

    2011-01-01

    We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments.

  3. Accelerator Modeling with MATLAB Accelerator Toolbox

    International Nuclear Information System (INIS)

    2002-01-01

    This paper introduces Accelerator Toolbox (AT)--a collection of tools to model storage rings and beam transport lines in the MATLAB environment. The objective is to illustrate the flexibility and efficiency of the AT-MATLAB framework. The paper discusses three examples of problems that are analyzed frequently in connection with ring-based synchrotron light sources

  4. TMS modeling toolbox for realistic simulation.

    Science.gov (United States)

    Cho, Young Sun; Suh, Hyun Sang; Lee, Won Hee; Kim, Tae-Seong

    2010-01-01

    Transcranial magnetic stimulation (TMS) is a technique for brain stimulation using rapidly changing magnetic fields generated by coils. It has been established as an effective stimulation technique to treat patients suffering from damaged brain functions. Although TMS is known to be painless and noninvasive, it can also be harmful to the brain by incorrect focusing and excessive stimulation which might result in seizure. Therefore there is ongoing research effort to elucidate and better understand the effect and mechanism of TMS. Lately Boundary element method (BEM) and Finite element method (FEM) have been used to simulate the electromagnetic phenomenon of TMS. However, there is a lack of general tools to generate the models of TMS due to some difficulties in realistic modeling of the human head and TMS coils. In this study, we have developed a toolbox through which one can generate high-resolution FE TMS models. The toolbox allows creating FE models of the head with isotropic and anisotropic electrical conductivities in five different tissues of the head and the coils in 3D. The generated TMS model is importable to FE software packages such as ANSYS for further and efficient electromagnetic analysis. We present a set of demonstrative results of realistic simulation of TMS with our toolbox.

  5. Object Oriented Toolbox for Modelling and Simulation of Dynamical Systems

    DEFF Research Database (Denmark)

    Poulsen, Mikael Zebbelin; Wagner, Falko Jens; Thomsen, Per Grove

    1998-01-01

    This paper presents the results of an ongoing project, dealing with design and implementation of a simulation toolbox based on object oriented modelling techniques. The paper describes an experimental implementation of parts of such a toolbox in C++, and discusses the experiences drawn from that ...... that process. Essential to the work is the focus on simulation of complex dynamical systems, from modelling the single components/subsystems to building complete systemssuch a toolbox in C++, and discusses the experiences drawn from that process....

  6. MMM: A toolbox for integrative structure modeling.

    Science.gov (United States)

    Jeschke, Gunnar

    2018-01-01

    Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM (Multiscale Modeling of Macromolecules) is a Matlab-based open-source modeling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models. MMM does not only integrate various types of restraints, but also various existing modeling tools by providing a common graphical user interface to them. The types of restraints that can support such modeling and the available model types are illustrated by recent application examples. © 2017 The Protein Society.

  7. Testing adaptive toolbox models: a Bayesian hierarchical approach.

    Science.gov (United States)

    Scheibehenne, Benjamin; Rieskamp, Jörg; Wagenmakers, Eric-Jan

    2013-01-01

    Many theories of human cognition postulate that people are equipped with a repertoire of strategies to solve the tasks they face. This theoretical framework of a cognitive toolbox provides a plausible account of intra- and interindividual differences in human behavior. Unfortunately, it is often unclear how to rigorously test the toolbox framework. How can a toolbox model be quantitatively specified? How can the number of toolbox strategies be limited to prevent uncontrolled strategy sprawl? How can a toolbox model be formally tested against alternative theories? The authors show how these challenges can be met by using Bayesian inference techniques. By means of parameter recovery simulations and the analysis of empirical data across a variety of domains (i.e., judgment and decision making, children's cognitive development, function learning, and perceptual categorization), the authors illustrate how Bayesian inference techniques allow toolbox models to be quantitatively specified, strategy sprawl to be contained, and toolbox models to be rigorously tested against competing theories. The authors demonstrate that their approach applies at the individual level but can also be generalized to the group level with hierarchical Bayesian procedures. The suggested Bayesian inference techniques represent a theoretical and methodological advancement for toolbox theories of cognition and behavior.

  8. A Module for Graphical Display of Model Results with the CBP Toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-04-21

    This report describes work performed by the Savannah River National Laboratory (SRNL) in fiscal year 2014 to add enhanced graphical capabilities to display model results in the Cementitious Barriers Project (CBP) Toolbox. Because Version 2.0 of the CBP Toolbox has just been released, the graphing enhancements described in this report have not yet been integrated into a new version of the Toolbox. Instead they have been tested using a standalone GoldSim model and, while they are substantially complete, may undergo further refinement before full implementation. Nevertheless, this report is issued to document the FY14 development efforts which will provide a basis for further development of the CBP Toolbox.

  9. Inspection of NFT-type cask fabrication

    International Nuclear Information System (INIS)

    Takani, M.; Umegaki, O.

    1998-01-01

    NFT-type cask has been developed to transport the high burn-up spent fuel from Japanese nuclear power stations to the reprocessing plant of Japan Nuclear Fuel Limited which is under construction in Rokkasho-mura, Aomori prefecture. NFT placed orders of 53 casks to 5 fabricators in Japan and overseas, and these casks have been fabricated since 1994. There are two types of NFT-type casks for PWR spent fuel and four types of NFT-type cask for BWR spent fuel. These are designed in consideration of the number of spent fuels accommodated into each type of casks and the handling conditions at domestic nuclear power stations. According to Japanese notification, it is required to be confirmed by competent authority that casks are manufactured in accordance with approved designs. Furthermore, additional tests are performed such as through-gauge test for basket and pressure test on the shielding material space to ensure the performance of cask by NFT other than items inspected by the competent authority. In order to enhance maintainability of casks, replacement parts such as bolts and valves are shared as much as possible. (authors)

  10. Reinforcement Toolbox, a Parametric Reinforcement Modelling Tool for Curved Surface Structures

    NARCIS (Netherlands)

    Lauppe, J.; Rolvink, A.; Coenders, J.L.

    2013-01-01

    This paper presents a computational strategy and parametric modelling toolbox which aim at enhancing the design- and production process of reinforcement in freeform curved surface structures. The computational strategy encompasses the necessary steps of raising an architectural curved surface model

  11. A Statistical Toolbox For Mining And Modeling Spatial Data

    Directory of Open Access Journals (Sweden)

    D’Aubigny Gérard

    2016-12-01

    Full Text Available Most data mining projects in spatial economics start with an evaluation of a set of attribute variables on a sample of spatial entities, looking for the existence and strength of spatial autocorrelation, based on the Moran’s and the Geary’s coefficients, the adequacy of which is rarely challenged, despite the fact that when reporting on their properties, many users seem likely to make mistakes and to foster confusion. My paper begins by a critical appraisal of the classical definition and rational of these indices. I argue that while intuitively founded, they are plagued by an inconsistency in their conception. Then, I propose a principled small change leading to corrected spatial autocorrelation coefficients, which strongly simplifies their relationship, and opens the way to an augmented toolbox of statistical methods of dimension reduction and data visualization, also useful for modeling purposes. A second section presents a formal framework, adapted from recent work in statistical learning, which gives theoretical support to our definition of corrected spatial autocorrelation coefficients. More specifically, the multivariate data mining methods presented here, are easily implementable on the existing (free software, yield methods useful to exploit the proposed corrections in spatial data analysis practice, and, from a mathematical point of view, whose asymptotic behavior, already studied in a series of papers by Belkin & Niyogi, suggests that they own qualities of robustness and a limited sensitivity to the Modifiable Areal Unit Problem (MAUP, valuable in exploratory spatial data analysis.

  12. Testing adaptive toolbox models: a Bayesian hierarchical approach

    NARCIS (Netherlands)

    Scheibehenne, B.; Rieskamp, J.; Wagenmakers, E.-J.

    2013-01-01

    Many theories of human cognition postulate that people are equipped with a repertoire of strategies to solve the tasks they face. This theoretical framework of a cognitive toolbox provides a plausible account of intra- and interindividual differences in human behavior. Unfortunately, it is often

  13. Nutrient Film Technique (NFT Hydroponic Monitoring System

    Directory of Open Access Journals (Sweden)

    Helmy Helmy

    2016-10-01

    Full Text Available Plant cultivation using hydroponic is very popular today. Nutrient Film Technique (NFT hydroponic system is commonly used by people. It can be applied indoor or outdoor. Plants in this systemneed nutrient solution to grow well. pH, TDS and temperature of the nutrient solution must be check to ensure plant gets sufficient nutrients. This research aims todevelop monitoring system of NFT hydroponic. Farmer will be able to monitor pH, TDS and temperature online. It will ease farmer to decide which plant is suitable to be cultivated and time to boost growth.Delay of the system will be measured to know system performance. Result shows that pH is directly proportional with TDS. Temperature value has no correlation with pH and TDS. System has highest delay during daylight and afternoon but it will decline in the night and morning. Average of delay in the morning is 11 s, 28.5 s in daylight, 32 s in the afternoon and 17.5 s in the night.

  14. DACE - A Matlab Kriging Toolbox

    DEFF Research Database (Denmark)

    2002-01-01

    DACE, Design and Analysis of Computer Experiments, is a Matlab toolbox for working with kriging approximations to computer models.......DACE, Design and Analysis of Computer Experiments, is a Matlab toolbox for working with kriging approximations to computer models....

  15. A comprehensive validation toolbox for regional ocean models - Outline, implementation and application to the Baltic Sea

    Science.gov (United States)

    Jandt, Simon; Laagemaa, Priidik; Janssen, Frank

    2014-05-01

    The systematic and objective comparison between output from a numerical ocean model and a set of observations, called validation in the context of this presentation, is a beneficial activity at several stages, starting from early steps in model development and ending at the quality control of model based products delivered to customers. Even though the importance of this kind of validation work is widely acknowledged it is often not among the most popular tasks in ocean modelling. In order to ease the validation work a comprehensive toolbox has been developed in the framework of the MyOcean-2 project. The objective of this toolbox is to carry out validation integrating different data sources, e.g. time-series at stations, vertical profiles, surface fields or along track satellite data, with one single program call. The validation toolbox, implemented in MATLAB, features all parts of the validation process - ranging from read-in procedures of datasets to the graphical and numerical output of statistical metrics of the comparison. The basic idea is to have only one well-defined validation schedule for all applications, in which all parts of the validation process are executed. Each part, e.g. read-in procedures, forms a module in which all available functions of this particular part are collected. The interface between the functions, the module and the validation schedule is highly standardized. Functions of a module are set up for certain validation tasks, new functions can be implemented into the appropriate module without affecting the functionality of the toolbox. The functions are assigned for each validation task in user specific settings, which are externally stored in so-called namelists and gather all information of the used datasets as well as paths and metadata. In the framework of the MyOcean-2 project the toolbox is frequently used to validate the forecast products of the Baltic Sea Marine Forecasting Centre. Hereby the performance of any new product

  16. ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling.

    Science.gov (United States)

    Streif, Stefan; Savchenko, Anton; Rumschinski, Philipp; Borchers, Steffen; Findeisen, Rolf

    2012-05-01

    Often competing hypotheses for biochemical networks exist in the form of different mathematical models with unknown parameters. Considering available experimental data, it is then desired to reject model hypotheses that are inconsistent with the data, or to estimate the unknown parameters. However, these tasks are complicated because experimental data are typically sparse, uncertain, and are frequently only available in form of qualitative if-then observations. ADMIT (Analysis, Design and Model Invalidation Toolbox) is a MatLab(TM)-based tool for guaranteed model invalidation, state and parameter estimation. The toolbox allows the integration of quantitative measurement data, a priori knowledge of parameters and states, and qualitative information on the dynamic or steady-state behavior. A constraint satisfaction problem is automatically generated and algorithms are implemented for solving the desired estimation, invalidation or analysis tasks. The implemented methods built on convex relaxation and optimization and therefore provide guaranteed estimation results and certificates for invalidity. ADMIT, tutorials and illustrative examples are available free of charge for non-commercial use at http://ifatwww.et.uni-magdeburg.de/syst/ADMIT/

  17. ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative–quantitative modeling

    Science.gov (United States)

    Streif, Stefan; Savchenko, Anton; Rumschinski, Philipp; Borchers, Steffen; Findeisen, Rolf

    2012-01-01

    Summary: Often competing hypotheses for biochemical networks exist in the form of different mathematical models with unknown parameters. Considering available experimental data, it is then desired to reject model hypotheses that are inconsistent with the data, or to estimate the unknown parameters. However, these tasks are complicated because experimental data are typically sparse, uncertain, and are frequently only available in form of qualitative if–then observations. ADMIT (Analysis, Design and Model Invalidation Toolbox) is a MatLabTM-based tool for guaranteed model invalidation, state and parameter estimation. The toolbox allows the integration of quantitative measurement data, a priori knowledge of parameters and states, and qualitative information on the dynamic or steady-state behavior. A constraint satisfaction problem is automatically generated and algorithms are implemented for solving the desired estimation, invalidation or analysis tasks. The implemented methods built on convex relaxation and optimization and therefore provide guaranteed estimation results and certificates for invalidity. Availability: ADMIT, tutorials and illustrative examples are available free of charge for non-commercial use at http://ifatwww.et.uni-magdeburg.de/syst/ADMIT/ Contact: stefan.streif@ovgu.de PMID:22451270

  18. The SSI TOOLBOX Source Term Model SOSIM - Screening for important radionuclides and parameter sensitivity analysis

    Energy Technology Data Exchange (ETDEWEB)

    Avila Moreno, R.; Barrdahl, R.; Haegg, C.

    1995-05-01

    The main objective of the present study was to carry out a screening and a sensitivity analysis of the SSI TOOLBOX source term model SOSIM. This model is a part of the SSI TOOLBOX for radiological impact assessment of the Swedish disposal concept for high-level waste KBS-3. The outputs of interest for this purpose were: the total released fraction, the time of total release, the time and value of maximum release rate, the dose rates after direct releases of the biosphere. The source term equations were derived and simple equations and methods were proposed for calculation of these. A literature survey has been performed in order to determine a characteristic variation range and a nominal value for each model parameter. In order to reduce the model uncertainties the authors recommend a change in the initial boundary condition for solution of the diffusion equation for highly soluble nuclides. 13 refs.

  19. Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) Users' Workshop Presentations

    Science.gov (United States)

    Litt, Jonathan S. (Compiler)

    2018-01-01

    NASA Glenn Research Center hosted a Users' Workshop on the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) on August 21, 2017. The objective of this workshop was to update the user community on the latest features of T-MATS, and to provide a forum to present work performed using T-MATS. Presentations highlighted creative applications and the development of new features and libraries, and emphasized the flexibility and simulation power of T-MATS.

  20. Model Updating Nonlinear System Identification Toolbox, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology (ZONA) proposes to develop an enhanced model updating nonlinear system identification (MUNSID) methodology that utilizes flight data with...

  1. Tolerance of continuous NFT spectrum to the optical fiber channel impairments

    DEFF Research Database (Denmark)

    Gaiarin, Simone; Da Ros, Francesco; Sørensen, Mads Peter

    2016-01-01

    The impact of launch power, additive white Gaussian noise and fiber loss on the nonlinear Fourier transform (NFT) continuous spectrum is investigated. NFT is shown to undergo lower spectral distortion than the discrete Fourier transform.......The impact of launch power, additive white Gaussian noise and fiber loss on the nonlinear Fourier transform (NFT) continuous spectrum is investigated. NFT is shown to undergo lower spectral distortion than the discrete Fourier transform....

  2. Model Updating Nonlinear System Identification Toolbox, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology proposes to develop an enhanced model updating nonlinear system identification (MUNSID) methodology by adopting the flight data with state-of-the-art...

  3. ECISVIEW. An interactive toolbox for optical model development

    International Nuclear Information System (INIS)

    Koning, A.J.; Van Wijk, J.J.; Delaroche, J.P.

    1997-01-01

    The software package ECISVIEW is a graphical interface built around the multi-disciplinary nuclear reaction code ECIS-95. The key feature of the working method is that the user can specify the value of optical potential parameters as any mathematical function of the energy, A, Z or user defined parameters. This enables us to obtain conveniently the optimal optical potential parameters for a given nucleus over the whole energy region of interest. ECISVIEW makes it possible to simultaneously study the dependence of all calculated angular distributions, polarizations and total cross sections on optical model parameters. This method is perhaps more than 100 times faster than the conventional method of preparing an input file, running the code, editing the output file and finally viewing the data with a graphical program. As an example, a spherical 0-200 MeV nucleon optical model for 90 Zr is presented. A demonstration of ECISVIEW has been given at this Specialist's Meeting. (author)

  4. ECISVIEW. An interactive toolbox for optical model development

    International Nuclear Information System (INIS)

    Koning, A.J.; Van Wijk, J.J.; Delaroche, J.P.

    1997-09-01

    The software package ECISVIEW is a graphical interface built around the multi-disciplinary nuclear reaction code ECIS-95. The basic purpose of ECISVIEW is the possibility to change optical potential parameters interactively, with the keyboard or the mouse, and to display the calculated result immediately on the screen. The key feature of the working method is that the user can specify the value of optical potential parameters as any mathematical function of the energy, A, Z or user defined parameters. This enables us to obtain conveniently the optimal optical potential parameters for a given nucleus over the whole energy region of interest. ECISVIEW makes it possible to simultaneously study the dependence of all calculated angular distributions, polarizations and total cross sections on optical model parameters. This method is perhaps more than 100 times faster than the conventional method of preparing an input file, running the code, editing the output file and finally viewing the data with a graphical program. ECISVIEW has been developed at ECN in Petten, Netherlands, and has been extensively used at CEA, Bruyeres-le-Chatel, France. A spherical 0-200 MeV nucleon optical model for 90 Zr is presented as an example. 4 figs., 1 tab., 5 refs

  5. Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

    Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

    2014-01-01

    NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

  6. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    Science.gov (United States)

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  7. An Emulator Toolbox to Approximate Radiative Transfer Models with Statistical Learning

    Directory of Open Access Journals (Sweden)

    Juan Pablo Rivera

    2015-07-01

    Full Text Available Physically-based radiative transfer models (RTMs help in understanding the processes occurring on the Earth’s surface and their interactions with vegetation and atmosphere. When it comes to studying vegetation properties, RTMs allows us to study light interception by plant canopies and are used in the retrieval of biophysical variables through model inversion. However, advanced RTMs can take a long computational time, which makes them unfeasible in many real applications. To overcome this problem, it has been proposed to substitute RTMs through so-called emulators. Emulators are statistical models that approximate the functioning of RTMs. Emulators are advantageous in real practice because of the computational efficiency and excellent accuracy and flexibility for extrapolation. We hereby present an “Emulator toolbox” that enables analysing multi-output machine learning regression algorithms (MO-MLRAs on their ability to approximate an RTM. The toolbox is included in the free-access ARTMO’s MATLAB suite for parameter retrieval and model inversion and currently contains both linear and non-linear MO-MLRAs, namely partial least squares regression (PLSR, kernel ridge regression (KRR and neural networks (NN. These MO-MLRAs have been evaluated on their precision and speed to approximate the soil vegetation atmosphere transfer model SCOPE (Soil Canopy Observation, Photochemistry and Energy balance. SCOPE generates, amongst others, sun-induced chlorophyll fluorescence as the output signal. KRR and NN were evaluated as capable of reconstructing fluorescence spectra with great precision. Relative errors fell below 0.5% when trained with 500 or more samples using cross-validation and principal component analysis to alleviate the underdetermination problem. Moreover, NN reconstructed fluorescence spectra about 50-times faster and KRR about 800-times faster than SCOPE. The Emulator toolbox is foreseen to open new opportunities in the use of advanced

  8. LIMO EEG: a toolbox for hierarchical LInear MOdeling of ElectroEncephaloGraphic data.

    Science.gov (United States)

    Pernet, Cyril R; Chauveau, Nicolas; Gaspar, Carl; Rousselet, Guillaume A

    2011-01-01

    Magnetic- and electric-evoked brain responses have traditionally been analyzed by comparing the peaks or mean amplitudes of signals from selected channels and averaged across trials. More recently, tools have been developed to investigate single trial response variability (e.g., EEGLAB) and to test differences between averaged evoked responses over the entire scalp and time dimensions (e.g., SPM, Fieldtrip). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data. In addition, LIMO EEG provides robust parametric tests, therefore providing a new and complementary tool in the analysis of neural evoked responses.

  9. DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.

    Science.gov (United States)

    Sherfey, Jason S; Soplata, Austin E; Ardid, Salva; Roberts, Erik A; Stanley, David A; Pittman-Polletta, Benjamin R; Kopell, Nancy J

    2018-01-01

    DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.

  10. LASSIM-A network inference toolbox for genome-wide mechanistic modeling.

    Directory of Open Access Journals (Sweden)

    Rasmus Magnusson

    2017-06-01

    Full Text Available Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM, which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE for gene regulatory networks (GRNs. LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM works in two steps, where it first infers a non-linear ODE system of the pre-specified core gene expression. Second, LASSIM in parallel optimizes the parameters that model the regulation of peripheral genes by core system genes. We showed the usefulness of this method by applying LASSIM to infer a large-scale non-linear model of naïve Th2 cell differentiation, made possible by integrating Th2 specific bindings, time-series together with six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models

  11. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

    Directory of Open Access Journals (Sweden)

    Jensen Paul A

    2011-09-01

    Full Text Available Abstract Background Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model. Results We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae. Conclusion The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.

  12. Production of calla lily grown in an NFT system

    Directory of Open Access Journals (Sweden)

    Paulo Roberto Correa Landgraf

    2017-12-01

    Full Text Available The objective of this study was to evaluate the production of calla lily in an NFT system. The experiment was carried out in a greenhouse, using a 2 x 2 factorial scheme in a completely randomized design (CRD, with fifteen replications. The treatments were a combination of two hydroponic profiles (100 and 150 mm of height and two nutrient solutions. Calla lily plantlets obtained from rhizome buds in trays containing nutrient solution, were transferred to a laminar flow of nutrients, and the experiment lasted 12 months. The height of stems and inflorescences were evaluated, as well as the length and diameter of the inflorescence, the number of flowers per plant and number of flowers per m2 . Growing calla lily plants in an NFT system is feasible. The nutrient solution with the highest concentration of nutrients, particularly N and K, and the profile of 150 mm, are the most suitable for the production of calla lily as a cut flower in a laminar flow of nutrients.

  13. Building the Nanoplasmonics Toolbox Through Shape Modeling and Single Particle Optical Studies

    Science.gov (United States)

    Ringe, Emilie

    Interest in nanotechnology is driven by unprecedented properties tailorability, achievable by controlling particle structure and composition. Unlike bulk components, minute changes in size and shape affect the optical and electronic properties of nanoparticles. Characterization of such structure-function relationships and better understanding of structure control mechanisms is crucial to the development of applications such as plasmonic sensors and devices. The objective of the current research is thus twofold: to theoretically predict and understand how shape is controlled by synthesis conditions, and to experimentally unravel, through single particle studies, how shape, composition, size, and surrounding environment affect plasmonic properties in noble metal particles. Quantitative, predictive rules and fundamental knowledge obtained from this research contributes to the "nanoplasmonics toolbox", a library designed to provide scientists and engineers the tools to create and optimize novel nanotechnology applications. In this dissertation, single particle approaches are developed and used to unravel the effects of size, shape, substrate, aggregation state and surrounding environment on the optical response of metallic nanoparticles. Ag and Au nanocubes on different substrates are first presented, followed by the discussion of the concept of plasmon length, a universal parameter to describe plasmon energy for a variety of particle shapes and plasmon modes. Plasmonic sensing (both refractive index sensing and surface-enhanced Raman spectroscopy) and polarization effects are then studied at the single particle level. In the last two Chapters, analytical shape models based on the Wulff construction provide unique modeling tools for alloy and kinetically grown nanoparticles. The former reveals a size-dependence of the shape of small alloy particles (such as those used in catalysis) because of surface segregation, while the latter uniquely models the shape of many

  14. A Data Analysis Toolbox for Modeling the Global Food-Energy-Water Nexus

    Science.gov (United States)

    AghaKouchak, A.; Sadegh, M.; Mallakpour, I.

    2017-12-01

    Water, Food and energy systems are highly interconnected. More than seventy percent of global water resource is used for food production. Water withdrawal, purification, and transfer systems are energy intensive. Furthermore, energy generation strongly depends on water availability. Therefore, considering the interactions in the nexus of water, food and energy is crucial for sustainable management of available resources. In this presentation, we introduce a user-friendly data analysis toolbox that mines the available global data on food, energy and water, and analyzes their interactions. This toolbox provides estimates of water footprint for a wide range of food types in different countries and also approximates the required energy and water resources. The toolbox also provides estimates of the corresponding emissions and biofuel production of different crops. In summary, this toolbox allows evaluating dependencies of the food, energy, and water systems at the country scale. We present global analysis of the interactions between water, food and energy from different perspectives including efficiency and diversity of resources use.

  15. Virtual toolbox

    Science.gov (United States)

    Jacobus, Charles J.; Jacobus, Heidi N.; Mitchell, Brian T.; Riggs, A. J.; Taylor, Mark J.

    1993-04-01

    At least three of the five senses must be fully addressed in a successful virtual reality (VR) system. Sight, sound, and touch are the most critical elements for the creation of the illusion of presence. Since humans depend so much on sight to collect information about their environment, this area has been the focus of much of the prior art in virtual reality, however, it is also crucial that we provide facilities for force, torque, and touch reflection, and sound replay and 3-D localization. In this paper we present a sampling of hardware and software in the virtual environment maker's `toolbox' which can support rapidly building up of customized VR systems. We provide demonstrative examples of how some of the tools work and we speculate about VR applications and future technology needs.

  16. a Matlab Toolbox for Basin Scale Fluid Flow Modeling Applied to Hydrology and Geothermal Energy

    Science.gov (United States)

    Alcanie, M.; Lupi, M.; Carrier, A.

    2017-12-01

    Recent boosts in the development of geothermal energy were fostered by the latest oil crises and by the need of reducing CO2 emissions generated by the combustion of fossil fuels. Various numerical codes (e.g. FEHM, CSMP++, HYDROTHERM, TOUGH) have thus been implemented for the simulation and quantification of fluid flow in the upper crust. One possible limitation of such codes is the limited accessibility and the complex structure of the simulators. For this reason, we began to develop a Hydrothermal Fluid Flow Matlab library as part of MRST (Matlab Reservoir Simulation Toolbox). MRST is designed for the simulation of oil and gas problems including carbon capture storage. However, a geothermal module is still missing. We selected the Geneva Basin as a natural laboratory because of the large amount of data available in the region. The Geneva Basin has been intensely investigated in the past with exploration wells, active seismic and gravity surveys. In addition, the energy strategy of Switzerland promotes the development of geothermal energy that lead to recent geophysical prospections. Previous and ongoing projects have shown the geothermal potential of the Geneva Basin but a consistent fluid flow model assessing the deep circulation in the region is yet to be defined. The first step of the study was to create the basin-scale static model. We integrated available active seismic, gravity inversions and borehole data to describe the principal geologic and tectonic features of the Geneva Basin. Petrophysical parameters were obtained from available and widespread well logs. This required adapting MRST to standard text format file imports and outline a new methodology for quick static model creation in an open source environment. We implemented several basin-scale fluid flow models to test the effects of petrophysical properties on the circulation dynamics of deep fluids in the Geneva Basin. Preliminary results allow the identification of preferential fluid flow

  17. The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

    Science.gov (United States)

    Agren, Rasmus; Liu, Liming; Shoaie, Saeed; Vongsangnak, Wanwipa; Nookaew, Intawat; Nielsen, Jens

    2013-01-01

    We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production. PMID:23555215

  18. ESA Atmospheric Toolbox

    Science.gov (United States)

    Niemeijer, Sander

    2017-04-01

    The ESA Atmospheric Toolbox (BEAT) is one of the ESA Sentinel Toolboxes. It consists of a set of software components to read, analyze, and visualize a wide range of atmospheric data products. In addition to the upcoming Sentinel-5P mission it supports a wide range of other atmospheric data products, including those of previous ESA missions, ESA Third Party missions, Copernicus Atmosphere Monitoring Service (CAMS), ground based data, etc. The toolbox consists of three main components that are called CODA, HARP and VISAN. CODA provides interfaces for direct reading of data from earth observation data files. These interfaces consist of command line applications, libraries, direct interfaces to scientific applications (IDL and MATLAB), and direct interfaces to programming languages (C, Fortran, Python, and Java). CODA provides a single interface to access data in a wide variety of data formats, including ASCII, binary, XML, netCDF, HDF4, HDF5, CDF, GRIB, RINEX, and SP3. HARP is a toolkit for reading, processing and inter-comparing satellite remote sensing data, model data, in-situ data, and ground based remote sensing data. The main goal of HARP is to assist in the inter-comparison of datasets. By appropriately chaining calls to HARP command line tools one can pre-process datasets such that two datasets that need to be compared end up having the same temporal/spatial grid, same data format/structure, and same physical unit. The toolkit comes with its own data format conventions, the HARP format, which is based on netcdf/HDF. Ingestion routines (based on CODA) allow conversion from a wide variety of atmospheric data products to this common format. In addition, the toolbox provides a wide range of operations to perform conversions on the data such as unit conversions, quantity conversions (e.g. number density to volume mixing ratios), regridding, vertical smoothing using averaging kernels, collocation of two datasets, etc. VISAN is a cross-platform visualization and

  19. Accelerator Toolbox for MATLAB

    International Nuclear Information System (INIS)

    Terebilo, Andrei

    2001-01-01

    This paper introduces Accelerator Toolbox (AT)--a collection of tools to model particle accelerators and beam transport lines in the MATLAB environment. At SSRL, it has become the modeling code of choice for the ongoing design and future operation of the SPEAR 3 synchrotron light source. AT was designed to take advantage of power and simplicity of MATLAB--commercially developed environment for technical computing and visualization. Many examples in this paper illustrate the advantages of the AT approach and contrast it with existing accelerator code frameworks

  20. Watershed Modeling Applications with the Open-Access Modular Distributed Watershed Educational Toolbox (MOD-WET) and Introductory Hydrology Textbook

    Science.gov (United States)

    Huning, L. S.; Margulis, S. A.

    2014-12-01

    Traditionally, introductory hydrology courses focus on hydrologic processes as independent or semi-independent concepts that are ultimately integrated into a watershed model near the end of the term. When an "off-the-shelf" watershed model is introduced in the curriculum, this approach can result in a potential disconnect between process-based hydrology and the inherent interconnectivity of processes within the water cycle. In order to curb this and reduce the learning curve associated with applying hydrologic concepts to complex real-world problems, we developed the open-access Modular Distributed Watershed Educational Toolbox (MOD-WET). The user-friendly, MATLAB-based toolbox contains the same physical equations for hydrological processes (i.e. precipitation, snow, radiation, evaporation, unsaturated flow, infiltration, groundwater, and runoff) that are presented in the companion e-textbook (http://aqua.seas.ucla.edu/margulis_intro_to_hydro_textbook.html) and taught in the classroom. The modular toolbox functions can be used by students to study individual hydrologic processes. These functions are integrated together to form a simple spatially-distributed watershed model, which reinforces a holistic understanding of how hydrologic processes are interconnected and modeled. Therefore when watershed modeling is introduced, students are already familiar with the fundamental building blocks that have been unified in the MOD-WET model. Extensive effort has been placed on the development of a highly modular and well-documented code that can be run on a personal computer within the commonly-used MATLAB environment. MOD-WET was designed to: 1) increase the qualitative and quantitative understanding of hydrological processes at the basin-scale and demonstrate how they vary with watershed properties, 2) emphasize applications of hydrologic concepts rather than computer programming, 3) elucidate the underlying physical processes that can often be obscured with a complicated

  1. Improving student comprehension of the interconnectivity of the hydrologic cycle with a novel 'hydrology toolbox', integrated watershed model, and companion textbook

    Science.gov (United States)

    Huning, L. S.; Margulis, S. A.

    2013-12-01

    Concepts in introductory hydrology courses are often taught in the context of process-based modeling that ultimately is integrated into a watershed model. In an effort to reduce the learning curve associated with applying hydrologic concepts to real-world applications, we developed and incorporated a 'hydrology toolbox' that complements a new, companion textbook into introductory undergraduate hydrology courses. The hydrology toolbox contains the basic building blocks (functions coded in MATLAB) for an integrated spatially-distributed watershed model that makes hydrologic topics (e.g. precipitation, snow, radiation, evaporation, unsaturated flow, infiltration, groundwater, and runoff) more user-friendly and accessible for students. The toolbox functions can be used in a modular format so that students can study individual hydrologic processes and become familiar with the hydrology toolbox. This approach allows such courses to emphasize understanding and application of hydrologic concepts rather than computer coding or programming. While topics in introductory hydrology courses are often introduced and taught independently or semi-independently, they are inherently interconnected. These toolbox functions are therefore linked together at the end of the course to reinforce a holistic understanding of how these hydrologic processes are measured, interconnected, and modeled. They are integrated into a spatially-distributed watershed model or numerical laboratory where students can explore a range of topics such as rainfall-runoff modeling, urbanization, deforestation, watershed response to changes in parameters or forcings, etc. Model output can readily be visualized and analyzed by students to understand watershed response in a real river basin or a simple 'toy' basin. These tools complement the textbook, each of which has been well received by students in multiple hydrology courses with various disciplinary backgrounds. The same governing equations that students have

  2. GOCE User Toolbox and Tutorial

    Science.gov (United States)

    Knudsen, Per; Benveniste, Jerome

    2017-04-01

    The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products.
GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information
and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced
computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations,
and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT
Install Guide. A set of a-priori data and models are made available as well. Without any doubt the development
of the GOCE user toolbox have played a major role in paving the way to successful use of the GOCE data for
oceanography. The GUT version 2.2 was released in April 2014 and beside some bug-fixes it adds the capability for the computation of Simple Bouguer Anomaly (Solid-Earth). During this fall a new GUT version 3 has been released. GUTv3 was further developed through a collaborative effort where the scientific communities participate aiming
on an implementation of remaining functionalities facilitating a wider span of research in the fields of Geodesy,
Oceanography and Solid earth studies.
Accordingly, the GUT version 3 has:
 - An attractive and easy to use Graphic User Interface (GUI) for the toolbox,
 - Enhance the toolbox with some further software functionalities such as to facilitate the use of gradients,
anisotropic diffusive filtering and computation of Bouguer and isostatic gravity anomalies.
 - An associated GUT VCM tool for analyzing the GOCE variance covariance matrices.

  3. GOCE user toolbox and tutorial

    DEFF Research Database (Denmark)

    Knudsen, Per; Benveniste, Jerome

    2011-01-01

    consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made...

  4. The Life Cycle Analysis Toolbox

    International Nuclear Information System (INIS)

    Bishop, L.; Tonn, B.E.; Williams, K.A.; Yerace, P.; Yuracko, K.L.

    1999-01-01

    The life cycle analysis toolbox is a valuable integration of decision-making tools and supporting materials developed by Oak Ridge National Laboratory (ORNL) to help Department of Energy managers improve environmental quality, reduce costs, and minimize risk. The toolbox provides decision-makers access to a wide variety of proven tools for pollution prevention (P2) and waste minimization (WMin), as well as ORNL expertise to select from this toolbox exactly the right tool to solve any given P2/WMin problem. The central element of the toolbox is a multiple criteria approach to life cycle analysis developed specifically to aid P2/WMin decision-making. ORNL has developed numerous tools that support this life cycle analysis approach. Tools are available to help model P2/WMin processes, estimate human health risks, estimate costs, and represent and manipulate uncertainties. Tools are available to help document P2/WMin decision-making and implement programs. Tools are also available to help track potential future environmental regulations that could impact P2/WMin programs and current regulations that must be followed. An Internet-site will provide broad access to the tools

  5. Channel Access Client Toolbox for Matlab

    International Nuclear Information System (INIS)

    2002-01-01

    This paper reports on MATLAB Channel Access (MCA) Toolbox--MATLAB [1] interface to EPICS Channel Access (CA) client library. We are developing the toolbox for SPEAR3 accelerator controls, but it is of general use for accelerator and experimental physics applications programming. It is packaged as a MATLAB toolbox to allow easy development of complex CA client applications entirely in MATLAB. The benefits include: the ability to calculate and display parameters that use EPICS process variables as inputs, availability of MATLAB graphics tools for user interface design, and integration with the MATLABbased accelerator modeling software - Accelerator Toolbox [2-4]. Another purpose of this paper is to propose a feasible path to a synergy between accelerator control systems and accelerator simulation codes, the idea known as on-line accelerator model

  6. Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order.

    Science.gov (United States)

    Aron, Miles; Browning, Richard; Carugo, Dario; Sezgin, Erdinc; Bernardino de la Serna, Jorge; Eggeling, Christian; Stride, Eleanor

    2017-05-12

    Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually characterized by the generalized polarization (GP) parameter. With the development of commercial microscopes equipped with spectral detectors, spectral imaging has become a convenient and powerful technique for measuring GP and other membrane properties. The existing tools for spectral image processing, however, are insufficient for processing the large data sets afforded by this technological advancement, and are unsuitable for processing images acquired with rapidly internalized fluorescent probes. Here we present a MATLAB spectral imaging toolbox with the aim of overcoming these limitations. In addition to common operations, such as the calculation of distributions of GP values, generation of pseudo-colored GP maps, and spectral analysis, a key highlight of this tool is reliable membrane segmentation for probes that are rapidly internalized. Furthermore, handling for hyperstacks, 3D reconstruction and batch processing facilitates analysis of data sets generated by time series, z-stack, and area scan microscope operations. Finally, the object size distribution is determined, which can provide insight into the mechanisms underlying changes in membrane properties and is desirable for e.g. studies involving model membranes and surfactant coated particles. Analysis is demonstrated for cell membranes, cell-derived vesicles, model membranes, and microbubbles with environmentally-sensitive probes Laurdan, carboxyl-modified Laurdan (C-Laurdan), Di-4-ANEPPDHQ, and Di-4-AN(F)EPPTEA (FE), for quantification of the local lateral density of lipids or lipid packing. The Spectral Imaging Toolbox is a powerful tool for the segmentation and processing of large spectral imaging datasets with a reliable method for membrane segmentation and no ability in programming required. The

  7. Air Sensor Toolbox

    Science.gov (United States)

    Air Sensor Toolbox provides information to citizen scientists, researchers and developers interested in learning more about new lower-cost compact air sensor technologies and tools for measuring air quality.

  8. The Modular Modeling System (MMS): A toolbox for water- and environmental-resources management

    Science.gov (United States)

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

    2005-01-01

    The increasing complexity of water- and environmental-resource problems require modeling approaches that incorporate knowledge from a broad range of scientific and software disciplines. To address this need, the U.S. Geological Survey (USGS) has developed the Modular Modeling System (MMS). MMS is an integrated system of computer software for model development, integration, and application. Its modular design allows a high level of flexibility and adaptability to enable modelers to incorporate their own software into a rich array of built-in models and modeling tools. These include individual process models, tightly coupled models, loosely coupled models, and fully- integrated decision support systems. A geographic information system (GIS) interface, the USGS GIS Weasel, has been integrated with MMS to enable spatial delineation and characterization of basin and ecosystem features, and to provide objective parameter-estimation methods for models using available digital data. MMS provides optimization and sensitivity-analysis tools to analyze model parameters and evaluate the extent to which uncertainty in model parameters affects uncertainty in simulation results. MMS has been coupled with the Bureau of Reclamation object-oriented reservoir and river-system modeling framework, RiverWare, to develop models to evaluate and apply optimal resource-allocation and management strategies to complex, operational decisions on multipurpose reservoir systems and watersheds. This decision support system approach has been developed, tested, and implemented in the Gunnison, Yakima, San Joaquin, Rio Grande, and Truckee River basins of the western United States. MMS is currently being coupled with the U.S. Forest Service model SIMulating Patterns and Processes at Landscape Scales (SIMPPLLE) to assess the effects of alternative vegetation-management strategies on a variety of hydrological and ecological responses. Initial development and testing of the MMS-SIMPPLLE integration is

  9. GOCE User Toolbox and Tutorial

    Science.gov (United States)

    Knudsen, P.; Benveniste, J.

    2011-07-01

    The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made available as well. GUT has been developed in a collaboration within the GUT Core Group. The GUT Core Group: S. Dinardo, D. Serpe, B.M. Lucas, R. Floberghagen, A. Horvath (ESA), O. Andersen, M. Herceg (DTU), M.-H. Rio, S. Mulet, G. Larnicol (CLS), J. Johannessen, L.Bertino (NERSC), H. Snaith, P. Challenor (NOC), K. Haines, D. Bretherton (NCEO), C. Hughes (POL), R.J. Bingham (NU), G. Balmino, S. Niemeijer, I. Price, L. Cornejo (S&T), M. Diament, I Panet (IPGP), C.C. Tscherning (KU), D. Stammer, F. Siegismund (UH), T. Gruber (TUM),

  10. The ABRAVIBE toolbox for teaching vibration analysis and structural dynamics

    DEFF Research Database (Denmark)

    Brandt, A.

    2013-01-01

    , a MATLAB toolbox (the ABRAVIBE toolbox) has been developed as an accompanying toolbox for the recent book "Noise and Vibration Analysis" by the author. This free, open software, published under GNU Public License, can be used with GNU Octave, if an entirely free software platform is wanted, with a few...... functional limitations. The toolbox includes functionality for simulation of mechanical models as well as advanced analysis such as time series analysis, spectral analysis, frequency response and correlation function estimation, modal parameter extraction, and rotating machinery analysis (order tracking...

  11. An open-source Java-based Toolbox for environmental model evaluation: The MOUSE Software Application

    Science.gov (United States)

    A consequence of environmental model complexity is that the task of understanding how environmental models work and identifying their sensitivities/uncertainties, etc. becomes progressively more difficult. Comprehensive numerical and visual evaluation tools have been developed such as the Monte Carl...

  12. Overview and application of the Model Optimization, Uncertainty, and SEnsitivity Analysis (MOUSE) toolbox

    Science.gov (United States)

    For several decades, optimization and sensitivity/uncertainty analysis of environmental models has been the subject of extensive research. Although much progress has been made and sophisticated methods developed, the growing complexity of environmental models to represent real-world systems makes it...

  13. A Simulation Platform To Model, Optimize And Design Wind Turbines. The Matlab/Simulink Toolbox

    Directory of Open Access Journals (Sweden)

    Anca Daniela HANSEN

    2002-12-01

    Full Text Available In the last years Matlab / Simulink® has become the most used software for modeling and simulation of dynamic systems. Wind energy conversion systems are for example such systems, containing subsystems with different ranges of the time constants: wind, turbine, generator, power electronics, transformer and grid. The electrical generator and the power converter need the smallest simulation step and therefore, these blocks decide the simulation speed. This paper presents a new and integrated simulation platform for modeling, optimizing and designing wind turbines. The platform contains different simulation tools: Matlab / Simulink - used as basic modeling tool, HAWC, DIgSilent and Saber.

  14. Traffic analysis toolbox volume XI : weather and traffic analysis, modeling and simulation.

    Science.gov (United States)

    2010-12-01

    This document presents a weather module for the traffic analysis tools program. It provides traffic engineers, transportation modelers and decisions makers with a guide that can incorporate weather impacts into transportation system analysis and mode...

  15. MOtoNMS : A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation

    NARCIS (Netherlands)

    Mantoan, Alice; Pizzolato, Claudio; Sartori, Massimo; Sawacha, Zimi; Cobelli, Claudio; Reggiani, Monica

    2015-01-01

    Background: Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical practice. However, a major factor limiting this translation is the lack of robust

  16. Regensim – Matlab toolbox for renewable energy sources modelling and simulation

    Directory of Open Access Journals (Sweden)

    Cristian Dragoş Dumitru

    2011-12-01

    Full Text Available This paper deals with the implementation and development of a Matlab Simulink library named RegenSim designed for modeling, simulations and analysis of real hybrid solarwind-hydro systems connected to local grids. Blocks like wind generators, hydro generators, solar photovoltaic modules and accumulators are implemented. The main objective is the study of the hybrid power system behavior, which allows employing renewable and variable in time energy sources while providing a continuous supply.

  17. TecDEM: A MATLAB Based Toolbox for understanding Tectonics from Digital Elevation Models

    Science.gov (United States)

    Shahzad, F.; Mahmood, S. A.; Gloaguen, R.

    2009-04-01

    TecDEM is a MATLAB based tool box for understanding the tectonics from digital elevation models (DEMs) of any area. These DEMs can be derived from data of any spatial resolution (Low, medium and High). In the first step we extract drainage network from the DEMs using flow grid approach. Drainage network is a group of streams having elevation and catchment area information as a function of spatial locations. We implement an array of stream structure to study this drainage network. Knickpoints can be identified on each stream of the drainage network by a graphical user interface and are helpful for understanding stream morphology. Stream profile analysis in steady state condition is applied on all streams to calculate geomorphic parameters and regional uplift rates. Hack index is calculated for all the profiles at a certain interval and over the change of knickpoints. Reports menu of this tool box generates detailed statistics report, complete tabulated report, graphical output of each analyzed stream profile and Hack index profile. All the calculated values are part of stream structure and is saved as .mat file for later use with this tool box. The spatial distribution of geomorphic parameters, uplift rates and knickpoints are exported as a shape files for visualization in professional GIS software. We test this tool box on DEMs from different tectonic settings worldwide and received verifiable results with other studies.

  18. The renormalization of collective states and the improper initial or final states in NFT

    International Nuclear Information System (INIS)

    Bes, D.R.; Dussel, G.G.; Perazzo, R.P.J.; Sofia, H.M.

    1978-01-01

    The collective lines in a given diagram are renormalized by including higher order processes. The problem is cast into the form of a conventional linear algebraic matrix equation that allows a simple treatment of the normalization conditions. It is shown that the states entering in the renormalization of the phonons become improper initial or final states, if dressed phonons are used in the intermediate states. A simple extension of this argument allows one to justify one of the rules given in the formulation of the NFT. (Auth.)

  19. The ROC Toolbox: A toolbox for analyzing receiver-operating characteristics derived from confidence ratings.

    Science.gov (United States)

    Koen, Joshua D; Barrett, Frederick S; Harlow, Iain M; Yonelinas, Andrew P

    2017-08-01

    Signal-detection theory, and the analysis of receiver-operating characteristics (ROCs), has played a critical role in the development of theories of episodic memory and perception. The purpose of the current paper is to present the ROC Toolbox. This toolbox is a set of functions written in the Matlab programming language that can be used to fit various common signal detection models to ROC data obtained from confidence rating experiments. The goals for developing the ROC Toolbox were to create a tool (1) that is easy to use and easy for researchers to implement with their own data, (2) that can flexibly define models based on varying study parameters, such as the number of response options (e.g., confidence ratings) and experimental conditions, and (3) that provides optimal routines (e.g., Maximum Likelihood estimation) to obtain parameter estimates and numerous goodness-of-fit measures.The ROC toolbox allows for various different confidence scales and currently includes the models commonly used in recognition memory and perception: (1) the unequal variance signal detection (UVSD) model, (2) the dual process signal detection (DPSD) model, and (3) the mixture signal detection (MSD) model. For each model fit to a given data set the ROC toolbox plots summary information about the best fitting model parameters and various goodness-of-fit measures. Here, we present an overview of the ROC Toolbox, illustrate how it can be used to input and analyse real data, and finish with a brief discussion on features that can be added to the toolbox.

  20. Broadview Radar Altimetry Toolbox

    Science.gov (United States)

    Garcia-Mondejar, Albert; Escolà, Roger; Moyano, Gorka; Roca, Mònica; Terra-Homem, Miguel; Friaças, Ana; Martinho, Fernando; Schrama, Ernst; Naeije, Marc; Ambrózio, Américo; Restano, Marco; Benveniste, Jérôme

    2017-04-01

    The universal altimetry toolbox, BRAT (Broadview Radar Altimetry Toolbox) which can read all previous and current altimetry missions' data, incorporates now the capability to read the upcoming Sentinel3 L1 and L2 products. ESA endeavoured to develop and supply this capability to support the users of the future Sentinel3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats. The BratGUI is the frontend for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with MATLAB/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the dataformatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as NetCDF, ASCII text files, KML (Google Earth) and raster images (JPEG, PNG, etc.). Several kinds of computations can be done within BRAT involving combinations of data fields that the user can save for posterior reuse or using the already embedded formulas that include the standard oceanographic altimetry formulas. The Radar Altimeter Tutorial, that contains a strong introduction to altimetry, shows its applications in different fields such as Oceanography, Cryosphere, Geodesy, Hydrology among others. Included are also "use cases", with step-by-step examples, on how to use the toolbox in the different contexts. The Sentinel3 SAR Altimetry Toolbox shall benefit from the current BRAT version. While developing the toolbox we will revamp of the Graphical User Interface and provide, among other enhancements, support for reading the upcoming S3 datasets and specific

  1. Implementasi Fuzzy Logic Controller untuk Mengatur Ph Nutrisi pada Sistem Hidroponik Nutrient Film Technique (NFT

    Directory of Open Access Journals (Sweden)

    Dian Pancawati

    2016-07-01

    Full Text Available One solution to solve limited agricultural land is applying hydroponics Nutrient Film Technique (NFT. The advantage of NFT is using water circulated as a growing medium in order to obtain water, nutrients and oxygen to accelerate the growth of plants with good results. The most important parameter is the pH of nutrients. This article discusses how to design an automatic nutritional pH control system by implementing the method of Fuzzy Logic Controller. The control system use Arduino Mega2560, Analog pH Meter Kit as input, and the solenoid valve as actuators. The best response of the implementation of Fuzzy Logic Controller with the system which has 25 rules. The response shows that the system has in 1200 millisecond rise time and the steady state in 5530 milliseconds to increase the pH. While to decrease the pH system has response of rise time at 2000 milliseconds and steady state at the time of 3000 milliseconds. The system is able to maintain the pH at 5.5, with the result of the growth of lettuce as high as 20 cm and seven leaves for 54 days.

  2. ICT: isotope correction toolbox.

    Science.gov (United States)

    Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

    2016-01-01

    Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Development of a Twin-Spool Turbofan Engine Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

    Zinnecker, Alicia M.; Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.

    2014-01-01

    The Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) is a tool that has been developed to allow a user to build custom models of systems governed by thermodynamic principles using a template to model each basic process. Validation of this tool in an engine model application was performed through reconstruction of the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) (v2) using the building blocks from the T-MATS (v1) library. In order to match the two engine models, it was necessary to address differences in several assumptions made in the two modeling approaches. After these modifications were made, validation of the engine model continued by integrating both a steady-state and dynamic iterative solver with the engine plant and comparing results from steady-state and transient simulation of the T-MATS and C-MAPSS models. The results show that the T-MATS engine model was accurate within 3% of the C-MAPSS model, with inaccuracy attributed to the increased dimension of the iterative solver solution space required by the engine model constructed using the T-MATS library. This demonstrates that, given an understanding of the modeling assumptions made in T-MATS and a baseline model, the T-MATS tool provides a viable option for constructing a computational model of a twin-spool turbofan engine that may be used in simulation studies.

  4. Development of a Twin-spool Turbofan Engine Simulation Using the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

    Zinnecker, Alicia M.; Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Johathan S.

    2014-01-01

    The Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS) is a tool that has been developed to allow a user to build custom models of systems governed by thermodynamic principles using a template to model each basic process. Validation of this tool in an engine model application was performed through reconstruction of the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) (v2) using the building blocks from the T-MATS (v1) library. In order to match the two engine models, it was necessary to address differences in several assumptions made in the two modeling approaches. After these modifications were made, validation of the engine model continued by integrating both a steady-state and dynamic iterative solver with the engine plant and comparing results from steady-state and transient simulation of the T-MATS and C-MAPSS models. The results show that the T-MATS engine model was accurate within 3 of the C-MAPSS model, with inaccuracy attributed to the increased dimension of the iterative solver solution space required by the engine model constructed using the T-MATS library. This demonstrates that, given an understanding of the modeling assumptions made in T-MATS and a baseline model, the T-MATS tool provides a viable option for constructing a computational model of a twin-spool turbofan engine that may be used in simulation studies.

  5. A DOE Computer Code Toolbox: Issues and Opportunities

    International Nuclear Information System (INIS)

    Vincent, A.M. III

    2001-01-01

    The initial activities of a Department of Energy (DOE) Safety Analysis Software Group to establish a Safety Analysis Toolbox of computer models are discussed. The toolbox shall be a DOE Complex repository of verified and validated computer models that are configuration-controlled and made available for specific accident analysis applications. The toolbox concept was recommended by the Defense Nuclear Facilities Safety Board staff as a mechanism to partially address Software Quality Assurance issues. Toolbox candidate codes have been identified through review of a DOE Survey of Software practices and processes, and through consideration of earlier findings of the Accident Phenomenology and Consequence Evaluation program sponsored by the DOE National Nuclear Security Agency/Office of Defense Programs. Planning is described to collect these high-use codes, apply tailored SQA specific to the individual codes, and implement the software toolbox concept. While issues exist such as resource allocation and the interface among code developers, code users, and toolbox maintainers, significant benefits can be achieved through a centralized toolbox and subsequent standardized applications

  6. Presentation of the International Building Physics Toolbox for Simulink

    DEFF Research Database (Denmark)

    Weitzmann, Peter; Sasic Kalagasidis, Angela; Nielsen, Toke Rammer

    2003-01-01

    The international building physics toolbox (IBPT) is a software library specially constructed for HAM system analysis in building physics. The toolbox is constructed as a modular structure of the standard building elements using the graphical programming language Simulink. Two research groups have...... participated in this project. In order to enable the development of the toolbox, a common modelling platform was defined: a set of unique communication signals, material database and documentation protocol. The IBPT is open source and publicly available on the Internet. Any researcher and student can use...

  7. Ubuntu Linux toolbox

    CERN Document Server

    Negus, Christopher

    2012-01-01

    This bestseller from Linux guru Chris Negus is packed with an array of new and revised material As a longstanding bestseller, Ubuntu Linux Toolbox has taught you how to get the most out Ubuntu, the world?s most popular Linux distribution. With this eagerly anticipated new edition, Christopher Negus returns with a host of new and expanded coverage on tools for managing file systems, ways to connect to networks, techniques for securing Ubuntu systems, and a look at the latest Long Term Support (LTS) release of Ubuntu, all aimed at getting you up and running with Ubuntu Linux quickly.

  8. NEMO: A Stellar Dynamics Toolbox

    Science.gov (United States)

    Barnes, Joshua; Hut, Piet; Teuben, Peter

    2010-10-01

    NEMO is an extendible Stellar Dynamics Toolbox, following an Open-Source Software model. It has various programs to create, integrate, analyze and visualize N-body and SPH like systems, following the pipe and filter architecture. In addition there are various tools to operate on images, tables and orbits, including FITS files to export/import to/from other astronomical data reduction packages. A large growing fraction of NEMO has been contributed by a growing list of authors. The source code consist of a little over 4000 files and a little under 1,000,000 lines of code and documentation, mostly C, and some C++ and Fortran. NEMO development started in 1986 in Princeton (USA) by Barnes, Hut and Teuben. See also ZENO (ascl:1102.027) for the version that Barnes maintains.

  9. ESA BRAT (Broadview Radar Altimetry Toolbox) and GUT (GOCE User Toolbox) toolboxes

    Science.gov (United States)

    Benveniste, J.; Ambrozio, A.; Restano, M.

    2016-12-01

    The Broadview Radar Altimetry Toolbox (BRAT) is a collection of tools designed to facilitate the processing of radar altimetry data from previous and current altimetry missions, including the upcoming Sentinel-3A L1 and L2 products. A tutorial is included providing plenty of use cases. BRAT's future release (4.0.0) is planned for September 2016. Based on the community feedback, the frontend has been further improved and simplified whereas the capability to use BRAT in conjunction with MATLAB/IDL or C/C++/Python/Fortran, allowing users to obtain desired data bypassing the data-formatting hassle, remains unchanged. Several kinds of computations can be done within BRAT involving the combination of data fields, that can be saved for future uses, either by using embedded formulas including those from oceanographic altimetry, or by implementing ad-hoc Python modules created by users to meet their needs. BRAT can also be used to quickly visualise data, or to translate data into other formats, e.g. from NetCDF to raster images. The GOCE User Toolbox (GUT) is a compilation of tools for the use and the analysis of GOCE gravity field models. It facilitates using, viewing and post-processing GOCE L2 data and allows gravity field data, in conjunction and consistently with any other auxiliary data set, to be pre-processed by beginners in gravity field processing, for oceanographic and hydrologic as well as for solid earth applications at both regional and global scales. Hence, GUT facilitates the extensive use of data acquired during GRACE and GOCE missions. In the current 3.0 version, GUT has been outfitted with a graphical user interface allowing users to visually program data processing workflows. Further enhancements aiming at facilitating the use of gradients, the anisotropic diffusive filtering, and the computation of Bouguer and isostatic gravity anomalies have been introduced. Packaged with GUT is also GUT's VCM (Variance-Covariance Matrix) tool for analysing GOCE

  10. PENGENDALIAN KUALITAS PADA RANTAI PASOK SAYURAN SELADA DENGAN TEKNIK BUDIDAYA HIDROPONIK NFT

    Directory of Open Access Journals (Sweden)

    Fristy Yuanita

    2017-07-01

    Full Text Available Tujuan dari penelitian mengenai pengendalian kualitas pada rantai pasok sayuran selada NFT (Nutrient Film Technique adalah untuk melihat kinerja pelaku yang ada dalam rantai pasok sebagai upaya dalam pengendalian kualitas produk dalam bisnis pertanian. Penelitian dilakukan pada PT. Momenta Agrikultura “Amazing Farm” yang berlokasi di Desa Cikahuripan Kampung Cisaroni RT 002/008, Kecamatan Lembang, Kabupaten Bandung Barat, Jawa Barat Indonesia. Desain penelitian yang digunakan dalam penelitian ini adalah desain kualitatif didukung data kuantitatif dengan teknik penelitian yang digunakan adalah studi kasus. Pengambilan sampel yang digunakan adalah metode purposive sampling. Data yang diperoleh adalah data primer dan data sekunder. Analisis data menggunakan analisis deskriptif. Hasil penelitian menunjukkan permasalahan utama adalah kontrak yang tidak memadai serta penanganan yang kasar disebabkan kurangnya pengawasan dan evaluasi kinerja secara rutin, serta pengendalian kualitas proses produksi pada rantai pasok selada dilakukan oleh pemasok dan PT Momenta Agrikultura “Amazing Farm”. Kinerja PT Momenta Agrikultura “Amazing Farm” mendekati empat sigma, yang mana merupakan standar industri Amerika dan melebihi standar kebanyakan industri di Indonesia. Tindakan pada perbaikan dan pengendalian yang diusulkan yaitu pembenahan kontrak, pembagian informasi, perbaikan metode kerja dan mengu-rangi resiko penurunan kualitas dengan Standard Operating Procedure (SOP pada Packing House agar lebih steril, efektif, dan efisien.

  11. HYDRORECESSION: A toolbox for streamflow recession analysis

    Science.gov (United States)

    Arciniega, S.

    2015-12-01

    Streamflow recession curves are hydrological signatures allowing to study the relationship between groundwater storage and baseflow and/or low flows at the catchment scale. Recent studies have showed that streamflow recession analysis can be quite sensitive to the combination of different models, extraction techniques and parameter estimation methods. In order to better characterize streamflow recession curves, new methodologies combining multiple approaches have been recommended. The HYDRORECESSION toolbox, presented here, is a Matlab graphical user interface developed to analyse streamflow recession time series with the support of different tools allowing to parameterize linear and nonlinear storage-outflow relationships through four of the most useful recession models (Maillet, Boussinesq, Coutagne and Wittenberg). The toolbox includes four parameter-fitting techniques (linear regression, lower envelope, data binning and mean squared error) and three different methods to extract hydrograph recessions segments (Vogel, Brutsaert and Aksoy). In addition, the toolbox has a module that separates the baseflow component from the observed hydrograph using the inverse reservoir algorithm. Potential applications provided by HYDRORECESSION include model parameter analysis, hydrological regionalization and classification, baseflow index estimates, catchment-scale recharge and low-flows modelling, among others. HYDRORECESSION is freely available for non-commercial and academic purposes.

  12. PENERAPAN PANJANG TALANG DAN JARAK TANAM DENGAN SISTEM HIDROPONIK NFT (Nutrient Film Technique PADA TANAMAN KAILAN (Brassica oleraceae var. alboglabra

    Directory of Open Access Journals (Sweden)

    Daviv Zali Vidianto

    2013-09-01

    Full Text Available Kailan vegetables is one kind of high economic value that can be grown in hydroponic NFT (Nutrient Film Technique. The purpose of this study to determine the effect of chamfer length and spacing of the system hydroponic NFT (Nutrient Film Technique on the growth and yield kailan (Brassica oleraceae var. Alboglabra. The research has been done in the greenhouse of the Faculty of Agriculture, University Department Agroekoteknologi Trunojoyo Madura District Kamal village Telang Bangkalan. Tat is was conducted in February-May 2012. Research using methods completely randomized design (CRD with non factorial treatment chamfer length 2 m with spacing of 15 cm (P1J1, chamfer length 2 m with spacing of 20 cm (P1J2, chamfer length of 4 m with spacing of 15 cm (P2J1 and chamfer length of 4 m with spacing of 20 cm (P2J2. The materials used are kailan seeds, fertilizers and hydroponics Goodplant acetic acid (CH3COOH. Observations were analyzed using analysis of variance and Duncan continued Test Distance (UJD level of 5%. P1J1 (chamfer length of 2 meters and 15 cm plant spacing gives the best effect on the variable root length, number of leaves and plant canopy wet weight. The treatment does’n effect to variable leaf area, root wet weight, dry weight, and root dry weight of the plant canopyKeyword : Brassica oleraceae var. Alboglabra, hydroponik NFT, chamfer length and spacing

  13. Comparison of Fatty Acid Methyl Ester Analysis with the Use of API 20E and NFT Strips for Identification of Aquatic Bacteria

    OpenAIRE

    Brown, B. J.; Leff, L. G.

    1996-01-01

    Aquatic bacteria grown on MacConkey agar and modified nutrient agar were identified by using API 20E and NFT strips and fatty acid methyl ester (FAME) analysis. Identifications agreed at the species level 35.7% of the time when API 20E strips and FAME analysis were used and in 4.3% of the cases when API NFT strips and FAME analysis were used. These techniques require further development before extended use in ecological studies.

  14. Smoke Ready Toolbox for Wildfires

    Science.gov (United States)

    This site provides an online Smoke Ready Toolbox for Wildfires, which lists resources and tools that provide information on health impacts from smoke exposure, current fire conditions and forecasts and strategies to reduce exposure to smoke.

  15. CONTINEX: A Toolbox for Continuation in Experiments

    DEFF Research Database (Denmark)

    Schilder, Frank; Bureau, Emil; Santos, Ilmar

    2014-01-01

    CONTINEX is a MATLAB toolbox for bifurcation analysis based on the development platform COCO (computational continuation core). CONTINEX is specifically designed for coupling to experimental test specimen via DSPACE, but provides also interfaces to SIMULINK-, ODE-, and so-called equation-free mod......CONTINEX is a MATLAB toolbox for bifurcation analysis based on the development platform COCO (computational continuation core). CONTINEX is specifically designed for coupling to experimental test specimen via DSPACE, but provides also interfaces to SIMULINK-, ODE-, and so-called equation......-free models. The current version of the interface for experimental set-ups implements an algorithm for tuning control parameters, a robust noise-tolerant covering algorithm, and functions for monitoring (in)stability. In this talk we will report on experiments with an impact oscillator with magnetic actuators...

  16. PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

    Science.gov (United States)

    Morales, Yeimy; Bosque, Gabriel; Vehí, Josep; Picó, Jesús; Llaneras, Francisco

    2016-07-11

    Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments. The PFA Toolbox can be used to face those scenarios. Here we present the PFA (Possibilistic Flux Analysis) Toolbox for MATLAB, which simplifies the use of Interval and Possibilistic Metabolic Flux Analysis. The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format. In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples. The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

  17. Development of a model using the MATLAB System identification toolbox to estimate (222)Rn equilibrium factor from CR-39 based passive measurements.

    Science.gov (United States)

    Abo-Elmagd, M; Sadek, A M

    2014-12-01

    Can and Bare method is a widely used passive method for measuring the equilibrium factor F through the determination of the track density ratio between bare (D) and filtered (Do) detectors. The dimensions of the used diffusion chamber are altering the deposition ratios of Po-isotopes on the chamber walls as well as the ratios of the existing alpha emitters in air. Then the measured filtered track density and therefore the resultant equilibrium factor is changed according to the diffusion chamber dimensions. For this reason, high uncertainty was expected in the measured F using different diffusion chambers. In the present work, F is derived as a function of both track density ratio (D/Do) and the dimensions of the used diffusion chambers (its volume to the total internal surface area; V/A). The accuracy of the derived formula was verified using the black-box modeling technique via the MATLAB System identification toolbox. The results show that the uncertainty of the calculated F by using the derived formula of F (D/Do, V/A) is only 5%. The obtained uncertainty ensures the quality of the derived function to calculate F using diffusion chambers with wide range of dimensions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Extension of Aquaponic Water Use for NFT Baby-Leaf Production: Mizuna and Rocket Salad

    Directory of Open Access Journals (Sweden)

    Carlo Nicoletto

    2018-05-01

    Full Text Available Aquaponics is a recirculating technology that combines aquaculture with hydroponics. It allows nutrients from fish waste to feed plants and thus saves water and nutrients. However, there is a mismatch between the nutrients provided by the fish waste and plant needs. Because of this, some nutrients, notably N, tend to accumulate in the aquaponic water (APW or AP water. The aim of this study was to investigate how APW, which is depleted of P and K but still rich in N, could be further utilized. APW was used in a mesocosm and compared with APW from the same source that had been supplemented with macro-nutrients (complemented AP water or CAPW and a hydroponic control (HC. Mizuna (M and rocket salad (R were used as short-cycle vegetable crops in a NFT system. The results revealed that the low production potential of APW was mainly caused by the lack of P and K. If these were supplemented, the yields were comparable to those in the HC. M yield in CAPW was significantly higher than that of HC, probably due to biostimulant effects connected to the organic components in the water as a result of fish farming. Water type, cultivation density, and intercropping significantly influenced the qualitative characteristics of the crop in terms of antioxidant compounds and minerals. Nitrate content in vegetables was lower than European regulation limits. The extended use of APW is viable if the missing nutrients are supplemented; this could be a strategy to increase the efficiency of water and nitrogen use, while further reducing environmental impact.

  19. Integrated Budget Office Toolbox

    Science.gov (United States)

    Rushing, Douglas A.; Blakeley, Chris; Chapman, Gerry; Robertson, Bill; Horton, Allison; Besser, Thomas; McCarthy, Debbie

    2010-01-01

    The Integrated Budget Office Toolbox (IBOT) combines budgeting, resource allocation, organizational funding, and reporting features in an automated, integrated tool that provides data from a single source for Johnson Space Center (JSC) personnel. Using a common interface, concurrent users can utilize the data without compromising its integrity. IBOT tracks planning changes and updates throughout the year using both phasing and POP-related (program-operating-plan-related) budget information for the current year, and up to six years out. Separating lump-sum funds received from HQ (Headquarters) into separate labor, travel, procurement, Center G&A (general & administrative), and servicepool categories, IBOT creates a script that significantly reduces manual input time. IBOT also manages the movement of travel and procurement funds down to the organizational level and, using its integrated funds management feature, helps better track funding at lower levels. Third-party software is used to create integrated reports in IBOT that can be generated for plans, actuals, funds received, and other combinations of data that are currently maintained in the centralized format. Based on Microsoft SQL, IBOT incorporates generic budget processes, is transportable, and is economical to deploy and support.

  20. Design and Implementation of a Space Environment Simulation Toolbox for Small Satellites

    DEFF Research Database (Denmark)

    Amini, Rouzbeh; Larsen, Jesper A.; Izadi-Zamanabadi, Roozbeh

    This paper presents a developed toolbox for space environment model in SIMULINK that facilitates development and design of Attitude Determination and Control Systems (ADCS) for a Low Earth Orbit (LEO) spacecraft. The toolbox includes, among others, models of orbit propagators, disturbances, Earth...

  1. Development of a model using the MATLAB System identification toolbox to estimate 222Rn equilibrium factor from CR-39 based passive measurements

    International Nuclear Information System (INIS)

    Abo-Elmagd, M.; Sadek, A.M.

    2014-01-01

    Can and Bare method is a widely used passive method for measuring the equilibrium factor F through the determination of the track density ratio between bare (D) and filtered (D o ) detectors. The dimensions of the used diffusion chamber are altering the deposition ratios of Po-isotopes on the chamber walls as well as the ratios of the existing alpha emitters in air. Then the measured filtered track density and therefore the resultant equilibrium factor is changed according to the diffusion chamber dimensions. For this reason, high uncertainty was expected in the measured F using different diffusion chambers. In the present work, F is derived as a function of both track density ratio (D/D o ) and the dimensions of the used diffusion chambers (its volume to the total internal surface area; V/A). The accuracy of the derived formula was verified using the black-box modeling technique via the MATLAB System identification toolbox. The results show that the uncertainty of the calculated F by using the derived formula of F (D/D o , V/A) is only 5%. The obtained uncertainty ensures the quality of the derived function to calculate F using diffusion chambers with wide range of dimensions. - Highlights: • The manuscript is aimed to develop the Can and Bare method for measuring the equilibrium factor F. • A new formula F (D/D o , V/A) is obtained taking the dimension of the used cup (V/A) into consideration. • The accuracy of the derived formula was verified using the black-box modeling technique via the MATLAB. • The derived function covers the range of the widely used diffusion chambers (r ≤ 3.5 cm and h ≤ 10 cm). • The reproducibility of F estimated using this model is quite good (5% deviation) for different 8 cups

  2. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    Directory of Open Access Journals (Sweden)

    Jason Gunther Lomnitz

    2016-07-01

    Full Text Available Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1 enumeration of the repertoire of model phenotypes, (2 prediction of values for the parameters for any model phenotype and (3 analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3 and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between 3 stable states by transient stimulation through one of two input channels: a positive channel that increases

  3. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    Science.gov (United States)

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  4. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  5. Particle Swarm Optimization Toolbox

    Science.gov (United States)

    Grant, Michael J.

    2010-01-01

    The Particle Swarm Optimization Toolbox is a library of evolutionary optimization tools developed in the MATLAB environment. The algorithms contained in the library include a genetic algorithm (GA), a single-objective particle swarm optimizer (SOPSO), and a multi-objective particle swarm optimizer (MOPSO). Development focused on both the SOPSO and MOPSO. A GA was included mainly for comparison purposes, and the particle swarm optimizers appeared to perform better for a wide variety of optimization problems. All algorithms are capable of performing unconstrained and constrained optimization. The particle swarm optimizers are capable of performing single and multi-objective optimization. The SOPSO and MOPSO algorithms are based on swarming theory and bird-flocking patterns to search the trade space for the optimal solution or optimal trade in competing objectives. The MOPSO generates Pareto fronts for objectives that are in competition. A GA, based on Darwin evolutionary theory, is also included in the library. The GA consists of individuals that form a population in the design space. The population mates to form offspring at new locations in the design space. These offspring contain traits from both of the parents. The algorithm is based on this combination of traits from parents to hopefully provide an improved solution than either of the original parents. As the algorithm progresses, individuals that hold these optimal traits will emerge as the optimal solutions. Due to the generic design of all optimization algorithms, each algorithm interfaces with a user-supplied objective function. This function serves as a "black-box" to the optimizers in which the only purpose of this function is to evaluate solutions provided by the optimizers. Hence, the user-supplied function can be numerical simulations, analytical functions, etc., since the specific detail of this function is of no concern to the optimizer. These algorithms were originally developed to support entry

  6. Experiencia de producción de lechuga americana (Lactuca sativa hidropónica, tipo NFT

    Directory of Open Access Journals (Sweden)

    Laura Brenes-Peralta

    2014-06-01

    En el Centro de Prácticas Docentes e Investigación Agropecuaria de la Escuela de Agronegocios del Instituto Tecnológico de Costa Rica (TEC se cuenta, actualmente, con un sistema de este tipo NFT donde estableció una actividad de fortalecimiento que ha resultado en la observación de ciertas características a partir de la experiencia generada, de la cual se espera fomentar el uso de la hidroponía, así como divulgar información técnica y de buenas prácticas en este tipo de cultivo entre usuarios interesados.

  7. The GMT/MATLAB Toolbox

    Science.gov (United States)

    Wessel, Paul; Luis, Joaquim F.

    2017-02-01

    The GMT/MATLAB toolbox is a basic interface between MATLAB® (or Octave) and GMT, the Generic Mapping Tools, which allows MATLAB users full access to all GMT modules. Data may be passed between the two programs using intermediate MATLAB structures that organize the metadata needed; these are produced when GMT modules are run. In addition, standard MATLAB matrix data can be used directly as input to GMT modules. The toolbox improves interoperability between two widely used tools in the geosciences and extends the capability of both tools: GMT gains access to the powerful computational capabilities of MATLAB while the latter gains the ability to access specialized gridding algorithms and can produce publication-quality PostScript-based illustrations. The toolbox is available on all platforms and may be downloaded from the GMT website.

  8. FIT3D toolbox: multiple view geometry and 3D reconstruction for Matlab

    NARCIS (Netherlands)

    Esteban, I.; Dijk, J.; Groen, F.

    2010-01-01

    FIT3D is a Toolbox built for Matlab that aims at unifying and distributing a set of tools that will allow the researcher to obtain a complete 3D model from a set of calibrated images. In this paper we motivate and present the structure of the toolbox in a tutorial and example based approach. Given

  9. CBP TOOLBOX VERSION 2.0: CODE INTEGRATION ENHANCEMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F.; Flach, G.; BROWN, K.

    2013-06-01

    This report describes enhancements made to code integration aspects of the Cementitious Barriers Project (CBP) Toolbox as a result of development work performed at the Savannah River National Laboratory (SRNL) in collaboration with Vanderbilt University (VU) in the first half of fiscal year 2013. Code integration refers to the interfacing to standalone CBP partner codes, used to analyze the performance of cementitious materials, with the CBP Software Toolbox. The most significant enhancements are: 1) Improved graphical display of model results. 2) Improved error analysis and reporting. 3) Increase in the default maximum model mesh size from 301 to 501 nodes. 4) The ability to set the LeachXS/Orchestra simulation times through the GoldSim interface. These code interface enhancements have been included in a new release (Version 2.0) of the CBP Toolbox.

  10. A toolbox for European judges

    NARCIS (Netherlands)

    Hesselink, M.W.

    2011-01-01

    The forthcoming instrument on European contract law, be it in the shape of an optional code for cross-border contracts or as an official toolbox for the European legislator, is likely to have a spill-over effect on private law adjudication in Europe. Judges will have no great difficulty in finding

  11. Extend your toolbox with R

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    R seems to be ideal tool for visualising your data as well as practically all other data-related tasks. Learn how to start with R as it is worth to be included not only in statistician's or data scientist's toolboxes.

  12. OpenNFT: An open-source Python/Matlab framework for real-time fMRI neurofeedback training based on activity, connectivity and multivariate pattern analysis.

    Science.gov (United States)

    Koush, Yury; Ashburner, John; Prilepin, Evgeny; Sladky, Ronald; Zeidman, Peter; Bibikov, Sergei; Scharnowski, Frank; Nikonorov, Artem; De Ville, Dimitri Van

    2017-08-01

    Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments. This framework is implemented using Python and Matlab source code to allow for diverse functionality, high modularity, and rapid extendibility of the software depending on the user's needs. In addition, it provides an easy interface to the functionality of Statistical Parametric Mapping (SPM) that is also open-source and one of the most widely used fMRI data analysis software. We demonstrate the functionality of our new framework by describing case studies that include neurofeedback protocols based on brain activity levels, effective connectivity models, and pattern classification approaches. This open-source initiative provides a suitable framework to actively engage in the development of novel neurofeedback approaches, so that local methodological developments can be easily made accessible to a wider range of users. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Design and Implementation of a Space Environment Simulation Toolbox for Small Satellites

    DEFF Research Database (Denmark)

    Amini, Rouzbeh; Larsen, Jesper A.; Izadi-Zamanabadi, Roozbeh

    2005-01-01

    This paper presents a developed toolbox for space environment model in SIMULINK that facilitates development and design of Attitude Determination and Control Systems (ADCS) for a Low Earth Orbit (LEO) spacecraft. The toolbox includes, among others, models of orbit propagators, disturbances, Earth...... gravity field, Earth magnetic field and eclipse. The structure and facilities within the toolbox are described and exemplified using a student satellite case (AAUSAT-II). The validity of developed models is confirmed by comparing the simulation results with the realistic data obtained from the Danish...

  14. MTpy: A Python toolbox for magnetotellurics

    Science.gov (United States)

    Krieger, Lars; Peacock, Jared R.

    2014-11-01

    We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software. In its current state, modules and functions of MTpy work on raw and pre-processed MT data. However, opposite to providing a static compilation of software, we prefer to introduce MTpy as a flexible software toolbox, whose contents can be combined and utilised according to the respective needs of the user. Just as the overall functionality of a mechanical toolbox can be extended by adding new tools, MTpy is a flexible framework, which will be dynamically extended in the future. Furthermore, it can help to unify and extend existing codes and algorithms within the (academic) MT community. In this paper, we introduce the structure and concept of MTpy. Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

  15. Wave data processing toolbox manual

    Science.gov (United States)

    Sullivan, Charlene M.; Warner, John C.; Martini, Marinna A.; Lightsom, Frances S.; Voulgaris, George; Work, Paul

    2006-01-01

    Researchers routinely deploy oceanographic equipment in estuaries, coastal nearshore environments, and shelf settings. These deployments usually include tripod-mounted instruments to measure a suite of physical parameters such as currents, waves, and pressure. Instruments such as the RD Instruments Acoustic Doppler Current Profiler (ADCP(tm)), the Sontek Argonaut, and the Nortek Aquadopp(tm) Profiler (AP) can measure these parameters. The data from these instruments must be processed using proprietary software unique to each instrument to convert measurements to real physical values. These processed files are then available for dissemination and scientific evaluation. For example, the proprietary processing program used to process data from the RD Instruments ADCP for wave information is called WavesMon. Depending on the length of the deployment, WavesMon will typically produce thousands of processed data files. These files are difficult to archive and further analysis of the data becomes cumbersome. More imperative is that these files alone do not include sufficient information pertinent to that deployment (metadata), which could hinder future scientific interpretation. This open-file report describes a toolbox developed to compile, archive, and disseminate the processed wave measurement data from an RD Instruments ADCP, a Sontek Argonaut, or a Nortek AP. This toolbox will be referred to as the Wave Data Processing Toolbox. The Wave Data Processing Toolbox congregates the processed files output from the proprietary software into two NetCDF files: one file contains the statistics of the burst data and the other file contains the raw burst data (additional details described below). One important advantage of this toolbox is that it converts the data into NetCDF format. Data in NetCDF format is easy to disseminate, is portable to any computer platform, and is viewable with public-domain freely-available software. Another important advantage is that a metadata

  16. The Linear Time Frequency Analysis Toolbox

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Torrésani, Bruno; Balazs, Peter

    2011-01-01

    The Linear Time Frequency Analysis Toolbox is a Matlab/Octave toolbox for computational time-frequency analysis. It is intended both as an educational and computational tool. The toolbox provides the basic Gabor, Wilson and MDCT transform along with routines for constructing windows (lter...... prototypes) and routines for manipulating coe cients. It also provides a bunch of demo scripts devoted either to demonstrating the main functions of the toolbox, or to exemplify their use in specic signal processing applications. In this paper we describe the used algorithms, their mathematical background...

  17. Object-oriented Matlab adaptive optics toolbox

    Science.gov (United States)

    Conan, R.; Correia, C.

    2014-08-01

    Object-Oriented Matlab Adaptive Optics (OOMAO) is a Matlab toolbox dedicated to Adaptive Optics (AO) systems. OOMAO is based on a small set of classes representing the source, atmosphere, telescope, wavefront sensor, Deformable Mirror (DM) and an imager of an AO system. This simple set of classes allows simulating Natural Guide Star (NGS) and Laser Guide Star (LGS) Single Conjugate AO (SCAO) and tomography AO systems on telescopes up to the size of the Extremely Large Telescopes (ELT). The discrete phase screens that make the atmosphere model can be of infinite size, useful for modeling system performance on large time scales. OOMAO comes with its own parametric influence function model to emulate different types of DMs. The cone effect, altitude thickness and intensity profile of LGSs are also reproduced. Both modal and zonal modeling approach are implemented. OOMAO has also an extensive library of theoretical expressions to evaluate the statistical properties of turbulence wavefronts. The main design characteristics of the OOMAO toolbox are object-oriented modularity, vectorized code and transparent parallel computing. OOMAO has been used to simulate and to design the Multi-Object AO prototype Raven at the Subaru telescope and the Laser Tomography AO system of the Giant Magellan Telescope. In this paper, a Laser Tomography AO system on an ELT is simulated with OOMAO. In the first part, we set-up the class parameters and we link the instantiated objects to create the source optical path. Then we build the tomographic reconstructor and write the script for the pseudo-open-loop controller.

  18. Concentração e conteúdo de nutrientes em lisianto, cultivado em hidroponia, em sistema NFT = Concentration and nutrient content in lisianthus grown in a hydroponic NFT system

    Directory of Open Access Journals (Sweden)

    Fernanda Alice Antonello Londero Backes

    2008-10-01

    Full Text Available O diagnóstico nutricional é fundamental para determinar as exigências das plantas quanto aos nutrientes, de forma a se proceder a um manejo adequado, de acordo com a espécie. Assim, para determinar as concentrações e conteúdos nutricionais adequados à produção e qualidade de plantas de lisianto em cultivo hidropônico, instalou-se um experimento onde as plantas foram cultivadas em sistema NFT, em diferentes soluções nutritivas. O experimento foi conduzido, segundo delineamento experimental em blocos casualizados, em esquema fatorial 4x3, totalizando 12 tratamentos, com três repetições. Ostratamentos foram compostos de quatro cultivares (Echo Champagne, Mariachi Pure White, Balboa Yellow e Ávila Blue Rim e três soluções nutritivas (Teste, Steiner modificada e Barbosa. Foram avaliadas as concentrações e os conteúdos dos nutrientes nas folhas e conteúdos na parte aérea das plantas. As plantas cultivadas nas soluções Barbosa eTeste apresentaram resultados satisfatórios quanto às concentrações e aos conteúdos de nutrientes, enquanto a solução Steiner modificada produziu plantas com limitações nutricionais.The nutritional diagnosis is fundamental for determining plantnutrients, in order to correctly manage the nutritional requirements for each species. Thus, in order to determine the ideal nutrient amount and concentration for obtaining the best yield and quality of lisianthus grown hydroponically, an experiment was conducted inwhich the plants were grown under the NFT system in different nutrient solutions. The experiment was conducted according to a random block design arrangement in a 4x3 factorial scheme, totaling 12 treatments with three repetitions. The treatments werecomprised of four cultivars (Echo Champagne, Mariachi Pure White, Balboa Yellow and Ávila Blue Rim and three nutrient solutions (Test, modified Steiner and Barbosa. In the leaves, nutrient concentration and content were evaluated; in the aerial

  19. Non-stationary Condition Monitoring of large diesel engines with the AEWATT toolbox

    DEFF Research Database (Denmark)

    Pontoppidan, Niels Henrik; Larsen, Jan; Sigurdsson, Sigurdur

    2005-01-01

    We are developing a specialized toolbox for non-stationary condition monitoring of large 2-stroke diesel engines based on acoustic emission measurements. The main contribution of this toolbox has so far been the utilization of adaptive linear models such as Principal and Independent Component Ana......, the inversion of those angular timing changes called “event alignment”, has allowed for condition monitoring across operation load settings, successfully enabling a single model to be used with realistic data under varying operational conditions-...

  20. Structural Time Domain Identification Toolbox User's Guide

    DEFF Research Database (Denmark)

    Andersen, P.; Kirkegaard, Poul Henning; Brincker, Rune

    This manual describes the Structural Time Domain Identification toolbox for use with MA TLAB. This version of the tool box has been developed using the PC-based MA TLAB version 4.2c, but is compatible with prior versions of MATLAB and UNIX-based versions. The routines of the toolbox are the so...

  1. User's manual for Ecolego Toolbox and the Discretization Block

    International Nuclear Information System (INIS)

    Broed, Robert; Shulan Xu

    2008-03-01

    The CLIMB modelling team (Catchment LInked Models of radiological effects in the Biosphere) was instituted in 2004 to provide SSI with an independent modelling capability when reviewing SKB's assessment of long-term safety for a geological repository. Modelling in CLIMB covers all aspects of performance assessment (PA) from near-field releases to radiological consequences in the surface environment. Software used to implement assessment models has been developed within the project. The software comprises a toolbox based on the commercial packages Matlab and Simulink used to solve compartment based differential equation systems, but with an added user friendly graphical interface. This report documents the new simulation toolbox and a newly developed Discretisation Block, which is a powerful tool for solving problems involving a network of compartments in two dimensions

  2. DeltaProt: a software toolbox for comparative genomics

    Directory of Open Access Journals (Sweden)

    Willassen Nils P

    2010-11-01

    Full Text Available Abstract Background Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, orthologous sequences from different habitats may be explored and compared. The main goal of the DeltaProt Toolbox is to provide users with important functionality that is needed for comparative screening and studies of extremophile proteins and protein classes. Visualization of the data sets is also the focus of this article, since visualizations can play a key role in making the various relationships transparent. This application paper is intended to inform the reader of the existence, functionality, and applicability of the toolbox. Results We present the DeltaProt Toolbox, a software toolbox that may be useful in importing, analyzing and visualizing data from multiple alignments of proteins. The toolbox has been written in MATLAB™ to provide an easy and user-friendly platform, including a graphical user interface, while ensuring good numerical performance. Problems in genome biology may be easily stated thanks to a compact input format. The toolbox also offers the possibility of utilizing structural information from the SABLE or other structure predictors. Different sequence plots can then be viewed and compared in order to find their similarities and differences. Detailed statistics are also calculated during the procedure. Conclusions The DeltaProt package is open source and freely available for academic, non-commercial use. The latest version of DeltaProt can be obtained from http://services.cbu.uib.no/software/deltaprot/. The website also contains documentation, and the toolbox comes with real data sets that are intended for training in applying the models to carry out bioinformatical and statistical analyses of protein sequences. Equipped with the new algorithms proposed here, DeltaProt serves as an auxiliary

  3. Integrated system dynamics toolbox for water resources planning.

    Energy Technology Data Exchange (ETDEWEB)

    Reno, Marissa Devan; Passell, Howard David; Malczynski, Leonard A.; Peplinski, William J.; Tidwell, Vincent Carroll; Coursey, Don (University of Chicago, Chicago, IL); Hanson, Jason (University of New Mexico, Albuquerque, NM); Grimsrud, Kristine (University of New Mexico, Albuquerque, NM); Thacher, Jennifer (University of New Mexico, Albuquerque, NM); Broadbent, Craig (University of New Mexico, Albuquerque, NM); Brookshire, David (University of New Mexico, Albuquerque, NM); Chemak, Janie (University of New Mexico, Albuquerque, NM); Cockerill, Kristan (Cockeril Consulting, Boone, NC); Aragon, Carlos (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Hallett, Heather (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Vivoni, Enrique (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Roach, Jesse

    2006-12-01

    Public mediated resource planning is quickly becoming the norm rather than the exception. Unfortunately, supporting tools are lacking that interactively engage the public in the decision-making process and integrate over the myriad values that influence water policy. In the pages of this report we document the first steps toward developing a specialized decision framework to meet this need; specifically, a modular and generic resource-planning ''toolbox''. The technical challenge lies in the integration of the disparate systems of hydrology, ecology, climate, demographics, economics, policy and law, each of which influence the supply and demand for water. Specifically, these systems, their associated processes, and most importantly the constitutive relations that link them must be identified, abstracted, and quantified. For this reason, the toolbox forms a collection of process modules and constitutive relations that the analyst can ''swap'' in and out to model the physical and social systems unique to their problem. This toolbox with all of its modules is developed within the common computational platform of system dynamics linked to a Geographical Information System (GIS). Development of this resource-planning toolbox represents an important foundational element of the proposed interagency center for Computer Aided Dispute Resolution (CADRe). The Center's mission is to manage water conflict through the application of computer-aided collaborative decision-making methods. The Center will promote the use of decision-support technologies within collaborative stakeholder processes to help stakeholders find common ground and create mutually beneficial water management solutions. The Center will also serve to develop new methods and technologies to help federal, state and local water managers find innovative and balanced solutions to the nation's most vexing water problems. The toolbox is an important step toward

  4. A 'Toolbox' Equivalent Process for Safety Analysis Software

    International Nuclear Information System (INIS)

    O'Kula, K.R.; Eng, Tony

    2004-01-01

    Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 2002-1 (Quality Assurance for Safety-Related Software) identified a number of quality assurance issues on the use of software in Department of Energy (DOE) facilities for analyzing hazards, and designing and operating controls that prevent or mitigate potential accidents. The development and maintenance of a collection, or 'toolbox', of multiple-site use, standard solution, Software Quality Assurance (SQA)-compliant safety software is one of the major improvements identified in the associated DOE Implementation Plan (IP). The DOE safety analysis toolbox will contain a set of appropriately quality-assured, configuration-controlled, safety analysis codes, recognized for DOE-broad, safety basis applications. Currently, six widely applied safety analysis computer codes have been designated for toolbox consideration. While the toolbox concept considerably reduces SQA burdens among DOE users of these codes, many users of unique, single-purpose, or single-site software may still have sufficient technical justification to continue use of their computer code of choice, but are thwarted by the multiple-site condition on toolbox candidate software. The process discussed here provides a roadmap for an equivalency argument, i.e., establishing satisfactory SQA credentials for single-site software that can be deemed ''toolbox-equivalent''. The process is based on the model established to meet IP Commitment 4.2.1.2: Establish SQA criteria for the safety analysis ''toolbox'' codes. Implementing criteria that establish the set of prescriptive SQA requirements are based on implementation plan/procedures from the Savannah River Site, also incorporating aspects of those from the Waste Isolation Pilot Plant (SNL component) and the Yucca Mountain Project. The major requirements are met with evidence of a software quality assurance plan, software requirements and design documentation, user's instructions, test report, a

  5. Sentinel-3 SAR Altimetry Toolbox

    Science.gov (United States)

    Benveniste, Jerome; Lucas, Bruno; DInardo, Salvatore

    2015-04-01

    The prime objective of the SEOM (Scientific Exploitation of Operational Missions) element is to federate, support and expand the large international research community that the ERS, ENVISAT and the Envelope programmes have build up over the last 20 years for the future European operational Earth Observation missions, the Sentinels. Sentinel-3 builds directly on a proven heritage of ERS-2 and Envisat, and CryoSat-2, with a dual-frequency (Ku and C band) advanced Synthetic Aperture Radar Altimeter (SRAL) that provides measurements at a resolution of ~300m in SAR mode along track. Sentinel-3 will provide exact measurements of sea-surface height along with accurate topography measurements over sea ice, ice sheets, rivers and lakes. The first of the two Sentinels is expected to be launched in early 2015. The current universal altimetry toolbox is BRAT (Basic Radar Altimetry Toolbox) which can read all previous and current altimetry mission's data, but it does not have the capabilities to read the upcoming Sentinel-3 L1 and L2 products. ESA will endeavour to develop and supply this capability to support the users of the future Sentinel-3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats, the BratGUI is the front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as netCDF, ASCII text files, KML (Google Earth

  6. The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Aarle, Wim van, E-mail: wim.vanaarle@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Palenstijn, Willem Jan, E-mail: willemjan.palenstijn@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam (Netherlands); De Beenhouwer, Jan, E-mail: jan.debeenhouwer@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Altantzis, Thomas, E-mail: thomas.altantzis@uantwerpen.be [Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk (Belgium); Bals, Sara, E-mail: sara.bals@uantwerpen.be [Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk (Belgium); Batenburg, K. Joost, E-mail: joost.batenburg@cwi.nl [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam (Netherlands); Mathematical Institute, Leiden University, P.O. Box 9512, NL-2300 RA Leiden (Netherlands); Sijbers, Jan, E-mail: jan.sijbers@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium)

    2015-10-15

    We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series. - Highlights: • The ASTRA Toolbox is an open platform for 3D image reconstruction in tomography. • Advanced reconstruction algorithms can be prototyped using the fast and flexible building blocks. • This flexibility is demonstrated on a common use case: dual-axis tilt series reconstruction with prior knowledge. • The computational efficiency is validated on an experimentally measured tilt series.

  7. The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

    International Nuclear Information System (INIS)

    Aarle, Wim van; Palenstijn, Willem Jan; De Beenhouwer, Jan; Altantzis, Thomas; Bals, Sara; Batenburg, K. Joost; Sijbers, Jan

    2015-01-01

    We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series. - Highlights: • The ASTRA Toolbox is an open platform for 3D image reconstruction in tomography. • Advanced reconstruction algorithms can be prototyped using the fast and flexible building blocks. • This flexibility is demonstrated on a common use case: dual-axis tilt series reconstruction with prior knowledge. • The computational efficiency is validated on an experimentally measured tilt series

  8. What's in Your Teaching Toolbox?

    Science.gov (United States)

    Mormer, Elaine

    2018-02-01

    Educators are faced with an array of tools available to enhance learning outcomes in the classroom and clinic. These tools range from those that are very simple to those that are sufficiently complex to require an investment in learning time. This article summarizes a collection of teaching tools, ordered by the time involved in learning proficient use. Simple tools described include specific online blogs providing support for faculty and student writing and a simple method to capture and download videos from YouTube for classroom use. More complex tools described include a Web-based application for custom-created animated videos and an interactive audience polling system. Readers are encouraged to reflect on the tools most appropriate for use in their own teaching toolbox by considering the requisite time to proficiency and suitability to address desired learner outcomes.

  9. Competição de cultivares de alface sob cultivo hidropônico 'NFT' em três diferentes espaçamentos Butterhead lettuce cultivars under 'NFT' hydroponic cultivation in three different spacings

    Directory of Open Access Journals (Sweden)

    Ronan Gualberto

    1999-07-01

    Full Text Available Com o objetivo de avaliar o desempenho de seis cultivares de alface do tipo lisa (Babá de Verão, Brasil 303, Elisa, Karla, Lívia e Monalisa em três espaçamentos (25 x 20, 25 x 25 e 25 x 30 cm, cultivadas em sistema hidropônico 'NFT', realizou-se um experimento na Fazenda Experimental da Universidade de Marília (SP, no período de 23 de setembro a 21 de novembro de 1997. Foram avaliadas as características comprimento de caule, produção de matéria fresca por planta e por área e produção de matéria seca da parte aérea, da raiz e total. O delineamento experimental adotado foi o de blocos casualizados, em esquema fatorial 6 x 3, com três repetições. Não houve efeito significativo da interação entre cultivares e espaçamentos. As cultivares Babá de Verão, Lívia e Elisa se destacaram pela produção de matéria fresca e matéria seca total. As cultivares Monalisa e Karla mostraram-se menos suscetíveis ao pendoamento precoce, enquanto a 'Babá de Verão' foi a mais suscetível. Não foi verificada influência significativa dos espaçamentos sobre as características estudadas, exceto para a produção por área, onde independente das cultivares utilizadas, o espaçamento 25 x 20 propiciou uma produção de 4,465 Kg/m², superior aos demais espaçamentos utilizados. Assim. Produções significativamente inferiores foram obtidas nos tratamentos 25 x 25 cm e 25 x 30 cm: 3,583 e 3,304 Kg/m², respectivamente, devido à redução no número de plantas por m².An experiment was carried out at the Experimental Farm, of Marília University, from September 23th 1997 to November 21st 1997 with the objective of evaluating the performance of six butterhead lettuce cultivars (Babá de Verão, Brasil 303, Elisa, Karla, Lívia and Monalisa in three spacings (25 x 20, 25 x 25 and 25 x 30 cm, cultivated under a hydroponic system 'NFT'. Stem length, fresh matter yield per plant and per area, and aerial part and root dry matter weight were

  10. Estratégias de uso de água salobra na produção de alface em hidroponia NFT Strategies for use of brackish water in NFT hydroponic lettuce production

    Directory of Open Access Journals (Sweden)

    Márcio S. Alves

    2011-05-01

    Full Text Available Plantas de alface crespa 'Verônica' foram cultivadas em condições hidropônicas, objetivando avaliar três diferentes estratégias de emprego de águas salobras: 1 águas salobras para reposição das perdas por evapotranspiração (ETc e água doce para o preparo da solução nutritiva (SN; 2 águas salobras para o preparo da SN e água doce para reposição da ETc; 3 águas salobras para o preparo da SN e reposição da ETc. Os níveis de salinidade da água foram obtidos pela adição de NaCl à água doce (0,27 dS m-1: 1,45; 2,51; 3,6; 5,41 e 7,5 dS m-1. O experimento foi conduzido em quatro blocos aleatorizados, com quatro repetições por tratamento. Uma estrutura de pesquisa foi construída com 72 parcelas que simulam a técnica do fluxo laminar de nutrientes (NFT. O uso de água salobra apenas para repor a ETc não produziu efeito sobre a produção da alface. Por outro lado, o uso de águas salobras para o preparo da SN e água doce para reposição da ETc, reduziu o rendimento da alface (massa de matéria fresca da parte aérea em 4,99% por (dS m-1. O rendimento foi reduzido em 7% por dS m-1 quando águas salobras foram usadas tanto para o preparo da SN quanto para reposição da ETc. Apesar da redução linear da produção da alface com o aumento da salinidade da água, sintomas depreciativos para a qualidade da alface hidropônica não foram registrados.Plants of crisphead lettuce cv. 'Verônica' were grown under hydroponic conditions aiming to evaluate three different strategies of brackish waters utilization: 1 brackish waters to replace the evapotranspiration loss (ETc and fresh water to prepare nutrient solution (NS; 2 brackish waters to prepare NS and fresh water to replace the ETc; 3 brackish waters to prepare NS and replace ETc. The levels of water salinity were obtained by addition of NaCl to fresh water (0.27 dS m-1: 1.45; 2.51; 3.6; 5.41 and 7.5 dS m-1. The experiment was conducted in randomized blocks with four

  11. Produção de girassol ornamental com uso de águas salobras em sistema hidropônico NFT Production of ornamental sunflower with use of brackish waters in NFT hydroponic system

    Directory of Open Access Journals (Sweden)

    Marlo P Maciel

    2012-02-01

    Full Text Available Plantas de girassol ornamental 'Sol Vermelho' foram cultivadas em hidroponia com o objetivo de avaliar o uso de águas salobras sobre seu rendimento e qualidade da inflorescência. As águas salobras foram usadas para preparar a solução nutritiva e repor as perdas por evapotranspiração. O experimento foi conduzido em delineamento inteiramente aleatorizado com cinco níveis de salinidade da água: 1,51; 2,56; 3,86 e 6,19 dS m-1, obtidos pela adição de NaCl na água doce local (0,47 dS m-1 que também foi usada como testemunha. Cada tratamento foi repetido quatro vezes e cada parcela (com quatro plantas foi construída para simular um sistema independente da técnica do fluxo laminar de nutrientes (NFT. Observou-se uma redução linear causada pelo aumento da salinidade da água sobre a altura das plantas, o diâmetro do caule e a massa da matéria seca da parte aérea. Tanto a altura da planta quanto o diâmetro do caule foram reduzidos em 3,2% e a massa de matéria seca da parte aérea foi reduzida em 5,78% (dS m-1-1, para cada acréscimo unitário da salinidade da água (dS m-1. Por outro lado, a salinidade da água não afetou o tamanho do capítulo do girassol e não foram registrados sintomas de toxicidade causados pela salinidade. Esses resultados sustentam a viabilidade técnica do uso de águas salobras para produção hidropônica de girassol ornamental.Plants of ornamental sunflower 'Sol Vermelho' were grown under hydroponic conditions aiming to evaluate the effects of use of brackish water on its yield and inflorescence (capitulum quality. The brackish waters were utilized to prepare nutrient solution and to replace water due to evapotranspiration loss. The experiment was carried out in a completely randomized experimental design with five levels of water salinity: 1.51; 2.56; 3.86 and 6.19 dS m-1, obtained by addition of NaCl to local fresh water; this fresh water (0.47 dS m-1 was also studied as control treatment. Each

  12. Produção de alface em NFT e Floating aproveitando água salobra e o rejeito da dessalinização Lettuce production under NFT and Floating using brackish groundwater and the reject from its desalination

    Directory of Open Access Journals (Sweden)

    Alexandre Nascimento dos Santos

    2011-06-01

    Full Text Available Plantas de alface cv. Elba foram cultivadas em dois sistemas hidropônicos, Floating e NFT, com o objetivo de avaliar três tipos de água: a água salobra natural (2,47 dS m-1 obtida a partir de um poço profundo; água doce (0,11 dS m-1 produzido por dessalinização por osmose inversa, e o rejeito salino (5,15 dS m-1, um efluente do processo de dessalinização. Estas águas foram combinadas em seis tratamentos resultantes da sua utilização alternada para preparar a solução nutritiva (SN e/ou substituir as perdas por evapotranspiração (ETc. O experimento foi conduzido em casa de vegetação na região semiárida de Pernambuco, utilizando 48 unidades experimentais em blocos casualizados em esquema fatorial 6x2 com quatro repetições. O rendimento da alface (massa de matéria fresca foi maior nas condições do Floating. O uso exclusivo da água do poço profundo e do rejeito de dessalinizadores diminuiu 22,7 e 39,6% a produção de alface, respectivamente. Para uma melhor combinação de águas doces e salobras, o uso de água salobra para repor a perda por ETc pode aumentar a produção de alface em relação ao uso dessas águas para preparar a SN, estes resultados foram registrados para a água do poço profundo e o rejeito.Plants of lettuce cv. Elba were grown under two hydroponic systems, Floating and NFT, aiming to evaluate three water resources: natural brackish water (2,47 dS m-1 obtained from a deep well; fresh water (0,11 dS m-1 produced by reverse osmosis desalination; and reject brine (5,15 dS m-1, a wastewater from desalination process. These waters were combined in six treatments resulted from their alternated use to prepare nutrient solution (NS and/or replace the evapotranspiration loss (ETc. The experiment was carried out under a greenhouse condition in the semiarid region of Pernambuco State, Brazil; 48 experimental units were used for both hydroponic systems. The lettuce yield (shoot fresh matter was higher under

  13. Drinking Water Cyanotoxin Risk Communication Toolbox

    Science.gov (United States)

    The drinking water cyanotoxin risk communication toolbox is a ready-to-use, “one-stop-shop” to support public water systems, states, and local governments in developing, as they deem appropriate, their own risk communication materials.

  14. An Open-Source Toolbox for PEM Fuel Cell Simulation

    Directory of Open Access Journals (Sweden)

    Jean-Paul Kone

    2018-05-01

    Full Text Available In this paper, an open-source toolbox that can be used to accurately predict the distribution of the major physical quantities that are transported within a proton exchange membrane (PEM fuel cell is presented. The toolbox has been developed using the Open Source Field Operation and Manipulation (OpenFOAM platform, which is an open-source computational fluid dynamics (CFD code. The base case results for the distribution of velocity, pressure, chemical species, Nernst potential, current density, and temperature are as expected. The plotted polarization curve was compared to the results from a numerical model and experimental data taken from the literature. The conducted simulations have generated a significant amount of data and information about the transport processes that are involved in the operation of a PEM fuel cell. The key role played by the concentration constant in shaping the cell polarization curve has been explored. The development of the present toolbox is in line with the objectives outlined in the International Energy Agency (IEA, Paris, France Advanced Fuel Cell Annex 37 that is devoted to developing open-source computational tools to facilitate fuel cell technologies. The work therefore serves as a basis for devising additional features that are not always feasible with a commercial code.

  15. A conceptual toolbox for designing CSCW applications

    DEFF Research Database (Denmark)

    Bødker, Susanne; Christiansen, Ellen

    1995-01-01

    This paper presents a conceptual toolbox, developed to support the design of CSCW applications in a large Esprit project, EuroCODE. Here, several groups of designers work to investigate computer support for cooperative work in large use organizations, at the same time as they work to develop...... an open development platform for CSCW applications. The conceptual toolbox has been developed to support communication in and among these design groups, between designers and users and in future use of the open development platform. Rejecting the idea that one may design from a framework describing CSCW......, the toolbox aims to support design by doing and help bridging between work with users, technical design, and insights gained from theoretical and empirical CSCW research....

  16. Multimodal Imaging Brain Connectivity Analysis (MIBCA toolbox

    Directory of Open Access Journals (Sweden)

    Andre Santos Ribeiro

    2015-07-01

    Full Text Available Aim. In recent years, connectivity studies using neuroimaging data have increased the understanding of the organization of large-scale structural and functional brain networks. However, data analysis is time consuming as rigorous procedures must be assured, from structuring data and pre-processing to modality specific data procedures. Until now, no single toolbox was able to perform such investigations on truly multimodal image data from beginning to end, including the combination of different connectivity analyses. Thus, we have developed the Multimodal Imaging Brain Connectivity Analysis (MIBCA toolbox with the goal of diminishing time waste in data processing and to allow an innovative and comprehensive approach to brain connectivity.Materials and Methods. The MIBCA toolbox is a fully automated all-in-one connectivity toolbox that offers pre-processing, connectivity and graph theoretical analyses of multimodal image data such as diffusion-weighted imaging, functional magnetic resonance imaging (fMRI and positron emission tomography (PET. It was developed in MATLAB environment and pipelines well-known neuroimaging softwares such as Freesurfer, SPM, FSL, and Diffusion Toolkit. It further implements routines for the construction of structural, functional and effective or combined connectivity matrices, as well as, routines for the extraction and calculation of imaging and graph-theory metrics, the latter using also functions from the Brain Connectivity Toolbox. Finally, the toolbox performs group statistical analysis and enables data visualization in the form of matrices, 3D brain graphs and connectograms. In this paper the MIBCA toolbox is presented by illustrating its capabilities using multimodal image data from a group of 35 healthy subjects (19–73 years old with volumetric T1-weighted, diffusion tensor imaging, and resting state fMRI data, and 10 subjets with 18F-Altanserin PET data also.Results. It was observed both a high inter

  17. A Total Factor Productivity Toolbox for MATLAB

    NARCIS (Netherlands)

    B.M. Balk (Bert); J. Barbero (Javier); J.L. Zofío (José)

    2018-01-01

    textabstractTotal Factor Productivity Toolbox is a new package for MATLAB that includes functions to calculate the main Total Factor Productivity (TFP) indices and their decompositions, based on Shephard’s distance functions and using Data Envelopment Analysis (DEA) programming techniques. The

  18. The RTMM Toolbox for DMM Applications

    DEFF Research Database (Denmark)

    Sharp, Robin; Todirica, Edward Alexandru

    2002-01-01

    This paper describes an approach to implementing distributed multimedia applications based on the use of a software toolbox. The tools in the box allow the designer to specify which components are to be used, how they are logically connected and what properties the streams of data to be passed...

  19. Tolkku - a toolbox for decision support from condition monitoring data

    International Nuclear Information System (INIS)

    Saarela, Olli; Lehtonen, Mikko; Halme, Jari; Aikala, Antti; Raivio, Kimmo

    2012-01-01

    This paper describes a software toolbox (a software library) designed for condition monitoring and diagnosis of machines. This toolbox implements both new methods and prior art and is aimed for practical down-to-earth data analysis work. The target is to improve knowledge of the operation and behaviour of machines and processes throughout their entire life-cycles. The toolbox supports different phases of condition based maintenance with tools that extract essential information and automate data processing. The paper discusses principles that have guided toolbox design and the implemented toolbox structure. Case examples are used to illustrate how condition monitoring applications can be built using the toolbox. In the first case study the toolbox is applied to fault detection of industrial centrifuges based on measured electrical current. The second case study outlines an application for centralized monitoring of a fleet of machines that supports organizational learning.

  20. SIPPI: A Matlab toolbox for sampling the solution to inverse problems with complex prior information

    DEFF Research Database (Denmark)

    Hansen, Thomas Mejer; Cordua, Knud Skou; Looms, Majken Caroline

    2013-01-01

    We present an application of the SIPPI Matlab toolbox, to obtain a sample from the a posteriori probability density function for the classical tomographic inversion problem. We consider a number of different forward models, linear and non-linear, such as ray based forward models that rely...

  1. Open Babel: An open chemical toolbox

    Directory of Open Access Journals (Sweden)

    O'Boyle Noel M

    2011-10-01

    Full Text Available Abstract Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language and de facto standards have arisen (for example, SMILES format, the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example, and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

  2. Open Babel: An open chemical toolbox

    Science.gov (United States)

    2011-01-01

    Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

  3. FAST: FAST Analysis of Sequences Toolbox

    Directory of Open Access Journals (Sweden)

    Travis J. Lawrence

    2015-05-01

    Full Text Available FAST (FAST Analysis of Sequences Toolbox provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU’s Not Unix Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics makes FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format. Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  4. NATbox: a network analysis toolbox in R.

    Science.gov (United States)

    Chavan, Shweta S; Bauer, Michael A; Scutari, Marco; Nagarajan, Radhakrishnan

    2009-10-08

    There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as opposed to independent entities hence may provide preliminary insights into biological pathways and signalling mechanisms. Bayesian structure learning (BSL) techniques and its extensions have been used successfully for modelling FRs from expression profiles. Such techniques are especially useful in discovering undocumented FRs, investigating non-canonical signalling mechanisms and cross-talk between pathways. The objective of the present study is to develop a graphical user interface (GUI), NATbox: Network Analysis Toolbox in the language R that houses a battery of BSL algorithms in conjunction with suitable statistical tools for modelling FRs in the form of acyclic networks from gene expression profiles and their subsequent analysis. NATbox is a menu-driven open-source GUI implemented in the R statistical language for modelling and analysis of FRs from gene expression profiles. It provides options to (i) impute missing observations in the given data (ii) model FRs and network structure from gene expression profiles using a battery of BSL algorithms and identify robust dependencies using a bootstrap procedure, (iii) present the FRs in the form of acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve FRs of interest from published literature. Subsequently, use these FRs as structural priors in BSL (v) enhance scalability of BSL across high-dimensional data by parallelizing the bootstrap routines. NATbox provides a menu-driven GUI for modelling and analysis of FRs from gene expression profiles. By incorporating readily available functions from existing R-packages, it minimizes redundancy and improves reproducibility, transparency and sustainability, characteristic of open-source environments

  5. A part toolbox to tune genetic expression in Bacillus subtilis

    Science.gov (United States)

    Guiziou, Sarah; Sauveplane, Vincent; Chang, Hung-Ju; Clerté, Caroline; Declerck, Nathalie; Jules, Matthieu; Bonnet, Jerome

    2016-01-01

    Libraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli, such libraries are lacking for the Gram-positive model Bacillus subtilis, a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis. We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ∼14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis. PMID:27402159

  6. SCoT: a Python toolbox for EEG source connectivity.

    Science.gov (United States)

    Billinger, Martin; Brunner, Clemens; Müller-Putz, Gernot R

    2014-01-01

    Analysis of brain connectivity has become an important research tool in neuroscience. Connectivity can be estimated between cortical sources reconstructed from the electroencephalogram (EEG). Such analysis often relies on trial averaging to obtain reliable results. However, some applications such as brain-computer interfaces (BCIs) require single-trial estimation methods. In this paper, we present SCoT-a source connectivity toolbox for Python. This toolbox implements routines for blind source decomposition and connectivity estimation with the MVARICA approach. Additionally, a novel extension called CSPVARICA is available for labeled data. SCoT estimates connectivity from various spectral measures relying on vector autoregressive (VAR) models. Optionally, these VAR models can be regularized to facilitate ill posed applications such as single-trial fitting. We demonstrate basic usage of SCoT on motor imagery (MI) data. Furthermore, we show simulation results of utilizing SCoT for feature extraction in a BCI application. These results indicate that CSPVARICA and correct regularization can significantly improve MI classification. While SCoT was mainly designed for application in BCIs, it contains useful tools for other areas of neuroscience. SCoT is a software package that (1) brings combined source decomposition and connectivtiy estimation to the open Python platform, and (2) offers tools for single-trial connectivity estimation. The source code is released under the MIT license and is available online at github.com/SCoT-dev/SCoT.

  7. SCoT: A Python Toolbox for EEG Source Connectivity

    Directory of Open Access Journals (Sweden)

    Martin eBillinger

    2014-03-01

    Full Text Available Analysis of brain connectivity has become an important research tool in neuroscience. Connectivity can be estimated between cortical sources reconstructed from the electroencephalogram (EEG. Such analysis often relies on trial averaging to obtain reliable results. However, some applications such as brain-computer interfaces (BCIs require single-trial estimation methods.In this paper, we present SCoT – a source connectivity toolbox for Python. This toolbox implements routines for blind source decomposition and connectivity estimation with theMVARICA approach. Additionally, a novel extension called CSPVARICA is available for labeled data. SCoT estimates connectivity from various spectral measures relying on vector autoregressive (VAR models. Optionally, these VAR models can be regularized to facilitate ill posed applications such as single-trial fitting.We demonstrate basic usage of SCoT on motor imagery (MI data. Furthermore, we show simulation results of utilizing SCoT for feature extraction in a BCI application. These results indicate that CSPVARICA and correct regularization can significantly improve MI classification. While SCoT was mainly designed for application in BCIs, it contains useful tools for other areas of neuroscience. SCoT is a software package that (1 brings combined source decomposition and connectivtiy estimation to the open Python platform, and (2 offers tools for single-trial connectivity estimation. The source code is released under the MIT license and is available online at github.com/SCoT-dev/SCoT.

  8. Construction of multi-functional open modulized Matlab simulation toolbox for imaging ladar system

    Science.gov (United States)

    Wu, Long; Zhao, Yuan; Tang, Meng; He, Jiang; Zhang, Yong

    2011-06-01

    Ladar system simulation is to simulate the ladar models using computer simulation technology in order to predict the performance of the ladar system. This paper presents the developments of laser imaging radar simulation for domestic and overseas studies and the studies of computer simulation on ladar system with different application requests. The LadarSim and FOI-LadarSIM simulation facilities of Utah State University and Swedish Defence Research Agency are introduced in details. This paper presents the low level of simulation scale, un-unified design and applications of domestic researches in imaging ladar system simulation, which are mostly to achieve simple function simulation based on ranging equations for ladar systems. Design of laser imaging radar simulation with open and modularized structure is proposed to design unified modules for ladar system, laser emitter, atmosphere models, target models, signal receiver, parameters setting and system controller. Unified Matlab toolbox and standard control modules have been built with regulated input and output of the functions, and the communication protocols between hardware modules. A simulation based on ICCD gain-modulated imaging ladar system for a space shuttle is made based on the toolbox. The simulation result shows that the models and parameter settings of the Matlab toolbox are able to simulate the actual detection process precisely. The unified control module and pre-defined parameter settings simplify the simulation of imaging ladar detection. Its open structures enable the toolbox to be modified for specialized requests. The modulization gives simulations flexibility.

  9. The laboratory test utilization management toolbox.

    Science.gov (United States)

    Baird, Geoffrey

    2014-01-01

    Efficiently managing laboratory test utilization requires both ensuring adequate utilization of needed tests in some patients and discouraging superfluous tests in other patients. After the difficult clinical decision is made to define the patients that do and do not need a test, a wealth of interventions are available to the clinician and laboratorian to help guide appropriate utilization. These interventions are collectively referred to here as the utilization management toolbox. Experience has shown that some tools in the toolbox are weak and other are strong, and that tools are most effective when many are used simultaneously. While the outcomes of utilization management studies are not always as concrete as may be desired, what data is available in the literature indicate that strong utilization management interventions are safe and effective measures to improve patient health and reduce waste in an era of increasing financial pressure.

  10. ESA's Multi-mission Sentinel-1 Toolbox

    Science.gov (United States)

    Veci, Luis; Lu, Jun; Foumelis, Michael; Engdahl, Marcus

    2017-04-01

    The Sentinel-1 Toolbox is a new open source software for scientific learning, research and exploitation of the large archives of Sentinel and heritage missions. The Toolbox is based on the proven BEAM/NEST architecture inheriting all current NEST functionality including multi-mission support for most civilian satellite SAR missions. The project is funded through ESA's Scientific Exploitation of Operational Missions (SEOM). The Sentinel-1 Toolbox will strive to serve the SEOM mandate by providing leading-edge software to the science and application users in support of ESA's operational SAR mission as well as by educating and growing a SAR user community. The Toolbox consists of a collection of processing tools, data product readers and writers and a display and analysis application. A common architecture for all Sentinel Toolboxes is being jointly developed by Brockmann Consult, Array Systems Computing and C-S called the Sentinel Application Platform (SNAP). The SNAP architecture is ideal for Earth Observation processing and analysis due the following technological innovations: Extensibility, Portability, Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory Management, and a Graph Processing Framework. The project has developed new tools for working with Sentinel-1 data in particular for working with the new Interferometric TOPSAR mode. TOPSAR Complex Coregistration and a complete Interferometric processing chain has been implemented for Sentinel-1 TOPSAR data. To accomplish this, a coregistration following the Spectral Diversity[4] method has been developed as well as special azimuth handling in the coherence, interferogram and spectral filter operators. The Toolbox includes reading of L0, L1 and L2 products in SAFE format, calibration and de-noising, slice product assembling, TOPSAR deburst and sub-swath merging, terrain flattening radiometric normalization, and visualization for L2 OCN products. The Toolbox also provides several new tools for

  11. Segmentation Toolbox for Tomographic Image Data

    DEFF Research Database (Denmark)

    Einarsdottir, Hildur

    , techniques to automatically analyze such data becomes ever more important. Most segmentation methods for large datasets, such as CT images, deal with simple thresholding techniques, where intensity values cut offs are predetermined and hard coded. For data where the intensity difference is not sufficient......Motivation: Image acquisition has vastly improved over the past years, introducing techniques such as X-ray computed tomography (CT). CT images provide the means to probe a sample non-invasively to investigate its inner structure. Given the wide usage of this technique and massive data amounts......, and partial volume voxels occur frequently, thresholding methods do not suffice and more advanced methods are required. Contribution: To meet these requirements a toolbox has been developed, combining well known methods within the image analysis field. The toolbox includes cluster-based methods...

  12. Insights into the European Years’ Communication Toolboxes

    Directory of Open Access Journals (Sweden)

    Camelia-Mihaela Cmeciu

    2012-08-01

    Full Text Available Since 1983 the European syntagm “unity in diversity” has been implemented in the European Years’ communication campaigns. Dependent on subsidiarity and decentralization, European Years focus on a specific issue which constitutes the subject of a year-long awareness campaign. Beyond the involvement of Europe’s citizens through their local, regional and national authorities in the implementation of the European Years’ policies, there is a unity at the level of the visual communication of the EU by two important image-building elements: EY logos and communication toolboxes. The European Years’ communication toolboxes can be considered signs of inclusion since every organization is expected to customize the templates in the official campaign design of the European Year. The analysis will focus on the image-building elements of three European Years (2010, 2011, 2012. Having social semiotics as the qualitative research method and the analytical framework based on the distinction between design resources and representational resources, I will analyze the double layers of the high intensity point of inclusion: (1 the European Years’ branding process; (2 the visual deontic modality within the visual guidelines of the EY communication toolbox.

  13. Interval Coded Scoring: a toolbox for interpretable scoring systems

    Directory of Open Access Journals (Sweden)

    Lieven Billiet

    2018-04-01

    Full Text Available Over the last decades, clinical decision support systems have been gaining importance. They help clinicians to make effective use of the overload of available information to obtain correct diagnoses and appropriate treatments. However, their power often comes at the cost of a black box model which cannot be interpreted easily. This interpretability is of paramount importance in a medical setting with regard to trust and (legal responsibility. In contrast, existing medical scoring systems are easy to understand and use, but they are often a simplified rule-of-thumb summary of previous medical experience rather than a well-founded system based on available data. Interval Coded Scoring (ICS connects these two approaches, exploiting the power of sparse optimization to derive scoring systems from training data. The presented toolbox interface makes this theory easily applicable to both small and large datasets. It contains two possible problem formulations based on linear programming or elastic net. Both allow to construct a model for a binary classification problem and establish risk profiles that can be used for future diagnosis. All of this requires only a few lines of code. ICS differs from standard machine learning through its model consisting of interpretable main effects and interactions. Furthermore, insertion of expert knowledge is possible because the training can be semi-automatic. This allows end users to make a trade-off between complexity and performance based on cross-validation results and expert knowledge. Additionally, the toolbox offers an accessible way to assess classification performance via accuracy and the ROC curve, whereas the calibration of the risk profile can be evaluated via a calibration curve. Finally, the colour-coded model visualization has particular appeal if one wants to apply ICS manually on new observations, as well as for validation by experts in the specific application domains. The validity and applicability

  14. Identification of Molecular Fingerprints in Human Heat Pain Thresholds by Use of an Interactive Mixture Model R Toolbox (AdaptGauss).

    Science.gov (United States)

    Ultsch, Alfred; Thrun, Michael C; Hansen-Goos, Onno; Lötsch, Jörn

    2015-10-28

    Biomedical data obtained during cell experiments, laboratory animal research, or human studies often display a complex distribution. Statistical identification of subgroups in research data poses an analytical challenge. Here were introduce an interactive R-based bioinformatics tool, called "AdaptGauss". It enables a valid identification of a biologically-meaningful multimodal structure in the data by fitting a Gaussian mixture model (GMM) to the data. The interface allows a supervised selection of the number of subgroups. This enables the expectation maximization (EM) algorithm to adapt more complex GMM than usually observed with a noninteractive approach. Interactively fitting a GMM to heat pain threshold data acquired from human volunteers revealed a distribution pattern with four Gaussian modes located at temperatures of 32.3, 37.2, 41.4, and 45.4 °C. Noninteractive fitting was unable to identify a meaningful data structure. Obtained results are compatible with known activity temperatures of different TRP ion channels suggesting the mechanistic contribution of different heat sensors to the perception of thermal pain. Thus, sophisticated analysis of the modal structure of biomedical data provides a basis for the mechanistic interpretation of the observations. As it may reflect the involvement of different TRP thermosensory ion channels, the analysis provides a starting point for hypothesis-driven laboratory experiments.

  15. The Biopsychology-Toolbox: a free, open-source Matlab-toolbox for the control of behavioral experiments.

    Science.gov (United States)

    Rose, Jonas; Otto, Tobias; Dittrich, Lars

    2008-10-30

    The Biopsychology-Toolbox is a free, open-source Matlab-toolbox for the control of behavioral experiments. The major aim of the project was to provide a set of basic tools that allow programming novices to control basic hardware used for behavioral experimentation without limiting the power and flexibility of the underlying programming language. The modular design of the toolbox allows portation of parts as well as entire paradigms between different types of hardware. In addition to the toolbox, this project offers a platform for the exchange of functions, hardware solutions and complete behavioral paradigms.

  16. Matlab Stability and Control Toolbox: Trim and Static Stability Module

    Science.gov (United States)

    Crespo, Luis G.; Kenny, Sean P.

    2006-01-01

    This paper presents the technical background of the Trim and Static module of the Matlab Stability and Control Toolbox. This module performs a low-fidelity stability and control assessment of an aircraft model for a set of flight critical conditions. This is attained by determining if the control authority available for trim is sufficient and if the static stability characteristics are adequate. These conditions can be selected from a prescribed set or can be specified to meet particular requirements. The prescribed set of conditions includes horizontal flight, take-off rotation, landing flare, steady roll, steady turn and pull-up/ push-over flight, for which several operating conditions can be specified. A mathematical model was developed allowing for six-dimensional trim, adjustable inertial properties, asymmetric vehicle layouts, arbitrary number of engines, multi-axial thrust vectoring, engine(s)-out conditions, crosswind and gyroscopic effects.

  17. The Matlab Radial Basis Function Toolbox

    Directory of Open Access Journals (Sweden)

    Scott A. Sarra

    2017-03-01

    Full Text Available Radial Basis Function (RBF methods are important tools for scattered data interpolation and for the solution of Partial Differential Equations in complexly shaped domains. The most straight forward approach used to evaluate the methods involves solving a linear system which is typically poorly conditioned. The Matlab Radial Basis Function toolbox features a regularization method for the ill-conditioned system, extended precision floating point arithmetic, and symmetry exploitation for the purpose of reducing flop counts of the associated numerical linear algebra algorithms.

  18. User's manual for Ecolego Toolbox and the Discretization Block

    Energy Technology Data Exchange (ETDEWEB)

    Broed, Robert (Facilia consulting AB (Sweden)); Shulan Xu (Swedish Radiation Protection Authority, Stockholm (Sweden))

    2008-03-15

    The CLIMB modelling team (Catchment LInked Models of radiological effects in the Biosphere) was instituted in 2004 to provide SSI with an independent modelling capability when reviewing SKB's assessment of long-term safety for a geological repository. Modelling in CLIMB covers all aspects of performance assessment (PA) from near-field releases to radiological consequences in the surface environment. Software used to implement assessment models has been developed within the project. The software comprises a toolbox based on the commercial packages Matlab and Simulink used to solve compartment based differential equation systems, but with an added user friendly graphical interface. This report documents the new simulation toolbox and a newly developed Discretisation Block, which is a powerful tool for solving problems involving a network of compartments in two dimensions

  19. The 'Toolbox' of strategies for managing Haemonchus contortus in goats: What's in and what's out.

    Science.gov (United States)

    Kearney, P E; Murray, P J; Hoy, J M; Hohenhaus, M; Kotze, A

    2016-04-15

    A dynamic and innovative approach to managing the blood-consuming nematode Haemonchus contortus in goats is critical to crack dependence on veterinary anthelmintics. H. contortus management strategies have been the subject of intense research for decades, and must be selected to create a tailored, individualized program for goat farms. Through the selection and combination of strategies from the Toolbox, an effective management program for H. contortus can be designed according to the unique conditions of each particular farm. This Toolbox investigates strategies including vaccines, bioactive forages, pasture/grazing management, behavioural management, natural immunity, FAMACHA, Refugia and strategic drenching, mineral/vitamin supplementation, copper Oxide Wire Particles (COWPs), breeding and selection/selecting resistant and resilient individuals, biological control and anthelmintic drugs. Barbervax(®), the ground-breaking Haemonchus vaccine developed and currently commercially available on a pilot scale for sheep, is prime for trialling in goats and would be an invaluable inclusion to this Toolbox. The specialised behaviours of goats, specifically their preferences to browse a variety of plants and accompanying physiological adaptations to the consumption of secondary compounds contained in browse, have long been unappreciated and thus overlooked as a valuable, sustainable strategy for Haemonchus management. These strategies are discussed in this review as to their value for inclusion into the 'Toolbox' currently, and the future implications of ongoing research for goat producers. Combining and manipulating strategies such as browsing behaviour, pasture management, bioactive forages and identifying and treating individual animals for haemonchosis, in addition to continuous evaluation of strategy effectiveness, is conducted using a model farm scenario. Selecting strategies from the Toolbox, with regard to their current availability, feasibility, economical cost

  20. Rad Toolbox User's Guide

    Energy Technology Data Exchange (ETDEWEB)

    Eckerman, Keith F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sjoreen, Andrea L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-05-01

    The Radiological Toolbox software developed by Oak Ridge National Laboratory (ORNL) for U. S. Nuclear Regulatory Commission (NRC) is designed to provide electronic access to the vast and varied data that underlies the field of radiation protection. These data represent physical, chemical, anatomical, physiological, and mathematical parameters detailed in various handbooks which a health physicist might consult while in his office. The initial motivation for the software was to serve the needs of the health physicist away from his office and without access to his handbooks; e.g., NRC inspectors. The earlier releases of the software were widely used and accepted around the world by not only practicing health physicist but also those within educational programs. This release updates the software to accommodate changes in Windows operating systems and, in some aspects, radiation protection. This release has been tested on Windows 7 and 8 and on 32- and 64-bit machines. The nuclear decay data has been updated and thermal neutron capture cross sections and cancer risk coefficients have been included. This document and the software’s user’s guide provide further details and documentation of the information captured within the Radiological Toolbox.

  1. Distributed Aerodynamic Sensing and Processing Toolbox

    Science.gov (United States)

    Brenner, Martin; Jutte, Christine; Mangalam, Arun

    2011-01-01

    A Distributed Aerodynamic Sensing and Processing (DASP) toolbox was designed and fabricated for flight test applications with an Aerostructures Test Wing (ATW) mounted under the fuselage of an F-15B on the Flight Test Fixture (FTF). DASP monitors and processes the aerodynamics with the structural dynamics using nonintrusive, surface-mounted, hot-film sensing. This aerodynamic measurement tool benefits programs devoted to static/dynamic load alleviation, body freedom flutter suppression, buffet control, improvement of aerodynamic efficiency through cruise control, supersonic wave drag reduction through shock control, etc. This DASP toolbox measures local and global unsteady aerodynamic load distribution with distributed sensing. It determines correlation between aerodynamic observables (aero forces) and structural dynamics, and allows control authority increase through aeroelastic shaping and active flow control. It offers improvements in flutter suppression and, in particular, body freedom flutter suppression, as well as aerodynamic performance of wings for increased range/endurance of manned/ unmanned flight vehicles. Other improvements include inlet performance with closed-loop active flow control, and development and validation of advanced analytical and computational tools for unsteady aerodynamics.

  2. Expanding the UniFrac Toolbox.

    Directory of Open Access Journals (Sweden)

    Ruth G Wong

    Full Text Available The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work properly. Here we demonstrate that unweighted UniFrac is highly sensitive to rarefaction instance and to sequencing depth in uniform data sets with no clear structure or separation between groups. We show that this arises because of subcompositional effects. We introduce information UniFrac and ratio UniFrac, two new weightings that are not as sensitive to rarefaction and allow greater separation of outliers than classic unweighted and weighted UniFrac. With this expansion of the UniFrac toolbox, we hope to empower researchers to extract more varied information from their data.

  3. SU-E-J-253: The Radiomics Toolbox in the Computational Environment for Radiological Research (CERR)

    Energy Technology Data Exchange (ETDEWEB)

    Apte, A; Veeraraghavan, H; Oh, J; Kijewski, P; Deasy, J [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

    2015-06-15

    Purpose: To present an open source and free platform to facilitate radiomics research — The “Radiomics toolbox” in CERR. Method: There is scarcity of open source tools that support end-to-end modeling of image features to predict patient outcomes. The “Radiomics toolbox” strives to fill the need for such a software platform. The platform supports (1) import of various kinds of image modalities like CT, PET, MR, SPECT, US. (2) Contouring tools to delineate structures of interest. (3) Extraction and storage of image based features like 1st order statistics, gray-scale co-occurrence and zonesize matrix based texture features and shape features and (4) Statistical Analysis. Statistical analysis of the extracted features is supported with basic functionality that includes univariate correlations, Kaplan-Meir curves and advanced functionality that includes feature reduction and multivariate modeling. The graphical user interface and the data management are performed with Matlab for the ease of development and readability of code and features for wide audience. Open-source software developed with other programming languages is integrated to enhance various components of this toolbox. For example: Java-based DCM4CHE for import of DICOM, R for statistical analysis. Results: The Radiomics toolbox will be distributed as an open source, GNU copyrighted software. The toolbox was prototyped for modeling Oropharyngeal PET dataset at MSKCC. The analysis will be presented in a separate paper. Conclusion: The Radiomics Toolbox provides an extensible platform for extracting and modeling image features. To emphasize new uses of CERR for radiomics and image-based research, we have changed the name from the “Computational Environment for Radiotherapy Research” to the “Computational Environment for Radiological Research”.

  4. ARC Code TI: X-Plane Communications Toolbox (XPC)

    Data.gov (United States)

    National Aeronautics and Space Administration — The X-Plane Communications Toolbox (XPC) is an open source research tool used to interact with the commercial flight simulator software X-Plane. XPC allows users to...

  5. iamxt: Max-tree toolbox for image processing and analysis

    Directory of Open Access Journals (Sweden)

    Roberto Souza

    2017-01-01

    Full Text Available The iamxt is an array-based max-tree toolbox implemented in Python using the NumPy library for array processing. It has state of the art methods for building and processing the max-tree, and a large set of visualization tools that allow to view the tree and the contents of its nodes. The array-based programming style and max-tree representation used in the toolbox make it simple to use. The intended audience of this toolbox includes mathematical morphology students and researchers that want to develop research in the field and image processing researchers that need a toolbox simple to use and easy to integrate in their applications.

  6. Managing Fieldwork Data with Toolbox and the Natural Language Toolkit

    Directory of Open Access Journals (Sweden)

    Stuart Robinson

    2007-06-01

    Full Text Available This paper shows how fieldwork data can be managed using the program Toolbox together with the Natural Language Toolkit (NLTK for the Python programming language. It provides background information about Toolbox and describes how it can be downloaded and installed. The basic functionality of the program for lexicons and texts is described, and its strengths and weaknesses are reviewed. Its underlying data format is briefly discussed, and Toolbox processing capabilities of NLTK are introduced, showing ways in which it can be used to extend the functionality of Toolbox. This is illustrated with a few simple scripts that demonstrate basic data management tasks relevant to language documentation, such as printing out the contents of a lexicon as HTML.

  7. III. NIH TOOLBOX COGNITION BATTERY (CB): MEASURING EPISODIC MEMORY

    OpenAIRE

    Bauer, Patricia J.; Dikmen, Sureyya S.; Heaton, Robert K.; Mungas, Dan; Slotkin, Jerry; Beaumont, Jennifer L.

    2013-01-01

    One of the most significant domains of cognition is episodic memory, which allows for rapid acquisition and long-term storage of new information. For purposes of the NIH Toolbox, we devised a new test of episodic memory. The nonverbal NIH Toolbox Picture Sequence Memory Test (TPSMT) requires participants to reproduce the order of an arbitrarily ordered sequence of pictures presented on a computer. To adjust for ability, sequence length varies from 6 to 15 pictures. Multiple trials are adminis...

  8. An open-source toolbox for automated phenotyping of mice in behavioral tasks

    Directory of Open Access Journals (Sweden)

    Tapan P Patel

    2014-10-01

    Full Text Available Classifying behavior patterns in mouse models of neurological, psychiatric and neurodevelopmental disorders is critical for understanding disease causality and treatment. However, complete characterization of behavior is time-intensive, prone to subjective scoring, and often requires specialized equipment. Although several reports describe automated home-cage monitoring and individual task scoring methods, we report the first open source, comprehensive toolbox for automating the scoring of several common behavior tasks used by the neuroscience community. We show this new toolbox is robust and achieves equal or better consistency when compared to manual scoring methods. We use this toolbox to study the alterations in behavior that occur following blast-induced traumatic brain injury (bTBI, and study if these behavior patterns are altered following genetic deletion of the transcription factor Ets-like kinase 1 (Elk-1. Due to the role of Elk-1 in neuronal survival and proposed role in synaptic plasticity, we hypothesized that Elk-1 deletion would improve some neurobehavioral deficits, while impairing others, following blast exposure. In Elk-1 knockout animals, deficits in open field, spatial object recognition and elevated zero maze performance after blast exposure disappeared, while new significant deficits appeared in spatial and associative memory. These are the first data suggesting a molecular mediator of anxiety deficits following blast-induced traumatic brain injury, and represent the utility of the broad screening tool we developed. More broadly, we envision this open-source toolbox will provide a more consistent and rapid analysis of behavior across many neurological diseases, promoting the rapid discovery of novel pathways mediating disease progression and treatment.

  9. Aerospace Toolbox---a flight vehicle design, analysis, simulation ,and software development environment: I. An introduction and tutorial

    Science.gov (United States)

    Christian, Paul M.; Wells, Randy

    2001-09-01

    This paper presents a demonstrated approach to significantly reduce the cost and schedule of non real-time modeling and simulation, real-time HWIL simulation, and embedded code development. The tool and the methodology presented capitalize on a paradigm that has become a standard operating procedure in the automotive industry. The tool described is known as the Aerospace Toolbox, and it is based on the MathWorks Matlab/Simulink framework, which is a COTS application. Extrapolation of automotive industry data and initial applications in the aerospace industry show that the use of the Aerospace Toolbox can make significant contributions in the quest by NASA and other government agencies to meet aggressive cost reduction goals in development programs. The part I of this paper provides a detailed description of the GUI based Aerospace Toolbox and how it is used in every step of a development program; from quick prototyping of concept developments that leverage built-in point of departure simulations through to detailed design, analysis, and testing. Some of the attributes addressed include its versatility in modeling 3 to 6 degrees of freedom, its library of flight test validated library of models (including physics, environments, hardware, and error sources), and its built-in Monte Carlo capability. Other topics to be covered in this part include flight vehicle models and algorithms, and the covariance analysis package, Navigation System Covariance Analysis Tools (NavSCAT). Part II of this paper, to be published at a later date, will conclude with a description of how the Aerospace Toolbox is an integral part of developing embedded code directly from the simulation models by using the Mathworks Real Time Workshop and optimization tools. It will also address how the Toolbox can be used as a design hub for Internet based collaborative engineering tools such as NASA's Intelligent Synthesis Environment (ISE) and Lockheed Martin's Interactive Missile Design Environment

  10. Design of a Toolbox of RNA Thermometers.

    Science.gov (United States)

    Sen, Shaunak; Apurva, Divyansh; Satija, Rohit; Siegal, Dan; Murray, Richard M

    2017-08-18

    Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. Although RNA-based sensors, called "thermometers", have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature differing in sensitivity and threshold. We address this issue by constructing a library of RNA thermometers based on thermodynamic computations and experimentally measuring their activities in cell-free biomolecular "breadboards". Using free energies of the minimum free energy structures as well as melt profile computations, we estimated that a diverse set of temperature responses were possible. We experimentally found a wide range of responses to temperature in the range 29-37 °C with fold-changes varying over 3-fold around the starting thermometer. The sensitivities of these responses ranged over 10-fold around the starting thermometer. We correlated these measurements with computational expectations, finding that although there was no strong correlation for the individual thermometers, overall trends of diversity, fold-changes, and sensitivities were similar. These results present a toolbox of RNA-based circuit elements with diverse temperature responses.

  11. Robotic inspection technology-process an toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Hermes, Markus [ROSEN Group (United States). R and D Dept.

    2005-07-01

    Pipeline deterioration grows progressively with ultimate aging of pipeline systems (on-plot and cross country). This includes both, very localized corrosion as well as increasing failure probability due to fatigue cracking. Limiting regular inspecting activities to the 'scrapable' part of the pipelines only, will ultimately result into a pipeline system with questionable integrity. The confidence level in the integrity of these systems will drop below acceptance levels. Inspection of presently un-inspectable sections of the pipeline system becomes a must. This paper provides information on ROSEN's progress on the 'robotic inspection technology' project. The robotic inspection concept developed by ROSEN is based on a modular toolbox principle. This is mandatory. A universal 'all purpose' robot would not be reliable and efficient in resolving the postulated inspection task. A preparatory Quality Function Deployment (QFD) analysis is performed prior to the decision about the adequate robotic solution. This enhances the serviceability and efficiency of the provided technology. The word 'robotic' can be understood in its full meaning of Recognition - Strategy - Motion - Control. Cooperation of different individual systems with an established communication, e.g. utilizing Bluetooth technology, support the robustness of the ROSEN robotic inspection approach. Beside the navigation strategy, the inspection strategy is also part of the QFD process. Multiple inspection technologies combined on a single carrier or distributed across interacting container must be selected with a clear vision of the particular goal. (author)

  12. DETECT: a MATLAB toolbox for event detection and identification in time series, with applications to artifact detection in EEG signals.

    Science.gov (United States)

    Lawhern, Vernon; Hairston, W David; Robbins, Kay

    2013-01-01

    Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG) data as an additional illustration.

  13. DETECT: a MATLAB toolbox for event detection and identification in time series, with applications to artifact detection in EEG signals.

    Directory of Open Access Journals (Sweden)

    Vernon Lawhern

    Full Text Available Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG data as an additional illustration.

  14. Hallmarks of Alzheimer disease are evolving relentlessly in Metropolitan Mexico City infants, children and young adults. APOE4 carriers have higher suicide risk and higher odds of reaching NFT stage V at ≤ 40 years of age.

    Science.gov (United States)

    Calderón-Garcidueñas, Lilian; Gónzalez-Maciel, Angélica; Reynoso-Robles, Rafael; Delgado-Chávez, Ricardo; Mukherjee, Partha S; Kulesza, Randy J; Torres-Jardón, Ricardo; Ávila-Ramírez, José; Villarreal-Ríos, Rodolfo

    2018-07-01

    Exposures to fine particulate matter (PM 2.5 ) and ozone (O 3 ) above USEPA standards are associated with Alzheimer's disease (AD) risk. Metropolitan Mexico City (MMC) residents have life time exposures to PM 2.5 and O 3 above USEPA standards. We investigated AD intra and extracellular protein aggregates and ultrastructural neurovascular pathology in 203 MMC residents age 25.36 ± 9.23 y. Immunohistochemical methods were used to identify AT8 hyperphosphorilated tau (Htau) and 4G8 (amyloid β 17-24). Primary outcomes: staging of Htau and amyloid, per decade and cumulative PM 2.5 (CPM 2.5 ) above standard. Apolipoprotein E allele 4 (APOE4), age and cause of death were secondary outcomes. Subcortical pretangle stage b was identified in an 11month old baby. Cortical tau pre-tangles, neurofibrillary tangles (NFT) Stages I-II, amyloid phases 1-2, Htau in substantia nigrae, auditory, oculomotor, trigeminal and autonomic systems were identified by the 2nd decade. Progression to NFT stages III-V was present in 24.8% of 30-40 y old subjects. APOE4 carriers have 4.92 times higher suicide odds (p = 0.0006), and 23.6 times higher odds of NFT V (p < 0.0001) v APOE4 non-carriers having similar CPM 2.5 exposure and age. Age (p = 0.0062) and CPM 2.5 (p = 0.0178) were significant for developing NFT V. Combustion-derived nanoparticles were associated with early and progressive damage to the neurovascular unit. Alzheimer's disease starting in the brainstem of young children and affecting 99.5% of young urbanites is a serious health crisis. Air pollution control should be prioritised. Childhood relentless Htau makes a fundamental target for neuroprotective interventions and the first two decades are critical. We recommend the concept of preclinical AD be revised and emphasize the need to define paediatric environmental, nutritional, metabolic and genetic risk factor interactions of paramount importance to prevent AD. AD evolving from childhood is threating the

  15. A preclinical cognitive test battery to parallel the National Institute of Health Toolbox in humans: bridging the translational gap.

    Science.gov (United States)

    Snigdha, Shikha; Milgram, Norton W; Willis, Sherry L; Albert, Marylin; Weintraub, S; Fortin, Norbert J; Cotman, Carl W

    2013-07-01

    A major goal of animal research is to identify interventions that can promote successful aging and delay or reverse age-related cognitive decline in humans. Recent advances in standardizing cognitive assessment tools for humans have the potential to bring preclinical work closer to human research in aging and Alzheimer's disease. The National Institute of Health (NIH) has led an initiative to develop a comprehensive Toolbox for Neurologic Behavioral Function (NIH Toolbox) to evaluate cognitive, motor, sensory and emotional function for use in epidemiologic and clinical studies spanning 3 to 85 years of age. This paper aims to analyze the strengths and limitations of animal behavioral tests that can be used to parallel those in the NIH Toolbox. We conclude that there are several paradigms available to define a preclinical battery that parallels the NIH Toolbox. We also suggest areas in which new tests may benefit the development of a comprehensive preclinical test battery for assessment of cognitive function in animal models of aging and Alzheimer's disease. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Introduction to TAFI - A Matlab® toolbox for analysis of flexural isostasy

    Science.gov (United States)

    Jha, S.; Harry, D. L.; Schutt, D.

    2016-12-01

    The isostatic response of vertical tectonic loads emplaced on thin elastic plates overlying inviscid substrate and the corresponding gravity anomalies are commonly modeled using well established theories and methodologies of flexural analysis. However, such analysis requires some mathematical and coding expertise on part of users. With that in mind, we designed a new interactive Matlab® toolbox called Toolbox for Analysis of Flexural Isostasy (TAFI). TAFI allows users to create forward models (2-D and 3-D) of flexural deformation of the lithosphere and resulting gravity anomaly. TAFI computes Green's Functions for flexure of the elastic plate subjected to point or line loads, and analytical solution for harmonic loads. Flexure due to non-impulsive, distributed 2-D or 3-D loads are computed by convolving the appropriate Green's function with a user-supplied spatially discretized load function. The gravity anomaly associated with each density interface is calculated by using the Fourier Transform of flexural deflection of these interfaces and estimating the gravity in the wavenumber domain. All models created in TAFI are based on Matlab's intrinsic functions and do not require any specialized toolbox, function or library except those distributed with TAFI. Modeling functions within TAFI can be called from Matlab workspace, from within user written programs or from the TAFI's graphical user interface (GUI). The GUI enables the user to model the flexural deflection of lithosphere interactively, enabling real time comparison of model fit with observed data constraining the flexural deformation and gravity, facilitating rapid search for best fitting flexural model. TAFI is a very useful teaching and research tool and have been tested rigorously in graduate level teaching and basic research environment.

  17. Wheat Rust Toolbox Related to New Initiatives on Yellow Rust

    DEFF Research Database (Denmark)

    Hansen, Jens Grønbech; Lassen, Poul

    ://www.fao.org/agriculture/crops/rust/stem/rust-report/en/). The Wheat rust toolbox is one of several International research platforms hosted by Aarhus University, and it uses the same ICT framework and databases as EuroWheat (www.eurowheat.org) and EuroBlight (www.EuroBlight.net). The Wheat Rust Toolbox will also serve the Global Rust Reference Centre (GRRC) as well...... – 2009), and as soon as possible this will be expanded to cover all global yellow rust data available via the GRRC. The presentation will focus on experiences from the previous work on global databases and web based information systems, as well as propose ideas how the toolbox can be helpful regarding...

  18. VQone MATLAB toolbox: A graphical experiment builder for image and video quality evaluations: VQone MATLAB toolbox.

    Science.gov (United States)

    Nuutinen, Mikko; Virtanen, Toni; Rummukainen, Olli; Häkkinen, Jukka

    2016-03-01

    This article presents VQone, a graphical experiment builder, written as a MATLAB toolbox, developed for image and video quality ratings. VQone contains the main elements needed for the subjective image and video quality rating process. This includes building and conducting experiments and data analysis. All functions can be controlled through graphical user interfaces. The experiment builder includes many standardized image and video quality rating methods. Moreover, it enables the creation of new methods or modified versions from standard methods. VQone is distributed free of charge under the terms of the GNU general public license and allows code modifications to be made so that the program's functions can be adjusted according to a user's requirements. VQone is available for download from the project page (http://www.helsinki.fi/psychology/groups/visualcognition/).

  19. SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

    Science.gov (United States)

    Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

    2013-01-01

    We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

  20. Evidence for a common toolbox based on necrotrophy in a fungal lineage spanning necrotrophs, biotrophs, endophytes, host generalists and specialists.

    Directory of Open Access Journals (Sweden)

    Marion Andrew

    Full Text Available The Sclerotiniaceae (Ascomycotina, Leotiomycetes is a relatively recently evolved lineage of necrotrophic host generalists, and necrotrophic or biotrophic host specialists, some latent or symptomless. We hypothesized that they inherited a basic toolbox of genes for plant symbiosis from their common ancestor. Maintenance and evolutionary diversification of symbiosis could require selection on toolbox genes or on timing and magnitude of gene expression. The genes studied were chosen because their products have been previously investigated as pathogenicity factors in the Sclerotiniaceae. They encode proteins associated with cell wall degradation: acid protease 1 (acp1, aspartyl protease (asps, and polygalacturonases (pg1, pg3, pg5, pg6, and the oxalic acid (OA pathway: a zinc finger transcription factor (pac1, and oxaloacetate acetylhydrolase (oah, catalyst in OA production, essential for full symptom production in Sclerotinia sclerotiorum. Site-specific likelihood analyses provided evidence for purifying selection in all 8 pathogenicity-related genes. Consistent with an evolutionary arms race model, positive selection was detected in 5 of 8 genes. Only generalists produced large, proliferating disease lesions on excised Arabidopsis thaliana leaves and oxalic acid by 72 hours in vitro. In planta expression of oah was 10-300 times greater among the necrotrophic host generalists than necrotrophic and biotrophic host specialists; pac1 was not differentially expressed. Ability to amplify 6/8 pathogenicity related genes and produce oxalic acid in all genera are consistent with the common toolbox hypothesis for this gene sample. That our data did not distinguish biotrophs from necrotrophs is consistent with 1 a common toolbox based on necrotrophy and 2 the most conservative interpretation of the 3-locus housekeeping gene phylogeny--a baseline of necrotrophy from which forms of biotrophy emerged at least twice. Early oah overexpression likely expands the

  1. Toolboxes for cyanobacteria: Recent advances and future direction.

    Science.gov (United States)

    Sun, Tao; Li, Shubin; Song, Xinyu; Diao, Jinjin; Chen, Lei; Zhang, Weiwen

    2018-05-03

    Photosynthetic cyanobacteria are important primary producers and model organisms for studying photosynthesis and elements cycling on earth. Due to the ability to absorb sunlight and utilize carbon dioxide, cyanobacteria have also been proposed as renewable chassis for carbon-neutral "microbial cell factories". Recent progresses on cyanobacterial synthetic biology have led to the successful production of more than two dozen of fuels and fine chemicals directly from CO 2 , demonstrating their potential for scale-up application in the future. However, compared with popular heterotrophic chassis like Escherichia coli and Saccharomyces cerevisiae, where abundant genetic tools are available for manipulations at levels from single gene, pathway to whole genome, limited genetic tools are accessible to cyanobacteria. Consequently, this significant technical hurdle restricts both the basic biological researches and further development and application of these renewable systems. Though still lagging the heterotrophic chassis, the vital roles of genetic tools in tuning of gene expression, carbon flux re-direction as well as genome-wide manipulations have been increasingly recognized in cyanobacteria. In recent years, significant progresses on developing and introducing new and efficient genetic tools have been made for cyanobacteria, including promoters, riboswitches, ribosome binding site engineering, clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease (CRISPR/Cas) systems, small RNA regulatory tools and genome-scale modeling strategies. In this review, we critically summarize recent advances on development and applications as well as technical limitations and future directions of the genetic tools in cyanobacteria. In addition, toolboxes feasible for using in large-scale cultivation are also briefly discussed. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. GPELab, a Matlab toolbox to solve Gross-Pitaevskii equations II: Dynamics and stochastic simulations

    Science.gov (United States)

    Antoine, Xavier; Duboscq, Romain

    2015-08-01

    GPELab is a free Matlab toolbox for modeling and numerically solving large classes of systems of Gross-Pitaevskii equations that arise in the physics of Bose-Einstein condensates. The aim of this second paper, which follows (Antoine and Duboscq, 2014), is to first present the various pseudospectral schemes available in GPELab for computing the deterministic and stochastic nonlinear dynamics of Gross-Pitaevskii equations (Antoine, et al., 2013). Next, the corresponding GPELab functions are explained in detail. Finally, some numerical examples are provided to show how the code works for the complex dynamics of BEC problems.

  3. OSSIM wave-optics toolbox and its use to simulate AEOS

    Science.gov (United States)

    Smith, Carey A.; Forgham, James L.; Jones, Bruce W.; Jones, Kenneth D.

    2001-12-01

    OSSim (Optical System Simulation) is a simulation toolbox of optical and processing components. By using full wave-optics in the time-domain, OSSim simulates diffractive effects and control loop interactions missed by simpler analyses. OSSim also models the atmosphere, with user customizable turbulence strength, wind, and slew. This paper first presents 2 introductory examples: a simple 2-lens imaging system and a simple tilt-control system. Then it presents a simulation of the 3.67-meter AEOS (Advanced Electro-Optics System) telescope on Maui. The OSSim simulation agrees well with the AEOS experimental results.

  4. Versatile Cas9-driven subpopulation selection toolbox for Lactococcus lactis

    NARCIS (Netherlands)

    Els, van der Simon; James, Jennelle K.; Kleerebezem, Michiel; Bron, Peter A.

    2018-01-01

    CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here, we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis. The Cas9 expression vector

  5. 40 CFR 141.719 - Additional filtration toolbox components.

    Science.gov (United States)

    2010-07-01

    ... taken from a surface water or GWUDI source. A cap, such as GAC, on a single stage of filtration is not... separate stage of filtration if both filtration stages treat entire plant flow taken from a surface water... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Additional filtration toolbox...

  6. Geoplotlib: a Python Toolbox for Visualizing Geographical Data

    OpenAIRE

    Cuttone, Andrea; Lehmann, Sune; Larsen, Jakob Eg

    2016-01-01

    We introduce geoplotlib, an open-source python toolbox for visualizing geographical data. geoplotlib supports the development of hardware-accelerated interactive visualizations in pure python, and provides implementations of dot maps, kernel density estimation, spatial graphs, Voronoi tesselation, shapefiles and many more common spatial visualizations. We describe geoplotlib design, functionalities and use cases.

  7. Wyrm: A Brain-Computer Interface Toolbox in Python.

    Science.gov (United States)

    Venthur, Bastian; Dähne, Sven; Höhne, Johannes; Heller, Hendrik; Blankertz, Benjamin

    2015-10-01

    In the last years Python has gained more and more traction in the scientific community. Projects like NumPy, SciPy, and Matplotlib have created a strong foundation for scientific computing in Python and machine learning packages like scikit-learn or packages for data analysis like Pandas are building on top of it. In this paper we present Wyrm ( https://github.com/bbci/wyrm ), an open source BCI toolbox in Python. Wyrm is applicable to a broad range of neuroscientific problems. It can be used as a toolbox for analysis and visualization of neurophysiological data and in real-time settings, like an online BCI application. In order to prevent software defects, Wyrm makes extensive use of unit testing. We will explain the key aspects of Wyrm's software architecture and design decisions for its data structure, and demonstrate and validate the use of our toolbox by presenting our approach to the classification tasks of two different data sets from the BCI Competition III. Furthermore, we will give a brief analysis of the data sets using our toolbox, and demonstrate how we implemented an online experiment using Wyrm. With Wyrm we add the final piece to our ongoing effort to provide a complete, free and open source BCI system in Python.

  8. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    1997-01-01

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  9. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  10. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

    Science.gov (United States)

    Minas, Giorgos; Momiji, Hiroshi; Jenkins, Dafyd J; Costa, Maria J; Rand, David A; Finkenstädt, Bärbel

    2017-06-26

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to researchers. The ReTrOS toolbox (Reconstructing Transcription Open Software) provides MATLAB-based implementations of two related methods, namely ReTrOS-Smooth and ReTrOS-Switch, for reconstructing the temporal transcriptional activity profile of a gene from given mRNA expression time series or protein reporter time series. The methods are based on fitting a differential equation model incorporating the processes of transcription, translation and degradation. The toolbox provides a framework for model fitting along with statistical analyses of the model with a graphical interface and model visualisation. We highlight several applications of the toolbox, including the reconstruction of the temporal cascade of transcriptional activity inferred from mRNA expression data and protein reporter data in the core circadian clock in Arabidopsis thaliana, and how such reconstructed transcription profiles can be used to study the effects of different cell lines and conditions. The ReTrOS toolbox allows users to analyse gene and/or protein expression time series where, with appropriate formulation of prior information about a minimum of kinetic parameters, in particular rates of degradation, users are able to infer timings of changes in transcriptional activity. Data from any organism and obtained from a range of technologies can be used as input due to the flexible and generic nature of the model and implementation. The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation.

  11. CBP Toolbox Version 3.0 “Beta Testing” Performance Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Smith, III, F. G. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-07-29

    One function of the Cementitious Barriers Partnership (CBP) is to assess available models of cement degradation and to assemble suitable models into a “Toolbox” that would be made available to members of the partnership, as well as the DOE Complex. To this end, SRNL and Vanderbilt University collaborated to develop an interface using the GoldSim software to the STADIUM@ code developed by SIMCO Technologies, Inc. and LeachXS/ORCHESTRA developed by Energy research Centre of the Netherlands (ECN). Release of Version 3.0 of the CBP Toolbox is planned in the near future. As a part of this release, an increased level of quality assurance for the partner codes and the GoldSim interface has been developed. This report documents results from evaluation testing of the ability of CBP Toolbox 3.0 to perform simulations of concrete degradation applicable to performance assessment of waste disposal facilities. Simulations of the behavior of Savannah River Saltstone Vault 2 and Vault 1/4 concrete subject to sulfate attack and carbonation over a 500- to 1000-year time period were run using a new and upgraded version of the STADIUM@ code and the version of LeachXS/ORCHESTRA released in Version 2.0 of the CBP Toolbox. Running both codes allowed comparison of results from two models which take very different approaches to simulating cement degradation. In addition, simulations of chloride attack on the two concretes were made using the STADIUM@ code. The evaluation sought to demonstrate that: 1) the codes are capable of running extended realistic simulations in a reasonable amount of time; 2) the codes produce “reasonable” results; the code developers have provided validation test results as part of their code QA documentation; and 3) the two codes produce results that are consistent with one another. Results of the evaluation testing showed that the three criteria listed above were met by the CBP partner codes. Therefore, it is concluded that

  12. An open-source toolbox for multiphase flow in porous media

    Science.gov (United States)

    Horgue, P.; Soulaine, C.; Franc, J.; Guibert, R.; Debenest, G.

    2015-02-01

    Multiphase flow in porous media provides a wide range of applications: from the environmental understanding (aquifer, site-pollution) to industrial process improvements (oil production, waste management). Modeling of such flows involves specific volume-averaged equations and therefore specific computational fluid dynamics (CFD) tools. In this work, we develop a toolbox for modeling multiphase flow in porous media with OpenFOAM®, an open-source platform for CFD. The underlying idea of this approach is to provide an easily adaptable tool that can be used in further studies to test new mathematical models or numerical methods. The package provides the most common effective properties models of the literature (relative permeability, capillary pressure) and specific boundary conditions related to porous media flows. To validate this package, solvers based on the IMplicit Pressure Explicit Saturation (IMPES) method are developed in the toolbox. The numerical validation is performed by comparison with analytical solutions on academic cases. Then, a satisfactory parallel efficiency of the solver is shown on a more complex configuration.

  13. DIRT: Dust InfraRed Toolbox

    Science.gov (United States)

    Pound, Marc W.; Wolfire, Mark G.; Mundy, Lee G.; Teuben, Peter; Lord, Steve

    2011-02-01

    DIRT is a Java applet for modelling astrophysical processes in circumstellar dust shells around young and evolved stars. With DIRT, you can: select and display over 500,000 pre-run model spectral energy distributions (SEDs) find the best-fit model to your data set account for beam size in model fitting manipulate data and models with an interactive viewer display gas and dust density and temperature profiles display model intensity profiles at various wavelengths

  14. Uso do rejeito da dessalinização de água salobra no cultivo da alface (Lactuca sativa L. em sistema hidropônico NFT Use of the desalted wastewater for lettuce (Lactuca sativa L. production in NFT hydroponic system

    Directory of Open Access Journals (Sweden)

    Rafaelly Suzanye da Silva Santos

    2010-08-01

    Full Text Available A dessalinização por osmose reversa tem sido bastante utilizada para o tratamento de água salobra, possibilitando a sua utilização para o consumo humano, especialmente em regiões semiáridas. Esse processo tem um fator limitante que é a produção de um rejeito de água com alta salinidade. Com o objetivo de avaliar os efeitos da utilização de água de rejeito da dessalinização no cultivo de alface cultivar Vera (Lactuca sativa L. em sistema hidropônico NFT foi conduzido um experimento em casa de vegetação no departamento de ciências ambientais da UFERSA, em delineamento em blocos casualizados, com seis tratamentos e quatro repetições. Os níveis de salinidade da água entre os tratamentos foram obtidos com, ou sem a necessidade de diluição da água de rejeito da dessalinização acrescido da solução nutritiva com salinidade de 1 dS m-1 (100% de água potável de abastecimento - 1,4 dS m-1; 85% abastecimento e 15% água de rejeito - 1,9 dS m-1; 75 % água de rejeito + 25 % água de abastecimento - 2,7 dS m-1; 50% água de rejeito e 50% água de abastecimento - 3,8 dS m-1; 25 % água de rejeito e 75 % água de abastecimento - 4,9 dS m-1 e água de rejeito coletada no dessalinizador - 5,5 dS m-1. Os parâmetros analisados foram área foliar, diâmetro do caule, número de folhas, peso de matéria fresca e o peso de matéria seca. Todas as variáveis estudadas foram influenciadas negativamente de forma linear pelo efeito da concentração de sais na água de irrigação, sendo que a área foliar e a matéria fresca da parte aérea são as que melhor representam a sensibilidade ao estresse salino na cultivar estudada, tendo a produção em termos de matéria fresca uma redução de 94,83%, ao se elevar a CEa de 1,4 a 5,5 dS m-1.The desalination process by reverse osmosis was used for the treatment of brackish water, making possible the usage human consume in semiarid zones. This process has a limiting factor: it produces

  15. III. NIH Toolbox Cognition Battery (CB): measuring episodic memory.

    Science.gov (United States)

    Bauer, Patricia J; Dikmen, Sureyya S; Heaton, Robert K; Mungas, Dan; Slotkin, Jerry; Beaumont, Jennifer L

    2013-08-01

    One of the most significant domains of cognition is episodic memory, which allows for rapid acquisition and long-term storage of new information. For purposes of the NIH Toolbox, we devised a new test of episodic memory. The nonverbal NIH Toolbox Picture Sequence Memory Test (TPSMT) requires participants to reproduce the order of an arbitrarily ordered sequence of pictures presented on a computer. To adjust for ability, sequence length varies from 6 to 15 pictures. Multiple trials are administered to increase reliability. Pediatric data from the validation study revealed the TPSMT to be sensitive to age-related changes. The task also has high test-retest reliability and promising construct validity. Steps to further increase the sensitivity of the instrument to individual and age-related variability are described. © 2013 The Society for Research in Child Development, Inc.

  16. The panacea toolbox of a PhD biomedical student.

    Science.gov (United States)

    Skaik, Younis

    2014-01-01

    Doing a PhD (doctor of philosophy) for the sake of contribution to knowledge should give the student an immense enthusiasm through the PhD period. It is the time in one's life that one spends to "hit the nail on the head" in a specific area and topic of interest. A PhD consists mostly of hard work and tenacity; however, luck and genius might also play a little role. You can pass all PhD phases without having both luck and genius. The PhD student should have pre-PhD and PhD toolboxes, which are "sine quibus non" for getting successfully a PhD degree. In this manuscript, the toolboxes of the PhD student are discussed.

  17. Tadarida: A Toolbox for Animal Detection on Acoustic Recordings

    Directory of Open Access Journals (Sweden)

    Yves Bas

    2017-02-01

    Full Text Available Passive Acoustic Monitoring (PAM recently extended to a very wide range of animals, but no available open software has been sufficiently generic to automatically treat several taxonomic groups. Here we present Tadarida, a software toolbox allowing for the detection and labelling of recorded sound events, and to classify any new acoustic data into known classes. It is made up of three modules handling Detection, Labelling and Classification and running on either Linux or Windows. This development resulted in the first open software (1 allowing generic sound event detection (multi-taxa, (2 providing graphical sound labelling at a single-instance level and (3 covering the whole process from sound detection to classification. This generic and modular design opens numerous reuse opportunities among (bioacoustics researchers, especially for those managing and/or developing PAM schemes. The whole toolbox is openly developed in C++ (Detection and Labelling and R (Classification and stored at https://github.com/YvesBas.

  18. System design through Matlab, control toolbox and Simulink

    CERN Document Server

    Singh, Krishna K

    2001-01-01

    MATLAB , a software package developed by Math Works, Inc. is powerful, versatile and interactive software for scientific and technical computations including simulations. Specialised toolboxes provided with several built-in functions are a special feature of MATLAB . This book titled System Design through MATLAB , Control Toolbox and SIMULINK aims at getting the reader started with computations and simulations in system engineering quickly and easily and then proceeds to build concepts for advanced computations and simulations that includes the control and compensation of systems. Simulation through SIMULINK has also been described to allow the reader to get the feel of the real world situation. This book is appropriate for undergraduate students undergoing final semester of their project work, postgraduate students who have MATLAB integrated in their course or wish to take up simulation problem in the area of system engineering for their dissertation work and research scholars for whom MATLABÊ

  19. PSYCHOACOUSTICS: a comprehensive MATLAB toolbox for auditory testing.

    Science.gov (United States)

    Soranzo, Alessandro; Grassi, Massimo

    2014-01-01

    PSYCHOACOUSTICS is a new MATLAB toolbox which implements three classic adaptive procedures for auditory threshold estimation. The first includes those of the Staircase family (method of limits, simple up-down and transformed up-down); the second is the Parameter Estimation by Sequential Testing (PEST); and the third is the Maximum Likelihood Procedure (MLP). The toolbox comes with more than twenty built-in experiments each provided with the recommended (default) parameters. However, if desired, these parameters can be modified through an intuitive and user friendly graphical interface and stored for future use (no programming skills are required). Finally, PSYCHOACOUSTICS is very flexible as it comes with several signal generators and can be easily extended for any experiment.

  20. RenderToolbox3: MATLAB tools that facilitate physically based stimulus rendering for vision research.

    Science.gov (United States)

    Heasly, Benjamin S; Cottaris, Nicolas P; Lichtman, Daniel P; Xiao, Bei; Brainard, David H

    2014-02-07

    RenderToolbox3 provides MATLAB utilities and prescribes a workflow that should be useful to researchers who want to employ graphics in the study of vision and perhaps in other endeavors as well. In particular, RenderToolbox3 facilitates rendering scene families in which various scene attributes and renderer behaviors are manipulated parametrically, enables spectral specification of object reflectance and illuminant spectra, enables the use of physically based material specifications, helps validate renderer output, and converts renderer output to physical units of radiance. This paper describes the design and functionality of the toolbox and discusses several examples that demonstrate its use. We have designed RenderToolbox3 to be portable across computer hardware and operating systems and to be free and open source (except for MATLAB itself). RenderToolbox3 is available at https://github.com/DavidBrainard/RenderToolbox3.

  1. fMRI Artefact Rejection and Sleep Scoring Toolbox

    Directory of Open Access Journals (Sweden)

    Yves Leclercq

    2011-01-01

    Full Text Available We started writing the “fMRI artefact rejection and sleep scoring toolbox”, or “FAST”, to process our sleep EEG-fMRI data, that is, the simultaneous recording of electroencephalographic and functional magnetic resonance imaging data acquired while a subject is asleep. FAST tackles three crucial issues typical of this kind of data: (1 data manipulation (viewing, comparing, chunking, etc. of long continuous M/EEG recordings, (2 rejection of the fMRI-induced artefact in the EEG signal, and (3 manual sleep-scoring of the M/EEG recording. Currently, the toolbox can efficiently deal with these issues via a GUI, SPM8 batching system or hand-written script. The tools developed are, of course, also useful for other EEG applications, for example, involving simultaneous EEG-fMRI acquisition, continuous EEG eye-balling, and manipulation. Even though the toolbox was originally devised for EEG data, it will also gracefully handle MEG data without any problem. “FAST” is developed in Matlab as an add-on toolbox for SPM8 and, therefore, internally uses its SPM8-meeg data format. “FAST” is available for free, under the GNU-GPL.

  2. Cumulative Risk Assessment Toolbox: Methods and Approaches for the Practitioner

    Directory of Open Access Journals (Sweden)

    Margaret M. MacDonell

    2013-01-01

    Full Text Available The historical approach to assessing health risks of environmental chemicals has been to evaluate them one at a time. In fact, we are exposed every day to a wide variety of chemicals and are increasingly aware of potential health implications. Although considerable progress has been made in the science underlying risk assessments for real-world exposures, implementation has lagged because many practitioners are unaware of methods and tools available to support these analyses. To address this issue, the US Environmental Protection Agency developed a toolbox of cumulative risk resources for contaminated sites, as part of a resource document that was published in 2007. This paper highlights information for nearly 80 resources from the toolbox and provides selected updates, with practical notes for cumulative risk applications. Resources are organized according to the main elements of the assessment process: (1 planning, scoping, and problem formulation; (2 environmental fate and transport; (3 exposure analysis extending to human factors; (4 toxicity analysis; and (5 risk and uncertainty characterization, including presentation of results. In addition to providing online access, plans for the toolbox include addressing nonchemical stressors and applications beyond contaminated sites and further strengthening resource accessibility to support evolving analyses for cumulative risk and sustainable communities.

  3. Semi-automated Robust Quantification of Lesions (SRQL Toolbox

    Directory of Open Access Journals (Sweden)

    Kaori Ito

    2017-02-01

    Full Text Available Quantifying lesions in a robust manner is fundamental for studying the effects of neuroanatomical changes in the post-stroke brain on recovery. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. We developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.267213 Toolbox that performs several analysis steps: 1 a white matter intensity correction that removes healthy white matter voxels from the lesion mask, thereby making lesions slightly more robust to subjective errors; 2 an automated report of descriptive statistics on lesions for simplified comparison between or across groups, and 3 an option to perform analyses in both native and standard space to facilitate analyses in either space, or comparisons between spaces. Here, we describe the methods implemented in the toolbox and demonstrate the outputs of the SRQL toolbox.

  4. MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

    Directory of Open Access Journals (Sweden)

    Xia Xuhua

    2005-03-01

    Full Text Available Abstract Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454.

  5. SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer.

    Science.gov (United States)

    Li, Jiannong; Smalley, Inna; Schell, Michael J; Smalley, Keiran S M; Chen, Y Ann

    2017-09-15

    Single-cell technologies allow characterization of transcriptomes and epigenomes for individual cells under different conditions and provide unprecedented resolution for researchers to investigate cellular heterogeneity in cancer. The SinCHet ( gle ell erogeneity) toolbox is developed in MATLAB and has a graphical user interface (GUI) for visualization and user interaction. It analyzes both continuous (e.g. mRNA expression) and binary omics data (e.g. discretized methylation data). The toolbox does not only quantify cellular heterogeneity using S hannon P rofile (SP) at different clonal resolutions but also detects heterogeneity differences using a D statistic between two populations. It is defined as the area under the P rofile of S hannon D ifference (PSD). This flexible tool provides a default clonal resolution using the change point of PSD detected by multivariate adaptive regression splines model; it also allows user-defined clonal resolutions for further investigation. This tool provides insights into emerging or disappearing clones between conditions, and enables the prioritization of biomarkers for follow-up experiments based on heterogeneity or marker differences between and/or within cell populations. The SinCHet software is freely available for non-profit academic use. The source code, example datasets, and the compiled package are available at http://labpages2.moffitt.org/chen/software/ . ann.chen@moffitt.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  6. COMETS2: An advanced MATLAB toolbox for the numerical analysis of electric fields generated by transcranial direct current stimulation.

    Science.gov (United States)

    Lee, Chany; Jung, Young-Jin; Lee, Sang Jun; Im, Chang-Hwan

    2017-02-01

    Since there is no way to measure electric current generated by transcranial direct current stimulation (tDCS) inside the human head through in vivo experiments, numerical analysis based on the finite element method has been widely used to estimate the electric field inside the head. In 2013, we released a MATLAB toolbox named COMETS, which has been used by a number of groups and has helped researchers to gain insight into the electric field distribution during stimulation. The aim of this study was to develop an advanced MATLAB toolbox, named COMETS2, for the numerical analysis of the electric field generated by tDCS. COMETS2 can generate any sizes of rectangular pad electrodes on any positions on the scalp surface. To reduce the large computational burden when repeatedly testing multiple electrode locations and sizes, a new technique to decompose the global stiffness matrix was proposed. As examples of potential applications, we observed the effects of sizes and displacements of electrodes on the results of electric field analysis. The proposed mesh decomposition method significantly enhanced the overall computational efficiency. We implemented an automatic electrode modeler for the first time, and proposed a new technique to enhance the computational efficiency. In this paper, an efficient toolbox for tDCS analysis is introduced (freely available at http://www.cometstool.com). It is expected that COMETS2 will be a useful toolbox for researchers who want to benefit from the numerical analysis of electric fields generated by tDCS. Copyright © 2016. Published by Elsevier B.V.

  7. Turbo-Satori: a neurofeedback and brain-computer interface toolbox for real-time functional near-infrared spectroscopy.

    Science.gov (United States)

    Lührs, Michael; Goebel, Rainer

    2017-10-01

    Turbo-Satori is a neurofeedback and brain-computer interface (BCI) toolbox for real-time functional near-infrared spectroscopy (fNIRS). It incorporates multiple pipelines from real-time preprocessing and analysis to neurofeedback and BCI applications. The toolbox is designed with a focus in usability, enabling a fast setup and execution of real-time experiments. Turbo-Satori uses an incremental recursive least-squares procedure for real-time general linear model calculation and support vector machine classifiers for advanced BCI applications. It communicates directly with common NIRx fNIRS hardware and was tested extensively ensuring that the calculations can be performed in real time without a significant change in calculation times for all sampling intervals during ongoing experiments of up to 6 h of recording. Enabling immediate access to advanced processing features also allows the use of this toolbox for students and nonexperts in the field of fNIRS data acquisition and processing. Flexible network interfaces allow third party stimulus applications to access the processed data and calculated statistics in real time so that this information can be easily incorporated in neurofeedback or BCI presentations.

  8. DIRT: The Dust InfraRed Toolbox

    Science.gov (United States)

    Pound, M. W.; Wolfire, M. G.; Mundy, L. G.; Teuben, P. J.; Lord, S.

    We present DIRT, a Java applet geared toward modeling a variety of processes in envelopes of young and evolved stars. Users can automatically and efficiently search grids of pre-calculated models to fit their data. A large set of physical parameters and dust types are included in the model database, which contains over 500,000 models. The computing cluster for the database is described in the accompanying paper by Teuben et al. (2000). A typical user query will return about 50-100 models, which the user can then interactively filter as a function of 8 model parameters (e.g., extinction, size, flux, luminosity). A flexible, multi-dimensional plotter (Figure 1) allows users to view the models, rotate them, tag specific parameters with color or symbol size, and probe individual model points. For any given model, auxiliary plots such as dust grain properties, radial intensity profiles, and the flux as a function of wavelength and beamsize can be viewed. The user can fit observed data to several models simultaneously and see the results of the fit; the best fit is automatically selected for plotting. The URL for this project is http://dustem.astro.umd.edu.

  9. ERP Reliability Analysis (ERA) Toolbox: An open-source toolbox for analyzing the reliability of event-related brain potentials.

    Science.gov (United States)

    Clayson, Peter E; Miller, Gregory A

    2017-01-01

    Generalizability theory (G theory) provides a flexible, multifaceted approach to estimating score reliability. G theory's approach to estimating score reliability has important advantages over classical test theory that are relevant for research using event-related brain potentials (ERPs). For example, G theory does not require parallel forms (i.e., equal means, variances, and covariances), can handle unbalanced designs, and provides a single reliability estimate for designs with multiple sources of error. This monograph provides a detailed description of the conceptual framework of G theory using examples relevant to ERP researchers, presents the algorithms needed to estimate ERP score reliability, and provides a detailed walkthrough of newly-developed software, the ERP Reliability Analysis (ERA) Toolbox, that calculates score reliability using G theory. The ERA Toolbox is open-source, Matlab software that uses G theory to estimate the contribution of the number of trials retained for averaging, group, and/or event types on ERP score reliability. The toolbox facilitates the rigorous evaluation of psychometric properties of ERP scores recommended elsewhere in this special issue. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. The Timeseries Toolbox - A Web Application to Enable Accessible, Reproducible Time Series Analysis

    Science.gov (United States)

    Veatch, W.; Friedman, D.; Baker, B.; Mueller, C.

    2017-12-01

    The vast majority of data analyzed by climate researchers are repeated observations of physical process or time series data. This data lends itself of a common set of statistical techniques and models designed to determine trends and variability (e.g., seasonality) of these repeated observations. Often, these same techniques and models can be applied to a wide variety of different time series data. The Timeseries Toolbox is a web application designed to standardize and streamline these common approaches to time series analysis and modeling with particular attention to hydrologic time series used in climate preparedness and resilience planning and design by the U. S. Army Corps of Engineers. The application performs much of the pre-processing of time series data necessary for more complex techniques (e.g. interpolation, aggregation). With this tool, users can upload any dataset that conforms to a standard template and immediately begin applying these techniques to analyze their time series data.

  11. Enhancing Organizational Performance: A Toolbox for Self ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Do you know if your organization is performing efficiently? If it isn't, do you know why? This guidebook presents an innovative and thoroughly tested model for organizational self-assessment. The tools and tips in Enhancing Organizational Performance go beyond measuring the impact of programs, products, and services.

  12. Desempenho de cultivares de alface crespa em dois ambientes de cultivo em sistema hidropônico Performance of lettuce cultivars grown in two environments, in the NFT hydroponic system

    Directory of Open Access Journals (Sweden)

    SF Blat

    2011-03-01

    Full Text Available Este trabalho foi desenvolvido em Ribeirão Preto-SP, de 06/02 a 07/04 de 2006. O objetivo foi avaliar o desempenho de cinco cultivares de alface (Pira Roxa, Belíssima, Locarno, Crespona Gigante e Verônica em dois ambientes de cultivo (casa de vegetação climatizada e não climatizada em sistema hidropônico NFT. O delineamento experimental foi em blocos casualizados para cada ambiente com três repetições sendo cinco cultivares. Os ambientes foram comparados por meio de análise conjunta. Avaliaram-se a massa fresca e seca da parte aérea, massas fresca e seca do caule, massa fresca e seca da raiz, número de folhas maiores que 10 cm e número total de folhas. Não houve efeito significativo da interação cultivares e ambientes, demonstrando que as cultivares tiveram comportamento similar em ambos os ambientes.This research was carried out in Ribeirão Preto, São Paulo State, Brazil, from February to April, 2006. The performance of five lettuce cultivars (Pira Roxa, Belíssima, Locarno, Crespona Gigante and Verônica was evaluated, growing the plants in two environments (conventional and acclimatized greenhouse in hydroponic system NFT. A randomized-block experimental design was used for each environment, with three replications and five cultivars. The environments were compared through joint analysis. Evaluations were done for fresh and dry mater of the aboveground part, stem, and roots; number of leaves larger than 10 cm and total number of leaves. The cultivars Crespona Gigante and Verônica were prominent with regard to green and dry mass of the aboveground part, leaves, and roots, as well as to the number of leaves larger than 10 cm. The interaction cultivar x environment was not significant, demonstrating that the cultivars had similar behavior in both environments.

  13. IMPROVEMENT TOOLBOX DESIGN FOR EFQM CRITERIA

    Directory of Open Access Journals (Sweden)

    Ipek Deveci Kocakoç

    2012-12-01

    Full Text Available The EFQM Excellence Model is a framework that helps organizations to achieve competitive advantage by measuring where they are on their path to excellence. However, it does not tell the organization what to do or how it should manage any of these areas. In this study, we suggest a structure to overcome this gap. We present a method, matrix reflections, to find a tool set that can be used for designing improvement approaches in order to reach desired results.

  14. MTpy: A Python toolbox for magnetotellurics

    Science.gov (United States)

    Krieger, Lars; Peacock, Jared R.

    2014-01-01

    We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software.

  15. Evaluation Toolbox: Ex-Ante Impact Assessment and Value Network Analysis for SI

    NARCIS (Netherlands)

    Dhondt, S.; Ven, H. van de; Cressey, P.; Kaderabkova, A.; Luna, Á.; Moghadam Saman, S.; Castro Spila, J.; Ziauberyte, R.; Torre, W. van der; Terstriep, J.

    2016-01-01

    This report contains a toolbox for use with the Ex-Ante Impact Assessment for social innovations as was developed in the report D7.1. This toolbox proposes a series of convenient and useful tools to apply in an ex-ante assessment of social innovation within SIMPACT's policy areas unemployment,

  16. Adding tools to the open source toolbox: The Internet

    Science.gov (United States)

    Porth, Tricia

    1994-01-01

    The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

  17. Offsets, one tool in the toolbox

    CSIR Research Space (South Africa)

    Garland, Rebecca M

    2014-01-01

    Full Text Available for PM2.5 tons) in the eastern United States. • 100:1 (NOx tons for PM2.5 tons) in the western United States 12 EPA 2011, revised policy for inter-pollutant trading provisions • Obama EPA had litigation and administrative petitions filed against....5 nonattainment area in which it will be applied.” 13 EPA 2011, revised policy for interpollutant trading provisions • “We expect existing models and techniques to be adequate for states to conduct local demonstrations leading to the development of area...

  18. Leptoquark toolbox for precision collider studies

    Science.gov (United States)

    Doršner, Ilja; Greljo, Admir

    2018-05-01

    We implement scalar and vector leptoquark (LQ) models in the universal FeynRules output (UFO) format assuming the Standard Model fermion content and conservation of baryon and lepton numbers. Scalar LQ implementations include next-to-leading order (NLO) QCD corrections. We report the NLO QCD inclusive cross sections in proton-proton collisions at 13 TeV, 14 TeV, and 27 TeV for all on-shell LQ production processes. These comprise (i) LQ pair production ( pp → ΦΦ) and (ii) single LQ + lepton production ( pp → Φ ℓ) for all initial quark flavours ( u, d, s, c, and b). Vector LQ implementation includes adjustable non-minimal QCD coupling. We discuss several aspects of LQ searches at a hadron collider, emphasising the implications of SU(2) gauge invariance, electroweak and flavour constraints, on the possible signatures. Finally, we outline the high- p T search strategy for LQs recently proposed in the literature to resolve experimental anomalies in B-meson decays. In this context, we stress the importance of complementarity of the three LQ related processes, namely, pp → ΦΦ, pp → Φ ℓ, and pp → ℓℓ.

  19. morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python

    Directory of Open Access Journals (Sweden)

    Michael James Hull

    2014-01-01

    Full Text Available The broad structure of a modelling study can often be explained over a cup of coffee, butconverting this high-level conceptual idea into graphs of the final simulation results may requiremany weeks of sitting at a computer. Although models themselves can be complex, oftenmany mental resources are wasted working around complexities of the software ecosystemsuch as fighting to manage files, interfacing between tools and data formats, finding mistakesin code or working out the units of variables. morphforge is a high-level, Python toolboxfor building and managing simulations of small populations of multicompartmental biophysicalmodel neurons. An entire in silico experiment, including the definition of neuronal morphologies,channel descriptions, stimuli, visualisation and analysis of results can be written within a singleshort Python script using high-level objects. Multiple independent simulations can be createdand run from a single script, allowing parameter spaces to be investigated. Consideration hasbeen given to the reuse of both algorithmic and parameterisable components to allow bothspecific and stochastic parameter variations. Some other features of the toolbox include: theautomatic generation of human-readable documentation (e. g. PDF-files about a simulation; thetransparent handling of different biophysical units; a novel mechanism for plotting simulationresults based on a system of tags; and an architecture that supports both the use of establishedformats for defining channels and synapses (e. g. MODL files, and the possibility to supportother libraries and standards easily. We hope that this toolbox will allow scientists to quicklybuild simulations of multicompartmental model neurons for research and serve as a platform forfurther tool development.

  20. SPATIAL DATA MINING TOOLBOX FOR MAPPING SUITABILITY OF LANDFILL SITES USING NEURAL NETWORKS

    Directory of Open Access Journals (Sweden)

    S. K. M. Abujayyab

    2016-09-01

    Full Text Available Mapping the suitability of landfill sites is a complex field and is involved with multidiscipline. The purpose of this research is to create an ArcGIS spatial data mining toolbox for mapping the suitability of landfill sites at a regional scale using neural networks. The toolbox is constructed from six sub-tools to prepare, train, and process data. The employment of the toolbox is straightforward. The multilayer perceptron (MLP neural networks structure with a backpropagation learning algorithm is used. The dataset is mined from the north states in Malaysia. A total of 14 criteria are utilized to build the training dataset. The toolbox provides a platform for decision makers to implement neural networks for mapping the suitability of landfill sites in the ArcGIS environment. The result shows the ability of the toolbox to produce suitability maps for landfill sites.

  1. An expression tag toolbox for microbial production of membrane bound plant cytochromes P450

    DEFF Research Database (Denmark)

    Vazquez Albacete, Dario; Cavaleiro, Mafalda; Christensen, Ulla

    2017-01-01

    of the intermediate and the final product of the pathway. Finally, the effect of a robustly performing expression tag was explored with a library of 49 different P450s from medicinal plants and nearly half of these were improved in expression by more than 2-fold. The developed toolbox serves as platform to tune P450...... tag chimeras of the model plant P450 CYP79A1 in different Escherichia coli strains. Using a high-throughput screening platform based on C-terminal GFP fusions, we identify several highly expressing and robustly performing chimeric designs. Analysis of long-term cultures by flow cytometry showed...... homogeneous populations for some of the conditions. Three chimeric designs were chosen for a more complex combinatorial assembly of a multigene pathway consisting of two P450s and a redox partner. Cells expressing these recombinant enzymes catalysed the conversion of the substrate to highly different ratios...

  2. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.

    2011-02-25

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.

  3. ParTIES: a toolbox for Paramecium interspersed DNA elimination studies.

    Science.gov (United States)

    Denby Wilkes, Cyril; Arnaiz, Olivier; Sperling, Linda

    2016-02-15

    Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available. We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms. ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Parallel Sequential Monte Carlo for Efficient Density Combination: The Deco Matlab Toolbox

    DEFF Research Database (Denmark)

    Casarin, Roberto; Grassi, Stefano; Ravazzolo, Francesco

    This paper presents the Matlab package DeCo (Density Combination) which is based on the paper by Billio et al. (2013) where a constructive Bayesian approach is presented for combining predictive densities originating from different models or other sources of information. The combination weights...... for standard CPU computing and for Graphical Process Unit (GPU) parallel computing. For the GPU implementation we use the Matlab parallel computing toolbox and show how to use General Purposes GPU computing almost effortless. This GPU implementation comes with a speed up of the execution time up to seventy...... times compared to a standard CPU Matlab implementation on a multicore CPU. We show the use of the package and the computational gain of the GPU version, through some simulation experiments and empirical applications....

  5. ARTS, the Atmospheric Radiative Transfer Simulator - version 2.2, the planetary toolbox edition

    Science.gov (United States)

    Buehler, Stefan A.; Mendrok, Jana; Eriksson, Patrick; Perrin, Agnès; Larsson, Richard; Lemke, Oliver

    2018-04-01

    This article describes the latest stable release (version 2.2) of the Atmospheric Radiative Transfer Simulator (ARTS), a public domain software for radiative transfer simulations in the thermal spectral range (microwave to infrared). The main feature of this release is a planetary toolbox that allows simulations for the planets Venus, Mars, and Jupiter, in addition to Earth. This required considerable model adaptations, most notably in the area of gaseous absorption calculations. Other new features are also described, notably radio link budgets (including the effect of Faraday rotation that changes the polarization state) and the treatment of Zeeman splitting for oxygen spectral lines. The latter is relevant, for example, for the various operational microwave satellite temperature sensors of the Advanced Microwave Sounding Unit (AMSU) family.

  6. Computational Performance of a Parallelized Three-Dimensional High-Order Spectral Element Toolbox

    Science.gov (United States)

    Bosshard, Christoph; Bouffanais, Roland; Clémençon, Christian; Deville, Michel O.; Fiétier, Nicolas; Gruber, Ralf; Kehtari, Sohrab; Keller, Vincent; Latt, Jonas

    In this paper, a comprehensive performance review of an MPI-based high-order three-dimensional spectral element method C++ toolbox is presented. The focus is put on the performance evaluation of several aspects with a particular emphasis on the parallel efficiency. The performance evaluation is analyzed with help of a time prediction model based on a parameterization of the application and the hardware resources. A tailor-made CFD computation benchmark case is introduced and used to carry out this review, stressing the particular interest for clusters with up to 8192 cores. Some problems in the parallel implementation have been detected and corrected. The theoretical complexities with respect to the number of elements, to the polynomial degree, and to communication needs are correctly reproduced. It is concluded that this type of code has a nearly perfect speed up on machines with thousands of cores, and is ready to make the step to next-generation petaflop machines.

  7. TAF(II)250: a transcription toolbox.

    Science.gov (United States)

    Wassarman, D A; Sauer, F

    2001-08-01

    Activation of RNA-polymerase-II-dependent transcription involves conversion of signals provided by gene-specific activator proteins into the synthesis of messenger RNA. This conversion requires dynamic structural changes in chromatin and assembly of general transcription factors (GTFs) and RNA polymerase II at core promoter sequence elements surrounding the transcription start site of genes. One hallmark of transcriptional activation is the interaction of DNA-bound activators with coactivators such as the TATA-box binding protein (TBP)-associated factors (TAF(II)s) within the GTF TFIID. TAF(II)250 possesses a variety of activities that are likely to contribute to the initial steps of RNA polymerase II transcription. TAF(II)250 is a scaffold for assembly of other TAF(II)s and TBP into TFIID, TAF(II)250 binds activators to recruit TFIID to particular promoters, TAF(II)250 regulates binding of TBP to DNA, TAF(II)250 binds core promoter initiator elements, TAF(II)250 binds acetylated lysine residues in core histones, and TAF(II)250 possesses protein kinase, ubiquitin-activating/conjugating and acetylase activities that modify histones and GTFs. We speculate that these activities achieve two goals--(1) they aid in positioning and stabilizing TFIID at particular promoters, and (2) they alter chromatin structure at the promoter to allow assembly of GTFs--and we propose a model for how TAF(II)250 converts activation signals into active transcription.

  8. A Sommerfeld toolbox for colored dark sectors

    Energy Technology Data Exchange (ETDEWEB)

    El Hedri, Sonia; Kaminska, Anna; Vries, Maikel de [Mainz Univ., PRISMA Cluster of Excellence and Mainz Inst. for Theoretical Physics (Germany)

    2017-09-15

    We present analytical formulas for the Sommerfeld corrections to the annihilation of massive colored particles into quarks and gluons through the strong interaction. These corrections are essential to accurately compute the dark matter relic density for coannihilation with colored partners. Our formulas allow us to compute the Sommerfeld effect, not only for the lowest term in the angular momentum expansion of the amplitude, but for all orders in the partial wave expansion. In particular, we carefully account for the effects of the spin of the annihilating particle on the symmetry of the two-particle wave function. This work focuses on strongly interacting particles of arbitrary spin in the triplet, sextet and octet color representations. For typical velocities during freeze-out, we find that including Sommerfeld corrections on the next-to-leading order partial wave leads to modifications of up to 10 to 20 percent on the total annihilation cross section. Complementary to QCD, we generalize our results to particles charged under an arbitrary unbroken SU(N) gauge group, as encountered in dark glueball models. In connection with this paper a Mathematica notebook is provided to compute the Sommerfeld corrections for colored particles up to arbitrary order in the angular momentum expansion. (orig.)

  9. A Sommerfeld toolbox for colored dark sectors

    International Nuclear Information System (INIS)

    El Hedri, Sonia; Kaminska, Anna; Vries, Maikel de

    2017-01-01

    We present analytical formulas for the Sommerfeld corrections to the annihilation of massive colored particles into quarks and gluons through the strong interaction. These corrections are essential to accurately compute the dark matter relic density for coannihilation with colored partners. Our formulas allow us to compute the Sommerfeld effect, not only for the lowest term in the angular momentum expansion of the amplitude, but for all orders in the partial wave expansion. In particular, we carefully account for the effects of the spin of the annihilating particle on the symmetry of the two-particle wave function. This work focuses on strongly interacting particles of arbitrary spin in the triplet, sextet and octet color representations. For typical velocities during freeze-out, we find that including Sommerfeld corrections on the next-to-leading order partial wave leads to modifications of up to 10 to 20 percent on the total annihilation cross section. Complementary to QCD, we generalize our results to particles charged under an arbitrary unbroken SU(N) gauge group, as encountered in dark glueball models. In connection with this paper a Mathematica notebook is provided to compute the Sommerfeld corrections for colored particles up to arbitrary order in the angular momentum expansion. (orig.)

  10. A Sommerfeld toolbox for colored dark sectors

    Science.gov (United States)

    El Hedri, Sonia; Kaminska, Anna; de Vries, Maikel

    2017-09-01

    We present analytical formulas for the Sommerfeld corrections to the annihilation of massive colored particles into quarks and gluons through the strong interaction. These corrections are essential to accurately compute the dark matter relic density for coannihilation with colored partners. Our formulas allow us to compute the Sommerfeld effect, not only for the lowest term in the angular momentum expansion of the amplitude, but for all orders in the partial wave expansion. In particular, we carefully account for the effects of the spin of the annihilating particle on the symmetry of the two-particle wave function. This work focuses on strongly interacting particles of arbitrary spin in the triplet, sextet and octet color representations. For typical velocities during freeze-out, we find that including Sommerfeld corrections on the next-to-leading order partial wave leads to modifications of up to 10 to 20 percent on the total annihilation cross section. Complementary to QCD, we generalize our results to particles charged under an arbitrary unbroken SU( N) gauge group, as encountered in dark glueball models. In connection with this paper a Mathematica notebook is provided to compute the Sommerfeld corrections for colored particles up to arbitrary order in the angular momentum expansion.

  11. Cementitious Barriers Partnership (CBP): Training and Release of CBP Toolbox Software, Version 1.0 - 13480

    Energy Technology Data Exchange (ETDEWEB)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S. [Vanderbilt University, School of Engineering, CRESP, Nashville, TN 37235 (United States); Flach, G.; Langton, C.; Smith, F.G. III; Burns, H. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Van der Sloot, H. [Hans Van der Sloot Consultancy, Dorpsstraat 216, 1721BV Langedijk (Netherlands); Meeussen, J.C.L. [Nuclear Research and Consultancy Group, Westerduinweg 3, Petten (Netherlands); Samson, E. [SIMCO Technologies, Inc., Quebec (Canada); Mallick, P.; Suttora, L. [U.S. Department of Energy, Washington, DC (United States); Esh, D.; Fuhrmann, M.; Philip, J. [U.S. Nuclear Regulatory Commission, Washington, DC (United States)

    2013-07-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the Office of Tank Waste Management within the Office of Environmental Management of U.S. Department of Energy (US DOE). The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that improve understanding and predictions of the long-term hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program are intended to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1,000 years for waste management purposes. CBP software tools were made available to selected DOE Office of Environmental Management and field site users for training and evaluation based on a set of important degradation scenarios, including sulfate ingress/attack and carbonation of cementitious materials. The tools were presented at two-day training workshops held at U.S. National Institute of Standards and Technology (NIST), Savannah River, and Hanford included LeachXS{sup TM}/ORCHESTRA, STADIUM{sup R}, and a CBP-developed GoldSim Dashboard interface. Collectively, these components form the CBP Software Toolbox. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF) were also presented. The CBP Dashboard uses a custom Dynamic-link library developed by CBP to couple to the LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} codes to simulate reactive transport and degradation in cementitious materials for selected performance assessment scenarios. The first day of the workshop introduced participants to the software components via presentation materials, and the second day included hands-on tutorial exercises followed

  12. Cementitious Barriers Partnership (CBP): Training and Release of CBP Toolbox Software, Version 1.0 - 13480

    International Nuclear Information System (INIS)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S.; Flach, G.; Langton, C.; Smith, F.G. III; Burns, H.; Van der Sloot, H.; Meeussen, J.C.L.; Samson, E.; Mallick, P.; Suttora, L.; Esh, D.; Fuhrmann, M.; Philip, J.

    2013-01-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the Office of Tank Waste Management within the Office of Environmental Management of U.S. Department of Energy (US DOE). The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that improve understanding and predictions of the long-term hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program are intended to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1,000 years for waste management purposes. CBP software tools were made available to selected DOE Office of Environmental Management and field site users for training and evaluation based on a set of important degradation scenarios, including sulfate ingress/attack and carbonation of cementitious materials. The tools were presented at two-day training workshops held at U.S. National Institute of Standards and Technology (NIST), Savannah River, and Hanford included LeachXS TM /ORCHESTRA, STADIUM R , and a CBP-developed GoldSim Dashboard interface. Collectively, these components form the CBP Software Toolbox. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF) were also presented. The CBP Dashboard uses a custom Dynamic-link library developed by CBP to couple to the LeachXS TM /ORCHESTRA and STADIUM R codes to simulate reactive transport and degradation in cementitious materials for selected performance assessment scenarios. The first day of the workshop introduced participants to the software components via presentation materials, and the second day included hands-on tutorial exercises followed by discussions

  13. The BRAT and GUT Couple: Broadview Radar Altimetry and GOCE User Toolboxes

    Science.gov (United States)

    Benveniste, J.; Restano, M.; Ambrózio, A.

    2017-12-01

    The Broadview Radar Altimetry Toolbox (BRAT) is a collection of tools designed to facilitate the processing of radar altimetry data from previous and current altimetry missions, including Sentinel-3A L1 and L2 products. A tutorial is included providing plenty of use cases. BRAT's next release (4.2.0) is planned for October 2017. Based on the community feedback, the front-end has been further improved and simplified whereas the capability to use BRAT in conjunction with MATLAB/IDL or C/C++/Python/Fortran, allowing users to obtain desired data bypassing the data-formatting hassle, remains unchanged. Several kinds of computations can be done within BRAT involving the combination of data fields, that can be saved for future uses, either by using embedded formulas including those from oceanographic altimetry, or by implementing ad-hoc Python modules created by users to meet their needs. BRAT can also be used to quickly visualise data, or to translate data into other formats, e.g. from NetCDF to raster images. The GOCE User Toolbox (GUT) is a compilation of tools for the use and the analysis of GOCE gravity field models. It facilitates using, viewing and post-processing GOCE L2 data and allows gravity field data, in conjunction and consistently with any other auxiliary data set, to be pre-processed by beginners in gravity field processing, for oceanographic and hydrologic as well as for solid earth applications at both regional and global scales. Hence, GUT facilitates the extensive use of data acquired during GRACE and GOCE missions. In the current 3.1 version, GUT has been outfitted with a graphical user interface allowing users to visually program data processing workflows. Further enhancements aiming at facilitating the use of gradients, the anisotropic diffusive filtering, and the computation of Bouguer and isostatic gravity anomalies have been introduced. Packaged with GUT is also GUT's Variance-Covariance Matrix tool (VCM). BRAT and GUT toolboxes can be freely

  14. Production de minitubercules de pomme de terre par hydroponie: évaluation d'un système combinant les techniques NFT et Gravel Culture pour deux types de solutions nutritives

    Directory of Open Access Journals (Sweden)

    Rolot J.L.

    2002-01-01

    Full Text Available Potato minituber production through hydropony: assessment of a system combining the NFT and Gravel Culture techniques for two types of nutrient solutions. The potato minituber production is the classical intermediate stage enabling field use of potato materials with an in vitro origin. This production of minitubers may be achieved through various techniques. Most often however they are based upon bedding vitroplantlets or vitroplantlets cuttings in an organic substratum which is disinfected or not. The soilless culture of plants stemming from vitrotubers to produce minitubers with a superior health quality was tested within a hydroponic system. Two types of nutrient solutions were compared: a nitrogen rich one (NPK, mg/l, 180-40-300 and a phosphorus rich one (NPK, mg/l, 60-150-300. In order to initiate the cultures, presprouting microtubers of several varieties (Bintje, Kennebec, Spunta, Saturna, Desiree and Gasore were used. Multiplication rates ranged between 13.2 (Saturna and 3.8 (Kennebec minitubers with a grade higher than 10 mm (more than 1.5 g. As the selected density of the plants was 59 plants per square metre, the yield per square metre varied from 224 to 779 minitubers with a grade higher than 10 mm. The obtained number of minitubers depended especially on the variety. The phosphorus enrichment of the nutrient solution induced an increased number of minitubers produced with a grade higher than 15 mm (more than 5 g. The health state of the produced tubers was excellent.

  15. The Expanded Capabilities Of The Cementitious Barriers Partnership Software Toolbox Version 2.0 - 14331

    Energy Technology Data Exchange (ETDEWEB)

    Burns, Heather; Flach, Greg; Smith, Frank; Langton, Christine; Brown, Kevin; Kosson, David; Samson, Eric; Mallick, Pramod

    2014-01-10

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. The CBP Software Toolbox – “Version 1.0” was released early in FY2013 and was used to support DOE-EM performance assessments in evaluating various degradation mechanisms that included sulfate attack, carbonation and constituent leaching. The sulfate attack analysis predicted the extent and damage that sulfate ingress will have on concrete vaults over extended time (i.e., > 1000 years) and the carbonation analysis provided concrete degradation predictions from rebar corrosion. The new release “Version 2.0” includes upgraded carbonation software and a new software module to evaluate degradation due to chloride attack. Also included in the newer version are a dual regime module allowing evaluation of contaminant release in two regimes – both fractured and un-fractured. The integrated software package has also been upgraded with new plotting capabilities and many other features that increase the “user-friendliness” of the package. Experimental work has been generated to provide data to calibrate the models to improve the credibility of the analysis and reduce the uncertainty. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox is and will continue to produce tangible benefits to the working DOE

  16. Semi-automated Robust Quantification of Lesions (SRQL Toolbox

    Directory of Open Access Journals (Sweden)

    Kaori L Ito

    2017-05-01

    Full Text Available Quantifying lesions in a reliable manner is fundamental for studying the effects of neuroanatomical changes related to recovery in the post-stroke brain. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This often makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. Thus, we developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.557114 Toolbox that performs several analysis steps: 1 a white matter intensity correction that removes healthy white matter voxels from the lesion mask, thereby making lesions slightly more robust to subjective errors; 2 an automated report of descriptive statistics on lesions for simplified comparison between or across groups, and 3 an option to perform analyses in both native and standard space to facilitate analyses in either space. Here, we describe the methods implemented in the toolbox.

  17. FracPaQ: a MATLAB™ toolbox for the quantification of fracture patterns

    Science.gov (United States)

    Healy, David; Rizzo, Roberto; Farrell, Natalie; Watkins, Hannah; Cornwell, David; Gomez-Rivas, Enrique; Timms, Nick

    2017-04-01

    The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, shapes and spatial distributions often exhibit some kind of order. In detail, there may be relationships among the different fracture attributes e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture patterns and fracture attributes. This presentation describes an open source toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales. Our current focus for the application of the software is on quantifying crack and fracture patterns in and around fault zones. There is a large body of published work on the quantification of relatively simple joint patterns, but fault zones present a bigger, and arguably more important, challenge. The methods presented are inherently scale independent, and a key task will be to analyse and integrate quantitative fracture pattern data from micro- to macro-scales. New features in this release include multi-scale analyses based on a wavelet method to look for scale transitions, support for multi-colour traces in the input file processed as separate fracture sets, and combining fracture traces

  18. Technical skills assessment toolbox: a review using the unitary framework of validity.

    Science.gov (United States)

    Ghaderi, Iman; Manji, Farouq; Park, Yoon Soo; Juul, Dorthea; Ott, Michael; Harris, Ilene; Farrell, Timothy M

    2015-02-01

    The purpose of this study was to create a technical skills assessment toolbox for 35 basic and advanced skills/procedures that comprise the American College of Surgeons (ACS)/Association of Program Directors in Surgery (APDS) surgical skills curriculum and to provide a critical appraisal of the included tools, using contemporary framework of validity. Competency-based training has become the predominant model in surgical education and assessment of performance is an essential component. Assessment methods must produce valid results to accurately determine the level of competency. A search was performed, using PubMed and Google Scholar, to identify tools that have been developed for assessment of the targeted technical skills. A total of 23 assessment tools for the 35 ACS/APDS skills modules were identified. Some tools, such as Operative Performance Rating System (OSATS) and Objective Structured Assessment of Technical Skill (OPRS), have been tested for more than 1 procedure. Therefore, 30 modules had at least 1 assessment tool, with some common surgical procedures being addressed by several tools. Five modules had none. Only 3 studies used Messick's framework to design their validity studies. The remaining studies used an outdated framework on the basis of "types of validity." When analyzed using the contemporary framework, few of these studies demonstrated validity for content, internal structure, and relationship to other variables. This study provides an assessment toolbox for common surgical skills/procedures. Our review shows that few authors have used the contemporary unitary concept of validity for development of their assessment tools. As we progress toward competency-based training, future studies should provide evidence for various sources of validity using the contemporary framework.

  19. SpaSM: A MATLAB Toolbox for Sparse Statistical Modeling

    DEFF Research Database (Denmark)

    Sjöstrand, Karl; Clemmensen, Line Harder; Larsen, Rasmus

    2018-01-01

    Applications in biotechnology such as gene expression analysis and image processing have led to a tremendous development of statistical methods with emphasis on reliable solutions to severely underdetermined systems. Furthermore, interpretations of such solutions are of importance, meaning...

  20. DYNAMIC SYSTEM ANALYSIS WITH pplane8.m (MATLAB® toolbox

    Directory of Open Access Journals (Sweden)

    Alejandro Regalado-Méndez

    2013-12-01

    Full Text Available In this work, four dynamic systems were analyzed (physical, chemical, ecological and economical, represented by autonomous systems of two ordinary differential equations. Main objective is proving that pplane8.m is an adequate and efficient computer tool. The analysis of autonomous systems was given by characterization of their critical points according to Coughanowr & LeBlanc (2009, with the MATLAB® toolbox pplane8.m. The main results are that pplane8.m (Polking, 2009 can quickly and precisely draw trajectories of each phase plane, it easily computes each critical point, and correctly characterize each equilibrium point of all autonomous studied systems. Finally, we can say that pplane8.m is a powerful tool to help the teaching-learning process for engineering students.

  1. The influence of industrial applications on a control system toolbox

    International Nuclear Information System (INIS)

    Clout, P.

    1992-01-01

    Vsystem is as an open, advanced software application toolbox for rapidly creating fast, efficient and cost-effective control and data-acquisition systems. Vsystem's modular architecture is designed for single computers, networked computers and workstations running under VAX/VMS or VAX/ELN. At the heart of Vsystem lies Vaccess, a user extendible real-time database and library of access routines. The application database provides the link to the hardware of the application and can be organized as one database or separate database installed in different computers on the network. Vsystem has found application in charged-particle accelerator control, tokamak control, and industrial research, as well as its more recent industrial applications. This paper describes the broad feature of Vsystem and the influence that recent industrial applications have had on the software. (author)

  2. Neuro-QOL and the NIH Toolbox: implications for epilepsy

    Science.gov (United States)

    Nowinski, Cindy J; Victorson, David; Cavazos, Jose E; Gershon, Richard; Cella, David

    2011-01-01

    The impact of neurological disorders on the lives of patients is often far more complex than what is measured in routine examination. Measurement of this impact can be challenging owing to a lack of brief, psychometrically sound and generally accepted instruments. Two NIH-funded initiatives are developing assessment tools, in English and Spanish, which address these issues, and should prove useful to the study and treatment of epilepsy and other neurological conditions. The first, Neuro-QOL, has created a set of health-related quality of life measures that are applicable for people with common neurological disorders. The second, the NIH Toolbox for the Assessment of Neurological and Behavioral Function, is assembling measures of cognitive, emotional, motor and sensory health and function that can be used across all ages, from 3 to 85 years. This article describes both the projects and their potential value to epilepsy treatment and research. PMID:21552344

  3. A fractured rock geophysical toolbox method selection tool

    Science.gov (United States)

    Day-Lewis, F. D.; Johnson, C.D.; Slater, L.D.; Robinson, J.L.; Williams, J.H.; Boyden, C.L.; Werkema, D.D.; Lane, J.W.

    2016-01-01

    Geophysical technologies have the potential to improve site characterization and monitoring in fractured rock, but the appropriate and effective application of geophysics at a particular site strongly depends on project goals (e.g., identifying discrete fractures) and site characteristics (e.g., lithology). No method works at every site or for every goal. New approaches are needed to identify a set of geophysical methods appropriate to specific project goals and site conditions while considering budget constraints. To this end, we present the Excel-based Fractured-Rock Geophysical Toolbox Method Selection Tool (FRGT-MST). We envision the FRGT-MST (1) equipping remediation professionals with a tool to understand what is likely to be realistic and cost-effective when contracting geophysical services, and (2) reducing applications of geophysics with unrealistic objectives or where methods are likely to fail.

  4. Peptide chemistry toolbox - Transforming natural peptides into peptide therapeutics.

    Science.gov (United States)

    Erak, Miloš; Bellmann-Sickert, Kathrin; Els-Heindl, Sylvia; Beck-Sickinger, Annette G

    2018-06-01

    The development of solid phase peptide synthesis has released tremendous opportunities for using synthetic peptides in medicinal applications. In the last decades, peptide therapeutics became an emerging market in pharmaceutical industry. The need for synthetic strategies in order to improve peptidic properties, such as longer half-life, higher bioavailability, increased potency and efficiency is accordingly rising. In this mini-review, we present a toolbox of modifications in peptide chemistry for overcoming the main drawbacks during the transition from natural peptides to peptide therapeutics. Modifications at the level of the peptide backbone, amino acid side chains and higher orders of structures are described. Furthermore, we are discussing the future of peptide therapeutics development and their impact on the pharmaceutical market. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. PANDA: a pipeline toolbox for analyzing brain diffusion images.

    Science.gov (United States)

    Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

    2013-01-01

    Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named "Pipeline for Analyzing braiN Diffusion imAges" (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

  6. PANDA: a pipeline toolbox for analyzing brain diffusion images

    Directory of Open Access Journals (Sweden)

    Zaixu eCui

    2013-02-01

    Full Text Available Diffusion magnetic resonance imaging (dMRI is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named Pipeline for Analyzing braiN Diffusion imAges (PANDA for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL, Pipeline System for Octave and Matlab (PSOM, Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics (e.g., FA and MD that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI, allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

  7. GISMO: A MATLAB toolbox for seismic research, monitoring, & education

    Science.gov (United States)

    Thompson, G.; Reyes, C. G.; Kempler, L. A.

    2017-12-01

    GISMO is an open-source MATLAB toolbox which provides an object-oriented framework to build workflows and applications that read, process, visualize and write seismic waveform, catalog and instrument response data. GISMO can retrieve data from a variety of sources (e.g. FDSN web services, Earthworm/Winston servers) and data formats (SAC, Seisan, etc.). It can handle waveform data that crosses file boundaries. All this alleviates one of the most time consuming part for scientists developing their own codes. GISMO simplifies seismic data analysis by providing a common interface for your data, regardless of its source. Several common plots are built-in to GISMO, such as record section plots, spectrograms, depth-time sections, event count per unit time, energy release per unit time, etc. Other visualizations include map views and cross-sections of hypocentral data. Several common processing methods are also included, such as an extensive set of tools for correlation analysis. Support is being added to interface GISMO with ObsPy. GISMO encourages community development of an integrated set of codes and accompanying documentation, eliminating the need for seismologists to "reinvent the wheel". By sharing code the consistency and repeatability of results can be enhanced. GISMO is hosted on GitHub with documentation both within the source code and in the project wiki. GISMO has been used at the University of South Florida and University of Alaska Fairbanks in graduate-level courses including Seismic Data Analysis, Time Series Analysis and Computational Seismology. GISMO has also been tailored to interface with the common seismic monitoring software and data formats used by volcano observatories in the US and elsewhere. As an example, toolbox training was delivered to researchers at INETER (Nicaragua). Applications built on GISMO include IceWeb (e.g. web-based spectrograms), which has been used by Alaska Volcano Observatory since 1998 and became the prototype for the USGS

  8. Development of an Ontology-Directed Signal Processing Toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Stephen W. Lang

    2011-05-27

    This project was focused on the development of tools for the automatic configuration of signal processing systems. The goal is to develop tools that will be useful in a variety of Government and commercial areas and useable by people who are not signal processing experts. In order to get the most benefit from signal processing techniques, deep technical expertise is often required in order to select appropriate algorithms, combine them into a processing chain, and tune algorithm parameters for best performance on a specific problem. Therefore a significant benefit would result from the assembly of a toolbox of processing algorithms that has been selected for their effectiveness in a group of related problem areas, along with the means to allow people who are not signal processing experts to reliably select, combine, and tune these algorithms to solve specific problems. Defining a vocabulary for problem domain experts that is sufficiently expressive to drive the configuration of signal processing functions will allow the expertise of signal processing experts to be captured in rules for automated configuration. In order to test the feasibility of this approach, we addressed a lightning classification problem, which was proposed by DOE as a surrogate for problems encountered in nuclear nonproliferation data processing. We coded a toolbox of low-level signal processing algorithms for extracting features of RF waveforms, and demonstrated a prototype tool for screening data. We showed examples of using the tool for expediting the generation of ground-truth metadata, for training a signal recognizer, and for searching for signals with particular characteristics. The public benefits of this approach, if successful, will accrue to Government and commercial activities that face the same general problem - the development of sensor systems for complex environments. It will enable problem domain experts (e.g. analysts) to construct signal and image processing chains without

  9. Expanding access to rheumatology care: the rheumatology general practice toolbox.

    LENUS (Irish Health Repository)

    Conway, R

    2015-02-01

    Management guidelines for many rheumatic diseases are published in specialty rheumatology literature but rarely in general medical journals. Musculoskeletal disorders comprise 14% of all consultations in primary care. Formal post-graduate training in rheumatology is limited or absent for many primary care practitioners. Primary care practitioners can be trained to effectively treat complex diseases and have expressed a preference for interactive educational courses. The Rheumatology General Practice (GP) Toolbox is an intensive one day course designed to offer up to date information to primary care practitioners on the latest diagnostic and treatment guidelines for seven common rheumatic diseases. The course structure involves a short lecture on each topic and workshops on arthrocentesis, joint injection and DXA interpretation. Participants evaluated their knowledge and educational experience before, during and after the course. Thirty-two primary care practitioners attended, who had a median of 13 (IQR 6.5, 20) years experience in their specialty. The median number of educational symposia attended in the previous 5 years was 10 (IQR-5, 22.5), with a median of 0 (IQR 0, 1) in rheumatology. All respondents agreed that the course format was appropriate. Numerical improvements were demonstrated in participant\\'s confidence in diagnosing and managing all seven common rheumatologic conditions, with statistically significant improvements (p < 0.05) in 11 of the 14 aspects assessed. The Rheumatology Toolbox is an effective educational method for disseminating current knowledge in rheumatology to primary care physicians and improved participant\\'s self-assessed competence in diagnosis and management of common rheumatic diseases.

  10. Developing a Conceptual Design Engineering Toolbox and its Tools

    Directory of Open Access Journals (Sweden)

    R. W. Vroom

    2004-01-01

    Full Text Available In order to develop a successful product, a design engineer needs to pay attention to all relevant aspects of that product. Many tools are available, software, books, websites, and commercial services. To unlock these potentially useful sources of knowledge, we are developing C-DET, a toolbox for conceptual design engineering. The idea of C-DET is that designers are supported by a system that provides them with a knowledge portal on one hand, and a system to store their current work on the other. The knowledge portal is to help the designer to find the most appropriate sites, experts, tools etc. at a short notice. Such a toolbox offers opportunities to incorporate extra functionalities to support the design engineering work. One of these functionalities could be to help the designer to reach a balanced comprehension in his work. Furthermore C-DET enables researchers in the area of design engineering and design engineers themselves to find each other or their work earlier and more easily. Newly developed design tools that can be used by design engineers but have not yet been developed up to a commercial level could be linked to by C-DET. In this way these tools can be evaluated in an early stage by design engineers who would like to use them. This paper describes the first prototypes of C-DET, an example of the development of a design tool that enables designers to forecast the use process and an example of the future functionalities of C-DET such as balanced comprehension.

  11. FRACOR-software toolbox for deterministic mapping of fracture corridors in oil fields on AutoCAD platform

    Science.gov (United States)

    Ozkaya, Sait I.

    2018-03-01

    Fracture corridors are interconnected large fractures in a narrow sub vertical tabular array, which usually traverse entire reservoir vertically and extended for several hundreds of meters laterally. Fracture corridors with their huge conductivities constitute an important element of many fractured reservoirs. Unlike small diffuse fractures, actual fracture corridors must be mapped deterministically for simulation or field development purposes. Fracture corridors can be identified and quantified definitely with borehole image logs and well testing. However, there are rarely sufficient image logs or well tests, and it is necessary to utilize various fracture corridor indicators with varying degrees of reliability. Integration of data from many different sources, in turn, requires a platform with powerful editing and layering capability. Available commercial reservoir characterization software packages, with layering and editing capabilities, can be cost intensive. CAD packages are far more affordable and may easily acquire the versatility and power of commercial software packages with addition of a small software toolbox. The objective of this communication is to present FRACOR, a software toolbox which enables deterministic 2D fracture corridor mapping and modeling on AutoCAD platform. The FRACOR toolbox is written in AutoLISPand contains several independent routines to import and integrate available fracture corridor data from an oil field, and export results as text files. The resulting fracture corridor maps consists mainly of fracture corridors with different confidence levels from combination of static and dynamic data and exclusion zones where no fracture corridor can exist. The exported text file of fracture corridors from FRACOR can be imported into an upscaling programs to generate fracture grid for dual porosity simulation or used for field development and well planning.

  12. Switch of Sensitivity Dynamics Revealed with DyGloSA Toolbox for Dynamical Global Sensitivity Analysis as an Early Warning for System's Critical Transition

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA – a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits. PMID:24367574

  13. Switch of sensitivity dynamics revealed with DyGloSA toolbox for dynamical global sensitivity analysis as an early warning for system's critical transition.

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA - a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits.

  14. A microfluidic toolbox for the development of in-situ product removal strategies in biocatalysis

    DEFF Research Database (Denmark)

    Heintz, Søren; Mitic, Aleksandar; Ringborg, Rolf Hoffmeyer

    2016-01-01

    A microfluidic toolbox for accelerated development of biocatalytic processes has great potential. This is especially the case for the development of advanced biocatalytic process concepts, where reactors and product separation methods are closely linked together to intensify the process performan...

  15. A toolbox for safety instrumented system evaluation based on improved continuous-time Markov chain

    Science.gov (United States)

    Wardana, Awang N. I.; Kurniady, Rahman; Pambudi, Galih; Purnama, Jaka; Suryopratomo, Kutut

    2017-08-01

    Safety instrumented system (SIS) is designed to restore a plant into a safe condition when pre-hazardous event is occur. It has a vital role especially in process industries. A SIS shall be meet with safety requirement specifications. To confirm it, SIS shall be evaluated. Typically, the evaluation is calculated by hand. This paper presents a toolbox for SIS evaluation. It is developed based on improved continuous-time Markov chain. The toolbox supports to detailed approach of evaluation. This paper also illustrates an industrial application of the toolbox to evaluate arch burner safety system of primary reformer. The results of the case study demonstrates that the toolbox can be used to evaluate industrial SIS in detail and to plan the maintenance strategy.

  16. Review of Qualitative Approaches for the Construction Industry: Designing a Risk Management Toolbox

    Directory of Open Access Journals (Sweden)

    David M. Zalk

    2011-06-01

    Conclusion: The Construction Toolbox presents a review-generated format to harness multiple solutions-based national programs and publications for controlling construction-related risks with simplified approaches across the occupational safety, health and hygiene professions.

  17. The NNSYSID Toolbox - A MATLAB Toolbox for System Identification with Neural Networks

    DEFF Research Database (Denmark)

    Nørgård, Peter Magnus; Ravn, Ole; Hansen, Lars Kai

    1996-01-01

    To assist the identification of nonlinear dynamic systems, a set of tools has been developed for the MATLAB(R) environment. The tools include a number of different model structures, highly effective training algorithms, functions for validating trained networks, and pruning algorithms for determi......To assist the identification of nonlinear dynamic systems, a set of tools has been developed for the MATLAB(R) environment. The tools include a number of different model structures, highly effective training algorithms, functions for validating trained networks, and pruning algorithms...

  18. The Basic Radar Altimetry Toolbox for Sentinel 3 Users

    Science.gov (United States)

    Lucas, Bruno; Rosmorduc, Vinca; Niemeijer, Sander; Bronner, Emilie; Dinardo, Salvatore; Benveniste, Jérôme

    2013-04-01

    The Basic Radar Altimetry Toolbox (BRAT) is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2006 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales). The latest version of the software, 3.1, was released on March 2012. The tools enable users to interact with the most common altimetry data formats, being the most used way, the Graphical User Interface (BratGui). This GUI is a front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. The BratDisplay (graphic visualizer) can be launched from BratGui, or used as a stand-alone tool to visualize netCDF files - it is distributed with another ESA toolbox (GUT) as the visualizer. The most frequent uses of BRAT are teaching remote sensing, altimetry data reading (all missions from ERS-1 to Saral and soon Sentinel-3), quick data visualization/export and simple computation on the data fields. BRAT can be used for importing data and having a quick look at his contents, with several different types of plotting available. One can also use it to translate the data into other formats such as netCDF, ASCII text files, KML (Google Earth) and raster images (JPEG, PNG, etc.). Several kinds of computations can be done within BratGui involving combinations of data fields that the user can save for posterior reuse or using the already embedded formulas that include the standard oceanographic altimetry formulas (MSS, -SSH, MSLA, editing of spurious data, etc.). The documentation collection includes the standard user manual explaining all the ways to interact with the set of software tools but the most important item is the Radar Altimeter Tutorial, that contains a strong introduction to

  19. Versatile Cas9-Driven Subpopulation Selection Toolbox for Lactococcus lactis.

    Science.gov (United States)

    van der Els, Simon; James, Jennelle K; Kleerebezem, Michiel; Bron, Peter A

    2018-04-15

    CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here, we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis The Cas9 expression vector pLABTarget, encoding the Streptocccus pyogenes Cas9 under the control of a constitutive promoter, was constructed, allowing plug and play introduction of short guide RNA (sgRNA) sequences to target specific genetic loci. Introduction of a pepN -targeting derivative of pLABTarget into L. lactis strain MG1363 led to a strong reduction in the number of transformants obtained, which did not occur in a pepN deletion derivative of the same strain, demonstrating the specificity and lethality of the Cas9-mediated double-strand breaks in the lactococcal chromosome. Moreover, the same pLABTarget derivative allowed the selection of a pepN deletion subpopulation from its corresponding single-crossover plasmid integrant precursor, accelerating the construction and selection of gene-specific deletion derivatives in L. lactis Finally, pLABTarget, which contained sgRNAs designed to target mobile genetic elements, allowed the effective curing of plasmids, prophages, and integrative conjugative elements (ICEs). These results establish that pLABTarget enables the effective exploitation of Cas9 targeting in L. lactis , while the broad-host-range vector used suggests that this toolbox could readily be expanded to other Gram-positive bacteria. IMPORTANCE Mobile genetic elements in Lactococcus lactis and other lactic acid bacteria (LAB) play an important role in dairy fermentation, having both positive and detrimental effects during the production of fermented dairy products. The pLABTarget vector offers an efficient cloning platform for Cas9 application in lactic acid bacteria. Targeting Cas9 toward mobile genetic elements enabled their effective curing, which is of particular interest in the

  20. European Studies and Public Engagement: A Conceptual Toolbox

    Directory of Open Access Journals (Sweden)

    Andreas Müllerleile

    2014-11-01

    Full Text Available Journal of Contemporary European Research User Username Password Remember me Subscribe... Sign up for issue alerts Follow JCER on Twitter Font Size Make font size smaller Make font size default Make font size larger Journal Content Search Search Scope Browse By Issue By Author By Title Information For Readers For Authors For Librarians Journal Help Keywords CFSP Communication ESDP EU EU enlargement EU trade policy Energy, EU, External Policy Europe European Commission European Parliament European Union European integration Europeanisation First Enlargement Germany Liberty Lisbon Treaty Poland Russia Security teaching European studies The UACES Blog The Commission after the 2014 EP... Power shift? The EU’s pivot to Asia 100 Books on Europe to be Remembered For a Global European Studies? EU Member State Building in the... Open Journal Systems Home About Login Register Search Current Archives Announcements UACES Home > Vol 10, No 4 (2014 > Müllerleile European Studies and Public Engagement: A Conceptual Toolbox Andreas Müllerleile Abstract This article examines public engagement strategies for academics working in the field of European Studies. Should academics engage with the public? What are the most effective outreach strategies? And what are the implications for universities and departments? The article argues that engaging with the public should be considered an integral part for academics working on topics that relate to the European Union or European politics. The article has a theoretical and a practical dimension. The first part of the paper deals with the nature of public engagement, explaining why it is an important issue and how it differs from the mainstream understanding of public engagement. The practical part of the paper presents the idea of building an online presence through which academics can engage with the public debate both during periods of low issue salience and high issue salience. The final section includes a toolbox

  1. ObsPy - A Python Toolbox for Seismology - and Applications

    Science.gov (United States)

    Krischer, L.; Megies, T.; Barsch, R.; MacCarthy, J.; Lecocq, T.; Koymans, M. R.; Carothers, L.; Eulenfeld, T.; Reyes, C. G.; Falco, N.; Sales de Andrade, E.

    2017-12-01

    Recent years witnessed the evolution of Python's ecosystem into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It is a Python toolbox offering: Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, SC3ML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. Newest features include: Full interoperability of SEED and StationXML/Inventory objects Access to the Nominal Response Library (NRL) for easy and quick creation of station metadata from scratch Support for the IRIS Federated Catalog Service Improved performance of the EarthWorm client Several improvements to MiniSEED read/write module Improved plotting capabilities for PPSD (spectrograms, PSD of discrete frequencies over time, ..) Support for.. Reading ArcLink Inventory XML Reading Reftek data format Writing SeisComp3 ML (SC3ML) Writing StationTXT format This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases and show-case some projects that are based on ObsPy, e.g.: seismo

  2. An adaptive toolbox approach to the route to expertise in sport

    Directory of Open Access Journals (Sweden)

    Rita F De Oliveira

    2014-07-01

    Full Text Available Expertise is characterized by fast decision-making which is highly adaptive to new situations. Here we propose that athletes use a toolbox of heuristics which they develop on their route to expertise. The development of heuristics occurs within the context of the athletes’ natural abilities, past experiences, developed skills, and situational context, but does not pertain to any of these factors separately. This is a novel approach because it integrates separate factors into a comprehensive heuristic description. The novelty of this approach lies within the integration of separate factors determining expertise into a comprehensive heuristic description. It is our contention that talent identification methods and talent development models should therefore be geared towards the assessment and development of specific heuristics. Specifically, in addition to identifying and developing separate natural abilities and skills as per usual, heuristics should be identified and developed. The application of heuristics to talent and expertise models can bring the field one step away from dichotomized models of nature and nurture towards a comprehensive approach to the route to expertise.

  3. An adaptive toolbox approach to the route to expertise in sport.

    Science.gov (United States)

    de Oliveira, Rita F; Lobinger, Babett H; Raab, Markus

    2014-01-01

    Expertise is characterized by fast decision-making which is highly adaptive to new situations. Here we propose that athletes use a toolbox of heuristics which they develop on their route to expertise. The development of heuristics occurs within the context of the athletes' natural abilities, past experiences, developed skills, and situational context, but does not pertain to any of these factors separately. This is a novel approach because it integrates separate factors into a comprehensive heuristic description. The novelty of this approach lies within the integration of separate factors determining expertise into a comprehensive heuristic description. It is our contention that talent identification methods and talent development models should therefore be geared toward the assessment and development of specific heuristics. Specifically, in addition to identifying and developing separate natural abilities and skills as per usual, heuristics should be identified and developed. The application of heuristics to talent and expertise models can bring the field one step away from dichotomized models of nature and nurture toward a comprehensive approach to the route to expertise.

  4. Software Toolbox for Low-Frequency Conductivity and Current Density Imaging Using MRI.

    Science.gov (United States)

    Sajib, Saurav Z K; Katoch, Nitish; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2017-11-01

    Low-frequency conductivity and current density imaging using MRI includes magnetic resonance electrical impedance tomography (MREIT), diffusion tensor MREIT (DT-MREIT), conductivity tensor imaging (CTI), and magnetic resonance current density imaging (MRCDI). MRCDI and MREIT provide current density and isotropic conductivity images, respectively, using current-injection phase MRI techniques. DT-MREIT produces anisotropic conductivity tensor images by incorporating diffusion weighted MRI into MREIT. These current-injection techniques are finding clinical applications in diagnostic imaging and also in transcranial direct current stimulation (tDCS), deep brain stimulation (DBS), and electroporation where treatment currents can function as imaging currents. To avoid adverse effects of nerve and muscle stimulations due to injected currents, conductivity tensor imaging (CTI) utilizes B1 mapping and multi-b diffusion weighted MRI to produce low-frequency anisotropic conductivity tensor images without injecting current. This paper describes numerical implementations of several key mathematical functions for conductivity and current density image reconstructions in MRCDI, MREIT, DT-MREIT, and CTI. To facilitate experimental studies of clinical applications, we developed a software toolbox for these low-frequency conductivity and current density imaging methods. This MR-based conductivity imaging (MRCI) toolbox includes 11 toolbox functions which can be used in the MATLAB environment. The MRCI toolbox is available at http://iirc.khu.ac.kr/software.html . Its functions were tested by using several experimental datasets, which are provided together with the toolbox. Users of the toolbox can focus on experimental designs and interpretations of reconstructed images instead of developing their own image reconstruction softwares. We expect more toolbox functions to be added from future research outcomes. Low-frequency conductivity and current density imaging using MRI includes

  5. An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave.

    Science.gov (United States)

    Silva, Ikaro; Moody, George B

    The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox provides access over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by metadata such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

  6. ALEA: a toolbox for allele-specific epigenomics analysis.

    Science.gov (United States)

    Younesy, Hamid; Möller, Torsten; Heravi-Moussavi, Alireza; Cheng, Jeffrey B; Costello, Joseph F; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

    2014-04-15

    The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data. The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. ObsPy: A Python Toolbox for Seismology

    Science.gov (United States)

    Krischer, Lion; Megies, Tobias; Sales de Andrade, Elliott; Barsch, Robert; MacCarthy, Jonathan

    2017-04-01

    In recent years the Python ecosystem evolved into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community-driven, open-source project dedicated to providing a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than seven years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases. Additionally we will discuss the road ahead as well as the long-term sustainability of open-source scientific software.

  8. MATLAB Stability and Control Toolbox Trim and Static Stability Module

    Science.gov (United States)

    Kenny, Sean P.; Crespo, Luis

    2012-01-01

    MATLAB Stability and Control Toolbox (MASCOT) utilizes geometric, aerodynamic, and inertial inputs to calculate air vehicle stability in a variety of critical flight conditions. The code is based on fundamental, non-linear equations of motion and is able to translate results into a qualitative, graphical scale useful to the non-expert. MASCOT was created to provide the conceptual aircraft designer accurate predictions of air vehicle stability and control characteristics. The code takes as input mass property data in the form of an inertia tensor, aerodynamic loading data, and propulsion (i.e. thrust) loading data. Using fundamental nonlinear equations of motion, MASCOT then calculates vehicle trim and static stability data for the desired flight condition(s). Available flight conditions include six horizontal and six landing rotation conditions with varying options for engine out, crosswind, and sideslip, plus three take-off rotation conditions. Results are displayed through a unique graphical interface developed to provide the non-stability and control expert conceptual design engineer a qualitative scale indicating whether the vehicle has acceptable, marginal, or unacceptable static stability characteristics. If desired, the user can also examine the detailed, quantitative results.

  9. SELANSI: a toolbox for simulation of stochastic gene regulatory networks.

    Science.gov (United States)

    Pájaro, Manuel; Otero-Muras, Irene; Vázquez, Carlos; Alonso, Antonio A

    2018-03-01

    Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort. This work presents SELANSI (SEmi-LAgrangian SImulation of GRNs), a software toolbox for the simulation of stochastic multidimensional gene regulatory networks. SELANSI exploits intrinsic structural properties of gene regulatory networks to accurately approximate the corresponding Chemical Master Equation with a partial integral differential equation that is solved by a semi-lagrangian method with high efficiency. Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors. Moreover, the validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options. SELANSI runs under the MATLAB environment, and is available under GPLv3 license at https://sites.google.com/view/selansi. antonio@iim.csic.es. © The Author(s) 2017. Published by Oxford University Press.

  10. Dem Generation from Close-Range Photogrammetry Using Extended Python Photogrammetry Toolbox

    Science.gov (United States)

    Belmonte, A. A.; Biong, M. M. P.; Macatulad, E. G.

    2017-10-01

    Digital elevation models (DEMs) are widely used raster data for different applications concerning terrain, such as for flood modelling, viewshed analysis, mining, land development, engineering design projects, to name a few. DEMs can be obtained through various methods, including topographic survey, LiDAR or photogrammetry, and internet sources. Terrestrial close-range photogrammetry is one of the alternative methods to produce DEMs through the processing of images using photogrammetry software. There are already powerful photogrammetry software that are commercially-available and can produce high-accuracy DEMs. However, this entails corresponding cost. Although, some of these software have free or demo trials, these trials have limits in their usable features and usage time. One alternative is the use of free and open-source software (FOSS), such as the Python Photogrammetry Toolbox (PPT), which provides an interface for performing photogrammetric processes implemented through python script. For relatively small areas such as in mining or construction excavation, a relatively inexpensive, fast and accurate method would be advantageous. In this study, PPT was used to generate 3D point cloud data from images of an open pit excavation. The PPT was extended to add an algorithm converting the generated point cloud data into a usable DEM.

  11. moviEEG: An animation toolbox for visualization of intracranial electroencephalography synchronization dynamics.

    Science.gov (United States)

    Wong, Simeon M; Ibrahim, George M; Ochi, Ayako; Otsubo, Hiroshi; Rutka, James T; Snead, O Carter; Doesburg, Sam M

    2016-06-01

    We introduce and describe the functions of moviEEG (Multiple Overlay Visualizations for Intracranial ElectroEncephaloGraphy), a novel MATLAB-based toolbox for spatiotemporal mapping of network synchronization dynamics in intracranial electroencephalography (iEEG) data. The toolbox integrates visualizations of inter-electrode phase-locking relationships in peri-ictal epileptogenic networks with signal spectral properties and graph-theoretical network measures overlaid upon operating room images of the electrode grid. Functional connectivity between every electrode pair is evaluated over a sliding window indexed by phase synchrony. Two case studies are presented to provide preliminary evidence for the application of the toolbox to guide network-based mapping of epileptogenic cortex and to distinguish these regions from eloquent brain networks. In both cases, epileptogenic cortex was visually distinct. We introduce moviEEG, a novel toolbox for animation of oscillatory network dynamics in iEEG data, and provide two case studies showing preliminary evidence for utility of the toolbox in delineating the epileptogenic zone. Despite evidence that atypical network synchronization has shown to be altered in epileptogenic brain regions, network based techniques have yet to be incorporated into clinical pre-surgical mapping. moviEEG provides a set of functions to enable easy visualization with network based techniques. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  12. CFS MATLAB toolbox: An experiment builder for continuous flash suppression (CFS) task.

    Science.gov (United States)

    Nuutinen, Mikko; Mustonen, Terhi; Häkkinen, Jukka

    2017-09-15

    CFS toolbox is an open-source collection of MATLAB functions that utilizes PsychToolbox-3 (PTB-3). It is designed to allow a researcher to create and run continuous flash suppression experiments using a variety of experimental parameters (i.e., stimulus types and locations, noise characteristics, and experiment window settings). In a CFS experiment, one of the eyes at a time is presented with a dynamically changing noise pattern, while the other eye is concurrently presented with a static target stimulus, such as a Gabor patch. Due to the strong interocular suppression created by the dominant noise pattern mask, the target stimulus is rendered invisible for an extended duration. Very little knowledge of MATLAB is required for using the toolbox; experiments are generated by modifying csv files with the required parameters, and result data are output to text files for further analysis. The open-source code is available on the project page under a Creative Commons License ( http://www.mikkonuutinen.arkku.net/CFS_toolbox/ and https://bitbucket.org/mikkonuutinen/cfs_toolbox ).

  13. MATLAB Toolboxes for Reference Electrode Standardization Technique (REST) of Scalp EEG.

    Science.gov (United States)

    Dong, Li; Li, Fali; Liu, Qiang; Wen, Xin; Lai, Yongxiu; Xu, Peng; Yao, Dezhong

    2017-01-01

    Reference electrode standardization technique (REST) has been increasingly acknowledged and applied as a re-reference technique to transform an actual multi-channels recordings to approximately zero reference ones in electroencephalography/event-related potentials (EEG/ERPs) community around the world in recent years. However, a more easy-to-use toolbox for re-referencing scalp EEG data to zero reference is still lacking. Here, we have therefore developed two open-source MATLAB toolboxes for REST of scalp EEG. One version of REST is closely integrated into EEGLAB, which is a popular MATLAB toolbox for processing the EEG data; and another is a batch version to make it more convenient and efficient for experienced users. Both of them are designed to provide an easy-to-use for novice researchers and flexibility for experienced researchers. All versions of the REST toolboxes can be freely downloaded at http://www.neuro.uestc.edu.cn/rest/Down.html, and the detailed information including publications, comments and documents on REST can also be found from this website. An example of usage is given with comparative results of REST and average reference. We hope these user-friendly REST toolboxes could make the relatively novel technique of REST easier to study, especially for applications in various EEG studies.

  14. Neural Parallel Engine: A toolbox for massively parallel neural signal processing.

    Science.gov (United States)

    Tam, Wing-Kin; Yang, Zhi

    2018-05-01

    Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs). It offers a selection of the most commonly used routines in neural signal processing such as spike detection and spike sorting, including advanced algorithms such as exponential-component-power-component (EC-PC) spike detection and binary pursuit spike sorting. We also propose a new method for detecting peaks in parallel through a parallel compact operation. Our toolbox is able to offer a 5× to 110× speedup compared with its CPU counterparts depending on the algorithms. A user-friendly MATLAB interface is provided to allow easy integration of the toolbox into existing workflows. Previous efforts on GPU neural signal processing only focus on a few rudimentary algorithms, are not well-optimized and often do not provide a user-friendly programming interface to fit into existing workflows. There is a strong need for a comprehensive toolbox for massively parallel neural signal processing. A new toolbox for massively parallel neural signal processing has been created. It can offer significant speedup in processing signals from large-scale recordings up to thousands of channels. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Toolbox for the design of LiNbO3-based passive and active integrated quantum circuits

    Science.gov (United States)

    Sharapova, P. R.; Luo, K. H.; Herrmann, H.; Reichelt, M.; Meier, T.; Silberhorn, C.

    2017-12-01

    We present and discuss perspectives of current developments on advanced quantum optical circuits monolithically integrated in the lithium niobate platform. A set of basic components comprising photon pair sources based on parametric down conversion (PDC), passive routing elements and active electro-optically controllable switches and polarisation converters are building blocks of a toolbox which is the basis for a broad range of diverse quantum circuits. We review the state-of-the-art of these components and provide models that properly describe their performance in quantum circuits. As an example for applications of these models we discuss design issues for a circuit providing on-chip two-photon interference. The circuit comprises a PDC section for photon pair generation followed by an actively controllable modified mach-Zehnder structure for observing Hong-Ou-Mandel interference. The performance of such a chip is simulated theoretically by taking even imperfections of the properties of the individual components into account.

  16. Toolbox for Research and Exploration (TREX): Investigations of Fine-Grained Materials on Small Bodies

    Science.gov (United States)

    Domingue, D. L.; Allain, J.-P.; Banks, M.; Christoffersen, R.; Cintala, M.; Clark, R.; Cloutis, E.; Graps, A.; Hendrix, A. R.; Hsieh, H.; hide

    2018-01-01

    The Toolbox for Research and Exploration (TREX) is a NASA SSERVI (Solar System Exploration Research Virtual Institute) node. TREX (trex.psi.edu) aims to decrease risk to future missions, specifically to the Moon, the Martian moons, and near- Earth asteroids, by improving mission success and assuring the safety of astronauts, their instruments, and spacecraft. TREX studies will focus on characteristics of the fine grains that cover the surfaces of these target bodies - their spectral characteristics and the potential resources (such as H2O) they may harbor. TREX studies are organized into four Themes (Laboratory- Studies, Moon-Studies, Small-Bodies Studies, and Field-Work). In this presentation, we focus on the work targeted by the Small-Bodies Theme. The Small-Bodies' Theme delves into several topics, many which overlap or are synergistic with the other TREX Themes. The main topics include photometry, spectral modeling, laboratory simulations of space weathering processes relevant to asteroids, the assembly of an asteroid regolith database, the dichotomy between nuclear and reflectance spectroscopy, and the dynamical evolution of asteroids and the implications for the retention of volatiles.

  17. Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Immethun, Cheryl M; DeLorenzo, Drew M; Focht, Caroline M; Gupta, Dinesh; Johnson, Charles B; Moon, Tae Seok

    2017-07-01

    Many under-developed organisms possess important traits that can boost the effectiveness and sustainability of microbial biotechnology. Photoautotrophic cyanobacteria can utilize the energy captured from light to fix carbon dioxide for their metabolic needs while living in environments not suited for growing crops. Various value-added compounds have been produced by cyanobacteria in the laboratory; yet, the products' titers and yields are often not industrially relevant and lag behind what have been accomplished in heterotrophic microbes. Genetic tools for biological process control are needed to take advantage of cyanobacteria's beneficial qualities, as tool development also lags behind what has been created in common heterotrophic hosts. To address this problem, we developed a suite of sensors that regulate transcription in the model cyanobacterium Synechocystis sp. PCC 6803 in response to metabolically relevant signals, including light and the cell's nitrogen status, and a family of sensors that respond to the inexpensive chemical, l-arabinose. Increasing the number of available tools enables more complex and precise control of gene expression. Expanding the synthetic biology toolbox for this cyanobacterium also improves our ability to utilize this important under-developed organism in biotechnology. Biotechnol. Bioeng. 2017;114: 1561-1569. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

    International Nuclear Information System (INIS)

    Li, R N; Liu, X; Liu, S J

    2013-01-01

    In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission

  19. Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

    Science.gov (United States)

    Li, R. N.; Liu, X.; Liu, S. J.

    2013-12-01

    In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission.

  20. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

    Science.gov (United States)

    Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

    2011-04-15

    The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

  1. Travel demand management : a toolbox of strategies to reduce single\\0x2010occupant vehicle trips and increase alternate mode usage in Arizona.

    Science.gov (United States)

    2012-02-01

    The report provides a suite of recommended strategies to reduce single-occupant vehicle traffic in the urban : areas of Phoenix and Tucson, Arizona, which are presented as a travel demand management toolbox. The : toolbox includes supporting research...

  2. Hemostats, sealants, and adhesives: components of the surgical toolbox.

    Science.gov (United States)

    Spotnitz, William D; Burks, Sandra

    2008-07-01

    The surgical toolbox is expanding, and newer products are being developed to improve results. Reducing blood loss so that bloodless surgery can be performed may help minimize morbidity and length of stay. As patients, hospital administrators, and government regulators desire less invasive procedures, the surgical technical challenge is increasing. More operations are being performed through minimally invasive incisions with laparoscopic, endoscopic, and robotic approaches. In this setting, tools that can reduce bleeding by causing blood to clot, sealing vessels, or gluing tissues are gaining an increasing importance. Thus, hemostats, sealants, and adhesives are becoming a more important element of surgical practice. This review is designed to facilitate the reader's basic knowledge of these tools so that informed choices are made for controlling bleeding in specific clinical situations. Such information is useful for all members of the operative team. The team includes surgeons, anesthesiologists, residents, and nurses as well as hematologists and other medical specialists who may be involved in the perioperative care of surgical patients. An understanding of these therapeutic options may also be helpful to the transfusion service. In some cases, these materials may be stored in the blood bank, and their appropriate use may reduce demand for other transfusion components. The product classification used in this review includes hemostats as represented by product categories that include mechanical agents, active agents, flowables, and fibrin sealants; sealants as represented by fibrin sealants and polyethylene glycol hydrogels; and adhesives as represented by cyanoacrylates and albumin cross-linked with glutaraldehyde. Only those agents approved by the Food and Drug Administration (FDA) and presently available (February 2008) for sale in the United States are discussed in this review.

  3. A DICOM-RT-based toolbox for the evaluation and verification of radiotherapy plans

    International Nuclear Information System (INIS)

    Spezi, E; Lewis, D G; Smith, C W

    2002-01-01

    The verification of radiotherapy plans is an essential step in the treatment planning process. This is especially important for highly conformal and IMRT plans which produce non-intuitive fluence maps and complex 3D dose distributions. In this work we present a DICOM (Digital Imaging and Communication in Medicine) based toolbox, developed for the evaluation and the verification of radiotherapy treatment plans. The toolbox offers the possibility of importing treatment plans generated with different calculation algorithms and/or different optimization engines and evaluating dose distributions on an independent platform. Furthermore the radiotherapy set-up can be exported to the BEAM Monte Carlo code system for dose verification. This can be done by simulating the irradiation of the patient CT dataset or the irradiation of a software-generated water phantom. We show the application of some of the functions implemented in this toolbox for the evaluation and verification of an IMRT treatment of the head and neck region

  4. Designed Green Toolbox as built environment educating method-analytical comparison between two groups of students with different cultural background

    NARCIS (Netherlands)

    El Fiky, U.; Hamdy, I.; Fikry, M.

    2006-01-01

    This paper is concerned with evaluating and testing the application process of green architecture design strategies using a tool-box as a built environment educating method and a pre-design reminder. Understanding the suggested green design strategies, testing the tool-box effectiveness,

  5. Wind Turbine Blockset in Matlab/Simulink. General Overview and Description of the Model

    DEFF Research Database (Denmark)

    Iov, Florin; Hansen, A. D.; Soerensen, P.

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project ?Simulation Platform to model, optimize and design wind turbines? and it has been used as a general developer tool for other three simulation tools......: Saber, DIgSILENT, HAWC. The report provides first a quick overview over Matlab issues and then explains the structure of the developed toolbox. The attention in the report is mainly drawn to the description of the most important mathematical models, which have been developed in the Toolbox. Then, some...

  6. NeoAnalysis: a Python-based toolbox for quick electrophysiological data processing and analysis.

    Science.gov (United States)

    Zhang, Bo; Dai, Ji; Zhang, Tao

    2017-11-13

    In a typical electrophysiological experiment, especially one that includes studying animal behavior, the data collected normally contain spikes, local field potentials, behavioral responses and other associated data. In order to obtain informative results, the data must be analyzed simultaneously with the experimental settings. However, most open-source toolboxes currently available for data analysis were developed to handle only a portion of the data and did not take into account the sorting of experimental conditions. Additionally, these toolboxes require that the input data be in a specific format, which can be inconvenient to users. Therefore, the development of a highly integrated toolbox that can process multiple types of data regardless of input data format and perform basic analysis for general electrophysiological experiments is incredibly useful. Here, we report the development of a Python based open-source toolbox, referred to as NeoAnalysis, to be used for quick electrophysiological data processing and analysis. The toolbox can import data from different data acquisition systems regardless of their formats and automatically combine different types of data into a single file with a standardized format. In cases where additional spike sorting is needed, NeoAnalysis provides a module to perform efficient offline sorting with a user-friendly interface. Then, NeoAnalysis can perform regular analog signal processing, spike train, and local field potentials analysis, behavioral response (e.g. saccade) detection and extraction, with several options available for data plotting and statistics. Particularly, it can automatically generate sorted results without requiring users to manually sort data beforehand. In addition, NeoAnalysis can organize all of the relevant data into an informative table on a trial-by-trial basis for data visualization. Finally, NeoAnalysis supports analysis at the population level. With the multitude of general-purpose functions provided

  7. CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation.

    Science.gov (United States)

    Wilke, Marko; Altaye, Mekibib; Holland, Scott K

    2017-01-01

    Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating "unusual" populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php.

  8. Process evaluation of a Toolbox-training program for construction foremen in Denmark

    DEFF Research Database (Denmark)

    Jeschke, Katharina Christiane; Kines, Pete; Rasmussen, Liselotte

    2017-01-01

    foremen’s knowledge and communication skills in daily planning of work tasks and their related OSH risks on construction sites. The program builds on the popular 'toolbox meeting' concept, however there is very little research evaluating these types of meetings. This article describes the development...... and revised until the final version after the fifth group. The evaluation utilized an action research strategy with a mixed–methods approach of triangulating questionnaire, interview, and observation data. Process evaluation results showed that the eight Toolbox-training topics were relevant and useful...

  9. ElectroMagnetoEncephalography software: overview and integration with other EEG/MEG toolboxes.

    Science.gov (United States)

    Peyk, Peter; De Cesarei, Andrea; Junghöfer, Markus

    2011-01-01

    EMEGS (electromagnetic encephalography software) is a MATLAB toolbox designed to provide novice as well as expert users in the field of neuroscience with a variety of functions to perform analysis of EEG and MEG data. The software consists of a set of graphical interfaces devoted to preprocessing, analysis, and visualization of electromagnetic data. Moreover, it can be extended using a plug-in interface. Here, an overview of the capabilities of the toolbox is provided, together with a simple tutorial for both a standard ERP analysis and a time-frequency analysis. Latest features and future directions of the software development are presented in the final section.

  10. Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine Learning

    OpenAIRE

    Lemaitre , Guillaume; Nogueira , Fernando; Aridas , Christos ,

    2017-01-01

    International audience; imbalanced-learn is an open-source python toolbox aiming at providing a wide range of methods to cope with the problem of imbalanced dataset frequently encountered in machine learning and pattern recognition. The implemented state-of-the-art methods can be categorized into 4 groups: (i) under-sampling, (ii) over-sampling, (iii) combination of over-and under-sampling, and (iv) ensemble learning methods. The proposed toolbox depends only on numpy, scipy, and scikit-learn...

  11. PEANO, a toolbox for real-time process signal validation and estimation

    Energy Technology Data Exchange (ETDEWEB)

    Fantoni, Paolo F.; Figedy, Stefan; Racz, Attila

    1998-02-01

    PEANO (Process Evaluation and Analysis by Neural Operators), a toolbox for real time process signal validation and condition monitoring has been developed. This system analyses the signals, which are e.g. the readings of process monitoring sensors, computes their expected values and alerts if real values are deviated from the expected ones more than limits allow. The reliability level of the current analysis is also produced. The system is based on neuro-fuzzy techniques. Artificial Neural Networks and Fuzzy Logic models can be combined to exploit learning and generalisation capability of the first technique with the approximate reasoning embedded in the second approach. Real-time process signal validation is an application field where the use of this technique can improve the diagnosis of faulty sensors and the identification of outliers in a robust and reliable way. This study implements a fuzzy and possibilistic clustering algorithm to classify the operating region where the validation process has to be performed. The possibilistic approach (rather than probabilistic) allows a ''don't know'' classification that results in a fast detection of unforeseen plant conditions or outliers. Specialised Artificial Neural Networks are used for the validation process, one for each fuzzy cluster in which the operating map has been divided. There are two main advantages in using this technique: the accuracy and generalisation capability is increased compared to the case of a single network working in the entire operating region, and the ability to identify abnormal conditions, where the system is not capable to operate with a satisfactory accuracy, is improved. This model has been tested in a simulated environment on a French PWR, to monitor safety-related reactor variables over the entire power-flow operating map. (author)

  12. PEANO, a toolbox for real-time process signal validation and estimation

    International Nuclear Information System (INIS)

    Fantoni, Paolo F.; Figedy, Stefan; Racz, Attila

    1998-02-01

    PEANO (Process Evaluation and Analysis by Neural Operators), a toolbox for real time process signal validation and condition monitoring has been developed. This system analyses the signals, which are e.g. the readings of process monitoring sensors, computes their expected values and alerts if real values are deviated from the expected ones more than limits allow. The reliability level of the current analysis is also produced. The system is based on neuro-fuzzy techniques. Artificial Neural Networks and Fuzzy Logic models can be combined to exploit learning and generalisation capability of the first technique with the approximate reasoning embedded in the second approach. Real-time process signal validation is an application field where the use of this technique can improve the diagnosis of faulty sensors and the identification of outliers in a robust and reliable way. This study implements a fuzzy and possibilistic clustering algorithm to classify the operating region where the validation process has to be performed. The possibilistic approach (rather than probabilistic) allows a ''don't know'' classification that results in a fast detection of unforeseen plant conditions or outliers. Specialised Artificial Neural Networks are used for the validation process, one for each fuzzy cluster in which the operating map has been divided. There are two main advantages in using this technique: the accuracy and generalisation capability is increased compared to the case of a single network working in the entire operating region, and the ability to identify abnormal conditions, where the system is not capable to operate with a satisfactory accuracy, is improved. This model has been tested in a simulated environment on a French PWR, to monitor safety-related reactor variables over the entire power-flow operating map. (author)

  13. Toolbox for Urban Mobility Simulation: High Resolution Population Dynamics for Global Cities

    Science.gov (United States)

    Bhaduri, B. L.; Lu, W.; Liu, C.; Thakur, G.; Karthik, R.

    2015-12-01

    In this rapidly urbanizing world, unprecedented rate of population growth is not only mirrored by increasing demand for energy, food, water, and other natural resources, but has detrimental impacts on environmental and human security. Transportation simulations are frequently used for mobility assessment in urban planning, traffic operation, and emergency management. Previous research, involving purely analytical techniques to simulations capturing behavior, has investigated questions and scenarios regarding the relationships among energy, emissions, air quality, and transportation. Primary limitations of past attempts have been availability of input data, useful "energy and behavior focused" models, validation data, and adequate computational capability that allows adequate understanding of the interdependencies of our transportation system. With increasing availability and quality of traditional and crowdsourced data, we have utilized the OpenStreetMap roads network, and has integrated high resolution population data with traffic simulation to create a Toolbox for Urban Mobility Simulations (TUMS) at global scale. TUMS consists of three major components: data processing, traffic simulation models, and Internet-based visualizations. It integrates OpenStreetMap, LandScanTM population, and other open data (Census Transportation Planning Products, National household Travel Survey, etc.) to generate both normal traffic operation and emergency evacuation scenarios. TUMS integrates TRANSIMS and MITSIM as traffic simulation engines, which are open-source and widely-accepted for scalable traffic simulations. Consistent data and simulation platform allows quick adaption to various geographic areas that has been demonstrated for multiple cities across the world. We are combining the strengths of geospatial data sciences, high performance simulations, transportation planning, and emissions, vehicle and energy technology development to design and develop a simulation

  14. A multiplexed microfluidic toolbox for the rapid optimization of affinity-driven partition in aqueous two phase systems.

    Science.gov (United States)

    Bras, Eduardo J S; Soares, Ruben R G; Azevedo, Ana M; Fernandes, Pedro; Arévalo-Rodríguez, Miguel; Chu, Virginia; Conde, João P; Aires-Barros, M Raquel

    2017-09-15

    Antibodies and other protein products such as interferons and cytokines are biopharmaceuticals of critical importance which, in order to be safely administered, have to be thoroughly purified in a cost effective and efficient manner. The use of aqueous two-phase extraction (ATPE) is a viable option for this purification, but these systems are difficult to model and optimization procedures require lengthy and expensive screening processes. Here, a methodology for the rapid screening of antibody extraction conditions using a microfluidic channel-based toolbox is presented. A first microfluidic structure allows a simple negative-pressure driven rapid screening of up to 8 extraction conditions simultaneously, using less than 20μL of each phase-forming solution per experiment, while a second microfluidic structure allows the integration of multi-step extraction protocols based on the results obtained with the first device. In this paper, this microfluidic toolbox was used to demonstrate the potential of LYTAG fusion proteins used as affinity tags to optimize the partitioning of antibodies in ATPE processes, where a maximum partition coefficient (K) of 9.2 in a PEG 3350/phosphate system was obtained for the antibody extraction in the presence of the LYTAG-Z dual ligand. This represents an increase of approx. 3.7 fold when compared with the same conditions without the affinity molecule (K=2.5). Overall, this miniaturized and versatile approach allowed the rapid optimization of molecule partition followed by a proof-of-concept demonstration of an integrated back extraction procedure, both of which are critical procedures towards obtaining high purity biopharmaceuticals using ATPE. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The Psychometric Toolbox: An Excel Package for Use in Measurement and Psychometrics Courses

    Science.gov (United States)

    Ferrando, Pere J.; Masip-Cabrera, Antoni; Navarro-González, David; Lorenzo-Seva, Urbano

    2017-01-01

    The Psychometric Toolbox (PT) is a user-friendly, non-commercial package mainly intended to be used for instructional purposes in introductory courses of educational and psychological measurement, psychometrics and statistics. The PT package is organized in six separate modules or sub-programs: Data preprocessor (descriptive analyses and data…

  16. 40 CFR 141.717 - Pre-filtration treatment toolbox components.

    Science.gov (United States)

    2010-07-01

    ... surface water or GWUDI source. (c) Bank filtration. Systems receive Cryptosporidium treatment credit for... paragraph. Systems using bank filtration when they begin source water monitoring under § 141.701(a) must... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Pre-filtration treatment toolbox...

  17. A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction

    Science.gov (United States)

    Abulnaga, S. Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M.; Onyike, Chiadi U.; Ying, Sarah H.; Prince, Jerry L.

    2016-03-01

    The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

  18. A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction.

    Science.gov (United States)

    Abulnaga, S Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M; Onyike, Chiadi U; Ying, Sarah H; Prince, Jerry L

    2016-02-27

    The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

  19. Par@Graph - a parallel toolbox for the construction and analysis of large complex climate networks

    NARCIS (Netherlands)

    Tantet, A.J.J.

    2015-01-01

    In this paper, we present Par@Graph, a software toolbox to reconstruct and analyze complex climate networks having a large number of nodes (up to at least 106) and edges (up to at least 1012). The key innovation is an efficient set of parallel software tools designed to leverage the inherited hybrid

  20. MatTAP: A MATLAB toolbox for the control and analysis of movement synchronisation experiments.

    Science.gov (United States)

    Elliott, Mark T; Welchman, Andrew E; Wing, Alan M

    2009-02-15

    Investigating movement timing and synchronisation at the sub-second range relies on an experimental setup that has high temporal fidelity, is able to deliver output cues and can capture corresponding responses. Modern, multi-tasking operating systems make this increasingly challenging when using standard PC hardware and programming languages. This paper describes a new free suite of tools (available from http://www.snipurl.com/mattap) for use within the MATLAB programming environment, compatible with Microsoft Windows and a range of data acquisition hardware. The toolbox allows flexible generation of timing cues with high temporal accuracy, the capture and automatic storage of corresponding participant responses and an integrated analysis module for the rapid processing of results. A simple graphical user interface is used to navigate the toolbox and so can be operated easily by users not familiar with programming languages. However, it is also fully extensible and customisable, allowing adaptation for individual experiments and facilitating the addition of new modules in future releases. Here we discuss the relevance of the MatTAP (MATLAB Timing Analysis Package) toolbox to current timing experiments and compare its use to alternative methods. We validate the accuracy of the analysis module through comparison to manual observation methods and replicate a previous sensorimotor synchronisation experiment to demonstrate the versatility of the toolbox features demanded by such movement synchronisation paradigms.

  1. SIPPI: A Matlab toolbox for sampling the solution to inverse problems with complex prior information

    DEFF Research Database (Denmark)

    Hansen, Thomas Mejer; Cordua, Knud Skou; Caroline Looms, Majken

    2013-01-01

    on the solution. The combined states of information (i.e. the solution to the inverse problem) is a probability density function typically referred to as the a posteriori probability density function. We present a generic toolbox for Matlab and Gnu Octave called SIPPI that implements a number of methods...

  2. An integrated GIS-MARKAL toolbox for designing a CO2 infrastructure network in the Netherlands

    NARCIS (Netherlands)

    van den Broek, M.A.; Brederode, E.; Ramirez, C.A.; Kramers, K.; van der Kuip, M.; Wildenborg, T.; Faaij, A.P.C.; Turkenburg, W.C.

    2009-01-01

    Large-scale implementation of carbon capture and storage needs a whole new infrastructure to transport and store CO2. Tools that can support planning and designing of such infrastructure require incorporation of both temporal and spatial aspects. Therefore, a toolbox that integrates ArcGIS, a

  3. Screening and assessment of chronic pain among children with cerebral palsy: a process evaluation of a pain toolbox.

    Science.gov (United States)

    Orava, Taryn; Provvidenza, Christine; Townley, Ashleigh; Kingsnorth, Shauna

    2018-06-08

    Though high numbers of children with cerebral palsy experience chronic pain, it remains under-recognized. This paper describes an evaluation of implementation supports and adoption of the Chronic Pain Assessment Toolbox for Children with Disabilities (the Toolbox) to enhance pain screening and assessment practices within a pediatric rehabilitation and complex continuing care hospital. A multicomponent knowledge translation strategy facilitated Toolbox adoption, inclusive of a clinical practice guideline, cerebral palsy practice points and assessment tools. Across the hospital, seven ambulatory care clinics with cerebral palsy caseloads participated in a staggered roll-out (Group 1: exclusive CP caseloads, March-December; Group 2: mixed diagnostic caseloads, August-December). Evaluation measures included client electronic medical record audit, document review and healthcare provider survey and interviews. A significant change in documentation of pain screening and assessment practice from pre-Toolbox (<2%) to post-Toolbox adoption (53%) was found. Uptake in Group 2 clinics lagged behind Group 1. Opportunities to use the Toolbox consistently (based on diagnostic caseload) and frequently (based on client appointments) were noted among contextual factors identified. Overall, the Toolbox was positively received and clinically useful. Findings affirm that the Toolbox, in conjunction with the application of integrated knowledge translation principles and an established knowledge translation framework, has potential to be a useful resource to enrich and standardize chronic pain screening and assessment practices among children with cerebral palsy. Implications for Rehabilitation It is important to engage healthcare providers in the conceptualization, development, implementation and evaluation of a knowledge-to-action best practice product. The Chronic Pain Toolbox for Children with Disabilities provides rehabilitation staff with guidance on pain screening and assessment

  4. DICOM router: an open source toolbox for communication and correction of DICOM objects.

    Science.gov (United States)

    Hackländer, Thomas; Kleber, Klaus; Martin, Jens; Mertens, Heinrich

    2005-03-01

    Today, the exchange of medical images and clinical information is well defined by the digital imaging and communications in medicine (DICOM) and Health Level Seven (ie, HL7) standards. The interoperability among information systems is specified by the integration profiles of IHE (Integrating the Healthcare Enterprise). However, older imaging modalities frequently do not correctly support these interfaces and integration profiles, and some use cases are not yet specified by IHE. Therefore, corrections of DICOM objects are necessary to establish conformity. The aim of this project was to develop a toolbox that can automatically perform these recurrent corrections of the DICOM objects. The toolbox is composed of three main components: 1) a receiver to receive DICOM objects, 2) a processing pipeline to correct each object, and 3) one or more senders to forward each corrected object to predefined addressees. The toolbox is implemented under Java as an open source project. The processing pipeline is realized by means of plug ins. One of the plug ins can be programmed by the user via an external eXtensible Stylesheet Language (ie, XSL) file. Using this plug in, DICOM objects can also be converted into eXtensible Markup Language (ie, XML) documents or other data formats. DICOM storage services, DICOM CD-ROMs, and the local file system are defined as input and output channel. The toolbox is used clinically for different application areas. These are the automatic correction of DICOM objects from non-IHE-conforming modalities, the import of DICOM CD-ROMs into the picture archiving and communication system and the pseudo naming of DICOM images. The toolbox has been accepted by users in a clinical setting. Because of the open programming interfaces, the functionality can easily be adapted to future applications.

  5. ObsPy: A Python Toolbox for Seismology - Recent Developments and Applications

    Science.gov (United States)

    Megies, T.; Krischer, L.; Barsch, R.; Sales de Andrade, E.; Beyreuther, M.

    2014-12-01

    ObsPy (http://www.obspy.org) is a community-driven, open-source project dedicated to building a bridge for seismology into the scientific Python ecosystem. It offersa) read and write support for essentially all commonly used waveform, station, and event metadata file formats with a unified interface,b) a comprehensive signal processing toolbox tuned to the needs of seismologists,c) integrated access to all large data centers, web services and databases, andd) convenient wrappers to legacy codes like libtau and evalresp.Python, currently the most popular language for teaching introductory computer science courses at top-ranked U.S. departments, is a full-blown programming language with the flexibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. Together with packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy enables the construction of complete workflows in Python. These vary from reading locally stored data or requesting data from one or more different data centers through to signal analysis and data processing and on to visualizations in GUI and web applications, output of modified/derived data and the creation of publication-quality figures.ObsPy enjoys a large world-wide rate of adoption in the community. Applications successfully using it include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. All functionality is extensively documented and the ObsPy tutorial and gallery give a good impression of the wide range of possible use cases.We will present the basic features of ObsPy, new developments and applications, and a roadmap for the near future and discuss the sustainability of our open-source development model.

  6. EasyCloneYALI: CRISPR/Cas9-based synthetic toolbox for engineering of the yeast Yarrowia lipolytica

    DEFF Research Database (Denmark)

    Holkenbrink, Carina; Dam, Marie Inger; Kildegaard, Kanchana Rueksomtawin

    2018-01-01

    . Here, we present the EasyCloneYALI genetic toolbox, which allows streamlined strain construction with high genome editing efficiencies in Y. lipolytica via the CRISPR/Cas9 technology. The toolbox allows marker-free integration of gene expression vectors into characterized genome sites as well as marker......-free deletion of genes with the help of CRISPR/Cas9. Genome editing efficiencies above 80% were achieved with transformation protocols using non-replicating DNA repair fragments (such as DNA oligos). Furthermore, the toolbox includes a set of integrative gene expression vectors with prototrophic markers...

  7. An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave

    Directory of Open Access Journals (Sweden)

    Ikaro Silva

    2014-09-01

    Full Text Available The WaveForm DataBase (WFDB Toolbox for MATLAB/Octave enables  integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox allows direct loading into MATLAB/Octave's workspace of over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by meta data such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

  8. The simulation of a non-linear unstable system of motion, utilising the Solid-Works and Matlab/Simulink extended libraries/toolboxes

    Directory of Open Access Journals (Sweden)

    Zátopek Jiří

    2016-01-01

    Full Text Available This text discusses the use and integration of various support software tools for the purpose of designing the motion control law governing mechanical structures with strongly non-linear behaviour. The detailed mathematical model is derived using Lagrange Equations of the Second Type. The physical model was designed by using SolidWorks 3D CAD software and a SimMechanics library. It extends Simulink with modelling tools for the simulation of mechanical “multi-domain” physical systems. The visualization of Simulink outputs is performed using the 3D Animation toolbox. Control law - designed on the basis of the mathematical model, is tested for both models (i.e. mathematical and physical and the regulatory processes’ results are compared.

  9. OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

    Directory of Open Access Journals (Sweden)

    Lucian A B Purvis

    Full Text Available In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

  10. A toolbox and sample object perception data for equalization of natural images

    Directory of Open Access Journals (Sweden)

    Wilma A. Bainbridge

    2015-12-01

    Full Text Available For psychologists and neuroscientists, careful selection of their stimuli is essential, so that low-level visual features such as color or spatial frequency do not serve as confounds between conditions of interest. Here, we detail the Natural Image Statistical Toolbox, which allows scientists to measure, visualize, and control stimulus sets along a set of low-level visual properties. Additionally, we provide a set of object images varying along several perceptual object properties, including physical size and interaction envelope size (i.e., the space around an object transversed during an interaction, serving as a test-bed for the Natural Image Statistical Toolbox. This stimulus set is also a highly characterized set useful to psychology and neuroscience studies on object perception.

  11. Genetic toolbox for controlled expression of functional proteins in Geobacillus spp.

    Directory of Open Access Journals (Sweden)

    Ivan Pogrebnyakov

    Full Text Available Species of genus Geobacillus are thermophilic bacteria and play an ever increasing role as hosts for biotechnological applications both in academia and industry. Here we screened a number of Geobacillus strains to determine which industrially relevant carbon sources they can utilize. One of the strains, G. thermoglucosidasius C56-YS93, was then chosen to develop a toolbox for controlled gene expression over a wide range of levels. It includes a library of semi-synthetic constitutive promoters (76-fold difference in expression levels and an inducible promoter from the xylA gene. A library of synthetic in silico designed ribosome binding sites was also created for further tuning of translation. The PxylA was further used to successfully express native and heterologous xylanases in G. thermoglucosidasius. This toolbox enables fine-tuning of gene expression in Geobacillus species for metabolic engineering approaches in production of biochemicals and heterologous proteins.

  12. OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

    Science.gov (United States)

    Purvis, Lucian A B; Clarke, William T; Biasiolli, Luca; Valkovič, Ladislav; Robson, Matthew D; Rodgers, Christopher T

    2017-01-01

    In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA) toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM) standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

  13. Building a symbolic computer algebra toolbox to compute 2D Fourier transforms in polar coordinates.

    Science.gov (United States)

    Dovlo, Edem; Baddour, Natalie

    2015-01-01

    The development of a symbolic computer algebra toolbox for the computation of two dimensional (2D) Fourier transforms in polar coordinates is presented. Multidimensional Fourier transforms are widely used in image processing, tomographic reconstructions and in fact any application that requires a multidimensional convolution. By examining a function in the frequency domain, additional information and insights may be obtained. The advantages of our method include: •The implementation of the 2D Fourier transform in polar coordinates within the toolbox via the combination of two significantly simpler transforms.•The modular approach along with the idea of lookup tables implemented help avoid the issue of indeterminate results which may occur when attempting to directly evaluate the transform.•The concept also helps prevent unnecessary computation of already known transforms thereby saving memory and processing time.

  14. Wind Turbine Blockset in Matlab/Simulink - General overview and description of the models

    Energy Technology Data Exchange (ETDEWEB)

    Iov, F.; Hansen, A.D.; Soerensen, P.; Blaabjerg, F.

    2004-03-01

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project 'Simulation Platform to model, optimize and design wind turbines' and it has been used as a general developer tool for other three simulation tools: Saber, DIgSILENT, HAWC. The report provides first a quick overview over Matlab issues and then explains the structure of the developed toolbox. The attention in the report is mainly drawn to the description of the most important mathematical models, which have been developed in the Toolbox. Then, some simulation results using the developed models are shown. Finally, some general conclusions regarding this new developed Toolbox as well as some directions for future work are made. (au)

  15. Wind turbine blockset in Matlab/Simulink. General overview and description of the models

    Energy Technology Data Exchange (ETDEWEB)

    Iov, F.; Timbus, A.V.; Hansen, A.D.; Soerensen, P.; Blaabjerg, F.

    2004-03-01

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project 'Simulation Platform to model, optimize and design wind turbines' and it has been used as a general developer tool for other three simulation tools: Saber, DIgSILENT, HAWC. The report provides first a quick overview over Matlab issues and then explains the structure of the developed toolbox. The attention in the report is mainly drawn to the description of the most important mathematical models, which have been developed in the Toolbox. Then, some simulation results using the developed models are shown. Finally, some general conclusions regarding this new developed Toolbox as well as some directions for future work are made. (au)

  16. Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum.

    Science.gov (United States)

    Liu, Jiao; Wang, Yu; Lu, Yujiao; Zheng, Ping; Sun, Jibin; Ma, Yanhe

    2017-11-16

    Corynebacterium glutamicum is an important industrial workhorse and advanced genetic engineering tools are urgently demanded. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) have revolutionized the field of genome engineering. The CRISPR/Cas9 system that utilizes NGG as protospacer adjacent motif (PAM) and has good targeting specificity can be developed into a powerful tool for efficient and precise genome editing of C. glutamicum. Herein, we developed a versatile CRISPR/Cas9 genome editing toolbox for C. glutamicum. Cas9 and gRNA expression cassettes were reconstituted to combat Cas9 toxicity and facilitate effective termination of gRNA transcription. Co-transformation of Cas9 and gRNA expression plasmids was exploited to overcome high-frequency mutation of cas9, allowing not only highly efficient gene deletion and insertion with plasmid-borne editing templates (efficiencies up to 60.0 and 62.5%, respectively) but also simple and time-saving operation. Furthermore, CRISPR/Cas9-mediated ssDNA recombineering was developed to precisely introduce small modifications and single-nucleotide changes into the genome of C. glutamicum with efficiencies over 80.0%. Notably, double-locus editing was also achieved in C. glutamicum. This toolbox works well in several C. glutamicum strains including the widely-used strains ATCC 13032 and ATCC 13869. In this study, we developed a CRISPR/Cas9 toolbox that could facilitate markerless gene deletion, gene insertion, precise base editing, and double-locus editing in C. glutamicum. The CRISPR/Cas9 toolbox holds promise for accelerating the engineering of C. glutamicum and advancing its application in the production of biochemicals and biofuels.

  17. Review of Qualitative Approaches for the Construction Industry: Designing a Risk Management Toolbox

    Science.gov (United States)

    Spee, Ton; Gillen, Matt; Lentz, Thomas J.; Garrod, Andrew; Evans, Paul; Swuste, Paul

    2011-01-01

    Objectives This paper presents the framework and protocol design for a construction industry risk management toolbox. The construction industry needs a comprehensive, systematic approach to assess and control occupational risks. These risks span several professional health and safety disciplines, emphasized by multiple international occupational research agenda projects including: falls, electrocution, noise, silica, welding fumes, and musculoskeletal disorders. Yet, the International Social Security Association says, "whereas progress has been made in safety and health, the construction industry is still a high risk sector." Methods Small- and medium-sized enterprises (SMEs) employ about 80% of the world's construction workers. In recent years a strategy for qualitative occupational risk management, known as Control Banding (CB) has gained international attention as a simplified approach for reducing work-related risks. CB groups hazards into stratified risk 'bands', identifying commensurate controls to reduce the level of risk and promote worker health and safety. We review these qualitative solutions-based approaches and identify strengths and weaknesses toward designing a simplified CB 'toolbox' approach for use by SMEs in construction trades. Results This toolbox design proposal includes international input on multidisciplinary approaches for performing a qualitative risk assessment determining a risk 'band' for a given project. Risk bands are used to identify the appropriate level of training to oversee construction work, leading to commensurate and appropriate control methods to perform the work safely. Conclusion The Construction Toolbox presents a review-generated format to harness multiple solutions-based national programs and publications for controlling construction-related risks with simplified approaches across the occupational safety, health and hygiene professions. PMID:22953194

  18. PredPsych: A toolbox for predictive machine learning based approach in experimental psychology research

    OpenAIRE

    Cavallo, Andrea; Becchio, Cristina; Koul, Atesh

    2016-01-01

    Recent years have seen an increased interest in machine learning based predictive methods for analysing quantitative behavioural data in experimental psychology. While these methods can achieve relatively greater sensitivity compared to conventional univariate techniques, they still lack an established and accessible software framework. The goal of this work was to build an open-source toolbox – “PredPsych” – that could make these methods readily available to all psychologists. PredPsych is a...

  19. Orfeo Toolbox: A Free And Open Source Solution For Research And Operational Remote Sensing Projects

    Science.gov (United States)

    Savinaud, Mickael; OTB-CS Team

    2013-12-01

    The free and open source solution, Orfeo ToolBox (OTB), offers the possibility to deal with large data processing. This library designed by CNES in the frame of the ORFEO accompaniment program to promote use of Pleiades data and other VHR data offers now a larger number of applications designed to end users. Due to its modular design, OTB is now used in different context from R&D studies to operational chain.

  20. Numerical solution of multi groups point kinetic equations by simulink toolbox of Matlab software

    International Nuclear Information System (INIS)

    Hadad, K.; Mohamadi, A.; Sabet, H.; Ayobian, N.; Khani, M.

    2004-01-01

    The simulink toolbox of Matlab Software was employed to solve the point kinetics equation with six group delayed neutrons. The method of Adams-Bash ford showed a good convergence in solving the system of simultaneous equations and the obtained results showed good agreements with other numerical schemes. The flexibility of the package in changing the system parameters and the user friendly interface makes this approach a reliable educational package in revealing the affects of reactivity changes on power incursions

  1. Evaluation of an Advanced Harmonic Filter for Adjustable Speed Drives using a Toolbox Approach

    DEFF Research Database (Denmark)

    Asiminoaei, Lucian; Hansen, Steffan; Blaabjerg, Frede

    2004-01-01

    A large diversity of solutions exists to reduce the harmonic emission of the 6-pulse Adjustable Speed Drive in order to fulfill the requirements of the international harmonic standards. Among them, new types of advanced harmonic filters recently gained an increased attention due to their good...... a combination of a pre-stored database and new interpolation techniques the toolbox can provide the harmonic data on real applications allowing comparisons between different mitigation solutions....

  2. Visualizing flow fields using acoustic Doppler current profilers and the Velocity Mapping Toolbox

    Science.gov (United States)

    Jackson, P. Ryan

    2013-01-01

    The purpose of this fact sheet is to provide examples of how the U.S. Geological Survey is using acoustic Doppler current profilers for much more than routine discharge measurements. These instruments are capable of mapping complex three-dimensional flow fields within rivers, lakes, and estuaries. Using the Velocity Mapping Toolbox to process the ADCP data allows detailed visualization of the data, providing valuable information for a range of studies and applications.

  3. Review of qualitative approaches for the construction industry: designing a risk management toolbox.

    Science.gov (United States)

    Zalk, David M; Spee, Ton; Gillen, Matt; Lentz, Thomas J; Garrod, Andrew; Evans, Paul; Swuste, Paul

    2011-06-01

    This paper presents the framework and protocol design for a construction industry risk management toolbox. The construction industry needs a comprehensive, systematic approach to assess and control occupational risks. These risks span several professional health and safety disciplines, emphasized by multiple international occupational research agenda projects including: falls, electrocution, noise, silica, welding fumes, and musculoskeletal disorders. Yet, the International Social Security Association says, "whereas progress has been made in safety and health, the construction industry is still a high risk sector." Small- and medium-sized enterprises (SMEs) employ about 80% of the world's construction workers. In recent years a strategy for qualitative occupational risk management, known as Control Banding (CB) has gained international attention as a simplified approach for reducing work-related risks. CB groups hazards into stratified risk 'bands', identifying commensurate controls to reduce the level of risk and promote worker health and safety. We review these qualitative solutions-based approaches and identify strengths and weaknesses toward designing a simplified CB 'toolbox' approach for use by SMEs in construction trades. This toolbox design proposal includes international input on multidisciplinary approaches for performing a qualitative risk assessment determining a risk 'band' for a given project. Risk bands are used to identify the appropriate level of training to oversee construction work, leading to commensurate and appropriate control methods to perform the work safely. The Construction Toolbox presents a review-generated format to harness multiple solutions-based national programs and publications for controlling construction-related risks with simplified approaches across the occupational safety, health and hygiene professions.

  4. IV. NIH Toolbox Cognition Battery (CB): measuring language (vocabulary comprehension and reading decoding).

    Science.gov (United States)

    Gershon, Richard C; Slotkin, Jerry; Manly, Jennifer J; Blitz, David L; Beaumont, Jennifer L; Schnipke, Deborah; Wallner-Allen, Kathleen; Golinkoff, Roberta Michnick; Gleason, Jean Berko; Hirsh-Pasek, Kathy; Adams, Marilyn Jager; Weintraub, Sandra

    2013-08-01

    Mastery of language skills is an important predictor of daily functioning and health. Vocabulary comprehension and reading decoding are relatively quick and easy to measure and correlate highly with overall cognitive functioning, as well as with success in school and work. New measures of vocabulary comprehension and reading decoding (in both English and Spanish) were developed for the NIH Toolbox Cognition Battery (CB). In the Toolbox Picture Vocabulary Test (TPVT), participants hear a spoken word while viewing four pictures, and then must choose the picture that best represents the word. This approach tests receptive vocabulary knowledge without the need to read or write, removing the literacy load for children who are developing literacy and for adults who struggle with reading and writing. In the Toolbox Oral Reading Recognition Test (TORRT), participants see a letter or word onscreen and must pronounce or identify it. The examiner determines whether it was pronounced correctly by comparing the response to the pronunciation guide on a separate computer screen. In this chapter, we discuss the importance of language during childhood and the relation of language and brain function. We also review the development of the TPVT and TORRT, including information about the item calibration process and results from a validation study. Finally, the strengths and weaknesses of the measures are discussed. © 2013 The Society for Research in Child Development, Inc.

  5. Wind wave analysis in depth limited water using OCEANLYZ, A MATLAB toolbox

    Science.gov (United States)

    Karimpour, Arash; Chen, Qin

    2017-09-01

    There are a number of well established methods in the literature describing how to assess and analyze measured wind wave data. However, obtaining reliable results from these methods requires adequate knowledge on their behavior, strengths and weaknesses. A proper implementation of these methods requires a series of procedures including a pretreatment of the raw measurements, and adjustment and refinement of the processed data to provide quality assurance of the outcomes, otherwise it can lead to untrustworthy results. This paper discusses potential issues in these procedures, explains what parameters are influential for the outcomes and suggests practical solutions to avoid and minimize the errors in the wave results. The procedure of converting the water pressure data into the water surface elevation data, treating the high frequency data with a low signal-to-noise ratio, partitioning swell energy from wind sea, and estimating the peak wave frequency from the weighted integral of the wave power spectrum are described. Conversion and recovery of the data acquired by a pressure transducer, particularly in depth-limited water like estuaries and lakes, are explained in detail. To provide researchers with tools for a reliable estimation of wind wave parameters, the Ocean Wave Analyzing toolbox, OCEANLYZ, is introduced. The toolbox contains a number of MATLAB functions for estimation of the wave properties in time and frequency domains. The toolbox has been developed and examined during a number of the field study projects in Louisiana's estuaries.

  6. A Transcription Activator-Like Effector (TALE) Toolbox for Genome Engineering

    Science.gov (United States)

    Sanjana, Neville E.; Cong, Le; Zhou, Yang; Cunniff, Margaret M.; Feng, Guoping; Zhang, Feng

    2013-01-01

    Transcription activator-like effectors (TALEs) are a class of naturally occurring DNA binding proteins found in the plant pathogen Xanthomonas sp. The DNA binding domain of each TALE consists of tandem 34-amino acid repeat modules that can be rearranged according to a simple cipher to target new DNA sequences. Customized TALEs can be used for a wide variety of genome engineering applications, including transcriptional modulation and genome editing. Here we describe a toolbox for rapid construction of custom TALE transcription factors (TALE-TFs) and nucleases (TALENs) using a hierarchical ligation procedure. This toolbox facilitates affordable and rapid construction of custom TALE-TFs and TALENs within one week and can be easily scaled up to construct TALEs for multiple targets in parallel. We also provide details for testing the activity in mammalian cells of custom TALE-TFs and TALENs using, respectively, qRT-PCR and Surveyor nuclease. The TALE toolbox described here will enable a broad range of biological applications. PMID:22222791

  7. NIH Toolbox Cognitive Function Battery (CFB): Composite Scores of Crystallized, Fluid, and Overall Cognition

    Science.gov (United States)

    Akshoomoff, Natacha; Beaumont, Jennifer L.; Bauer, Patricia J.; Dikmen, Sureyya; Gershon, Richard; Mungas, Dan; Slotkin, Jerry; Tulsky, David; Weintraub, Sandra; Zelazzo, Philip; Heaton, Robert K.

    2014-01-01

    The NIH Toolbox Cognitive Function Battery (CFB) includes 7 tests covering 8 cognitive abilities considered to be important in adaptive functioning across the lifespan (from early childhood to late adulthood). Here we present data on psychometric characteristics in children (N = 208; ages 3–15 years) of a total summary score and composite scores reflecting two major types of cognitive abilities: “crystallized” (more dependent upon past learning experiences) and “fluid” (capacity for new learning and information processing in novel situations). Both types of cognition are considered important in everyday functioning, but are thought to be differently affected by brain health status throughout life, from early childhood through older adulthood. All three Toolbox composite scores showed excellent test-retest reliability, robust developmental effects across the childhood age range considered here, and strong correlations with established, “gold standard” measures of similar abilities. Additional preliminary evidence of validity includes significant associations between all three Toolbox composite scores and maternal reports of children’s health status and school performance. PMID:23952206

  8. ARCTIS — A MATLAB® Toolbox for Archaeological Imaging Spectroscopy

    Directory of Open Access Journals (Sweden)

    Clement Atzberger

    2014-09-01

    Full Text Available Imaging spectroscopy acquires imagery in hundreds or more narrow contiguous spectral bands. This offers unprecedented information for archaeological research. To extract the maximum of useful archaeological information from it, however, a number of problems have to be solved. Major problems relate to data redundancy and the visualization of the large amount of data. This makes data mining approaches necessary, as well as efficient data visualization tools. Additional problems relate to data quality. Indeed, the upwelling electromagnetic radiation is recorded in small spectral bands that are only about ten nanometers wide. The signal received by the sensor is, thus quite low compared to sensor noise and possible atmospheric perturbations. The often small, instantaneous field of view (IFOV—essential for archaeologically relevant imaging spectrometer datasets—further limits the useful signal stemming from the ground. The combination of both effects makes radiometric smoothing techniques mandatory. The present study details the functionality of a MATLAB®-based toolbox, called ARCTIS (ARChaeological Toolbox for Imaging Spectroscopy, for filtering, enhancing, analyzing, and visualizing imaging spectrometer datasets. The toolbox addresses the above-mentioned problems. Its Graphical User Interface (GUI is designed to allow non-experts in remote sensing to extract a wealth of information from imaging spectroscopy for archaeological research. ARCTIS will be released under creative commons license, free of charge, via website (http://luftbildarchiv.univie.ac.at.

  9. ERPLAB: An Open-Source Toolbox for the Analysis of Event-Related Potentials

    Directory of Open Access Journals (Sweden)

    Javier eLopez-Calderon

    2014-04-01

    Full Text Available ERPLAB Toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (ERP data in the MATLAB environment. ERPLAB is closely integrated with EEGLAB, a popular open-source toolbox that provides many EEG preprocessing steps and an excellent user interface design. ERPLAB adds to EEGLAB’s EEG processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. ERPLAB also provides robust tools for averaging EEG segments together to create averaged ERPs, for creating difference waves and other recombinations of ERP waveforms through algebraic expressions, for filtering and re-referencing the averaged ERPs, for plotting ERP waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. ERPLAB’s tools can be accessed either from an easy-to-learn graphical user interface or from MATLAB scripts, and a command history function makes it easy for users with no programming experience to write scripts. Consequently, ERPLAB provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex ERP experiments. Several forms of documentation are available, including a detailed user’s guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations.

  10. Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving-vessel ADCP measurements

    Science.gov (United States)

    Parsons, D.R.; Jackson, P.R.; Czuba, J.A.; Engel, F.L.; Rhoads, B.L.; Oberg, K.A.; Best, J.L.; Mueller, D.S.; Johnson, K.K.; Riley, J.D.

    2013-01-01

    The use of acoustic Doppler current profilers (ADCP) for discharge measurements and three-dimensional flow mapping has increased rapidly in recent years and has been primarily driven by advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross-section vector and contouring), and analysis of a range of ADCP-derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open-source code along with this publication.

  11. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 2: Line Segments Linking and Merging

    Directory of Open Access Journals (Sweden)

    Mehdi Rahnama

    2014-11-01

    Full Text Available Extraction and interpretation of tectonic lineaments is one of the routines for mapping large areas using remote sensing data. However, this is a subjective and time-consuming process. It is difficult to choose an optimal lineament extraction method in order to reduce subjectivity and obtain vectors similar to what an analyst would manually extract. The objective of this study is the implementation, evaluation and comparison of Hough transform, segment merging and polynomial fitting methods towards automated tectonic lineament mapping. For this purpose we developed a new MATLAB-based toolbox (TecLines. The proposed toolbox capabilities were validated using a synthetic Digital Elevation Model (DEM and tested along in the Andarab fault zone (Afghanistan where specific fault structures are known. In this study, we used filters in both frequency and spatial domains and the tensor voting framework to produce binary edge maps. We used the Hough transform to extract linear image discontinuities. We used B-spline as a polynomial curve fitting method to eliminate artificial line segments that are out of interest and to link discontinuous segments with similar trends. We performed statistical analyses in order to compare the final image discontinuities maps with existing references map.

  12. National Institutes of Health Toolbox Emotion Battery for English- and Spanish-speaking adults: normative data and factor-based summary scores.

    Science.gov (United States)

    Babakhanyan, Ida; McKenna, Benjamin S; Casaletto, Kaitlin B; Nowinski, Cindy J; Heaton, Robert K

    2018-01-01

    The National Institutes of Health Toolbox Emotion Battery (NIHTB-EB) is a "common currency", computerized assessment developed to measure the full spectrum of emotional health. Though comprehensive, the NIHTB-EB's 17 scales may be unwieldy for users aiming to capture more global indices of emotional functioning. NIHTB-EB was administered to 1,036 English-speaking and 408 Spanish-speaking adults as a part of the NIH Toolbox norming project. We examined the factor structure of the NIHTB-EB in English- and Spanish-speaking adults and developed factor analysis-based summary scores. Census-weighted norms were presented for English speakers, and sample-weighted norms were presented for Spanish speakers. Exploratory factor analysis for both English- and Spanish-speaking cohorts resulted in the same 3-factor solution: 1) negative affect, 2) social satisfaction, and 3) psychological well-being. Confirmatory factor analysis supported similar factor structures for English- and Spanish-speaking cohorts. Model fit indices fell within the acceptable/good range, and our final solution was optimal compared to other solutions. Summary scores based upon the normative samples appear to be psychometrically supported and should be applied to clinical samples to further validate the factor structures and investigate rates of problematic emotions in medical and psychiatric populations.

  13. The Cementitious Barriers Partnership (CBP) Software Toolbox Capabilities in Assessing the Degradation of Cementitious Barriers - 13487

    Energy Technology Data Exchange (ETDEWEB)

    Flach, G.P.; Burns, H.H.; Langton, C.; Smith, F.G. III [Savannah River National Laboratory, Savannah River Site, Aiken SC 29808 (United States); Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S. [Vanderbilt University, Nashville, TN (United States); Van der Sloot, H. [Hans Van der Sloot Consultancy (Netherlands); Meeussen, J.C.L. [Nuclear Research and Consultancy Group, Petten (Netherlands); Samson, E. [SIMCO Technologies Inc., 1400, boul. du Parc-Technologique, Suite 203, Quebec (Canada); Mallick, P.; Suttora, L. [United States Department of Energy, 1000 Independence Ave. SW, Washington, DC (United States); Esh, D.W.; Fuhrmann, M.J.; Philip, J. [U.S. Nuclear Regulatory Commission, Washington, DC (United States)

    2013-07-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste and Nuclear Materials Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to 100 years and longer for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox has produced tangible benefits to the DOE Performance Assessment (PA) community. A review of prior DOE PAs has provided a list of potential opportunities for improving cementitious barrier performance predictions through the use of the CBP software tools. These opportunities include: 1) impact of atmospheric exposure to concrete and grout before closure, such as accelerated slag and Tc-99 oxidation, 2) prediction of changes in K{sub d}/mobility as a function of time that result from changing pH and redox conditions, 3) concrete degradation from rebar corrosion due to carbonation, 4) early age cracking from drying and/or thermal shrinkage and 5) degradation due to sulfate attack. The CBP has already had opportunity to provide near-term, tangible support to ongoing DOE-EM PAs such as the Savannah River Saltstone Disposal Facility (SDF) by providing a sulfate attack analysis that predicts the extent and damage that sulfate ingress will have on the concrete vaults over extended time (i.e., > 1000 years). This analysis is one of the many technical opportunities in cementitious barrier performance that can be addressed by the DOE-EM sponsored CBP

  14. The Cementitious Barriers Partnership (CBP) Software Toolbox Capabilities In Assessing The Degradation Of Cementitious Barriers

    Energy Technology Data Exchange (ETDEWEB)

    Flach, G. P. [Savannah River Site (SRS), Aiken, SC (United States); Burns, H. H. [Savannah River Site (SRS), Aiken, SC (United States); Langton, C. [Savannah River Site (SRS), Aiken, SC (United States); Smith, F. G. III [Savannah River Site (SRS), Aiken, SC (United States); Brown, K. G. [Vanderbilt University, Nashville, TN (United States); Kosson, D. S. [Vanderbilt University, Nashville, TN (United States); Garrabrants, A. C. [Vanderbilt University, Nashville, TN (United States); Sarkar, S. [Vanderbilt University, Nashville, TN (United States); van der Sloot, H. [Hans van der Sloot Consultancy (The Netherlands); Meeussen, J. C.L. [Nuclear Research and Consultancy Group, Petten (The Netherlands); Samson, E. [SIMCO Technologies Inc. , 1400, boul. du Parc - Technologique , Suite 203, Quebec (Canada); Mallick, P. [United States Department of Energy, 1000 Independence Ave. SW , Washington, DC (United States); Suttora, L. [United States Department of Energy, 1000 Independence Ave. SW , Washington, DC (United States); Esh, D. W. [U .S. Nuclear Regulatory Commission , Washington, DC (United States); Fuhrmann, M. J. [U .S. Nuclear Regulatory Commission , Washington, DC (United States); Philip, J. [U .S. Nuclear Regulatory Commission , Washington, DC (United States)

    2013-01-11

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste and Nuclear Materials Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to 100 years and longer for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox has produced tangible benefits to the DOE Performance Assessment (PA) community. A review of prior DOE PAs has provided a list of potential opportunities for improving cementitious barrier performance predictions through the use of the CBP software tools. These opportunities include: 1) impact of atmospheric exposure to concrete and grout before closure, such as accelerated slag and Tc-99 oxidation, 2) prediction of changes in Kd/mobility as a function of time that result from changing pH and redox conditions, 3) concrete degradation from rebar corrosion due to carbonation, 4) early age cracking from drying and/or thermal shrinkage and 5) degradation due to sulfate attack. The CBP has already had opportunity to provide near-term, tangible support to ongoing DOE-EM PAs such as the Savannah River Saltstone Disposal Facility (SDF) by providing a sulfate attack analysis that predicts the extent and damage that sulfate ingress will have on the concrete vaults over extended time (i.e., > 1000 years). This analysis is one of the many technical opportunities in cementitious barrier performance that can be addressed by the DOE-EM sponsored CBP software

  15. A Python Software Toolbox for the Analysis of SO2 Camera Data. Implications in Geosciences

    Directory of Open Access Journals (Sweden)

    Jonas Gliß

    2017-12-01

    Full Text Available Ultraviolet (UV SO2 cameras have become a common tool to measure and monitor SO2 emission rates, mostly from volcanoes but also from anthropogenic sources (e.g., power plants or ships. Over the past decade, the analysis of UV SO2 camera data has seen many improvements. As a result, for many of the required analysis steps, several alternatives exist today (e.g., cell vs. DOAS based camera calibration; optical flow vs. cross-correlation based gas-velocity retrieval. This inspired the development of Pyplis (Python plume imaging software, an open-source software toolbox written in Python 2.7, which unifies the most prevalent methods from literature within a single, cross-platform analysis framework. Pyplis comprises a vast collection of algorithms relevant for the analysis of UV SO2 camera data. These include several routines to retrieve plume background radiances as well as routines for cell and DOAS based camera calibration. The latter includes two independent methods to identify the DOAS field-of-view (FOV within the camera images (based on (1 Pearson correlation and (2 IFR inversion method. Plume velocities can be retrieved using an optical flow algorithm as well as signal cross-correlation. Furthermore, Pyplis includes a routine to perform a first order correction of the signal dilution effect (also referred to as light dilution. All required geometrical calculations are performed within a 3D model environment allowing for distance retrievals to plume and local terrain features on a pixel basis. SO2 emission rates can be retrieved simultaneously for an arbitrary number of plume intersections. Hence, Pyplis provides a state-of-the-art framework for more efficient and flexible analyses of UV SO2 camera data and, therefore, marks an important step forward towards more transparency, reliability and inter-comparability of the results. Pyplis has been extensively and successfully tested using data from several field campaigns. Here, the main features

  16. GCE Data Toolbox for MATLAB - a software framework for automating environmental data processing, quality control and documentation

    Science.gov (United States)

    Sheldon, W.; Chamblee, J.; Cary, R. H.

    2013-12-01

    developing automated workflows for unattended processing. Finalized data and structured metadata can be exported in a wide variety of text and MATLAB formats or uploaded to a relational database for long-term archiving and distribution. The GCE Data Toolbox can be used as a complete, light-weight solution for environmental data and metadata management, but it can also be used in conjunction with other cyber infrastructure to provide a more comprehensive solution. For example, newly acquired data can be retrieved from a Data Turbine or Campbell LoggerNet Database server for quality control and processing, then transformed to CUAHSI Observations Data Model format and uploaded to a HydroServer for distribution through the CUAHSI Hydrologic Information System. The GCE Data Toolbox can also be leveraged in analytical workflows developed using Kepler or other systems that support MATLAB integration or tool chaining. This software can therefore be leveraged in many ways to help researchers manage, analyze and distribute the data they collect.

  17. PyCoTools: A Python Toolbox for COPASI.

    Science.gov (United States)

    Welsh, Ciaran M; Fullard, Nicola; Proctor, Carole J; Martinez-Guimera, Alvaro; Isfort, Robert J; Bascom, Charles C; Tasseff, Ryan; Przyborski, Stefan A; Shanley, Daryl P

    2018-05-22

    COPASI is an open source software package for constructing, simulating and analysing dynamic models of biochemical networks. COPASI is primarily intended to be used with a graphical user interface but often it is desirable to be able to access COPASI features programmatically, with a high level interface. PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. PyCoTools enables the construction of COPASI models and the execution of a subset of COPASI tasks including time courses, parameter scans and parameter estimations. Additional 'composite' tasks which use COPASI tasks as building blocks are available for increasing parameter estimation throughput, performing identifiability analysis and performing model selection. PyCoTools supports exploratory data analysis on parameter estimation data to assist with troubleshooting model calibrations. We demonstrate PyCoTools by posing a model selection problem designed to show case PyCoTools within a realistic scenario. The aim of the model selection problem is to test the feasibility of three alternative hypotheses in explaining experimental data derived from neonatal dermal fibroblasts in response to TGF-β over time. PyCoTools is used to critically analyse the parameter estimations and propose strategies for model improvement. PyCoTools can be downloaded from the Python Package Index (PyPI) using the command 'pip install pycotools' or directly from GitHub (https://github.com/CiaranWelsh/pycotools). Documentation at http://pycotools.readthedocs.io. Supplementary data are available at Bioinformatics.

  18. Toolbox for Research, or how to facilitate a central data management in small-scale research projects.

    Science.gov (United States)

    Bialke, Martin; Rau, Henriette; Thamm, Oliver C; Schuldt, Ronny; Penndorf, Peter; Blumentritt, Arne; Gött, Robert; Piegsa, Jens; Bahls, Thomas; Hoffmann, Wolfgang

    2018-01-25

    In most research projects budget, staff and IT infrastructures are limiting resources. Especially for small-scale registries and cohort studies professional IT support and commercial electronic data capture systems are too expensive. Consequently, these projects use simple local approaches (e.g. Excel) for data capture instead of a central data management including web-based data capture and proper research databases. This leads to manual processes to merge, analyze and, if possible, pseudonymize research data of different study sites. To support multi-site data capture, storage and analyses in small-scall research projects, corresponding requirements were analyzed within the MOSAIC project. Based on the identified requirements, the Toolbox for Research was developed as a flexible software solution for various research scenarios. Additionally, the Toolbox facilitates data integration of research data as well as metadata by performing necessary procedures automatically. Also, Toolbox modules allow the integration of device data. Moreover, separation of personally identifiable information and medical data by using only pseudonyms for storing medical data ensures the compliance to data protection regulations. This pseudonymized data can then be exported in SPSS format in order to enable scientists to prepare reports and analyses. The Toolbox for Research was successfully piloted in the German Burn Registry in 2016 facilitating the documentation of 4350 burn cases at 54 study sites. The Toolbox for Research can be downloaded free of charge from the project website and automatically installed due to the use of Docker technology.

  19. PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory.

    Science.gov (United States)

    Niknam, Niloofar; Khakzad, Hamed; Arab, Seyed Shahriar; Naderi-Manesh, Hossein

    2016-05-01

    The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis.

    Science.gov (United States)

    Delorme, Arnaud; Makeig, Scott

    2004-03-15

    We have developed a toolbox and graphic user interface, EEGLAB, running under the crossplatform MATLAB environment (The Mathworks, Inc.) for processing collections of single-trial and/or averaged EEG data of any number of channels. Available functions include EEG data, channel and event information importing, data visualization (scrolling, scalp map and dipole model plotting, plus multi-trial ERP-image plots), preprocessing (including artifact rejection, filtering, epoch selection, and averaging), independent component analysis (ICA) and time/frequency decompositions including channel and component cross-coherence supported by bootstrap statistical methods based on data resampling. EEGLAB functions are organized into three layers. Top-layer functions allow users to interact with the data through the graphic interface without needing to use MATLAB syntax. Menu options allow users to tune the behavior of EEGLAB to available memory. Middle-layer functions allow users to customize data processing using command history and interactive 'pop' functions. Experienced MATLAB users can use EEGLAB data structures and stand-alone signal processing functions to write custom and/or batch analysis scripts. Extensive function help and tutorial information are included. A 'plug-in' facility allows easy incorporation of new EEG modules into the main menu. EEGLAB is freely available (http://www.sccn.ucsd.edu/eeglab/) under the GNU public license for noncommercial use and open source development, together with sample data, user tutorial and extensive documentation.

  1. Multi-hazard Assessment and Scenario Toolbox (MhAST): A Framework for Analyzing Compounding Effects of Multiple Hazards

    Science.gov (United States)

    Sadegh, M.; Moftakhari, H.; AghaKouchak, A.

    2017-12-01

    Many natural hazards are driven by multiple forcing variables, and concurrence/consecutive extreme events significantly increases risk of infrastructure/system failure. It is a common practice to use univariate analysis based upon a perceived ruling driver to estimate design quantiles and/or return periods of extreme events. A multivariate analysis, however, permits modeling simultaneous occurrence of multiple forcing variables. In this presentation, we introduce the Multi-hazard Assessment and Scenario Toolbox (MhAST) that comprehensively analyzes marginal and joint probability distributions of natural hazards. MhAST also offers a wide range of scenarios of return period and design levels and their likelihoods. Contribution of this study is four-fold: 1. comprehensive analysis of marginal and joint probability of multiple drivers through 17 continuous distributions and 26 copulas, 2. multiple scenario analysis of concurrent extremes based upon the most likely joint occurrence, one ruling variable, and weighted random sampling of joint occurrences with similar exceedance probabilities, 3. weighted average scenario analysis based on a expected event, and 4. uncertainty analysis of the most likely joint occurrence scenario using a Bayesian framework.

  2. The Self-Powered Detector Simulation `MATiSSe' Toolbox applied to SPNDs for severe accident monitoring in PWRs

    Science.gov (United States)

    Barbot, Loïc; Villard, Jean-François; Fourrez, Stéphane; Pichon, Laurent; Makil, Hamid

    2018-01-01

    In the framework of the French National Research Agency program on nuclear safety and radioprotection, the `DIstributed Sensing for COrium Monitoring and Safety' project aims at developing innovative instrumentation for corium monitoring in case of severe accident in a Pressurized Water nuclear Reactor. Among others, a new under-vessel instrumentation based on Self-Powered Neutron Detectors is developed using a numerical simulation toolbox, named `MATiSSe'. The CEA Instrumentation Sensors and Dosimetry Lab developed MATiSSe since 2010 for Self-Powered Neutron Detectors material selection and geometry design, as well as for their respective partial neutron and gamma sensitivity calculations. MATiSSe is based on a comprehensive model of neutron and gamma interactions which take place in Selfpowered neutron detector components using the MCNP6 Monte Carlo code. As member of the project consortium, the THERMOCOAX SAS Company is currently manufacturing some instrumented pole prototypes to be tested in 2017. The full severe accident monitoring equipment, including the standalone low current acquisition system, will be tested during a joined CEA-THERMOCOAX experimental campaign in some realistic irradiation conditions, in the Slovenian TRIGA Mark II research reactor.

  3. HERMES: towards an integrated toolbox to characterize functional and effective brain connectivity.

    Science.gov (United States)

    Niso, Guiomar; Bruña, Ricardo; Pereda, Ernesto; Gutiérrez, Ricardo; Bajo, Ricardo; Maestú, Fernando; del-Pozo, Francisco

    2013-10-01

    The analysis of the interdependence between time series has become an important field of research in the last years, mainly as a result of advances in the characterization of dynamical systems from the signals they produce, the introduction of concepts such as generalized and phase synchronization and the application of information theory to time series analysis. In neurophysiology, different analytical tools stemming from these concepts have added to the 'traditional' set of linear methods, which includes the cross-correlation and the coherency function in the time and frequency domain, respectively, or more elaborated tools such as Granger Causality.This increase in the number of approaches to tackle the existence of functional (FC) or effective connectivity (EC) between two (or among many) neural networks, along with the mathematical complexity of the corresponding time series analysis tools, makes it desirable to arrange them into a unified-easy-to-use software package. The goal is to allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of these analysis methods from a single integrated toolbox.Here we present HERMES ( http://hermes.ctb.upm.es ), a toolbox for the Matlab® environment (The Mathworks, Inc), which is designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. We believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

  4. MagPy: A Python toolbox for controlling Magstim transcranial magnetic stimulators.

    Science.gov (United States)

    McNair, Nicolas A

    2017-01-30

    To date, transcranial magnetic stimulation (TMS) studies manipulating stimulation parameters have largely used blocked paradigms. However, altering these parameters on a trial-by-trial basis in Magstim stimulators is complicated by the need to send regular (1Hz) commands to the stimulator. Additionally, effecting such control interferes with the ability to send TMS pulses or simultaneously present stimuli with high-temporal precision. This manuscript presents the MagPy toolbox, a Python software package that provides full control over Magstim stimulators via the serial port. It is able to maintain this control with no impact on concurrent processing, such as stimulus delivery. In addition, a specially-designed "QuickFire" serial cable is specified that allows MagPy to trigger TMS pulses with very low-latency. In a series of experimental simulations, MagPy was able to maintain uninterrupted remote control over the connected Magstim stimulator across all testing sessions. In addition, having MagPy enabled had no effect on stimulus timing - all stimuli were presented for precisely the duration specified. Finally, using the QuickFire cable, MagPy was able to elicit TMS pulses with sub-millisecond latencies. The MagPy toolbox allows for experiments that require manipulating stimulation parameters from trial to trial. Furthermore, it can achieve this in contexts that require tight control over timing, such as those seeking to combine TMS with fMRI or EEG. Together, the MagPy toolbox and QuickFire serial cable provide an effective means for controlling Magstim stimulators during experiments while ensuring high-precision timing. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. PETPVC: a toolbox for performing partial volume correction techniques in positron emission tomography

    Science.gov (United States)

    Thomas, Benjamin A.; Cuplov, Vesna; Bousse, Alexandre; Mendes, Adriana; Thielemans, Kris; Hutton, Brian F.; Erlandsson, Kjell

    2016-11-01

    Positron emission tomography (PET) images are degraded by a phenomenon known as the partial volume effect (PVE). Approaches have been developed to reduce PVEs, typically through the utilisation of structural information provided by other imaging modalities such as MRI or CT. These methods, known as partial volume correction (PVC) techniques, reduce PVEs by compensating for the effects of the scanner resolution, thereby improving the quantitative accuracy. The PETPVC toolbox described in this paper comprises a suite of methods, both classic and more recent approaches, for the purposes of applying PVC to PET data. Eight core PVC techniques are available. These core methods can be combined to create a total of 22 different PVC techniques. Simulated brain PET data are used to demonstrate the utility of toolbox in idealised conditions, the effects of applying PVC with mismatched point-spread function (PSF) estimates and the potential of novel hybrid PVC methods to improve the quantification of lesions. All anatomy-based PVC techniques achieve complete recovery of the PET signal in cortical grey matter (GM) when performed in idealised conditions. Applying deconvolution-based approaches results in incomplete recovery due to premature termination of the iterative process. PVC techniques are sensitive to PSF mismatch, causing a bias of up to 16.7% in GM recovery when over-estimating the PSF by 3 mm. The recovery of both GM and a simulated lesion was improved by combining two PVC techniques together. The PETPVC toolbox has been written in C++, supports Windows, Mac and Linux operating systems, is open-source and publicly available.

  6. FACET - a "Flexible Artifact Correction and Evaluation Toolbox" for concurrently recorded EEG/fMRI data.

    Science.gov (United States)

    Glaser, Johann; Beisteiner, Roland; Bauer, Herbert; Fischmeister, Florian Ph S

    2013-11-09

    In concurrent EEG/fMRI recordings, EEG data are impaired by the fMRI gradient artifacts which exceed the EEG signal by several orders of magnitude. While several algorithms exist to correct the EEG data, these algorithms lack the flexibility to either leave out or add new steps. The here presented open-source MATLAB toolbox FACET is a modular toolbox for the fast and flexible correction and evaluation of imaging artifacts from concurrently recorded EEG datasets. It consists of an Analysis, a Correction and an Evaluation framework allowing the user to choose from different artifact correction methods with various pre- and post-processing steps to form flexible combinations. The quality of the chosen correction approach can then be evaluated and compared to different settings. FACET was evaluated on a dataset provided with the FMRIB plugin for EEGLAB using two different correction approaches: Averaged Artifact Subtraction (AAS, Allen et al., NeuroImage 12(2):230-239, 2000) and the FMRI Artifact Slice Template Removal (FASTR, Niazy et al., NeuroImage 28(3):720-737, 2005). Evaluation of the obtained results were compared to the FASTR algorithm implemented in the EEGLAB plugin FMRIB. No differences were found between the FACET implementation of FASTR and the original algorithm across all gradient artifact relevant performance indices. The FACET toolbox not only provides facilities for all three modalities: data analysis, artifact correction as well as evaluation and documentation of the results but it also offers an easily extendable framework for development and evaluation of new approaches.

  7. Using a Toolbox of Tailored Educational Lessons to Improve Fruit, Vegetable, and Physical Activity Behaviors among African American Women in California

    Science.gov (United States)

    Backman, Desiree; Scruggs, Valarie; Atiedu, Akpene Ama; Bowie, Shene; Bye, Larry; Dennis, Angela; Hall, Melanie; Ossa, Alexandra; Wertlieb, Stacy; Foerster, Susan B.

    2011-01-01

    Objective: Evaluate the effectiveness of the "Fruit, Vegetable, and Physical Activity Toolbox for Community Educators" ("Toolbox"), an intervention originally designed for Spanish- and English-speaking audiences, in changing knowledge, attitudes, and behavior among low-income African American women. Design: Quasi-experimental…

  8. Process Evaluation of a Toolbox-training Program for Construction Foremen in Denmark

    DEFF Research Database (Denmark)

    Jeschke, Katharina Christiane; Kines, Pete; Rasmussen, Liselotte

    2017-01-01

    for the majority of the foremen, who experienced positive changes in their daily work methods and interactions with their crews, colleagues, leaders, customers and other construction professions. The program is a unique contribution to leadership training in the construction industry, and can potentially......Daily dialogue between leaders and workers on traditional construction sites is primarily focused on production, quality and time issues, and rarely involves occupational safety and health (OSH) issues. A leadership training program entitled 'Toolbox-training' was developed to improve construction...

  9. ACCEPT: Introduction of the Adverse Condition and Critical Event Prediction Toolbox

    Science.gov (United States)

    Martin, Rodney A.; Santanu, Das; Janakiraman, Vijay Manikandan; Hosein, Stefan

    2015-01-01

    The prediction of anomalies or adverse events is a challenging task, and there are a variety of methods which can be used to address the problem. In this paper, we introduce a generic framework developed in MATLAB (sup registered mark) called ACCEPT (Adverse Condition and Critical Event Prediction Toolbox). ACCEPT is an architectural framework designed to compare and contrast the performance of a variety of machine learning and early warning algorithms, and tests the capability of these algorithms to robustly predict the onset of adverse events in any time-series data generating systems or processes.

  10. Recent advances of molecular toolbox construction expand Pichia pastoris in synthetic biology applications.

    Science.gov (United States)

    Kang, Zhen; Huang, Hao; Zhang, Yunfeng; Du, Guocheng; Chen, Jian

    2017-01-01

    Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P. pastoris. Furthermore, the applications of P. pastoris towards synthetic biology were also discussed and prospected especially in the context of genome-scale metabolic pathway analysis.

  11. Cognitive functioning in socially anxious adults: Insights from the NIH Toolbox Cognition Battery

    Directory of Open Access Journals (Sweden)

    Sonya Violet Troller-Renfree

    2015-06-01

    Full Text Available Theory suggests that individuals with social anxiety manifest unique patterns of cognition with less efficient fluid cognition and unperturbed crystallized cognition; however, empirical support for these ideas remains inconclusive. The heterogeneity of past findings may reflect unreliability in cognitive assessments or the influence of confounding variables. The present study examined the relations among social anxiety and performance on the reliable, newly established NIH Toolbox Cognition Battery. Results indicate that high socially anxious adults performed as well as low anxious participants on all measures of fluid cognition. However, highly socially anxious adults demonstrated enhanced crystallized cognitive abilities relative to a low socially anxious comparison group.

  12. An educational model for ensemble streamflow simulation and uncertainty analysis

    Directory of Open Access Journals (Sweden)

    A. AghaKouchak

    2013-02-01

    Full Text Available This paper presents the hands-on modeling toolbox, HBV-Ensemble, designed as a complement to theoretical hydrology lectures, to teach hydrological processes and their uncertainties. The HBV-Ensemble can be used for in-class lab practices and homework assignments, and assessment of students' understanding of hydrological processes. Using this modeling toolbox, students can gain more insights into how hydrological processes (e.g., precipitation, snowmelt and snow accumulation, soil moisture, evapotranspiration and runoff generation are interconnected. The educational toolbox includes a MATLAB Graphical User Interface (GUI and an ensemble simulation scheme that can be used for teaching uncertainty analysis, parameter estimation, ensemble simulation and model sensitivity. HBV-Ensemble was administered in a class for both in-class instruction and a final project, and students submitted their feedback about the toolbox. The results indicate that this educational software had a positive impact on students understanding and knowledge of uncertainty in hydrological modeling.

  13. PM Synchronous Motor Dynamic Modeling with Genetic Algorithm ...

    African Journals Online (AJOL)

    Adel

    This paper proposes dynamic modeling simulation for ac Surface Permanent Magnet Synchronous ... Simulations are implemented using MATLAB with its genetic algorithm toolbox. .... selection, the process that drives biological evolution.

  14. LESTO: an Open Source GIS-based toolbox for LiDAR analysis

    Science.gov (United States)

    Franceschi, Silvia; Antonello, Andrea; Tonon, Giustino

    2015-04-01

    During the last five years different research institutes and private companies stared to implement new algorithms to analyze and extract features from LiDAR data but only a few of them also created a public available software. In the field of forestry there are different examples of software that can be used to extract the vegetation parameters from LiDAR data, unfortunately most of them are closed source (even if free), which means that the source code is not shared with the public for anyone to look at or make changes to. In 2014 we started the development of the library LESTO (LiDAR Empowered Sciences Toolbox Opensource): a set of modules for the analysis of LiDAR point cloud with an Open Source approach with the aim of improving the performance of the extraction of the volume of biomass and other vegetation parameters on large areas for mixed forest structures. LESTO contains a set of modules for data handling and analysis implemented within the JGrassTools spatial processing library. The main subsections are dedicated to 1) preprocessing of LiDAR raw data mainly in LAS format (utilities and filtering); 2) creation of raster derived products; 3) flight-lines identification and normalization of the intensity values; 4) tools for extraction of vegetation and buildings. The core of the LESTO library is the extraction of the vegetation parameters. We decided to follow the single tree based approach starting with the implementation of some of the most used algorithms in literature. These have been tweaked and applied on LiDAR derived raster datasets (DTM, DSM) as well as point clouds of raw data. The methods range between the simple extraction of tops and crowns from local maxima, the region growing method, the watershed method and individual tree segmentation on point clouds. The validation procedure consists in finding the matching between field and LiDAR-derived measurements at individual tree and plot level. An automatic validation procedure has been developed

  15. Outcome quantification using SPHARM-PDM toolbox in orthognathic surgery

    Science.gov (United States)

    Cevidanes, Lucia; Zhu, HongTu; Styner, Martin

    2011-01-01

    Purpose Quantification of surgical outcomes in longitudinal studies has led to significant progress in the treatment of dentofacial deformity, both by offering options to patients who might not otherwise have been recommended for treatment and by clarifying the selection of appropriate treatment methods. Most existing surgical treatments have not been assessed in a systematic way. This paper presents the quantification of surgical outcomes in orthognathic surgery via our localized shape analysis framework. Methods In our setting, planning and surgical simulation is performed using the surgery planning software CMFapp. We then employ the SPHARM-PDM to measure the difference between pre-surgery and virtually simulated post-surgery models. This SPHARM-PDM shape framework is validated for use with craniofacial structures via simulating known 3D surgical changes within CMFapp. Results Our results show that SPHARM-PDM analysis accurately measures surgical displacements, compared with known displacement values. Visualization of color maps of virtually simulated surgical displacements describe corresponding surface distances that precisely describe location of changes, and difference vectors indicate directionality and magnitude of changes. Conclusions SPHARM-PDM-based quantification of surgical outcome is feasible. When compared to prior solutions, our method has the potential to make the surgical planning process more flexible, increase the level of detail and accuracy of the plan, yield higher operative precision and control and enhance the follow-up and documentation of clinical cases. PMID:21161693

  16. Yeast synthetic biology toolbox and applications for biofuel production.

    Science.gov (United States)

    Tsai, Ching-Sung; Kwak, Suryang; Turner, Timothy L; Jin, Yong-Su

    2015-02-01

    Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  17. Data processing and analysis with the autoPROC toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Vonrhein, Clemens, E-mail: vonrhein@globalphasing.com; Flensburg, Claus; Keller, Peter; Sharff, Andrew; Smart, Oliver; Paciorek, Wlodek; Womack, Thomas; Bricogne, Gérard [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom)

    2011-04-01

    Typical topics and problems encountered during data processing of diffraction experiments are discussed and the tools provided in the autoPROC software are described. A typical diffraction experiment will generate many images and data sets from different crystals in a very short time. This creates a challenge for the high-throughput operation of modern synchrotron beamlines as well as for the subsequent data processing. Novice users in particular may feel overwhelmed by the tables, plots and numbers that the different data-processing programs and software packages present to them. Here, some of the more common problems that a user has to deal with when processing a set of images that will finally make up a processed data set are shown, concentrating on difficulties that may often show up during the first steps along the path of turning the experiment (i.e. data collection) into a model (i.e. interpreted electron density). Difficulties such as unexpected crystal forms, issues in crystal handling and suboptimal choices of data-collection strategies can often be dealt with, or at least diagnosed, by analysing specific data characteristics during processing. In the end, one wants to distinguish problems over which one has no immediate control once the experiment is finished from problems that can be remedied a posteriori. A new software package, autoPROC, is also presented that combines third-party processing programs with new tools and an automated workflow script that is intended to provide users with both guidance and insight into the offline processing of data affected by the difficulties mentioned above, with particular emphasis on the automated treatment of multi-sweep data sets collected on multi-axis goniostats.

  18. PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

    Science.gov (United States)

    Huang, Huiyuan; Ding, Zhongxiang; Mao, Dewang; Yuan, Jianhua; Zhu, Fangmei; Chen, Shuda; Xu, Yan; Lou, Lin; Feng, Xiaoyan; Qi, Le; Qiu, Wusi; Zhang, Han; Zang, Yu-Feng

    2016-10-01

    The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy.

  19. KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis.

    Science.gov (United States)

    Hastreiter, Maximilian; Jeske, Tim; Hoser, Jonathan; Kluge, Michael; Ahomaa, Kaarin; Friedl, Marie-Sophie; Kopetzky, Sebastian J; Quell, Jan-Dominik; Mewes, H Werner; Küffner, Robert

    2017-05-15

    Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME. See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license). robert.kueffner@helmholtz-muenchen.de. Supplementary data are available at Bioinformatics online.

  20. PredPsych: A toolbox for predictive machine learning-based approach in experimental psychology research.

    Science.gov (United States)

    Koul, Atesh; Becchio, Cristina; Cavallo, Andrea

    2017-12-12

    Recent years have seen an increased interest in machine learning-based predictive methods for analyzing quantitative behavioral data in experimental psychology. While these methods can achieve relatively greater sensitivity compared to conventional univariate techniques, they still lack an established and accessible implementation. The aim of current work was to build an open-source R toolbox - "PredPsych" - that could make these methods readily available to all psychologists. PredPsych is a user-friendly, R toolbox based on machine-learning predictive algorithms. In this paper, we present the framework of PredPsych via the analysis of a recently published multiple-subject motion capture dataset. In addition, we discuss examples of possible research questions that can be addressed with the machine-learning algorithms implemented in PredPsych and cannot be easily addressed with univariate statistical analysis. We anticipate that PredPsych will be of use to researchers with limited programming experience not only in the field of psychology, but also in that of clinical neuroscience, enabling computational assessment of putative bio-behavioral markers for both prognosis and diagnosis.

  1. Integration of Lead Discovery Tactics and the Evolution of the Lead Discovery Toolbox.

    Science.gov (United States)

    Leveridge, Melanie; Chung, Chun-Wa; Gross, Jeffrey W; Phelps, Christopher B; Green, Darren

    2018-06-01

    There has been much debate around the success rates of various screening strategies to identify starting points for drug discovery. Although high-throughput target-based and phenotypic screening has been the focus of this debate, techniques such as fragment screening, virtual screening, and DNA-encoded library screening are also increasingly reported as a source of new chemical equity. Here, we provide examples in which integration of more than one screening approach has improved the campaign outcome and discuss how strengths and weaknesses of various methods can be used to build a complementary toolbox of approaches, giving researchers the greatest probability of successfully identifying leads. Among others, we highlight case studies for receptor-interacting serine/threonine-protein kinase 1 and the bromo- and extra-terminal domain family of bromodomains. In each example, the unique insight or chemistries individual approaches provided are described, emphasizing the synergy of information obtained from the various tactics employed and the particular question each tactic was employed to answer. We conclude with a short prospective discussing how screening strategies are evolving, what this screening toolbox might look like in the future, how to maximize success through integration of multiple tactics, and scenarios that drive selection of one combination of tactics over another.

  2. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  3. Robust Correlation Analyses: False Positive and Power Validation Using a New Open Source Matlab Toolbox

    Science.gov (United States)

    Pernet, Cyril R.; Wilcox, Rand; Rousselet, Guillaume A.

    2012-01-01

    Pearson’s correlation measures the strength of the association between two variables. The technique is, however, restricted to linear associations and is overly sensitive to outliers. Indeed, a single outlier can result in a highly inaccurate summary of the data. Yet, it remains the most commonly used measure of association in psychology research. Here we describe a free Matlab(R) based toolbox (http://sourceforge.net/projects/robustcorrtool/) that computes robust measures of association between two or more random variables: the percentage-bend correlation and skipped-correlations. After illustrating how to use the toolbox, we show that robust methods, where outliers are down weighted or removed and accounted for in significance testing, provide better estimates of the true association with accurate false positive control and without loss of power. The different correlation methods were tested with normal data and normal data contaminated with marginal or bivariate outliers. We report estimates of effect size, false positive rate and power, and advise on which technique to use depending on the data at hand. PMID:23335907

  4. SPP Toolbox: Supporting Sustainable Public Procurement in the Context of Socio-Technical Transitions

    Directory of Open Access Journals (Sweden)

    Paula Cayolla Trindade

    2017-12-01

    Full Text Available Public procurement can shape production and consumption trends and represents a stimulus for both innovation and diversification in products and services, through a direct increase in demand. In recent years, the interest in demand-side policies has grown and several approaches have emerged, such as Green Public Procurement (GPP, Sustainable Public Procurement (SPP and Public Procurement of Innovation (PPI, representing strategic goals to be achieved through public procurement. In this context, there is a need to guide and support public organizations in the uptake of GPP, SPP and PPI practices. To respond to the challenges raised by the operationalization of such strategies, this paper proposes a new tool—the SPP Toolbox—for guiding public organizations as they re-think the procurement process, raising their ambitions and broadening their vision, thus changing the organizational approach towards culture, strategies, structures and practices. This toolbox integrates insights from GPP, SPP and PPI objectives and practices, in the context of the emergence of socio-technical transitions. The toolbox coherently links GPP, SPP and PPI, allowing flexibility in terms of goals, yet promoting an increasing complexity of institutionalized practices and skills—from GPP to SPP and then from SPP to PPI, organized in a framework fully integrated into the organizational strategy.

  5. Robust correlation analyses: false positive and power validation using a new open source matlab toolbox.

    Science.gov (United States)

    Pernet, Cyril R; Wilcox, Rand; Rousselet, Guillaume A

    2012-01-01

    Pearson's correlation measures the strength of the association between two variables. The technique is, however, restricted to linear associations and is overly sensitive to outliers. Indeed, a single outlier can result in a highly inaccurate summary of the data. Yet, it remains the most commonly used measure of association in psychology research. Here we describe a free Matlab((R)) based toolbox (http://sourceforge.net/projects/robustcorrtool/) that computes robust measures of association between two or more random variables: the percentage-bend correlation and skipped-correlations. After illustrating how to use the toolbox, we show that robust methods, where outliers are down weighted or removed and accounted for in significance testing, provide better estimates of the true association with accurate false positive control and without loss of power. The different correlation methods were tested with normal data and normal data contaminated with marginal or bivariate outliers. We report estimates of effect size, false positive rate and power, and advise on which technique to use depending on the data at hand.

  6. BOLDSync: a MATLAB-based toolbox for synchronized stimulus presentation in functional MRI.

    Science.gov (United States)

    Joshi, Jitesh; Saharan, Sumiti; Mandal, Pravat K

    2014-02-15

    Precise and synchronized presentation of paradigm stimuli in functional magnetic resonance imaging (fMRI) is central to obtaining accurate information about brain regions involved in a specific task. In this manuscript, we present a new MATLAB-based toolbox, BOLDSync, for synchronized stimulus presentation in fMRI. BOLDSync provides a user friendly platform for design and presentation of visual, audio, as well as multimodal audio-visual (AV) stimuli in functional imaging experiments. We present simulation experiments that demonstrate the millisecond synchronization accuracy of BOLDSync, and also illustrate the functionalities of BOLDSync through application to an AV fMRI study. BOLDSync gains an advantage over other available proprietary and open-source toolboxes by offering a user friendly and accessible interface that affords both precision in stimulus presentation and versatility across various types of stimulus designs and system setups. BOLDSync is a reliable, efficient, and versatile solution for synchronized stimulus presentation in fMRI study. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. A Toolbox of Genetically Encoded FRET-Based Biosensors for Rapid l-Lysine Analysis

    Directory of Open Access Journals (Sweden)

    Victoria Steffen

    2016-09-01

    Full Text Available Background: The fast development of microbial production strains for basic and fine chemicals is increasingly carried out in small scale cultivation systems to allow for higher throughput. Such parallelized systems create a need for new rapid online detection systems to quantify the respective target compound. In this regard, biosensors, especially genetically encoded Förster resonance energy transfer (FRET-based biosensors, offer tremendous opportunities. As a proof-of-concept, we have created a toolbox of FRET-based biosensors for the ratiometric determination of l-lysine in fermentation broth. Methods: The sensor toolbox was constructed based on a sensor that consists of an optimized central lysine-/arginine-/ornithine-binding protein (LAO-BP flanked by two fluorescent proteins (enhanced cyan fluorescent protein (ECFP, Citrine. Further sensor variants with altered affinity and sensitivity were obtained by circular permutation of the binding protein as well as the introduction of flexible and rigid linkers between the fluorescent proteins and the LAO-BP, respectively. Results: The sensor prototype was applied to monitor the extracellular l-lysine concentration of the l-lysine producing Corynebacterium glutamicum (C. glutamicum strain DM1933 in a BioLector® microscale cultivation device. The results matched well with data obtained by HPLC analysis and the Ninhydrin assay, demonstrating the high potential of FRET-based biosensors for high-throughput microbial bioprocess optimization.

  8. Sentinel-3 SAR Altimetry Toolbox - Scientific Exploitation of Operational Missions (SEOM) Program Element

    Science.gov (United States)

    Benveniste, Jérôme; Lucas, Bruno; Dinardo, Salvatore

    2014-05-01

    The prime objective of the SEOM (Scientific Exploitation of Operational Missions) element is to federate, support and expand the large international research community that the ERS, ENVISAT and the Envelope programmes have build up over the last 20 years for the future European operational Earth Observation missions, the Sentinels. Sentinel-3 builds directly on a proven heritage pioneered by ERS-1, ERS-2, Envisat and CryoSat-2, with a dual-frequency (Ku and C band) advanced Synthetic Aperture Radar Altimeter (SRAL) that provides measurements at a resolution of ~300m in SAR mode along track. Sentinel-3 will provide exact measurements of sea-surface height along with accurate topography measurements over sea ice, ice sheets, rivers and lakes. The first of the Sentinel-3 series is planned for launch in early 2015. The current universal altimetry toolbox is BRAT (Basic Radar Altimetry Toolbox) which can read all previous and current altimetry mission's data, but it does not have the capabilities to read the upcoming Sentinel-3 L1 and L2 products. ESA will endeavour to develop and supply this capability to support the users of the future Sentinel-3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales, the French Space Agency), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats, the BratGUI is the front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as net

  9. Various Solution Methods, Accompanied by Dynamic Investigation, for the Same Problem as a Means for Enriching the Mathematical Toolbox

    Science.gov (United States)

    Oxman, Victor; Stupel, Moshe

    2018-01-01

    A geometrical task is presented with multiple solutions using different methods, in order to show the connection between various branches of mathematics and to highlight the importance of providing the students with an extensive 'mathematical toolbox'. Investigation of the property that appears in the task was carried out using a computerized tool.

  10. A molecular toolbox for rapid generation of viral vectors to up- or down-regulate in vivo neuronal gene expression

    Directory of Open Access Journals (Sweden)

    Melanie D. White

    2011-07-01

    Full Text Available We introduce a molecular toolbox for manipulation of neuronal gene expression in vivo. The toolbox includes promoters, ion channels, optogenetic tools, fluorescent proteins and intronic artificial microRNAs. The components are easily assembled into adeno-associated virus (AAV or lentivirus vectors using recombination cloning. We demonstrate assembly of toolbox components into lentivirus and AAV vectors and use these vectors for in vivo expression of inwardly rectifying potassium channels (Kir2.1, Kir3.1 and Kir3.2 and an artificial microRNA targeted against the ion channel HCN1 (HCN1 miR. We show that AAV assembled to express HCN1 miR produces efficacious and specific in vivo knockdown of HCN1 channels. Comparison of in vivo viral transduction using HCN1 miR with mice containing a germ line deletion of HCN1 reveals similar physiological phenotypes in cerebellar Purkinje cells. The easy assembly and re-usability of the toolbox components, together with the ability to up- or down-regulate neuronal gene expression in vivo, may be useful for applications in many areas of neuroscience.

  11. User Guide for Compressible Flow Toolbox Version 2.1 for Use With MATLAB(Registered Trademark); Version 7

    Science.gov (United States)

    Melcher, Kevin J.

    2006-01-01

    This report provides a user guide for the Compressible Flow Toolbox, a collection of algorithms that solve almost 300 linear and nonlinear classical compressible flow relations. The algorithms, implemented in the popular MATLAB programming language, are useful for analysis of one-dimensional steady flow with constant entropy, friction, heat transfer, or shock discontinuities. The solutions do not include any gas dissociative effects. The toolbox also contains functions for comparing and validating the equation-solving algorithms against solutions previously published in the open literature. The classical equations solved by the Compressible Flow Toolbox are: isentropic-flow equations, Fanno flow equations (pertaining to flow of an ideal gas in a pipe with friction), Rayleigh flow equations (pertaining to frictionless flow of an ideal gas, with heat transfer, in a pipe of constant cross section.), normal-shock equations, oblique-shock equations, and Prandtl-Meyer expansion equations. At the time this report was published, the Compressible Flow Toolbox was available without cost from the NASA Software Repository.

  12. TopoToolbox: using sensor topography to calculate psychologically meaningful measures from event-related EEG/MEG.

    Science.gov (United States)

    Tian, Xing; Poeppel, David; Huber, David E

    2011-01-01

    The open-source toolbox "TopoToolbox" is a suite of functions that use sensor topography to calculate psychologically meaningful measures (similarity, magnitude, and timing) from multisensor event-related EEG and MEG data. Using a GUI and data visualization, TopoToolbox can be used to calculate and test the topographic similarity between different conditions (Tian and Huber, 2008). This topographic similarity indicates whether different conditions involve a different distribution of underlying neural sources. Furthermore, this similarity calculation can be applied at different time points to discover when a response pattern emerges (Tian and Poeppel, 2010). Because the topographic patterns are obtained separately for each individual, these patterns are used to produce reliable measures of response magnitude that can be compared across individuals using conventional statistics (Davelaar et al. Submitted and Huber et al., 2008). TopoToolbox can be freely downloaded. It runs under MATLAB (The MathWorks, Inc.) and supports user-defined data structure as well as standard EEG/MEG data import using EEGLAB (Delorme and Makeig, 2004).

  13. SAINTS toolbox

    DEFF Research Database (Denmark)

    Petersen, Anders

    2000-01-01

    En virtuel redskabskasse der bl.a. indeholder materiale om forretningsmodeller, analysemodeller, cases, WebQuests mm.......En virtuel redskabskasse der bl.a. indeholder materiale om forretningsmodeller, analysemodeller, cases, WebQuests mm....

  14. A toolbox for the fast information analysis of multiple-site LFP, EEG and spike train recordings

    Directory of Open Access Journals (Sweden)

    Logothetis Nikos K

    2009-07-01

    Full Text Available Abstract Background Information theory is an increasingly popular framework for studying how the brain encodes sensory information. Despite its widespread use for the analysis of spike trains of single neurons and of small neural populations, its application to the analysis of other types of neurophysiological signals (EEGs, LFPs, BOLD has remained relatively limited so far. This is due to the limited-sampling bias which affects calculation of information, to the complexity of the techniques to eliminate the bias, and to the lack of publicly available fast routines for the information analysis of multi-dimensional responses. Results Here we introduce a new C- and Matlab-based information theoretic toolbox, specifically developed for neuroscience data. This toolbox implements a novel computationally-optimized algorithm for estimating many of the main information theoretic quantities and bias correction techniques used in neuroscience applications. We illustrate and test the toolbox in several ways. First, we verify that these algorithms provide accurate and unbiased estimates of the information carried by analog brain signals (i.e. LFPs, EEGs, or BOLD even when using limited amounts of experimental data. This test is important since existing algorithms were so far tested primarily on spike trains. Second, we apply the toolbox to the analysis of EEGs recorded from a subject watching natural movies, and we characterize the electrodes locations, frequencies and signal features carrying the most visual information. Third, we explain how the toolbox can be used to break down the information carried by different features of the neural signal into distinct components reflecting different ways in which correlations between parts of the neural signal contribute to coding. We illustrate this breakdown by analyzing LFPs recorded from primary visual cortex during presentation of naturalistic movies. Conclusion The new toolbox presented here implements fast

  15. A toolbox for the fast information analysis of multiple-site LFP, EEG and spike train recordings.

    Science.gov (United States)

    Magri, Cesare; Whittingstall, Kevin; Singh, Vanessa; Logothetis, Nikos K; Panzeri, Stefano

    2009-07-16

    Information theory is an increasingly popular framework for studying how the brain encodes sensory information. Despite its widespread use for the analysis of spike trains of single neurons and of small neural populations, its application to the analysis of other types of neurophysiological signals (EEGs, LFPs, BOLD) has remained relatively limited so far. This is due to the limited-sampling bias which affects calculation of information, to the complexity of the techniques to eliminate the bias, and to the lack of publicly available fast routines for the information analysis of multi-dimensional responses. Here we introduce a new C- and Matlab-based information theoretic toolbox, specifically developed for neuroscience data. This toolbox implements a novel computationally-optimized algorithm for estimating many of the main information theoretic quantities and bias correction techniques used in neuroscience applications. We illustrate and test the toolbox in several ways. First, we verify that these algorithms provide accurate and unbiased estimates of the information carried by analog brain signals (i.e. LFPs, EEGs, or BOLD) even when using limited amounts of experimental data. This test is important since existing algorithms were so far tested primarily on spike trains. Second, we apply the toolbox to the analysis of EEGs recorded from a subject watching natural movies, and we characterize the electrodes locations, frequencies and signal features carrying the most visual information. Third, we explain how the toolbox can be used to break down the information carried by different features of the neural signal into distinct components reflecting different ways in which correlations between parts of the neural signal contribute to coding. We illustrate this breakdown by analyzing LFPs recorded from primary visual cortex during presentation of naturalistic movies. The new toolbox presented here implements fast and data-robust computations of the most relevant

  16. Wind turbine blockset in Saber. General overview and description of the models

    DEFF Research Database (Denmark)

    Iov, Florin; Timbus, Adrian Vasile; Hansen, Anca Daniela

    This report presents a new developed Saber Toolbox for wind turbine applications. This toolbox has been developed during the research project “Simulation Platform to model, optimize and design wind turbines”. The report provides a quick overview of the Saber and then explains the structure...... of this simulation package, which is different than other tools e.g. Matlab/Simulink. Then the structure of the toolbox is shown as well as the description of the developed models. The main focus here is to underline the special structure of the models, which are a mixture of Saber built-in blocks and new developed...... blocks. Since the developed models are based on Saber built-in blocks, a description of the libraries from Saber is given. Then some simulation results using the developed models are shown. Finally some general conclusions regarding this new developed Toolbox as well as some directions for future work...

  17. Wind Turbine Blockset in Saber. General Overview and Description of the Model

    DEFF Research Database (Denmark)

    Iov, Florin; Timbus, Adrian Vasile; Hansen, A. D.

    This report presents a new developed Saber Toolbox for wind turbine applications. This toolbox has been developed during the research project ?Simulation Platform to model, optimize and design wind turbines?. The report provides a quick overview of the Saber and then explains the structure...... of this simulation package, which is different than other tools e.g. Matlab/Simulink. Then the structure of the toolbox is shown as well as the description of the developed models. The main focus here is to underline the special structure of the models, which are a mixture of Saber built-in blocks and new developed...... blocks. Since the developed models are based on Saber built-in blocks, a description of the libraries from Saber is given. Then some simulation results using the developed models are shown. Finally some general conclusions regarding this new developed Toolbox as well as some directions for future work...

  18. Multimodal Imaging of Brain Connectivity Using the MIBCA Toolbox: Preliminary Application to Alzheimer's Disease

    Science.gov (United States)

    Ribeiro, André Santos; Lacerda, Luís Miguel; Silva, Nuno André da; Ferreira, Hugo Alexandre

    2015-06-01

    The Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox is a fully automated all-in-one connectivity analysis toolbox that offers both pre-processing, connectivity, and graph theory analysis of multimodal images such as anatomical, diffusion, and functional MRI, and PET. In this work, the MIBCA functionalities were used to study Alzheimer's Disease (AD) in a multimodal MR/PET approach. Materials and Methods: Data from 12 healthy controls, and 36 patients with EMCI, LMCI and AD (12 patients for each group) were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (adni.loni.usc.edu), including T1-weighted (T1-w), Diffusion Tensor Imaging (DTI) data, and 18F-AV-45 (florbetapir) dynamic PET data from 40-60 min post injection (4x5 min). Both MR and PET data were automatically pre-processed for all subjects using MIBCA. T1-w data was parcellated into cortical and subcortical regions-of-interest (ROIs), and the corresponding thicknesses and volumes were calculated. DTI data was used to compute structural connectivity matrices based on fibers connecting pairs of ROIs. Lastly, dynamic PET images were summed, and the relative Standard Uptake Values calculated for each ROI. Results: An overall higher uptake of 18F-AV-45, consistent with an increased deposition of beta-amyloid, was observed for the AD group. Additionally, patients showed significant cortical atrophy (thickness and volume) especially in the entorhinal cortex and temporal areas, and a significant increase in Mean Diffusivity (MD) in the hippocampus, amygdala and temporal areas. Furthermore, patients showed a reduction of fiber connectivity with the progression of the disease, especially for intra-hemispherical connections. Conclusion: This work shows the potential of the MIBCA toolbox for the study of AD, as findings were shown to be in agreement with the literature. Here, only structural changes and beta-amyloid accumulation were considered. Yet, MIBCA is further able to

  19. Basic Radar Altimetry Toolbox: Tools and Tutorial to Use Cryosat Data

    Science.gov (United States)

    Benveniste, J.; Bronner, E.; Dinardo, S.; Lucas, B. M.; Rosmorduc, V.; Earith, D.; Niemeijer, S.

    2011-12-01

    Radar altimetry is very much a technique expanding its applications. Even If quite a lot of effort has been invested for oceanography users, the use of Altimetry data for cryosphere application, especially with the new ESA CryoSat-2 mission data is still somehow tedious for new Altimetry data products users. ESA and CNES therfore developed the Basic Radar Altimetry Toolbox a few years ago, and are improving and upgrading it to fit new missions and the growing number of altimetry uses. The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data. The software is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason-1, Envisat, Jason- 2, CryoSat, the future Saral missions and is ready for adaptation to Sentinel-3 products - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. It is an opportunity to teach remote sensing with practical training. It has been available since April 2007, and had been demonstrated during training courses and scientific meetings. About 2000 people downloaded it (Summer 2011), with many "newcomers" to altimetry among them

  20. Basic Radar Altimetry Toolbox: Tools and Tutorial To Use Radar Altimetry For Cryosphere

    Science.gov (United States)

    Benveniste, J. J.; Bronner, E.; Dinardo, S.; Lucas, B. M.; Rosmorduc, V.; Earith, D.

    2010-12-01

    Radar altimetry is very much a technique expanding its applications. If quite a lot of efforts have been made for oceanography users (including easy-to-use data), the use of those data for cryosphere application, especially with the new ESA CryoSat-2 mission data is still somehow tedious, especially for new Altimetry data products users. ESA and CNES thus had the Basic Radar Altimetry Toolbox developed a few years ago, and are improving and upgrading it to fit new missions and the growing number of altimetry uses. The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data. The software is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason-1, Envisat, Jason- 2, CryoSat and the future Saral missions, - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. It is an opportunity to teach remote sensing with practical training. It has been available from April 2007, and had been demonstrated during training courses and scientific meetings. About 1200 people downloaded it (Summer 2010), with many "newcomers" to altimetry among them, including teachers

  1. Incorporation of support vector machines in the LIBS toolbox for sensitive and robust classification amidst unexpected sample and system variability.

    Science.gov (United States)

    Dingari, Narahara Chari; Barman, Ishan; Myakalwar, Ashwin Kumar; Tewari, Surya P; Kumar Gundawar, Manoj

    2012-03-20

    Despite the intrinsic elemental analysis capability and lack of sample preparation requirements, laser-induced breakdown spectroscopy (LIBS) has not been extensively used for real-world applications, e.g., quality assurance and process monitoring. Specifically, variability in sample, system, and experimental parameters in LIBS studies present a substantive hurdle for robust classification, even when standard multivariate chemometric techniques are used for analysis. Considering pharmaceutical sample investigation as an example, we propose the use of support vector machines (SVM) as a nonlinear classification method over conventional linear techniques such as soft independent modeling of class analogy (SIMCA) and partial least-squares discriminant analysis (PLS-DA) for discrimination based on LIBS measurements. Using over-the-counter pharmaceutical samples, we demonstrate that the application of SVM enables statistically significant improvements in prospective classification accuracy (sensitivity), because of its ability to address variability in LIBS sample ablation and plasma self-absorption behavior. Furthermore, our results reveal that SVM provides nearly 10% improvement in correct allocation rate and a concomitant reduction in misclassification rates of 75% (cf. PLS-DA) and 80% (cf. SIMCA)-when measurements from samples not included in the training set are incorporated in the test data-highlighting its robustness. While further studies on a wider matrix of sample types performed using different LIBS systems is needed to fully characterize the capability of SVM to provide superior predictions, we anticipate that the improved sensitivity and robustness observed here will facilitate application of the proposed LIBS-SVM toolbox for screening drugs and detecting counterfeit samples, as well as in related areas of forensic and biological sample analysis.

  2. PREVIEW behavior modification intervention toolbox (PREMIT: a study protocol for a psychological element of a multicenter project

    Directory of Open Access Journals (Sweden)

    Daniela Kahlert

    2016-08-01

    Full Text Available Background: Losing excess body weight and preventing weight regain by changing lifestyle is a challenging but promising task to prevent the incidence of type-2 diabetes. To be successful, it is necessary to use evidence-based and theory-driven interventions, which also contribute to the science of behavior modification by providing a deeper understanding of successful intervention components. Objective: To develop a physical activity and dietary behavior modification intervention toolbox (PREMIT that fulfills current requirements of being theory-driven and evidence-based, comprehensively described and feasible to evaluate. PREMIT is part of an intervention trial, which aims to prevent the onset of type-2 diabetes in pre-diabetics in eight clinical centers across the world by guiding them in changing their physical activity and dietary behavior through a group counselling approach. Methods: The program development took five progressive steps, in line with the Public Health Action Cycle: (1 Summing-up the intervention goal(s, target group and the setting, (2 uncovering the generative psychological mechanisms, (3 identifying behavior change techniques and tools, (4 preparing for evaluation and (5 implementing the intervention and assuring quality. Results: PREMIT is based on a trans-theoretical approach referring to valid behavior modification theories, models and approaches. A major ‘product’ of PREMIT is a matrix, constructed for use by onsite-instructors. The matrix includes objectives, tasks and activities ordered by periods. PREMIT is constructed to help instructors guide participant’s behavior change. To ensure high fidelity and adherence of program-implementation across the eight intervention centers standardized operational procedures were defined and train-the-trainer workshops were held. In summary PREMIT is a theory-driven, evidence-based program carefully developed to change physical activity and dietary behaviors in pre

  3. PREVIEW Behavior Modification Intervention Toolbox (PREMIT): A Study Protocol for a Psychological Element of a Multicenter Project.

    Science.gov (United States)

    Kahlert, Daniela; Unyi-Reicherz, Annelie; Stratton, Gareth; Meinert Larsen, Thomas; Fogelholm, Mikael; Raben, Anne; Schlicht, Wolfgang

    2016-01-01

    Losing excess body weight and preventing weight regain by changing lifestyle is a challenging but promising task to prevent the incidence of type-2 diabetes. To be successful, it is necessary to use evidence-based and theory-driven interventions, which also contribute to the science of behavior modification by providing a deeper understanding of successful intervention components. To develop a physical activity and dietary behavior modification intervention toolbox (PREMIT) that fulfills current requirements of being theory-driven and evidence-based, comprehensively described and feasible to evaluate. PREMIT is part of an intervention trial, which aims to prevent the onset of type-2 diabetes in pre-diabetics in eight clinical centers across the world by guiding them in changing their physical activity and dietary behavior through a group counseling approach. The program development took five progressive steps, in line with the Public Health Action Cycle: (1) Summing-up the intervention goal(s), target group and the setting, (2) uncovering the generative psychological mechanisms, (3) identifying behavior change techniques and tools, (4) preparing for evaluation and (5) implementing the intervention and assuring quality. PREMIT is based on a trans-theoretical approach referring to valid behavior modification theories, models and approaches. A major "product" of PREMIT is a matrix, constructed for use by onsite-instructors. The matrix includes objectives, tasks and activities ordered by periods. PREMIT is constructed to help instructors guide participants' behavior change. To ensure high fidelity and adherence of program-implementation across the eight intervention centers standardized operational procedures were defined and "train-the-trainer" workshops were held. In summary PREMIT is a theory-driven, evidence-based program carefully developed to change physical activity and dietary behaviors in pre-diabetic people.

  4. Improving Flood Risk Management for California's Central Valley: How the State Developed a Toolbox for Large, System-wide Studies

    Science.gov (United States)

    Pingel, N.; Liang, Y.; Bindra, A.

    2016-12-01

    More than 1 million Californians live and work in the floodplains of the Sacramento-San Joaquin Valley where flood risks are among the highest in the nation. In response to this threat to people, property and the environment, the Department of Water Resources (DWR) has been called to action to improve flood risk management. This has transpired through significant advances in development of flood information and tools, analysis, and planning. Senate Bill 5 directed DWR to prepare the Central Valley Flood Protection Plan (CVFPP) and update it every 5 years. A key component of this aggressive planning approach is answering the question: What is the current flood risk, and how would proposed improvements change flood risk throughout the system? Answering this question is a substantial challenge due to the size and complexity of the watershed and flood control system. The watershed is roughly 42,000 sq mi, and flows are controlled by numerous reservoirs, bypasses, and levees. To overcome this challenge, the State invested in development of a comprehensive analysis "tool box" through various DWR programs. Development of the tool box included: collection of hydro-meteorological, topographic, geotechnical, and economic data; development of rainfall-runoff, reservoir operation, hydraulic routing, and flood risk analysis models; and development of specialized applications and computing schemes to accelerate the analysis. With this toolbox, DWR is analyzing flood hazard, flood control system performance, exposure and vulnerability of people and property to flooding, consequence of flooding for specific events, and finally flood risk for a range of CVFPP alternatives. Based on the results, DWR will put forward a State Recommended Plan in the 2017 CVFPP. Further, the value of the analysis tool box extends beyond the CVFPP. It will serve as a foundation for other flood studies for years to come and has already been successfully applied for inundation mapping to support emergency

  5. Cementitious Barriers Partnership (CBP): Using the CBP Software Toolbox to Simulate Sulfate Attack and Carbonation of Concrete Structures - 13481

    Energy Technology Data Exchange (ETDEWEB)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S. [Vanderbilt University, School of Engineering, CRESP, Nashville, TN 37235 (United States); Flach, G.; Langton, C.; Smith, F.G.III; Burns, H. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Van der Sloot, H. [Hans Van der Sloot Consultancy, Dorpsstraat 216, 1721BV Langedijk (Netherlands); Meeussen, J.C.L. [Nuclear Research and Consultancy Group, Westerduinweg 3, Petten (Netherlands); Seignette, P.F.A.B. [Energy Research Center of The Netherlands, Petten (Netherlands); Samson, E. [SIMCO Technologies, Inc., Quebec (Canada); Mallick, P.; Suttora, L. [U.S. Department of Energy, Washington, DC (United States); Esh, D.; Fuhrmann, M.; Philip, J. [U.S. Nuclear Regulatory Commission, Washington, DC (United States)

    2013-07-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy Office of Tank Waste Management. The CBP project has developed a set of integrated modeling tools and leaching test methods to help improve understanding and prediction of the long-term hydraulic and chemical performance of cementitious materials used in nuclear applications. State-of-the-art modeling tools, including LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R}, were selected for their demonstrated abilities to simulate reactive transport and degradation in cementitious materials. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF), now adopted as part of the SW-846 RCRA methods, have been used to help make the link between modeling and experiment. Although each of the CBP tools has demonstrated utility as a standalone product, coupling the models over relevant spatial and temporal solution domains can provide more accurate predictions of cementitious materials behavior over relevant periods of performance. The LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} models were first linked to the GoldSim Monte Carlo simulator to better and more easily characterize model uncertainties and as a means to coupling the models allowing linking to broader performance assessment evaluations that use CBP results for a source term. Two important degradation scenarios were selected for initial demonstration: sulfate ingress / attack and carbonation of cementitious materials. When sufficient sulfate is present in the pore solution external to a concrete barrier, sulfate can diffuse into the concrete, react with the concrete solid phases, and cause cracking that significantly changes the transport and structural properties of the concrete. The penetration of gaseous carbon dioxide within partially saturated concrete usually initiates a series of carbonation

  6. Cementitious Barriers Partnership (CBP): Using the CBP Software Toolbox to Simulate Sulfate Attack and Carbonation of Concrete Structures - 13481

    International Nuclear Information System (INIS)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S.; Flach, G.; Langton, C.; Smith, F.G.III; Burns, H.; Van der Sloot, H.; Meeussen, J.C.L.; Seignette, P.F.A.B.; Samson, E.; Mallick, P.; Suttora, L.; Esh, D.; Fuhrmann, M.; Philip, J.

    2013-01-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy Office of Tank Waste Management. The CBP project has developed a set of integrated modeling tools and leaching test methods to help improve understanding and prediction of the long-term hydraulic and chemical performance of cementitious materials used in nuclear applications. State-of-the-art modeling tools, including LeachXS TM /ORCHESTRA and STADIUM R , were selected for their demonstrated abilities to simulate reactive transport and degradation in cementitious materials. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF), now adopted as part of the SW-846 RCRA methods, have been used to help make the link between modeling and experiment. Although each of the CBP tools has demonstrated utility as a standalone product, coupling the models over relevant spatial and temporal solution domains can provide more accurate predictions of cementitious materials behavior over relevant periods of performance. The LeachXS TM /ORCHESTRA and STADIUM R models were first linked to the GoldSim Monte Carlo simulator to better and more easily characterize model uncertainties and as a means to coupling the models allowing linking to broader performance assessment evaluations that use CBP results for a source term. Two important degradation scenarios were selected for initial demonstration: sulfate ingress / attack and carbonation of cementitious materials. When sufficient sulfate is present in the pore solution external to a concrete barrier, sulfate can diffuse into the concrete, react with the concrete solid phases, and cause cracking that significantly changes the transport and structural properties of the concrete. The penetration of gaseous carbon dioxide within partially saturated concrete usually initiates a series of carbonation reactions with

  7. NIH Toolbox Cognition Battery (NIHTB-CB): list sorting test to measure working memory.

    Science.gov (United States)

    Tulsky, David S; Carlozzi, Noelle; Chiaravalloti, Nancy D; Beaumont, Jennifer L; Kisala, Pamela A; Mungas, Dan; Conway, Kevin; Gershon, Richard

    2014-07-01

    The List Sorting Working Memory Test was designed to assess working memory (WM) as part of the NIH Toolbox Cognition Battery. List Sorting is a sequencing task requiring children and adults to sort and sequence stimuli that are presented visually and auditorily. Validation data are presented for 268 participants ages 20 to 85 years. A subset of participants (N=89) was retested 7 to 21 days later. As expected, the List Sorting Test had moderately high correlations with other measures of working memory and executive functioning (convergent validity) but a low correlation with a test of receptive vocabulary (discriminant validity). Furthermore, List Sorting demonstrates expected changes over the age span and has excellent test-retest reliability. Collectively, these results provide initial support for the construct validity of the List Sorting Working Memory Measure as a measure of working memory. However, the relationship between the List Sorting Test and general executive function has yet to be determined.

  8. Fast modal simulation of paraxial optical systems: the MIST open source toolbox

    International Nuclear Information System (INIS)

    Vajente, Gabriele

    2013-01-01

    This paper presents a new approach to the simulation of optical laser systems in the paraxial approximation, with particular applications to interferometric gravitational wave detectors. The method presented here is based on a standard decomposition of the laser field in terms of Hermite–Gauss transverse modes. The innovative feature consists of a symbolic manipulation of the equations describing the field propagation. This approach allows a huge reduction in the computational time, especially when a large number of higher order modes is needed to properly simulate the system. The new algorithm has been implemented in an open source toolbox, called the MIST, based on the MATLAB® environment. The MIST has been developed and is being used in the framework of the design of advanced gravitational wave detectors. Examples from this field of application will be discussed to illustrate the capabilities and performance of the simulation tool. (paper)

  9. EEGVIS: A MATLAB toolbox for browsing, exploring, and viewing large datasets

    Directory of Open Access Journals (Sweden)

    Kay A Robbins

    2012-05-01

    Full Text Available Recent advances in data monitoring and sensor technology have accelerated the acquisition of very large data sets. Streaming data sets from instrumentation such as multi-channel EEG recording usually must undergo substantial pre-processing and artifact removal. Even when using automated procedures, most scientists engage in laborious manual examination and processing to assure high quality data and to indentify interesting or problematic data segments. Researchers also do not have a convenient method of method of visually assessing the effects of applying any stage in a processing pipeline. EEGVIS is a MATLAB toolbox that allows users to quickly explore multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. Customizable summary views reveal potentially interesting sections of data, which users can explore further by clicking to examine using detailed viewing components. The viewer and a companion browser are built on our MoBBED framework, which has a library of modular viewing components that can be mixed and matched to best reveal structure. Users can easily create new viewers for their specific data without any programming during the exploration process. These viewers automatically support pan, zoom, resizing of individual components, and cursor exploration. The toolbox can be used directly in MATLAB at any stage in a processing pipeline, as a plug in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license at http://visual.cs.utsa.edu/ eegvis.

  10. Reliability and Validity of Composite Scores from the NIH Toolbox Cognition Battery in Adults

    Science.gov (United States)

    Heaton, Robert K.; Akshoomoff, Natacha; Tulsky, David; Mungas, Dan; Weintraub, Sandra; Dikmen, Sureyya; Beaumont, Jennifer; Casaletto, Kaitlin B.; Conway, Kevin; Slotkin, Jerry; Gershon, Richard

    2014-01-01

    This study describes psychometric properties of the NIH Toolbox Cognition Battery (NIHTB-CB) Composite Scores in an adult sample. The NIHTB-CB was designed for use in epidemiologic studies and clinical trials for ages 3 to 85. A total of 268 self-described healthy adults were recruited at four university-based sites, using stratified sampling guidelines to target demographic variability for age (20–85 years), gender, education, and ethnicity. The NIHTB-CB contains seven computer-based instruments assessing five cognitive sub-domains: Language, Executive Function, Episodic Memory, Processing Speed, and Working Memory. Participants completed the NIHTB-CB, corresponding gold standard validation measures selected to tap the same cognitive abilities, and sociodemographic questionnaires. Three Composite Scores were derived for both the NIHTB-CB and gold standard batteries: “Crystallized Cognition Composite,” “Fluid Cognition Composite,” and “Total Cognition Composite” scores. NIHTB Composite Scores showed acceptable internal consistency (Cronbach’s alphas = 0.84 Crystallized, 0.83 Fluid, 0.77 Total), excellent test–retest reliability (r: 0.86–0.92), strong convergent (r: 0.78–0.90) and discriminant (r: 0.19–0.39) validities versus gold standard composites, and expected age effects (r = 0.18 crystallized, r = − 0.68 fluid, r = − 0.26 total). Significant relationships with self-reported prior school difficulties and current health status, employment, and presence of a disability provided evidence of external validity. The NIH Toolbox Cognition Battery Composite Scores have excellent reliability and validity, suggesting they can be used effectively in epidemiologic and clinical studies. PMID:24960398

  11. EEGVIS: A MATLAB Toolbox for Browsing, Exploring, and Viewing Large Datasets.

    Science.gov (United States)

    Robbins, Kay A

    2012-01-01

    Recent advances in data monitoring and sensor technology have accelerated the acquisition of very large data sets. Streaming data sets from instrumentation such as multi-channel EEG recording usually must undergo substantial pre-processing and artifact removal. Even when using automated procedures, most scientists engage in laborious manual examination and processing to assure high quality data and to indentify interesting or problematic data segments. Researchers also do not have a convenient method of method of visually assessing the effects of applying any stage in a processing pipeline. EEGVIS is a MATLAB toolbox that allows users to quickly explore multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. Customizable summary views reveal potentially interesting sections of data, which users can explore further by clicking to examine using detailed viewing components. The viewer and a companion browser are built on our MoBBED framework, which has a library of modular viewing components that can be mixed and matched to best reveal structure. Users can easily create new viewers for their specific data without any programming during the exploration process. These viewers automatically support pan, zoom, resizing of individual components, and cursor exploration. The toolbox can be used directly in MATLAB at any stage in a processing pipeline, as a plug-in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license at http://visual.cs.utsa.edu/eegvis.

  12. Load forecasting using different architectures of neural networks with the assistance of the MATLAB toolboxes; Previsao de cargas eletricas utilizando diferentes arquiteturas de redes neurais artificiais com o auxilio das toolboxes do MATLAB

    Energy Technology Data Exchange (ETDEWEB)

    Nose Filho, Kenji; Araujo, Klayton A.M.; Maeda, Jorge L.Y.; Lotufo, Anna Diva P. [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Ilha Solteira, SP (Brazil)], Emails: kenjinose@yahoo.com.br, klayton_ama@hotmail.com, jorge-maeda@hotmail.com, annadiva@dee.feis.unesp.br

    2009-07-01

    This paper presents a development and implementation of a program to electrical load forecasting with data from a Brazilian electrical company, using four different architectures of neural networks of the MATLAB toolboxes: multilayer backpropagation gradient descendent with momentum, multilayer backpropagation Levenberg-Marquardt, adaptive network based fuzzy inference system and general regression neural network. The program presented a satisfactory performance, guaranteeing very good results. (author)

  13. A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

    Science.gov (United States)

    Lefebvre, Baptiste; Deny, Stéphane; Gardella, Christophe; Stimberg, Marcel; Jetter, Florian; Zeck, Guenther; Picaud, Serge; Duebel, Jens

    2018-01-01

    In recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here, we developed a new toolbox to sort spikes from these large-scale extracellular data. To validate our method, we performed simultaneous extracellular and loose patch recordings in rodents to obtain ‘ground truth’ data, where the solution to this sorting problem is known for one cell. The performance of our algorithm was always close to the best expected performance, over a broad range of signal-to-noise ratios, in vitro and in vivo. The algorithm is entirely parallelized and has been successfully tested on recordings with up to 4225 electrodes. Our toolbox thus offers a generic solution to sort accurately spikes for up to thousands of electrodes. PMID:29557782

  14. From black box to toolbox: Outlining device functionality, engagement activities, and the pervasive information architecture of mHealth interventions

    Directory of Open Access Journals (Sweden)

    Brian G. Danaher

    2015-03-01

    Full Text Available mHealth interventions that deliver content via mobile phones represent a burgeoning area of health behavior change. The current paper examines two themes that can inform the underlying design of mHealth interventions: (1 mobile device functionality, which represents the technological toolbox available to intervention developers; and (2 the pervasive information architecture of mHealth interventions, which determines how intervention content can be delivered concurrently using mobile phones, personal computers, and other devices. We posit that developers of mHealth interventions will be able to better achieve the promise of this burgeoning arena by leveraging the toolbox and functionality of mobile devices in order to engage participants and encourage meaningful behavior change within the context of a carefully designed pervasive information architecture.

  15. From black box to toolbox: Outlining device functionality, engagement activities, and the pervasive information architecture of mHealth interventions.

    Science.gov (United States)

    Danaher, Brian G; Brendryen, Håvar; Seeley, John R; Tyler, Milagra S; Woolley, Tim

    2015-03-01

    mHealth interventions that deliver content via mobile phones represent a burgeoning area of health behavior change. The current paper examines two themes that can inform the underlying design of mHealth interventions: (1) mobile device functionality, which represents the technological toolbox available to intervention developers; and (2) the pervasive information architecture of mHealth interventions, which determines how intervention content can be delivered concurrently using mobile phones, personal computers, and other devices. We posit that developers of mHealth interventions will be better able to achieve the promise of this burgeoning arena by leveraging the toolbox and functionality of mobile devices in order to engage participants and encourage meaningful behavior change within the context of a carefully designed pervasive information architecture.

  16. Assessing the health status of managed honeybee colonies (HEALTHY-B): a toolbox to facilitate harmonised data collection

    DEFF Research Database (Denmark)

    Nielsen, Søren Saxmose

    2016-01-01

    Tools are provided to assess the health status of managed honeybee colonies by facilitating further harmonisation of data collection and reporting, design of field surveys across the European Union (EU) and analysis of data on bee health. The toolbox is based on characteristics of a healthy managed...... is very important when assessing its health status, but tools are currently lacking that could be used at apiary level in field surveys across the EU. Data on ‘beekeeping management practices’ and ‘environmental drivers’ can be collected via questionnaires and available databases, respectively....... Integrating multiple attributes of honeybee health, for instance, via a Health Status Index, is required to support a holistic assessment. Examples are provided on how the toolbox could be used by different stakeholders. Continued interaction between the Member State organisations, the EU Reference Laboratory...

  17. Image processing and pattern recognition with CVIPtools MATLAB toolbox: automatic creation of masks for veterinary thermographic images

    Science.gov (United States)

    Mishra, Deependra K.; Umbaugh, Scott E.; Lama, Norsang; Dahal, Rohini; Marino, Dominic J.; Sackman, Joseph

    2016-09-01

    CVIPtools is a software package for the exploration of computer vision and image processing developed in the Computer Vision and Image Processing Laboratory at Southern Illinois University Edwardsville. CVIPtools is available in three variants - a) CVIPtools Graphical User Interface, b) CVIPtools C library and c) CVIPtools MATLAB toolbox, which makes it accessible to a variety of different users. It offers students, faculty, researchers and any user a free and easy way to explore computer vision and image processing techniques. Many functions have been implemented and are updated on a regular basis, the library has reached a level of sophistication that makes it suitable for both educational and research purposes. In this paper, the detail list of the functions available in the CVIPtools MATLAB toolbox are presented and how these functions can be used in image analysis and computer vision applications. The CVIPtools MATLAB toolbox allows the user to gain practical experience to better understand underlying theoretical problems in image processing and pattern recognition. As an example application, the algorithm for the automatic creation of masks for veterinary thermographic images is presented.

  18. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production.

    Science.gov (United States)

    Bi, Changhao; Su, Peter; Müller, Jana; Yeh, Yi-Chun; Chhabra, Swapnil R; Beller, Harry R; Singer, Steven W; Hillson, Nathan J

    2013-11-13

    The chemoautotrophic bacterium Ralstonia eutropha can utilize H2/CO2 for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhydroxybutyrate) directly from CO2, little work has been done to develop genetic part libraries to enable such endeavors. We report the development of a toolbox for the metabolic engineering of Ralstonia eutropha H16. We have constructed a set of broad-host-range plasmids bearing a variety of origins of replication, promoters, 5' mRNA stem-loop structures, and ribosomal binding sites. Specifically, we analyzed the origins of replication pCM62 (IncP), pBBR1, pKT (IncQ), and their variants. We tested the promoters P(BAD), T7, P(xyls/PM), P(lacUV5), and variants thereof for inducible expression. We also evaluated a T7 mRNA stem-loop structure sequence and compared a set of ribosomal binding site (RBS) sequences derived from Escherichia coli, R. eutropha, and a computational RBS design tool. Finally, we employed the toolbox to optimize hydrocarbon production in R. eutropha and demonstrated a 6-fold titer improvement using the appropriate combination of parts. We constructed and evaluated a versatile synthetic biology toolbox for Ralstonia eutropha metabolic engineering that could apply to other microbial hosts as well.

  19. PLDAPS: A Hardware Architecture and Software Toolbox for Neurophysiology Requiring Complex Visual Stimuli and Online Behavioral Control.

    Science.gov (United States)

    Eastman, Kyler M; Huk, Alexander C

    2012-01-01

    Neurophysiological studies in awake, behaving primates (both human and non-human) have focused with increasing scrutiny on the temporal relationship between neural signals and behaviors. Consequently, laboratories are often faced with the problem of developing experimental equipment that can support data recording with high temporal precision and also be flexible enough to accommodate a wide variety of experimental paradigms. To this end, we have developed a MATLAB toolbox that integrates several modern pieces of equipment, but still grants experimenters the flexibility of a high-level programming language. Our toolbox takes advantage of three popular and powerful technologies: the Plexon apparatus for neurophysiological recordings (Plexon, Inc., Dallas, TX, USA), a Datapixx peripheral (Vpixx Technologies, Saint-Bruno, QC, Canada) for control of analog, digital, and video input-output signals, and the Psychtoolbox MATLAB toolbox for stimulus generation (Brainard, 1997; Pelli, 1997; Kleiner et al., 2007). The PLDAPS ("Platypus") system is designed to support the study of the visual systems of awake, behaving primates during multi-electrode neurophysiological recordings, but can be easily applied to other related domains. Despite its wide range of capabilities and support for cutting-edge video displays and neural recording systems, the PLDAPS system is simple enough for someone with basic MATLAB programming skills to design their own experiments.

  20. Pt based PEMFC catalysts prepared from colloidal particle suspensions--a toolbox for model studies.

    Science.gov (United States)

    Speder, Jozsef; Altmann, Lena; Roefzaad, Melanie; Bäumer, Marcus; Kirkensgaard, Jacob J K; Mortensen, Kell; Arenz, Matthias

    2013-03-14

    A colloidal synthesis approach is presented that allows systematic studies of the properties of supported proton exchange membrane fuel cell (PEMFC) catalysts. The applied synthesis route is based on the preparation of monodisperse nanoparticles in the absence of strong binding organic stabilizing agents. No temperature post-treatment of the catalyst is required rendering the synthesis route ideally suitable for comparative studies. We report work concerning a series of catalysts based on the same colloidal Pt nanoparticle (NP) suspension, but with different high surface area (HSA) carbon supports. It is shown that for the prepared catalysts the carbon support has no catalytic co-function, but carbon pre-treatment leads to enhanced sticking of the Pt NPs on the support. An unwanted side effect, however, is NP agglomeration during synthesis. By contrast, enhanced NP sticking without agglomeration can be accomplished by the addition of an ionomer to the NP suspension. The catalytic activity of the prepared catalysts for the oxygen reduction reaction is comparable to industrial catalysts and no influence of the particle size is found in the range of 2-5 nm.

  1. C++ Toolbox for Object-Oriented Modeling and Dynamic Simulation of Physical Systems

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1999-01-01

    This paper presents the efforts made in an ongoing project that exploits the advantages of using object-oriented methodologies for describing and simulating dynamical systems. The background for this work is a search for new and better ways to simulate physical systems.......This paper presents the efforts made in an ongoing project that exploits the advantages of using object-oriented methodologies for describing and simulating dynamical systems. The background for this work is a search for new and better ways to simulate physical systems....

  2. An Educational Model for Hands-On Hydrology Education

    Science.gov (United States)

    AghaKouchak, A.; Nakhjiri, N.; Habib, E. H.

    2014-12-01

    This presentation provides an overview of a hands-on modeling tool developed for students in civil engineering and earth science disciplines to help them learn the fundamentals of hydrologic processes, model calibration, sensitivity analysis, uncertainty assessment, and practice conceptual thinking in solving engineering problems. The toolbox includes two simplified hydrologic models, namely HBV-EDU and HBV-Ensemble, designed as a complement to theoretical hydrology lectures. The models provide an interdisciplinary application-oriented learning environment that introduces the hydrologic phenomena through the use of a simplified conceptual hydrologic model. The toolbox can be used for in-class lab practices and homework assignments, and assessment of students' understanding of hydrological processes. Using this modeling toolbox, students can gain more insights into how hydrological processes (e.g., precipitation, snowmelt and snow accumulation, soil moisture, evapotranspiration and runoff generation) are interconnected. The educational toolbox includes a MATLAB Graphical User Interface (GUI) and an ensemble simulation scheme that can be used for teaching more advanced topics including uncertainty analysis, and ensemble simulation. Both models have been administered in a class for both in-class instruction and a final project, and students submitted their feedback about the toolbox. The results indicate that this educational software had a positive impact on students understanding and knowledge of hydrology.

  3. Evolutionary process development towards next generation crystalline silicon solar cells : a semiconductor process toolbox application

    Directory of Open Access Journals (Sweden)

    Tous L.

    2012-08-01

    Full Text Available Bulk crystalline Silicon solar cells are covering more than 85% of the world’s roof top module installation in 2010. With a growth rate of over 30% in the last 10 years this technology remains the working horse of solar cell industry. The full Aluminum back-side field (Al BSF technology has been developed in the 90’s and provides a production learning curve on module price of constant 20% in average. The main reason for the decrease of module prices with increasing production capacity is due to the effect of up scaling industrial production. For further decreasing of the price per wattpeak silicon consumption has to be reduced and efficiency has to be improved. In this paper we describe a successive efficiency improving process development starting from the existing full Al BSF cell concept. We propose an evolutionary development includes all parts of the solar cell process: optical enhancement (texturing, polishing, anti-reflection coating, junction formation and contacting. Novel processes are benchmarked on industrial like baseline flows using high-efficiency cell concepts like i-PERC (Passivated Emitter and Rear Cell. While the full Al BSF crystalline silicon solar cell technology provides efficiencies of up to 18% (on cz-Si in production, we are achieving up to 19.4% conversion efficiency for industrial fabricated, large area solar cells with copper based front side metallization and local Al BSF applying the semiconductor toolbox.

  4. ObspyDMT: a Python toolbox for retrieving and processing large seismological data sets

    Directory of Open Access Journals (Sweden)

    K. Hosseini

    2017-10-01

    Full Text Available We present obspyDMT, a free, open-source software toolbox for the query, retrieval, processing and management of seismological data sets, including very large, heterogeneous and/or dynamically growing ones. ObspyDMT simplifies and speeds up user interaction with data centers, in more versatile ways than existing tools. The user is shielded from the complexities of interacting with different data centers and data exchange protocols and is provided with powerful diagnostic and plotting tools to check the retrieved data and metadata. While primarily a productivity tool for research seismologists and observatories, easy-to-use syntax and plotting functionality also make obspyDMT an effective teaching aid. Written in the Python programming language, it can be used as a stand-alone command-line tool (requiring no knowledge of Python or can be integrated as a module with other Python codes. It facilitates data archiving, preprocessing, instrument correction and quality control – routine but nontrivial tasks that can consume much user time. We describe obspyDMT's functionality, design and technical implementation, accompanied by an overview of its use cases. As an example of a typical problem encountered in seismogram preprocessing, we show how to check for inconsistencies in response files of two example stations. We also demonstrate the fully automated request, remote computation and retrieval of synthetic seismograms from the Synthetics Engine (Syngine web service of the Data Management Center (DMC at the Incorporated Research Institutions for Seismology (IRIS.

  5. PyMVPA: A python toolbox for multivariate pattern analysis of fMRI data.

    Science.gov (United States)

    Hanke, Michael; Halchenko, Yaroslav O; Sederberg, Per B; Hanson, Stephen José; Haxby, James V; Pollmann, Stefan

    2009-01-01

    Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.

  6. SWToolbox: A surface-water tool-box for statistical analysis of streamflow time series

    Science.gov (United States)

    Kiang, Julie E.; Flynn, Kate; Zhai, Tong; Hummel, Paul; Granato, Gregory

    2018-03-07

    This report is a user guide for the low-flow analysis methods provided with version 1.0 of the Surface Water Toolbox (SWToolbox) computer program. The software combines functionality from two software programs—U.S. Geological Survey (USGS) SWSTAT and U.S. Environmental Protection Agency (EPA) DFLOW. Both of these programs have been used primarily for computation of critical low-flow statistics. The main analysis methods are the computation of hydrologic frequency statistics such as the 7-day minimum flow that occurs on average only once every 10 years (7Q10), computation of design flows including biologically based flows, and computation of flow-duration curves and duration hydrographs. Other annual, monthly, and seasonal statistics can also be computed. The interface facilitates retrieval of streamflow discharge data from the USGS National Water Information System and outputs text reports for a record of the analysis. Tools for graphing data and screening tests are available to assist the analyst in conducting the analysis.

  7. ANÁLISIS DE SISTEMAS DINÁMICOS CON pplane8.m (MATLAB® toolbox

    Directory of Open Access Journals (Sweden)

    Alejandro Regalado-Méndez

    2013-01-01

    Full Text Available En este trabajo se analizaron cuatro sistemas dinámicos (físico, químico, ecológico y económico, los cuales son representados por sistemas autónomos de dos ecuaciones diferenciales ordinarias. El objetivo principal es demostrar que pplane8.m es una herramienta computacional adecuada y eficiente. El análisis de los sistemas autónomos se llevó a cabo con base en la caracterización de sus puntos críticos de acuerdo a lo citado por Coughanowr & LeBlanc (2009 y con ayuda de pplane8.m (MATLAB® toolbox. Los principales resultados de este trabajo son que, pplane8.m (Polking, 2009 dibuja rápida y precisamente las trayectorias de todos los planos de fases, calcula con facilidad todos los puntos críticos y caracteriza correctamente cada uno de los puntos de equilibrio de los sistemas autónomos estudiados. Finalmente se puede decir que pplane8.m es una herramienta poderosa para ayudar en el proceso de enseñanza aprendizaje para estudiantes de un programa de ingeniería.

  8. The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding

    Directory of Open Access Journals (Sweden)

    Victoria C. Blake

    2016-07-01

    Full Text Available The Triticeae Toolbox (; T3 is the database schema enabling plant breeders and researchers to combine, visualize, and interrogate the wealth of phenotype and genotype data generated by the Triticeae Coordinated Agricultural Project (TCAP. T3 enables users to define specific data sets for download in formats compatible with the external tools TASSEL, Flapjack, and R; or to use by software residing on the T3 server for operations such as Genome Wide Association and Genomic Prediction. New T3 tools to assist plant breeders include a Selection Index Generator, analytical tools to compare phenotype trials using common or user-defined indices, and a histogram generator for nursery reports, with applications using the Android OS, and a Field Plot Layout Designer in development. Researchers using T3 will soon enjoy the ability to design training sets, define core germplasm sets, and perform multivariate analysis. An increased collaboration with GrainGenes and integration with the small grains reference sequence resources will place T3 in a pivotal role for on-the-fly data analysis, with instant access to the knowledge databases for wheat and barley. T3 software is available under the GNU General Public License and is freely downloadable.

  9. MiToBo - A Toolbox for Image Processing and Analysis

    Directory of Open Access Journals (Sweden)

    Birgit Möller

    2016-04-01

    Full Text Available MiToBo is a toolbox and Java library for solving basic as well as advanced image processing and analysis tasks. It features a rich collection of fundamental, intermediate and high-level image processing operators and algorithms as well as a couple of sophisticated tools for specific biological and biomedical applications. These tools include operators for elucidating cellular morphology and locomotion as well as operators for the characterization of certain intracellular particles and structures. MiToBo builds upon and integrates into the widely-used image analysis software packages ImageJ and Fiji [11, 10], and all of its operators can easily be run in ImageJ and Fiji via a generic operator runner plugin. Alternatively MiToBo operators can directly be run from command line, and using its functionality as a library for developing own applications is also supported. Thanks to the Alida library [8] forming the base of MiToBo all operators share unified APIs fostering reusability, and graphical as well as command line user interfaces for operators are automatically generated. MiToBo is available from its website http://www.informatik.uni-halle.de/mitobo, on Github, via an Apache Archiva Maven repository server, and it can easily be activated in Fiji via its own update site.

  10. The emerging molecular biology toolbox for the study of long noncoding RNA biology.

    Science.gov (United States)

    Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

    2017-10-01

    Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

  11. ASAP (Automatic Software for ASL Processing): A toolbox for processing Arterial Spin Labeling images.

    Science.gov (United States)

    Mato Abad, Virginia; García-Polo, Pablo; O'Daly, Owen; Hernández-Tamames, Juan Antonio; Zelaya, Fernando

    2016-04-01

    The method of Arterial Spin Labeling (ASL) has experienced a significant rise in its application to functional imaging, since it is the only technique capable of measuring blood perfusion in a truly non-invasive manner. Currently, there are no commercial packages for processing ASL data and there is no recognized standard for normalizing ASL data to a common frame of reference. This work describes a new Automated Software for ASL Processing (ASAP) that can automatically process several ASL datasets. ASAP includes functions for all stages of image pre-processing: quantification, skull-stripping, co-registration, partial volume correction and normalization. To assess the applicability and validity of the toolbox, this work shows its application in the study of hypoperfusion in a sample of healthy subjects at risk of progressing to Alzheimer's disease. ASAP requires limited user intervention, minimizing the possibility of random and systematic errors, and produces cerebral blood flow maps that are ready for statistical group analysis. The software is easy to operate and results in excellent quality of spatial normalization. The results found in this evaluation study are consistent with previous studies that find decreased perfusion in Alzheimer's patients in similar regions and demonstrate the applicability of ASAP. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. ObspyDMT: a Python toolbox for retrieving and processing large seismological data sets

    Science.gov (United States)

    Hosseini, Kasra; Sigloch, Karin

    2017-10-01

    We present obspyDMT, a free, open-source software toolbox for the query, retrieval, processing and management of seismological data sets, including very large, heterogeneous and/or dynamically growing ones. ObspyDMT simplifies and speeds up user interaction with data centers, in more versatile ways than existing tools. The user is shielded from the complexities of interacting with different data centers and data exchange protocols and is provided with powerful diagnostic and plotting tools to check the retrieved data and metadata. While primarily a productivity tool for research seismologists and observatories, easy-to-use syntax and plotting functionality also make obspyDMT an effective teaching aid. Written in the Python programming language, it can be used as a stand-alone command-line tool (requiring no knowledge of Python) or can be integrated as a module with other Python codes. It facilitates data archiving, preprocessing, instrument correction and quality control - routine but nontrivial tasks that can consume much user time. We describe obspyDMT's functionality, design and technical implementation, accompanied by an overview of its use cases. As an example of a typical problem encountered in seismogram preprocessing, we show how to check for inconsistencies in response files of two example stations. We also demonstrate the fully automated request, remote computation and retrieval of synthetic seismograms from the Synthetics Engine (Syngine) web service of the Data Management Center (DMC) at the Incorporated Research Institutions for Seismology (IRIS).

  13. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 1: Line Segment Detection and Extraction

    Directory of Open Access Journals (Sweden)

    Mehdi Rahnama

    2014-06-01

    Full Text Available Geological structures, such as faults and fractures, appear as image discontinuities or lineaments in remote sensing data. Geologic lineament mapping is a very important issue in geo-engineering, especially for construction site selection, seismic, and risk assessment, mineral exploration and hydrogeological research. Classical methods of lineaments extraction are based on semi-automated (or visual interpretation of optical data and digital elevation models. We developed a freely available Matlab based toolbox TecLines (Tectonic Lineament Analysis for locating and quantifying lineament patterns using satellite data and digital elevation models. TecLines consists of a set of functions including frequency filtering, spatial filtering, tensor voting, Hough transformation, and polynomial fitting. Due to differences in the mathematical background of the edge detection and edge linking procedure as well as the breadth of the methods, we introduce the approach in two-parts. In this first study, we present the steps that lead to edge detection. We introduce the data pre-processing using selected filters in spatial and frequency domains. We then describe the application of the tensor-voting framework to improve position and length accuracies of the detected lineaments. We demonstrate the robustness of the approach in a complex area in the northeast of Afghanistan using a panchromatic QUICKBIRD-2 image with 1-meter resolution. Finally, we compare the results of TecLines with manual lineament extraction, and other lineament extraction algorithms, as well as a published fault map of the study area.

  14. ObsPy: A Python toolbox for seismology - Sustainability, New Features, and Applications

    Science.gov (United States)

    Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; MacCarthy, J.

    2016-12-01

    ObsPy (https://www.obspy.org) is a community-driven, open-source project dedicated to offer a bridge for seismology into the scientific Python ecosystem. Amongst other things, it provides Read and write support for essentially every commonly used data format in seismology with a unified interface. This includes waveform data as well as station and event meta information. A signal processing toolbox tuned to the specific needs of seismologists. Integrated access to the largest data centers, web services, and databases. Wrappers around third party codes like libmseed and evalresp. Using ObsPy enables users to take advantage of the vast scientific ecosystem that has developed around Python. In contrast to many other programming languages and tools, Python is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often must be translated to stable and production ready environments, especially in the age of big data. ObsPy has seen constant development for more than six years and enjoys a large rate of adoption in the seismological community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. We will present a short overview of the capabilities of ObsPy and point out several representative use cases and more specialized software built around ObsPy. Additionally we will discuss new and upcoming features, as well as the sustainability of open-source scientific software.

  15. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

    Science.gov (United States)

    2013-01-01

    The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

  16. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data.

    Science.gov (United States)

    De Leener, Benjamin; Lévy, Simon; Dupont, Sara M; Fonov, Vladimir S; Stikov, Nikola; Louis Collins, D; Callot, Virginie; Cohen-Adad, Julien

    2017-01-15

    For the past 25 years, the field of neuroimaging has witnessed the development of several software packages for processing multi-parametric magnetic resonance imaging (mpMRI) to study the brain. These software packages are now routinely used by researchers and clinicians, and have contributed to important breakthroughs for the understanding of brain anatomy and function. However, no software package exists to process mpMRI data of the spinal cord. Despite the numerous clinical needs for such advanced mpMRI protocols (multiple sclerosis, spinal cord injury, cervical spondylotic myelopathy, etc.), researchers have been developing specific tools that, while necessary, do not provide an integrative framework that is compatible with most usages and that is capable of reaching the community at large. This hinders cross-validation and the possibility to perform multi-center studies. In this study we introduce the Spinal Cord Toolbox (SCT), a comprehensive software dedicated to the processing of spinal cord MRI data. SCT builds on previously-validated methods and includes state-of-the-art MRI templates and atlases of the spinal cord, algorithms to segment and register new data to the templates, and motion correction methods for diffusion and functional time series. SCT is tailored towards standardization and automation of the processing pipeline, versatility, modularity, and it follows guidelines of software development and distribution. Preliminary applications of SCT cover a variety of studies, from cross-sectional area measures in large databases of patients, to the precise quantification of mpMRI metrics in specific spinal pathways. We anticipate that SCT will bring together the spinal cord neuroimaging community by establishing standard templates and analysis procedures. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. FZUImageReg: A toolbox for medical image registration and dose fusion in cervical cancer radiotherapy.

    Directory of Open Access Journals (Sweden)

    Qinquan Gao

    Full Text Available The combination external-beam radiotherapy and high-dose-rate brachytherapy is a standard form of treatment for patients with locally advanced uterine cervical cancer. Personalized radiotherapy in cervical cancer requires efficient and accurate dose planning and assessment across these types of treatment. To achieve radiation dose assessment, accurate mapping of the dose distribution from HDR-BT onto EBRT is extremely important. However, few systems can achieve robust dose fusion and determine the accumulated dose distribution during the entire course of treatment. We have therefore developed a toolbox (FZUImageReg, which is a user-friendly dose fusion system based on hybrid image registration for radiation dose assessment in cervical cancer radiotherapy. The main part of the software consists of a collection of medical image registration algorithms and a modular design with a user-friendly interface, which allows users to quickly configure, test, monitor, and compare different registration methods for a specific application. Owing to the large deformation, the direct application of conventional state-of-the-art image registration methods is not sufficient for the accurate alignment of EBRT and HDR-BT images. To solve this problem, a multi-phase non-rigid registration method using local landmark-based free-form deformation is proposed for locally large deformation between EBRT and HDR-BT images, followed by intensity-based free-form deformation. With the transformation, the software also provides a dose mapping function according to the deformation field. The total dose distribution during the entire course of treatment can then be presented. Experimental results clearly show that the proposed system can achieve accurate registration between EBRT and HDR-BT images and provide radiation dose warping and fusion results for dose assessment in cervical cancer radiotherapy in terms of high accuracy and efficiency.

  18. The oceanographic toolbox for the collection of sinking and suspended marine particles

    Science.gov (United States)

    McDonnell, Andrew M. P.; Lam, Phoebe J.; Lamborg, Carl H.; Buesseler, Ken O.; Sanders, Richard; Riley, Jennifer S.; Marsay, Chris; Smith, Helen E. K.; Sargent, Elizabeth C.; Lampitt, Richard S.; Bishop, James K. B.

    2015-04-01

    Marine particles play a central role in controlling the transport, cycling, and inventories of many major elements and trace elements and isotopes throughout the oceans. Studies seeking to elucidate the biogeochemical roles of marine particles often require reliable ways to collect them from the ocean. Here, we review the oceanographic toolbox of techniques and instrumentation that are employed to collect both suspended and sinking particles. With these tools, it is possible to determine both the concentrations and vertical fluxes of important elements and individual particle types. We describe the various methods for quantifying the concentrations of particulate matter with in situ pumps, towed sampling devices, bottle collectors, and large volume capture devices. The uses of various types of flux collection platforms are discussed including surface tethered, neutrally buoyant, and bottom moored devices. We address the issues of sediment trap collection biases and the apparent inconsistencies that can arise due to differences in the temporal and spatial scales sampled by the various methodologies. Special attention is given to collection considerations made for the analysis of trace metals and isotopes, as these methodologies are of high importance to the ongoing GEOTRACES program which seeks to identify the processes and quantify fluxes that control the distributions of key trace elements and isotopes in the ocean. With the emergence of new particle collection methodologies and the continued reliance on traditional collection methods, it is imperative that we combine these multiple approaches in ways that will help improve their accuracy and precision while enhancing their utility in advancing understanding of the biogeochemical and ecological roles of marine particles.

  19. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis

    Science.gov (United States)

    Stata, Matt; Wang, Wei; White, Merlin M.; Moncalvo, Jean-Marc

    2018-01-01

    ABSTRACT Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects. PMID:29764946

  20. iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data.

    Science.gov (United States)

    Groppe, David M; Bickel, Stephan; Dykstra, Andrew R; Wang, Xiuyuan; Mégevand, Pierre; Mercier, Manuel R; Lado, Fred A; Mehta, Ashesh D; Honey, Christopher J

    2017-04-01

    Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. NEW METHOD: iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging. Subsequently, iELVis implements methods for correcting electrode locations for postimplant brain shift with millimeter-scale accuracy and provides interactive visualization on 3D surfaces or in 2D slices with optional functional neuroimaging overlays. iELVis also localizes electrodes relative to FreeSurfer-based atlases and can combine data across subjects via the FreeSurfer average brain. It takes 30-60min of user time and 12-24h of computer time to localize and visualize electrodes from one brain. We demonstrate iELVis's functionality by showing that three methods for mapping primary hand somatosensory cortex (iEEG, iEBS, and functional MRI) provide highly concordant results. COMPARISON WITH EXISTING METHODS: iELVis is the first public software for electrode localization that corrects for brain shift, maps electrodes to an average brain, and supports neuroimaging overlays. Moreover, its interactive visualizations are powerful and its tutorial material is extensive. iELVis promises to speed the progress and enhance the robustness of intracranial electrode research. The software and extensive tutorial materials are freely available as part of the EpiSurg software project: https://github.com/episurg/episurg. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. RMBNToolbox: random models for biochemical networks

    Directory of Open Access Journals (Sweden)

    Niemi Jari

    2007-05-01

    Full Text Available Abstract Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models. Results We present a computational toolbox for generating random biochemical network models which mimic real biochemical networks. The toolbox is called Random Models for Biochemical Networks. The toolbox works in the Matlab environment, and it makes it possible to generate various network structures, stoichiometries, kinetic laws for reactions, and parameters therein. The generation can be based on statistical rules and distributions, and more detailed information of real biochemical networks can be used in situations where it is known. The toolbox can be easily extended. The resulting network models can be exported in the format of Systems Biology Markup Language. Conclusion While more information is accumulating on biochemical networks, random networks can be used as an intermediate step towards their better understanding. Random networks make it possible to study the effects of various network characteristics to the overall behavior of the network. Moreover, the construction of artificial network models provides the ground truth data needed in the validation of various computational methods in the fields of parameter estimation and data analysis.

  2. Systematic identification of crystallization kinetics within a generic modelling framework

    DEFF Research Database (Denmark)

    Abdul Samad, Noor Asma Fazli Bin; Meisler, Kresten Troelstrup; Gernaey, Krist

    2012-01-01

    A systematic development of constitutive models within a generic modelling framework has been developed for use in design, analysis and simulation of crystallization operations. The framework contains a tool for model identification connected with a generic crystallizer modelling tool-box, a tool...

  3. SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets.

    Science.gov (United States)

    Navratil, Vincent; Pontoizeau, Clément; Billoir, Elise; Blaise, Benjamin J

    2013-05-15

    Supervised multivariate statistical analyses are often required to analyze the high-density spectral information in metabolic datasets acquired from complex mixtures in metabolic phenotyping studies. Here we present an implementation of the SRV-Statistical Recoupling of Variables-algorithm as an open-source Matlab and GNU Octave toolbox. SRV allows the identification of similarity between consecutive variables resulting from the high-resolution bucketing. Similar variables are gathered to restore the spectral dependency within the datasets and identify metabolic NMR signals. The correlation and significance of these new NMR variables for a given effect under study can then be measured and represented on a loading plot to allow a visual and efficient identification of candidate biomarkers. Further on, correlations between these candidate biomarkers can be visualized on a two-dimensional pseudospectrum, representing a correlation map, helping to understand the modifications of the underlying metabolic network. SRV toolbox is encoded in MATLAB R2008A (Mathworks, Natick, MA) and in GNU Octave. It is available free of charge at http://www.prabi.fr/redmine/projects/srv/repository with a tutorial. benjamin.blaise@chu-lyon.fr or vincent.navratil@univ-lyon1.fr.

  4. Expanding the toolbox for studying the biological responses of individual fish to hydropower infrastructure and operating strategies

    International Nuclear Information System (INIS)

    Hasler, C.T.; Cooke, S.J.; Patterson, D.A.

    2009-01-01

    Hydropower infrastructure and the operational strategies used by power utilities have the potential to change local aquatic environments. However, few studies have evaluated sub-organismal responses such as physiological consequences of individual fish to fluctuating flows or hydropower infrastructure such as fishways or turbines. Rather than review the impacts of hydropower on fish, this paper detailed the behavioural, energetic, genomic, molecular, forensic, isotopic, and physiological tools available for studying sub-organismal responses of fish to hydropower infrastructure and operating procedures with a critical assessment of their benefits and limitations. A brief summary of the current state of knowledge regarding the 12 types of tools was provided along with their usefulness in fisheries science and environmental management. The benefits and limitations of using these techniques for evaluating hydropower impacts on fish and fish habitat were discussed. Two case studies were presented to demonstrate how the inclusion of individual-based information into hydropower research has helped to improve the understanding of complex fish and hydropower issues. Practitioners can use the expanded toolbox to assess fishway performance, migration delays, and fish responses to fluctuating flows through a mechanistic approach. These tools are also relevant for evaluating other anthropogenic impacts such as water withdrawal for irrigation or drinking water, habitat alteration, and fisheries interactions. The expanded toolbox can contribute to a more sustainable hydropower industry by providing regulators with tools for making informed decisions and evaluating compliance issues. 150 refs., 1 tab., 4 figs

  5. Rangeland Brush Estimation Toolbox (RaBET): An Approach for Evaluating Brush Management Conservation Efforts in Western Grazing Lands

    Science.gov (United States)

    Holifield Collins, C.; Kautz, M. A.; Skirvin, S. M.; Metz, L. J.

    2016-12-01

    There are over 180 million hectares of rangelands and grazed forests in the central and western United States. Due to the loss of perennial grasses and subsequent increased runoff and erosion that can degrade the system, woody cover species cannot be allowed to proliferate unchecked. The USDA-Natural Resources Conservation Service (NRCS) has allocated extensive resources to employ brush management (removal) as a conservation practice to control woody species encroachment. The Rangeland-Conservation Effects Assessment Project (CEAP) has been tasked with determining how effective the practice has been, however their land managers lack a cost-effective means to conduct these assessments at the necessary scale. An ArcGIS toolbox for generating large-scale, Landsat-based, spatial maps of woody cover on grazing lands in the western United States was developed through a collaboration with NRCS Rangeland-CEAP. The toolbox contains two main components of operation, image generation and temporal analysis, and utilizes simple interfaces requiring minimum user inputs. The image generation tool utilizes geographically specific algorithms developed from combining moderate-resolution (30-m) Landsat imagery and high-resolution (1-m) National Agricultural Imagery Program (NAIP) aerial photography to produce the woody cover scenes at the Major Land Resource (MLRA) scale. The temporal analysis tool can be used on these scenes to assess treatment effectiveness and monitor woody cover reemergence. RaBET provides rangeland managers an operational, inexpensive decision support tool to aid in the application of brush removal treatments and assessing their effectiveness.

  6. Self-advocacy training for cancer survivors. The Cancer Survival Toolbox.

    Science.gov (United States)

    Walsh-Burke, K; Marcusen, C

    1999-01-01

    With the advent of managed healthcare, self-advocacy has been identified as an essential skill for cancer survivors. This article describes a self-advocacy training program, the Cancer Survival Toolbox, developed through a unique collaborative effort by the National Coalition for Cancer Survivorship, the Association of Oncology Social Work, and the Oncology Nursing Society. Self-advocacy training is provided in audiotape format, as well as through the Internet and in interactive groups. The need for this training was established through surveys completed by 569 cancer survivors and 833 oncology professionals. Essential skills were identified through a literature review, and the content of the training was pilot tested with bicoastal groups of cancer survivors and with feedback from representatives of 15 national cancer organizations. While the majority of the 569 respondents to the survivor survey were highly educated and between the ages of 31 and 60 years, fewer than half reported that when they first received a diagnosis of cancer they were able to communicate their needs effectively, had the skills necessary to make decisions, or were able to negotiate with healthcare providers, insurers, and employers. Results of the survey of professional oncology nurses and social workers also supported the need for self-advocacy training. Fewer than one third of the 833 respondents to the professional survey reported that their patients who had received new diagnoses of cancer had essential self-advocacy skills. This self-advocacy training program is currently available on audiotape in English and Spanish. It is available in print in Chinese on the Internet. Data from the pilot groups indicate the program effectively addresses the self-advocacy skills of communication, information seeking, problem solving, decision making, and negotiating. Data are currently being collected to assess the efficacy of the audiotape format and the impact of the training on survivors and

  7. An evaluative study of the impact of the "Curriculum Alignment Toolbox" on middle school science achievement

    Science.gov (United States)

    Jones, Carol L.

    The number of computer-assisted education programs on the market is overwhelming science teachers all over the Michigan. Though the need is great, many teachers are reluctant to procure computer-assisted science education programs because they are unsure of the effectiveness of such programs. The Curriculum Alignment Toolbox (CAT) is a computer-based program, aligned to the Michigan Curriculum Framework's Benchmarks for Science Education and designed to supplement science instruction in Michigan middle schools. The purpose of this study was to evaluate the effectiveness of CAT in raising the standardized test scores of Michigan students. This study involved 419 students from one urban, one suburban and one rural middle school. Data on these students was collected from 4 sources: (1) the 8th grade Michigan Education Assessment Program (MEAP) test, (2) a 9 question, 5-point Likert-type scale student survey, (3) 4 open-response student survey questions and (4) classroom observations. Results of this study showed that the experimental group of 226 students who utilized the CAT program in addition to traditional instruction did significantly better on the Science MEAP test than the control group of 193 students who received only traditional instruction. The study also showed that the urban students from a "high needs" school seemed to benefit most from the program. Additionally, though both genders and all identified ethnic groups benefited from the program, males benefited more than females and whites, blacks and Asian/Pacific Islander students benefited more than Hispanic and multi-racial students. The CAT program's success helping raise the middle school MEAP scores may well be due to some of its components. CAT provided students with game-like experiences all based on the benchmarks required for science education and upon which the MEAP test is based. The program also provided visual and auditory stimulation as well as numerous references which students indicated

  8. Development of a harmonized risk mitigation toolbox dedicated to environmental risks of pesticides in farmland in Europe: outcome of the MAgPIE workshop

    Directory of Open Access Journals (Sweden)

    Alix, A.

    2015-11-01

    Full Text Available Risk mitigation measures are a key component in designing conditions of use of pesticides in crop protection. A 2-step workshop was organized under the auspices of SETAC and the European Commission and gathered risk assessors and risk managers of 21 European countries, industry, academia and agronomical advisors/extension services, in order to provide European regulatory authorities with a toolbox of risk mitigation measures designed to reduce environmental risks of pesticides used in agriculture, and thus contribute to a better harmonization within Europe in the area. The workshop gathered an inventory of the risk mitigation tools for pesticides being implemented or in development in European countries. The inventory was discussed in order to identify the most promising tools for a harmonized toolbox in the European area. The discussions concerned the level of confidence in the technical data on which the tools identified rely, possible regulatory hurdles, expectations as regards the implementation of these tools by farmers and links with risk assessment. Finally, this workshop was a first step towards a network gathering all stakeholders, i.e. experts from national authorities, research sector, industry and farmers, to share information and further develop this toolbox. This paper presents an outline of the content of the toolbox with an emphasis on spray drift reducing techniques, in line with the discussions ongoing in the SPISE workshop.

  9. PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eye-tracking experiments

    NARCIS (Netherlands)

    Dalmaijer, E.S.; Mathôt, S.; van der Stigchel, S.

    2014-01-01

    he PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and

  10. PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments.

    Science.gov (United States)

    Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

    2014-12-01

    The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

  11. PyTRiP - a toolbox and GUI for the proton/ion therapy planning system TRiP

    International Nuclear Information System (INIS)

    Toftegaard, J; Bassler, N; Petersen, J B

    2014-01-01

    Purpose: Only very few treatment planning systems (TPS) are capable of handling heavy ions. Commercial heavy ion TPS are costly and normally restrict the possibility to implement new functionalities. PyTRiP provides Python bindings and a platform-independent graphical user interface (GUI) for the heavy ion treatment program TRiP, and adds seamless support of DICOM files. We aim to provide a front-end for TRiP which does not require any special computer skills. Methods: PyTRiP is written in Python combined with C for fast computing. Routines for DICOM file import/export to TRiPs native file format are implemented. The GUI comes as an executable with all its dependencies including PyTRiP making it easy to install on Windows, Mac and Linux. Results: PyTRiP is a comprehensive toolbox for handling TRiP. Treatment plans are handled using an object oriented structure. Bindings to TRiP (which only runs on Linux, either locally or on a remote server) are performed through a single function call. GUI users can intuitively create treatment plans without much knowledge about the TRiP user interface. Advanced users still have full access to all TRiP functionality. The user interface comes with a comprehensive plotting tool, which can visualize 2D contours, volume histograms, as well as dose- and linear energy transfer (LET) distributions. Conclusion: We developed a powerful toolbox for ion therapy research using TRiP as backend. The corresponding GUI allows to easily and intuitively create, calculate and visualize treatment plans. TRiP is thereby more accessible and simpler to use.

  12. D and D Toolbox Project - Technology Demonstration of Fixatives Applied to Hot Cell Facilities via Remote Sprayer Platforms

    International Nuclear Information System (INIS)

    Lagos, L.; Shoffner, P.; Espinosa, E.; Pena, G.; Kirk, P.; Conley, T.

    2009-01-01

    The objective of the US Department of Energy Office of Environmental Management's (DOE-EM's) D and D Toolbox Project is to use an integrated systems approach to develop a suite of decontamination and decommissioning (D and D) technologies, a D and D toolbox, that can be readily used across the DOE complex to improve safety, reduce technical risks, and limit uncertainty within D and D operations. Florida International University's Applied Research Center (FIU-ARC) is supporting this initiative by identifying technologies suitable to meet specific facility D and D requirements, assessing the readiness of those technologies for field deployment, and conducting technology demonstrations of selected technologies at FIU-ARC facilities in Miami, Florida. To meet the technology gap challenge for a technology to remotely apply strippable/fixative coatings, FIU-ARC identified and demonstrated of a remote fixative sprayer platform. During this process, FIU-ARC worked closely with the Oak Ridge National Laboratory in the selection of typical fixatives and in the design of a hot cell mockup facility for demonstrations at FIUARC. For this demonstration and for future demonstrations, FIU-ARC built a hot cell mockup facility at the FIU-ARC Technology Demonstration/Evaluation site in Miami, Florida. FIU-ARC selected the International Climbing Machines' (ICM's) Robotic Climber to perform this technology demonstration. The selected technology was demonstrated at the hot cell mockup facility at FIU-ARC during the week of November 10, 2008. Fixative products typically used inside hot cells were investigated and selected for this remote application. The fixatives tested included Sherwin Williams' Promar 200 and DTM paints and Bartlett's Polymeric Barrier System (PBS). The technology evaluation documented the ability of the remote system to spray fixative products on horizontal and vertical concrete surfaces. The technology performance, cost, and health and safety issues were evaluated

  13. modelling of queuing process at airport check-in system

    African Journals Online (AJOL)

    HOD

    Key words: Airport check-in system, discrete time events, analytical models, simulation model, SimEvents toolbox. 1. ..... [6] Gross, D. and Harris, C. M. Fundamentals of. Queueing ... [11] Manataki I. E. and Zogra os K. G. “A Generic. System ...

  14. Online model evaluation of large-eddy simulations covering Germany with a horizontal resolution of 156 m

    Science.gov (United States)

    Hansen, Akio; Ament, Felix; Lammert, Andrea

    2017-04-01

    Large-eddy simulations have been performed since several decades, but due to computational limits most studies were restricted to small domains or idealised initial-/boundary conditions. Within the High definition clouds and precipitation for advancing climate prediction (HD(CP)2) project realistic weather forecasting like LES simulations were performed with the newly developed ICON LES model for several days. The domain covers central Europe with a horizontal resolution down to 156 m. The setup consists of more than 3 billion grid cells, by what one 3D dump requires roughly 500 GB. A newly developed online evaluation toolbox was created to check instantaneously for realistic model simulations. The toolbox automatically combines model results with observations and generates several quicklooks for various variables. So far temperature-/humidity profiles, cloud cover, integrated water vapour, precipitation and many more are included. All kind of observations like aircraft observations, soundings or precipitation radar networks are used. For each dataset, a specific module is created, which allows for an easy handling and enhancement of the toolbox. Most of the observations are automatically downloaded from the Standardized Atmospheric Measurement Database (SAMD). The evaluation tool should support scientists at monitoring computational costly model simulations as well as to give a first overview about model's performance. The structure of the toolbox as well as the SAMD database are presented. Furthermore, the toolbox was applied on an ICON LES sensitivity study, where example results are shown.

  15. Proposal for Classifying the Severity of Speech Disorder Using a Fuzzy Model in Accordance with the Implicational Model of Feature Complexity

    Science.gov (United States)

    Brancalioni, Ana Rita; Magnago, Karine Faverzani; Keske-Soares, Marcia

    2012-01-01

    The objective of this study is to create a new proposal for classifying the severity of speech disorders using a fuzzy model in accordance with a linguistic model that represents the speech acquisition of Brazilian Portuguese. The fuzzy linguistic model was run in the MATLAB software fuzzy toolbox from a set of fuzzy rules, and it encompassed…

  16. An Early Years Toolbox for Assessing Early Executive Function, Language, Self-Regulation, and Social Development: Validity, Reliability, and Preliminary Norms.

    Science.gov (United States)

    Howard, Steven J; Melhuish, Edward

    2017-06-01

    Several methods of assessing executive function (EF), self-regulation, language development, and social development in young children have been developed over previous decades. Yet new technologies make available methods of assessment not previously considered. In resolving conceptual and pragmatic limitations of existing tools, the Early Years Toolbox (EYT) offers substantial advantages for early assessment of language, EF, self-regulation, and social development. In the current study, results of our large-scale administration of this toolbox to 1,764 preschool and early primary school students indicated very good reliability, convergent validity with existing measures, and developmental sensitivity. Results were also suggestive of better capture of children's emerging abilities relative to comparison measures. Preliminary norms are presented, showing a clear developmental trajectory across half-year age groups. The accessibility of the EYT, as well as its advantages over existing measures, offers considerably enhanced opportunities for objective measurement of young children's abilities to enable research and educational applications.

  17. Evaluation of an educational "toolbox" for improving nursing staff competence and psychosocial work environment in elderly care: results of a prospective, non-randomized controlled intervention.

    Science.gov (United States)

    Arnetz, J E; Hasson, H

    2007-07-01

    Lack of professional development opportunities among nursing staff is a major concern in elderly care and has been associated with work dissatisfaction and staff turnover. There is a lack of prospective, controlled studies evaluating the effects of educational interventions on nursing competence and work satisfaction. The aim of this study was to evaluate the possible effects of an educational "toolbox" intervention on nursing staff ratings of their competence, psychosocial work environment and overall work satisfaction. The study was a prospective, non-randomized, controlled intervention. Nursing staff in two municipal elderly care organizations in western Sweden. In an initial questionnaire survey, nursing staff in the intervention municipality described several areas in which they felt a need for competence development. Measurement instruments and educational materials for improving staff knowledge and work practices were then collated by researchers and managers in a "toolbox." Nursing staff ratings of their competence and work were measured pre and post-intervention by questionnaire. Staff ratings in the intervention municipality were compared to staff ratings in the reference municipality, where no toolbox was introduced. Nursing staff ratings of their competence and psychosocial work environment, including overall work satisfaction, improved significantly over time in the intervention municipality, compared to the reference group. Both competence and work environment ratings were largely unchanged among reference municipality staff. Multivariate analysis revealed a significant interaction effect between municipalities over time for nursing staff ratings of participation, leadership, performance feedback and skills' development. Staff ratings for these four scales improved significantly in the intervention municipality as compared to the reference municipality. Compared to a reference municipality, nursing staff ratings of their competence and the

  18. Three-dimensional mapping of mechanical activation patterns, contractile dyssynchrony and dyscoordination by two-dimensional strain echocardiography: Rationale and design of a novel software toolbox

    Directory of Open Access Journals (Sweden)

    Cramer Maarten J

    2008-05-01

    Full Text Available Abstract Background Dyssynchrony of myocardial deformation is usually described in terms of variability only (e.g. standard deviations SD's. A description in terms of the spatio-temporal distribution pattern (vector-analysis of dyssynchrony or by indices estimating its impact by expressing dyscoordination of shortening in relation to the global ventricular shortening may be preferential. Strain echocardiography by speckle tracking is a new non-invasive, albeit 2-D imaging modality to study myocardial deformation. Methods A post-processing toolbox was designed to incorporate local, speckle tracking-derived deformation data into a 36 segment 3-D model of the left ventricle. Global left ventricular shortening, standard deviations and vectors of timing of shortening were calculated. The impact of dyssynchrony was estimated by comparing the end-systolic values with either early peak values only (early shortening reserve ESR or with all peak values (virtual shortening reserve VSR, and by the internal strain fraction (ISF expressing dyscoordination as the fraction of deformation lost internally due to simultaneous shortening and stretching. These dyssynchrony parameters were compared in 8 volunteers (NL, 8 patients with Wolff-Parkinson-White syndrome (WPW, and 7 patients before (LBBB and after cardiac resynchronization therapy (CRT. Results Dyssynchrony indices merely based on variability failed to detect differences between WPW and NL and failed to demonstrate the effect of CRT. Only the 3-D vector of onset of shortening could distinguish WPW from NL, while at peak shortening and by VSR, ESR and ISF no differences were found. All tested dyssynchrony parameters yielded higher values in LBBB compared to both NL and WPW. CRT reduced the spatial divergence of shortening (both vector magnitude and direction, and improved global ventricular shortening along with reductions in ESR and dyscoordination of shortening expressed by ISF. Conclusion Incorporation

  19. Modelling Project Feasibility Robustness by Use of Scenarios

    DEFF Research Database (Denmark)

    Moshøj, Claus Rehfeld; Leleur, Steen

    1998-01-01

    , SEAM secures a consistent inclusion of actual scenario elements in the quantitative impact modelling and facilitates a transparent project feasibility robustness analysis. SEAM is implemented as part of a decision support system with a toolbox structure applicable to different types of transport...

  20. TLM.open: a SystemC/TLM Frontend for the CADP Verification Toolbox

    Directory of Open Access Journals (Sweden)

    Claude Helmstetter

    2014-04-01

    Full Text Available SystemC/TLM models, which are C++ programs, allow the simulation of embedded software before hardware low-level descriptions are available and are used as golden models for hardware verification. The verification of the SystemC/TLM models is an important issue since an error in the model can mislead the system designers or reveal an error in the specifications. An open-source simulator for SystemC/TLM is provided but there are no tools for formal verification.In order to apply model checking to a SystemC/TLM model, a semantics for standard C++ code and for specific SystemC/TLM features must be provided. The usual approach relies on the translation of the SystemC/TLM code into a formal language for which a model checker is available.We propose another approach that suppresses the error-prone translation effort. Given a SystemC/TLM program, the transitions are obtained by executing the original code using g++ and an extended SystemC library, and we ask the user to provide additional functions to store the current model state. These additional functions generally represent less than 20% of the size of the original model, and allow it to apply all CADP verification tools to the SystemC/TLM model itself.

  1. The cognition battery of the NIH toolbox for assessment of neurological and behavioral function: validation in an adult sample.

    Science.gov (United States)

    Weintraub, Sandra; Dikmen, Sureyya S; Heaton, Robert K; Tulsky, David S; Zelazo, Philip David; Slotkin, Jerry; Carlozzi, Noelle E; Bauer, Patricia J; Wallner-Allen, Kathleen; Fox, Nathan; Havlik, Richard; Beaumont, Jennifer L; Mungas, Dan; Manly, Jennifer J; Moy, Claudia; Conway, Kevin; Edwards, Emmeline; Nowinski, Cindy J; Gershon, Richard

    2014-07-01

    This study introduces a special series on validity studies of the Cognition Battery (CB) from the U.S. National Institutes of Health Toolbox for the Assessment of Neurological and Behavioral Function (NIHTB) (Gershon, Wagster et al., 2013) in an adult sample. This first study in the series describes the sample, each of the seven instruments in the NIHTB-CB briefly, and the general approach to data analysis. Data are provided on test-retest reliability and practice effects, and raw scores (mean, standard deviation, range) are presented for each instrument and the gold standard instruments used to measure construct validity. Accompanying papers provide details on each instrument, including information about instrument development, psychometric properties, age and education effects on performance, and convergent and discriminant construct validity. One study in the series is devoted to a factor analysis of the NIHTB-CB in adults and another describes the psychometric properties of three composite scores derived from the individual measures representing fluid and crystallized abilities and their combination. The NIHTB-CB is designed to provide a brief, comprehensive, common set of measures to allow comparisons among disparate studies and to improve scientific communication.

  2. Reprocessing Close Range Terrestrial and Uav Photogrammetric Projects with the Dbat Toolbox for Independent Verification and Quality Control

    Science.gov (United States)

    Murtiyoso, A.; Grussenmeyer, P.; Börlin, N.

    2017-11-01

    Photogrammetry has recently seen a rapid increase in many applications, thanks to developments in computing power and algorithms. Furthermore with the democratisation of UAVs (Unmanned Aerial Vehicles), close range photogrammetry has seen more and more use due to the easier capability to acquire aerial close range images. In terms of photogrammetric processing, many commercial software solutions exist in the market that offer results from user-friendly environments. However, in most commercial solutions, a black-box approach to photogrammetric calculations is often used. This is understandable in light of the proprietary nature of the algorithms, but it may pose a problem if the results need to be validated in an independent manner. In this paper, the Damped Bundle Adjustment Toolbox (DBAT) developed for Matlab was used to reprocess some photogrammetric projects that were processed using the commercial software Agisoft Photoscan. Several scenarios were experimented on in order to see the performance of DBAT in reprocessing terrestrial and UAV close range photogrammetric projects in several configurations of self-calibration setting. Results show that DBAT managed to reprocess PS projects and generate metrics which can be useful for project verification.

  3. Creating Qungasvik (a Yup'ik intervention "toolbox"): case examples from a community-developed and culturally-driven intervention.

    Science.gov (United States)

    Rasmus, Stacy M; Charles, Billy; Mohatt, Gerald V

    2014-09-01

    This paper describes the development of a Yup'ik Alaska Native approach to suicide and alcohol abuse prevention that resulted in the creation of the Qungasvik, a toolbox promoting reasons for life and sobriety among youth. The Qungasvik is made up of thirty-six modules that function as cultural scripts for creating experiences in Yup'ik communities that build strengths and protection against suicide and alcohol abuse. The Qungasvik manual represents the results of a community based participatory research intervention development process grounded in culture and local process, and nurtured through a syncretic blending of Indigenous and Western theories and practices. This paper will provide a description of the collaborative steps taken at the community-level to develop the intervention modules. This process involved university researchers and community members coming together and drawing from multiple sources of data and knowledge to inform the development of prevention activities addressing youth suicide and alcohol abuse. We will present case examples describing the development of three keystone modules; Qasgiq (The Men's House), Yup'ik Kinship Terms, and Surviving Your Feelings. These modules each are representative of the process that the community co-researcher team took to develop and implement protective experiences that: (1) create supportive community, (2) strengthen families, and (3) give individuals tools to be healthy and strong.

  4. REPROCESSING CLOSE RANGE TERRESTRIAL AND UAV PHOTOGRAMMETRIC PROJECTS WITH THE DBAT TOOLBOX FOR INDEPENDENT VERIFICATION AND QUALITY CONTROL

    Directory of Open Access Journals (Sweden)

    A. Murtiyoso

    2017-11-01

    Full Text Available Photogrammetry has recently seen a rapid increase in many applications, thanks to developments in computing power and algorithms. Furthermore with the democratisation of UAVs (Unmanned Aerial Vehicles, close range photogrammetry has seen more and more use due to the easier capability to acquire aerial close range images. In terms of photogrammetric processing, many commercial software solutions exist in the market that offer results from user-friendly environments. However, in most commercial solutions, a black-box approach to photogrammetric calculations is often used. This is understandable in light of the proprietary nature of the algorithms, but it may pose a problem if the results need to be validated in an independent manner. In this paper, the Damped Bundle Adjustment Toolbox (DBAT developed for Matlab was used to reprocess some photogrammetric projects that were processed using the commercial software Agisoft Photoscan. Several scenarios were experimented on in order to see the performance of DBAT in reprocessing terrestrial and UAV close range photogrammetric projects in several configurations of self-calibration setting. Results show that DBAT managed to reprocess PS projects and generate metrics which can be useful for project verification.

  5. Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater.

    Science.gov (United States)

    Tran, Ngoc Han; Gin, Karina Yew-Hoong; Ngo, Huu Hao

    2015-12-15

    The quality of surface waters/groundwater of a geographical region can be affected by anthropogenic activities, land use patterns and fecal pollution sources from humans and animals. Therefore, the development of an efficient fecal pollution source tracking toolbox for identifying the origin of the fecal pollution sources in surface waters/groundwater is especially helpful for improving management efforts and remediation actions of water resources in a more cost-effective and efficient manner. This review summarizes the updated knowledge on the use of fecal pollution source tracking markers for detecting, evaluating and characterizing fecal pollution sources in receiving surface waters and groundwater. The suitability of using chemical markers (i.e. fecal sterols, fluorescent whitening agents, pharmaceuticals and personal care products, and artificial sweeteners) and/or microbial markers (e.g. F+RNA coliphages, enteric viruses, and host-specific anaerobic bacterial 16S rDNA genetic markers) for tracking fecal pollution sources in receiving water bodies is discussed. In addition, this review also provides a comprehensive approach, which is based on the detection ratios (DR), detection frequencies (DF), and fate of potential microbial and chemical markers. DR and DF are considered as the key criteria for selecting appropriate markers for identifying and evaluating the impacts of fecal contamination in surface waters/groundwater. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. PL-DA-PS: A hardware architecture and software toolbox for neurophysiology requiring complex visual stimuli and online behavioral control

    Directory of Open Access Journals (Sweden)

    Kyler M. Eastman

    2012-01-01

    Full Text Available Neurophysiological studies in awake, behaving primates (both human and nonhuman primates have focused with increasing scrutiny on the temporal relationship between neural signals and behaviors. Consequently, laboratories are often faced with the problem of developing experimental equipment that can support data recording with high temporal precision and also be flexible enough to accommodate a wide variety of experimental paradigms. To this end, we have developed an architecture that integrates several modern pieces of equipment, but still grants experimenters a high degree of flexibility. Our hardware architecture and software tools take advantage of three popular and powerful technologies: the PLexon apparatus for neurophysiological recordings (Plexon, Inc., Dallas TX, a DAtapixx box (Vpixx Technologies, Saint-Bruno, QC, Canada for analog, digital, and video signal input-output control, and the PSychtoolbox MATLAB toolbox for stimulus generation (Brainard, 1997. The PL-DA-PS (Platypus system is designed to support the study of the visual systems of awake, behaving primates during multi-electrode neurophysiological recordings, but can be easily applied to other related domains. Despite its wide range of capabilities and support for cutting-edge video displays and neural recording systems, the PLDAPS system is simple enough for someone with basic MATLAB programming skills to design their own experiments.

  7. The EnMAP-Box—A Toolbox and Application Programming Interface for EnMAP Data Processing

    Directory of Open Access Journals (Sweden)

    Sebastian van der Linden

    2015-09-01

    Full Text Available The EnMAP-Box is a toolbox that is developed for the processing and analysis of data acquired by the German spaceborne imaging spectrometer EnMAP (Environmental Mapping and Analysis Program. It is developed with two aims in mind in order to guarantee full usage of future EnMAP data, i.e., (1 extending the EnMAP user community and (2 providing access to recent approaches for imaging spectroscopy data processing. The software is freely available and offers a range of tools and applications for the processing of spectral imagery, including classical processing tools for imaging spectroscopy data as well as powerful machine learning approaches or interfaces for the integration of methods available in scripting languages. A special developer version includes the full open source code, an application programming interface and an application wizard for easy integration and documentation of new developments. This paper gives an overview of the EnMAP-Box for users and developers, explains typical workflows along an application example and exemplifies the concept for making it a frequently used and constantly extended platform for imaging spectroscopy applications.

  8. iSpectra: An Open Source Toolbox For The Analysis of Spectral Images Recorded on Scanning Electron Microscopes.

    Science.gov (United States)

    Liebske, Christian

    2015-08-01

    iSpectra is an open source and system-independent toolbox for the analysis of spectral images (SIs) recorded on energy-dispersive spectroscopy (EDS) systems attached to scanning electron microscopes (SEMs). The aim of iSpectra is to assign pixels with similar spectral content to phases, accompanied by cumulative phase spectra with superior counting statistics for quantification. Pixel-to-phase assignment starts with a threshold-based pre-sorting of spectra to create groups of pixels with identical elemental budgets, similar to a method described by van Hoek (2014). Subsequent merging of groups and re-assignments of pixels using elemental or principle component histogram plots enables the user to generate chemically and texturally plausible phase maps. A variety of standard image processing algorithms can be applied to groups of pixels to optimize pixel-to-phase assignments, such as morphology operations to account for overlapping excitation volumes over pixels located at phase boundaries. iSpectra supports batch processing and allows pixel-to-phase assignments to be applied to an unlimited amount of SIs, thus enabling phase mapping of large area samples like petrographic thin sections.

  9. DAFNE: A Matlab toolbox for Bayesian multi-source remote sensing and ancillary data fusion, with application to flood mapping

    Science.gov (United States)

    D'Addabbo, Annarita; Refice, Alberto; Lovergine, Francesco P.; Pasquariello, Guido

    2018-03-01

    High-resolution, remotely sensed images of the Earth surface have been proven to be of help in producing detailed flood maps, thanks to their synoptic overview of the flooded area and frequent revisits. However, flood scenarios can be complex situations, requiring the integration of different data in order to provide accurate and robust flood information. Several processing approaches have been recently proposed to efficiently combine and integrate heterogeneous information sources. In this paper, we introduce DAFNE, a Matlab®-based, open source toolbox, conceived to produce flood maps from remotely sensed and other ancillary information, through a data fusion approach. DAFNE is based on Bayesian Networks, and is composed of several independent modules, each one performing a different task. Multi-temporal and multi-sensor data can be easily handled, with the possibility of following the evolution of an event through multi-temporal output flood maps. Each DAFNE module can be easily modified or upgraded to meet different user needs. The DAFNE suite is presented together with an example of its application.

  10. A House Full of Trap Doors. Identifying barriers to resilient drylands in the toolbox of pastoral development

    Science.gov (United States)

    Krätli, Saverio; Kaufmann, Brigitte; Roba, Hassan; Hiernaux, Pierre; Li, Wenjun; Easdale, Marcos H.; Huelsebusch, Christian

    2016-04-01

    The theoretical understanding of drylands and pastoral systems has long undergone a U-turn from the initial perspective rooted in classical ecology. The shift has hinged on the way to represent asymmetric variability, from a disturbance in an ecosystem that naturally tends towards uniformity and stability, to a constitutive part of a dynamic ecosystem. Operationalising the new reversed perspective, including the need to update the methodological infrastructure to plan around drylands and pastoral development, remains a challenge. Underlying assumptions about stability and uniformity, that are a legacy of equilibrium thinking, remain embedded in the toolbox of pastoral development, starting from the technical language to talk about the subject. This effectively gets in the way of operationalizing state of the art understanding of pastoral systems and the drylands. Unless these barriers are identified, unpacked and managed, even the present calls for increasing the rigour and intensity of data collection - for example as part of the ongoing global process to revise and improve agricultural data - cannot deliver a realistic representation of pastoral systems in statistics and policy making. This contribution presents the case for understanding variability as an asset, and provides a range of examples of methodological barriers, including classifications of livestock systems, scale of observation, key parameters in animal production, indicators in the measurement of ecological efficiency, concepts of ecological fragility, natural resources, and pastoral risk. The need to update this legacy is a pressing challenge for policy makers concerned with both modernisation and resilience in the drylands.

  11. The Irie Classroom Toolbox: developing a violence prevention, preschool teacher training program using evidence, theory, and practice.

    Science.gov (United States)

    Baker-Henningham, Helen

    2018-05-01

    In this paper, I describe the development of the Irie Classroom Toolbox, a school-based violence prevention, teacher training program for use with children aged 3-6 years. In-depth interviews were conducted with Jamaican preschool teachers, who had participated in a trial of a classroom behavior management program, at posttest (n = 35) and 5 years later (n = 20). An on-going process evaluation was also conducted. Teachers' preferred behavior management strategies and training methods were documented, and enablers and barriers to implementation were identified. Teachers were most likely to adopt strategies that they liked, found easy to use, and were effective. These included paying attention to positive behavior and explicitly teaching children the expected behavior. Teachers preferred active, hands-on training strategies based on social-cognitive theories. Enablers to intervention implementation included positive teacher-facilitator relationships, choice, collaborative problem solving, teachers recognizing benefits of the intervention, group support, and provision of materials. Barriers to intervention implementation were also identified. These data were integrated with behavior change theory (i.e., the behavior change wheel and theoretical domains framework) to develop an intervention grounded in common core elements of evidence-based programs while also utilizing teachers' perspectives. The resulting program is a low cost, adaptable intervention that should be suitable for training preschool teachers in other low-resource settings. © 2018 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of The New York Academy of Sciences.

  12. MODELLING OF THE RISK FACTORS AND CHRONIC DISEASESTHAT INFLUENCE THE DEVELOPMENT OF SERIOUS HEALTHCOMPLICATIONS

    Directory of Open Access Journals (Sweden)

    Maja Atanasijević-Kunc

    2008-08-01

    For a quantitative evaluation of the mentioned patient groups, the age distribution andan estimation of the treatment expenses a dynamic mathematical model was developed,where special attention was devoted to its structure, as it should enable the sequentialconstruction and representation of different forms of data information. The model wasrealized in the Matlab program package with the Simulink Toolbox.

  13. A problem-solving environment for data assimilation in air quality modelling

    NARCIS (Netherlands)

    Velzen, N. van; Segers, A.J.

    2010-01-01

    A generic toolbox for data assimilation called COSTA (COmmon Set of Tools for the Assimilation of data) makes it possible to simplify the application of data assimilation to models and to try out various methods for a particular model. Concepts of object oriented programming are used to define

  14. Power system dynamics and stability with synchrophasor measurement and power system toolbox

    CERN Document Server

    Sauer, Peter W; Chow, Joe H

    2017-01-01

    This new edition addresses the needs of dynamic modeling and simulation relevant to power system planning, design, and operation, including a systematic derivation of synchronous machine dynamic models together with speed and voltage control subsystems. Reduced-order modeling based on integral manifolds is used as a firm basis for understanding the derivations and limitations of lower-order dynamic models. Following these developments, a multi-machine model interconnected through the transmission network is formulated and simulated using numerical simulation methods. Energy function methods are discussed for direct evaluation of stability. Small-signal analysis is used for determining the electromechanical modes and mode-shapes, and for power system stabilizer design. Time-synchronized high-sampling-rate phasor measurement units (PMUs) to monitor power system disturbances ave been implemented throughout North America and many other countries. In this second edition, new chapters on synchrophasor measurement ...

  15. A Few Insights Into Romanian Information Systems Analysts and Designers Toolbox

    Directory of Open Access Journals (Sweden)

    Fotache Marin

    2017-06-01

    Full Text Available Information Systems (IS analysts and designers have been key members in software development teams. From waterfall to Rational Unified Process, from UML to agile development, IS modelers have faced many trends and buzzwords. Even if the topic of models and modeling tools in software development is important, there are no many detailed studies to identify for what the developers, customers and managers decide to use the modeling and specific tools. Despite the popularity of the subject, studies showing what tools the IS modelers prefer are scarce, and quasi-non-existent, when talking about Romanian market. As Romania is an important IT outsourcing market, this paper investigated what methods and tools Romanian IS analysts and designers apply. In this context, the starting question of our research focuses on the preference of the developers to choose between agile or non-agile methods in IT projects. As a result, the research questions targeted the main drivers in choosing specific methods and tools for IT projects deployed in Romanian companies. Also, one of the main objectives of this paper was to approach the relationship between the methodologies (agile or non-agile, diagrams and other tools (we refer in our study to the CASE features with other variables/metrics of the system/software development project. The observational study was conducted based on a survey filled by IS modelers in Romanian IT companies. The data collected were processed and analyzed using Exploratory Data Analysis. The platform for data visualization and analysis was R.

  16. A wave generation toolbox for the open‐source CFD library: OpenFoam

    DEFF Research Database (Denmark)

    Jacobsen, Niels Gjøl; Fuhrman, David R.; Fredsøe, Jørgen

    2012-01-01

    The open‐source CFD library OpenFoam® contains a method for solving free surface Newtonian flows using the Reynolds averaged Navier–Stokes equations coupled with a volume of fluid method. In this paper, it is demonstrated how this has been extended with a generic wave generation and absorption...... method termed ‘wave relaxation zones’, on which a detailed account is given. The ability to use OpenFoam for the modelling of waves is demonstrated using two benchmark test cases, which show the ability to model wave propagation and wave breaking. Furthermore, the reflection coefficient from outlet...... made freely available through the OpenFoam‐Extend Community....

  17. Expanding the Tissue Toolbox : Deriving Colon Tissue from Human Pluripotent Stem Cells

    NARCIS (Netherlands)

    Bruens, Lotte; Snippert, Hugo J.G.

    2017-01-01

    Organoid technology holds great potential for disease modeling and regenerative medicine. In this issue of Cell Stem Cell, Múnera et al. (2017) establish the generation of pluripotent stem cell-derived colon organoids that upon transplantation in mice, resembling human colon to a large extent,

  18. LEA in Private: A Privacy and Data Protection Framework for a Learning Analytics Toolbox

    Science.gov (United States)

    Steiner, Christina M.; Kickmeier-Rust, Michael D.; Albert, Dietrich

    2016-01-01

    To find a balance between learning analytics research and individual privacy, learning analytics initiatives need to appropriately address ethical, privacy, and data protection issues. A range of general guidelines, model codes, and principles for handling ethical issues and for appropriate data and privacy protection are available, which may…

  19. A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels.

    Science.gov (United States)

    Keator, David Bryant; Gadde, Syam; Grethe, Jeffrey S; Taylor, Derek V; Potkin, Steven G

    2006-01-01

    With the increased frequency of multisite, large-scale collaborative neuro-imaging studies, the need for a general, self-documenting framework for the storage and retrieval of activation maps and anatomical labels becomes evident. To address this need, we have developed and extensible markup language (XML) schema and associated tools for the storage of neuro-imaging activation maps and anatomical labels. This schema, as part of the XML-based Clinical Experiment Data Exchange (XCEDE) schema, provides storage capabilities for analysis annotations, activation threshold parameters, and cluster and voxel-level statistics. Activation parameters contain information describing the threshold, degrees of freedom, FWHM smoothness, search volumes, voxel sizes, expected voxels per cluster, and expected number of clusters in the statistical map. Cluster and voxel statistics can be stored along with the coordinates, threshold, and anatomical label information. Multiple threshold types can be documented for a given cluster or voxel along with the uncorrected and corrected probability values. Multiple atlases can be used to generate anatomical labels and stored for each significant voxel or cluter. Additionally, a toolbox for Statistical Parametric Mapping software (http://www. fil. ion.ucl.ac.uk/spm/) was created to capture the results from activation maps using the XML schema that supports both SPM99 and SPM2 versions (http://nbirn.net/Resources/Users/ Applications/xcede/SPM_XMLTools.htm). Support for anatomical labeling is available via the Talairach Daemon (http://ric.uthscsa. edu/projects/talairachdaemon.html) and Automated Anatomical Labeling (http://www. cyceron.fr/freeware/).

  20. AREVA's toolbox for long-term best performance and reliable operation of nuclear steam generators

    International Nuclear Information System (INIS)

    Drexler, Andreas; Weiss, Steffen; Caris, Neil; Stiepani, Christoph

    2015-01-01

    Long-term integrity and high performance of major plant systems and components are of uppermost importance for the successful operation of any power plant. AREVA's experience gathered with water-steam cycle chemistry treatments in more than 40 years yields the conclusion: Accumulation of corrosion products in SGs may result in local overheating and enrichment of impurities up to critical levels. This can lead to several degradation phenomena of the structural materials of the SGs. Therefore, minimization of corrosion product generation and prevention of deposit accumulation is required. The objective of AREVA's asset management program is to support operators by minimizing corrosion damage and performance losses of water-steam cycle systems and components and thereby to maximize the availability and economic performance of the plant. Such asset management program is in principle a closed cycle process. It is based on control, corrective and preventive measures. The objective of control measure is deriving a widespread assessment of the corrosion status of the steam-water cycle which yields to weak points and identifying the best suited corrective and/or preventive measures. In the subsequent steps appropriate measures which improve the current status or counteract on identified issues are identified and applied. Corrective measures, likes mechanical and/or chemical cleaning are targeting the minimization of negative influence on plant performance caused by corrosion in the steam-water cycle. Complementary to corrective measures are preventive ones, like optimization of pH strategy and AREVA's FFA technology could by applied. They are focusing on the origin of corrosion product generation. AREVA is offering a toolbox for long-term best performance and reliable operation of NPPs. (author)

  1. A novel FbFP-based biosensor toolbox for sensitive in vivo determination of intracellular pH.

    Science.gov (United States)

    Rupprecht, Christian; Wingen, Marcus; Potzkei, Janko; Gensch, Thomas; Jaeger, Karl-Erich; Drepper, Thomas

    2017-09-20

    The intracellular pH is an important modulator of various bio(techno)logical processes such as enzymatic conversion of metabolites or transport across the cell membrane. Changes of intracellular pH due to altered proton distribution can thus cause dysfunction of cellular processes. Consequently, accurate monitoring of intracellular pH allows elucidating the pH-dependency of (patho)physiological and biotechnological processes. In this context, genetically encoded biosensors represent a powerful tool to determine intracellular pH values non-invasively and with high spatiotemporal resolution. We have constructed a toolbox of novel genetically encoded FRET-based pH biosensors (named Fluorescence Biosensors for pH or FluBpH) that utilizes the FMN-binding fluorescent protein EcFbFP as donor domain. In contrast to many fluorescent proteins of the GFP family, EcFbFP exhibits a remarkable tolerance towards acidic pH (pK a ∼3.2). To cover the broad range of physiologically relevant pH values, three EYFP variants exhibiting pK a values of 5.7, 6.1 and 7.5 were used as pH-sensing FRET acceptor domains. The resulting biosensors FluBpH 5.7, FluBpH 6.1 and FluBpH 7.5 were calibrated in vitro and in vivo to accurately evaluate their pH indicator properties. To demonstrate the in vivo applicability of FluBpH, changes of intracellular pH were ratiometrically measured in E. coli cells during acid stress. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Analysis of Power Laws, Shape Collapses, and Neural Complexity: New Techniques and MATLAB Support via the NCC Toolbox.

    Science.gov (United States)

    Marshall, Najja; Timme, Nicholas M; Bennett, Nicholas; Ripp, Monica; Lautzenhiser, Edward; Beggs, John M

    2016-01-01

    Neural systems include interactions that occur across many scales. Two divergent methods for characterizing such interactions have drawn on the physical analysis of critical phenomena and the mathematical study of information. Inferring criticality in neural systems has traditionally rested on fitting power laws to the property distributions of "neural avalanches" (contiguous bursts of activity), but the fractal nature of avalanche shapes has recently emerged as another signature of criticality. On the other hand, neural complexity, an information theoretic measure, has been used to capture the interplay between the functional localization of brain regions and their integration for higher cognitive functions. Unfortunately, treatments of all three methods-power-law fitting, avalanche shape collapse, and neural complexity-have suffered from shortcomings. Empirical data often contain biases that introduce deviations from true power law in the tail and head of the distribution, but deviations in the tail have often been unconsidered; avalanche shape collapse has required manual parameter tuning; and the estimation of neural complexity has relied on small data sets or statistical assumptions for the sake of computational efficiency. In this paper we present technical advancements in the analysis of criticality and complexity in neural systems. We use maximum-likelihood estimation to automatically fit power laws with left and right cutoffs, present the first automated shape collapse algorithm, and describe new techniques to account for large numbers of neural variables and small data sets in the calculation of neural complexity. In order to facilitate future research in criticality and complexity, we have made the software utilized in this analysis freely available online in the MATLAB NCC (Neural Complexity and Criticality) Toolbox.

  3. Expanding the Strained Alkyne Toolbox: Generation and Utility of Oxygen-Containing Strained Alkynes.

    Science.gov (United States)

    Shah, Tejas K; Medina, Jose M; Garg, Neil K

    2016-04-13

    We report synthetic methodology that permits access to two oxacyclic strained intermediates, the 4,5-benzofuranyne and the 3,4-oxacyclohexyne. In situ trapping of these intermediates affords an array of heterocyclic scaffolds by the formation of one or more new C-C or C-heteroatom bonds. Experimentally determined regioselectivities were consistent with predictions made using the distortion/interaction model and were also found to be greater compared to selectivities seen in the case of trapping experiments of the corresponding N-containing intermediates. These studies demonstrate the synthetic versatility of oxacyclic arynes and alkynes for the synthesis of functionalized heterocycles, while further expanding the scope of the distortion/interaction model. Moreover, these efforts underscore the value of harnessing strained heterocyclic intermediates as a unique approach to building polycyclic heteroatom-containing frameworks.

  4. Toolbox for uncertainty; Introduction of adaptive heuristics as strategies for project decision making

    DEFF Research Database (Denmark)

    Stingl, Verena; Geraldi, Joana

    2017-01-01

    This article presents adaptive heuristics as an alternative approach to navigate uncertainty in project decision-making. Adaptive heuristic are a class of simple decision strategies that have received only scant attention in project studies. Yet, they can strive in contexts of high uncertainty...... they are ‘ecologically rational’. The model builds on the individual definitions of ecological rationality and organizes them according to two types of uncertainty (‘knowable’ and ‘unknowable’). Decision problems and heuristics are furthermore grouped by decision task (choice and judgement). The article discusses...... and limited information, which are the typical project decision context. This article develops a conceptual model that supports a systematic connection between adaptive heuristics and project decisions. Individual adaptive heuristics succeed only in specific decision environments, in which...

  5. Development of a Simulink® toolbox for friction control design and compensation

    Directory of Open Access Journals (Sweden)

    Teodor DUMITRIU

    2005-12-01

    Full Text Available This paper focuses on the development of a MATLAB/Simulink® library for servo-systems with friction as a part of a new simulation platform dedicated to model, analysis and control design of friction. It is well known that friction is a very important process for the control engineering both for high-precision servo – mechanisms and simple pneumatic and hydraulic systems. Highly nonlinear process, friction may result in steady state errors, limit cycles and poor performance. It is therefore important for control engineering to understand friction phenomena and to know how to deal with them. Moreover, a reliable library of friction models that captures the friction behavior provides an important tool in order to investigate by analysis and simulation the properties of friction that are relevant to control design.

  6. Understanding socio-groundwater systems: framework, toolbox, and stakeholders’ efforts for analysis and monitoring groundwater resources

    OpenAIRE

    López Maldonado, Yolanda Cristina

    2018-01-01

    Groundwater, the predominant accessible reservoir of freshwater storage on Earth, plays an important role as a human-natural life sustaining resource. In recent decades there has been an increasing concern that human activities are placing too much pressure on the resource, affecting the health of the ecosystem. However, because groundwater it is out of sight, its monitoring on both global and local scales is challenging. In the field of groundwater monitoring, modelling tools have been devel...

  7. Stress, strain, and structural dynamics an interactive handbook of formulas, solutions, and Matlab toolboxes

    CERN Document Server

    Yang, Bingen

    2005-01-01

    Stress, Strain, and Structural Dynamics is a comprehensive and definitive reference to statics and dynamics of solids and structures, including mechanics of materials, structural mechanics, elasticity, rigid-body dynamics, vibrations, structural dynamics, and structural controls. This text integrates the development of fundamental theories, formulas and mathematical models with user-friendly interactive computer programs, written in the powerful and popular MATLAB. This unique merger of technical referencing and interactive computing allows instant solution of a variety of engineering problems

  8. Electronic audit and feedback intervention with action implementation toolbox to improve pain management in intensive care: protocol for a laboratory experiment and cluster randomised trial.

    Science.gov (United States)

    Gude, Wouter T; Roos-Blom, Marie-José; van der Veer, Sabine N; de Jonge, Evert; Peek, Niels; Dongelmans, Dave A; de Keizer, Nicolette F

    2017-05-25

    Audit and feedback is often used as a strategy to improve quality of care, however, its effects are variable and often marginal. In order to learn how to design and deliver effective feedback, we need to understand their mechanisms of action. This theory-informed study will investigate how electronic audit and feedback affects improvement intentions (i.e. information-intention gap), and whether an action implementation toolbox with suggested actions and materials helps translating those intentions into action (i.e. intention-behaviour gap). The study will be executed in Dutch intensive care units (ICUs) and will be focused on pain management. We will conduct a laboratory experiment with individual ICU professionals to assess the impact of feedback on their intentions to improve practice. Next, we will conduct a cluster randomised controlled trial with ICUs allocated to feedback without or feedback with action implementation toolbox group. Participants will not be told explicitly what aspect of the intervention is randomised; they will only be aware that there are two variations of providing feedback. ICUs are eligible for participation if they submit indicator data to the Dutch National Intensive Care Evaluation (NICE) quality registry and agree to allocate a quality improvement team that spends 4 h per month on the intervention. All participating ICUs will receive access to an online quality dashboard that provides two functionalities: gaining insight into clinical performance on pain management indicators and developing action plans. ICUs with access to the toolbox can develop their action plans guided by a list of potential barriers in the care process, associated suggested actions, and supporting materials to facilitate implementation of the actions. The primary outcome measure for the laboratory experiment is the proportion of improvement intentions set by participants that are consistent with recommendations based on peer comparisons; for the randomised

  9. Integration of 3D printing and additive manufacturing in the interventional pulmonologist's toolbox.

    Science.gov (United States)

    Guibert, Nicolas; Mhanna, Laurent; Didier, Alain; Moreno, Benjamin; Leyx, Pierre; Plat, Gavin; Mazieres, Julien; Hermant, Christophe

    2018-01-01

    New 3D technologies are rapidly entering into the surgical landscape, including in interventional pulmonology. The transition of 2D restricted data into a physical model of pathological airways by three-dimensional printing (3DP) allows rapid prototyping and fabrication of complex and patient-specific shapes and can thus help the physician to plan and guide complex procedures. Furthermore, computer-assisted designed (CAD) patient-specific devices have already helped surgeons overcome several therapeutic impasses and are likely to rapidly cover a wider range of situations. We report herein with a special focus on our clinical experience: i) how additive manufacturing is progressively integrated into the management of complex central airways diseases; ii) the appealing future directions of these new technologies, including the potential of the emerging technique of bioprinting; iii) the main pitfalls that could delay its introduction into routine care. Copyright © 2017. Published by Elsevier Ltd.

  10. A model library for simulation and benchmarking of integrated urban wastewater systems

    DEFF Research Database (Denmark)

    Saagi, R.; Flores Alsina, Xavier; Kroll, J. S.

    2017-01-01

    This paper presents a freely distributed, open-source toolbox to predict the behaviour of urban wastewater systems (UWS). The proposed library is used to develop a system-wide Benchmark Simulation Model (BSM-UWS) for evaluating (local/global) control strategies in urban wastewater systems (UWS...

  11. C code generation applied to nonlinear model predictive control for an artificial pancreas

    DEFF Research Database (Denmark)

    Boiroux, Dimitri; Jørgensen, John Bagterp

    2017-01-01

    This paper presents a method to generate C code from MATLAB code applied to a nonlinear model predictive control (NMPC) algorithm. The C code generation uses the MATLAB Coder Toolbox. It can drastically reduce the time required for development compared to a manual porting of code from MATLAB to C...

  12. Expanding the Immunology Toolbox: Embracing Public-Data Reuse and Crowdsourcing.

    Science.gov (United States)

    Sparks, Rachel; Lau, William W; Tsang, John S

    2016-12-20

    New technologies have been propelling dramatic increases in the volume and diversity of large-scale public data, which can potentially be reused to answer questions beyond those originally envisioned. However, this often requires computational and statistical skills beyond the reach of most bench scientists. The development of educational and accessible computational tools is thus critical, as are crowdsourcing efforts that utilize the community's expertise to curate public data for hypothesis generation and testing. Here we review the history of public-data reuse and argue for greater incorporation of computational and statistical sciences into the biomedical education curriculum and the development of biologist-friendly crowdsourcing tools. Finally, we provide a resource list for the reuse of public data and highlight an illustrative crowdsourcing exercise to explore public gene-expression data of human autoimmune diseases and corresponding mouse models. Through education, tool development, and community engagement, immunologists will be poised to transform public data into biological insights. Copyright © 2016. Published by Elsevier Inc.

  13. Augmenting the Genetic Toolbox for Sulfolobus islandicus with a Stringent Positive Selectable Marker for Agmatine Prototrophy

    Science.gov (United States)

    Cooper, Tara E.; Krause, David J.

    2013-01-01

    Sulfolobus species have become the model organisms for studying the unique biology of the crenarchaeal division of the archaeal domain. In particular, Sulfolobus islandicus provides a powerful opportunity to explore natural variation via experimental functional genomics. To support these efforts, we further expanded genetic tools for S. islandicus by developing a stringent positive selection for agmatine prototrophs in strains in which the argD gene, encoding arginine decarboxylase, has been deleted. Strains with deletions in argD were shown to be auxotrophic for agmatine even in nutrient-rich medium, but growth could be restored by either supplementation of exogenous agmatine or reintroduction of a functional copy of the argD gene from S. solfataricus P2 into the ΔargD host. Using this stringent selection, a robust targeted gene knockout system was established via an improved next generation of the MID (marker insertion and unmarked target gene deletion) method. Application of this novel system was validated by targeted knockout of the upsEF genes involved in UV-inducible cell aggregation formation. PMID:23835176

  14. A toolbox of lectins for translating the sugar code: the galectin network in phylogenesis and tumors.

    Science.gov (United States)

    Kaltner, H; Gabius, H-J

    2012-04-01

    Lectin histochemistry has revealed cell-type-selective glycosylation. It is under dynamic and spatially controlled regulation. Since their chemical properties allow carbohydrates to reach unsurpassed structural diversity in oligomers, they are ideal for high density information coding. Consequently, the concept of the sugar code assigns a functional dimension to the glycans of cellular glycoconjugates. Indeed, multifarious cell processes depend on specific recognition of glycans by their receptors (lectins), which translate the sugar-encoded information into effects. Duplication of ancestral genes and the following divergence of sequences account for the evolutionary dynamics in lectin families. Differences in gene number can even appear among closely related species. The adhesion/growth-regulatory galectins are selected as an instructive example to trace the phylogenetic diversification in several animals, most of them popular models in developmental and tumor biology. Chicken galectins are identified as a low-level-complexity set, thus singled out for further detailed analysis. The various operative means for establishing protein diversity among the chicken galectins are delineated, and individual characteristics in expression profiles discerned. To apply this galectin-fingerprinting approach in histopathology has potential for refining differential diagnosis and for obtaining prognostic assessments. On the grounds of in vitro work with tumor cells a strategically orchestrated co-regulation of galectin expression with presentation of cognate glycans is detected. This coordination epitomizes the far-reaching physiological significance of sugar coding.

  15. Geocoding uncertainty analysis for the automated processing of Sentinel-1 data using Sentinel-1 Toolbox software

    Science.gov (United States)

    Dostálová, Alena; Naeimi, Vahid; Wagner, Wolfgang; Elefante, Stefano; Cao, Senmao; Persson, Henrik

    2016-10-01

    One of the major advantages of the Sentinel-1 data is its capability to provide very high spatio-temporal coverage allowing the mapping of large areas as well as creation of dense time-series of the Sentinel-1 acquisitions. The SGRT software developed at TU Wien aims at automated processing of Sentinel-1 data for global and regional products. The first step of the processing consists of the Sentinel-1 data geocoding with the help of S1TBX software and their resampling to a common grid. These resampled images serve as an input for the product derivation. Thus, it is very important to select the most reliable processing settings and assess the geocoding uncertainty for both backscatter and projected local incidence angle images. Within this study, selection of Sentinel-1 acquisitions over 3 test areas in Europe were processed manually in the S1TBX software, testing multiple software versions, processing settings and digital elevation models (DEM) and the accuracy of the resulting geocoded images were assessed. Secondly, all available Sentinel-1 data over the areas were processed using selected settings and detailed quality check was performed. Overall, strong influence of the used DEM on the geocoding quality was confirmed with differences up to 80 meters in areas with higher terrain variations. In flat areas, the geocoding accuracy of backscatter images was overall good, with observed shifts between 0 and 30m. Larger systematic shifts were identified in case of projected local incidence angle images. These results encourage the automated processing of large volumes of Sentinel-1 data.

  16. U.S. Geological Survey groundwater toolbox, a graphical and mapping interface for analysis of hydrologic data (version 1.0): user guide for estimation of base flow, runoff, and groundwater recharge from streamflow data

    Science.gov (United States)

    Barlow, Paul M.; Cunningham, William L.; Zhai, Tong; Gray, Mark

    2015-01-01

    This report is a user guide for the streamflow-hydrograph analysis methods provided with version 1.0 of the U.S. Geological Survey (USGS) Groundwater Toolbox computer program. These include six hydrograph-separation methods to determine the groundwater-discharge (base-flow) and surface-runoff components of streamflow—the Base-Flow Index (BFI; Standard and Modified), HYSEP (Fixed Interval, Sliding Interval, and Local Minimum), and PART methods—and the RORA recession-curve displacement method and associated RECESS program to estimate groundwater recharge from streamflow data. The Groundwater Toolbox is a customized interface built on the nonproprietary, open source MapWindow geographic information system software. The program provides graphing, mapping, and analysis capabilities in a Microsoft Windows computing environment. In addition to the four hydrograph-analysis methods, the Groundwater Toolbox allows for the retrieval of hydrologic time-series data (streamflow, groundwater levels, and precipitation) from the USGS National Water Information System, downloading of a suite of preprocessed geographic information system coverages and meteorological data from the National Oceanic and Atmospheric Administration National Climatic Data Center, and analysis of data with several preprocessing and postprocessing utilities. With its data retrieval and analysis tools, the Groundwater Toolbox provides methods to estimate many of the components of the water budget for a hydrologic basin, including precipitation; streamflow; base flow; runoff; groundwater recharge; and total, groundwater, and near-surface evapotranspiration.

  17. Evaluation of FITC-induced atopic dermatitis-like disease in NC/Nga mice and BALB/c mice using computer-assisted stereological toolbox, a computer-aided morphometric system

    DEFF Research Database (Denmark)

    Hvid, Malene; Jensen, Helene Kofoed; Deleuran, Bent

    2009-01-01

    Stereological Toolbox as a stereological method, the mice were sensitized to FITC and the histological efficiency of disease induction with regard to inflammation and CD4+ and CD8+ lymphocytes, in addition to mast cells, was evaluated. The method was validated by comparison to a conventional semiquantitative...

  18. A distributed multimedia toolbox

    NARCIS (Netherlands)

    Scholten, Johan; Jansen, P.G.

    1997-01-01

    Emphasis of our research lies on the application of realtime multimedia technology: tele-teaching, teleconferencing and collaborative work. To support this research we need a real-time environment that supports rapid prototyping of distributed multimedia applications. Because other systems were not

  19. Photogrammetry Toolbox Reference Manual

    Science.gov (United States)

    Liu, Tianshu; Burner, Alpheus W.

    2014-01-01

    Specialized photogrammetric and image processing MATLAB functions useful for wind tunnel and other ground-based testing of aerospace structures are described. These functions include single view and multi-view photogrammetric solutions, basic image processing to determine image coordinates, 2D and 3D coordinate transformations and least squares solutions, spatial and radiometric camera calibration, epipolar relations, and various supporting utility functions.

  20. Isotope toolbox turns 10

    DEFF Research Database (Denmark)

    Wenander, Fredrik; Riisager, Karsten

    2012-01-01

    REX-ISOLDE, one of CERN’s most compact accelerators, has just celebrated its 10th anniversary. The machine’s versatility provides radioactive ion beams across the range of nuclear isotopes.......REX-ISOLDE, one of CERN’s most compact accelerators, has just celebrated its 10th anniversary. The machine’s versatility provides radioactive ion beams across the range of nuclear isotopes....

  1. Toolbox for Electric Fences

    Directory of Open Access Journals (Sweden)

    Melissa Gregg

    2013-09-01

    Full Text Available An affective dimension is often at work in constructions of political ‘reality’. Such a recognition might be seen to reinforce the value of certain legacies in cultural studies, particularly the role of articulation in public debate, and the renewed importance of such work in framing responses to volatile issues like the mandatory detention of asylum seekers. Revisiting the work of Stuart Hall on Thatcherism, and taking note of Judith Brett’s recent history of the Australian Liberal Party, I want to contemplate the prominent role language plays in political life, and, alongside Watson and others, question the priority the Left accords this key element of contemporary politics. In doing so, I use Hall as an example of what might be called scholarly affect: a voice of intervention that catalyses the Left in moments of crisis, and a voice that deploys cultural theory to make sense of concrete political problems.

  2. Mescoscopic Toolbox for Biophotonics

    DEFF Research Database (Denmark)

    Glückstad, Jesper

    I will outline the “spec’s” of our Biophotonics Workstation that we have developed in PPO at DTU Fotonik that utilizes high‐speed spatial light modulation to generate a plurality of independently reconfigurable optical traps making real‐time laser manipulation of biological or micro‐fabricated st......I will outline the “spec’s” of our Biophotonics Workstation that we have developed in PPO at DTU Fotonik that utilizes high‐speed spatial light modulation to generate a plurality of independently reconfigurable optical traps making real‐time laser manipulation of biological or micro...

  3. Mobile Context Toolbox

    DEFF Research Database (Denmark)

    Stopczynski, Arkadiusz; Larsen, Jakob Eg; Skomail, Lukasz

    2010-01-01

    In this paper we describe an open framework utilizing sensors and application data on the Maemo mobile platform enabling rapid prototyping of context-aware mobile applications. The framework has an extensible layered architecture allowing new hardware and software sensors and features to be added...... to the context framework. We present initial results from in-the-wild experiments where contextual data was acquired using the tool. In the experiments 6 participants were using a Nokia N900 mobile phone continuously with a logger application for an average of 33 days. The study has provided valuable insights...

  4. Matlab laser toolbox

    NARCIS (Netherlands)

    Römer, Gerardus Richardus, Bernardus, Engelina; Huis in 't Veld, Bert; Schmidt, M.; Vollertsen, F.; Geiger, M.

    2010-01-01

    Matlab® is a program for numeric computation, simulation and visualization, developed by The Mathworks, Inc. It is used heavily in education, research, and industry, for solving general, as well as application area-specific problems, that arise in various disciplines. For this purpose Matlab has

  5. Benchmarking in University Toolbox

    Directory of Open Access Journals (Sweden)

    Katarzyna Kuźmicz

    2015-06-01

    Full Text Available In the face of global competition and rising challenges that higher education institutions (HEIs meet, it is imperative to increase innovativeness and efficiency of their management. Benchmarking can be the appropriate tool to search for a point of reference necessary to assess institution’s competitive position and learn from the best in order to improve. The primary purpose of the paper is to present in-depth analysis of benchmarking application in HEIs worldwide. The study involves indicating premises of using benchmarking in HEIs. It also contains detailed examination of types, approaches and scope of benchmarking initiatives. The thorough insight of benchmarking applications enabled developing classification of benchmarking undertakings in HEIs. The paper includes review of the most recent benchmarking projects and relating them to the classification according to the elaborated criteria (geographical range, scope, type of data, subject, support and continuity. The presented examples were chosen in order to exemplify different approaches to benchmarking in higher education setting. The study was performed on the basis of the published reports from benchmarking projects, scientific literature and the experience of the author from the active participation in benchmarking projects. The paper concludes with recommendations for university managers undertaking benchmarking, derived on the basis of the conducted analysis.

  6. Putting computational modeling at the fingertips of bench biologists

    DEFF Research Database (Denmark)

    Sonnenschein, Nikolaus; Herrgard, Markus

    Communication is key in successful collaborations between theoretical and experimental life scientists. In our line of work we integrate physiological and systems-level data of cell factories with constraint-based Modeling approaches to predict suitable targets for metabolic engineering. The most......-level programming environment Mathematica and an open source metabolic modeling package (MASS Toolbox) to quickly prototype maps and other interactive widgets. In the long term, we would like to make those publicly accessible using open web technologies....

  7. Pareto design of state feedback tracking control of a biped robot via multiobjective PSO in comparison with sigma method and genetic algorithms: modified NSGAII and MATLAB's toolbox.

    Science.gov (United States)

    Mahmoodabadi, M J; Taherkhorsandi, M; Bagheri, A

    2014-01-01

    An optimal robust state feedback tracking controller is introduced to control a biped robot. In the literature, the parameters of the controller are usually determined by a tedious trial and error process. To eliminate this process and design the parameters of the proposed controller, the multiobjective evolutionary algorithms, that is, the proposed method, modified NSGAII, Sigma method, and MATLAB's Toolbox MOGA, are employed in this study. Among the used evolutionary optimization algorithms to design the controller for biped robots, the proposed method operates better in the aspect of designing the controller since it provides ample opportunities for designers to choose the most appropriate point based upon the design criteria. Three points are chosen from the nondominated solutions of the obtained Pareto front based on two conflicting objective functions, that is, the normalized summation of angle errors and normalized summation of control effort. Obtained results elucidate the efficiency of the proposed controller in order to control a biped robot.

  8. Performance of Hispanics and Non-Hispanic Whites on the NIH Toolbox Cognition Battery: the roles of ethnicity and language backgrounds.

    Science.gov (United States)

    Flores, Ilse; Casaletto, Kaitlin B; Marquine, Maria J; Umlauf, Anya; Moore, David J; Mungas, Dan; Gershon, Richard C; Beaumont, Jennifer L; Heaton, Robert K

    2017-05-01

    This study examined the influence of Hispanic ethnicity and language/cultural background on performance on the NIH Toolbox Cognition Battery (NIHTB-CB). Participants included healthy, primarily English-speaking Hispanic (n = 93; Hispanic-English), primarily Spanish-speaking Hispanic (n = 93; Hispanic-Spanish), and English speaking Non-Hispanic white (n = 93; NH white) adults matched on age, sex, and education levels. All participants were in the NIH Toolbox national norming project and completed the Fluid and Crystallized components of the NIHTB-CB. T-scores (demographically-unadjusted) were developed based on the current sample and were used in analyses. Spanish-speaking Hispanics performed worse than English-speaking Hispanics and NH whites on demographically unadjusted NIHTB-CB Fluid Composite scores (ps differences on tests of executive inhibitory control (p = .001), processing speed (p = .003), and working memory (p language/cultural backgrounds in the Hispanic-Spanish group: better vocabularies and reading were predicted by being born outside the U.S., having Spanish as a first language, attending school outside the U.S., and speaking more Spanish at home. However, many of these same background factors were associated with worse Fluid Composites within the Hispanic-Spanish group. On tests of Fluid cognition, the Hispanic-Spanish group performed the poorest of all groups. Socio-demographic and linguistic factors were associated with those differences. These findings highlight the importance of considering language/cultural backgrounds when interpreting neuropsychological test performances. Importantly, after applying previously published NIHTB-CB norms with demographic corrections, these language/ethnic group differences are eliminated.

  9. GAT: a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks.

    Science.gov (United States)

    Hosseini, S M Hadi; Hoeft, Fumiko; Kesler, Shelli R

    2012-01-01

    In recent years, graph theoretical analyses of neuroimaging data have increased our understanding of the organization of large-scale structural and functional brain networks. However, tools for pipeline application of graph theory for analyzing topology of brain networks is still lacking. In this report, we describe the development of a graph-analysis toolbox (GAT) that facilitates analysis and comparison of structural and functional network brain networks. GAT provides a graphical user interface (GUI) that facilitates construction and analysis of brain networks, comparison of regional and global topological properties between networks, analysis of network hub and modules, and analysis of resilience of the networks to random failure and targeted attacks. Area under a curve (AUC) and functional data analyses (FDA), in conjunction with permutation testing, is employed for testing the differences in network topologies; analyses that are less sensitive to the thresholding process. We demonstrated the capabilities of GAT by investigating the differences in the organization of regional gray-matter correlation networks in survivors of acute lymphoblastic leukemia (ALL) and healthy matched Controls (CON). The results revealed an alteration in small-world characteristics of the brain networks in the ALL survivors; an observation that confirm our hypothesis suggesting widespread neurobiological injury in ALL survivors. Along with demonstration of the capabilities of the GAT, this is the first report of altered large-scale structural brain networks in ALL survivors.

  10. GAT: a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks.

    Directory of Open Access Journals (Sweden)

    S M Hadi Hosseini

    Full Text Available In recent years, graph theoretical analyses of neuroimaging data have increased our understanding of the organization of large-scale structural and functional brain networks. However, tools for pipeline application of graph theory for analyzing topology of brain networks is still lacking. In this report, we describe the development of a graph-analysis toolbox (GAT that facilitates analysis and comparison of structural and functional network brain networks. GAT provides a graphical user interface (GUI that facilitates construction and analysis of brain networks, comparison of regional and global topological properties between networks, analysis of network hub and modules, and analysis of resilience of the networks to random failure and targeted attacks. Area under a curve (AUC and functional data analyses (FDA, in conjunction with permutation testing, is employed for testing the differences in network topologies; analyses that are less sensitive to the thresholding process. We demonstrated the capabilities of GAT by investigating the differences in the organization of regional gray-matter correlation networks in survivors of acute lymphoblastic leukemia (ALL and healthy matched Controls (CON. The results revealed an alteration in small-world characteristics of the brain networks in the ALL survivors; an observation that confirm our hypothesis suggesting widespread neurobiological injury in ALL survivors. Along with demonstration of the capabilities of the GAT, this is the first report of altered large-scale structural brain networks in ALL survivors.

  11. Psychophysics in a Web browser? Comparing response times collected with JavaScript and Psychophysics Toolbox in a visual search task.

    Science.gov (United States)

    de Leeuw, Joshua R; Motz, Benjamin A

    2016-03-01

    Behavioral researchers are increasingly using Web-based software such as JavaScript to conduct response time experiments. Although there has been some research on the accuracy and reliability of response time measurements collected using JavaScript, it remains unclear how well this method performs relative to standard laboratory software in psychologically relevant experimental manipulations. Here we present results from a visual search experiment in which we measured response time distributions with both Psychophysics Toolbox (PTB) and JavaScript. We developed a methodology that allowed us to simultaneously run the visual search experiment with both systems, interleaving trials between two independent computers, thus minimizing the effects of factors other than the experimental software. The response times measured by JavaScript were approximately 25 ms longer than those measured by PTB. However, we found no reliable difference in the variability of the distributions related to the software, and both software packages were equally sensitive to changes in the response times as a result of the experimental manipulations. We concluded that JavaScript is a suitable tool for measuring response times in behavioral research.

  12. An initial investigation of the GOCE error variance-covariance matrices in the context of the GOCE user toolbox project

    DEFF Research Database (Denmark)

    Bingham, Rory J.; Tscherning, Christian; Knudsen, Per

    2011-01-01

    The availability of the full error variance-covariance matrices for the GOCE gravity field models is an important feature of the GOCE mission. Potentially, it will allow users to evaluate the accuracy of a geoid or mean dynamic topography (MDT) derived from the gravity field model at any particul...

  13. Modeling nuclear processes by Simulink

    Energy Technology Data Exchange (ETDEWEB)

    Rashid, Nahrul Khair Alang Md, E-mail: nahrul@iium.edu.my [Faculty of Engineering, International Islamic University Malaysia, Jalan Gombak, Selangor (Malaysia)

    2015-04-29

    Modelling and simulation are essential parts in the study of dynamic systems behaviours. In nuclear engineering, modelling and simulation are important to assess the expected results of an experiment before the actual experiment is conducted or in the design of nuclear facilities. In education, modelling can give insight into the dynamic of systems and processes. Most nuclear processes can be described by ordinary or partial differential equations. Efforts expended to solve the equations using analytical or numerical solutions consume time and distract attention from the objectives of modelling itself. This paper presents the use of Simulink, a MATLAB toolbox software that is widely used in control engineering, as a modelling platform for the study of nuclear processes including nuclear reactor behaviours. Starting from the describing equations, Simulink models for heat transfer, radionuclide decay process, delayed neutrons effect, reactor point kinetic equations with delayed neutron groups, and the effect of temperature feedback are used as examples.

  14. Modeling nuclear processes by Simulink

    International Nuclear Information System (INIS)

    Rashid, Nahrul Khair Alang Md

    2015-01-01

    Modelling and simulation are essential parts in the study of dynamic systems behaviours. In nuclear engineering, modelling and simulation are important to assess the expected results of an experiment before the actual experiment is conducted or in the design of nuclear facilities. In education, modelling can give insight into the dynamic of systems and processes. Most nuclear processes can be described by ordinary or partial differential equations. Efforts expended to solve the equations using analytical or numerical solutions consume time and distract attention from the objectives of modelling itself. This paper presents the use of Simulink, a MATLAB toolbox software that is widely used in control engineering, as a modelling platform for the study of nuclear processes including nuclear reactor behaviours. Starting from the describing equations, Simulink models for heat transfer, radionuclide decay process, delayed neutrons effect, reactor point kinetic equations with delayed neutron groups, and the effect of temperature feedback are used as examples

  15. Wave optics modeling of real-time holographic wavefront compensation systems using OSSim

    Science.gov (United States)

    Carbon, Margarita A.; Guthals, Dennis M.; Logan, Jerry D.

    2005-08-01

    OSSim (Optical System Simulation) is a wave-optics, time-domain simulation toolbox with both optical and data processing components developed for adaptive optics (AO) systems. Diffractive wavefront control elements have recently been added that accurately model optically and electrically addressed spatial light modulators as real time holographic (RTH) devices in diffractive wavefront control systems. The developed RTH toolbox has found multiple applications for a variety of Boeing programs in solving problems of AO system analysis and design. Several complex diffractive wavefront control systems have been modeled for compensation of static and dynamic aberrations such as imperfect segmented primary mirrors and atmospheric and boundary layer turbulence. The results of OSSim simulations of RTH wavefront compensation show very good agreement with available experimental data.

  16. Obtaining of Analytical Relations for Hydraulic Parameters of Channels With Two Phase Flow Using Open CFD Toolbox

    Science.gov (United States)

    Varseev, E.

    2017-11-01

    The present work is dedicated to verification of numerical model in standard solver of open-source CFD code OpenFOAM for two-phase flow simulation and to determination of so-called “baseline” model parameters. Investigation of heterogeneous coolant flow parameters, which leads to abnormal friction increase of channel in two-phase adiabatic “water-gas” flows with low void fractions, presented.

  17. Modeling, Simulation and Position Control of 3DOF Articulated Manipulator

    Directory of Open Access Journals (Sweden)

    Hossein Sadegh Lafmejani

    2014-08-01

    Full Text Available In this paper, the modeling, simulation and control of 3 degrees of freedom articulated robotic manipulator have been studied. First, we extracted kinematics and dynamics equations of the mentioned manipulator by using the Lagrange method. In order to validate the analytical model of the manipulator we compared the model simulated in the simulation environment of Matlab with the model was simulated with the SimMechanics toolbox. A sample path has been designed for analyzing the tracking subject. The system has been linearized with feedback linearization and then a PID controller was applied to track a reference trajectory. Finally, the control results have been compared with a nonlinear PID controller.

  18. USE OF THE SIMPLE LINEAR REGRESSION MODEL IN MACRO-ECONOMICAL ANALYSES

    Directory of Open Access Journals (Sweden)

    Constantin ANGHELACHE

    2011-10-01

    Full Text Available The article presents the fundamental aspects of the linear regression, as a toolbox which can be used in macroeconomic analyses. The article describes the estimation of the parameters, the statistical tests used, the homoscesasticity and heteroskedasticity. The use of econometrics instrument in macroeconomics is an important factor that guarantees the quality of the models, analyses, results and possible interpretation that can be drawn at this level.

  19. Characterisation of large catastrophic landslides using an integrated field, remote sensing and numerical modelling approach

    OpenAIRE

    Wolter, Andrea Elaine

    2014-01-01

    I apply a forensic, multidisciplinary approach that integrates engineering geology field investigations, engineering geomorphology mapping, long-range terrestrial photogrammetry, and a numerical modelling toolbox to two large rock slope failures to study their causes, initiation, kinematics, and dynamics. I demonstrate the significance of endogenic and exogenic processes, both separately and in concert, in contributing to landscape evolution and conditioning slopes for failure, and use geomor...

  20. IASM: Individualized activity space modeler

    Science.gov (United States)

    Hasanzadeh, Kamyar

    2018-01-01

    Researchers from various disciplines have long been interested in analyzing and describing human mobility patterns. Activity space (AS), defined as an area encapsulating daily human mobility and activities, has been at the center of this interest. However, given the applied nature of research in this field and the complexity that advanced geographical modeling can pose to its users, the proposed models remain simplistic and inaccurate in many cases. Individualized Activity Space Modeler (IASM) is a geographic information system (GIS) toolbox, written in Python programming language using ESRI's Arcpy module, comprising four tools aiming to facilitate the use of advanced activity space models in empirical research. IASM provides individual-based and context-sensitive tools to estimate home range distances, delineate activity spaces, and model place exposures using individualized geographical data. In this paper, we describe the design and functionality of IASM, and provide an example of how it performs on a spatial dataset collected through an online map-based survey.

  1. MeProRisk - a toolbox for evaluating risks in exploration, development, and operation of geothermal reservoirs

    Science.gov (United States)

    Clauser, C.

    2009-04-01

    When developing geothermal resources, the risk of failure is still high when compared to hydrocarbon exploration. The MeProRisk projects aims at the improvement of strategies in all phases of the reservoir life cycle. It is a joint enterprise of five university institutes at RWTH Aachen University, Free University Berlin, and Kiel University. Two partners, namely Geophysica Beratunggesellschaft mbH, (Aachen), and RWE Dea AG (Hamburg) present the industrial side. It is funded by the German Ministry of Education and Science (BMBF). The key idea followed in this project is that the development of the understanding of a given reservoir is an iterative process. Starting from geological base knowledge and geophysical exploration one or more conceptual models will emerge, which will be incorporated in first numerical models. The use of inverse techniques in a broad sense will not only lead to an optimal model, but will produce uncertainty and resolution estimates for this model. This information may be used for further setup of optimal experiments, including the choice of exploration well locations. In later stages of reservoir development, the numerical models will be continuously updated based on the most recent models. Once wells have been drilled, the character of experiments shifts from static methods to dynamic interaction with the reservoir, e.g. by injection experiments and their monitoring. The use of all the methods with one simulation tool poses large challenges. Inverse problems require orders of magnitude larger computer resources, and the development of appropriate theoretical and numerical methods for this is on of the primary aims of this project. Due to the less obvious signatures of geothermally relevant targets, it is also necessary to improve the experimental base for model setup and update by developing new and better methods for some of the key problems in the case of geothermal targets. Among these are the development of methods to estimate

  2. Implementation of the DINEOF ArcGIS Toolbox: Case study of reconstruction of Chlorophyll-a missing data over the Mediterranean using MyOcean satellite data products.

    Science.gov (United States)

    Nikolaidis, Andreas; Stylianou, Stavros; Georgiou, Georgios; Hadjimitsis, Diofantos; Akylas, Evangelos

    2014-05-01

    ArcGIS® is a well known standard on Geographical Information Systems, used over the years for various remote sensing procedures. During the last decade, Rixen (2003) and Azcarate (2011) presented the DINEOF (Data Interpolating Empirical Orthogonal Functions) method, a EOF-based technique to reconstruct missing data in satellite images. The recent results of the DINEOF method in various experimental trials (Wang and Liu, 2013; Nikolaidis et al., 2013;2014) showed that this computationally affordable method leads to effective reconstruction of missing data from geophysical fields, such as chlorophyll-a, sea surface temperatures or salinities and geophysical fields derived from satellite data. Implementing the method in a GIS system will lead to a complete and integrated approach, enhancing its applicability. The inclusion of statistical tools within the GIS, will multiply the effectiveness, providing interoperability with other sources in the same application environment. This may be especially useful in studies where various different kinds of data are of interest. For this purpose, in this study we have implemented a new GIS toolbox that aims at automating the usage of the algorithm, incorporating the DINEOF codes provided by GHER (GeoHydrodynamics and Environment Research Group of University of Liege) into the ArcGIS®. A case-study of filling the chlorophyll-a missing data in the Mediterranean Sea area, for a 18-day period is analyzed, as an example for the effectiveness and simplicity of the toolbox. More specifically, we focus on chlorophyll-a MODIS satellite data collected by CNR-ISAC (Italian National Research Council, Institute of Atmospheric Sciences and Climate), from the respective products of MyOcean2® organization, that provides free online access to Level 3, with 1 km resolution. All the daily products with an initial level of only 27% data coverage were successfully reconstructed over the Mediterranean Sea. [1] Alvera-Azcárate A., Barth A

  3. Power1D: a Python toolbox for numerical power estimates in experiments involving one-dimensional continua

    Directory of Open Access Journals (Sweden)

    Todd C. Pataky

    2017-07-01

    Full Text Available The unit of experimental measurement in a variety of scientific applications is the one-dimensional (1D continuum: a dependent variable whose value is measured repeatedly, often at regular intervals, in time or space. A variety of software packages exist for computing continuum-level descriptive statistics and also for conducting continuum-level hypothesis testing, but very few offer power computing capabilities, where ‘power’ is the probability that an experiment will detect a true continuum signal given experimental noise. Moreover, no software package yet exists for arbitrary continuum-level signal/noise modeling. This paper describes a package called power1d which implements (a two analytical 1D power solutions based on random field theory (RFT and (b a high-level framework for computational power analysis using arbitrary continuum-level signal/noise modeling. First power1d’s two RFT-based analytical solutions are numerically validated using its random continuum generators. Second arbitrary signal/noise modeling is demonstrated to show how power1d can be used for flexible modeling well beyond the assumptions of RFT-based analytical solutions. Its computational demands are non-excessive, requiring on the order of only 30 s to execute on standard desktop computers, but with approximate solutions available much more rapidly. Its broad signal/noise modeling capabilities along with relatively rapid computations imply that power1d may be a useful tool for guiding experimentation involving multiple measurements of similar 1D continua, and in particular to ensure that an adequate number of measurements is made to detect assumed continuum signals.

  4. ASKI: A modular toolbox for scattering-integral-based seismic full waveform inversion and sensitivity analysis utilizing external forward codes

    Directory of Open Access Journals (Sweden)

    Florian Schumacher

    2016-01-01

    Full Text Available Due to increasing computational resources, the development of new numerically demanding methods and software for imaging Earth’s interior remains of high interest in Earth sciences. Here, we give a description from a user’s and programmer’s perspective of the highly modular, flexible and extendable software package ASKI–Analysis of Sensitivity and Kernel Inversion–recently developed for iterative scattering-integral-based seismic full waveform inversion. In ASKI, the three fundamental steps of solving the seismic forward problem, computing waveform sensitivity kernels and deriving a model update are solved by independent software programs that interact via file output/input only. Furthermore, the spatial discretizations of the model space used for solving the seismic forward problem and for deriving model updates, respectively, are kept completely independent. For this reason, ASKI does not contain a specific forward solver but instead provides a general interface to established community wave propagation codes. Moreover, the third fundamental step of deriving a model update can be repeated at relatively low costs applying different kinds of model regularization or re-selecting/weighting the inverted dataset without need to re-solve the forward problem or re-compute the kernels. Additionally, ASKI offers the user sensitivity and resolution analysis tools based on the full sensitivity matrix and allows to compose customized workflows in a consistent computational environment. ASKI is written in modern Fortran and Python, it is well documented and freely available under terms of the GNU General Public License (http://www.rub.de/aski.

  5. Sustainable knowledge development across cultural boundaries: Experiences from the EU-project SILMAS (Toolbox for conflict solving instruments in Alpine Lake Management)

    Science.gov (United States)

    Fegerl, Michael; Wieden, Wilfried

    2013-04-01

    Increasingly people have to communicate knowledge across cultural and language boundaries. Even though recent technologies offer powerful communication facilities people often feel confronted with barriers which clearly reduce their chances of making their interaction a success. Concrete evidence concerning such problems derives from a number of projects, where generated knowledge often results in dead-end products. In the Alpine Space-project SILMAS (Sustainable Instruments for Lake Management in Alpine Space), in which both authors were involved, a special approach (syneris® ) was taken to avoid this problem and to manage project knowledge in sustainable form. Under this approach knowledge input and output are handled interactively: Relevant knowledge can be developed continuously and users can always access the latest state of expertise. Resort to the respective tools and procedures can also assist in closing knowledge gaps and in developing innovative responses to familiar or novel problems. This contribution intends to describe possible ways and means which have been found to increase the chances of success of knowledge communication across cultural boundaries. The process of trans-cultural discussions of experts to find a standardized solution is highlighted as well as the problem of dissemination of expert knowledge to variant stakeholders. Finally lessons learned are made accessible, where a main task lies in the creation of a tool box for conflict solving instruments, as a demonstrable result of the project and for the time thereafter. The interactive web-based toolbox enables lake managers to access best practice instruments in standardized, explicit and cross-linguistic form.

  6. Exact and grid-free solutions to the Lighthill-Whitham-Richards traffic flow model with bounded acceleration for a class of fundamental diagrams

    KAUST Repository

    Qiu, Shanwen

    2013-09-01

    In this article, we propose a new exact and grid-free numerical scheme for computing solutions associated with an hybrid traffic flow model based on the Lighthill-Whitham-Richards (LWR) partial differential equation, for a class of fundamental diagrams. In this hybrid flow model, the vehicles satisfy the LWR equation whenever possible, and have a constant acceleration otherwise. We first propose a mathematical definition of the solution as a minimization problem. We use this formulation to build a grid-free solution method for this model based on the minimization of component function. We then derive these component functions analytically for triangular fundamental diagrams, which are commonly used to model traffic flow. We also show that the proposed computational method can handle fixed or moving bottlenecks. A toolbox implementation of the resulting algorithm is briefly discussed, and posted at https://dl.dropbox.com/u/1318701/Toolbox.zip. © 2013 Elsevier Ltd.

  7. Creating a business toolbox for a start-up : a case study of SnapSwap International

    OpenAIRE

    Kovshikov, Iaroslav

    2017-01-01

    This thesis was implemented at SnapSwap International in spring and summer 2017. The case company is a fin-tech start-up established in 2015 and located in Luxembourg. The company aims to develop a new payment solution (money messenger) for the European market. The purpose of the thesis is to observe commonly used business techniques (SWOT, Business Model Canvas (BMC), Persona, and Empathy Map) and analyze current business activities of the company employing these tools. The theoretic...

  8. Deep Belief Nets for Topic Modeling

    DEFF Research Database (Denmark)

    Maaløe, Lars; Arngren, Morten; Winther, Ole

    2015-01-01

    -formative. In this paper we describe large-scale content based collaborative filtering for digital publishing. To solve the digital publishing recommender problem we compare two approaches: latent Dirichlet allocation (LDA) and deep be-lief nets (DBN) that both find low-dimensional latent representations for documents....... Efficient retrieval can be carried out in the latent representation. We work both on public benchmarks and digital media content provided by Issuu, an on-line publishing platform. This article also comes with a newly developed deep belief nets toolbox for topic modeling tailored towards performance...

  9. Simulation of ODE/PDE models with MATLAB, OCTAVE and SCILAB scientific and engineering applications

    CERN Document Server

    Vande Wouwer, Alain; Vilas, Carlos

    2014-01-01

    Simulation of ODE/PDE Models with MATLAB®, OCTAVE and SCILAB shows the reader how to exploit a fuller array of numerical methods for the analysis of complex scientific and engineering systems than is conventionally employed. The book is dedicated to numerical simulation of distributed parameter systems described by mixed systems of algebraic equations, ordinary differential equations (ODEs) and partial differential equations (PDEs). Special attention is paid to the numerical method of lines (MOL), a popular approach to the solution of time-dependent PDEs, which proceeds in two basic steps: spatial discretization and time integration. Besides conventional finite-difference and -element techniques, more advanced spatial-approximation methods are examined in some detail, including nonoscillatory schemes and adaptive-grid approaches. A MOL toolbox has been developed within MATLAB®/OCTAVE/SCILAB. In addition to a set of spatial approximations and time integrators, this toolbox includes a collection of applicatio...

  10. OXlearn: a new MATLAB-based simulation tool for connectionist models.

    Science.gov (United States)

    Ruh, Nicolas; Westermann, Gert

    2009-11-01

    OXlearn is a free, platform-independent MATLAB toolbox in which standard connectionist neural network models can be set up, run, and analyzed by means of a user-friendly graphical interface. Due to its seamless integration with the MATLAB programming environment, the inner workings of the simulation tool can be easily inspected and/or extended using native MATLAB commands or components. This combination of usability, transparency, and extendability makes OXlearn an efficient tool for the implementation of basic research projects or the prototyping of more complex research endeavors, as well as for teaching. Both the MATLAB toolbox and a compiled version that does not require access to MATLAB can be downloaded from http://psych.brookes.ac.uk/oxlearn/.

  11. Novel human neuronal tau model exhibiting neurofibrillary tangles and transcellular propagation.

    Science.gov (United States)

    Reilly, Patrick; Winston, Charisse N; Baron, Kelsey R; Trejo, Margarita; Rockenstein, Edward M; Akers, Johnny C; Kfoury, Najla; Diamond, Marc; Masliah, Eliezer; Rissman, Robert A; Yuan, Shauna H

    2017-10-01

    Tauopathies are a class of neurodegenerative diseases, including Alzheimer's disease, frontotemporal dementia and progressive supranuclear palsy, which are associated with the pathological aggregation of tau protein into neurofibrillary tangles (NFT). Studies have characterized tau as a "prion-like" protein given its ability to form distinct, stable amyloid conformations capable of transcellular and multigenerational propagation in clonal fashion. It has been proposed that progression of tauopathy could be due to the prion-like propagation of tau, suggesting the possibility that end-stage pathologies, like NFT formation, may require an instigating event such as tau seeding. To investigate this, we applied a novel human induced pluripotent stem cell (hiPSC) system we have developed to serve as a human neuronal model. We introduced the tau repeat domain (tau-RD) with P301L and V337M (tau-RD-LM) mutations into hiPSC-derived neurons and observed expression of tau-RD at levels similar to total tau in postmortem AD brains. Tau aggregation occurred without the addition of recombinant tau fibrils. The conditioned media from tau-RD cultures contained tau-RD seeds, which were capable of inducing aggregate formation in homotypic mode in non-transduced recipient neuronal cultures. The resultant NFTs were thioflavin-positive, silver stain-positive, and assumed fibrillary appearance on transmission electron microscopy (TEM) with immunogold, which revealed paired helical filament 1 (PHF1)-positive NFTs, representing possible recruitment of endogenous tau in the aggregates. Functionally, expression of tau-RD caused neurotoxicity that manifested as axon retraction, synaptic density reduction, and enlargement of lysosomes. The results of our hiPSC study were reinforced by the observation that Tau-RD-LM is excreted in exosomes, which mediated the transfer of human tau to wild-type mouse neurons in vivo. Our hiPSC human neuronal system provides a model for further studies of tau

  12. Can a GIS toolbox assess the environmental risk of oil spills? Implementation for oil facilities in harbors.

    Science.gov (United States)

    Valdor, Paloma F; Gómez, Aina G; Velarde, Víctor; Puente, Araceli

    2016-04-01

    Oil spills are one of the most widespread problems in port areas (loading/unloading of bulk liquid, fuel supply). Specific environmental risk analysis procedures for diffuse oil sources that are based on the evolution of oil in the marine environment are needed. Diffuse sources such as oil spills usually present a lack of information, which makes the use of numerical models an arduous and occasionally impossible task. For that reason, a tool that can assess the risk of oil spills in near-shore areas by using Geographical Information System (GIS) is presented. The SPILL Tool provides immediate results by automating the process without miscalculation errors. The tool was developed using the Python and ArcGIS scripting library to build a non-ambiguous geoprocessing workflow. The SPILL Tool was implemented for oil facilities at Tarragona Harbor (NE Spain) and validated showing a satisfactory correspondence (around 0.60 RSR error index) with the results obtained using a 2D calibrated oil transport numerical model. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Similarity and Modeling in Science and Engineering

    CERN Document Server

    Kuneš, Josef

    2012-01-01

    The present text sets itself in relief to other titles on the subject in that it addresses the means and methodologies versus a narrow specific-task oriented approach. Concepts and their developments which evolved to meet the changing needs of applications are addressed. This approach provides the reader with a general tool-box to apply to their specific needs. Two important tools are presented: dimensional analysis and the similarity analysis methods. The fundamental point of view, enabling one to sort all models, is that of information flux between a model and an original expressed by the similarity and abstraction. Each chapter includes original examples and ap-plications. In this respect, the models can be divided into several groups. The following models are dealt with separately by chapter; mathematical and physical models, physical analogues, deterministic, stochastic, and cybernetic computer models. The mathematical models are divided into asymptotic and phenomenological models. The phenomenological m...

  14. The LIKE system, a novel protein expression toolbox for Bacillus subtilis based on the liaI promoter

    Science.gov (United States)

    2012-01-01

    Background Bacillus subtilis is a very important Gram-positive model organism of high biotechnological relevance, which is widely used as a host for the production of both secreted and cytoplasmic proteins. We developed a novel and efficient expression system, based on the liaI promoter (PliaI) from B. subtilis, which is under control of the LiaRS antibiotic-inducible two-component system. In the absence of a stimulus, this promoter is kept tightly inactive. Upon induction by cell wall antibiotics, it shows an over 100-fold increase in activity within 10 min. Results Based on these traits of PliaI, we developed a novel LiaRS-controlled gene expression system for B. subtilis (the “LIKE" system). Two expression vectors, the integrative pLIKE-int and the replicative pLIKE-rep, were constructed. To enhance the performance of the PliaI-derived system, site-directed mutagenesis was employed to optimize the ribosome binding site and alter its spacing to the initiation codon used for the translational fusion. The impact of these genetic modifications on protein production yield was measured using GFP as a model protein. Moreover, a number of tailored B. subtilis expression strains containing different markerless chromosomal deletions of the liaIH region were constructed to circumvent undesired protein production, enhance the positive autoregulation of the LiaRS system and thereby increase target gene expression strength from the PliaI promoter. Conclusions The LIKE protein expression system is a novel protein expression system, which offers a number of advantages over existing systems. Its major advantages are (i) a tightly switched-off promoter during exponential growth in the absence of a stimulus, (ii) a concentration-dependent activation of PliaI in the presence of suitable inducers, (iii) a very fast but transient response with a very high dynamic range of over 100-fold (up to 1,000-fold) induction, (iv) a choice from a range of well-defined, commercially available

  15. The terrestrial isopod microbiome: An all-in-one toolbox for animal-microbe interactions of ecological relevance

    Directory of Open Access Journals (Sweden)

    Didier Bouchon

    2016-09-01

    Full Text Available Bacterial symbionts represent essential drivers of arthropod ecology and evolution, influencing host traits such as nutrition, reproduction, immunity and speciation. However, the majority of work on arthropod microbiota has been conducted in insects and more studies in non-model species across different ecological niches will be needed to complete our understanding of host-microbiota interactions. In this review, we present terrestrial isopod crustaceans as an emerging model organism to investigate symbiotic associations with potential relevance to ecosystem functioning. Terrestrial isopods comprise a group of crustaceans that have evolved a terrestrial lifestyle and represent keystone species in terrestrial ecosystems, contributing to the decomposition of organic matter and regulating the microbial food web. Since their nutrition is based on plant detritus, it has long been suspected that bacterial symbionts located in the digestive tissues might play an important role in host nutrition via the provisioning of digestive enzymes, thereby enabling the utilization of recalcitrant food compounds (e.g. cellulose or lignins. If this were the case, then (i the acquisition of these bacteria might have been an important evolutionary prerequisite for the colonization of land by isopods, and (ii these bacterial symbionts would directly mediate the role of their hosts in ecosystem functioning. Several bacterial symbionts have indeed been discovered in the midgut caeca of terrestrial isopods and some of them might be specific to this group of animals (i.e. Candidatus Hepatoplasma crinochetorum, Candidatus Hepatincola porcellionum and Rhabdochlamydia porcellionis, while others are well-known intracellular pathogens (Rickettsiella spp. or reproductive parasites (Wolbachia sp.. Moreover, a recent investigation of the microbiota in Armadillidium vulgare has revealed that this species harbors a highly diverse bacterial community which varies between host

  16. The Terrestrial Isopod Microbiome: An All-in-One Toolbox for Animal-Microbe Interactions of Ecological Relevance.

    Science.gov (United States)

    Bouchon, Didier; Zimmer, Martin; Dittmer, Jessica

    2016-01-01

    Bacterial symbionts represent essential drivers of arthropod ecology and evolution, influencing host traits such as nutrition, reproduction, immunity, and speciation. However, the majority of work on arthropod microbiota has been conducted in insects and more studies in non-model species across different ecological niches will be needed to complete our understanding of host-microbiota interactions. In this review, we present terrestrial isopod crustaceans as an emerging model organism to investigate symbiotic associations with potential relevance to ecosystem functioning. Terrestrial isopods comprise a group of crustaceans that have evolved a terrestrial lifestyle and represent keystone species in terrestrial ecosystems, contributing to the decomposition of organic matter and regulating the microbial food web. Since their nutrition is based on plant detritus, it has long been suspected that bacterial symbionts located in the digestive tissues might play an important role in host nutrition via the provisioning of digestive enzymes, thereby enabling the utilization of recalcitrant food compounds (e.g., cellulose or lignins). If this were the case, then (i) the acquisition of these bacteria might have been an important evolutionary prerequisite for the colonization of land by isopods, and (ii) these bacterial symbionts would directly mediate the role of their hosts in ecosystem functioning. Several bacterial symbionts have indeed been discovered in the midgut caeca of terrestrial isopods and some of them might be specific to this group of animals (i.e., Candidatus Hepatoplasma crinochetorum, Candidatus Hepatincola porcellionum, and Rhabdochlamydia porcellionis ), while others are well-known intracellular pathogens ( Rickettsiella spp.) or reproductive parasites ( Wolbachia sp.). Moreover, a recent investigation of the microbiota in Armadillidium vulgare has revealed that this species harbors a highly diverse bacterial community which varies between host populations

  17. 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.

  18. PerMallows: An R Package for Mallows and Generalized Mallows Models

    Directory of Open Access Journals (Sweden)

    Ekhine Irurozki

    2016-08-01

    Full Text Available In this paper we present the R package PerMallows, which is a complete toolbox to work with permutations, distances and some of the most popular probability models for permutations: Mallows and the Generalized Mallows models. The Mallows model is an exponential location model, considered as analogous to the Gaussian distribution. It is based on the definition of a distance between permutations. The Generalized Mallows model is its best-known extension. The package includes functions for making inference, sampling and learning such distributions. The distances considered in PerMallows are Kendall's τ , Cayley, Hamming and Ulam.

  19. The Need for Accurate Geometric and Radiometric Corrections of Drone-Borne Hyperspectral Data for Mineral Exploration: MEPHySTo—A Toolbox for Pre-Processing Drone-Borne Hyperspectral Data

    Directory of Open Access Journals (Sweden)

    Sandra Jakob

    2017-01-01

    Full Text Available Drone-borne hyperspectral imaging is a new and promising technique for fast and precise acquisition, as well as delivery of high-resolution hyperspectral data to a large variety of end-users. Drones can overcome the scale gap between field and air-borne remote sensing, thus providing high-resolution and multi-temporal data. They are easy to use, flexible and deliver data within cm-scale resolution. So far, however, drone-borne imagery has prominently and successfully been almost solely used in precision agriculture and photogrammetry. Drone technology currently mainly relies on structure-from-motion photogrammetry, aerial photography and agricultural monitoring. Recently, a few hyperspectral sensors became available for drones, but complex geometric and radiometric effects complicate their use for geology-related studies. Using two examples, we first show that precise corrections are required for any geological mapping. We then present a processing toolbox for frame-based hyperspectral imaging systems adapted for the complex correction of drone-borne hyperspectral imagery. The toolbox performs sensor- and platform-specific geometric distortion corrections. Furthermore, a topographic correction step is implemented to correct for rough terrain surfaces. We recommend the c-factor-algorithm for geological applications. To our knowledge, we demonstrate for the first time the applicability of the corrected dataset for lithological mapping and mineral exploration.

  20. From position-specific isotope labeling towards soil fluxomics: a novel toolbox to assess the microbial impact on biogeochemical cycles

    Science.gov (United States)

    Apostel, C.; Dippold, M. A.; Kuzyakov, Y.

    2015-12-01

    . Quantitative models to assess microbial group specific metabolic pathways can be generated and parameterized by this approach. The knowledge of submolecular C transformation steps and its regulating factors is essential for understanding C cycling and long-term C storage in soils.