WorldWideScience

Sample records for modeling system reproduced

  1. Bitwise identical compiling setup: prospective for reproducibility and reliability of earth system modeling

    Directory of Open Access Journals (Sweden)

    R. Li

    2015-11-01

    Full Text Available Reproducibility and reliability are fundamental principles of scientific research. A compiling setup that includes a specific compiler version and compiler flags is essential technical supports for Earth system modeling. With the fast development of computer software and hardware, compiling setup has to be updated frequently, which challenges the reproducibility and reliability of Earth system modeling. The existing results of a simulation using an original compiling setup may be irreproducible by a newer compiling setup because trivial round-off errors introduced by the change of compiling setup can potentially trigger significant changes in simulation results. Regarding the reliability, a compiler with millions of lines of codes may have bugs that are easily overlooked due to the uncertainties or unknowns in Earth system modeling. To address these challenges, this study shows that different compiling setups can achieve exactly the same (bitwise identical results in Earth system modeling, and a set of bitwise identical compiling setups of a model can be used across different compiler versions and different compiler flags. As a result, the original results can be more easily reproduced; for example, the original results with an older compiler version can be reproduced exactly with a newer compiler version. Moreover, this study shows that new test cases can be generated based on the differences of bitwise identical compiling setups between different models, which can help detect software bugs or risks in the codes of models and compilers and finally improve the reliability of Earth system modeling.

  2. Spatial-temporal reproducibility assessment of global seasonal forecasting system version 5 model for Dam Inflow forecasting

    Science.gov (United States)

    Moon, S.; Suh, A. S.; Soohee, H.

    2016-12-01

    The GloSea5(Global Seasonal forecasting system version 5) is provided and operated by the KMA(Korea Meteorological Administration). GloSea5 provides Forecast(FCST) and Hindcast(HCST) data and its horizontal resolution is about 60km (0.83° x 0.56°) in the mid-latitudes. In order to use this data in watershed-scale water management, GloSea5 needs spatial-temporal downscaling. As such, statistical downscaling was used to correct for systematic biases of variables and to improve data reliability. HCST data is provided in ensemble format, and the highest statistical correlation(R2 = 0.60, RMSE = 88.92, NSE = 0.57) of ensemble precipitation was reported for the Yongdam Dam watershed on the #6 grid. Additionally, the original GloSea5(600.1mm) showed the greatest difference(-26.5%) compared to observations(816.1mm) during the summer flood season. However, downscaled GloSea5 was shown to have only a ?3.1% error rate. Most of the underestimated results corresponded to precipitation levels during the flood season and the downscaled GloSea5 showed important results of restoration in precipitation levels. Per the analysis results of spatial autocorrelation using seasonal Moran's I, the spatial distribution was shown to be statistically significant. These results can improve the uncertainty of original GloSea5 and substantiate its spatial-temporal accuracy and validity. The spatial-temporal reproducibility assessment will play a very important role as basic data for watershed-scale water management.

  3. Reproducibility of neuroimaging analyses across operating systems.

    Science.gov (United States)

    Glatard, Tristan; Lewis, Lindsay B; Ferreira da Silva, Rafael; Adalat, Reza; Beck, Natacha; Lepage, Claude; Rioux, Pierre; Rousseau, Marc-Etienne; Sherif, Tarek; Deelman, Ewa; Khalili-Mahani, Najmeh; Evans, Alan C

    2015-01-01

    Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of these differences using library and system call interception. We find that these packages use mathematical functions based on single-precision floating-point arithmetic whose implementations in operating systems continue to evolve. While these differences have little or no impact on simple analysis pipelines such as brain extraction and cortical tissue classification, their accumulation creates important differences in longer pipelines such as subcortical tissue classification, fMRI analysis, and cortical thickness extraction. With FSL, most Dice coefficients between subcortical classifications obtained on different operating systems remain above 0.9, but values as low as 0.59 are observed. Independent component analyses (ICA) of fMRI data differ between operating systems in one third of the tested subjects, due to differences in motion correction. With Freesurfer and CIVET, in some brain regions we find an effect of build or operating system on cortical thickness. A first step to correct these reproducibility issues would be to use more precise representations of floating-point numbers in the critical sections of the pipelines. The numerical stability of pipelines should also be reviewed.

  4. A two-stage unsupervised learning algorithm reproduces multisensory enhancement in a neural network model of the corticotectal system.

    Science.gov (United States)

    Anastasio, Thomas J; Patton, Paul E

    2003-07-30

    Multisensory enhancement (MSE) is the augmentation of the response to sensory stimulation of one modality by stimulation of a different modality. It has been described for multisensory neurons in the deep superior colliculus (DSC) of mammals, which function to detect, and direct orienting movements toward, the sources of stimulation (targets). MSE would seem to improve the ability of DSC neurons to detect targets, but many mammalian DSC neurons are unimodal. MSE requires descending input to DSC from certain regions of parietal cortex. Paradoxically, the descending projections necessary for MSE originate from unimodal cortical neurons. MSE, and the puzzling findings associated with it, can be simulated using a model of the corticotectal system. In the model, a network of DSC units receives primary sensory input that can be augmented by modulatory cortical input. Connection weights from primary and modulatory inputs are trained in stages one (Hebb) and two (Hebb-anti-Hebb), respectively, of an unsupervised two-stage algorithm. Two-stage training causes DSC units to extract information concerning simulated targets from their inputs. It also causes the DSC to develop a mixture of unimodal and multisensory units. The percentage of DSC multisensory units is determined by the proportion of cross-modal targets and by primary input ambiguity. Multisensory DSC units develop MSE, which depends on unimodal modulatory connections. Removal of the modulatory influence greatly reduces MSE but has little effect on DSC unit responses to stimuli of a single modality. The correspondence between model and data suggests that two-stage training captures important features of self-organization in the real corticotectal system.

  5. Reproducibility Issues: Avoiding Pitfalls in Animal Inflammation Models.

    Science.gov (United States)

    Laman, Jon D; Kooistra, Susanne M; Clausen, Björn E

    2017-01-01

    In light of an enhanced awareness of ethical questions and ever increasing costs when working with animals in biomedical research, there is a dedicated and sometimes fierce debate concerning the (lack of) reproducibility of animal models and their relevance for human inflammatory diseases. Despite evident advancements in searching for alternatives, that is, replacing, reducing, and refining animal experiments-the three R's of Russel and Burch (1959)-understanding the complex interactions of the cells of the immune system, the nervous system and the affected tissue/organ during inflammation critically relies on in vivo models. Consequently, scientific advancement and ultimately novel therapeutic interventions depend on improving the reproducibility of animal inflammation models. As a prelude to the remaining hands-on protocols described in this volume, here, we summarize potential pitfalls of preclinical animal research and provide resources and background reading on how to avoid them.

  6. Assessment of Modeling Capability for Reproducing Storm Impacts on TEC

    Science.gov (United States)

    Shim, J. S.; Kuznetsova, M. M.; Rastaetter, L.; Bilitza, D.; Codrescu, M.; Coster, A. J.; Emery, B. A.; Foerster, M.; Foster, B.; Fuller-Rowell, T. J.; Huba, J. D.; Goncharenko, L. P.; Mannucci, A. J.; Namgaladze, A. A.; Pi, X.; Prokhorov, B. E.; Ridley, A. J.; Scherliess, L.; Schunk, R. W.; Sojka, J. J.; Zhu, L.

    2014-12-01

    During geomagnetic storm, the energy transfer from solar wind to magnetosphere-ionosphere system adversely affects the communication and navigation systems. Quantifying storm impacts on TEC (Total Electron Content) and assessment of modeling capability of reproducing storm impacts on TEC are of importance to specifying and forecasting space weather. In order to quantify storm impacts on TEC, we considered several parameters: TEC changes compared to quiet time (the day before storm), TEC difference between 24-hour intervals, and maximum increase/decrease during the storm. We investigated the spatial and temporal variations of the parameters during the 2006 AGU storm event (14-15 Dec. 2006) using ground-based GPS TEC measurements in the selected 5 degree eight longitude sectors. The latitudinal variations were also studied in two longitude sectors among the eight sectors where data coverage is relatively better. We obtained modeled TEC from various ionosphere/thermosphere (IT) models. The parameters from the models were compared with each other and with the observed values. We quantified performance of the models in reproducing the TEC variations during the storm using skill scores. This study has been supported by the Community Coordinated Modeling Center (CCMC) at the Goddard Space Flight Center. Model outputs and observational data used for the study will be permanently posted at the CCMC website (http://ccmc.gsfc.nasa.gov) for the space science communities to use.

  7. Towards reproducible descriptions of neuronal network models.

    Directory of Open Access Journals (Sweden)

    Eilen Nordlie

    2009-08-01

    Full Text Available Progress in science depends on the effective exchange of ideas among scientists. New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely. This applies to simulation studies as well as to experiments and theories. But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing network models in publications. This hinders the critical evaluation of network models as well as their re-use. We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the ordering and placement of material. We further observe great variation in the graphical representation of networks and the notation used in equations. Based on our observations, we propose a good model description practice, composed of guidelines for the organization of publications, a checklist for model descriptions, templates for tables presenting model structure, and guidelines for diagrams of networks. The main purpose of this good practice is to trigger a debate about the communication of neuronal network models in a manner comprehensible to humans, as opposed to machine-readable model description languages. We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and software-sharing, may lead to a deeper and more fruitful exchange of ideas among computational neuroscientists in years to come. We further hope that work on standardized ways of describing--and thinking about--complex neuronal networks will lead the scientific community to a clearer understanding of high-level concepts in network dynamics, and will thus lead to deeper insights into the function of the brain.

  8. Reproducibility and Transparency in Ocean-Climate Modeling

    Science.gov (United States)

    Hannah, N.; Adcroft, A.; Hallberg, R.; Griffies, S. M.

    2015-12-01

    Reproducibility is a cornerstone of the scientific method. Within geophysical modeling and simulation achieving reproducibility can be difficult, especially given the complexity of numerical codes, enormous and disparate data sets, and variety of supercomputing technology. We have made progress on this problem in the context of a large project - the development of new ocean and sea ice models, MOM6 and SIS2. Here we present useful techniques and experience.We use version control not only for code but the entire experiment working directory, including configuration (run-time parameters, component versions), input data and checksums on experiment output. This allows us to document when the solutions to experiments change, whether due to code updates or changes in input data. To avoid distributing large input datasets we provide the tools for generating these from the sources, rather than provide raw input data.Bugs can be a source of non-determinism and hence irreproducibility, e.g. reading from or branching on uninitialized memory. To expose these we routinely run system tests, using a memory debugger, multiple compilers and different machines. Additional confidence in the code comes from specialised tests, for example automated dimensional analysis and domain transformations. This has entailed adopting a code style where we deliberately restrict what a compiler can do when re-arranging mathematical expressions.In the spirit of open science, all development is in the public domain. This leads to a positive feedback, where increased transparency and reproducibility makes using the model easier for external collaborators, who in turn provide valuable contributions. To facilitate users installing and running the model we provide (version controlled) digital notebooks that illustrate and record analysis of output. This has the dual role of providing a gross, platform-independent, testing capability and a means to documents model output and analysis.

  9. Measurement of cerebral blood flow by intravenous xenon-133 technique and a mobile system. Reproducibility using the Obrist model compared to total curve analysis

    DEFF Research Database (Denmark)

    Schroeder, T; Holstein, P; Lassen, N A

    1986-01-01

    and side-to-side asymmetry. Data were analysed according to the Obrist model and the results compared with those obtained using a model correcting for the air passage artifact. Reproducibility was of the same order of magnitude as reported using stationary equipment. The side-to-side CBF asymmetry...... differences, but in low flow situations the artifact model yielded significantly more stable results. The present apparatus, equipped with 3-5 detectors covering each hemisphere, offers the opportunity of performing serial CBF measurements in situations not otherwise feasible....

  10. Safety and Reproducibility of a Clinical Trial System Using Induced Blood Stage Plasmodium vivax Infection and Its Potential as a Model to Evaluate Malaria Transmission

    Science.gov (United States)

    Elliott, Suzanne; Sekuloski, Silvana; Sikulu, Maggy; Hugo, Leon; Khoury, David; Cromer, Deborah; Davenport, Miles; Sattabongkot, Jetsumon; Ivinson, Karen; Ockenhouse, Christian; McCarthy, James

    2016-01-01

    Background Interventions to interrupt transmission of malaria from humans to mosquitoes represent an appealing approach to assist malaria elimination. A limitation has been the lack of systems to test the efficacy of such interventions before proceeding to efficacy trials in the field. We have previously demonstrated the feasibility of induced blood stage malaria (IBSM) infection with Plasmodium vivax. In this study, we report further validation of the IBSM model, and its evaluation for assessment of transmission of P. vivax to Anopheles stephensi mosquitoes. Methods Six healthy subjects (three cohorts, n = 2 per cohort) were infected with P. vivax by inoculation with parasitized erythrocytes. Parasite growth was monitored by quantitative PCR, and gametocytemia by quantitative reverse transcriptase PCR (qRT-PCR) for the mRNA pvs25. Parasite multiplication rate (PMR) and size of inoculum were calculated by linear regression. Mosquito transmission studies were undertaken by direct and membrane feeding assays over 3 days prior to commencement of antimalarial treatment, and midguts of blood fed mosquitoes dissected and checked for presence of oocysts after 7–9 days. Results The clinical course and parasitemia were consistent across cohorts, with all subjects developing mild to moderate symptoms of malaria. No serious adverse events were reported. Asymptomatic elevated liver function tests were detected in four of six subjects; these resolved without treatment. Direct feeding of mosquitoes was well tolerated. The estimated PMR was 9.9 fold per cycle. Low prevalence of mosquito infection was observed (1.8%; n = 32/1801) from both direct (4.5%; n = 20/411) and membrane (0.9%; n = 12/1360) feeds. Conclusion The P. vivax IBSM model proved safe and reliable. The clinical course and PMR were reproducible when compared with the previous study using this model. The IBSM model presented in this report shows promise as a system to test transmission-blocking interventions

  11. Theoretical Modeling and Computer Simulations for the Origins and Evolution of Reproducing Molecular Systems and Complex Systems with Many Interactive Parts

    Science.gov (United States)

    Liang, Shoudan

    2000-01-01

    Our research effort has produced nine publications in peer-reviewed journals listed at the end of this report. The work reported here are in the following areas: (1) genetic network modeling; (2) autocatalytic model of pre-biotic evolution; (3) theoretical and computational studies of strongly correlated electron systems; (4) reducing thermal oscillations in atomic force microscope; (5) transcription termination mechanism in prokaryotic cells; and (6) the low glutamine usage in thennophiles obtained by studying completely sequenced genomes. We discuss the main accomplishments of these publications.

  12. Research Spotlight: Improved model reproduces the 2003 European heat wave

    Science.gov (United States)

    Schultz, Colin

    2011-04-01

    In August 2003, record-breaking temperatures raged across much of Europe. In France, maximum temperatures of 37°C (99°F) persisted for 9 days straight, the longest such stretch since 1873. About 40,000 deaths (14,000 in France alone) were attributed to the extreme heat and low humidity. Various climate conditions must come into alignment to produce extreme weather like the 2003 heat wave, and despite a concerted effort, forecasting models have so far been unable to accurately reproduce the event—including the modern European Centre for Medium-Range Weather Forecasts (ECMWF) ensemble modeling system for seasonal forecasts, which went into operation in 2007. (Geophysical Research Letters, doi:10.1029/2010GL046455, 2011)

  13. Reproducing the Kinematics of Damped Lyman-alpha Systems

    CERN Document Server

    Bird, Simeon; Neeleman, Marcel; Genel, Shy; Vogelsberger, Mark; Hernquist, Lars

    2014-01-01

    We examine the kinematic structure of Damped Lyman-alpha Systems (DLAs) in a series of cosmological hydrodynamic simulations using the AREPO code. We are able to match the distribution of velocity widths of associated low ionisation metal absorbers substantially better than earlier work. Our simulations produce a population of DLAs dominated by halos with virial velocities around 70 km/s, consistent with a picture of relatively small, faint objects. In addition, we reproduce the observed correlation between velocity width and metallicity and the equivalent width distribution of SiII. Some discrepancies of moderate statistical significance remain; too many of our spectra show absorption concentrated at the edge of the profile and there are slight differences in the exact shape of the velocity width distribution. We show that the improvement over previous work is mostly due to our strong feedback from star formation and our detailed modelling of the metal ionisation state.

  14. Reproducibility of LCA models of crude oil production.

    Science.gov (United States)

    Vafi, Kourosh; Brandt, Adam R

    2014-11-04

    Scientific models are ideally reproducible, with results that converge despite varying methods. In practice, divergence between models often remains due to varied assumptions, incompleteness, or simply because of avoidable flaws. We examine LCA greenhouse gas (GHG) emissions models to test the reproducibility of their estimates for well-to-refinery inlet gate (WTR) GHG emissions. We use the Oil Production Greenhouse gas Emissions Estimator (OPGEE), an open source engineering-based life cycle assessment (LCA) model, as the reference model for this analysis. We study seven previous studies based on six models. We examine the reproducibility of prior results by successive experiments that align model assumptions and boundaries. The root-mean-square error (RMSE) between results varies between ∼1 and 8 g CO2 eq/MJ LHV when model inputs are not aligned. After model alignment, RMSE generally decreases only slightly. The proprietary nature of some of the models hinders explanations for divergence between the results. Because verification of the results of LCA GHG emissions is often not possible by direct measurement, we recommend the development of open source models for use in energy policy. Such practice will lead to iterative scientific review, improvement of models, and more reliable understanding of emissions.

  15. Reproducibility Issues : Avoiding Pitfalls in Animal Inflammation Models

    NARCIS (Netherlands)

    Laman, Jon D; Kooistra, Susanne M; Clausen, Björn E; Clausen, Björn E.; Laman, Jon D.

    2017-01-01

    In light of an enhanced awareness of ethical questions and ever increasing costs when working with animals in biomedical research, there is a dedicated and sometimes fierce debate concerning the (lack of) reproducibility of animal models and their relevance for human inflammatory diseases. Despite

  16. Modeling and evaluating repeatability and reproducibility of ordinal classifications

    NARCIS (Netherlands)

    J. de Mast; W.N. van Wieringen

    2010-01-01

    This paper argues that currently available methods for the assessment of the repeatability and reproducibility of ordinal classifications are not satisfactory. The paper aims to study whether we can modify a class of models from Item Response Theory, well established for the study of the reliability

  17. Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems.

    Science.gov (United States)

    Rhee, Minsoung; Light, Yooli K; Yilmaz, Suzan; Adams, Paul D; Saxena, Deepak; Meagher, Robert J; Singh, Anup K

    2014-12-07

    Picoinjection is a promising technique to add reagents into pre-formed emulsion droplets on chip however, it is sensitive to pressure fluctuation, making stable operation of the picoinjector challenging. We present a chip architecture using a simple pressure stabilizer for consistent and highly reproducible picoinjection in multi-step biochemical assays with droplets. Incorporation of the stabilizer immediately upstream of a picoinjector or a combination of injectors greatly reduces pressure fluctuations enabling reproducible and effective picoinjection in systems where the pressure varies actively during operation. We demonstrate the effectiveness of the pressure stabilizer for an integrated platform for on-demand encapsulation of bacterial cells followed by picoinjection of reagents for lysing the encapsulated cells. The pressure stabilizer was also used for picoinjection of multiple displacement amplification (MDA) reagents to achieve genomic DNA amplification of lysed bacterial cells.

  18. Reproducing wavelet kernel method in nonlinear system identification

    Institute of Scientific and Technical Information of China (English)

    WEN Xiang-jun; XU Xiao-ming; CAI Yun-ze

    2008-01-01

    By combining the wavelet decomposition with kernel method, a practical approach of universal multi-scale wavelet kernels constructed in reproducing kernel Hilbert space (RKHS) is discussed, and an identifica-tion scheme using wavelet support vector machines ( WSVM ) estimator is proposed for nonlinear dynamic sys-tems. The good approximating properties of wavelet kernel function enhance the generalization ability of the pro-posed method, and the comparison of some numerical experimental results between the novel approach and some existing methods is encouraging.

  19. Using a 1-D model to reproduce diurnal SST signals

    DEFF Research Database (Denmark)

    Karagali, Ioanna; Høyer, Jacob L.

    2014-01-01

    of measurement. A generally preferred approach to bridge the gap between in situ and remotely obtained measurements is through modelling of the upper ocean temperature. This ESA supported study focuses on the implementation of the 1 dimensional General Ocean Turbulence Model (GOTM), in order to resolve...... profiles, along with the selection of the coefficients for the 2-band parametrisation of light’s penetration in the water column, hold a key role in the agreement of the modelled output with observations. To improve the surface heat budget and the distribution of heat, the code was modified to include...... Institution Upper Ocean Processes Group archive. The successful implementation of the new parametrisations is verified while the model reproduces the diurnal signals seen from in situ measurements. Special focus is given to testing and validation of different set-ups using campaign data from the Atlantic...

  20. Hydrological Modeling Reproducibility Through Data Management and Adaptors for Model Interoperability

    Science.gov (United States)

    Turner, M. A.

    2015-12-01

    Because of a lack of centralized planning and no widely-adopted standards among hydrological modeling research groups, research communities, and the data management teams meant to support research, there is chaos when it comes to data formats, spatio-temporal resolutions, ontologies, and data availability. All this makes true scientific reproducibility and collaborative integrated modeling impossible without some glue to piece it all together. Our Virtual Watershed Integrated Modeling System provides the tools and modeling framework hydrologists need to accelerate and fortify new scientific investigations by tracking provenance and providing adaptors for integrated, collaborative hydrologic modeling and data management. Under global warming trends where water resources are under increasing stress, reproducible hydrological modeling will be increasingly important to improve transparency and understanding of the scientific facts revealed through modeling. The Virtual Watershed Data Engine is capable of ingesting a wide variety of heterogeneous model inputs, outputs, model configurations, and metadata. We will demonstrate one example, starting from real-time raw weather station data packaged with station metadata. Our integrated modeling system will then create gridded input data via geostatistical methods along with error and uncertainty estimates. These gridded data are then used as input to hydrological models, all of which are available as web services wherever feasible. Models may be integrated in a data-centric way where the outputs too are tracked and used as inputs to "downstream" models. This work is part of an ongoing collaborative Tri-state (New Mexico, Nevada, Idaho) NSF EPSCoR Project, WC-WAVE, comprised of researchers from multiple universities in each of the three states. The tools produced and presented here have been developed collaboratively alongside watershed scientists to address specific modeling problems with an eye on the bigger picture of

  1. Venusian Polar Vortex reproduced by a general circulation model

    Science.gov (United States)

    Ando, Hiroki; Sugimoto, Norihiko; Takagi, Masahiro

    2016-10-01

    Unlike the polar vortices observed in the Earth, Mars and Titan atmospheres, the observed Venus polar vortex is warmer than the mid-latitudes at cloud-top levels (~65 km). This warm polar vortex is zonally surrounded by a cold latitude band located at ~60 degree latitude, which is a unique feature called 'cold collar' in the Venus atmosphere [e.g. Taylor et al. 1980; Piccioni et al. 2007]. Although these structures have been observed in numerous previous observations, the formation mechanism is still unknown. In addition, an axi-asymmetric feature is always seen in the warm polar vortex. It changes temporally and sometimes shows a hot polar dipole or S-shaped structure as shown by a lot of infrared measurements [e.g. Garate-Lopez et al. 2013; 2015]. However, its vertical structure has not been investigated. To solve these problems, we performed a numerical simulation of the Venus atmospheric circulation using a general circulation model named AFES for Venus [Sugimoto et al. 2014] and reproduced these puzzling features.And then, the reproduced structures of the atmosphere and the axi-asymmetirc feature are compared with some previous observational results.In addition, the quasi-periodical zonal-mean zonal wind fluctuation is also seen in the Venus polar vortex reproduced in our model. This might be able to explain some observational results [e.g. Luz et al. 2007] and implies that the polar vacillation might also occur in the Venus atmosphere, which is silimar to the Earth's polar atmosphere. We will also show some initial results about this point in this presentation.

  2. Reproducibility of UAV-based photogrammetric surface models

    Science.gov (United States)

    Anders, Niels; Smith, Mike; Cammeraat, Erik; Keesstra, Saskia

    2016-04-01

    Soil erosion, rapid geomorphological change and vegetation degradation are major threats to the human and natural environment in many regions. Unmanned Aerial Vehicles (UAVs) and Structure-from-Motion (SfM) photogrammetry are invaluable tools for the collection of highly detailed aerial imagery and subsequent low cost production of 3D landscapes for an assessment of landscape change. Despite the widespread use of UAVs for image acquisition in monitoring applications, the reproducibility of UAV data products has not been explored in detail. This paper investigates this reproducibility by comparing the surface models and orthophotos derived from different UAV flights that vary in flight direction and altitude. The study area is located near Lorca, Murcia, SE Spain, which is a semi-arid medium-relief locale. The area is comprised of terraced agricultural fields that have been abandoned for about 40 years and have suffered subsequent damage through piping and gully erosion. In this work we focused upon variation in cell size, vertical and horizontal accuracy, and horizontal positioning of recognizable landscape features. The results suggest that flight altitude has a significant impact on reconstructed point density and related cell size, whilst flight direction affects the spatial distribution of vertical accuracy. The horizontal positioning of landscape features is relatively consistent between the different flights. We conclude that UAV data products are suitable for monitoring campaigns for land cover purposes or geomorphological mapping, but special care is required when used for monitoring changes in elevation.

  3. Reproducible quantitative proteotype data matrices for systems biology.

    Science.gov (United States)

    Röst, Hannes L; Malmström, Lars; Aebersold, Ruedi

    2015-11-05

    Historically, many mass spectrometry-based proteomic studies have aimed at compiling an inventory of protein compounds present in a biological sample, with the long-term objective of creating a proteome map of a species. However, to answer fundamental questions about the behavior of biological systems at the protein level, accurate and unbiased quantitative data are required in addition to a list of all protein components. Fueled by advances in mass spectrometry, the proteomics field has thus recently shifted focus toward the reproducible quantification of proteins across a large number of biological samples. This provides the foundation to move away from pure enumeration of identified proteins toward quantitative matrices of many proteins measured across multiple samples. It is argued here that data matrices consisting of highly reproducible, quantitative, and unbiased proteomic measurements across a high number of conditions, referred to here as quantitative proteotype maps, will become the fundamental currency in the field and provide the starting point for downstream biological analysis. Such proteotype data matrices, for example, are generated by the measurement of large patient cohorts, time series, or multiple experimental perturbations. They are expected to have a large effect on systems biology and personalized medicine approaches that investigate the dynamic behavior of biological systems across multiple perturbations, time points, and individuals. © 2015 Röst et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  4. A Robotic System to Scan and Reproduce Object

    Directory of Open Access Journals (Sweden)

    Cesare Rossi

    2011-01-01

    Full Text Available An application of a robotic system integrated with a vision system is presented. The robot is a 3-axis revolute prototype, while the vision system essentially consists in a laser scanner made up of a camera and a linear laser projector. Both the robotic and the video system were designed and built at DIME (Department of Mechanical Engineering for Energetics, University of Naples Federico II. The presented application essentially consists of a laser scanner that is installed on the robot arm; the scanner scans a 3D surface, and the data are converted in a cloud of points in the robot’s workspace. Then, starting from those points, the end-effector trajectories adopted to replicate the scanned surface are calculated; so, the same robot, by using a tool, can reproduce the scanned object. The software was developed also at the DIME. The adopted tool was a high-speed drill, installed on the last link of the robot arm, with a spherical milling cutter in order to obtain enough accurate surfaces by the data represented by the cloud of points. An algorithm to interpolate the paths and to plan the trajectories was also developed and successfully tested.

  5. Can a coupled meteorology–chemistry model reproduce the ...

    Science.gov (United States)

    The ability of a coupled meteorology–chemistry model, i.e., Weather Research and Forecast and Community Multiscale Air Quality (WRF-CMAQ), to reproduce the historical trend in aerosol optical depth (AOD) and clear-sky shortwave radiation (SWR) over the Northern Hemisphere has been evaluated through a comparison of 21-year simulated results with observation-derived records from 1990 to 2010. Six satellite-retrieved AOD products including AVHRR, TOMS, SeaWiFS, MISR, MODIS-Terra and MODIS-Aqua as well as long-term historical records from 11 AERONET sites were used for the comparison of AOD trends. Clear-sky SWR products derived by CERES at both the top of atmosphere (TOA) and surface as well as surface SWR data derived from seven SURFRAD sites were used for the comparison of trends in SWR. The model successfully captured increasing AOD trends along with the corresponding increased TOA SWR (upwelling) and decreased surface SWR (downwelling) in both eastern China and the northern Pacific. The model also captured declining AOD trends along with the corresponding decreased TOA SWR (upwelling) and increased surface SWR (downwelling) in the eastern US, Europe and the northern Atlantic for the period of 2000–2010. However, the model underestimated the AOD over regions with substantial natural dust aerosol contributions, such as the Sahara Desert, Arabian Desert, central Atlantic and northern Indian Ocean. Estimates of the aerosol direct radiative effect (DRE) at TOA a

  6. A reproducible nonlethal animal model for studying cyanide poisoning.

    Science.gov (United States)

    Vick, J; Marino, M T; von Bredow, J D; Kaminskis, A; Brewer, T

    2000-12-01

    Previous studies using bolus intravenous injections of sodium cyanide have been used to model the sudden exposure to high concentrations of cyanide that could occur on the battlefield. This study was designed to develop a model that would simulate the type of exposure to cyanide gas that could happen during actual low-level continuous types of exposure and then compare it with the bolus model. Cardiovascular and respiratory recordings taken from anesthetized dogs have been used previously to characterize the lethal effects of cyanide. The intravenous, bolus injection of 2.5 mg/kg sodium cyanide provides a model in which a greater than lethal concentration is attained. In contrast, our model uses a slow, intravenous infusion of cyanide to titrate each animal to its own inherent end point, which coincides with the amount of cyanide needed to induce death through respiratory arrest. In this model, therapeutic intervention can be used to restore respiration and allow for the complete recovery of the animals. After recovery, the same animal can be given a second infusion of cyanide, followed again by treatment and recovery, providing a reproducible end point. This end point can then be expressed as the total amount of cyanide per body weight (mg/kg) required to kill. In this study, the average dose of sodium cyanide among 12 animals was 1.21 mg/kg, which is approximately half the cyanide used in the bolus model. Thus, titration to respiratory arrest followed by resuscitation provides a repetitive-use animal model that can be used to test the efficacy of various forms of pretreatment and/or therapy without the loss of a single animal.

  7. A reproducible brain tumour model established from human glioblastoma biopsies

    Directory of Open Access Journals (Sweden)

    Li Xingang

    2009-12-01

    Full Text Available Abstract Background Establishing clinically relevant animal models of glioblastoma multiforme (GBM remains a challenge, and many commonly used cell line-based models do not recapitulate the invasive growth patterns of patient GBMs. Previously, we have reported the formation of highly invasive tumour xenografts in nude rats from human GBMs. However, implementing tumour models based on primary tissue requires that these models can be sufficiently standardised with consistently high take rates. Methods In this work, we collected data on growth kinetics from a material of 29 biopsies xenografted in nude rats, and characterised this model with an emphasis on neuropathological and radiological features. Results The tumour take rate for xenografted GBM biopsies were 96% and remained close to 100% at subsequent passages in vivo, whereas only one of four lower grade tumours engrafted. Average time from transplantation to the onset of symptoms was 125 days ± 11.5 SEM. Histologically, the primary xenografts recapitulated the invasive features of the parent tumours while endothelial cell proliferations and necrosis were mostly absent. After 4-5 in vivo passages, the tumours became more vascular with necrotic areas, but also appeared more circumscribed. MRI typically revealed changes related to tumour growth, several months prior to the onset of symptoms. Conclusions In vivo passaging of patient GBM biopsies produced tumours representative of the patient tumours, with high take rates and a reproducible disease course. The model provides combinations of angiogenic and invasive phenotypes and represents a good alternative to in vitro propagated cell lines for dissecting mechanisms of brain tumour progression.

  8. Voxel-level reproducibility assessment of modality independent elastography in a pre-clinical murine model

    Science.gov (United States)

    Flint, Katelyn M.; Weis, Jared A.; Yankeelov, Thomas E.; Miga, Michael I.

    2015-03-01

    Changes in tissue mechanical properties, measured non-invasively by elastography methods, have been shown to be an important diagnostic tool, particularly for cancer. Tissue elasticity information, tracked over the course of therapy, may be an important prognostic indicator of tumor response to treatment. While many elastography techniques exist, this work reports on the use of a novel form of elastography that uses image texture to reconstruct elastic property distributions in tissue (i.e., a modality independent elastography (MIE) method) within the context of a pre-clinical breast cancer system.1,2 The elasticity results have previously shown good correlation with independent mechanical testing.1 Furthermore, MIE has been successfully utilized to localize and characterize lesions in both phantom experiments and simulation experiments with clinical data.2,3 However, the reproducibility of this method has not been characterized in previous work. The goal of this study is to evaluate voxel-level reproducibility of MIE in a pre-clinical model of breast cancer. Bland-Altman analysis of co-registered repeat MIE scans in this preliminary study showed a reproducibility index of 24.7% (scaled to a percent of maximum stiffness) at the voxel level. As opposed to many reports in the magnetic resonance elastography (MRE) literature that speak to reproducibility measures of the bulk organ, these results establish MIE reproducibility at the voxel level; i.e., the reproducibility of locally-defined mechanical property measurements throughout the tumor volume.

  9. Reproducible in vitro regeneration system for purifying sugarcane ...

    African Journals Online (AJOL)

    Tansgenic Lab

    2012-05-24

    May 24, 2012 ... Full Length Research Paper. Reproducible in ... regeneration was varied from basal to top sections. Nevertheless ... 2005). The application of biotechnology to sugarcane is comparatively ..... Damon RA, Harvey WR (1987).

  10. Establishment of reproducible osteosarcoma rat model using orthotopic implantation technique.

    Science.gov (United States)

    Yu, Zhe; Sun, Honghui; Fan, Qingyu; Long, Hua; Yang, Tongtao; Ma, Bao'an

    2009-05-01

    negligible and the procedure was simple to perform and easily reproduced. It may be a useful tool in the investigation of antiangiogenic and anticancer therapeutics. Ultrasound was found to be a highly accurate tool for tumor diagnosis, localization and measurement and may be recommended for monitoring tumor growth in this model.

  11. Reproducing Phenomenology of Peroxidation Kinetics via Model Optimization

    Science.gov (United States)

    Ruslanov, Anatole D.; Bashylau, Anton V.

    2010-06-01

    We studied mathematical modeling of lipid peroxidation using a biochemical model system of iron (II)-ascorbate-dependent lipid peroxidation of rat hepatocyte mitochondrial fractions. We found that antioxidants extracted from plants demonstrate a high intensity of peroxidation inhibition. We simplified the system of differential equations that describes the kinetics of the mathematical model to a first order equation, which can be solved analytically. Moreover, we endeavor to algorithmically and heuristically recreate the processes and construct an environment that closely resembles the corresponding natural system. Our results demonstrate that it is possible to theoretically predict both the kinetics of oxidation and the intensity of inhibition without resorting to analytical and biochemical research, which is important for cost-effective discovery and development of medical agents with antioxidant action from the medicinal plants.

  12. A structured model of video reproduces primary visual cortical organisation.

    Directory of Open Access Journals (Sweden)

    Pietro Berkes

    2009-09-01

    Full Text Available The visual system must learn to infer the presence of objects and features in the world from the images it encounters, and as such it must, either implicitly or explicitly, model the way these elements interact to create the image. Do the response properties of cells in the mammalian visual system reflect this constraint? To address this question, we constructed a probabilistic model in which the identity and attributes of simple visual elements were represented explicitly and learnt the parameters of this model from unparsed, natural video sequences. After learning, the behaviour and grouping of variables in the probabilistic model corresponded closely to functional and anatomical properties of simple and complex cells in the primary visual cortex (V1. In particular, feature identity variables were activated in a way that resembled the activity of complex cells, while feature attribute variables responded much like simple cells. Furthermore, the grouping of the attributes within the model closely parallelled the reported anatomical grouping of simple cells in cat V1. Thus, this generative model makes explicit an interpretation of complex and simple cells as elements in the segmentation of a visual scene into basic independent features, along with a parametrisation of their moment-by-moment appearances. We speculate that such a segmentation may form the initial stage of a hierarchical system that progressively separates the identity and appearance of more articulated visual elements, culminating in view-invariant object recognition.

  13. A force-based model to reproduce stop-and-go waves in pedestrian dynamics

    CERN Document Server

    Chraibi, Mohcine; Schadschneider, Andreas

    2015-01-01

    Stop-and-go waves in single-file movement are a phenomenon that is ob- served empirically in pedestrian dynamics. It manifests itself by the co-existence of two phases: moving and stopping pedestrians. We show analytically based on a simplified one-dimensional scenario that under some conditions the system can have instable homogeneous solutions. Hence, oscillations in the trajectories and in- stabilities emerge during simulations. To our knowledge there exists no force-based model which is collision- and oscillation-free and meanwhile can reproduce phase separation. We develop a new force-based model for pedestrian dynamics able to reproduce qualitatively the phenomenon of phase separation. We investigate analytically the stability condition of the model and define regimes of parameter values where phase separation can be observed. We show by means of simulations that the predefined conditions lead in fact to the expected behavior and validate our model with respect to empirical findings.

  14. Pressure Stabilizer for Reproducible Picoinjection in Droplet Microfluidic Systems

    OpenAIRE

    Rhee, Minsoung; Light, Yooli K.; Yilmaz, Suzan; Adams, Paul D.; Saxena, Deepak; Meagher, Robert J.; Singh, Anup K.

    2014-01-01

    Picoinjection is a promising technique to add reagents into pre-formed emulsion droplets on chip; however, it is sensitive to pressure fluctuation, making stable operation of the picoinjector challenging. We present a chip architecture using a simple pressure stabilizer for consistent and highly reproducible picoinjection in multi-step biochemical assays with droplets. Incorporation of the stabilizer immediately upstream of a picoinjector or a combination of injectors greatly reduces pressure...

  15. New model for datasets citation and extraction reproducibility in VAMDC

    CERN Document Server

    Zwölf, Carlo Maria; Dubernet, Marie-Lise

    2016-01-01

    In this paper we present a new paradigm for the identification of datasets extracted from the Virtual Atomic and Molecular Data Centre (VAMDC) e-science infrastructure. Such identification includes information on the origin and version of the datasets, references associated to individual data in the datasets, as well as timestamps linked to the extraction procedure. This paradigm is described through the modifications of the language used to exchange data within the VAMDC and through the services that will implement those modifications. This new paradigm should enforce traceability of datasets, favour reproducibility of datasets extraction, and facilitate the systematic citation of the authors having originally measured and/or calculated the extracted atomic and molecular data.

  16. New model for datasets citation and extraction reproducibility in VAMDC

    Science.gov (United States)

    Zwölf, Carlo Maria; Moreau, Nicolas; Dubernet, Marie-Lise

    2016-09-01

    In this paper we present a new paradigm for the identification of datasets extracted from the Virtual Atomic and Molecular Data Centre (VAMDC) e-science infrastructure. Such identification includes information on the origin and version of the datasets, references associated to individual data in the datasets, as well as timestamps linked to the extraction procedure. This paradigm is described through the modifications of the language used to exchange data within the VAMDC and through the services that will implement those modifications. This new paradigm should enforce traceability of datasets, favor reproducibility of datasets extraction, and facilitate the systematic citation of the authors having originally measured and/or calculated the extracted atomic and molecular data.

  17. Can a regional climate model reproduce observed extreme temperatures?

    Directory of Open Access Journals (Sweden)

    Peter F. Craigmile

    2013-10-01

    Full Text Available Using output from a regional Swedish climate model and observations from the Swedish synoptic observational network, we compare seasonal minimum temperatures from model output and observations using marginal extreme value modeling techniques. We make seasonal comparisons using generalized extreme value models and empirically estimate the shift in the distribution as a function of the regional climate model values, using the Doksum shift function. Spatial and temporal comparisons over south central Sweden are made by building hierarchical Bayesian generalized extreme value models for the observed minima and regional climate model output. Generally speaking the regional model is surprisingly well calibrated for minimum temperatures. We do detect a problem in the regional model to produce minimum temperatures close to 0◦C. The seasonal spatial effects are quite similar between data and regional model. The observations indicate relatively strong warming, especially in the northern region. This signal is present in the regional model, but is not as strong.

  18. A model project for reproducible papers: critical temperature for the Ising model on a square lattice

    CERN Document Server

    Dolfi, M; Hehn, A; Imriška, J; Pakrouski, K; Rønnow, T F; Troyer, M; Zintchenko, I; Chirigati, F; Freire, J; Shasha, D

    2014-01-01

    In this paper we present a simple, yet typical simulation in statistical physics, consisting of large scale Monte Carlo simulations followed by an involved statistical analysis of the results. The purpose is to provide an example publication to explore tools for writing reproducible papers. The simulation estimates the critical temperature where the Ising model on the square lattice becomes magnetic to be Tc /J = 2.26934(6) using a finite size scaling analysis of the crossing points of Binder cumulants. We provide a virtual machine which can be used to reproduce all figures and results.

  19. Autonomous Agents: The Origins and Co-Evolution of Reproducing Molecular Systems

    Science.gov (United States)

    Kauffman, Stuart

    1999-01-01

    The central aim of this award concerned an investigation into, and adequate formulation of, the concept of an "autonomous agent." If we consider a bacterium swimming upstream in a glucose gradient, we are willing to say of the bacterium that it is going to get food. That is, we are willing, and do, describe the bacterium as acting on its own behalf in an environment. All free living cells are, in this sense, autonomous agents. But the bacterium is "just" a set of molecules. We define an autonomous agent as a physical system able to act on its own behalf in an environment, then ask, "What must a physical system be to be an autonomous agent?" The tentative definition for a molecular autonomous agent is that it must be self-reproducing and carry out at least one thermodynamic work cycle. The work carried out in this grant involved, among other features, the development of a detailed model of a molecular autonomous agent, and study of the kinetics of this system. In particular, a molecular autonomous agent must, by the above tentative definition, not only reproduce, but must carry out at least one work cycle. I took, as a simple example of a self-reproducing molecular system, the single-stranded DNA hexamer 3'CCGCGG5' which can line up and ligate its two complementary trimers, 5'CCG3' and 5'CGG3'. But the two ligated trimers constitute the same molecular sequence in the 3' to 5' direction as the initial hexamer, hence this system is autocatalytic. On the other hand the above system is not yet an autonomous agent. At the minimum, autonomous agents, as I have defined them, are a new class of chemical reaction network. At a maximum, they may constitute a proper definition of life itself.

  20. Using the Monte Carlo Simulation Methods in Gauge Repeatability and Reproducibility of Measurement System Analysis

    Directory of Open Access Journals (Sweden)

    Tsu-Ming Yeh

    2013-10-01

    Full Text Available Measurements are required to maintain the consistent quality of all finished and semi-finished products in a production line. Many firms in the automobile and general precision industries apply the TS 16949:2009 Technical Specifications and Measurement System Analysis (MSA manual to establish measurement systems. This work is undertaken to evaluate gauge repeatability and reproducibility (GR&R to verify the measuring ability and quality of the measurement frame, as well as to continuously improve and maintain the verification process. Nevertheless, the implementation of GR&R requires considerable time and manpower, and is likely to affect production adversely. In addition, the evaluation value for GR&R is always different owing to the sum of man-made and machine-made variations. Using a Monte Carlo simulation and the prediction of the repeatability and reproducibility of the measurement system analysis, this study aims to determine the distribution of %GR&R and the related number of distinct categories (ndc. This study uses two case studies of an automobile parts manufacturer and the combination of a Monte Carlo simulation, statistical bases, and the prediction of the repeatability and reproducibility of the measurement system analysis to determine the probability density function, the distribution of %GR&R, and the related number of distinct categories (ndc. The method used in this study could evaluate effectively the possible range of the GR&R of the measurement capability, in order to establish a prediction model for the evaluation of the measurement capacity of a measurement system.

  1. Reproducible Infection Model for Clostridium perfringens in Broiler Chickens

    DEFF Research Database (Denmark)

    Pedersen, Karl; Friis-Holm, Lotte Bjerrum; Heuer, Ole Eske

    2008-01-01

    Experiments were carried out to establish an infection and disease model for Clostridium perfringens in broiler chickens. Previous experiments had failed to induce disease and only a transient colonization with challenge strains had been obtained. In the present study, two series of experiments w...

  2. Quantitative Evaluation of Ionosphere Models for Reproducing Regional TEC During Geomagnetic Storms

    Science.gov (United States)

    Shim, J. S.; Kuznetsova, M.; Rastaetter, L.; Bilitza, D.; Codrescu, M.; Coster, A. J.; Emery, B.; Foster, B.; Fuller-Rowell, T. J.; Goncharenko, L. P.; Huba, J.; Mitchell, C. N.; Ridley, A. J.; Fedrizzi, M.; Scherliess, L.; Schunk, R. W.; Sojka, J. J.; Zhu, L.

    2015-12-01

    TEC (Total Electron Content) is one of the key parameters in description of the ionospheric variability that has influence on the accuracy of navigation and communication systems. To assess current TEC modeling capability of ionospheric models during geomagnetic storms and to establish a baseline against which future improvement can be compared, we quantified the ionospheric models' performance by comparing modeled vertical TEC values with ground-based GPS TEC measurements and Multi-Instrument Data Analysis System (MIDAS) TEC. The comparison focused on North America and Europe sectors during selected two storm events: 2006 AGU storm (14-15 Dec. 2006) and 2013 March storm (17-19 Mar. 2013). The ionospheric models used for this study range from empirical to physics-based, and physics-based data assimilation models. We investigated spatial and temporal variations of TEC during the storms. In addition, we considered several parameters to quantify storm impacts on TEC: TEC changes compared to quiet time, rate of TEC change, and maximum increase/decrease during the storms. In this presentation, we focus on preliminary results of the comparison of the models performance in reproducing the storm-time TEC variations using the parameters and skill scores. This study has been supported by the Community Coordinated Modeling Center (CCMC) at the Goddard Space Flight Center. Model outputs and observational data used for the study will be permanently posted at the CCMC website (http://ccmc.gsfc.nasa.gov) for the space science communities to use.

  3. On the reproducibility of spatiotemporal traffic dynamics with microscopic traffic models

    CERN Document Server

    Knorr, Florian

    2012-01-01

    Traffic flow is a very prominent example of a driven non-equilibrium system. A characteristic phenomenon of traffic dynamics is the spontaneous and abrupt drop of the average velocity on a stretch of road leading to congestion. Such a traffic breakdown corresponds to a boundary-induced phase transition from free flow to congested traffic. In this paper, we study the ability of selected microscopic traffic models to reproduce a traffic breakdown, and we investigate its spatiotemporal dynamics. For our analysis, we use empirical traffic data from stationary loop detectors on a German Autobahn showing a spontaneous breakdown. We then present several methods to assess the results and compare the models with each other. In addition, we will also discuss some important modeling aspects and their impact on the resulting spatiotemporal pattern. The investigation of different downstream boundary conditions, for example, shows that the physical origin of the traffic breakdown may be artificially induced by the setup of...

  4. On the reproducibility of spatiotemporal traffic dynamics with microscopic traffic models

    Science.gov (United States)

    Knorr, Florian; Schreckenberg, Michael

    2012-10-01

    Traffic flow is a very prominent example of a driven non-equilibrium system. A characteristic phenomenon of traffic dynamics is the spontaneous and abrupt drop of the average velocity on a stretch of road leading to congestion. Such a traffic breakdown corresponds to a boundary-induced phase transition from free flow to congested traffic. In this paper, we study the ability of selected microscopic traffic models to reproduce a traffic breakdown, and we investigate its spatiotemporal dynamics. For our analysis, we use empirical traffic data from stationary loop detectors on a German Autobahn showing a spontaneous breakdown. We then present several methods to assess the results and compare the models with each other. In addition, we will also discuss some important modeling aspects and their impact on the resulting spatiotemporal pattern. The investigation of different downstream boundary conditions, for example, shows that the physical origin of the traffic breakdown may be artificially induced by the setup of the boundaries.

  5. Accuracy and reproducibility of measurements on plaster models and digital models created using an intraoral scanner.

    Science.gov (United States)

    Camardella, Leonardo Tavares; Breuning, Hero; de Vasconcellos Vilella, Oswaldo

    2017-05-01

    The purpose of the present study was to evaluate the accuracy and reproducibility of measurements made on digital models created using an intraoral color scanner compared to measurements on dental plaster models. This study included impressions of 28 volunteers. Alginate impressions were used to make plaster models, and each volunteers' dentition was scanned with a TRIOS Color intraoral scanner. Two examiners performed measurements on the plaster models using a digital caliper and measured the digital models using Ortho Analyzer software. The examiners measured 52 distances, including tooth diameter and height, overjet, overbite, intercanine and intermolar distances, and the sagittal relationship. The paired t test was used to assess intra-examiner performance and measurement accuracy of the two examiners for both plaster and digital models. The level of clinically relevant differences between the measurements according to the threshold used was evaluated and a formula was applied to calculate the chance of finding clinically relevant errors on measurements on plaster and digital models. For several parameters, statistically significant differences were found between the measurements on the two different models. However, most of these discrepancies were not considered clinically significant. The measurement of the crown height of upper central incisors had the highest measurement error for both examiners. Based on the interexaminer performance, reproducibility of the measurements was poor for some of the parameters. Overall, our findings showed that most of the measurements on digital models created using the TRIOS Color scanner and measured with Ortho Analyzer software had a clinically acceptable accuracy compared to the same measurements made with a caliper on plaster models, but the measuring method can affect the reproducibility of the measurements.

  6. How well can DFT reproduce key interactions in Ziegler-Natta systems?

    KAUST Repository

    Correa, Andrea

    2013-08-08

    The performance of density functional theory in reproducing some of the main interactions occurring in MgCl2-supported Ziegler-Natta catalytic systems is assessed. Eight model systems, representatives of key interactions occurring in Ziegler-Natta catalysts, are selected. Fifteen density functionals are tested in combination with two different basis sets, namely, TZVP and cc-pVTZ. As a general result, we found that the best performances are achieved by the PBEh1PBE hybrid generalized gradient approximation (GGA) functional, but also the cheaper PBEh GGA functional gives rather good results. The failure of the popular B3LYP and BP86 functionals is noticeable. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Can a stepwise steady flow computational fluid dynamics model reproduce unsteady particulate matter separation for common unit operations?

    Science.gov (United States)

    Pathapati, Subbu-Srikanth; Sansalone, John J

    2011-07-01

    Computational fluid dynamics (CFD) is emerging as a model for resolving the fate of particulate matter (PM) by unit operations subject to rainfall-runoff loadings. However, compared to steady flow CFD models, there are greater computational requirements for unsteady hydrodynamics and PM loading models. Therefore this study examines if integrating a stepwise steady flow CFD model can reproduce PM separation by common unit operations loaded by unsteady flow and PM loadings, thereby reducing computational effort. Utilizing monitored unit operation data from unsteady events as a metric, this study compares the two CFD modeling approaches for a hydrodynamic separator (HS), a primary clarifier (PC) tank, and a volumetric clarifying filtration system (VCF). Results indicate that while unsteady CFD models reproduce PM separation of each unit operation, stepwise steady CFD models result in significant deviation for HS and PC models as compared to monitored data; overestimating the physical size requirements of each unit required to reproduce monitored PM separation results. In contrast, the stepwise steady flow approach reproduces PM separation by the VCF, a combined gravitational sedimentation and media filtration unit operation that provides attenuation of turbulent energy and flow velocity.

  8. Accuracy and reproducibility of dental replica models reconstructed by different rapid prototyping techniques

    NARCIS (Netherlands)

    Hazeveld, Aletta; Huddleston Slater, James J. R.; Ren, Yijin

    INTRODUCTION: Rapid prototyping is a fast-developing technique that might play a significant role in the eventual replacement of plaster dental models. The aim of this study was to investigate the accuracy and reproducibility of physical dental models reconstructed from digital data by several rapid

  9. Stochastic model of financial markets reproducing scaling and memory in volatility return intervals

    Science.gov (United States)

    Gontis, V.; Havlin, S.; Kononovicius, A.; Podobnik, B.; Stanley, H. E.

    2016-11-01

    We investigate the volatility return intervals in the NYSE and FOREX markets. We explain previous empirical findings using a model based on the interacting agent hypothesis instead of the widely-used efficient market hypothesis. We derive macroscopic equations based on the microscopic herding interactions of agents and find that they are able to reproduce various stylized facts of different markets and different assets with the same set of model parameters. We show that the power-law properties and the scaling of return intervals and other financial variables have a similar origin and could be a result of a general class of non-linear stochastic differential equations derived from a master equation of an agent system that is coupled by herding interactions. Specifically, we find that this approach enables us to recover the volatility return interval statistics as well as volatility probability and spectral densities for the NYSE and FOREX markets, for different assets, and for different time-scales. We find also that the historical S&P500 monthly series exhibits the same volatility return interval properties recovered by our proposed model. Our statistical results suggest that human herding is so strong that it persists even when other evolving fluctuations perturbate the financial system.

  10. Assessment of a climate model to reproduce rainfall variability and extremes over Southern Africa

    Science.gov (United States)

    Williams, C. J. R.; Kniveton, D. R.; Layberry, R.

    2010-01-01

    It is increasingly accepted that any possible climate change will not only have an influence on mean climate but may also significantly alter climatic variability. A change in the distribution and magnitude of extreme rainfall events (associated with changing variability), such as droughts or flooding, may have a far greater impact on human and natural systems than a changing mean. This issue is of particular importance for environmentally vulnerable regions such as southern Africa. The sub-continent is considered especially vulnerable to and ill-equipped (in terms of adaptation) for extreme events, due to a number of factors including extensive poverty, famine, disease and political instability. Rainfall variability and the identification of rainfall extremes is a function of scale, so high spatial and temporal resolution data are preferred to identify extreme events and accurately predict future variability. The majority of previous climate model verification studies have compared model output with observational data at monthly timescales. In this research, the assessment of ability of a state of the art climate model to simulate climate at daily timescales is carried out using satellite-derived rainfall data from the Microwave Infrared Rainfall Algorithm (MIRA). This dataset covers the period from 1993 to 2002 and the whole of southern Africa at a spatial resolution of 0.1° longitude/latitude. This paper concentrates primarily on the ability of the model to simulate the spatial and temporal patterns of present-day rainfall variability over southern Africa and is not intended to discuss possible future changes in climate as these have been documented elsewhere. Simulations of current climate from the UK Meteorological Office Hadley Centre's climate model, in both regional and global mode, are firstly compared to the MIRA dataset at daily timescales. Secondly, the ability of the model to reproduce daily rainfall extremes is assessed, again by a comparison with

  11. Exploring predictive and reproducible modeling with the single-subject FIAC dataset.

    Science.gov (United States)

    Chen, Xu; Pereira, Francisco; Lee, Wayne; Strother, Stephen; Mitchell, Tom

    2006-05-01

    Predictive modeling of functional magnetic resonance imaging (fMRI) has the potential to expand the amount of information extracted and to enhance our understanding of brain systems by predicting brain states, rather than emphasizing the standard spatial mapping. Based on the block datasets of Functional Imaging Analysis Contest (FIAC) Subject 3, we demonstrate the potential and pitfalls of predictive modeling in fMRI analysis by investigating the performance of five models (linear discriminant analysis, logistic regression, linear support vector machine, Gaussian naive Bayes, and a variant) as a function of preprocessing steps and feature selection methods. We found that: (1) independent of the model, temporal detrending and feature selection assisted in building a more accurate predictive model; (2) the linear support vector machine and logistic regression often performed better than either of the Gaussian naive Bayes models in terms of the optimal prediction accuracy; and (3) the optimal prediction accuracy obtained in a feature space using principal components was typically lower than that obtained in a voxel space, given the same model and same preprocessing. We show that due to the existence of artifacts from different sources, high prediction accuracy alone does not guarantee that a classifier is learning a pattern of brain activity that might be usefully visualized, although cross-validation methods do provide fairly unbiased estimates of true prediction accuracy. The trade-off between the prediction accuracy and the reproducibility of the spatial pattern should be carefully considered in predictive modeling of fMRI. We suggest that unless the experimental goal is brain-state classification of new scans on well-defined spatial features, prediction alone should not be used as an optimization procedure in fMRI data analysis.

  12. MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

    Science.gov (United States)

    Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

    2017-01-01

    Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

  13. A stable and reproducible human blood-brain barrier model derived from hematopoietic stem cells.

    Directory of Open Access Journals (Sweden)

    Romeo Cecchelli

    Full Text Available The human blood brain barrier (BBB is a selective barrier formed by human brain endothelial cells (hBECs, which is important to ensure adequate neuronal function and protect the central nervous system (CNS from disease. The development of human in vitro BBB models is thus of utmost importance for drug discovery programs related to CNS diseases. Here, we describe a method to generate a human BBB model using cord blood-derived hematopoietic stem cells. The cells were initially differentiated into ECs followed by the induction of BBB properties by co-culture with pericytes. The brain-like endothelial cells (BLECs express tight junctions and transporters typically observed in brain endothelium and maintain expression of most in vivo BBB properties for at least 20 days. The model is very reproducible since it can be generated from stem cells isolated from different donors and in different laboratories, and could be used to predict CNS distribution of compounds in human. Finally, we provide evidence that Wnt/β-catenin signaling pathway mediates in part the BBB inductive properties of pericytes.

  14. Reproducibility and reliability of hypoglycaemic episodes recorded with Continuous Glucose Monitoring System (CGMS) in daily life

    DEFF Research Database (Denmark)

    Høi-Hansen, T; Pedersen-Bjergaard, U; Thorsteinsson, B

    2005-01-01

    AIM: Continuous glucose monitoring may reveal episodes of unrecognized hypoglycaemia. We evaluated reproducibility and reliability of hypoglycaemic episodes recorded in daily life by the Medtronic MiniMed Continuous Glucose Monitoring System (CGMS). METHODS: Twenty-nine adult patients with Type 1...

  15. A standardised and reproducible model of intra-abdominal infection and abscess formation in rats

    NARCIS (Netherlands)

    Bosscha, K; Nieuwenhuijs, VB; Gooszen, AW; van Duijvenbode-Beumer, H; Visser, MR; Verweij, Willem; Akkermans, LMA

    2000-01-01

    Objective: To develop a standardised and reproducible model of intra-abdominal infection and abscess formation in rats. Design: Experimental study. Setting: University hospital, The Netherlands. Subjects: 36 adult male Wistar rats. Interventions: In 32 rats, peritonitis was produced using two differ

  16. Reliable and reproducible classification system for scoliotic radiograph using image processing techniques.

    Science.gov (United States)

    Anitha, H; Prabhu, G K; Karunakar, A K

    2014-11-01

    Scoliosis classification is useful for guiding the treatment and testing the clinical outcome. State-of-the-art classification procedures are inherently unreliable and non-reproducible due to technical and human judgmental error. In the current diagnostic system each examiner will have diagrammatic summary of classification procedure, number of scoliosis curves, apex level, etc. It is very difficult to define the required anatomical parameters in the noisy radiographs. The classification system demands automatic image understanding system. The proposed automated classification procedures extracts the anatomical features using image processing and applies classification procedures based on computer assisted algorithms. The reliability and reproducibility of the proposed computerized image understanding system are compared with manual and computer assisted system using Kappa values.

  17. A new paradigm for reproducing and analyzing N-body simulations of planetary systems

    Science.gov (United States)

    Rein, Hanno; Tamayo, Daniel

    2017-01-01

    The reproducibility of experiments is one of the main principles of the scientific method. However, numerical N-body experiments, especially those of planetary systems, are currently not reproducible. In the most optimistic scenario, they can only be replicated in an approximate or statistical sense. Even if authors share their full source code and initial conditions, differences in compilers, libraries, operating systems or hardware often lead to qualitatively different results. We provide a new set of easy-to-use, open-source tools that address the above issues, allowing for exact (bit-by-bit) reproducibility of N-body experiments. In addition to generating completely reproducible integrations, we show that our framework also offers novel and innovative ways to analyze these simulations. As an example, we present a high-accuracy integration of the Solar System spanning 10 Gyrs, requiring several weeks to run on a modern CPU. In our framework we can not only easily access simulation data at predefined intervals for which we save snapshots, but at any time during the integration. We achieve this by integrating an on-demand reconstructed simulation forward in time from the nearest snapshot. This allows us to extract arbitrary quantities at any point in the saved simulation exactly (bit-by-bit), and within seconds rather than weeks. We believe that the tools we present in this paper offer a new paradigm for how N-body simulations are run, analyzed, and shared across the community.

  18. Using the mouse to model human disease: increasing validity and reproducibility

    Directory of Open Access Journals (Sweden)

    Monica J. Justice

    2016-02-01

    Full Text Available Experiments that use the mouse as a model for disease have recently come under scrutiny because of the repeated failure of data, particularly derived from preclinical studies, to be replicated or translated to humans. The usefulness of mouse models has been questioned because of irreproducibility and poor recapitulation of human conditions. Newer studies, however, point to bias in reporting results and improper data analysis as key factors that limit reproducibility and validity of preclinical mouse research. Inaccurate and incomplete descriptions of experimental conditions also contribute. Here, we provide guidance on best practice in mouse experimentation, focusing on appropriate selection and validation of the model, sources of variation and their influence on phenotypic outcomes, minimum requirements for control sets, and the importance of rigorous statistics. Our goal is to raise the standards in mouse disease modeling to enhance reproducibility, reliability and clinical translation of findings.

  19. Anatomical Reproducibility of a Head Model Molded by a Three-dimensional Printer.

    Science.gov (United States)

    Kondo, Kosuke; Nemoto, Masaaki; Masuda, Hiroyuki; Okonogi, Shinichi; Nomoto, Jun; Harada, Naoyuki; Sugo, Nobuo; Miyazaki, Chikao

    2015-01-01

    We prepared rapid prototyping models of heads with unruptured cerebral aneurysm based on image data of computed tomography angiography (CTA) using a three-dimensional (3D) printer. The objective of this study was to evaluate the anatomical reproducibility and accuracy of these models by comparison with the CTA images on a monitor. The subjects were 22 patients with unruptured cerebral aneurysm who underwent preoperative CTA. Reproducibility of the microsurgical anatomy of skull bone and arteries, the length and thickness of the main arteries, and the size of cerebral aneurysm were compared between the CTA image and rapid prototyping model. The microsurgical anatomy and arteries were favorably reproduced, apart from a few minute regions, in the rapid prototyping models. No significant difference was noted in the measured lengths of the main arteries between the CTA image and rapid prototyping model, but errors were noted in their thickness (p 3D printer. It was concluded that these models are useful tools for neurosurgical simulation. The thickness of the main arteries and size of cerebral aneurysm should be comprehensively judged including other neuroimaging in consideration of errors.

  20. Rainfall variability and extremes over southern Africa: Assessment of a climate model to reproduce daily extremes

    Science.gov (United States)

    Williams, C. J. R.; Kniveton, D. R.; Layberry, R.

    2009-04-01

    It is increasingly accepted that that any possible climate change will not only have an influence on mean climate but may also significantly alter climatic variability. A change in the distribution and magnitude of extreme rainfall events (associated with changing variability), such as droughts or flooding, may have a far greater impact on human and natural systems than a changing mean. This issue is of particular importance for environmentally vulnerable regions such as southern Africa. The subcontinent is considered especially vulnerable to and ill-equipped (in terms of adaptation) for extreme events, due to a number of factors including extensive poverty, famine, disease and political instability. Rainfall variability and the identification of rainfall extremes is a function of scale, so high spatial and temporal resolution data are preferred to identify extreme events and accurately predict future variability. The majority of previous climate model verification studies have compared model output with observational data at monthly timescales. In this research, the assessment of ability of a state of the art climate model to simulate climate at daily timescales is carried out using satellite derived rainfall data from the Microwave Infra-Red Algorithm (MIRA). This dataset covers the period from 1993-2002 and the whole of southern Africa at a spatial resolution of 0.1 degree longitude/latitude. The ability of a climate model to simulate current climate provides some indication of how much confidence can be applied to its future predictions. In this paper, simulations of current climate from the UK Meteorological Office Hadley Centre's climate model, in both regional and global mode, are firstly compared to the MIRA dataset at daily timescales. This concentrates primarily on the ability of the model to simulate the spatial and temporal patterns of rainfall variability over southern Africa. Secondly, the ability of the model to reproduce daily rainfall extremes will

  1. Impact of soil parameter and physical process on reproducibility of hydrological processes by land surface model in semiarid grassland

    Science.gov (United States)

    Miyazaki, S.; Yorozu, K.; Asanuma, J.; Kondo, M.; Saito, K.

    2014-12-01

    The land surface model (LSM) takes part in the land-atmosphere interaction on the earth system model for the climate change research. In this study, we evaluated the impact of soil parameters and physical process on reproducibility of hydrological process by LSM Minimal Advanced Treatments of Surface Interaction and RunOff (MATSIRO; Takata et al, 2003, GPC) forced by the meteorological data observed at grassland in semiarid climate in China and Mongolia. The testing of MATSIRO was carried out offline mode over the semiarid grassland sites at Tongyu (44.42 deg. N, 122.87 deg. E, altitude: 184m) in China, Kherlen Bayan Ulaan (KBU; 47.21 deg. N, 108.74 deg. E, altitude: 1235m) and Arvaikheer (46.23 N, 102.82E, altitude: 1,813m) in Mongolia. Although all sites locate semiarid grassland, the climate condition is different among sites, which the annual air temperature and precipitation are 5.7 deg. C and 388mm (Tongyu), 1.2 deg.C and 180mm (KBU), and 0.4 deg. C and 245mm(Arvaikheer). We can evaluate the effect of climate condition on the model performance. Three kinds of experiments have been carried out, which was run with the default parameters (CTL), the observed parameters (OBS) for soil physics and hydrology, and vegetation, and refined MATSIRO with the effect of ice in thermal parameters and unfrozen water below the freezing with same parameters as OBS run (OBSr). The validation data has been provided by CEOP(http://www.ceop.net/) , RAISE(http://raise.suiri.tsukuba.ac.jp/), GAME-AAN (Miyazaki et al., 2004, JGR) for Tongyu, KBU, and Arvaikheer, respectively. The reproducibility of the net radiation, the soil temperature (Ts), and latent heat flux (LE) were well reproduced by OBS and OBSr run. The change of soil physical and hydraulic parameter affected the reproducibility of soil temperature (Ts) and soil moisture (SM) as well as energy flux component especially for the sensible heat flux (H) and soil heat flux (G). The reason for the great improvement on the

  2. A Reproducing Kernel Hilbert Space Method for Solving Systems of Fractional Integrodifferential Equations

    Directory of Open Access Journals (Sweden)

    Samia Bushnaq

    2014-01-01

    Full Text Available We present a new version of the reproducing kernel Hilbert space method (RKHSM for the solution of systems of fractional integrodifferential equations. In this approach, the solution is obtained as a convergent series with easily computable components. Several illustrative examples are given to demonstrate the effectiveness of the present method. The method described in this paper is expected to be further employed to solve similar nonlinear problems in fractional calculus.

  3. Reproducibility of the sella turcica landmark in three dimensions using a sella turcica-specific reference system

    Energy Technology Data Exchange (ETDEWEB)

    Pittayapat, Pisha; Jacobs, Reinhilde [University Hospitals Leuven, University of Leuven, Leuven (Belgium); Odri, Guillaume A. [Service de Chirurgie Orthopedique et Traumatologique, Centre Hospitalier Regional d' Orleans, Orleans Cedex2 (France); De Faria Vasconcelos, Karla [Dept. of Oral Diagnosis, Division of Oral Radiology, Piracicaba Dental School, University of Campinas, Sao Paulo (Brazil); Willems, Guy [Dept. of Oral Health Sciences, Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, University of Leuven, Leuven (Belgium); Olszewski, Raphael [Dept. of Oral and Maxillofacial Surgery, Cliniques Universitaires Saint Luc, Universite Catholique de Louvain, Brussels (Belgium)

    2015-03-15

    This study was performed to assess the reproducibility of identifying the sella turcica landmark in a three-dimensional (3D) model by using a new sella-specific landmark reference system. Thirty-two cone-beam computed tomographic scans (3D Accuitomo 170, J. Morita, Kyoto, Japan) were retrospectively collected. The 3D data were exported into the Digital Imaging and Communications in Medicine standard and then imported into the Maxilim software (Medicim NV, Sint-Niklaas, Belgium) to create 3D surface models. Five observers identified four osseous landmarks in order to create the reference frame and then identified two sella landmarks. The x, y, and z coordinates of each landmark were exported. The observations were repeated after four weeks. Statistical analysis was performed using the multiple paired t-test with Bonferroni correction (intraobserver precision: p<0.005, interobserver precision: p<0.0011). The intraobserver mean precision of all landmarks was <1 mm. Significant differences were found when comparing the intraobserver precision of each observer (p<0.005). For the sella landmarks, the intraobserver mean precision ranged from 0.43±0.34 mm to 0.51±0.46 mm. The intraobserver reproducibility was generally good. The overall interobserver mean precision was <1 mm. Significant differences between each pair of observers for all anatomical landmarks were found (p<0.0011). The interobserver reproducibility of sella landmarks was good, with >50% precision in locating the landmark within 1 mm. A newly developed reference system offers high precision and reproducibility for sella turcica identification in a 3D model without being based on two-dimensional images derived from 3D data.

  4. How well do CMIP5 climate models reproduce explosive cyclones in the extratropics of the Northern Hemisphere?

    Science.gov (United States)

    Seiler, C.; Zwiers, F. W.

    2016-02-01

    Extratropical explosive cyclones are rapidly intensifying low pressure systems with severe wind speeds and heavy precipitation, affecting livelihoods and infrastructure primarily in coastal and marine environments. This study evaluates how well the most recent generation of climate models reproduces extratropical explosive cyclones in the Northern Hemisphere for the period 1980-2005. An objective-feature tracking algorithm is used to identify and track cyclones from 25 climate models and three reanalysis products. Model biases are compared to biases in the sea surface temperature (SST) gradient, the polar jet stream, the Eady growth rate, and model resolution. Most models accurately reproduce the spatial distribution of explosive cyclones when compared to reanalysis data ( R = 0.94), with high frequencies along the Kuroshio Current and the Gulf Stream. Three quarters of the models however significantly underpredict explosive cyclone frequencies, by a third on average and by two thirds in the worst case. This frequency bias is significantly correlated with jet stream speed in the inter-model spread ( R ≥ 0.51), which in the Atlantic is correlated with a negative meridional SST gradient ( R = -0.56). The importance of the jet stream versus other variables considered in this study also applies to the interannual variability of explosive cyclone frequency. Furthermore, models with fewer explosive cyclones tend to underpredict the corresponding deepening rates ( R ≥ 0.88). A follow-up study will assess the impacts of climate change on explosive cyclones, and evaluate how model biases presented in this study affect the projections.

  5. Repeatability and reproducibility of the Tekscan HR-Walkway system in healthy children.

    Science.gov (United States)

    Coda, Andrea; Carline, Tom; Santos, Derek

    2014-06-01

    This study investigated the repeatability and reproducibility of the HR Walkway system with regards to peak pressure values (PP) and pressure time integral (PTI) in healthy children, ranging between 5 and 18 years of age. Subjects recruited took part in two non-invasive clinical assessments, at baseline and 1 week later. Gait analysis was carried out using the PP box approach, and plantar foot recording was divided into 10 anatomical areas. The PP and PTI was investigated for the left, right and both feet accounted together. Interclass Correlation Coefficient (ICC) test was adopted for statistical analysis. Overall, 30 healthy patients were recruited and 60 appointments were completed, 53.3% (n=16) were female and 46.7% (n=14) were male. Mean age was 13.3 years (SD=4.5), with an age-range of 5-18.6 years old. Results indicated that for all variables tested the repeatability data were 'good' ICC for 73.8% (n=121) and 'moderate' ICC for 26.2% (n=43). For all variables tested, the reproducibility data showed that 'good' ICC for 70.7% (n=58) and 'moderate' ICC for 29.3% (n=24). In conclusion, the HR Walkway system is able to provide repeatable and reproducible data.

  6. Cellular automaton model in the fundamental diagram approach reproducing the synchronized outflow of wide moving jams

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Jun-fang, E-mail: tianhustbjtu@hotmail.com [MOE Key Laboratory for Urban Transportation Complex Systems Theory and Technology, Beijing Jiaotong University, Beijing 100044 (China); Yuan, Zhen-zhou; Jia, Bin; Fan, Hong-qiang; Wang, Tao [MOE Key Laboratory for Urban Transportation Complex Systems Theory and Technology, Beijing Jiaotong University, Beijing 100044 (China)

    2012-09-10

    Velocity effect and critical velocity are incorporated into the average space gap cellular automaton model [J.F. Tian, et al., Phys. A 391 (2012) 3129], which was able to reproduce many spatiotemporal dynamics reported by the three-phase theory except the synchronized outflow of wide moving jams. The physics of traffic breakdown has been explained. Various congested patterns induced by the on-ramp are reproduced. It is shown that the occurrence of synchronized outflow, free outflow of wide moving jams is closely related with drivers time delay in acceleration at the downstream jam front and the critical velocity, respectively. -- Highlights: ► Velocity effect is added into average space gap cellular automaton model. ► The physics of traffic breakdown has been explained. ► The probabilistic nature of traffic breakdown is simulated. ► Various congested patterns induced by the on-ramp are reproduced. ► The occurrence of synchronized outflow of jams depends on drivers time delay.

  7. Spatial aspects of sound quality - and by multichannel systems subjective assessment of sound reproduced by stereo

    DEFF Research Database (Denmark)

    Choisel, Sylvain

    the fidelity with which sound reproduction systems can re-create the desired stereo image, a laser pointing technique was developed to accurately collect subjects' responses in a localization task. This method is subsequently applied in an investigation of the effects of loudspeaker directivity...... on the perceived direction of panned sources. The second part of the thesis addresses the identification of auditory attributes which play a role in the perception of sound reproduced by multichannel systems. Short musical excerpts were presented in mono, stereo and several multichannel formats to evoke various...

  8. Measurement of volatilized mercury by a mini-system: a simple, reliable and reproducible technique

    Directory of Open Access Journals (Sweden)

    Cursino Luciana

    2003-01-01

    Full Text Available A simple and easy new technique for volatilized mercury determination in biological systems was developed. This technique is fast and sensitive and can overcome the problems that arise due to the extremely low readings during the measurements and reproducibility in biological material (bacteria. It measures directly the volatilized metallic mercury of bacteria by means of a chemical adsorbent in a coupled mini-system, as a modified technique for mercury in air analysis. It is potentially of interest to the bioremediation and bacterial mercury resistance communities

  9. Hidden-variable models for the spin singlet: I. Non-local theories reproducing quantum mechanics

    CERN Document Server

    Di Lorenzo, Antonio

    2011-01-01

    A non-local hidden variable model reproducing the quantum mechanical probabilities for a spin singlet is presented. The non-locality is concentrated in the distribution of the hidden variables. The model otherwise satisfies both the hypothesis of outcome independence, made in the derivation of Bell inequality, and of compliance with Malus's law, made in the derivation of Leggett inequality. It is shown through the prescription of a protocol that the non-locality can be exploited to send information instantaneously provided that the hidden variables can be measured, even though they cannot be controlled.

  10. A novel, recovery, and reproducible minimally invasive cardiopulmonary bypass model with lung injury in rats

    Institute of Scientific and Technical Information of China (English)

    LI Ling-ke; CHENG Wei; LIU Dong-hai; ZHANG Jing; ZHU Yao-bin; QIAO Chen-hui; ZHANG Yan-bo

    2013-01-01

    Background Cardiopulmonary bypass (CPB) has been shown to be associated with a systemic inflammatory response leading to postoperative organ dysfunction.Elucidating the underlying mechanisms and developing protective strategies for the pathophysiological consequences of CPB have been hampered due to the absence of a satisfactory recovery animal model.The purpose of this study was to establish a good rat model of CPB to study the pathophysiology of potential complications.Methods Twenty adult male Sprague-Dawley rats weighing 450-560 g were randomly divided into a CPB group (n=10)and a control group (n=10).All rats were anaesthetized and mechanically ventilated.The carotid artery and jugular vein were cannulated.The blood was drained from the dght atrium via the right jugular and transferred by a miniaturized roller pump to a hollow fiber oxygenator and back to the rat via the left carotid artery.Priming consisted of 8 ml of homologous blood and 8 ml of colloid.The surface of the hollow fiber oxygenator was 0.075 m2.CPB was conducted for 60 minutes at a flow rate of 100-120 ml.kg-1.min-1 in the CPB group.Oxygen flow/perfusion flow was 0.8 to 1.0,and the mean arterial pressure remained 60-80 mmHg.Blood gas analysis,hemodynamic investigations,and lung histology were subsequently examined.Results All CPB rats recovered from the operative process without incident.Normal cardiac function after successful weaning was confirmed by electrocardiography and blood pressure measurements.Mean arterial pressure remained stable.The results of blood gas analysis at different times were within the normal range.Levels of IL-1β and TNF-α were higher in the lung tissue in the CPB group (P <0.005).Histological examination revealed marked increases in interstitial congestion,edema,and inflammation in the CPB group.Conclusion This novel,recovery,and reproducible minimally invasive CPB model may open the field for various studies on the pathophysiological process of CPB and systemic

  11. On some problems with reproducing the Standard Model fields and interactions in five-dimensional warped brane world models

    CERN Document Server

    Smolyakov, Mikhail N

    2015-01-01

    In the present paper we discuss some problems which arise, when the matter, gauge and Higgs fields are allowed to propagate in the bulk of five-dimensional brane world models with compact extra dimension and their zero Kaluza-Klein modes are supposed to exactly reproduce the Standard Model fields and their interactions.

  12. The general theory of the Quasi-reproducible experiments: How to describe the measured data of complex systems?

    Science.gov (United States)

    Nigmatullin, Raoul R.; Maione, Guido; Lino, Paolo; Saponaro, Fabrizio; Zhang, Wei

    2017-01-01

    In this paper, we suggest a general theory that enables to describe experiments associated with reproducible or quasi-reproducible data reflecting the dynamical and self-similar properties of a wide class of complex systems. Under complex system we understand a system when the model based on microscopic principles and suppositions about the nature of the matter is absent. This microscopic model is usually determined as "the best fit" model. The behavior of the complex system relatively to a control variable (time, frequency, wavelength, etc.) can be described in terms of the so-called intermediate model (IM). One can prove that the fitting parameters of the IM are associated with the amplitude-frequency response of the segment of the Prony series. The segment of the Prony series including the set of the decomposition coefficients and the set of the exponential functions (with k = 1,2,…,K) is limited by the final mode K. The exponential functions of this decomposition depend on time and are found by the original algorithm described in the paper. This approach serves as a logical continuation of the results obtained earlier in paper [Nigmatullin RR, W. Zhang and Striccoli D. General theory of experiment containing reproducible data: The reduction to an ideal experiment. Commun Nonlinear Sci Numer Simul, 27, (2015), pp 175-192] for reproducible experiments and includes the previous results as a partial case. In this paper, we consider a more complex case when the available data can create short samplings or exhibit some instability during the process of measurements. We give some justified evidences and conditions proving the validity of this theory for the description of a wide class of complex systems in terms of the reduced set of the fitting parameters belonging to the segment of the Prony series. The elimination of uncontrollable factors expressed in the form of the apparatus function is discussed. To illustrate how to apply the theory and take advantage of its

  13. Reproducibility blues.

    Science.gov (United States)

    Pulverer, Bernd

    2015-11-12

    Research findings advance science only if they are significant, reliable and reproducible. Scientists and journals must publish robust data in a way that renders it optimally reproducible. Reproducibility has to be incentivized and supported by the research infrastructure but without dampening innovation.

  14. Current reinforcement model reproduces center-in-center vein trajectory of Physarum polycephalum.

    Science.gov (United States)

    Akita, Dai; Schenz, Daniel; Kuroda, Shigeru; Sato, Katsuhiko; Ueda, Kei-Ichi; Nakagaki, Toshiyuki

    2017-06-01

    Vein networks span the whole body of the amoeboid organism in the plasmodial slime mould Physarum polycephalum, and the network topology is rearranged within an hour in response to spatio-temporal variations of the environment. It has been reported that this tube morphogenesis is capable of solving mazes, and a mathematical model, named the 'current reinforcement rule', was proposed based on the adaptability of the veins. Although it is known that this model works well for reproducing some key characters of the organism's maze-solving behaviour, one important issue is still open: In the real organism, the thick veins tend to trace the shortest possible route by cutting the corners at the turn of corridors, following a center-in-center trajectory, but it has not yet been examined whether this feature also appears in the mathematical model, using corridors of finite width. In this report, we confirm that the mathematical model reproduces the center-in-center trajectory of veins around corners observed in the maze-solving experiment. © 2017 Japanese Society of Developmental Biologists.

  15. [Amniocentesis trainer: development of a cheap and reproducible new training model].

    Science.gov (United States)

    Tassin, M; Cordier, A-G; Laher, G; Benachi, A; Mandelbrot, L

    2012-11-01

    Amniocentesis is the most common invasive procedure for prenatal diagnosis. It is essential to master this sampling technique prior to performing more complex ultrasound-guided interventions (cordocentesis, drain insertion). Training is a challenge because of the risks associated with the procedure, as well as the impact on the patient's anxiety. An amniocentesis simulator allows for safe training and repeats interventions, thus accelerating the learning curve, and also allows for periodic evaluation of proficiency. We present here a new, simple, and cost-effective amniotrainer model that reproduces real life conditions, using chicken breast and condoms filled with water.

  16. Extreme Rainfall Events Over Southern Africa: Assessment of a Climate Model to Reproduce Daily Extremes

    Science.gov (United States)

    Williams, C.; Kniveton, D.; Layberry, R.

    2007-12-01

    It is increasingly accepted that any possible climate change will not only have an influence on mean climate but may also significantly alter climatic variability. This issue is of particular importance for environmentally vulnerable regions such as southern Africa. The subcontinent is considered especially vulnerable extreme events, due to a number of factors including extensive poverty, disease and political instability. Rainfall variability and the identification of rainfall extremes is a function of scale, so high spatial and temporal resolution data are preferred to identify extreme events and accurately predict future variability. The majority of previous climate model verification studies have compared model output with observational data at monthly timescales. In this research, the assessment of a state-of-the-art climate model to simulate climate at daily timescales is carried out using satellite derived rainfall data from the Microwave Infra-Red Algorithm (MIRA). This dataset covers the period from 1993-2002 and the whole of southern Africa at a spatial resolution of 0.1 degree longitude/latitude. Once the model's ability to reproduce extremes has been assessed, idealised regions of SST anomalies are used to force the model, with the overall aim of investigating the ways in which SST anomalies influence rainfall extremes over southern Africa. In this paper, results from sensitivity testing of the UK Meteorological Office Hadley Centre's climate model's domain size are firstly presented. Then simulations of current climate from the model, operating in both regional and global mode, are compared to the MIRA dataset at daily timescales. Thirdly, the ability of the model to reproduce daily rainfall extremes will be assessed, again by a comparison with extremes from the MIRA dataset. Finally, the results from the idealised SST experiments are briefly presented, suggesting associations between rainfall extremes and both local and remote SST anomalies.

  17. Tackling the Reproducibility Problem in Systems Research with Declarative Experiment Specifications

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez, Ivo [Univ. of California, Santa Cruz, CA (United States); Maltzahn, Carlos [Univ. of California, Santa Cruz, CA (United States); Lofstead, Jay [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Moody, Adam [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mohror, Kathryn [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Arpaci-Dusseau, Remzi [Univ. of Wisconsin, Madison, WI (United States); Arpaci-Dusseau, Andrea [Univ. of Wisconsin, Madison, WI (United States)

    2015-05-04

    Validating experimental results in the field of computer systems is a challenging task, mainly due to the many changes in software and hardware that computational environments go through. Determining if an experiment is reproducible entails two separate tasks: re-executing the experiment and validating the results. Existing reproducibility efforts have focused on the former, envisioning techniques and infrastructures that make it easier to re-execute an experiment. In this work we focus on the latter by analyzing the validation workflow that an experiment re-executioner goes through. We notice that validating results is done on the basis of experiment design and high-level goals, rather than exact quantitative metrics. Based on this insight, we introduce a declarative format for specifying the high-level components of an experiment as well as describing generic, testable conditions that serve as the basis for validation. We present a use case in the area of storage systems to illustrate the usefulness of this approach. We also discuss limitations and potential benefits of using this approach in other areas of experimental systems research.

  18. Analysis of the reproducibility of the gray values and noise of a direct digital radiography system

    Directory of Open Access Journals (Sweden)

    Marcelo Lupion POLETI

    2015-01-01

    Full Text Available The aim of this study was to evaluate the reproducibility of the gray values and noise of a direct digital radiography system (Visualix eHD for various exposure times and analyzed regions. To obtain radiographic images in a standardized manner, the digital sensor of the system and a stepwedge were positioned in a phantom at a focus-film distance of 30 cm in a dental device at 70 kV, 7 mA and 2.2 mm filtration. Ten consecutive repetitions of X-ray imaging were performed at each exposure time (0.05, 0.07, 0.09 and 0.13 s. Gray values were analyzed using ImageJ software in five regions of interest (ROIs: alveolar bone (AB, soft tissue (ST and three steps of the stepwedge (S1, S2 and S3. The results showed that both the variability of the gray values and the noise were statistically greater (p < 0.05 in the most radiolucent region (ST. Only the noise was affected by the exposure time. In conclusion, the reproducibility of the gray values and the noise of the Visualix eHD system can vary in specific areas with different radiolucency.

  19. A novel highly reproducible and lethal nonhuman primate model for orthopox virus infection.

    Directory of Open Access Journals (Sweden)

    Marit Kramski

    Full Text Available The intentional re-introduction of Variola virus (VARV, the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV and Monkeypox virus (MPXV cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus.A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1-3 days after onset of symptoms, even when very low infectious viral doses of 5x10(2 pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed.We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID(50 (minimal monkey infectious dose 50% of 8.3x10(2 pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis.

  20. Digital versus plaster study models: how accurate and reproducible are they?

    Science.gov (United States)

    Abizadeh, Neilufar; Moles, David R; O'Neill, Julian; Noar, Joseph H

    2012-09-01

    To compare measurements of occlusal relationships and arch dimensions taken from digital study models with those taken from plaster models. Laboratory study The Orthodontic Department, Kettering General Hospital, Kettering, UK Methods and materials: One hundred and twelve sets of study models with a range of malocclusions and various degrees of crowding were selected. Occlusal features were measured manually with digital callipers on the plaster models. The same measurements were performed on digital images of the study models. Each method was carried out twice in order to check for intra-operator variability. The repeatability and reproducibility of the methods was assessed. Statistically significant differences between the two methods were found. In 8 of the 16 occlusal features measured, the plaster measurements were more repeatable. However, those differences were not of sufficient magnitude to have clinical relevance. In addition there were statistically significant systematic differences for 12 of the 16 occlusal features, with the plaster measurements being greater for 11 of these, indicating the digital model scans were not a true 11 representation of the plaster models. The repeatability of digital models compared with plaster models is satisfactory for clinical applications, although this study demonstrated some systematic differences. Digital study models can therefore be considered for use as an adjunct to clinical assessment of the occlusion, but as yet may not supersede current methods for scientific purposes.

  1. Fourier modeling of the BOLD response to a breath-hold task: Optimization and reproducibility.

    Science.gov (United States)

    Pinto, Joana; Jorge, João; Sousa, Inês; Vilela, Pedro; Figueiredo, Patrícia

    2016-07-15

    Cerebrovascular reactivity (CVR) reflects the capacity of blood vessels to adjust their caliber in order to maintain a steady supply of brain perfusion, and it may provide a sensitive disease biomarker. Measurement of the blood oxygen level dependent (BOLD) response to a hypercapnia-inducing breath-hold (BH) task has been frequently used to map CVR noninvasively using functional magnetic resonance imaging (fMRI). However, the best modeling approach for the accurate quantification of CVR maps remains an open issue. Here, we compare and optimize Fourier models of the BOLD response to a BH task with a preparatory inspiration, and assess the test-retest reproducibility of the associated CVR measurements, in a group of 10 healthy volunteers studied over two fMRI sessions. Linear combinations of sine-cosine pairs at the BH task frequency and its successive harmonics were added sequentially in a nested models approach, and were compared in terms of the adjusted coefficient of determination and corresponding variance explained (VE) of the BOLD signal, as well as the number of voxels exhibiting significant BOLD responses, the estimated CVR values, and their test-retest reproducibility. The brain average VE increased significantly with the Fourier model order, up to the 3rd order. However, the number of responsive voxels increased significantly only up to the 2nd order, and started to decrease from the 3rd order onwards. Moreover, no significant relative underestimation of CVR values was observed beyond the 2nd order. Hence, the 2nd order model was concluded to be the optimal choice for the studied paradigm. This model also yielded the best test-retest reproducibility results, with intra-subject coefficients of variation of 12 and 16% and an intra-class correlation coefficient of 0.74. In conclusion, our results indicate that a Fourier series set consisting of a sine-cosine pair at the BH task frequency and its two harmonics is a suitable model for BOLD-fMRI CVR measurements

  2. Reproducibility, reliability and validity of measurements obtained from Cecile3 digital models

    Directory of Open Access Journals (Sweden)

    Gustavo Adolfo Watanabe-Kanno

    2009-09-01

    Full Text Available The aim of this study was to determine the reproducibility, reliability and validity of measurements in digital models compared to plaster models. Fifteen pairs of plaster models were obtained from orthodontic patients with permanent dentition before treatment. These were digitized to be evaluated with the program Cécile3 v2.554.2 beta. Two examiners measured three times the mesiodistal width of all the teeth present, intercanine, interpremolar and intermolar distances, overjet and overbite. The plaster models were measured using a digital vernier. The t-Student test for paired samples and interclass correlation coefficient (ICC were used for statistical analysis. The ICC of the digital models were 0.84 ± 0.15 (intra-examiner and 0.80 ± 0.19 (inter-examiner. The average mean difference of the digital models was 0.23 ± 0.14 and 0.24 ± 0.11 for each examiner, respectively. When the two types of measurements were compared, the values obtained from the digital models were lower than those obtained from the plaster models (p < 0.05, although the differences were considered clinically insignificant (differences < 0.1 mm. The Cécile digital models are a clinically acceptable alternative for use in Orthodontics.

  3. Assessment of the reliability of reproducing two-dimensional resistivity models using an image processing technique.

    Science.gov (United States)

    Ishola, Kehinde S; Nawawi, Mohd Nm; Abdullah, Khiruddin; Sabri, Ali Idriss Aboubakar; Adiat, Kola Abdulnafiu

    2014-01-01

    This study attempts to combine the results of geophysical images obtained from three commonly used electrode configurations using an image processing technique in order to assess their capabilities to reproduce two-dimensional (2-D) resistivity models. All the inverse resistivity models were processed using the PCI Geomatica software package commonly used for remote sensing data sets. Preprocessing of the 2-D inverse models was carried out to facilitate further processing and statistical analyses. Four Raster layers were created, three of these layers were used for the input images and the fourth layer was used as the output of the combined images. The data sets were merged using basic statistical approach. Interpreted results show that all images resolved and reconstructed the essential features of the models. An assessment of the accuracy of the images for the four geologic models was performed using four criteria: the mean absolute error and mean percentage absolute error, resistivity values of the reconstructed blocks and their displacements from the true models. Generally, the blocks of the images of maximum approach give the least estimated errors. Also, the displacement of the reconstructed blocks from the true blocks is the least and the reconstructed resistivities of the blocks are closer to the true blocks than any other combined used. Thus, it is corroborated that when inverse resistivity models are combined, most reliable and detailed information about the geologic models is obtained than using individual data sets.

  4. Classical signal model reproducing quantum probabilities for single and coincidence detections

    Science.gov (United States)

    Khrennikov, Andrei; Nilsson, Börje; Nordebo, Sven

    2012-05-01

    We present a simple classical (random) signal model reproducing Born's rule. The crucial point of our approach is that the presence of detector's threshold and calibration procedure have to be treated not as simply experimental technicalities, but as the basic counterparts of the theoretical model. We call this approach threshold signal detection model (TSD). The experiment on coincidence detection which was done by Grangier in 1986 [22] played a crucial role in rejection of (semi-)classical field models in favour of quantum mechanics (QM): impossibility to resolve the wave-particle duality in favour of a purely wave model. QM predicts that the relative probability of coincidence detection, the coefficient g(2) (0), is zero (for one photon states), but in (semi-)classical models g(2)(0) >= 1. In TSD the coefficient g(2)(0) decreases as 1/ɛ2d, where ɛd > 0 is the detection threshold. Hence, by increasing this threshold an experimenter can make the coefficient g(2) (0) essentially less than 1. The TSD-prediction can be tested experimentally in new Grangier type experiments presenting a detailed monitoring of dependence of the coefficient g(2)(0) on the detection threshold. Structurally our model has some similarity with the prequantum model of Grossing et al. Subquantum stochasticity is composed of the two counterparts: a stationary process in the space of internal degrees of freedom and the random walk type motion describing the temporal dynamics.

  5. Accuracy and reproducibility of linear measurements of resin, plaster, digital and printed study-models.

    Science.gov (United States)

    Saleh, Waleed K; Ariffin, Emy; Sherriff, Martyn; Bister, Dirk

    2015-01-01

    To compare the accuracy and reproducibility of measurements of on-screen three-dimensional (3D) digital surface models captured by a 3Shape R700™ laser-scanner, with measurements made using a digital caliper on acrylic, plaster models or model replicas. Four sets of typodont models were used. Acrylic models, alginate impressions, plaster models and physical replicas were measured. The 3Shape R700™ laser-scanning device with 3Shape™ software was used for scans and measurements. Linear measurements were recorded for selected landmarks, on each of the physical models and on the 3D digital surface models on ten separate occasions by a single examiner. Comparing measurements taken on the physical models the mean difference of the measurements was 0.32 mm (SD 0.15 mm). For the different methods (physical versus digital) the mean difference was 0.112 mm (SD 0.15 mm). None of the values showed a statistically significant difference (p plaster and acrylic models. The comparison of measurements on the physical models showed no significant difference. The 3Shape R700™ is a reliable device for capturing surface details of models in a digital format. When comparing measurements taken manually and digitally there was no statistically significant difference. The Objet Eden 250™ 3D prints proved to be as accurate as the original acrylic, plaster, or alginate impressions as was shown by the accuracy of the measurements taken. This confirms that using virtual study models can be a reliable method, replacing traditional plaster models.

  6. Reproducibility of VPCT parameters in the normal pancreas: comparison of two different kinetic calculation models.

    Science.gov (United States)

    Kaufmann, Sascha; Schulze, Maximilian; Horger, Thomas; Oelker, Aenne; Nikolaou, Konstantin; Horger, Marius

    2015-09-01

    To assess the reproducibility of volume computed tomographic perfusion (VPCT) measurements in normal pancreatic tissue using two different kinetic perfusion calculation models at three different time points. Institutional ethical board approval was obtained for retrospective analysis of pancreas perfusion data sets generated by our prospective study for liver response monitoring to local therapy in patients experiencing unresectable hepatocellular carcinoma, which was approved by the institutional review board. VPCT of the entire pancreas was performed in 41 patients (mean age, 64.8 years) using 26 consecutive volume measurements and intravenous injection of 50 mL of iodinated contrast at a flow rate of 5 mL/s. Blood volume(BV) and blood flow (BF) were calculated using two mathematical methods: maximum slope + Patlak analysis versus deconvolution method. Pancreas perfusion was calculated using two volume of interests. Median interval between the first and the second VPCT was 2 days and between the second and the third VPCT 82 days. Variability was assessed with within-patient coefficients of variation (CVs) and Bland-Altman analyses. Interobserver agreement for all perfusion parameters was calculated using intraclass correlation coefficients (ICCs). BF and BV values varied widely by method of analysis as did within-patient CVs for BF and BV at the second versus the first VPCT by 22.4%/50.4% (method 1) and 24.6%/24.0% (method 2) measured in the pancreatic head and 18.4%/62.6% (method 1) and 23.8%/28.1% (method 2) measured in the pancreatic corpus and at the third versus the first VPCT by 21.7%/61.8% (method 1) and 25.7%/34.5% (method 2) measured also in the pancreatic head and 19.1%/66.1% (method 1) and 22.0%/31.8% (method 2) measured in the pancreatic corpus, respectively. Interobserver agreement measured with ICC shows fair-to-good reproducibility. VPCT performed with the presented examinational protocol is reproducible and can be used for monitoring

  7. Classical signal model reproducing quantum probabilities for single and coincidence detections

    CERN Document Server

    Khrennikov, Andrei; Nordebo, Sven

    2011-01-01

    We present a simple classical (random) signal model reproducing Born's rule. The crucial point of our approach is that the presence of detector's threshold and calibration procedure have to be treated not as simply experimental technicalities, but as the basic counterparts of the theoretical model. We call this approach threshold signal detection model (TSD). The experiment on coincidence detection which was done by Grangier in 1986 \\cite{Grangier} played a crucial role in rejection of (semi-)classical field models in favor of quantum mechanics (QM): impossibility to resolve the wave-particle duality in favor of a purely wave model. QM predicts that the relative probability of coincidence detection, the coefficient $g^{(2)}(0),$ is zero (for one photon states), but in (semi-)classical models $g^{(2)}(0)\\geq 1.$ In TSD the coefficient $g^{(2)}(0)$ decreases as $1/{\\cal E}_d^2,$ where ${\\cal E}_d>0$ is the detection threshold. Hence, by increasing this threshold an experimenter can make the coefficient $g^{(2)}...

  8. An analytical nonlinear model for laminate multiferroic composites reproducing the DC magnetic bias dependent magnetoelectric properties.

    Science.gov (United States)

    Lin, Lizhi; Wan, Yongping; Li, Faxin

    2012-07-01

    In this work, we propose an analytical nonlinear model for laminate multiferroic composites in which the magnetic-field-induced strain in magnetostrictive phase is described by a standard square law taking the stress effect into account, whereas the ferroelectric phase retains a linear piezoelectric response. Furthermore, differing from previous models which assume uniform deformation, we take into account the stress attenuation and adopt non-uniform deformation along the layer thickness in both piezoelectric and magnetostrictive phases. Analysis of this model on L-T and L-L modes of sandwiched Terfenol-D/lead zirconate titanate/Terfenol-D composites can well reproduce the observed dc magnetic field (H(dc)) dependent magnetoelectric coefficients, which reach their maximum with the H(dc) all at about 500 Oe. The model also suggests that stress attenuation along the layer thickness in practical composites should be taken into account. Furthermore, the model also indicates that a high volume fraction of magnetostrictive phase is required to get giant magnetoelectric coupling, coinciding with existing models.

  9. A small animal holding fixture system with positional reproducibility for longitudinal multimodal imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kokuryo, Daisuke; Kimura, Yuichi; Obata, Takayuki; Yamaya, Taiga; Kawamura, Kazunori; Zhang, Ming-Rong; Kanno, Iwao; Aoki, Ichio, E-mail: ukimura@ieee.or [Molecular Imaging Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan)

    2010-07-21

    This study presents a combined small animal holding fixture system, termed a 'bridge capsule', which provides for small animal re-fixation with positional reproducibility. This system comprises separate holding fixtures for the head and lower body and a connecting part to a gas anesthesia system. A mouse is fixed in place by the combination of a head fixture with a movable part made from polyacetal resin, a lower body fixture made from vinyl-silicone and a holder for the legs and tail. For re-fixation, a similar posture could be maintained by the same holding fixtures and a constant distance between the head and lower body fixtures is maintained. Artifacts caused by the bridge capsule system were not observed on magnetic resonance (MRI) and positron emission tomography (PET) images. The average position differences of the spinal column and the iliac body before and after re-fixation for the same modality were approximately 1.1 mm. The difference between the MRI and PET images was approximately 1.8 mm for the lower body fixture after image registration using fiducial markers. This system would be useful for longitudinal, repeated and multimodal imaging experiments requiring similar animal postures.

  10. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.

    Science.gov (United States)

    Benedetti, Fabrizio; Dorier, Julien; Burnier, Yannis; Stasiak, Andrzej

    2014-03-01

    Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of ∼1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.

  11. A novel, stable and reproducible acute lung injury model induced by oleic acid in immature piglet

    Institute of Scientific and Technical Information of China (English)

    ZHU Yao-bin; LING Feng; ZHANG Yan-bo; LIU Ai-jun; LIU Dong-hai; QIAO Chen-hui; WANG Qiang; LIU Ying-long

    2011-01-01

    Background Young children are susceptible to pulmonary injury,and acute lung injury (ALl) often results in a high mortality and financial costs in pediatric patients.A good ALl model will help us to gain a better understanding of the real pathophysiological picture and to evaluate novel treatment approaches to acute respiratory distress syndrome (ARDS) more accurately and liberally.This study aimed to establish a hemodynamically stable and reproducible model with ALl in piglet induced by oleic acid.Methods Six Chinese mini-piglets were used to establish ALl models by oleic acid.Hemodynamic and pulmonary function data were measured.Histopathological assessment was performed.Results Mean blood pressure,heart rate (HR),cardiac output (CO),central venous pressure (CVP) and left atrial pressure (LAP) were sharply decreased after oleic acid given,while the mean pulmonary arterial pressure (MPAP) was increased in comparison with baseline (P <0.05).pH,arterial partial pressure of O2 (PaO2),PaO2/inspired O2 fraction (FiO2) and lung compliance decreased,while PaCO2 and airway pressure increased in comparison with baseline (P <0.05).The lung histology showed severe inflammation,hyaline membranes,intra-alveolar and interstitial hemorrhage.Conclusion This experiment established a stable model which allows for a diversity of studies on early lung injury.

  12. Demography-based adaptive network model reproduces the spatial organization of human linguistic groups

    Science.gov (United States)

    Capitán, José A.; Manrubia, Susanna

    2015-12-01

    The distribution of human linguistic groups presents a number of interesting and nontrivial patterns. The distributions of the number of speakers per language and the area each group covers follow log-normal distributions, while population and area fulfill an allometric relationship. The topology of networks of spatial contacts between different linguistic groups has been recently characterized, showing atypical properties of the degree distribution and clustering, among others. Human demography, spatial conflicts, and the construction of networks of contacts between linguistic groups are mutually dependent processes. Here we introduce an adaptive network model that takes all of them into account and successfully reproduces, using only four model parameters, not only those features of linguistic groups already described in the literature, but also correlations between demographic and topological properties uncovered in this work. Besides their relevance when modeling and understanding processes related to human biogeography, our adaptive network model admits a number of generalizations that broaden its scope and make it suitable to represent interactions between agents based on population dynamics and competition for space.

  13. Validation and reproducibility assessment of modality independent elastography in a pre-clinical model of breast cancer

    Science.gov (United States)

    Weis, Jared A.; Kim, Dong K.; Yankeelov, Thomas E.; Miga, Michael I.

    2014-03-01

    Clinical observations have long suggested that cancer progression is accompanied by extracellular matrix remodeling and concomitant increases in mechanical stiffness. Due to the strong association of mechanics and tumor progression, there has been considerable interest in incorporating methodologies to diagnose cancer through the use of mechanical stiffness imaging biomarkers, resulting in commercially available US and MR elastography products. Extension of this approach towards monitoring longitudinal changes in mechanical properties along a course of cancer therapy may provide means for assessing early response to therapy; therefore a systematic study of the elasticity biomarker in characterizing cancer for therapeutic monitoring is needed. The elastography method we employ, modality independent elastography (MIE), can be described as a model-based inverse image-analysis method that reconstructs elasticity images using two acquired image volumes in a pre/post state of compression. In this work, we present preliminary data towards validation and reproducibility assessment of our elasticity biomarker in a pre-clinical model of breast cancer. The goal of this study is to determine the accuracy and reproducibility of MIE and therefore the magnitude of changes required to determine statistical differences during therapy. Our preliminary results suggest that the MIE method can accurately and robustly assess mechanical properties in a pre-clinical system and provide considerable enthusiasm for the extension of this technique towards monitoring therapy-induced changes to breast cancer tissue architecture.

  14. Server-side workflow execution using data grid technology for reproducible analyses of data-intensive hydrologic systems

    Science.gov (United States)

    Essawy, Bakinam T.; Goodall, Jonathan L.; Xu, Hao; Rajasekar, Arcot; Myers, James D.; Kugler, Tracy A.; Billah, Mirza M.; Whitton, Mary C.; Moore, Reagan W.

    2016-04-01

    Many geoscience disciplines utilize complex computational models for advancing understanding and sustainable management of Earth systems. Executing such models and their associated data preprocessing and postprocessing routines can be challenging for a number of reasons including (1) accessing and preprocessing the large volume and variety of data required by the model, (2) postprocessing large data collections generated by the model, and (3) orchestrating data processing tools, each with unique software dependencies, into workflows that can be easily reproduced and reused. To address these challenges, the work reported in this paper leverages the Workflow Structured Object functionality of the Integrated Rule-Oriented Data System and demonstrates how it can be used to access distributed data, encapsulate hydrologic data processing as workflows, and federate with other community-driven cyberinfrastructure systems. The approach is demonstrated for a study investigating the impact of drought on populations in the Carolinas region of the United States. The analysis leverages computational modeling along with data from the Terra Populus project and data management and publication services provided by the Sustainable Environment-Actionable Data project. The work is part of a larger effort under the DataNet Federation Consortium project that aims to demonstrate data and computational interoperability across cyberinfrastructure developed independently by scientific communities.

  15. Accuracy and reproducibility of dental measurements on tomographic digital models: a systematic review and meta-analysis.

    Science.gov (United States)

    Ferreira, Jamille B; Christovam, Ilana O; Alencar, David S; da Motta, Andréa F J; Mattos, Claudia T; Cury-Saramago, Adriana

    2017-04-26

    The aim of this systematic review with meta-analysis was to assess the accuracy and reproducibility of dental measurements obtained from digital study models generated from CBCT compared with those acquired from plaster models. The electronic databases Cochrane Library, Medline (via PubMed), Scopus, VHL, Web of Science, and System for Information on Grey Literature in Europe were screened to identify articles from 1998 until February 2016. The inclusion criteria were: prospective and retrospective clinical trials in humans; validation and/or comparison articles of dental study models obtained from CBCT and plaster models; and articles that used dental linear measurements as an assessment tool. The methodological quality of the studies was carried out by Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. A meta-analysis was performed to validate all comparative measurements. The databases search identified a total of 3160 items and 554 duplicates were excluded. After reading titles and abstracts, 12 articles were selected. Five articles were included after reading in full. The methodological quality obtained through QUADAS-2 was poor to moderate. In the meta-analysis, there were statistical differences between the mesiodistal widths of mandibular incisors, maxillary canines and premolars, and overall Bolton analysis. Therefore, the measurements considered accurate were maxillary and mandibular crowding, intermolar width and mesiodistal width of maxillary incisors, mandibular canines and premolars, in both arches for molars. Digital models obtained from CBCT were not accurate for all measures assessed. The differences were clinically acceptable for all dental linear measurements, except for maxillary arch perimeter. Digital models are reproducible for all measurements when intraexaminer assessment is considered and need improvement in interexaminer evaluation.

  16. Can a global model reproduce observed trends in summertime surface ozone levels?

    Directory of Open Access Journals (Sweden)

    S. Koumoutsaris

    2012-01-01

    Full Text Available Quantifying trends in surface ozone concentrations are critical for assessing pollution control strategies. Here we use observations and results from a global chemical transport model to examine the trends (1991–2005 in daily maximum 8-hour average concentrations in summertime surface ozone at rural sites in Europe and the United States. We find a decrease in observed ozone concentrations at the high end of the probability distribution at many of the sites in both regions. The model attributes these trends to a decrease in local anthropogenic ozone precursors, although simulated decreasing trends are overestimated in comparison with observed ones. The low end of observed distribution show small upward trends over Europe and the western US and downward trends in Eastern US. The model cannot reproduce these observed trends, especially over Europe and the western US. In particular, simulated changes between the low and high end of the distributions in these two regions are not significant. Sensitivity simulations indicate that emissions from far away source regions do not affect significantly ozone trends at both ends of the distribution. This is in contrast with previously available results, which indicated that increasing ozone trends at the low percentiles may reflect an increase in ozone background associated with increasing remote sources of ozone precursors. Possible reasons for discrepancies between observed and simulated trends are discussed.

  17. Animal models that best reproduce the clinical manifestations of human intoxication with organophosphorus compounds.

    Science.gov (United States)

    Pereira, Edna F R; Aracava, Yasco; DeTolla, Louis J; Beecham, E Jeffrey; Basinger, G William; Wakayama, Edgar J; Albuquerque, Edson X

    2014-08-01

    The translational capacity of data generated in preclinical toxicological studies is contingent upon several factors, including the appropriateness of the animal model. The primary objectives of this article are: 1) to analyze the natural history of acute and delayed signs and symptoms that develop following an acute exposure of humans to organophosphorus (OP) compounds, with an emphasis on nerve agents; 2) to identify animal models of the clinical manifestations of human exposure to OPs; and 3) to review the mechanisms that contribute to the immediate and delayed OP neurotoxicity. As discussed in this study, clinical manifestations of an acute exposure of humans to OP compounds can be faithfully reproduced in rodents and nonhuman primates. These manifestations include an acute cholinergic crisis in addition to signs of neurotoxicity that develop long after the OP exposure, particularly chronic neurologic deficits consisting of anxiety-related behavior and cognitive deficits, structural brain damage, and increased slow electroencephalographic frequencies. Because guinea pigs and nonhuman primates, like humans, have low levels of circulating carboxylesterases-the enzymes that metabolize and inactivate OP compounds-they stand out as appropriate animal models for studies of OP intoxication. These are critical points for the development of safe and effective therapeutic interventions against OP poisoning because approval of such therapies by the Food and Drug Administration is likely to rely on the Animal Efficacy Rule, which allows exclusive use of animal data as evidence of the effectiveness of a drug against pathologic conditions that cannot be ethically or feasibly tested in humans.

  18. A Semi-Analytic dynamical friction model that reproduces core stalling

    CERN Document Server

    Petts, James A; Read, Justin I

    2015-01-01

    We present a new semi-analytic model for dynamical friction based on Chandrasekhar's formalism. The key novelty is the introduction of physically motivated, radially varying, maximum and minimum impact parameters. With these, our model gives an excellent match to full N-body simulations for isotropic background density distributions, both cuspy and shallow, without any fine-tuning of the model parameters. In particular, we are able to reproduce the dramatic core-stalling effect that occurs in shallow/constant density cores, for the first time. This gives us new physical insight into the core-stalling phenomenon. We show that core stalling occurs in the limit in which the product of the Coulomb logarithm and the local fraction of stars with velocity lower than the infalling body tends to zero. For cuspy backgrounds, this occurs when the infalling mass approaches the enclosed background mass. For cored backgrounds, it occurs at larger distances from the centre, due to a combination of a rapidly increasing minim...

  19. Assessment of an ensemble of ocean-atmosphere coupled and uncoupled regional climate models to reproduce the climatology of Mediterranean cyclones

    Science.gov (United States)

    Flaounas, Emmanouil; Kelemen, Fanni Dora; Wernli, Heini; Gaertner, Miguel Angel; Reale, Marco; Sanchez-Gomez, Emilia; Lionello, Piero; Calmanti, Sandro; Podrascanin, Zorica; Somot, Samuel; Akhtar, Naveed; Romera, Raquel; Conte, Dario

    2016-11-01

    This study aims to assess the skill of regional climate models (RCMs) at reproducing the climatology of Mediterranean cyclones. Seven RCMs are considered, five of which were also coupled with an oceanic model. All simulations were forced at the lateral boundaries by the ERA-Interim reanalysis for a common 20-year period (1989-2008). Six different cyclone tracking methods have been applied to all twelve RCM simulations and to the ERA-Interim reanalysis in order to assess the RCMs from the perspective of different cyclone definitions. All RCMs reproduce the main areas of high cyclone occurrence in the region south of the Alps, in the Adriatic, Ionian and Aegean Seas, as well as in the areas close to Cyprus and to Atlas mountains. The RCMs tend to underestimate intense cyclone occurrences over the Mediterranean Sea and reproduce 24-40 % of these systems, as identified in the reanalysis. The use of grid nudging in one of the RCMs is shown to be beneficial, reproducing about 60 % of the intense cyclones and keeping a better track of the seasonal cycle of intense cyclogenesis. Finally, the most intense cyclones tend to be similarly reproduced in coupled and uncoupled model simulations, suggesting that modeling atmosphere-ocean coupled processes has only a weak impact on the climatology and intensity of Mediterranean cyclones.

  20. Experimental and Numerical Models of Complex Clinical Scenarios; Strategies to Improve Relevance and Reproducibility of Joint Replacement Research.

    Science.gov (United States)

    Bechtold, Joan E; Swider, Pascal; Goreham-Voss, Curtis; Soballe, Kjeld

    2016-02-01

    This research review aims to focus attention on the effect of specific surgical and host factors on implant fixation, and the importance of accounting for them in experimental and numerical models. These factors affect (a) eventual clinical applicability and (b) reproducibility of findings across research groups. Proper function and longevity for orthopedic joint replacement implants relies on secure fixation to the surrounding bone. Technology and surgical technique has improved over the last 50 years, and robust ingrowth and decades of implant survival is now routinely achieved for healthy patients and first-time (primary) implantation. Second-time (revision) implantation presents with bone loss with interfacial bone gaps in areas vital for secure mechanical fixation. Patients with medical comorbidities such as infection, smoking, congestive heart failure, kidney disease, and diabetes have a diminished healing response, poorer implant fixation, and greater revision risk. It is these more difficult clinical scenarios that require research to evaluate more advanced treatment approaches. Such treatments can include osteogenic or antimicrobial implant coatings, allo- or autogenous cellular or tissue-based approaches, local and systemic drug delivery, surgical approaches. Regarding implant-related approaches, most experimental and numerical models do not generally impose conditions that represent mechanical instability at the implant interface, or recalcitrant healing. Many treatments will work well in forgiving settings, but fail in complex human settings with disease, bone loss, or previous surgery. Ethical considerations mandate that we justify and limit the number of animals tested, which restricts experimental permutations of treatments. Numerical models provide flexibility to evaluate multiple parameters and combinations, but generally need to employ simplifying assumptions. The objectives of this paper are to (a) to highlight the importance of mechanical

  1. Reproducibility of summertime diurnal precipitation over northern Eurasia simulated by CMIP5 climate models

    Science.gov (United States)

    Hirota, N.; Takayabu, Y. N.

    2015-12-01

    Reproducibility of diurnal precipitation over northern Eurasia simulated by CMIP5 climate models in their historical runs were evaluated, in comparison with station data (NCDC-9813) and satellite data (GSMaP-V5). We first calculated diurnal cycles by averaging precipitation at each local solar time (LST) in June-July-August during 1981-2000 over the continent of northern Eurasia (0-180E, 45-90N). Then we examined occurrence time of maximum precipitation and a contribution of diurnally varying precipitation to the total precipitation.The contribution of diurnal precipitation was about 21% in both NCDC-9813 and GSMaP-V5. The maximum precipitation occurred at 18LST in NCDC-9813 but 16LST in GSMaP-V5, indicating some uncertainties even in the observational datasets. The diurnal contribution of the CMIP5 models varied largely from 11% to 62%, and their timing of the precipitation maximum ranged from 11LST to 20LST. Interestingly, the contribution and the timing had strong negative correlation of -0.65. The models with larger diurnal precipitation showed precipitation maximum earlier around noon. Next, we compared sensitivity of precipitation to surface temperature and tropospheric humidity between 5 models with large diurnal precipitation (LDMs) and 5 models with small diurnal precipitation (SDMs). Precipitation in LDMs showed high sensitivity to surface temperature, indicating its close relationship with local instability. On the other hand, synoptic disturbances were more active in SDMs with a dominant role of the large scale condensation, and precipitation in SDMs was more related with tropospheric moisture. Therefore, the relative importance of the local instability and the synoptic disturbances was suggested to be an important factor in determining the contribution and timing of the diurnal precipitation. Acknowledgment: This study is supported by Green Network of Excellence (GRENE) Program by the Ministry of Education, Culture, Sports, Science and Technology

  2. An update on the rotenone models of Parkinson's disease: their ability to reproduce the features of clinical disease and model gene-environment interactions.

    Science.gov (United States)

    Johnson, Michaela E; Bobrovskaya, Larisa

    2015-01-01

    Parkinson's disease (PD) is the second most common neurodegenerative disorder that is characterized by two major neuropathological hallmarks: the degeneration of dopaminergic neurons in the substantia nigra (SN) and the presence of Lewy bodies in the surviving SN neurons, as well as other regions of the central and peripheral nervous system. Animal models have been invaluable tools for investigating the underlying mechanisms of the pathogenesis of PD and testing new potential symptomatic, neuroprotective and neurorestorative therapies. However, the usefulness of these models is dependent on how precisely they replicate the features of clinical PD with some studies now employing combined gene-environment models to replicate more of the affected pathways. The rotenone model of PD has become of great interest following the seminal paper by the Greenamyre group in 2000 (Betarbet et al., 2000). This paper reported for the first time that systemic rotenone was able to reproduce the two pathological hallmarks of PD as well as certain parkinsonian motor deficits. Since 2000, many research groups have actively used the rotenone model worldwide. This paper will review rotenone models, focusing upon their ability to reproduce the two pathological hallmarks of PD, motor deficits, extranigral pathology and non-motor symptoms. We will also summarize the recent advances in neuroprotective therapies, focusing on those that investigated non-motor symptoms and review rotenone models used in combination with PD genetic models to investigate gene-environment interactions.

  3. Commentary on the integration of model sharing and reproducibility analysis to scholarly publishing workflow in computational biomechanics.

    Science.gov (United States)

    Erdemir, Ahmet; Guess, Trent M; Halloran, Jason P; Modenese, Luca; Reinbolt, Jeffrey A; Thelen, Darryl G; Umberger, Brian R; Erdemir, Ahmet; Guess, Trent M; Halloran, Jason P; Modenese, Luca; Reinbolt, Jeffrey A; Thelen, Darryl G; Umberger, Brian R; Umberger, Brian R; Erdemir, Ahmet; Thelen, Darryl G; Guess, Trent M; Reinbolt, Jeffrey A; Modenese, Luca; Halloran, Jason P

    2016-10-01

    The overall goal of this paper is to demonstrate that dissemination of models and analyses for assessing the reproducibility of simulation results can be incorporated in the scientific review process in biomechanics. As part of a special issue on model sharing and reproducibility in the IEEE Transactions on Biomedical Engineering, two manuscripts on computational biomechanics were submitted: Rajagopal et al., IEEE Trans. Biomed. Eng., 2016 and Schmitz and Piovesan, IEEE Trans. Biomed. Eng., 2016. Models used in these studies were shared with the scientific reviewers and the public. In addition to the standard review of the manuscripts, the reviewers downloaded the models and performed simulations that reproduced results reported in the studies. There was general agreement between simulation results of the authors and those of the reviewers. Discrepancies were resolved during the necessary revisions. The manuscripts and instructions for download and simulation were updated in response to the reviewers' feedback; changes that may otherwise have been missed if explicit model sharing and simulation reproducibility analysis was not conducted in the review process. Increased burden on the authors and the reviewers, to facilitate model sharing and to repeat simulations, were noted. When the authors of computational biomechanics studies provide access to models and data, the scientific reviewers can download and thoroughly explore the model, perform simulations, and evaluate simulation reproducibility beyond the traditional manuscript-only review process. Model sharing and reproducibility analysis in scholarly publishing will result in a more rigorous review process, which will enhance the quality of modeling and simulation studies and inform future users of computational models.

  4. Fast bootstrapping and permutation testing for assessing reproducibility and interpretability of multivariate fMRI decoding models.

    Directory of Open Access Journals (Sweden)

    Bryan R Conroy

    Full Text Available Multivariate decoding models are increasingly being applied to functional magnetic imaging (fMRI data to interpret the distributed neural activity in the human brain. These models are typically formulated to optimize an objective function that maximizes decoding accuracy. For decoding models trained on full-brain data, this can result in multiple models that yield the same classification accuracy, though some may be more reproducible than others--i.e. small changes to the training set may result in very different voxels being selected. This issue of reproducibility can be partially controlled by regularizing the decoding model. Regularization, along with the cross-validation used to estimate decoding accuracy, typically requires retraining many (often on the order of thousands of related decoding models. In this paper we describe an approach that uses a combination of bootstrapping and permutation testing to construct both a measure of cross-validated prediction accuracy and model reproducibility of the learned brain maps. This requires re-training our classification method on many re-sampled versions of the fMRI data. Given the size of fMRI datasets, this is normally a time-consuming process. Our approach leverages an algorithm called fast simultaneous training of generalized linear models (FaSTGLZ to create a family of classifiers in the space of accuracy vs. reproducibility. The convex hull of this family of classifiers can be used to identify a subset of Pareto optimal classifiers, with a single-optimal classifier selectable based on the relative cost of accuracy vs. reproducibility. We demonstrate our approach using full-brain analysis of elastic-net classifiers trained to discriminate stimulus type in an auditory and visual oddball event-related fMRI design. Our approach and results argue for a computational approach to fMRI decoding models in which the value of the interpretation of the decoding model ultimately depends upon optimizing a

  5. Composite model to reproduce the mechanical behaviour of methane hydrate bearing soils

    Science.gov (United States)

    De la Fuente, Maria

    2016-04-01

    Methane hydrate bearing sediments (MHBS) are naturally-occurring materials containing different components in the pores that may suffer phase changes under relative small temperature and pressure variations for conditions typically prevailing a few hundreds of meters below sea level. Their modelling needs to account for heat and mass balance equations of the different components, and several strategies already exist to combine them (e.g., Rutqvist & Moridis, 2009; Sánchez et al. 2014). These equations have to be completed by restrictions and constitutive laws reproducing the phenomenology of heat and fluid flows, phase change conditions and mechanical response. While the formulation of the non-mechanical laws generally includes explicitly the mass fraction of methane in each phase, which allows for a natural update of parameters during phase changes, mechanical laws are, in most cases, stated for the whole solid skeleton (Uchida et al., 2012; Soga et al. 2006). In this paper, a mechanical model is proposed to cope with the response of MHBS. It is based on a composite approach that allows defining the thermo-hydro-mechanical response of mineral skeleton and solid hydrates independently. The global stress-strain-temperature response of the solid phase (grains + hydrate) is then obtained by combining both responses according to energy principle following the work by Pinyol et al. (2007). In this way, dissociation of MH can be assessed on the basis of the stress state and temperature prevailing locally within the hydrate component. Besides, its structuring effect is naturally accounted for by the model according to patterns of MH inclusions within soil pores. This paper describes the fundamental hypothesis behind the model and its formulation. Its performance is assessed by comparison with laboratory data presented in the literature. An analysis of MHBS response to several stress-temperature paths representing potential field cases is finally presented. References

  6. Assessing reproducibility by the within-subject coefficient of variation with random effects models.

    Science.gov (United States)

    Quan, H; Shih, W J

    1996-12-01

    In this paper we consider the use of within-subject coefficient of variation (WCV) for assessing the reproducibility or reliability of a measurement. Application to assessing reproducibility of biochemical markers for measuring bone turnover is described and the comparison with intraclass correlation is discussed. Both maximum likelihood and moment confidence intervals of WCV are obtained through their corresponding asymptotic distributions. Normal and log-normal cases are considered. In general, WCV is preferred when the measurement scale bears intrinsic meaning and is not subject to arbitrary shifting. The intraclass correlation may be preferred when a fixed population of subjects can be well identified.

  7. Can cerebral blood volume be measured reproducibly with an improved near infrared spectroscopy system?

    NARCIS (Netherlands)

    Ven, M.T.P. van de; Colier, W.N.J.M.; Sluijs, M.C. van der; Walraven, D.; Oeseburg, B.; Folgering, H.T.M.

    2001-01-01

    In some circumstances, cerebral blood volume (CBV) can be used as a measure for cerebral blood flow. A new near infrared spectroscope was used for determining the reproducibility of CBV measurements assessed by the O2-method. Twenty-seven healthy subjects were investigated. An intrasubject coefficie

  8. Development of a flow chamber system for the reproducible in vitro analysis of biofilm formation on implant materials

    Science.gov (United States)

    Rath, Henryke; Stumpp, Sascha Nico; Stiesch, Meike

    2017-01-01

    Since the introduction of modern dental implants in the 1980s, the number of inserted implants has steadily increased. Implant systems have become more sophisticated and have enormously enhanced patients’ quality of life. Although there has been tremendous development in implant materials and clinical methods, bacterial infections are still one of the major causes of implant failure. These infections involve the formation of sessile microbial communities, called biofilms. Biofilms possess unique physical and biochemical properties and are hard to treat conventionally. There is a great demand for innovative methods to functionalize surfaces antibacterially, which could be used as the basis of new implant technologies. Present, there are few test systems to evaluate bacterial growth on these surfaces under physiological flow conditions. We developed a flow chamber model optimized for the assessment of dental implant materials. As a result it could be shown that biofilms of the five important oral bacteria Streptococcus gordonii, Streptococcus oralis, Streptococcus salivarius, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans, can be reproducibly formed on the surface of titanium, a frequent implant material. This system can be run automatically in combination with an appropriate microscopic device and is a promising approach for testing the antibacterial effect of innovative dental materials. PMID:28187188

  9. Reproducible long-term disc degeneration in a large animal model

    NARCIS (Netherlands)

    Hoogendoorn, R.J.W.; Helder, M.N.; Kroeze, R.J.; Bank, R.A.; Smit, T.H.; Wuisman, P.I.J.M.

    2008-01-01

    STUDY DESIGN. Twelve goats were chemically degenerated and the development of the degenerative signs was followed for 26 weeks to evaluate the progression of the induced degeneration. The results were also compared with a previous study to determine the reproducibility. OBJECTIVES. The purpose of th

  10. Reproducing the Wechsler Intelligence Scale for Children-Fifth Edition: Factor Model Results

    Science.gov (United States)

    Beaujean, A. Alexander

    2016-01-01

    One of the ways to increase the reproducibility of research is for authors to provide a sufficient description of the data analytic procedures so that others can replicate the results. The publishers of the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V) do not follow these guidelines when reporting their confirmatory factor…

  11. Assessment of the potential forecasting skill of a global hydrological model in reproducing the occurrence of monthly flow extremes

    NARCIS (Netherlands)

    Candogan Yossef, N.A.N.N.; Beek, L.P.H. van; Kwadijk, J.C.J.; Bierkens, M.F.P.

    2012-01-01

    As an initial step in assessing the prospect of using global hydrological models (GHMs) for hydrological forecasting, this study investigates the skill of the GHM PCRGLOBWB in reproducing the occurrence of past extremes in monthly discharge on a global scale. Global terrestrial hydrology from 1958

  12. Can a coupled meteorology–chemistry model reproduce the historical trend in aerosol direct radiative effects over the Northern Hemisphere?

    Science.gov (United States)

    The ability of a coupled meteorology–chemistry model, i.e., Weather Research and Forecast and Community Multiscale Air Quality (WRF-CMAQ), to reproduce the historical trend in aerosol optical depth (AOD) and clear-sky shortwave radiation (SWR) over the Northern Hemisphere h...

  13. Can a coupled meteorology–chemistry model reproduce the historical trend in aerosol direct radiative effects over the Northern Hemisphere?

    Science.gov (United States)

    The ability of a coupled meteorology–chemistry model, i.e., Weather Research and Forecast and Community Multiscale Air Quality (WRF-CMAQ), to reproduce the historical trend in aerosol optical depth (AOD) and clear-sky shortwave radiation (SWR) over the Northern Hemisphere h...

  14. Reproducibility of scratch assays is affected by the initial degree of confluence: Experiments, modelling and model selection.

    Science.gov (United States)

    Jin, Wang; Shah, Esha T; Penington, Catherine J; McCue, Scott W; Chopin, Lisa K; Simpson, Matthew J

    2016-02-01

    Scratch assays are difficult to reproduce. Here we identify a previously overlooked source of variability which could partially explain this difficulty. We analyse a suite of scratch assays in which we vary the initial degree of confluence (initial cell density). Our results indicate that the rate of re-colonisation is very sensitive to the initial density. To quantify the relative roles of cell migration and proliferation, we calibrate the solution of the Fisher-Kolmogorov model to cell density profiles to provide estimates of the cell diffusivity, D, and the cell proliferation rate, λ. This procedure indicates that the estimates of D and λ are very sensitive to the initial density. This dependence suggests that the Fisher-Kolmogorov model does not accurately represent the details of the collective cell spreading process, since this model assumes that D and λ are constants that ought to be independent of the initial density. Since higher initial cell density leads to enhanced spreading, we also calibrate the solution of the Porous-Fisher model to the data as this model assumes that the cell flux is an increasing function of the cell density. Estimates of D and λ associated with the Porous-Fisher model are less sensitive to the initial density, suggesting that the Porous-Fisher model provides a better description of the experiments.

  15. A novel porcine model of ataxia telangiectasia reproduces neurological features and motor deficits of human disease.

    Science.gov (United States)

    Beraldi, Rosanna; Chan, Chun-Hung; Rogers, Christopher S; Kovács, Attila D; Meyerholz, David K; Trantzas, Constantin; Lambertz, Allyn M; Darbro, Benjamin W; Weber, Krystal L; White, Katherine A M; Rheeden, Richard V; Kruer, Michael C; Dacken, Brian A; Wang, Xiao-Jun; Davis, Bryan T; Rohret, Judy A; Struzynski, Jason T; Rohret, Frank A; Weimer, Jill M; Pearce, David A

    2015-11-15

    Ataxia telangiectasia (AT) is a progressive multisystem disorder caused by mutations in the AT-mutated (ATM) gene. AT is a neurodegenerative disease primarily characterized by cerebellar degeneration in children leading to motor impairment. The disease progresses with other clinical manifestations including oculocutaneous telangiectasia, immune disorders, increased susceptibly to cancer and respiratory infections. Although genetic investigations and physiological models have established the linkage of ATM with AT onset, the mechanisms linking ATM to neurodegeneration remain undetermined, hindering therapeutic development. Several murine models of AT have been successfully generated showing some of the clinical manifestations of the disease, however they do not fully recapitulate the hallmark neurological phenotype, thus highlighting the need for a more suitable animal model. We engineered a novel porcine model of AT to better phenocopy the disease and bridge the gap between human and current animal models. The initial characterization of AT pigs revealed early cerebellar lesions including loss of Purkinje cells (PCs) and altered cytoarchitecture suggesting a developmental etiology for AT and could advocate for early therapies for AT patients. In addition, similar to patients, AT pigs show growth retardation and develop motor deficit phenotypes. By using the porcine system to model human AT, we established the first animal model showing PC loss and motor features of the human disease. The novel AT pig provides new opportunities to unmask functions and roles of ATM in AT disease and in physiological conditions.

  16. Some problems with reproducing the Standard Model fields and interactions in five-dimensional warped brane world models

    Science.gov (United States)

    Smolyakov, Mikhail N.; Volobuev, Igor P.

    2016-01-01

    In this paper we examine, from the purely theoretical point of view and in a model-independent way, the case, when matter, gauge and Higgs fields are allowed to propagate in the bulk of five-dimensional brane world models with compact extra dimension, and the Standard Model fields and their interactions are supposed to be reproduced by the corresponding zero Kaluza-Klein modes. An unexpected result is that in order to avoid possible pathological behavior in the fermion sector, it is necessary to impose constraints on the fermion field Lagrangian. In the case when the fermion zero modes are supposed to be localized at one of the branes, these constraints imply an additional relation between the vacuum profile of the Higgs field and the form of the background metric. Moreover, this relation between the vacuum profile of the Higgs field and the form of the background metric results in the exact reproduction of the gauge boson and fermion sectors of the Standard Model by the corresponding zero mode four-dimensional effective theory in all the physically relevant cases, allowed by the absence of pathologies. Meanwhile, deviations from these conditions can lead either back to pathological behavior in the fermion sector or to a variance between the resulting zero mode four-dimensional effective theory and the Standard Model, which, depending on the model at hand, may, in principle, result in constraints putting the theory out of the reach of the present day experiments.

  17. An independent evaluation on the interobserver reliability and intraobserver reproducibility of Toyama classification system for cervical dumbbell tumors.

    Science.gov (United States)

    Yin, Mengchen; Huang, Quan; Sun, Zhengwang; Gao, Xin; Chen, Guanghui; He, Shaohui; Xia, Ye; Ma, Junming; Mo, Wen; Xiao, Jianru

    2017-03-01

    Dumbbell tumors can not only cause the compression of cervical cord and nerve root, but also invade the important structures and the surrounding organs, causing great harm to the patient. Toyama classification that is commonly used has not been evaluated and still requires independent validation.The objectives of this study were to evaluate and analyze the interobserver reliability and intraobserver reproducibility of Toyama classification system, explore the differences, discover the shortages, and evaluate the clinical value for diagnosis.One hundred sixty-five consecutive patients of a cervical dumbbell tumor with complete clinical and radiologic data were enrolled. Six surgeons determined the classification according to Toyama system. The classification was repeated 12 weeks later. Correlation coefficient (ICC) and kappa coefficient (κ) test were used to determine interobserver reliability and intraobserver reproducibility.The interobserver reliability for Toyama classification was moderate with a value of 0.432. The interobserver reproducibility for Toyama classification was moderate with a value of 0.608.The Toyama classification has landmark value in clinical practice, but it is a relatively cumbersome system. This study shows that it has low reliability and reproducibility. Accordingly, surgical management of the resection of dumbbell cervical tumors raises several problems, including preservation of the cervical nerve root, control of the vertebral artery, and maintenance of spine. There is a need to optimize the classification in the future.

  18. Characterization of Adipogenic Chemicals in Three Different Cell Culture Systems: Implications for Reproducibility Based on Cell Source and Handling.

    Science.gov (United States)

    Kassotis, Christopher D; Masse, Lauren; Kim, Stephanie; Schlezinger, Jennifer J; Webster, Thomas F; Stapleton, Heather M

    2017-02-08

    The potential for chemical exposures to exacerbate the development and/or prevalence of metabolic disorders, such as obesity, is currently of great societal concern. Various in vitro assays are available to assess adipocyte differentiation, though little work has been done to standardize protocols and compare models effectively. This study compares several adipogenic cell culture systems under a variety of conditions to assess variability in responses. Two sources of 3T3-L1 preadipocytes as well as OP9 preadipocytes were assessed for cell proliferation and triglyceride accumulation following different induction periods and using various tissue culture plates. Both cell line and cell source had a significant impact on potencies and efficacies of adipogenic chemicals. Gene expression analyses suggested that differential expression of nuclear receptors involved in adipogenesis underlie the differences between OP9 and 3T3-L1 cells; however, there were also differences based on 3T3-L1 cell source. Induction period modulated potency and efficacy of response depending on cell line and test chemical, and large variations were observed in triglyceride accumulation and cell proliferation between brands of tissue culture plates. Our results suggest that the selection of a cell system and differentiation protocol significantly impacts the detection of adipogenic chemicals, and therefore, influences reproducibility of these studies.

  19. Reproducibility and geometric accuracy of the fixster system during hypofractionated stereotactic radiotherapy

    Directory of Open Access Journals (Sweden)

    Henriksson Roger

    2008-05-01

    Full Text Available Abstract Background Hypofractionated radiotherapy has been used for the treatment of AVMs and brain metastases. Hypofractionation necessitates the use of a relocatable stereotactic frame that has to be applied on several occasions. The stereotactic frame needs to have a high degree of reproducibility, and patient positioning is crucial to achieve a high accuracy of the treatment. Methods In this study we have, by radiological means, evaluated the reproducibility of the isocenter in consecutive treatment sessions using the Fixster frame. Deviations in the X, Y and Z-axis were measured in 10 patients treated with hypofractionated radiotherapy. Results The mean deviation in the X-axis was 0.4 mm (range -2.1 – 2.1, median 0.7 mm and in the Y-axis -0.3 mm (range -1.4 – 0.7, median -0.2 mm. The mean deviation in the Z-axis was -0.6 (range -1.4 – 1.4, median 0.0 mm. Conclusion There is a high degree of reproducibility of the isocenter during successive treatment sessions with HCSRT using the Fixster frame for stereotactic targeting. The high reducibility enables a safe treatment using hypofractionated stereotactic radiotherapy.

  20. [The Autocad system for planimetric study of the optic disc in glaucoma: technique and reproducibility study].

    Science.gov (United States)

    Sánchez Pérez, A; Honrubia López, F M; Larrosa Poves, J M; Polo Llorens, V; Melcon Sánchez-Frieras, B

    2001-09-01

    To develop a lens planimetry technique for the optic disc using AutoCAD. To determine variability magnitude of the optic disc morphological measurements. We employed AutoCAD R.14.0 Autodesk: image acquisition, contour delimitation by multiple lines fitting or ellipse adjustment, image sectorialization and measurements quantification (optic disc and excavation, vertical diameters, optic disc area, excavation area, neuroretinal sector area and Beta atrophy area). Intraimage or operator and interimage o total reproducibility was studied by coefficient of variability (CV) (n=10) in normal and myopic optic discs. This technique allows to obtain optic disc measurement in 5 to 10 minutes time. Total or interimage variability of measurements introduced by one observer presents CV range from 1.18-4.42. Operator or intraimage measurement presents CV range from 0.30-4.21. Optic disc contour delimitation by ellipse adjustment achieved better reproducibility results than multiple lines adjustment in all measurements. Computer assisted AutoCAD planimetry is an interactive method to analyse the optic disc, feasible to incorporate to clinical practice. Reproducibility results are comparable to other analyzers in quantification optic disc morphology. Ellipse adjustment improves results in optic disc contours delimitation.

  1. Elusive reproducibility.

    Science.gov (United States)

    Gori, Gio Batta

    2014-08-01

    Reproducibility remains a mirage for many biomedical studies because inherent experimental uncertainties generate idiosyncratic outcomes. The authentication and error rates of primary empirical data are often elusive, while multifactorial confounders beset experimental setups. Substantive methodological remedies are difficult to conceive, signifying that many biomedical studies yield more or less plausible results, depending on the attending uncertainties. Real life applications of those results remain problematic, with important exceptions for counterfactual field validations of strong experimental signals, notably for some vaccines and drugs, and for certain safety and occupational measures. It is argued that industrial, commercial and public policies and regulations could not ethically rely on unreliable biomedical results; rather, they should be rationally grounded on transparent cost-benefit tradeoffs.

  2. Reproducing Electric Field Observations during Magnetic Storms by means of Rigorous 3-D Modelling and Distortion Matrix Co-estimation

    Science.gov (United States)

    Püthe, Christoph; Manoj, Chandrasekharan; Kuvshinov, Alexey

    2015-04-01

    Electric fields induced in the conducting Earth during magnetic storms drive currents in power transmission grids, telecommunication lines or buried pipelines. These geomagnetically induced currents (GIC) can cause severe service disruptions. The prediction of GIC is thus of great importance for public and industry. A key step in the prediction of the hazard to technological systems during magnetic storms is the calculation of the geoelectric field. To address this issue for mid-latitude regions, we developed a method that involves 3-D modelling of induction processes in a heterogeneous Earth and the construction of a model of the magnetospheric source. The latter is described by low-degree spherical harmonics; its temporal evolution is derived from observatory magnetic data. Time series of the electric field can be computed for every location on Earth's surface. The actual electric field however is known to be perturbed by galvanic effects, arising from very local near-surface heterogeneities or topography, which cannot be included in the conductivity model. Galvanic effects are commonly accounted for with a real-valued time-independent distortion matrix, which linearly relates measured and computed electric fields. Using data of various magnetic storms that occurred between 2000 and 2003, we estimated distortion matrices for observatory sites onshore and on the ocean bottom. Strong correlations between modellings and measurements validate our method. The distortion matrix estimates prove to be reliable, as they are accurately reproduced for different magnetic storms. We further show that 3-D modelling is crucial for a correct separation of galvanic and inductive effects and a precise prediction of electric field time series during magnetic storms. Since the required computational resources are negligible, our approach is suitable for a real-time prediction of GIC. For this purpose, a reliable forecast of the source field, e.g. based on data from satellites

  3. Reproducible Research in Speech Sciences

    Directory of Open Access Journals (Sweden)

    Kandaacute;lmandaacute;n Abari

    2012-11-01

    Full Text Available Reproducible research is the minimum standard of scientific claims in cases when independent replication proves to be difficult. With the special combination of available software tools, we provide a reproducibility recipe for the experimental research conducted in some fields of speech sciences. We have based our model on the triad of the R environment, the EMU-format speech database, and the executable publication. We present the use of three typesetting systems (LaTeX, Markdown, Org, with the help of a mini research.

  4. From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.

    Science.gov (United States)

    González-Beltrán, Alejandra; Li, Peter; Zhao, Jun; Avila-Garcia, Maria Susana; Roos, Marco; Thompson, Mark; van der Horst, Eelke; Kaliyaperumal, Rajaram; Luo, Ruibang; Lee, Tin-Lap; Lam, Tak-Wah; Edmunds, Scott C; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

    2015-01-01

    Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler. Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata. SOAPdenovo2 scripts, data, and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP, and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2/. philippe

  5. Evaluating the Reliability and Reproducibility of the AO and Lauge-Hansen Classification Systems for Ankle Injuries.

    Science.gov (United States)

    Yin, Meng-Chen; Yuan, Xue-Fei; Ma, Jun-Ming; Xia, Ye; Wang, Tao; Xu, Xiao-Li; Yan, Yin-Jie; Xu, Jin-Hai; Ye, Jie; Tong, Zheng-Yi; Feng, Yan-Qi; Wang, Hong-Bo; Wu, Xue-Qun; Mo, Wen

    2015-07-01

    Ankle injuries are responsible for more than 5 million emergency department visits each year. The AO and Lauge-Hansen classification systems are widely used in the clinical diagnosis of ankle injuries. This study aimed to analyze the intraobserver reliability and interobserver reproducibility of the AO and Lauge-Hansen classification systems. In addition, the authors explored the differences among physicians' classification responses and evaluated the clinical value for diagnosis. Fifty-six patients with an ankle injury with complete clinical and radiologic data were enrolled. The definition of injury type, the index score typing methods, and the specific study criteria were explained in detail. Five observers, who were orthopedic surgeons, determined the classifications according to both the AO and Lauge-Hansen systems. The classification was repeated 1 month later. Cronbach's alpha and Cohen's kappa test were used to determine interobserver reliability and intraobserver reproducibility. The physicians conducted 560 classifications (56 cases × 5 physicians × 2 times per patient). Average inter- and intraobserver kappa values for the AO system were 0.708 and 0.608, respectively. Average inter- and intraobserver kappa values for the Lauge-Hansen system were 0.402 and 0.398, respectively. Cronbach's alpha coefficient was 96.7% for the AO system and 76.0% for the Lauge-Hansen system. The Lauge-Hansen classification system is a comprehensive yet cumbersome system. Comparatively, the AO classification system is easier to understand. This study shows that the AO classification system has more reliability and reproducibility, and thus has more value in clinical practice, than the Lauge-Hansen classification system.

  6. Assessing the relative effectiveness of statistical downscaling and distribution mapping in reproducing rainfall statistics based on climate model results

    Science.gov (United States)

    Langousis, Andreas; Mamalakis, Antonios; Deidda, Roberto; Marrocu, Marino

    2016-01-01

    To improve the level skill of climate models (CMs) in reproducing the statistics of daily rainfall at a basin level, two types of statistical approaches have been suggested. One is statistical correction of CM rainfall outputs based on historical series of precipitation. The other, usually referred to as statistical rainfall downscaling, is the use of stochastic models to conditionally simulate rainfall series, based on large-scale atmospheric forcing from CMs. While promising, the latter approach attracted reduced attention in recent years, since the developed downscaling schemes involved complex weather identification procedures, while demonstrating limited success in reproducing several statistical features of rainfall. In a recent effort, Langousis and Kaleris () developed a statistical framework for simulation of daily rainfall intensities conditional on upper-air variables, which is simpler to implement and more accurately reproduces several statistical properties of actual rainfall records. Here we study the relative performance of: (a) direct statistical correction of CM rainfall outputs using nonparametric distribution mapping, and (b) the statistical downscaling scheme of Langousis and Kaleris (), in reproducing the historical rainfall statistics, including rainfall extremes, at a regional level. This is done for an intermediate-sized catchment in Italy, i.e., the Flumendosa catchment, using rainfall and atmospheric data from four CMs of the ENSEMBLES project. The obtained results are promising, since the proposed downscaling scheme is more accurate and robust in reproducing a number of historical rainfall statistics, independent of the CM used and the characteristics of the calibration period. This is particularly the case for yearly rainfall maxima.

  7. The perceptual influence of the cabin acoustics on the reproduced sound of a car audio system

    DEFF Research Database (Denmark)

    Kaplanis, Neofytos; Bech, Søren; Sakari, Tervo

    2015-01-01

    . In this study, a sensory evaluation methodology [Lokki et al., J. Acoust. Soc. Am. 132, 3148–2161 (2012)] was employed to identify the most relevant attributes that characterize the influence of the physical properties of a car cabin on the reproduced sound field. A series of in-situ measurements of a high......A significant element of audio evaluation experiments is the availability of verbal descriptors that can accurately characterize the perceived auditory events. In terms of room acoustics, understanding the perceptual effects of the physical properties of the space would enable a better...... understanding of its acoustical qualities, and stipulate perceptually relevant ways to compensate for the subsequent degradations. In contrast to concert halls, perceptual evaluation of everyday-sized and less reverberant spaces has been a challenging task, and literature on the subject is limited...

  8. Assessing the reproducibility of high definition urethral pressure profilometry and its correlation with an air-charged system.

    Science.gov (United States)

    Klünder, Mario; Amend, Bastian; Sawodny, Oliver; Stenzl, Arnulf; Ederer, Michael; Kelp, Alexandra; Sievert, Karl-Dietrich; Feuer, Ronny

    2017-06-01

    Recently, a new urodynamic method for the assessment of stress urinary incontinence called high definition urethral pressure profilometry (HD-UPP) has been introduced. This method combines a novel microtip catheter with advanced signal processing to enable spatial data location and the reconstruction of a pressure image inside the urethra. In order to assess the reproducibility of HD-UPP data, we statistically evaluate HD-UPP datasets and compare them to data from a double balloon air-charged system. Both catheters are used on sedated female minipigs. Data from the microtip catheter are processed through a signal reconstruction algorithm, urodynamic features are extracted, and compared to the air-charged system. Reproducibility of HD-UPP data is assessed by statistically evaluating consecutive, intra-individual datasets. HD-UPP delivers results in agreement with previous comparisons of microtip and air-charged systems. The average deviation of two consecutive, intra-individual pressure images is very low at 7 cm H2 O. HD-UPP provides physicians with detailed information on the pressure distribution inside the urethra. Through comparison with an air-charged catheter, it is shown that HD-UPP delivers results in agreement with previous studies on the comparison of microtip and air-charged catheters. It provides excellent reproducibility, as the difference between sequentially measured profiles from the same minipig is significantly lower than the one between profiles from different minipigs. © 2016 Wiley Periodicals, Inc.

  9. A novel, comprehensive, and reproducible porcine model for determining the timing of bruises in forensic pathology

    DEFF Research Database (Denmark)

    Barington, Kristiane; Jensen, Henrik Elvang

    2016-01-01

    that resulted in bruises were inflicted on the back. In addition, 2 control pigs were included in the study. The pigs were euthanized consecutively from 1 to 10 h after the infliction of bruises. Following gross evaluation, skin, and muscle tissues were sampled for histology. Results Grossly, the bruises...... appeared uniform and identical to the tramline bruises seen in humans and pigs subjected to blunt trauma. Histologically, the number of neutrophils in the subcutis, the number of macrophages in the muscle tissue, and the localization of neutrophils and macrophages in muscle tissue showed a time...... in order to identify gross and histological parameters that may be useful in determining the age of a bruise. Methods The mechanical device was able to apply a single reproducible stroke with a plastic tube that was equivalent to being struck by a man. In each of 10 anesthetized pigs, four strokes...

  10. Assessment of the performance of numerical modeling in reproducing a replenishment of sediments in a water-worked channel

    Science.gov (United States)

    Juez, C.; Battisacco, E.; Schleiss, A. J.; Franca, M. J.

    2016-06-01

    The artificial replenishment of sediment is used as a method to re-establish sediment continuity downstream of a dam. However, the impact of this technique on the hydraulics conditions, and resulting bed morphology, is yet to be understood. Several numerical tools have been developed during last years for modeling sediment transport and morphology evolution which can be used for this application. These models range from 1D to 3D approaches: the first being over simplistic for the simulation of such a complex geometry; the latter requires often a prohibitive computational effort. However, 2D models are computationally efficient and in these cases may already provide sufficiently accurate predictions of the morphology evolution caused by the sediment replenishment in a river. Here, the 2D shallow water equations in combination with the Exner equation are solved by means of a weak-coupled strategy. The classical friction approach considered for reproducing the bed channel roughness has been modified to take into account the morphological effect of replenishment which provokes a channel bed fining. Computational outcomes are compared with four sets of experimental data obtained from several replenishment configurations studied in the laboratory. The experiments differ in terms of placement volume and configuration. A set of analysis parameters is proposed for the experimental-numerical comparison, with particular attention to the spreading, covered surface and travel distance of placed replenishment grains. The numerical tool is reliable in reproducing the overall tendency shown by the experimental data. The effect of fining roughness is better reproduced with the approach herein proposed. However, it is also highlighted that the sediment clusters found in the experiment are not well numerically reproduced in the regions of the channel with a limited number of sediment grains.

  11. geoKepler Workflow Module for Computationally Scalable and Reproducible Geoprocessing and Modeling

    Science.gov (United States)

    Cowart, C.; Block, J.; Crawl, D.; Graham, J.; Gupta, A.; Nguyen, M.; de Callafon, R.; Smarr, L.; Altintas, I.

    2015-12-01

    The NSF-funded WIFIRE project has developed an open-source, online geospatial workflow platform for unifying geoprocessing tools and models for for fire and other geospatially dependent modeling applications. It is a product of WIFIRE's objective to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. geoKepler includes a set of reusable GIS components, or actors, for the Kepler Scientific Workflow System (https://kepler-project.org). Actors exist for reading and writing GIS data in formats such as Shapefile, GeoJSON, KML, and using OGC web services such as WFS. The actors also allow for calling geoprocessing tools in other packages such as GDAL and GRASS. Kepler integrates functions from multiple platforms and file formats into one framework, thus enabling optimal GIS interoperability, model coupling, and scalability. Products of the GIS actors can be fed directly to models such as FARSITE and WRF. Kepler's ability to schedule and scale processes using Hadoop and Spark also makes geoprocessing ultimately extensible and computationally scalable. The reusable workflows in geoKepler can be made to run automatically when alerted by real-time environmental conditions. Here, we show breakthroughs in the speed of creating complex data for hazard assessments with this platform. We also demonstrate geoKepler workflows that use Data Assimilation to ingest real-time weather data into wildfire simulations, and for data mining techniques to gain insight into environmental conditions affecting fire behavior. Existing machine learning tools and libraries such as R and MLlib are being leveraged for this purpose in Kepler, as well as Kepler's Distributed Data Parallel (DDP) capability to provide a framework for scalable processing. geoKepler workflows can be executed via an iPython notebook as a part of a Jupyter hub at UC San Diego for sharing and reporting of the scientific analysis and results from

  12. Reproducibility of the Nottingham modification of the Scarff-Bloom-Richardson histological grading system and the complementary value of Ki-67 to this system

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rui; CHEN Hui-jiao; WEI Bing; ZHANG Hong-ying; PANG Zong-guo; ZHU Hong; ZHANG Zhang; FU Jing; BU Hong

    2010-01-01

    Background The reproducibility of the Nottingham modification of the Scarff-Bloom-Richardson (NSBR) histological grading system for invasive breast cancer (IBC) adopted by the World Health Organization (WHO) has previously not been studied in Chinese hospitals. The proliferation marker, Ki-67, has been widely applied in detecting IBC. The objective of this study was to assess the reproducibility of the NSBR system among Chinese pathologists and the complementary value that Ki-67 brings to this system.Methods Four general pathologists graded 100 IBC cases independently, which had previously been graded by specialists in breast pathology. The interobserver reproducibility among four general pathologists and pairwise reproducibility between each of them and the specialists were assessed. The Ki-67 labeling index (Ki-67LI) was determined by immunohistochemistry, and its correlations with histological grade and survival were determined.Results With respect to interobserver reproducibility, NSBR grading was fairly reproducible (kappa=0.34); as for the components of NSBR grading, agreement was best for tubule formation (kappa=0.46), intermediate for nuclear pleomorphism (kappa=0.42), and poorest for mitotic count (kappa=0.28). In terms of pairwise reproducibility, agreement was fair to substantial with NSBR grading (kappa=0.30-0.69) and nuclear pleomorphism (kappa=0.28-0.69), moderate to substantial for tubule formation (kappa=0.51-0.78), and slight to substantial for mitotic count (kappa=0.19-0.71).There were characteristic Ki-67LI ranges for grades 1,2 and 3 tumors. Univariate analysis showed that Ki-67 was able to divide grade 2 patients into two different prognostic subgroups. Multivariate analysis of grade 2 patients with negative lymph node demonstrated that Ki-67 was an independent prognosticator for overall survival.Conclusions The reproducibility of grading by general pathologists could be enhanced. Specialization in breast pathology is essential for accurate

  13. Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

    Science.gov (United States)

    Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

    2017-05-07

    A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

  14. Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

    Science.gov (United States)

    Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

    2017-05-01

    A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

  15. Validation of the 3D Skin Comet assay using full thickness skin models: transferability and reproducibility

    Directory of Open Access Journals (Sweden)

    Kerstin Reisinger

    2015-06-01

    Full Text Available The 3D Skin Comet assay was developed to improve the in vitro prediction of the genotoxic potential of dermally applied chemicals. For this purpose, a classical read-out for genotoxicity (i.e. comet formation was combined with reconstructed 3D skin models as well-established test systems. Five laboratories (BASF, BfR (Federal Institute for Risk Assessment, Henkel, Procter & Gamble and TNO Triskilion started to validate this assay using the Phenion® Full- Thickness (FT Skin Model and 8 coded chemicals with financial support by Cosmetics Europe and the German Ministry of Education & Research. There was an excellent overall predictivity of the expected genotoxicity (>90%. Four labs correctly identified all chemicals and the fifth correctly identified 80% of the chemicals. Background DNA damage was low and values for solvent (acetone and positive (methyl methanesulfonate (MMS controls were comparable among labs. Inclusion of the DNA-polymerase inhibitor, aphidicolin (APC, in the protocol improved the predictivity of the assay since it enabled robust detection of pro-mutagens e.g., 7,12-dimethylbenz[a]anthracene and benzo[a]pyrene. Therefore, all negative findings are now confirmed by additional APC experiments to come to a final conclusion. Furthermore, MMC, which intercalates between DNA strands causing covalent binding, was detected with the standard protocol, in which it gave weak but statistically significant responses. Stronger responses, however, were obtained using a cross-linker specific protocol in which MMC reduced the migration of MMS-induced DNA damage. These data support the use of the Phenion® FT in the Comet assay: no false-positives and only one false-negative finding in a single lab. Testing will continue to obtain data for 30 chemicals. Once validated, the 3D Skin Comet assay is foreseen to be used as a follow-up test for positive results from the current in vitro genotoxicity test battery.

  16. Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method

    KAUST Repository

    Prest, Emmanuelle I E C

    2013-12-01

    Flow cytometry (FCM) is a rapid, cultivation-independent tool to assess and evaluate bacteriological quality and biological stability of water. Here we demonstrate that a stringent, reproducible staining protocol combined with fixed FCM operational and gating settings is essential for reliable quantification of bacteria and detection of changes in aquatic bacterial communities. Triplicate measurements of diverse water samples with this protocol typically showed relative standard deviation values and 95% confidence interval values below 2.5% on all the main FCM parameters. We propose a straightforward and instrument-independent method for the characterization of water samples based on the combination of bacterial cell concentration and fluorescence distribution. Analysis of the fluorescence distribution (or so-called fluorescence fingerprint) was accomplished firstly through a direct comparison of the raw FCM data and subsequently simplified by quantifying the percentage of large and brightly fluorescent high nucleic acid (HNA) content bacteria in each sample. Our approach enables fast differentiation of dissimilar bacterial communities (less than 15min from sampling to final result), and allows accurate detection of even small changes in aquatic environments (detection above 3% change). Demonstrative studies on (a) indigenous bacterial growth in water, (b) contamination of drinking water with wastewater, (c) household drinking water stagnation and (d) mixing of two drinking water types, univocally showed that this FCM approach enables detection and quantification of relevant bacterial water quality changes with high sensitivity. This approach has the potential to be used as a new tool for application in the drinking water field, e.g. for rapid screening of the microbial water quality and stability during water treatment and distribution in networks and premise plumbing. © 2013 Elsevier Ltd.

  17. Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method.

    Science.gov (United States)

    Prest, E I; Hammes, F; Kötzsch, S; van Loosdrecht, M C M; Vrouwenvelder, J S

    2013-12-01

    Flow cytometry (FCM) is a rapid, cultivation-independent tool to assess and evaluate bacteriological quality and biological stability of water. Here we demonstrate that a stringent, reproducible staining protocol combined with fixed FCM operational and gating settings is essential for reliable quantification of bacteria and detection of changes in aquatic bacterial communities. Triplicate measurements of diverse water samples with this protocol typically showed relative standard deviation values and 95% confidence interval values below 2.5% on all the main FCM parameters. We propose a straightforward and instrument-independent method for the characterization of water samples based on the combination of bacterial cell concentration and fluorescence distribution. Analysis of the fluorescence distribution (or so-called fluorescence fingerprint) was accomplished firstly through a direct comparison of the raw FCM data and subsequently simplified by quantifying the percentage of large and brightly fluorescent high nucleic acid (HNA) content bacteria in each sample. Our approach enables fast differentiation of dissimilar bacterial communities (less than 15 min from sampling to final result), and allows accurate detection of even small changes in aquatic environments (detection above 3% change). Demonstrative studies on (a) indigenous bacterial growth in water, (b) contamination of drinking water with wastewater, (c) household drinking water stagnation and (d) mixing of two drinking water types, univocally showed that this FCM approach enables detection and quantification of relevant bacterial water quality changes with high sensitivity. This approach has the potential to be used as a new tool for application in the drinking water field, e.g. for rapid screening of the microbial water quality and stability during water treatment and distribution in networks and premise plumbing. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Cellular automaton model with dynamical 2D speed-gap relation reproduces empirical and experimental features of traffic flow

    CERN Document Server

    Tian, Junfang; Ma, Shoufeng; Zhu, Chenqiang; Jiang, Rui; Ding, YaoXian

    2015-01-01

    This paper proposes an improved cellular automaton traffic flow model based on the brake light model, which takes into account that the desired time gap of vehicles is remarkably larger than one second. Although the hypothetical steady state of vehicles in the deterministic limit corresponds to a unique relationship between speeds and gaps in the proposed model, the traffic states of vehicles dynamically span a two-dimensional region in the plane of speed versus gap, due to the various randomizations. It is shown that the model is able to well reproduce (i) the free flow, synchronized flow, jam as well as the transitions among the three phases; (ii) the evolution features of disturbances and the spatiotemporal patterns in a car-following platoon; (iii) the empirical time series of traffic speed obtained from NGSIM data. Therefore, we argue that a model can potentially reproduce the empirical and experimental features of traffic flow, provided that the traffic states are able to dynamically span a 2D speed-gap...

  19. Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.

    Science.gov (United States)

    Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C; Parisot, Sarah; Rueckert, Daniel

    2017-01-01

    OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A

  20. The quantum CP-violating kaon system reproduced in the electronic laboratory

    Science.gov (United States)

    Caruso, M.; Fanchiotti, H.; García Canal, C. A.; Mayosky, M.; Veiga, A.

    2016-11-01

    The equivalence between the Schrödinger dynamics of a quantum system with a finite number of basis states and a classical dynamics is realized in terms of electric networks. The isomorphism that connects in a univocal way both dynamical systems was applied to the case of neutral mesons, kaons in particular, and the class of electric networks univocally related to the quantum system was analysed. Moreover, under CPT invariance, the relevant ɛ parameter that measures CP violation in the kaon system is reinterpreted in terms of network parameters. All these results were explicitly shown by means of both a numerical simulation of the implied networks and by constructing the corresponding circuits.

  1. A measuring system for facial aesthetics in Caucasian adolescents: reproducibility and validity.

    NARCIS (Netherlands)

    Kiekens, R.M.A.; Maltha, J.C.; Hof, M.A. van 't; Kuijpers-Jagtman, A.M.

    2005-01-01

    A new measuring system to judge facial aesthetics in young Caucasians is presented. The system uses sets of three photographs (one frontal, one three-quarter smiling, and one lateral) as a stimulus. Scores are performed on a visual analogue scale (VAS) with separate sets of reference photographs for

  2. An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models.

    Science.gov (United States)

    Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie

    2014-10-07

    Constraint-based models are currently the only methodology that allows the study of metabolism at the whole-genome scale. Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic. Here we introduce MONGOOSE, a toolbox for analysing the structure of constraint-based metabolic models in exact arithmetic. We apply MONGOOSE to the analysis of 98 existing metabolic network models and find that the biomass reaction is surprisingly blocked (unable to sustain non-zero flux) in nearly half of them. We propose a principled approach for unblocking these reactions and extend it to the problems of identifying essential and synthetic lethal reactions and minimal media. Our structural insights enable a systematic study of constraint-based metabolic models, yielding a deeper understanding of their possibilities and limitations.

  3. A reproducible analytical system based on the multi-component analysis of triterpene acids in Ganoderma lucidum.

    Science.gov (United States)

    Da, Juan; Cheng, Chun-Ru; Yao, Shuai; Long, Hua-Li; Wang, Yan-Hong; Khan, Ikhlas A; Li, Yi-Feng; Wang, Qiu-Rong; Cai, Lu-Ying; Jiang, Bao-Hong; Liu, Xuan; Wu, Wan-Ying; Guo, De-An

    2015-06-01

    Ultra-performance liquid chromatography (UPLC) and Single Standard for Determination of Multi-Components (SSDMC) are becoming increasingly important for quality control of medicinal herbs; this approach was developed for Ganoderma lucidum. Special attention was necessary for the appropriate selection of markers, for determining the reproducibility of the relative retention times (RRT), and for the accuracy of conversion factors (F). Finally, ten components were determined, with ganoderic acid A serving as single standard. Stable system parameters were established, and with successful resolution of those issues, this analytical method could be used more broadly.

  4. Assessment of the urban water system with an open, reproducible process applied to Chicago

    Science.gov (United States)

    Urban water systems convey complex environmental and man-made flows. The relationships among water flows and networked storages remains difficult to comprehensively evaluate. Such evaluation is important, however, as interventions are designed (e.g, conservation measures, green...

  5. The quantum CP-violating kaon system reproduced in the electronic laboratory (Homage to Nolberto Martinez)

    CERN Document Server

    Caruso, M; Canal, C García; Mayosky, M; Veiga, V

    2016-01-01

    The equivalence between the $\\mathrm{Schr\\ddot{o}dinger}$ dynamics of a quantum system with a finite number of basis states and a classical dynamics is realized in terms of electric networks. The isomorphism that connects in a univocal way both dynamical systems was applied to the case of neutral mesons, kaons in particular, and the class of electric networks univocally related to the quantum system was analyzed. Moreover, under $CPT$ invariance, the relevant $\\epsilon$ parameter that measures $CP$ violation in the kaon system is reinterpreted in terms of network parameters. All these results were explicitly shown by means of both a numerical simulation of the implied networks and by constructing the corresponding circuits.

  6. Histologic grading of urothelial papillary neoplasms: impact of combined grading (two-numbered grading system) on reproducibility.

    Science.gov (United States)

    Tuna, Burçin; Yörükoglu, Kutsal; Düzcan, Ender; Sen, Sait; Nese, Nalan; Sarsık, Banu; Akder, Aysegul; Sayhan, Sehnaz; Mungan, Uğur; Kirkali, Ziya

    2011-06-01

    The clinical management of tumor patients is often strongly influenced by the tumor grade. The presence of heterogeneity is well recognized in a variety of tumors. Overall grade is based on highest grade area identified within a tumor. Urothelial carcinoma often contains different histological grades within the same tumor. This study investigates the impact of a combined grading system on the reproducibility of papillary urothelial neoplasms. A set prepared for an earlier study consisting of ten cases of each category (papillary urothelial neoplasm of low malignant potential (PUNLMP), LGPUC, and HGPUC) was used. Agreement between pairs of pathologists was evaluated using κ statistics for the combined scoring system. Interobserver agreement was fair to substantial as reflected by κ values ranging from 0.24 to 0.74 (mean κ = 0.43). The combined scores of 2 and 3 which included PUNLMP showed the lowest degree of agreement and when this category was excluded from the analysis, interobserver agreement increased significantly (mean κ = 0.65; ranging from 0.43 to 0.92) in terms of combined scores of 4, 5, and 6. PUNLMP has been shown to be the least reproducible component of a combined scoring system even among experienced observers. Exclusion of PUNLMP from grading scheme seems to improve interobserver variability.

  7. Can a global model reproduce observed trends in summertime surface ozone levels?

    OpenAIRE

    S. Koumoutsaris; I. Bey

    2012-01-01

    Quantifying trends in surface ozone concentrations are critical for assessing pollution control strategies. Here we use observations and results from a global chemical transport model to examine the trends (1991–2005) in daily maximum 8-hour average concentrations in summertime surface ozone at rural sites in Europe and the United States. We find a decrease in observed ozone concentrations at the high end of the probability distribution at many of the sites in both regions. The model attribut...

  8. A Versatile and Reproducible Multi-Frequency Electrical Impedance Tomography System.

    Science.gov (United States)

    Avery, James; Dowrick, Thomas; Faulkner, Mayo; Goren, Nir; Holder, David

    2017-01-31

    A highly versatile Electrical Impedance Tomography (EIT) system, nicknamed the ScouseTom, has been developed. The system allows control over current amplitude, frequency, number of electrodes, injection protocol and data processing. Current is injected using a Keithley 6221 current source, and voltages are recorded with a 24-bit EEG system with minimum bandwidth of 3.2 kHz. Custom PCBs interface with a PC to control the measurement process, electrode addressing and triggering of external stimuli. The performance of the system was characterised using resistor phantoms to represent human scalp recordings, with an SNR of 77.5 dB, stable across a four hour recording and 20 Hz to 20 kHz. In studies of both haeomorrhage using scalp electrodes, and evoked activity using epicortical electrode mats in rats, it was possible to reconstruct images matching established literature at known areas of onset. Data collected using scalp electrode in humans matched known tissue impedance spectra and was stable over frequency. The experimental procedure is software controlled and is readily adaptable to new paradigms. Where possible, commercial or open-source components were used, to minimise the complexity in reproduction. The hardware designs and software for the system have been released under an open source licence, encouraging contributions and allowing for rapid replication.

  9. A Versatile and Reproducible Multi-Frequency Electrical Impedance Tomography System

    Directory of Open Access Journals (Sweden)

    James Avery

    2017-01-01

    Full Text Available A highly versatile Electrical Impedance Tomography (EIT system, nicknamed the ScouseTom, has been developed. The system allows control over current amplitude, frequency, number of electrodes, injection protocol and data processing. Current is injected using a Keithley 6221 current source, and voltages are recorded with a 24-bit EEG system with minimum bandwidth of 3.2 kHz. Custom PCBs interface with a PC to control the measurement process, electrode addressing and triggering of external stimuli. The performance of the system was characterised using resistor phantoms to represent human scalp recordings, with an SNR of 77.5 dB, stable across a four hour recording and 20 Hz to 20 kHz. In studies of both haeomorrhage using scalp electrodes, and evoked activity using epicortical electrode mats in rats, it was possible to reconstruct images matching established literature at known areas of onset. Data collected using scalp electrode in humans matched known tissue impedance spectra and was stable over frequency. The experimental procedure is software controlled and is readily adaptable to new paradigms. Where possible, commercial or open-source components were used, to minimise the complexity in reproduction. The hardware designs and software for the system have been released under an open source licence, encouraging contributions and allowing for rapid replication.

  10. A Versatile and Reproducible Multi-Frequency Electrical Impedance Tomography System

    Science.gov (United States)

    Avery, James; Dowrick, Thomas; Faulkner, Mayo; Goren, Nir; Holder, David

    2017-01-01

    A highly versatile Electrical Impedance Tomography (EIT) system, nicknamed the ScouseTom, has been developed. The system allows control over current amplitude, frequency, number of electrodes, injection protocol and data processing. Current is injected using a Keithley 6221 current source, and voltages are recorded with a 24-bit EEG system with minimum bandwidth of 3.2 kHz. Custom PCBs interface with a PC to control the measurement process, electrode addressing and triggering of external stimuli. The performance of the system was characterised using resistor phantoms to represent human scalp recordings, with an SNR of 77.5 dB, stable across a four hour recording and 20 Hz to 20 kHz. In studies of both haeomorrhage using scalp electrodes, and evoked activity using epicortical electrode mats in rats, it was possible to reconstruct images matching established literature at known areas of onset. Data collected using scalp electrode in humans matched known tissue impedance spectra and was stable over frequency. The experimental procedure is software controlled and is readily adaptable to new paradigms. Where possible, commercial or open-source components were used, to minimise the complexity in reproduction. The hardware designs and software for the system have been released under an open source licence, encouraging contributions and allowing for rapid replication. PMID:28146122

  11. Validation of EURO-CORDEX regional climate models in reproducing the variability of precipitation extremes in Romania

    Science.gov (United States)

    Dumitrescu, Alexandru; Busuioc, Aristita

    2016-04-01

    EURO-CORDEX is the European branch of the international CORDEX initiative that aims to provide improved regional climate change projections for Europe. The main objective of this paper is to document the performance of the individual models in reproducing the variability of precipitation extremes in Romania. Here three EURO-CORDEX regional climate models (RCMs) ensemble (scenario RCP4.5) are analysed and inter-compared: DMI-HIRHAM5, KNMI-RACMO2.2 and MPI-REMO. Compared to previous studies, when the RCM validation regarding the Romanian climate has mainly been made on mean state and at station scale, a more quantitative approach of precipitation extremes is proposed. In this respect, to have a more reliable comparison with observation, a high resolution daily precipitation gridded data set was used as observational reference (CLIMHYDEX project). The comparison between the RCM outputs and observed grid point values has been made by calculating three extremes precipitation indices, recommended by the Expert Team on Climate Change Detection Indices (ETCCDI), for the 1976-2005 period: R10MM, annual count of days when precipitation ≥10mm; RX5DAY, annual maximum 5-day precipitation and R95P%, precipitation fraction of annual total precipitation due to daily precipitation > 95th percentile. The RCMs capability to reproduce the mean state for these variables, as well as the main modes of their spatial variability (given by the first three EOF patterns), are analysed. The investigation confirms the ability of RCMs to simulate the main features of the precipitation extreme variability over Romania, but some deficiencies in reproducing of their regional characteristics were found (for example, overestimation of the mea state, especially over the extra Carpathian regions). This work has been realised within the research project "Changes in climate extremes and associated impact in hydrological events in Romania" (CLIMHYDEX), code PN II-ID-2011-2-0073, financed by the Romanian

  12. Augmenting a Large-Scale Hydrology Model to Reproduce Groundwater Variability

    Science.gov (United States)

    Stampoulis, D.; Reager, J. T., II; Andreadis, K.; Famiglietti, J. S.

    2016-12-01

    To understand the influence of groundwater on terrestrial ecosystems and society, global assessment of groundwater temporal fluctuations is required. A water table was initialized in the Variable Infiltration Capacity (VIC) hydrologic model in a semi-realistic approach to account for groundwater variability. Global water table depth data derived from observations at nearly 2 million well sites compiled from government archives and published literature, as well as groundwater model simulations, were used to create a new soil layer of varying depth for each model grid cell. The new 4-layer version of VIC, hereafter named VIC-4L, was run with and without assimilating NASA's Gravity Recovery and Climate Experiment (GRACE) observations. The results were compared with simulations using the original VIC version (named VIC-3L) with GRACE assimilation, while all runs were compared with well data.

  13. Energy and nutrient deposition and excretion in the reproducing sow: model development and evaluation

    DEFF Research Database (Denmark)

    Hansen, A V; Strathe, A B; Theil, Peter Kappel;

    2014-01-01

    Air and nutrient emissions from swine operations raise environmental concerns. During the reproduction phase, sows consume and excrete large quantities of nutrients. The objective of this study was to develop a mathematical model to describe energy and nutrient partitioning and predict manure...... excretion and composition and methane emissions on a daily basis. The model was structured to contain gestation and lactation modules, which can be run separately or sequentially, with outputs from the gestation module used as inputs to the lactation module. In the gestating module, energy and protein...... production, and maternal growth with body tissue losses constrained within biological limits. Global sensitivity analysis showed that nonlinearity in the parameters was small. The model outputs considered were the total protein and fat deposition, average urinary and fecal N excretion, average methane...

  14. An exponent tunable network model for reproducing density driven superlinear relation

    CERN Document Server

    Qin, Yuhao; Xu, Lida; Gao, Zi-You

    2014-01-01

    Previous works have shown the universality of allometric scalings under density and total value at city level, but our understanding about the size effects of regions on them is still poor. Here, we revisit the scaling relations between gross domestic production (GDP) and population (POP) under total and density value. We first reveal that the superlinear scaling is a general feature under density value crossing different regions. The scaling exponent $\\beta$ under density value falls into the range $(1.0, 2.0]$, which unexpectedly goes beyond the range observed by Pan et al. (Nat. Commun. vol. 4, p. 1961 (2013)). To deal with the wider range, we propose a network model based on 2D lattice space with the spatial correlation factor $\\alpha$ as parameter. Numerical experiments prove that the generated scaling exponent $\\beta$ in our model is fully tunable by the spatial correlation factor $\\alpha$. We conjecture that our model provides a general platform for extensive urban and regional studies.

  15. A simple branching model that reproduces language family and language population distributions

    Science.gov (United States)

    Schwämmle, Veit; de Oliveira, Paulo Murilo Castro

    2009-07-01

    Human history leaves fingerprints in human languages. Little is known about language evolution and its study is of great importance. Here we construct a simple stochastic model and compare its results to statistical data of real languages. The model is based on the recent finding that language changes occur independently of the population size. We find agreement with the data additionally assuming that languages may be distinguished by having at least one among a finite, small number of different features. This finite set is also used in order to define the distance between two languages, similarly to linguistics tradition since Swadesh.

  16. An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

    National Research Council Canada - National Science Library

    Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie

    2014-01-01

    .... Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic...

  17. Reproducible infection model for Clostridium perfringens in broiler chickens

    DEFF Research Database (Denmark)

    Pedersen, Karl; Friis-Holm, Lotte Bjerrum; Heuer, Ole Eske

    2008-01-01

    Experiments were carried out to establish an infection and disease model for Clostridium perfringens in broiler chickens. Previous experiments had failed to induce disease and only a transient colonization with challenge strains had been obtained. In the present study, two series of experiments w...

  18. Establishing a Reproducible Hypertrophic Scar following Thermal Injury: A Porcine Model

    Directory of Open Access Journals (Sweden)

    Scott J. Rapp, MD

    2015-02-01

    Conclusions: Deep partial-thickness thermal injury to the back of domestic swine produces an immature hypertrophic scar by 10 weeks following burn with thickness appearing to coincide with the location along the dorsal axis. With minimal pig to pig variation, we describe our technique to provide a testable immature scar model.

  19. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

    OpenAIRE

    2014-01-01

    Background Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies. Therefore, there is an urgent need for accessible, modular, and sharable tools for phylogenetic analysis. Results We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris. ...

  20. Evaluation of Nitinol staples for the Lapidus arthrodesis in a reproducible biomechanical model

    Directory of Open Access Journals (Sweden)

    Nicholas Alexander Russell

    2015-12-01

    Full Text Available While the Lapidus procedure is a widely accepted technique for treatment of hallux valgus, the optimal fixation method to maintain joint stability remains controversial. The purpose of this study was to evaluate the biomechanical properties of new Shape Memory Alloy staples arranged in different configurations in a repeatable 1st Tarsometatarsal arthrodesis model. Ten sawbones models of the whole foot (n=5 per group were reconstructed using a single dorsal staple or two staples in a delta configuration. Each construct was mechanically tested in dorsal four-point bending, medial four-point bending, dorsal three-point bending and plantar cantilever bending with the staples activated at 37°C. The peak load, stiffness and plantar gapping were determined for each test. Pressure sensors were used to measure the contact force and area of the joint footprint in each group. There was a significant (p < 0.05 increase in peak load in the two staple constructs compared to the single staple constructs for all testing modalities. Stiffness also increased significantly in all tests except dorsal four-point bending. Pressure sensor readings showed a significantly higher contact force at time zero and contact area following loading in the two staple constructs (p < 0.05. Both groups completely recovered any plantar gapping following unloading and restored their initial contact footprint. The biomechanical integrity and repeatability of the models was demonstrated with no construct failures due to hardware or model breakdown. Shape memory alloy staples provide fixation with the ability to dynamically apply and maintain compression across a simulated arthrodesis following a range of loading conditions.

  1. Reproducibility of the heat/capsaicin skin sensitization model in healthy volunteers

    Directory of Open Access Journals (Sweden)

    Cavallone LF

    2013-11-01

    Full Text Available Laura F Cavallone,1 Karen Frey,1 Michael C Montana,1 Jeremy Joyal,1 Karen J Regina,1 Karin L Petersen,2 Robert W Gereau IV11Department of Anesthesiology, Washington University in St Louis, School of Medicine, St Louis, MO, USA; 2California Pacific Medical Center Research Institute, San Francisco, CA, USAIntroduction: Heat/capsaicin skin sensitization is a well-characterized human experimental model to induce hyperalgesia and allodynia. Using this model, gabapentin, among other drugs, was shown to significantly reduce cutaneous hyperalgesia compared to placebo. Since the larger thermal probes used in the original studies to produce heat sensitization are now commercially unavailable, we decided to assess whether previous findings could be replicated with a currently available smaller probe (heated area 9 cm2 versus 12.5–15.7 cm2.Study design and methods: After Institutional Review Board approval, 15 adult healthy volunteers participated in two study sessions, scheduled 1 week apart (Part A. In both sessions, subjects were exposed to the heat/capsaicin cutaneous sensitization model. Areas of hypersensitivity to brush stroke and von Frey (VF filament stimulation were measured at baseline and after rekindling of skin sensitization. Another group of 15 volunteers was exposed to an identical schedule and set of sensitization procedures, but, in each session, received either gabapentin or placebo (Part B.Results: Unlike previous reports, a similar reduction of areas of hyperalgesia was observed in all groups/sessions. Fading of areas of hyperalgesia over time was observed in Part A. In Part B, there was no difference in area reduction after gabapentin compared to placebo.Conclusion: When using smaller thermal probes than originally proposed, modifications of other parameters of sensitization and/or rekindling process may be needed to allow the heat/capsaicin sensitization protocol to be used as initially intended. Standardization and validation of

  2. The link between the Barents Sea and ENSO events reproduced by NEMO model

    Directory of Open Access Journals (Sweden)

    V. N. Stepanov

    2012-05-01

    Full Text Available An analysis of observational data in the Barents Sea along a meridian at 33°30´ E between 70°30´ and 72°30´ N has reported a negative correlation between El Niño/La Niña-Southern Oscillation (ENSO events and water temperature in the top 200 m: the temperature drops about 0.5 °C during warm ENSO events while during cold ENSO events the top 200 m layer of the Barents Sea is warmer. Results from 1 and 1/4-degree global NEMO models show a similar response for the whole Barents Sea. During the strong warm ENSO event in 1997–1998 an anticyclonic atmospheric circulation is settled over the Barents Sea instead of a usual cyclonic circulation. This change enhances heat loses in the Barents Sea, as well as substantially influencing the Barents Sea inflow from the North Atlantic, via changes in ocean currents. Under normal conditions along the Scandinavian peninsula there is a warm current entering the Barents sea from the North Atlantic, however after the 1997–1998 event this current is weakened.

    During 1997–1998 the model annual mean temperature in the Barents Sea is decreased by about 0.8 °C, also resulting in a higher sea ice volume. In contrast during the cold ENSO events in 1999–2000 and 2007–2008 the model shows a lower sea ice volume, and higher annual mean temperatures in the upper layer of the Barents Sea of about 0.7 °C.

    An analysis of model data shows that the Barents Sea inflow is the main source for the variability of Barents Sea heat content, and is forced by changing pressure and winds in the North Atlantic. However, surface heat-exchange with atmosphere can also play a dominant role in the Barents Sea annual heat balance, especially for the subsequent year after ENSO events.

  3. A computational model incorporating neural stem cell dynamics reproduces glioma incidence across the lifespan in the human population.

    Directory of Open Access Journals (Sweden)

    Roman Bauer

    Full Text Available Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstract way, and do not directly relate to empirical findings. To decrease this gap between theory and experimental observations, we incorporate recent data on cellular and molecular factors underlying gliomagenesis. Since evidence implicates the adult neural stem cell as the likely cell-of-origin of glioma, we have incorporated empirically-determined estimates of neural stem cell number, cell division rate, mutation rate and oncogenic potential into our model. We demonstrate that our model yields results which match actual demographic data in the human population. In particular, this model accounts for the observed peak incidence of glioma at approximately 80 years of age, without the need to assert differential susceptibility throughout the population. Overall, our model supports the hypothesis that glioma is caused by randomly-occurring oncogenic mutations within the neural stem cell population. Based on this model, we assess the influence of the (experimentally indicated decrease in the number of neural stem cells and increase of cell division rate during aging. Our model provides multiple testable predictions, and suggests that different temporal sequences of oncogenic mutations can lead to tumorigenesis. Finally, we conclude that four or five oncogenic mutations are sufficient for the formation of glioma.

  4. Can a global model chemical mechanism reproduce NO, NO2, and O3 measurements above a tropical rainforest?

    Directory of Open Access Journals (Sweden)

    C. N. Hewitt

    2009-12-01

    Full Text Available A cross-platform field campaign, OP3, was conducted in the state of Sabah in Malaysian Borneo between April and July of 2008. Among the suite of observations recorded, the campaign included measurements of NOx and O3–crucial outputs of any model chemistry mechanism. We describe the measurements of these species made from both the ground site and aircraft. We examine the output from the global model p-TOMCAT at two resolutions for this location during the April campaign period. The models exhibit reasonable ability in capturing the NOx diurnal cycle, but ozone is overestimated. We use a box model containing the same chemical mechanism to explore the weaknesses in the global model and the ability of the simplified global model chemical mechanism to capture the chemistry at the rainforest site. We achieve a good fit to the data for all three species (NO, NO2, and O3, though the model is much more sensitive to changes in the treatment of physical processes than to changes in the chemical mechanism. Indeed, without some parameterization of the nighttime boundary layer-free troposphere mixing, a time dependent box model will not reproduce the observations. The final simulation uses this mixing parameterization for NO and NO2 but not O3, as determined by the vertical structure of each species, and matches the measurements well.

  5. Can model observers be developed to reproduce radiologists' diagnostic performances? Our study says not so fast!

    Science.gov (United States)

    Lee, Juhun; Nishikawa, Robert M.; Reiser, Ingrid; Boone, John M.

    2016-03-01

    The purpose of this study was to determine radiologists' diagnostic performances on different image reconstruction algorithms that could be used to optimize image-based model observers. We included a total of 102 pathology proven breast computed tomography (CT) cases (62 malignant). An iterative image reconstruction (IIR) algorithm was used to obtain 24 reconstructions with different image appearance for each image. Using quantitative image feature analysis, three IIRs and one clinical reconstruction of 50 lesions (25 malignant) were selected for a reader study. The reconstructions spanned a range of smooth-low noise to sharp-high noise image appearance. The trained classifiers' AUCs on the above reconstructions ranged from 0.61 (for smooth reconstruction) to 0.95 (for sharp reconstruction). Six experienced MQSA radiologists read 200 cases (50 lesions times 4 reconstructions) and provided the likelihood of malignancy of each lesion. Radiologists' diagnostic performances (AUC) ranged from 0.7 to 0.89. However, there was no agreement among the six radiologists on which image appearance was the best, in terms of radiologists' having the highest diagnostic performances. Specifically, two radiologists indicated sharper image appearance was diagnostically superior, another two radiologists indicated smoother image appearance was diagnostically superior, and another two radiologists indicated all image appearances were diagnostically similar to each other. Due to the poor agreement among radiologists on the diagnostic ranking of images, it may not be possible to develop a model observer for this particular imaging task.

  6. The ability of a GCM-forced hydrological model to reproduce global discharge variability

    Directory of Open Access Journals (Sweden)

    F. C. Sperna Weiland

    2010-08-01

    Full Text Available Data from General Circulation Models (GCMs are often used to investigate hydrological impacts of climate change. However GCM data are known to have large biases, especially for precipitation. In this study the usefulness of GCM data for hydrological studies, with focus on discharge variability and extremes, was tested by using bias-corrected daily climate data of the 20CM3 control experiment from a selection of twelve GCMs as input to the global hydrological model PCR-GLOBWB. Results of these runs were compared with discharge observations of the GRDC and discharges calculated from model runs based on two meteorological datasets constructed from the observation-based CRU TS2.1 and ERA-40 reanalysis. In the first dataset the CRU TS 2.1 monthly timeseries were downscaled to daily timeseries using the ERA-40 dataset (ERA6190. This dataset served as a best guess of the past climate and was used to analyze the performance of PCR-GLOBWB. The second dataset was created from the ERA-40 timeseries bias-corrected with the CRU TS 2.1 dataset using the same bias-correction method as applied to the GCM datasets (ERACLM. Through this dataset the influence of the bias-correction method was quantified. The bias-correction was limited to monthly mean values of precipitation, potential evaporation and temperature, as our focus was on the reproduction of inter- and intra-annual variability.

    After bias-correction the spread in discharge results of the GCM based runs decreased and results were similar to results of the ERA-40 based runs, especially for rivers with a strong seasonal pattern. Overall the bias-correction method resulted in a slight reduction of global runoff and the method performed less well in arid and mountainous regions. However, deviations between GCM results and GRDC statistics did decrease for Q, Q90 and IAV. After bias-correction consistency amongst

  7. PAMELA positron and electron spectra are reproduced by 3-dimensional cosmic-ray modeling

    CERN Document Server

    Gaggero, Daniele; Maccione, Luca; Di Bernardo, Giuseppe; Evoli, Carmelo

    2013-01-01

    The PAMELA collaboration recently released the $e^+$ absolute spectrum between 1 and 300 GeV in addition to the positron fraction and $e^-$ spectrum previously measured in the same time period. We use the newly developed 3-dimensional upgrade of the DRAGON code and the charge dependent solar modulation HelioProp code to consistently describe those data. We obtain very good fits of all data sets if a $e^+$ + $e^-$ hard extra-component peaked at 1 TeV is added to a softer $e^-$ background and the secondary $e^\\pm$ produced by the spallation of cosmic ray proton and helium nuclei. All sources are assumed to follow a realistic spiral arm spatial distribution. Remarkably, PAMELA data do not display any need of charge asymmetric extra-component. Finally, plain diffusion, or low re-acceleration, propagation models which are tuned against nuclear data, nicely describe PAMELA lepton data with no need to introduce a low energy break in the proton and Helium spectra.

  8. The diverse broad-band light-curves of Swift GRBs reproduced with the cannonball model

    CERN Document Server

    Dado, Shlomo; De Rújula, A

    2009-01-01

    Two radiation mechanisms, inverse Compton scattering (ICS) and synchrotron radiation (SR), suffice within the cannonball (CB) model of long gamma ray bursts (LGRBs) and X-ray flashes (XRFs) to provide a very simple and accurate description of their observed prompt emission and afterglows. Simple as they are, the two mechanisms and the burst environment generate the rich structure of the light curves at all frequencies and times. This is demonstrated for 33 selected Swift LGRBs and XRFs, which are well sampled from early time until late time and well represent the entire diversity of the broad band light curves of Swift LGRBs and XRFs. Their prompt gamma-ray and X-ray emission is dominated by ICS of glory light. During their fast decline phase, ICS is taken over by SR which dominates their broad band afterglow. The pulse shape and spectral evolution of the gamma-ray peaks and the early-time X-ray flares, and even the delayed optical `humps' in XRFs, are correctly predicted. The canonical and non-canonical X-ra...

  9. A Detailed Data-Driven Network Model of Prefrontal Cortex Reproduces Key Features of In Vivo Activity.

    Science.gov (United States)

    Hass, Joachim; Hertäg, Loreen; Durstewitz, Daniel

    2016-05-01

    The prefrontal cortex is centrally involved in a wide range of cognitive functions and their impairment in psychiatric disorders. Yet, the computational principles that govern the dynamics of prefrontal neural networks, and link their physiological, biochemical and anatomical properties to cognitive functions, are not well understood. Computational models can help to bridge the gap between these different levels of description, provided they are sufficiently constrained by experimental data and capable of predicting key properties of the intact cortex. Here, we present a detailed network model of the prefrontal cortex, based on a simple computationally efficient single neuron model (simpAdEx), with all parameters derived from in vitro electrophysiological and anatomical data. Without additional tuning, this model could be shown to quantitatively reproduce a wide range of measures from in vivo electrophysiological recordings, to a degree where simulated and experimentally observed activities were statistically indistinguishable. These measures include spike train statistics, membrane potential fluctuations, local field potentials, and the transmission of transient stimulus information across layers. We further demonstrate that model predictions are robust against moderate changes in key parameters, and that synaptic heterogeneity is a crucial ingredient to the quantitative reproduction of in vivo-like electrophysiological behavior. Thus, we have produced a physiologically highly valid, in a quantitative sense, yet computationally efficient PFC network model, which helped to identify key properties underlying spike time dynamics as observed in vivo, and can be harvested for in-depth investigation of the links between physiology and cognition.

  10. The statistics of repeating patterns of cortical activity can be reproduced by a model network of stochastic binary neurons.

    Science.gov (United States)

    Roxin, Alex; Hakim, Vincent; Brunel, Nicolas

    2008-10-15

    Calcium imaging of the spontaneous activity in cortical slices has revealed repeating spatiotemporal patterns of transitions between so-called down states and up states (Ikegaya et al., 2004). Here we fit a model network of stochastic binary neurons to data from these experiments, and in doing so reproduce the distributions of such patterns. We use two versions of this model: (1) an unconnected network in which neurons are activated as independent Poisson processes; and (2) a network with an interaction matrix, estimated from the data, representing effective interactions between the neurons. The unconnected model (model 1) is sufficient to account for the statistics of repeating patterns in 11 of the 15 datasets studied. Model 2, with interactions between neurons, is required to account for pattern statistics of the remaining four. Three of these four datasets are the ones that contain the largest number of transitions, suggesting that long datasets are in general necessary to render interactions statistically visible. We then study the topology of the matrix of interactions estimated for these four datasets. For three of the four datasets, we find sparse matrices with long-tailed degree distributions and an overrepresentation of certain network motifs. The remaining dataset exhibits a strongly interconnected, spatially localized subgroup of neurons. In all cases, we find that interactions between neurons facilitate the generation of long patterns that do not repeat exactly.

  11. Isokinetic eccentric exercise as a model to induce and reproduce pathophysiological alterations related to delayed onset muscle soreness

    DEFF Research Database (Denmark)

    Lund, Henrik; Vestergaard-Poulsen, P; Kanstrup, I.L.

    1998-01-01

    Physiological alterations following unaccustomed eccentric exercise in an isokinetic dynamometer of the right m. quadriceps until exhaustion were studied, in order to create a model in which the physiological responses to physiotherapy could be measured. In experiment I (exp. I), seven selected...... parameters were measured bilaterally in 7 healthy subjects at day 0 as a control value. Then after a standardized bout of eccentric exercise the same parameters were measured daily for the following 7 d (test values). The measured parameters were: the ratio of phosphocreatine to inorganic phosphate (PCr...... (133Xenon washout technique). This was repeated in experiment II (exp. II) 6-12 months later in order to study reproducibility. In experiment III (exp. III), the normal fluctuations over 8 d of the seven parameters were measured, without intervention with eccentric exercise in 6 other subjects. All...

  12. Assessing the repeatability and reproducibility of the Leg Score: a Dutch Claw Health Scoring System for dairy cattle.

    Science.gov (United States)

    Holzhauer, M; Middelesch, H; Bartels, C J M; Frankena, K; Verhoeff, J; Noordhuizen-Stassen, E N; Noordhuizen, J P T M

    The optimal moment for trimming the claws of all dairy cows in a herd was investigated by assessing the external rotation of the hind claws of individual cows relative to the spinal column. This leg score consisted of three independent descriptors: 1 (good/normal), 2 (moderately deviant), and 3 (severely deviant). This study assessed the repeatability and the reproducibility of the leg score system, and the consistency of the advice given subsequently about trimming of the hind claws of all cows in the herd. Repeatability was assessed for 52 cows that were scored twice on the same day by 11 observers; the kappa value ranged from 0.17 to 0.66 (mean: 0.36). The probability of the same result for both assessments ranged from 0.49 to 0.80 (mean: 0.61). Claw trimming was advised if at least 20% of the cows had a leg score of 3. On the basis of the scores, 3 observers consistently advised trimming of the hind claws of all the cows in the herd, and 6 observers consistently advised against the need for trimming in the short term; 2 observers had an inconsistent advice. The reproducibility of the scoring system was assessed in two dairy herds (62 and 50 cows). Eight observers evaluated the leg score of the cows of both herds on the same day. The mean kappa value of the leg score for all pairs of different observers (A-B, A-C etcetera) was 0.24 [-0.08-0.49]. In conclusion, the leg score is not a reliable method for determining the optimal moment for claw trimming in dairy cattle. The reasons for the inconsistent observations require further investigation.

  13. Efficient and Reproducible Myogenic Differentiation from Human iPS Cells: Prospects for Modeling Miyoshi Myopathy In Vitro

    Science.gov (United States)

    Tanaka, Akihito; Woltjen, Knut; Miyake, Katsuya; Hotta, Akitsu; Ikeya, Makoto; Yamamoto, Takuya; Nishino, Tokiko; Shoji, Emi; Sehara-Fujisawa, Atsuko; Manabe, Yasuko; Fujii, Nobuharu; Hanaoka, Kazunori; Era, Takumi; Yamashita, Satoshi; Isobe, Ken-ichi; Kimura, En; Sakurai, Hidetoshi

    2013-01-01

    The establishment of human induced pluripotent stem cells (hiPSCs) has enabled the production of in vitro, patient-specific cell models of human disease. In vitro recreation of disease pathology from patient-derived hiPSCs depends on efficient differentiation protocols producing relevant adult cell types. However, myogenic differentiation of hiPSCs has faced obstacles, namely, low efficiency and/or poor reproducibility. Here, we report the rapid, efficient, and reproducible differentiation of hiPSCs into mature myocytes. We demonstrated that inducible expression of myogenic differentiation1 (MYOD1) in immature hiPSCs for at least 5 days drives cells along the myogenic lineage, with efficiencies reaching 70–90%. Myogenic differentiation driven by MYOD1 occurred even in immature, almost completely undifferentiated hiPSCs, without mesodermal transition. Myocytes induced in this manner reach maturity within 2 weeks of differentiation as assessed by marker gene expression and functional properties, including in vitro and in vivo cell fusion and twitching in response to electrical stimulation. Miyoshi Myopathy (MM) is a congenital distal myopathy caused by defective muscle membrane repair due to mutations in DYSFERLIN. Using our induced differentiation technique, we successfully recreated the pathological condition of MM in vitro, demonstrating defective membrane repair in hiPSC-derived myotubes from an MM patient and phenotypic rescue by expression of full-length DYSFERLIN (DYSF). These findings not only facilitate the pathological investigation of MM, but could potentially be applied in modeling of other human muscular diseases by using patient-derived hiPSCs. PMID:23626698

  14. Nonlinear System Identification and Behavioral Modeling

    CERN Document Server

    Huq, Kazi Mohammed Saidul; Kabir, A F M Sultanul

    2010-01-01

    The problem of determining a mathematical model for an unknown system by observing its input-output data pair is generally referred to as system identification. A behavioral model reproduces the required behavior of the original analyzed system, such as there is a one-to-one correspondence between the behavior of the original system and the simulated system. This paper presents nonlinear system identification and behavioral modeling using a work assignment.

  15. Long-term stability, reproducibility, and statistical sensitivity of a telemetry-instrumented dog model: A 27-month longitudinal assessment.

    Science.gov (United States)

    Fryer, Ryan M; Ng, Khing Jow; Chi, Liguo; Jin, Xidong; Reinhart, Glenn A

    2015-01-01

    ICH guidelines, as well as best-practice and ethical considerations, provide strong rationale for use of telemetry-instrumented dog colonies for cardiovascular safety assessment. However, few studies have investigated the long-term stability of cardiovascular function at baseline, reproducibility in response to pharmacologic challenge, and maintenance of statistical sensitivity to define the usable life of the colony. These questions were addressed in 3 identical studies spanning 27months and were performed in the same colony of dogs. Telemetry-instrumented dogs (n=4) received a single dose of dl-sotalol (10mg/kg, p.o.), a β1 adrenergic and IKr blocker, or vehicle, in 3 separate studies spanning 27months. Systemic hemodynamics, cardiovascular function, and ECG parameters were monitored for 18h post-dose; plasma drug concentrations (Cp) were measured at 1, 3, 5, and 24h post-dose. Baseline hemodynamic/ECG values were consistent across the 27-month study with the exception of modest age-dependent decreases in heart rate and the corresponding QT-interval. dl-Sotalol elicited highly reproducible effects in each study. Reductions in heart rate after dl-sotalol treatment ranged between -22 and -32 beats/min, and slight differences in magnitude could be ascribed to variability in dl-sotalol Cp (range=3230-5087ng/mL); dl-sotalol also reduced LV-dP/dtmax 13-22%. dl-Sotalol increased the slope of the PR-RR relationship suggesting inhibition of AV-conduction. Increases in the heart-rate corrected QT-interval were not significantly different across the 3 studies and results of a power analysis demonstrated that the detection limit for QTc values was not diminished throughout the 27month period and across a range of power assumptions despite modest, age-dependent changes in heart rate. These results demonstrate the long-term stability of a telemetry dog colony as evidenced by a stability of baseline values, consistently reproducible response to pharmacologic challenge and no

  16. A versatile and reproducible automatic injection system for liquid standard introduction: application to in-situ calibration

    Directory of Open Access Journals (Sweden)

    G. Isaacman

    2011-05-01

    Full Text Available The quantitation of trace organic compounds in ambient organic aerosol is difficult due to the chemical complexity of these mixtures, but is needed to provide insight into their sources and formation processes. Compound-level characterization of organic aerosols is typically performed through sample collection followed by gas or liquid chromatography. With these methods, introduction of liquid standards has long been used as an effective means of quantifying trace compounds, but automating this technique for use with in-situ instrumentation has not previously been achieved. Here we develop an automatic injection system (AutoInject for the introduction of liquids into a custom collection and analysis cell for improved quantitation in chromatographic measurements. The system consists of chilled reservoirs containing liquid standards from which a sample loop is loaded and then injected into the cell. The AutoInject is shown to have reproducibility over 106 injections with a relative standard deviation of 1.5 %, and have negligible injection-to-injection carryover. A 6-port selector allows injection of different liquid standards separately or simultaneously. Additionally, automatic injection of multiple sample loops is shown to generate a linear multi-point calibration curve. Tests conducted in this work focus on use with the Thermal desorption Aerosol Gas chromatograph (TAG, but the flexibility of the system allows it to be used for a variety of applications.

  17. A short-term mouse model that reproduces the immunopathological features of rhinovirus-induced exacerbation of COPD.

    Science.gov (United States)

    Singanayagam, Aran; Glanville, Nicholas; Walton, Ross P; Aniscenko, Julia; Pearson, Rebecca M; Pinkerton, James W; Horvat, Jay C; Hansbro, Philip M; Bartlett, Nathan W; Johnston, Sebastian L

    2015-08-01

    Viral exacerbations of chronic obstructive pulmonary disease (COPD), commonly caused by rhinovirus (RV) infections, are poorly controlled by current therapies. This is due to a lack of understanding of the underlying immunopathological mechanisms. Human studies have identified a number of key immune responses that are associated with RV-induced exacerbations including neutrophilic inflammation, expression of inflammatory cytokines and deficiencies in innate anti-viral interferon. Animal models of COPD exacerbation are required to determine the contribution of these responses to disease pathogenesis. We aimed to develop a short-term mouse model that reproduced the hallmark features of RV-induced exacerbation of COPD. Evaluation of complex protocols involving multiple dose elastase and lipopolysaccharide (LPS) administration combined with RV1B infection showed suppression rather than enhancement of inflammatory parameters compared with control mice infected with RV1B alone. Therefore, these approaches did not accurately model the enhanced inflammation associated with RV infection in patients with COPD compared with healthy subjects. In contrast, a single elastase treatment followed by RV infection led to heightened airway neutrophilic and lymphocytic inflammation, increased expression of tumour necrosis factor (TNF)-α, C-X-C motif chemokine 10 (CXCL10)/IP-10 (interferon γ-induced protein 10) and CCL5 [chemokine (C-C motif) ligand 5]/RANTES (regulated on activation, normal T-cell expressed and secreted), mucus hypersecretion and preliminary evidence for increased airway hyper-responsiveness compared with mice treated with elastase or RV infection alone. In summary, we have developed a new mouse model of RV-induced COPD exacerbation that mimics many of the inflammatory features of human disease. This model, in conjunction with human models of disease, will provide an essential tool for studying disease mechanisms and allow testing of novel therapies with potential to

  18. A first attempt to reproduce basaltic soil chronosequences using a process-based soil profile model: implications for our understanding of soil evolution

    Science.gov (United States)

    Johnson, M.; Gloor, M.; Lloyd, J.

    2012-04-01

    Soils are complex systems which hold a wealth of information on both current and past conditions and many biogeochemical processes. The ability to model soil forming processes and predict soil properties will enable us to quantify such conditions and contribute to our understanding of long-term biogeochemical cycles, particularly the carbon cycle and plant nutrient cycles. However, attempts to confront such soil model predictions with data are rare, although increasingly more data from chronosquence studies is becoming available for such a purpose. Here we present initial results of an attempt to reproduce soil properties with a process-based soil evolution model similar to the model of Kirkby (1985, J. Soil Science). We specifically focus on the basaltic soils in both Hawaii and north Queensland, Australia. These soils are formed on a series of volcanic lava flows which provide sequences of different aged soils all with a relatively uniform parent material. These soil chronosequences provide a snapshot of a soil profile during different stages of development. Steep rainfall gradients in these regions also provide a system which allows us to test the model's ability to reproduce soil properties under differing climates. The mechanistic, soil evolution model presented here includes the major processes of soil formation such as i) mineral weathering, ii) percolation of rainfall through the soil, iii) leaching of solutes out of the soil profile iv) surface erosion and v) vegetation and biotic interactions. The model consists of a vertical profile and assumes simple geometry with a constantly sloping surface. The timescales of interest are on the order of tens to hundreds of thousand years. The specific properties the model predicts are, soil depth, the proportion of original elemental oxides remaining in each soil layer, pH of the soil solution, organic carbon distribution and CO2 production and concentration. The presentation will focus on a brief introduction of the

  19. Can CFMIP2 models reproduce the leading modes of cloud vertical structure in the CALIPSO-GOCCP observations?

    Science.gov (United States)

    Wang, Fang; Yang, Song

    2017-02-01

    Using principal component (PC) analysis, three leading modes of cloud vertical structure (CVS) are revealed by the GCM-Oriented CALIPSO Cloud Product (GOCCP), i.e. tropical high, subtropical anticyclonic and extratropical cyclonic cloud modes (THCM, SACM and ECCM, respectively). THCM mainly reflect the contrast between tropical high clouds and clouds in middle/high latitudes. SACM is closely associated with middle-high clouds in tropical convective cores, few-cloud regimes in subtropical anticyclonic clouds and stratocumulus over subtropical eastern oceans. ECCM mainly corresponds to clouds along extratropical cyclonic regions. Models of phase 2 of Cloud Feedback Model Intercomparison Project (CFMIP2) well reproduce the THCM, but SACM and ECCM are generally poorly simulated compared to GOCCP. Standardized PCs corresponding to CVS modes are generally captured, whereas original PCs (OPCs) are consistently underestimated (overestimated) for THCM (SACM and ECCM) by CFMIP2 models. The effects of CVS modes on relative cloud radiative forcing (RSCRF/RLCRF) (RSCRF being calculated at the surface while RLCRF at the top of atmosphere) are studied in terms of principal component regression method. Results show that CFMIP2 models tend to overestimate (underestimated or simulate the opposite sign) RSCRF/RLCRF radiative effects (REs) of ECCM (THCM and SACM) in unit global mean OPC compared to observations. These RE biases may be attributed to two factors, one of which is underestimation (overestimation) of low/middle clouds (high clouds) (also known as stronger (weaker) REs in unit low/middle (high) clouds) in simulated global mean cloud profiles, the other is eigenvector biases in CVS modes (especially for SACM and ECCM). It is suggested that much more attention should be paid on improvement of CVS, especially cloud parameterization associated with particular physical processes (e.g. downwelling regimes with the Hadley circulation, extratropical storm tracks and others), which

  20. Can a coupled meteorology-chemistry model reproduce the historical trend in aerosol direct radiative effects over the Northern Hemisphere?

    Directory of Open Access Journals (Sweden)

    J. Xing

    2015-05-01

    Full Text Available The ability of a coupled meteorology-chemistry model, i.e., WRF-CMAQ, in reproducing the historical trend in AOD and clear-sky short-wave radiation (SWR over the Northern Hemisphere has been evaluated through a comparison of 21 year simulated results with observation-derived records from 1990–2010. Six satellite retrieved AOD products including AVHRR, TOMS, SeaWiFS, MISR, MODIS-terra and -aqua as well as long-term historical records from 11 AERONET sites were used for the comparison of AOD trends. Clear-sky SWR products derived by CERES at both TOA and surface as well as surface SWR data derived from seven SURFRAD sites were used for the comparison of trends in SWR. The model successfully captured increasing AOD trends along with the corresponding increased TOA SWR (upwelling and decreased surface SWR (downwelling in both eastern China and the northern Pacific. The model also captured declining AOD trends along with the corresponding decreased TOA SWR (upwelling and increased surface SWR (downwelling in eastern US, Europe and northern Atlantic for the period of 2000–2010. However, the model underestimated the AOD over regions with substantial natural dust aerosol contributions, such as the Sahara Desert, Arabian Desert, central Atlantic and north Indian Ocean. Estimates of aerosol direct radiative effect (DRE at TOA are comparable with those derived by measurements. Compared to GCMs, the model exhibits better estimates of surface- aerosol direct radiative efficiency (Eτ. However, surface-DRE tends to be underestimated due to the underestimated AOD in land and dust regions. Further investigation of TOA-Eτ estimations as well as the dust module used for estimates of windblown-dust emissions is needed.

  1. A Bloch-McConnell simulator with pharmacokinetic modeling to explore accuracy and reproducibility in the measurement of hyperpolarized pyruvate

    Science.gov (United States)

    Walker, Christopher M.; Bankson, James A.

    2015-03-01

    Magnetic resonance imaging (MRI) of hyperpolarized (HP) agents has the potential to probe in-vivo metabolism with sensitivity and specificity that was not previously possible. Biological conversion of HP agents specifically for cancer has been shown to correlate to presence of disease, stage and response to therapy. For such metabolic biomarkers derived from MRI of hyperpolarized agents to be clinically impactful, they need to be validated and well characterized. However, imaging of HP substrates is distinct from conventional MRI, due to the non-renewable nature of transient HP magnetization. Moreover, due to current practical limitations in generation and evolution of hyperpolarized agents, it is not feasible to fully experimentally characterize measurement and processing strategies. In this work we use a custom Bloch-McConnell simulator with pharmacokinetic modeling to characterize the performance of specific magnetic resonance spectroscopy sequences over a range of biological conditions. We performed numerical simulations to evaluate the effect of sequence parameters over a range of chemical conversion rates. Each simulation was analyzed repeatedly with the addition of noise in order to determine the accuracy and reproducibility of measurements. Results indicate that under both closed and perfused conditions, acquisition parameters can affect measurements in a tissue dependent manner, suggesting that great care needs to be taken when designing studies involving hyperpolarized agents. More modeling studies will be needed to determine what effect sequence parameters have on more advanced acquisitions and processing methods.

  2. An Effective and Reproducible Model of Ventricular Fibrillation in Crossbred Yorkshire Swine (Sus scrofa) for Use in Physiologic Research.

    Science.gov (United States)

    Burgert, James M; Johnson, Arthur D; Garcia-Blanco, Jose C; Craig, W John; O'Sullivan, Joseph C

    2015-10-01

    Transcutaneous electrical induction (TCEI) has been used to induce ventricular fibrillation (VF) in laboratory swine for physiologic and resuscitation research. Many studies do not describe the method of TCEI in detail, thus making replication by future investigators difficult. Here we describe a detailed method of electrically inducing VF that was used successfully in a prospective, experimental resuscitation study. Specifically, an electrical current was passed through the heart to induce VF in crossbred Yorkshire swine (n = 30); the current was generated by using two 22-gauge spinal needles, with one placed above and one below the heart, and three 9V batteries connected in series. VF developed in 28 of the 30 pigs (93%) within 10 s of beginning the procedure. In the remaining 2 swine, VF was induced successfully after medial redirection of the superior parasternal needle. The TCEI method is simple, reproducible, and cost-effective. TCEI may be especially valuable to researchers with limited access to funding, sophisticated equipment, or colleagues experienced in interventional cardiology techniques. The TCEI method might be most appropriate for pharmacologic studies requiring VF, VF resulting from the R-on-T phenomenon (as in prolonged QT syndrome), and VF arising from other ectopic or reentrant causes. However, the TCEI method does not accurately model the most common cause of VF, acute coronary occlusive disease. Researchers must consider the limitations of TCEI that may affect internal and external validity of collected data, when designing experiments using this model of VF.

  3. A rat tail temporary static compression model reproduces different stages of intervertebral disc degeneration with decreased notochordal cell phenotype.

    Science.gov (United States)

    Hirata, Hiroaki; Yurube, Takashi; Kakutani, Kenichiro; Maeno, Koichiro; Takada, Toru; Yamamoto, Junya; Kurakawa, Takuto; Akisue, Toshihiro; Kuroda, Ryosuke; Kurosaka, Masahiro; Nishida, Kotaro

    2014-03-01

    The intervertebral disc nucleus pulposus (NP) has two phenotypically distinct cell types-notochordal cells (NCs) and non-notochordal chondrocyte-like cells. In human discs, NCs are lost during adolescence, which is also when discs begin to show degenerative signs. However, little evidence exists regarding the link between NC disappearance and the pathogenesis of disc degeneration. To clarify this, a rat tail disc degeneration model induced by static compression at 1.3 MPa for 0, 1, or 7 days was designed and assessed for up to 56 postoperative days. Radiography, MRI, and histomorphology showed degenerative disc findings in response to the compression period. Immunofluorescence displayed that the number of DAPI-positive NP cells decreased with compression; particularly, the decrease was notable in larger, vacuolated, cytokeratin-8- and galectin-3-co-positive cells, identified as NCs. The proportion of TUNEL-positive cells, which predominantly comprised non-NCs, increased with compression. Quantitative PCR demonstrated isolated mRNA up-regulation of ADAMTS-5 in the 1-day loaded group and MMP-3 in the 7-day loaded group. Aggrecan-1 and collagen type 2α-1 mRNA levels were down-regulated in both groups. This rat tail temporary static compression model, which exhibits decreased NC phenotype, increased apoptotic cell death, and imbalanced catabolic and anabolic gene expression, reproduces different stages of intervertebral disc degeneration.

  4. MRI assessment of knee osteoarthritis: Knee Osteoarthritis Scoring System (KOSS) - inter-observer and intra-observer reproducibility of a compartment-based scoring system

    Energy Technology Data Exchange (ETDEWEB)

    Kornaat, Peter R.; Ceulemans, Ruth Y.T.; Kroon, Herman M.; Bloem, Johan L. [Leiden University Medical Center, Department of Radiology, Leiden (Netherlands); Riyazi, Naghmeh; Kloppenburg, Margreet [Leiden University Medical Center, Department of Rheumatology, Leiden (Netherlands); Carter, Wayne O.; Woodworth, Thasia G. [Pfizer Groton, Groton, Connecticut (United States)

    2005-02-01

    To develop a scoring system for quantifying osteoarthritic changes of the knee as identified by magnetic resonance (MR) imaging, and to determine its inter- and intra-observer reproducibility, in order to monitor medical therapy in research studies. Two independent observers evaluated 25 consecutive MR examinations of the knee in patients with previously defined clinical symptoms and radiological signs of osteoarthritis. We acquired on a 1.5 T system: coronal and sagittal proton density- and T2-weighted dual spin echo (SE) images, sagittal three-dimensional T1-weighted gradient echo (GE) images with fat suppression, and axial dual turbo SE images with fat suppression. Images were scored for the presence of cartilaginous lesions, osteophytes, subchondral cysts, bone marrow edema, and for meniscal abnormalities. Presence and size of effusion, synovitis and Baker's cyst were recorded. All parameters were ranked on a previously defined, semiquantitative scale, reflecting increasing severity of findings. Kappa, weighted kappa and intraclass correlation coefficient (ICC) were used to determine inter- and intra-observer variability. Inter-observer reproducibility was good (ICC value 0.77). Inter- and intra-observer reproducibility for individual parameters was good to very good (inter-observer ICC value 0.63-0.91; intra-observer ICC value 0.76-0.96). The presented comprehensive MR scoring system for osteoarthritic changes of the knee has a good to very good inter-observer and intra-observer reproducibility. Thus the score form with its definitions can be used for standardized assessment of osteoarthritic changes to monitor medical therapy in research studies. (orig.)

  5. QSAR model reproducibility and applicability: a case study of rate constants of hydroxyl radical reaction models applied to polybrominated diphenyl ethers and (benzo-)triazoles.

    Science.gov (United States)

    Roy, Partha Pratim; Kovarich, Simona; Gramatica, Paola

    2011-08-01

    The crucial importance of the three central OECD principles for quantitative structure-activity relationship (QSAR) model validation is highlighted in a case study of tropospheric degradation of volatile organic compounds (VOCs) by OH, applied to two CADASTER chemical classes (PBDEs and (benzo-)triazoles). The application of any QSAR model to chemicals without experimental data largely depends on model reproducibility by the user. The reproducibility of an unambiguous algorithm (OECD Principle 2) is guaranteed by redeveloping MLR models based on both updated version of DRAGON software for molecular descriptors calculation and some freely available online descriptors. The Genetic Algorithm has confirmed its ability to always select the most informative descriptors independently on the input pool of variables. The ability of the GA-selected descriptors to model chemicals not used in model development is verified by three different splittings (random by response, K-ANN and K-means clustering), thus ensuring the external predictivity of the new models, independently of the training/prediction set composition (OECD Principle 5). The relevance of checking the structural applicability domain becomes very evident on comparing the predictions for CADASTER chemicals, using the new models proposed herein, with those obtained by EPI Suite. Copyright © 2011 Wiley Periodicals, Inc.

  6. A rat model of post-traumatic stress disorder reproduces the hippocampal deficits seen in the human syndrome

    Directory of Open Access Journals (Sweden)

    Sonal eGoswami

    2012-06-01

    Full Text Available Despite recent progress, the causes and pathophysiology of post-traumatic stress disorder (PTSD remain poorly understood, partly because of ethical limitations inherent to human studies. One approach to circumvent this obstacle is to study PTSD in a valid animal model of the human syndrome. In one such model, extreme and long-lasting behavioral manifestations of anxiety develop in a subset of Lewis rats after exposure to an intense predatory threat that mimics the type of life-and-death situation known to precipitate PTSD in humans. This study aimed to assess whether the hippocampus-associated deficits observed in the human syndrome are reproduced in this rodent model. Prior to predatory threat, different groups of rats were each tested on one of three object recognition memory tasks that varied in the types of contextual clues (i.e. that require the hippocampus or not the rats could use to identify novel items. After task completion, the rats were subjected to predatory threat and, one week later, tested on the elevated plus maze. Based on their exploratory behavior in the plus maze, rats were then classified as resilient or PTSD-like and their performance on the pre-threat object recognition tasks compared. The performance of PTSD-like rats was inferior to that of resilient rats but only when subjects relied on an allocentric frame of reference to identify novel items, a process thought to be critically dependent on the hippocampus. Therefore, these results suggest that even prior to trauma, PTSD-like rats show a deficit in hippocampal-dependent functions, as reported in twin studies of human PTSD.

  7. Reproducing the organic matter model of anthropogenic dark earth of Amazonia and testing the ecotoxicity of functionalized charcoal compounds

    Directory of Open Access Journals (Sweden)

    Carolina Rodrigues Linhares

    2012-05-01

    Full Text Available The objective of this work was to obtain organic compounds similar to the ones found in the organic matter of anthropogenic dark earth of Amazonia (ADE using a chemical functionalization procedure on activated charcoal, as well as to determine their ecotoxicity. Based on the study of the organic matter from ADE, an organic model was proposed and an attempt to reproduce it was described. Activated charcoal was oxidized with the use of sodium hypochlorite at different concentrations. Nuclear magnetic resonance was performed to verify if the spectra of the obtained products were similar to the ones of humic acids from ADE. The similarity between spectra indicated that the obtained products were polycondensed aromatic structures with carboxyl groups: a soil amendment that can contribute to soil fertility and to its sustainable use. An ecotoxicological test with Daphnia similis was performed on the more soluble fraction (fulvic acids of the produced soil amendment. Aryl chloride was formed during the synthesis of the organic compounds from activated charcoal functionalization and partially removed through a purification process. However, it is probable that some aryl chloride remained in the final product, since the ecotoxicological test indicated that the chemical functionalized soil amendment is moderately toxic.

  8. Enhancement of accuracy and reproducibility of parametric modeling for estimating abnormal intra-QRS potentials in signal-averaged electrocardiograms.

    Science.gov (United States)

    Lin, Chun-Cheng

    2008-09-01

    This work analyzes and attempts to enhance the accuracy and reproducibility of parametric modeling in the discrete cosine transform (DCT) domain for the estimation of abnormal intra-QRS potentials (AIQP) in signal-averaged electrocardiograms. One hundred sets of white noise with a flat frequency response were introduced to simulate the unpredictable, broadband AIQP when quantitatively analyzing estimation error. Further, a high-frequency AIQP parameter was defined to minimize estimation error caused by the overlap between normal QRS and AIQP in low-frequency DCT coefficients. Seventy-two patients from Taiwan were recruited for the study, comprising 30 patients with ventricular tachycardia (VT) and 42 without VT. Analytical results showed that VT patients had a significant decrease in the estimated AIQP. The global diagnostic performance (area under the receiver operating characteristic curve) of AIQP rose from 73.0% to 84.2% in lead Y, and from 58.3% to 79.1% in lead Z, when the high-frequency range fell from 100% to 80%. The combination of AIQP and ventricular late potentials further enhanced performance to 92.9% (specificity=90.5%, sensitivity=90%). Therefore, the significantly reduced AIQP in VT patients, possibly also including dominant unpredictable potentials within the normal QRS complex, may be new promising evidence of ventricular arrhythmias.

  9. A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types.

    Science.gov (United States)

    Schwämmle, Veit; Jensen, Ole Nørregaard

    2013-01-01

    Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are implicated in the regulation of eukaryote genes and they carry numerous reversible post-translational modifications that control DNA-protein interactions and the recruitment of chromatin binding proteins. Heterochromatin, the transcriptionally inactive part of the genome, is densely packed and contains histone H3 that is methylated at Lys 9 (H3K9me). The propagation of H3K9me in nucleosomes along the DNA in chromatin is antagonizing by methylation of H3 Lysine 4 (H3K4me) and acetylations of several lysines, which is related to euchromatin and active genes. We show that the related histone modifications form antagonized domains on a coarse scale. These histone marks are assumed to be initiated within distinct nucleation sites in the DNA and to propagate bi-directionally. We propose a simple computer model that simulates the distribution of heterochromatin in human chromosomes. The simulations are in agreement with previously reported experimental observations from two different human cell lines. We reproduced different types of barriers between heterochromatin and euchromatin providing a unified model for their function. The effect of changes in the nucleation site distribution and of propagation rates were studied. The former occurs mainly with the aim of (de-)activation of single genes or gene groups and the latter has the power of controlling the transcriptional programs of entire chromosomes. Generally, the regulatory program of gene transcription is controlled by the distribution of nucleation sites along the DNA string.

  10. Reproducibility and accuracy of linear measurements on dental models derived from cone-beam computed tomography compared with digital dental casts

    NARCIS (Netherlands)

    Waard, O. de; Rangel, F.A.; Fudalej, P.S.; Bronkhorst, E.M.; Kuijpers-Jagtman, A.M.; Breuning, K.H.

    2014-01-01

    INTRODUCTION: The aim of this study was to determine the reproducibility and accuracy of linear measurements on 2 types of dental models derived from cone-beam computed tomography (CBCT) scans: CBCT images, and Anatomodels (InVivoDental, San Jose, Calif); these were compared with digital models gene

  11. Randomised reproducing graphs

    CERN Document Server

    Jordan, Jonathan

    2011-01-01

    We introduce a model for a growing random graph based on simultaneous reproduction of the vertices. The model can be thought of as a generalisation of the reproducing graphs of Southwell and Cannings and Bonato et al to allow for a random element, and there are three parameters, $\\alpha$, $\\beta$ and $\\gamma$, which are the probabilities of edges appearing between different types of vertices. We show that as the probabilities associated with the model vary there are a number of phase transitions, in particular concerning the degree sequence. If $(1+\\alpha)(1+\\gamma)1$ then the degree of a typical vertex grows to infinity, and the proportion of vertices having any fixed degree $d$ tends to zero. We also give some results on the number of edges and on the spectral gap.

  12. Current status of the ability of the GEMS/MACC models to reproduce the tropospheric CO vertical distribution as measured by MOZAIC

    Directory of Open Access Journals (Sweden)

    N. Elguindi

    2010-10-01

    Full Text Available Vertical profiles of CO taken from the MOZAIC aircraft database are used to globally evaluate the performance of the GEMS/MACC models, including the ECMWF-Integrated Forecasting System (IFS model coupled to the CTM MOZART-3 with 4DVAR data assimilation for the year 2004. This study provides a unique opportunity to compare the performance of three offline CTMs (MOZART-3, MOCAGE and TM5 driven by the same meteorology as well as one coupled atmosphere/CTM model run with data assimilation, enabling us to assess the potential gain brought by the combination of online transport and the 4DVAR chemical satellite data assimilation.

    First we present a global analysis of observed CO seasonal averages and interannual variability for the years 2002–2007. Results show that despite the intense boreal forest fires that occurred during the summer in Alaska and Canada, the year 2004 had comparably lower tropospheric CO concentrations. Next we present a validation of CO estimates produced by the MACC models for 2004, including an assessment of their ability to transport pollutants originating from the Alaskan/Canadian wildfires. In general, all the models tend to underestimate CO. The coupled model and the CTMs perform best in Europe and the US where biases range from 0 to -25% in the free troposphere and from 0 to -50% in the surface and boundary layers (BL. Using the 4DVAR technique to assimilate MOPITT V4 CO significantly reduces biases by up to 50% in most regions. However none of the models, even the IFS-MOZART-3 coupled model with assimilation, are able to reproduce well the CO plumes originating from the Alaskan/Canadian wildfires at downwind locations in the eastern US and Europe. Sensitivity tests reveal that deficiencies in the fire emissions inventory and injection height play a role.

  13. Attempting to train a digital human model to reproduce human subject reach capabilities in an ejection seat aircraft

    NARCIS (Netherlands)

    Zehner, G.F.; Hudson, J.A.; Oudenhuijzen, A.

    2006-01-01

    From 1997 through 2002, the Air Force Research Lab and TNO Defence, Security and Safety (Business Unit Human Factors) were involved in a series of tests to quantify the accuracy of five Human Modeling Systems (HMSs) in determining accommodation limits of ejection seat aircraft. The results of these

  14. The Need for Reproducibility

    Energy Technology Data Exchange (ETDEWEB)

    Robey, Robert W. [Los Alamos National Laboratory

    2016-06-27

    The purpose of this presentation is to consider issues of reproducibility, specifically it determines whether bitwise reproducible computation is possible, if computational research in DOE improves its publication process, and if reproducible results can be achieved apart from the peer review process?

  15. Physics and Psychophysics of High-Fidelity Sound. Part III: The Components of a Sound-Reproducing System: Amplifiers and Loudspeakers.

    Science.gov (United States)

    Rossing, Thomas D.

    1980-01-01

    Described are the components for a high-fidelity sound-reproducing system which focuses on various program sources, the amplifier, and loudspeakers. Discussed in detail are amplifier power and distortion, air suspension, loudspeaker baffles and enclosures, bass-reflex enclosure, drone cones, rear horn and acoustic labyrinth enclosures, horn…

  16. Physics and Psychophysics of High-Fidelity Sound. Part III: The Components of a Sound-Reproducing System: Amplifiers and Loudspeakers.

    Science.gov (United States)

    Rossing, Thomas D.

    1980-01-01

    Described are the components for a high-fidelity sound-reproducing system which focuses on various program sources, the amplifier, and loudspeakers. Discussed in detail are amplifier power and distortion, air suspension, loudspeaker baffles and enclosures, bass-reflex enclosure, drone cones, rear horn and acoustic labyrinth enclosures, horn…

  17. Reproducibility of Quantitative Brain Imaging Using a PET-Only and a Combined PET/MR System

    Science.gov (United States)

    Lassen, Martin L.; Muzik, Otto; Beyer, Thomas; Hacker, Marcus; Ladefoged, Claes Nøhr; Cal-González, Jacobo; Wadsak, Wolfgang; Rausch, Ivo; Langer, Oliver; Bauer, Martin

    2017-01-01

    The purpose of this study was to test the feasibility of migrating a quantitative brain imaging protocol from a positron emission tomography (PET)-only system to an integrated PET/MR system. Potential differences in both absolute radiotracer concentration as well as in the derived kinetic parameters as a function of PET system choice have been investigated. Five healthy volunteers underwent dynamic (R)-[11C]verapamil imaging on the same day using a GE-Advance (PET-only) and a Siemens Biograph mMR system (PET/MR). PET-emission data were reconstructed using a transmission-based attenuation correction (AC) map (PET-only), whereas a standard MR-DIXON as well as a low-dose CT AC map was applied to PET/MR emission data. Kinetic modeling based on arterial blood sampling was performed using a 1-tissue-2-rate constant compartment model, yielding kinetic parameters (K1 and k2) and distribution volume (VT). Differences for parametric values obtained in the PET-only and the PET/MR systems were analyzed using a 2-way Analysis of Variance (ANOVA). Comparison of DIXON-based AC (PET/MR) with emission data derived from the PET-only system revealed average inter-system differences of −33 ± 14% (p PET/MR resulted in slightly lower systematic differences of −16 ± 18% for K1 and −9 ± 10% for k2. The average differences in VT were −18 ± 10% (p PET/MR and PET-only imaging due to different standard AC methods employed. Therefore, a transfer of imaging protocols from PET-only to PET/MR systems is not straightforward without application of proper correction methods. Clinical Trial Registration: www.clinicaltrialsregister.eu, identifier 2013-001724-19 PMID:28769742

  18. Current status of the ability of the GEMS/MACC models to reproduce the tropospheric CO vertical distribution as measured by MOZAIC

    Directory of Open Access Journals (Sweden)

    N. Elguindi

    2010-04-01

    Full Text Available Vertical profiles of CO taken from the MOZAIC aircraft database are used to present (1 a global analysis of CO seasonal averages and interannual variability for the years 2002–2007 and (2 a global validation of CO estimates produced by the MACC models for 2004, including an assessment of their ability to transport pollutants originating from the Alaskan/Canadian wildfires. Seasonal averages and interannual variability from several MOZAIC sites representing different regions of the world show that CO concentrations are highest and most variable during the winter season. The inter-regional variability is significant with concentrations increasing eastward from Europe to Japan. The impact of the intense boreal fires, particularly in Russia, during the fall of 2002 on the Northern Hemisphere CO concentrations throughout the troposphere is well represented by the MOZAIC data.

    A global validation of the GEMS/MACC GRG models which include three stand-alone CTMs (MOZART, MOCAGE and TM5 and the coupled ECMWF Integrated Forecasting System (IFS/MOZART model with and without MOPITT CO data assimilation show that the models have a tendency to underestimate CO. The models perform best in Europe and the US where biases range from 0 to –25% in the free troposphere and from 0 to –50% in the surface and boundary layers (BL. The biases are largest in the winter and during the daytime when emissions are highest, indicating that current inventories are too low. Data assimilation is shown to reduce biases by up to 25% in some regions. The models are not able to reproduce well the CO plumes originating from the Alaskan/Canadian wildfires at downwind locations in the eastern US and Europe, not even with assimilation. Sensitivity tests reveal that this is mainly due to deficiencies in the fire emissions inventory and injection height.

  19. Opening Reproducible Research

    Science.gov (United States)

    Nüst, Daniel; Konkol, Markus; Pebesma, Edzer; Kray, Christian; Klötgen, Stephanie; Schutzeichel, Marc; Lorenz, Jörg; Przibytzin, Holger; Kussmann, Dirk

    2016-04-01

    Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. When science transforms to open access we not only mean access to papers, research data being collected, or data being generated, but also access to the data used and the procedures carried out in the research paper. Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are completely carried out computationally. Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method (Pebesma, Nüst and Bivand, 2012). As opposed to the collection of experimental data in labs or nature, computational experiments lend themselves very well for reproduction. Some of the reasons why scientists do not publish data and computational procedures that allow reproduction will be hard to change, e.g. privacy concerns in the data, fear for embarrassment or of losing a competitive advantage. Others reasons however involve technical aspects, and include the lack of standard procedures to publish such information and the lack of benefits after publishing them. We aim to resolve these two technical aspects. We propose a system that supports the evolution of scientific publications from static papers into dynamic, executable research documents. The DFG-funded experimental project Opening Reproducible Research (ORR) aims for the main aspects of open access, by improving the exchange of, by facilitating productive access to, and by simplifying reuse of research results that are published over the Internet. Central to the project is a new form for creating and providing research results, the executable research compendium (ERC), which not only enables third parties to

  20. Development of a Three-Dimensional Hand Model Using Three-Dimensional Stereophotogrammetry: Assessment of Image Reproducibility.

    Directory of Open Access Journals (Sweden)

    Inge A Hoevenaren

    Full Text Available Using three-dimensional (3D stereophotogrammetry precise images and reconstructions of the human body can be produced. Over the last few years, this technique is mainly being developed in the field of maxillofacial reconstructive surgery, creating fusion images with computed tomography (CT data for precise planning and prediction of treatment outcome. Though, in hand surgery 3D stereophotogrammetry is not yet being used in clinical settings.A total of 34 three-dimensional hand photographs were analyzed to investigate the reproducibility. For every individual, 3D photographs were captured at two different time points (baseline T0 and one week later T1. Using two different registration methods, the reproducibility of the methods was analyzed. Furthermore, the differences between 3D photos of men and women were compared in a distance map as a first clinical pilot testing our registration method.The absolute mean registration error for the complete hand was 1.46 mm. This reduced to an error of 0.56 mm isolating the region to the palm of the hand. When comparing hands of both sexes, it was seen that the male hand was larger (broader base and longer fingers than the female hand.This study shows that 3D stereophotogrammetry can produce reproducible images of the hand without harmful side effects for the patient, so proving to be a reliable method for soft tissue analysis. Its potential use in everyday practice of hand surgery needs to be further explored.

  1. Model Systems

    Directory of Open Access Journals (Sweden)

    Francisco Rodríguez-Trelles

    1998-12-01

    Full Text Available Current efforts to study the biological effects of global change have focused on ecological responses, particularly shifts in species ranges. Mostly ignored are microevolutionary changes. Genetic changes may be at least as important as ecological ones in determining species' responses. In addition, such changes may be a sensitive indicator of global changes that will provide different information than that provided by range shifts. We discuss potential candidate systems to use in such monitoring programs. Studies of Drosophila subobscura suggest that its chromosomal inversion polymorphisms are responding to global warming. Drosophila inversion polymorphisms can be useful indicators of the effects of climate change on populations and ecosystems. Other species also hold the potential to become important indicators of global change. Such studies might significantly influence ecosystem conservation policies and research priorities.

  2. Identification of Nonlinear Spatiotemporal Dynamical Systems With Nonuniform Observations Using Reproducing-Kernel-Based Integral Least Square Regulation.

    Science.gov (United States)

    Ning, Hanwen; Qing, Guangyan; Jing, Xingjian

    2016-11-01

    The identification of nonlinear spatiotemporal dynamical systems given by partial differential equations has attracted a lot of attention in the past decades. Several methods, such as searching principle-based algorithms, partially linear kernel methods, and coupled lattice methods, have been developed to address the identification problems. However, most existing methods have some restrictions on sampling processes in that the sampling intervals should usually be very small and uniformly distributed in spatiotemporal domains. These are actually not applicable for some practical applications. In this paper, to tackle this issue, a novel kernel-based learning algorithm named integral least square regularization regression (ILSRR) is proposed, which can be used to effectively achieve accurate derivative estimation for nonlinear functions in the time domain. With this technique, a discretization method named inverse meshless collocation is then developed to realize the dimensional reduction of the system to be identified. Thereafter, with this novel inverse meshless collocation model, the ILSRR, and a multiple-kernel-based learning algorithm, a multistep identification method is systematically proposed to address the identification problem of spatiotemporal systems with pointwise nonuniform observations. Numerical studies for benchmark systems with necessary discussions are presented to illustrate the effectiveness and the advantages of the proposed method.

  3. REPROVIS-DB: a benchmark system for ligand-based virtual screening derived from reproducible prospective applications.

    Science.gov (United States)

    Ripphausen, Peter; Wassermann, Anne Mai; Bajorath, Jürgen

    2011-10-24

    Benchmark calculations are essential for the evaluation of virtual screening (VS) methods. Typically, classes of known active compounds taken from the medicinal chemistry literature are divided into reference molecules (search templates) and potential hits that are added to background databases assumed to consist of compounds not sharing this activity. Then VS calculations are carried out, and the recall of known active compounds is determined. However, conventional benchmarking is affected by a number of problems that reduce its value for method evaluation. In addition to often insufficient statistical validation and the lack of generally accepted evaluation standards, the artificial nature of typical benchmark settings is often criticized. Retrospective benchmark calculations generally overestimate the potential of VS methods and do not scale with their performance in prospective applications. In order to provide additional opportunities for benchmarking that more closely resemble practical VS conditions, we have designed a publicly available compound database (DB) of reproducible virtual screens (REPROVIS-DB) that organizes information from successful ligand-based VS applications including reference compounds, screening databases, compound selection criteria, and experimentally confirmed hits. Using the currently available 25 hand-selected compound data sets, one can attempt to reproduce successful virtual screens with other than the originally applied methods and assess their potential for practical applications.

  4. Enabling dynamic access to dynamic petascale Earth Systems and Environmental data collections is easy: citing and reproducing the actual data extracts used in research publications is NOT

    Science.gov (United States)

    Wyborn, L. A.; Wang, J.; Si, W.; Druken, K. A.; Evans, B. J. K.; Klump, J. F.; Car, N. J.; Trenham, C.

    2015-12-01

    The National Computational Infrastructure (NCI) at the Australian National University (ANU) has collocated over 10 PB of national and international Earth Systems and Environmental data assets within a HPC facility to create the National Environmental Research Data Interoperability Platform (NERDIP). Data are replicated to, or are produced at, NCI: in many cases they are processed to higher-level data products. Individual data sets within these collections can range from multi-petabyte climate models and large volume raster arrays, down to gigabyte size, ultra-high resolution data sets. All data are quality assured to being 'published' and made accessible as services. Persistent identifiers are assigned during publishing at both the collection and data set level: the granularity and version control on persistent identifiers depend on the dataset. However, most NERDIP collections are dynamic: either new data is being appended, or else models/derivative products are being revised with new data, or changed as processing methods are improved. Further, because the data are accessible as services, researchers can log in and dynamically create user-defined subsets for specific research projects: inevitably such extracts underpin traditional 'publications'. Being able to reproduce these exact data extracts can be difficult and for the very larger data sets preserving a copy of large data extracts is out of the question. A solution is for the researcher to use provenance workflows that at a minimum capture the version of the data set used, the query and the time of extraction. In parallel, the data provider needs to implement version controls on the data and deploy tracking systems that time stamp when new data are appended, or when modifications are made to existing data and record what these changes are. Where, when and how persistent identifiers are minted on these large and dynamically changing data sets is still open to debate.

  5. Reproducibility of the NEPTUNE descriptor-based scoring system on whole-slide images and histologic and ultrastructural digital images.

    Science.gov (United States)

    Barisoni, Laura; Troost, Jonathan P; Nast, Cynthia; Bagnasco, Serena; Avila-Casado, Carmen; Hodgin, Jeffrey; Palmer, Matthew; Rosenberg, Avi; Gasim, Adil; Liensziewski, Chrysta; Merlino, Lino; Chien, Hui-Ping; Chang, Anthony; Meehan, Shane M; Gaut, Joseph; Song, Peter; Holzman, Lawrence; Gibson, Debbie; Kretzler, Matthias; Gillespie, Brenda W; Hewitt, Stephen M

    2016-07-01

    The multicenter Nephrotic Syndrome Study Network (NEPTUNE) digital pathology scoring system employs a novel and comprehensive methodology to document pathologic features from whole-slide images, immunofluorescence and ultrastructural digital images. To estimate inter- and intra-reader concordance of this descriptor-based approach, data from 12 pathologists (eight NEPTUNE and four non-NEPTUNE) with experience from training to 30 years were collected. A descriptor reference manual was generated and a webinar-based protocol for consensus/cross-training implemented. Intra-reader concordance for 51 glomerular descriptors was evaluated on jpeg images by seven NEPTUNE pathologists scoring 131 glomeruli three times (Tests I, II, and III), each test following a consensus webinar review. Inter-reader concordance of glomerular descriptors was evaluated in 315 glomeruli by all pathologists; interstitial fibrosis and tubular atrophy (244 cases, whole-slide images) and four ultrastructural podocyte descriptors (178 cases, jpeg images) were evaluated once by six and five pathologists, respectively. Cohen's kappa for inter-reader concordance for 48/51 glomerular descriptors with sufficient observations was moderate (0.40transformation. NEPTUNE digital pathology scoring system enables novel morphologic profiling of renal structures. For all histologic and ultrastructural descriptors tested with sufficient observations, moderate-to-excellent concordance was seen for 31/54 (57%). Descriptors not sufficiently represented will require further testing. This study proffers the NEPTUNE digital pathology scoring system as a model for standardization of renal biopsy interpretation extendable outside the NEPTUNE consortium, enabling international collaborations.

  6. Reproducibility study of [{sup 18}F]FPP(RGD){sub 2} uptake in murine models of human tumor xenografts

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Edwin; Liu, Shuangdong; Chin, Frederick; Cheng, Zhen [Stanford University, Molecular Imaging Program at Stanford, Department of Radiology, School of Medicine, Stanford, CA (United States); Gowrishankar, Gayatri; Yaghoubi, Shahriar [Stanford University, Molecular Imaging Program at Stanford, Department of Radiology, School of Medicine, Stanford, CA (United States); Stanford University, Molecular Imaging Program at Stanford, Department of Bioengineering, School of Medicine, Stanford, CA (United States); Wedgeworth, James Patrick [Stanford University, Molecular Imaging Program at Stanford, Department of Bioengineering, School of Medicine, Stanford, CA (United States); Berndorff, Dietmar; Gekeler, Volker [Bayer Schering Pharma AG, Global Drug Discovery, Berlin (Germany); Gambhir, Sanjiv S. [Stanford University, Molecular Imaging Program at Stanford, Department of Radiology, School of Medicine, Stanford, CA (United States); Stanford University, Molecular Imaging Program at Stanford, Department of Bioengineering, School of Medicine, Stanford, CA (United States); Canary Center at Stanford for Cancer Early Detection, Nuclear Medicine, Departments of Radiology and Bioengineering, Molecular Imaging Program at Stanford, Stanford, CA (United States)

    2011-04-15

    An {sup 18}F-labeled PEGylated arginine-glycine-aspartic acid (RGD) dimer [{sup 18}F]FPP(RGD){sub 2} has been used to image tumor {alpha}{sub v}{beta}{sub 3} integrin levels in preclinical and clinical studies. Serial positron emission tomography (PET) studies may be useful for monitoring antiangiogenic therapy response or for drug screening; however, the reproducibility of serial scans has not been determined for this PET probe. The purpose of this study was to determine the reproducibility of the integrin {alpha}{sub v}{beta}{sub 3}-targeted PET probe, [{sup 18}F ]FPP(RGD){sub 2} using small animal PET. Human HCT116 colon cancer xenografts were implanted into nude mice (n = 12) in the breast and scapular region and grown to mean diameters of 5-15 mm for approximately 2.5 weeks. A 3-min acquisition was performed on a small animal PET scanner approximately 1 h after administration of [{sup 18}F]FPP(RGD){sub 2} (1.9-3.8 MBq, 50-100 {mu}Ci) via the tail vein. A second small animal PET scan was performed approximately 6 h later after reinjection of the probe to assess for reproducibility. Images were analyzed by drawing an ellipsoidal region of interest (ROI) around the tumor xenograft activity. Percentage injected dose per gram (%ID/g) values were calculated from the mean or maximum activity in the ROIs. Coefficients of variation and differences in %ID/g values between studies from the same day were calculated to determine the reproducibility. The coefficient of variation (mean {+-}SD) for %ID{sub mean}/g and %ID{sub max}/g values between [{sup 18}F]FPP(RGD){sub 2} small animal PET scans performed 6 h apart on the same day were 11.1 {+-} 7.6% and 10.4 {+-} 9.3%, respectively. The corresponding differences in %ID{sub mean}/g and %ID{sub max}/g values between scans were -0.025 {+-} 0.067 and -0.039 {+-} 0.426. Immunofluorescence studies revealed a direct relationship between extent of {alpha}{sub {nu}}{beta}{sub 3} integrin expression in tumors and tumor vasculature

  7. A reliable and reproducible method for the lipase assay in an AOT/isooctane reversed micellar system: modification of the copper-soap colorimetric method.

    Science.gov (United States)

    Kwon, Chang Woo; Park, Kyung-Min; Choi, Seung Jun; Chang, Pahn-Shick

    2015-09-01

    The copper-soap method, which is based on the absorbance of a fatty acid-copper complex at 715 nm, is a widely used colorimetric assay to determine the lipase activity in reversed micellar system. However, the absorbance of the bis(2-ethylhexyl) sodium sulfosuccinate (AOT)-copper complex prevents the use of an AOT/isooctane reversed micellar system. An extraction step was added to the original procedure to remove AOT and eliminate interference from the AOT-copper complex. Among the solvents tested, acetonitrile was determined to be the most suitable because it allows for the generation of a reproducible calibration curve with oleic acid that is independent of the AOT concentrations. Based on the validation data, the modified method, which does not experience interference from the AOT-copper complex, could be a useful method with enhanced accuracy and reproducibility for the lipase assay.

  8. A right to reproduce?

    Science.gov (United States)

    Quigley, Muireann

    2010-10-01

    How should we conceive of a right to reproduce? And, morally speaking, what might be said to justify such a right? These are just two questions of interest that are raised by the technologies of assisted reproduction. This paper analyses the possible legitimate grounds for a right to reproduce within the two main theories of rights; interest theory and choice theory.

  9. Magni Reproducibility Example

    DEFF Research Database (Denmark)

    2016-01-01

    An example of how to use the magni.reproducibility package for storing metadata along with results from a computational experiment. The example is based on simulating the Mandelbrot set.......An example of how to use the magni.reproducibility package for storing metadata along with results from a computational experiment. The example is based on simulating the Mandelbrot set....

  10. Towards Reproducibility in Computational Hydrology

    Science.gov (United States)

    Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei

    2016-04-01

    The ability to reproduce published scientific findings is a foundational principle of scientific research. Independent observation helps to verify the legitimacy of individual findings; build upon sound observations so that we can evolve hypotheses (and models) of how catchments function; and move them from specific circumstances to more general theory. The rise of computational research has brought increased focus on the issue of reproducibility across the broader scientific literature. This is because publications based on computational research typically do not contain sufficient information to enable the results to be reproduced, and therefore verified. Given the rise of computational analysis in hydrology over the past 30 years, to what extent is reproducibility, or a lack thereof, a problem in hydrology? Whilst much hydrological code is accessible, the actual code and workflow that produced and therefore documents the provenance of published scientific findings, is rarely available. We argue that in order to advance and make more robust the process of hypothesis testing and knowledge creation within the computational hydrological community, we need to build on from existing open data initiatives and adopt common standards and infrastructures to: first make code re-useable and easy to find through consistent use of metadata; second, publish well documented workflows that combine re-useable code together with data to enable published scientific findings to be reproduced; finally, use unique persistent identifiers (e.g. DOIs) to reference re-useable and reproducible code, thereby clearly showing the provenance of published scientific findings. Whilst extra effort is require to make work reproducible, there are benefits to both the individual and the broader community in doing so, which will improve the credibility of the science in the face of the need for societies to adapt to changing hydrological environments.

  11. Reproducibility in Seismic Imaging

    Directory of Open Access Journals (Sweden)

    González-Verdejo O.

    2012-04-01

    Full Text Available Within the field of exploration seismology, there is interest at national level of integrating reproducibility in applied, educational and research activities related to seismic processing and imaging. This reproducibility implies the description and organization of the elements involved in numerical experiments. Thus, a researcher, teacher or student can study, verify, repeat, and modify them independently. In this work, we document and adapt reproducibility in seismic processing and imaging to spread this concept and its benefits, and to encourage the use of open source software in this area within our academic and professional environment. We present an enhanced seismic imaging example, of interest in both academic and professional environments, using Mexican seismic data. As a result of this research, we prove that it is possible to assimilate, adapt and transfer technology at low cost, using open source software and following a reproducible research scheme.

  12. Three-dimensional surgical modelling with an open-source software protocol: study of precision and reproducibility in mandibular reconstruction with the fibula free flap.

    Science.gov (United States)

    Ganry, L; Quilichini, J; Bandini, C M; Leyder, P; Hersant, B; Meningaud, J P

    2017-08-01

    Very few surgical teams currently use totally independent and free solutions to perform three-dimensional (3D) surgical modelling for osseous free flaps in reconstructive surgery. This study assessed the precision and technical reproducibility of a 3D surgical modelling protocol using free open-source software in mandibular reconstruction with fibula free flaps and surgical guides. Precision was assessed through comparisons of the 3D surgical guide to the sterilized 3D-printed guide, determining accuracy to the millimetre level. Reproducibility was assessed in three surgical cases by volumetric comparison to the millimetre level. For the 3D surgical modelling, a difference of less than 0.1mm was observed. Almost no deformations (modelling was between 0.1mm and 0.4mm, and the average precision of the complete reconstructed mandible was less than 1mm. The open-source software protocol demonstrated high accuracy without complications. However, the precision of the surgical case depends on the surgeon's 3D surgical modelling. Therefore, surgeons need training on the use of this protocol before applying it to surgical cases; this constitutes a limitation. Further studies should address the transfer of expertise. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  13. Cocaine addiction related reproducible brain regions of abnormal default-mode network functional connectivity: a group ICA study with different model orders.

    Science.gov (United States)

    Ding, Xiaoyu; Lee, Seong-Whan

    2013-08-26

    Model order selection in group independent component analysis (ICA) has a significant effect on the obtained components. This study investigated the reproducible brain regions of abnormal default-mode network (DMN) functional connectivity related with cocaine addiction through different model order settings in group ICA. Resting-state fMRI data from 24 cocaine addicts and 24 healthy controls were temporally concatenated and processed by group ICA using model orders of 10, 20, 30, 40, and 50, respectively. For each model order, the group ICA approach was repeated 100 times using the ICASSO toolbox and after clustering the obtained components, centrotype-based anterior and posterior DMN components were selected for further analysis. Individual DMN components were obtained through back-reconstruction and converted to z-score maps. A whole brain mixed effects factorial ANOVA was performed to explore the differences in resting-state DMN functional connectivity between cocaine addicts and healthy controls. The hippocampus, which showed decreased functional connectivity in cocaine addicts for all the tested model orders, might be considered as a reproducible abnormal region in DMN associated with cocaine addiction. This finding suggests that using group ICA to examine the functional connectivity of the hippocampus in the resting-state DMN may provide an additional insight potentially relevant for cocaine-related diagnoses and treatments. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  14. The Proximal Medial Sural Nerve Biopsy Model: A Standardised and Reproducible Baseline Clinical Model for the Translational Evaluation of Bioengineered Nerve Guides

    Directory of Open Access Journals (Sweden)

    Ahmet Bozkurt

    2014-01-01

    Full Text Available Autologous nerve transplantation (ANT is the clinical gold standard for the reconstruction of peripheral nerve defects. A large number of bioengineered nerve guides have been tested under laboratory conditions as an alternative to the ANT. The step from experimental studies to the implementation of the device in the clinical setting is often substantial and the outcome is unpredictable. This is mainly linked to the heterogeneity of clinical peripheral nerve injuries, which is very different from standardized animal studies. In search of a reproducible human model for the implantation of bioengineered nerve guides, we propose the reconstruction of sural nerve defects after routine nerve biopsy as a first or baseline study. Our concept uses the medial sural nerve of patients undergoing diagnostic nerve biopsy (≥2 cm. The biopsy-induced nerve gap was immediately reconstructed by implantation of the novel microstructured nerve guide, Neuromaix, as part of an ongoing first-in-human study. Here we present (i a detailed list of inclusion and exclusion criteria, (ii a detailed description of the surgical procedure, and (iii a follow-up concept with multimodal sensory evaluation techniques. The proximal medial sural nerve biopsy model can serve as a preliminarynature of the injuries or baseline nerve lesion model. In a subsequent step, newly developed nerve guides could be tested in more unpredictable and challenging clinical peripheral nerve lesions (e.g., following trauma which have reduced comparability due to the different nature of the injuries (e.g., site of injury and length of nerve gap.

  15. Whole-body skeletal imaging in mice utilizing microPET: optimization of reproducibility and applications in animal models of bone disease

    Energy Technology Data Exchange (ETDEWEB)

    Berger, Frank [The Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California School of Medicine, 700 Westwood Blvd., Los Angeles, CA 90095 (United States); Department of Nuclear Medicine, Ludwig-Maximilians-University, Munich (Germany); Lee, Yu-Po; Lieberman, Jay R. [Department of Orthopedic Surgery, University of California School of Medicine, Los Angeles, California (United States); Loening, Andreas M.; Chatziioannou, Arion [The Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California School of Medicine, 700 Westwood Blvd., Los Angeles, CA 90095 (United States); Freedland, Stephen J.; Belldegrun, Arie S. [Department of Urology, University of California School of Medicine, Los Angeles, California (United States); Leahy, Richard [University of Southern California School of Bioengineering, Los Angeles, California (United States); Sawyers, Charles L. [Department of Medicine, University of California School of Medicine, Los Angeles, California (United States); Gambhir, Sanjiv S. [The Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California School of Medicine, 700 Westwood Blvd., Los Angeles, CA 90095 (United States); UCLA-Jonsson Comprehensive Cancer Center and Department of Biomathematics, University of California School of Medicine, Los Angeles, California (United States)

    2002-09-01

    The aims were to optimize reproducibility and establish [{sup 18}F]fluoride ion bone scanning in mice, using a dedicated small animal positron emission tomography (PET) scanner (microPET) and to correlate functional findings with anatomical imaging using computed tomography (microCAT). Optimal tracer uptake time for [{sup 18}F]fluoride ion was determined by performing dynamic microPET scans. Quantitative reproducibility was measured using region of interest (ROI)-based counts normalized to (a) the injected dose, (b) integral of the heart time-activity curve, or (c) ROI over the whole skeleton. Bone lesions were repetitively imaged. Functional images were correlated with X-ray and microCAT. The plateau of [{sup 18}F]fluoride uptake occurs 60 min after injection. The highest reproducibility was achieved by normalizing to an ROI over the whole skeleton, with a mean percent coefficient of variation [(SD/mean) x 100] of <15%-20%. Benign and malignant bone lesions were successfully repetitively imaged. Preliminary correlation of microPET with microCAT demonstrated the high sensitivity of microPET and the ability of microCAT to detect small osteolytic lesions. Whole-body [{sup 18}F]fluoride ion bone imaging using microPET is reproducible and can be used to serially monitor normal and pathological changes to the mouse skeleton. Morphological imaging with microCAT is useful to display correlative changes in anatomy. Detailed in vivo studies of the murine skeleton in various small animal models of bone diseases should now be possible. (orig.)

  16. Continuous system modeling

    Science.gov (United States)

    Cellier, Francois E.

    1991-01-01

    A comprehensive and systematic introduction is presented for the concepts associated with 'modeling', involving the transition from a physical system down to an abstract description of that system in the form of a set of differential and/or difference equations, and basing its treatment of modeling on the mathematics of dynamical systems. Attention is given to the principles of passive electrical circuit modeling, planar mechanical systems modeling, hierarchical modular modeling of continuous systems, and bond-graph modeling. Also discussed are modeling in equilibrium thermodynamics, population dynamics, and system dynamics, inductive reasoning, artificial neural networks, and automated model synthesis.

  17. Can four-zero-texture mass matrix model reproduce the quark and lepton mixing angles and CP violating phases?

    CERN Document Server

    Matsuda, K; Matsuda, Koichi; Nishiura, Hiroyuki

    2006-01-01

    We reconsider an universal mass matrix model which has a seesaw-invariant structure with four-zero texture common to all quarks and leptons. The CKM quark and MNS lepton mixing matrices of the model are analyzed analytically.We show that the model can be consistent with all the experimental data of neutrino oscillation and quark mixings by tuning free parameters of the model. It is also shown that the model predicts a relatively large value for (1,3) element of the MNS lepton mixing matrix, |(U_{MNS})_{13}|^2 \\simeq 2.6 \\times 10^{-2}. Using the seesaw mechanism, we also discuss the conditions for the components of the Dirac and the right-handed Majorana neutrino mass matrices which lead to the neutrino mass matrix consistent with the experimental data.

  18. Assessment of a numerical model to reproduce event‐scale erosion and deposition distributions in a braided river

    Science.gov (United States)

    Measures, R.; Hicks, D. M.; Brasington, J.

    2016-01-01

    Abstract Numerical morphological modeling of braided rivers, using a physics‐based approach, is increasingly used as a technique to explore controls on river pattern and, from an applied perspective, to simulate the impact of channel modifications. This paper assesses a depth‐averaged nonuniform sediment model (Delft3D) to predict the morphodynamics of a 2.5 km long reach of the braided Rees River, New Zealand, during a single high‐flow event. Evaluation of model performance primarily focused upon using high‐resolution Digital Elevation Models (DEMs) of Difference, derived from a fusion of terrestrial laser scanning and optical empirical bathymetric mapping, to compare observed and predicted patterns of erosion and deposition and reach‐scale sediment budgets. For the calibrated model, this was supplemented with planform metrics (e.g., braiding intensity). Extensive sensitivity analysis of model functions and parameters was executed, including consideration of numerical scheme for bed load component calculations, hydraulics, bed composition, bed load transport and bed slope effects, bank erosion, and frequency of calculations. Total predicted volumes of erosion and deposition corresponded well to those observed. The difference between predicted and observed volumes of erosion was less than the factor of two that characterizes the accuracy of the Gaeuman et al. bed load transport formula. Grain size distributions were best represented using two φ intervals. For unsteady flows, results were sensitive to the morphological time scale factor. The approach of comparing observed and predicted morphological sediment budgets shows the value of using natural experiment data sets for model testing. Sensitivity results are transferable to guide Delft3D applications to other rivers. PMID:27708477

  19. Assessment of a numerical model to reproduce event-scale erosion and deposition distributions in a braided river.

    Science.gov (United States)

    Williams, R D; Measures, R; Hicks, D M; Brasington, J

    2016-08-01

    Numerical morphological modeling of braided rivers, using a physics-based approach, is increasingly used as a technique to explore controls on river pattern and, from an applied perspective, to simulate the impact of channel modifications. This paper assesses a depth-averaged nonuniform sediment model (Delft3D) to predict the morphodynamics of a 2.5 km long reach of the braided Rees River, New Zealand, during a single high-flow event. Evaluation of model performance primarily focused upon using high-resolution Digital Elevation Models (DEMs) of Difference, derived from a fusion of terrestrial laser scanning and optical empirical bathymetric mapping, to compare observed and predicted patterns of erosion and deposition and reach-scale sediment budgets. For the calibrated model, this was supplemented with planform metrics (e.g., braiding intensity). Extensive sensitivity analysis of model functions and parameters was executed, including consideration of numerical scheme for bed load component calculations, hydraulics, bed composition, bed load transport and bed slope effects, bank erosion, and frequency of calculations. Total predicted volumes of erosion and deposition corresponded well to those observed. The difference between predicted and observed volumes of erosion was less than the factor of two that characterizes the accuracy of the Gaeuman et al. bed load transport formula. Grain size distributions were best represented using two φ intervals. For unsteady flows, results were sensitive to the morphological time scale factor. The approach of comparing observed and predicted morphological sediment budgets shows the value of using natural experiment data sets for model testing. Sensitivity results are transferable to guide Delft3D applications to other rivers.

  20. How well can a convection-permitting climate model reproduce decadal statistics of precipitation, temperature and cloud characteristics?

    Science.gov (United States)

    Brisson, Erwan; Van Weverberg, Kwinten; Demuzere, Matthias; Devis, Annemarie; Saeed, Sajjad; Stengel, Martin; van Lipzig, Nicole P. M.

    2016-11-01

    Convection-permitting climate model are promising tools for improved representation of extremes, but the number of regions for which these models have been evaluated are still rather limited to make robust conclusions. In addition, an integrated interpretation of near-surface characteristics (typically temperature and precipitation) together with cloud properties is limited. The objective of this paper is to comprehensively evaluate the performance of a `state-of-the-art' regional convection-permitting climate model for a mid-latitude coastal region with little orographic forcing. For this purpose, an 11-year integration with the COSMO-CLM model at Convection-Permitting Scale (CPS) using a grid spacing of 2.8 km was compared with in-situ and satellite-based observations of precipitation, temperature, cloud properties and radiation (both at the surface and the top of the atmosphere). CPS clearly improves the representation of precipitation, in especially the diurnal cycle, intensity and spatial distribution of hourly precipitation. Improvements in the representation of temperature are less obvious. In fact the CPS integration overestimates both low and high temperature extremes. The underlying cause for the overestimation of high temperature extremes was attributed to deficiencies in the cloud properties: The modelled cloud fraction is only 46 % whereas a cloud fraction of 65 % was observed. Surprisingly, the effect of this deficiency was less pronounced at the radiation balance at the top of the atmosphere due to a compensating error, in particular an overestimation of the reflectivity of clouds when they are present. Overall, a better representation of convective precipitation and a very good representation of the daily cycle in different cloud types were demonstrated. However, to overcome remaining deficiencies, additional efforts are necessary to improve cloud characteristics in CPS. This will be a challenging task due to compensating deficiencies that currently

  1. Second edition of 'The Bethesda System for reporting cervical cytology' – atlas, website, and Bethesda interobserver reproducibility project

    Directory of Open Access Journals (Sweden)

    Nayar Ritu

    2004-10-01

    Full Text Available Abstract A joint task force of the American Society of Cytopathology (ASC and the National Cancer Institute (NCI recently completed a 2-year effort to revise the Bethesda System "blue book" atlas and develop a complementary web-based collection of cervical cytology images. The web-based collection of images is housed on the ASC website, which went live on November 5th, 2003; it can be directly accessed at http://www.cytopathology.org/NIH/.

  2. SU-E-J-182: Reproducibility of Tumor Motion Probability Distribution Function in Stereotactic Body Radiation Therapy of Lung Using Real-Time Tumor-Tracking Radiotherapy System

    Energy Technology Data Exchange (ETDEWEB)

    Shiinoki, T; Hanazawa, H; Park, S; Takahashi, T; Shibuya, K [Yamaguchi University, Ube, Yamaguchi (Japan); Kawamura, S; Uehara, T; Yuasa, Y; Koike, M [Yamaguchi University Hospital, Ube, Yamaguchi (Japan)

    2015-06-15

    Purpose: We aim to achieve new four-dimensional radiotherapy (4DRT) using the next generation real-time tumor-tracking (RTRT) system and flattening-filter-free techniques. To achieve new 4DRT, it is necessary to understand the respiratory motion of tumor. The purposes of this study were: 1.To develop the respiratory motion analysis tool using log files. 2.To evaluate the reproducibility of tumor motion probability distribution function (PDF) during stereotactic body RT (SBRT) of lung tumor. Methods: Seven patients having fiducial markers closely implanted to the lung tumor were enrolled in this study. The positions of fiducial markers were measured using the RTRT system (Mitsubishi Electronics Co., JP) and recorded as two types of log files during the course of SBRT. For each patients, tumor motion range and tumor motion PDFs in left-right (LR), anterior-posterior (AP) and superior-inferior (SI) directions were calculated using log files of all beams per fraction (PDFn). Fractional PDF reproducibility (Rn) was calculated as Kullback-Leibler (KL) divergence between PDF1 and PDFn of tumor motion. The mean of Rn (Rm) was calculated for each patient and correlated to the patient’s mean tumor motion range (Am). The change of Rm during the course of SBRT was also evluated. These analyses were performed using in-house developed software. Results: The Rm were 0.19 (0.07–0.30), 0.14 (0.07–0.32) and 0.16 (0.09–0.28) in LR, AP and SI directions, respectively. The Am were 5.11 mm (2.58–9.99 mm), 7.81 mm (2.87–15.57 mm) and 11.26 mm (3.80–21.27 mm) in LR, AP and SI directions, respectively. The PDF reproducibility decreased as the tumor motion range increased in AP and SI direction. That decreased slightly through the course of RT in SI direction. Conclusion: We developed the respiratory motion analysis tool for 4DRT using log files and quantified the range and reproducibility of respiratory motion for lung tumors.

  3. Comparison of interreader reproducibility of the prostate imaging reporting and data system and likert scales for evaluation of multiparametric prostate MRI.

    Science.gov (United States)

    Rosenkrantz, Andrew B; Lim, Ruth P; Haghighi, Mershad; Somberg, Molly B; Babb, James S; Taneja, Samir S

    2013-10-01

    The objective of our study was to compare interreader reproducibility of the recently proposed "Prostate Imaging Reporting and Data System," or "PI-RADS," scale incorporating fixed criteria and a standard Likert scale based on overall impression for prostate cancer localization using multiparametric MRI. Fifty-five patients who underwent a 3-T prostate MRI examination using a pelvic phased-array coil and incorporating T2-weighted imaging, diffusion-weighted imaging, and dynamic contrast-enhanced imaging were included in the study. Three radiologists (6, 4, and 1 year of experience) independently scored 18 regions (12 in the peripheral zone [PZ] and six in the transition zone [TZ]) using PI-RADS (range, 3-15) and Likert (range, 1-5) scales, which were based on fixed criteria and overall impression, respectively. Interreader reproducibility was evaluated using the concordance correlation coefficient (CCC), which assesses exact agreement between scores (minimal, Likert scales (CCC = 0.608-0.677), moderate in the TZ for the Likert scale (CCC = 0.519), and poor in the TZ for PI-RADS (CCC = 0.376). Agreement between experienced and inexperienced readers was moderate to poor in the PZ and TZ combined for PI-RADS (CCC = 0.340-0.477), moderate in the PZ and TZ combined for the Likert scale (CCC = 0.471-0.497), moderate in the PZ for PI-RADS and Likert scales (CCC = 0.472-0.542), minimal to poor in the TZ for PI-RADS (CCC = 0.094-0.283), and poor in the TZ for the Likert scale (CCC = 0.287-0.400). Interreader reproducibility tended to be higher for relatively experienced readers than for less experienced readers and to be higher in the PZ than in the TZ. For the relatively experienced readers, reproducibility was similar for PI-RADS and Likert scales in the PZ but was somewhat higher for the Likert scale than for PI-RADS in the TZ.

  4. Decadal Variability Shown by the Arctic Ocean Hydrochemical Data and Reproduced by an Ice-Ocean Model

    Institute of Scientific and Technical Information of China (English)

    M. Ikeda; R. Colony; H. Yamaguchi; T. Ikeda

    2005-01-01

    The Arctic is experiencing a significant warming trend as well as a decadal oscillation. The atmospheric circulation represented by the Polar Vortex and the sea ice cover show decadal variabilities, while it has been difficult to reveal the decadal oscillation from the ocean interior. The recent distribution of Russian hydrochemical data collected from the Arctic Basin provides useful information on ocean interior variabilities. Silicate is used to provide the most valuable data for showing the boundary between the silicate-rich Pacific Water and the opposite Atlantic Water. Here, it is assumed that the silicate distribution receives minor influence from seasonal biological productivity and Siberian Rivers outflow. It shows a clear maximum around 100m depth in the Canada Basin, along with a vertical gradient below 100 m, which provides information on the vertical motion of the upper boundary of the Atlantic Water at a decadal time scale. The boundary shifts upward (downward), as realized by the silicate reduction (increase) at a fixed depth, responding to a more intense (weaker) Polar Vortex or a positive (negative) phase of the Arctic Oscillation. A coupled ice-ocean model is employed to reconstruct this decadal oscillation.

  5. Reproducibility of haemodynamical simulations in a subject-specific stented aneurysm model--a report on the Virtual Intracranial Stenting Challenge 2007.

    Science.gov (United States)

    Radaelli, A G; Augsburger, L; Cebral, J R; Ohta, M; Rüfenacht, D A; Balossino, R; Benndorf, G; Hose, D R; Marzo, A; Metcalfe, R; Mortier, P; Mut, F; Reymond, P; Socci, L; Verhegghe, B; Frangi, A F

    2008-07-19

    This paper presents the results of the Virtual Intracranial Stenting Challenge (VISC) 2007, an international initiative whose aim was to establish the reproducibility of state-of-the-art haemodynamical simulation techniques in subject-specific stented models of intracranial aneurysms (IAs). IAs are pathological dilatations of the cerebral artery walls, which are associated with high mortality and morbidity rates due to subarachnoid haemorrhage following rupture. The deployment of a stent as flow diverter has recently been indicated as a promising treatment option, which has the potential to protect the aneurysm by reducing the action of haemodynamical forces and facilitating aneurysm thrombosis. The direct assessment of changes in aneurysm haemodynamics after stent deployment is hampered by limitations in existing imaging techniques and currently requires resorting to numerical simulations. Numerical simulations also have the potential to assist in the personalized selection of an optimal stent design prior to intervention. However, from the current literature it is difficult to assess the level of technological advancement and the reproducibility of haemodynamical predictions in stented patient-specific models. The VISC 2007 initiative engaged in the development of a multicentre-controlled benchmark to analyse differences induced by diverse grid generation and computational fluid dynamics (CFD) technologies. The challenge also represented an opportunity to provide a survey of available technologies currently adopted by international teams from both academic and industrial institutions for constructing computational models of stented aneurysms. The results demonstrate the ability of current strategies in consistently quantifying the performance of three commercial intracranial stents, and contribute to reinforce the confidence in haemodynamical simulation, thus taking a step forward towards the introduction of simulation tools to support diagnostics and

  6. Accuracy and reproducibility of voxel based superimposition of cone beam computed tomography models on the anterior cranial base and the zygomatic arches.

    Directory of Open Access Journals (Sweden)

    Rania M Nada

    Full Text Available Superimposition of serial Cone Beam Computed Tomography (CBCT scans has become a valuable tool for three dimensional (3D assessment of treatment effects and stability. Voxel based image registration is a newly developed semi-automated technique for superimposition and comparison of two CBCT scans. The accuracy and reproducibility of CBCT superimposition on the anterior cranial base or the zygomatic arches using voxel based image registration was tested in this study. 16 pairs of 3D CBCT models were constructed from pre and post treatment CBCT scans of 16 adult dysgnathic patients. Each pair was registered on the anterior cranial base three times and on the left zygomatic arch twice. Following each superimposition, the mean absolute distances between the 2 models were calculated at 4 regions: anterior cranial base, forehead, left and right zygomatic arches. The mean distances between the models ranged from 0.2 to 0.37 mm (SD 0.08-0.16 for the anterior cranial base registration and from 0.2 to 0.45 mm (SD 0.09-0.27 for the zygomatic arch registration. The mean differences between the two registration zones ranged between 0.12 to 0.19 mm at the 4 regions. Voxel based image registration on both zones could be considered as an accurate and a reproducible method for CBCT superimposition. The left zygomatic arch could be used as a stable structure for the superimposition of smaller field of view CBCT scans where the anterior cranial base is not visible.

  7. Adaptation and Validation of QUick, Easy, New, CHEap, and Reproducible (QUENCHER) Antioxidant Capacity Assays in Model Products Obtained from Residual Wine Pomace.

    Science.gov (United States)

    Del Pino-García, Raquel; García-Lomillo, Javier; Rivero-Pérez, María D; González-SanJosé, María L; Muñiz, Pilar

    2015-08-12

    Evaluation of the total antioxidant capacity of solid matrices without extraction steps is a very interesting alternative for food researchers and also for food industries. These methodologies have been denominated QUENCHER from QUick, Easy, New, CHEap, and Reproducible assays. To demonstrate and highlight the validity of QUENCHER (Q) methods, values of Q-method validation were showed for the first time, and they were tested with products of well-known different chemical properties. Furthermore, new QUENCHER assays to measure scavenging capacity against superoxide, hydroxyl, and lipid peroxyl radicals were developed. Calibration models showed good linearity (R(2) > 0.995), proportionality and precision (CV antioxidant capacity values significantly different from those obtained with water. The dilution of samples with powdered cellulose was discouraged because possible interferences with some of the matrices analyzed may take place.

  8. Reproducible ion-current-based approach for 24-plex comparison of the tissue proteomes of hibernating versus normal myocardium in swine models.

    Science.gov (United States)

    Qu, Jun; Young, Rebeccah; Page, Brian J; Shen, Xiaomeng; Tata, Nazneen; Li, Jun; Duan, Xiaotao; Fallavollita, James A; Canty, John M

    2014-05-02

    Hibernating myocardium is an adaptive response to repetitive myocardial ischemia that is clinically common, but the mechanism of adaptation is poorly understood. Here we compared the proteomes of hibernating versus normal myocardium in a porcine model with 24 biological replicates. Using the ion-current-based proteomic strategy optimized in this study to expand upon previous proteomic work, we identified differentially expressed proteins in new molecular pathways of cardiovascular interest. The methodological strategy includes efficient extraction with detergent cocktail; precipitation/digestion procedure with high, quantitative peptide recovery; reproducible nano-LC/MS analysis on a long, heated column packed with small particles; and quantification based on ion-current peak areas. Under the optimized conditions, high efficiency and reproducibility were achieved for each step, which enabled a reliable comparison of 24 the myocardial samples. To achieve confident discovery of differentially regulated proteins in hibernating myocardium, we used highly stringent criteria to define "quantifiable proteins". These included the filtering criteria of low peptide FDR and S/N > 10 for peptide ion currents, and each protein was quantified independently from ≥2 distinct peptides. For a broad methodological validation, the quantitative results were compared with a parallel, well-validated 2D-DIGE analysis of the same model. Excellent agreement between the two orthogonal methods was observed (R = 0.74), and the ion-current-based method quantified almost one order of magnitude more proteins. In hibernating myocardium, 225 significantly altered proteins were discovered with a low false-discovery rate (∼3%). These proteins are involved in biological processes including metabolism, apoptosis, stress response, contraction, cytoskeleton, transcription, and translation. This provides compelling evidence that hibernating myocardium adapts to chronic ischemia. The major metabolic

  9. Compliant bipedal model with the center of pressure excursion associated with oscillatory behavior of the center of mass reproduces the human gait dynamics.

    Science.gov (United States)

    Jung, Chang Keun; Park, Sukyung

    2014-01-03

    Although the compliant bipedal model could reproduce qualitative ground reaction force (GRF) of human walking, the model with a fixed pivot showed overestimations in stance leg rotation and the ratio of horizontal to vertical GRF. The human walking data showed a continuous forward progression of the center of pressure (CoP) during the stance phase and the suspension of the CoP near the forefoot before the onset of step transition. To better describe human gait dynamics with a minimal expense of model complexity, we proposed a compliant bipedal model with the accelerated pivot which associated the CoP excursion with the oscillatory behavior of the center of mass (CoM) with the existing simulation parameter and leg stiffness. Owing to the pivot acceleration defined to emulate human CoP profile, the arrival of the CoP at the limit of the stance foot over the single stance duration initiated the step-to-step transition. The proposed model showed an improved match of walking data. As the forward motion of CoM during single stance was partly accounted by forward pivot translation, the previously overestimated rotation of the stance leg was reduced and the corresponding horizontal GRF became closer to human data. The walking solutions of the model ranged over higher speed ranges (~1.7 m/s) than those of the fixed pivoted compliant bipedal model (~1.5m/s) and exhibited other gait parameters, such as touchdown angle, step length and step frequency, comparable to the experimental observations. The good matches between the model and experimental GRF data imply that the continuous pivot acceleration associated with CoM oscillatory behavior could serve as a useful framework of bipedal model.

  10. Reproducible research in palaeomagnetism

    Science.gov (United States)

    Lurcock, Pontus; Florindo, Fabio

    2015-04-01

    The reproducibility of research findings is attracting increasing attention across all scientific disciplines. In palaeomagnetism as elsewhere, computer-based analysis techniques are becoming more commonplace, complex, and diverse. Analyses can often be difficult to reproduce from scratch, both for the original researchers and for others seeking to build on the work. We present a palaeomagnetic plotting and analysis program designed to make reproducibility easier. Part of the problem is the divide between interactive and scripted (batch) analysis programs. An interactive desktop program with a graphical interface is a powerful tool for exploring data and iteratively refining analyses, but usually cannot operate without human interaction. This makes it impossible to re-run an analysis automatically, or to integrate it into a larger automated scientific workflow - for example, a script to generate figures and tables for a paper. In some cases the parameters of the analysis process itself are not saved explicitly, making it hard to repeat or improve the analysis even with human interaction. Conversely, non-interactive batch tools can be controlled by pre-written scripts and configuration files, allowing an analysis to be 'replayed' automatically from the raw data. However, this advantage comes at the expense of exploratory capability: iteratively improving an analysis entails a time-consuming cycle of editing scripts, running them, and viewing the output. Batch tools also tend to require more computer expertise from their users. PuffinPlot is a palaeomagnetic plotting and analysis program which aims to bridge this gap. First released in 2012, it offers both an interactive, user-friendly desktop interface and a batch scripting interface, both making use of the same core library of palaeomagnetic functions. We present new improvements to the program that help to integrate the interactive and batch approaches, allowing an analysis to be interactively explored and refined

  11. Can a Dusty Warm Absorber Model Reproduce the Soft X-ray Spectra of MCG-6-30-15 and Mrk 766?

    CERN Document Server

    Sako, M; Branduardi-Raymont, G; Kaastra, J S; Brinkman, A C; Page, M J; Behar, E; Paerels, F B S; Kinkhabwala, A; Liedahl, D A; Den Herder, J W A

    2003-01-01

    XMM-Newton RGS spectra of MCG-6-30-15 and Mrk 766 exhibit complex discrete structure, which was interpreted in a paper by Branduardi-Raymont et al. (2001) as evidence for the existence of relativistically broadened Lyman alpha emission from carbon, nitrogen, and oxygen, produced in the inner-most regions of an accretion disk around a Kerr black hole. This suggestion was subsequently criticized in a paper by Lee et al. (2001), who argued that for MCG-6-30-15, the Chandra HETG spectrum, which is partially overlapping the RGS in spectral coverage, is adequately fit by a dusty warm absorber model, with no relativistic line emission. We present a reanalysis of the original RGS data sets in terms of the Lee et al. (2001) model, and demonstrate that spectral models consisting of a smooth continuum with ionized and dust absorption alone cannot reproduce the RGS spectra of both objects. The original relativistic line model with warm absorption proposed by Branduardi-Raymont et al. (2001) provides a superior fit to the...

  12. 4D-Imaging of the lung: reproducibility of lesion size and displacement on helical CT, MRI, and cone beam CT in a ventilated ex vivo system.

    Science.gov (United States)

    Biederer, Juergen; Dinkel, Julien; Remmert, Gregor; Jetter, Siri; Nill, Simeon; Moser, Torsten; Bendl, Rolf; Thierfelder, Carsten; Fabel, Michael; Oelfke, Uwe; Bock, Michael; Plathow, Christian; Bolte, Hendrik; Welzel, Thomas; Hoffmann, Beata; Hartmann, Günter; Schlegel, Wolfgang; Debus, Jürgen; Heller, Martin; Kauczor, Hans-Ulrich

    2009-03-01

    Four-dimensional (4D) imaging is a key to motion-adapted radiotherapy of lung tumors. We evaluated in a ventilated ex vivo system how size and displacement of artificial pulmonary nodules are reproduced with helical 4D-CT, 4D-MRI, and linac-integrated cone beam CT (CBCT). Four porcine lungs with 18 agarose nodules (mean diameters 1.3-1.9 cm), were ventilated inside a chest phantom at 8/min and subject to 4D-CT (collimation 24 x 1.2 mm, pitch 0.1, slice/increment 24 x 10(2)/1.5/0.8 mm, pitch 0.1, temporal resolution 0.5 s), 4D-MRI (echo-shared dynamic three-dimensional-flash; repetition/echo time 2.13/0.72 ms, voxel size 2.7 x 2.7 x 4.0 mm, temporal resolution 1.4 s) and linac-integrated 4D-CBCT (720 projections, 3-min rotation, temporal resolution approximately 1 s). Static CT without respiration served as control. Three observers recorded lesion size (RECIST-diameters x/y/z) and axial displacement. Interobserver- and interphase-variation coefficients (IO/IP VC) of measurements indicated reproducibility. Mean x/y/z lesion diameters in cm were equal on static and dynamic CT (1.88/1.87; 1.30/1.39; 1.71/1.73; p > 0.05), but appeared larger on MRI and CBCT (2.06/1.95 [p CT]; 1.47/1.28 [MRI vs. CT/CBCT p CT vs. CBCT p CT), 2.29-4.48% (4D-CT); 5.44-6.22% (MRI) and 4.86-6.97% (CBCT). Interphase-VC for lesion sizes ranged from 2.28% (4D-CT) to 10.0% (CBCT). Mean displacement in cm decreased from static CT (1.65) to 4D-CT (1.40), CBCT (1.23) and MRI (1.16). Lesion sizes are exactly reproduced with 4D-CT but overestimated on 4D-MRI and CBCT with a larger variability due to limited temporal and spatial resolution. All 4D-modalities underestimate lesion displacement.

  13. Modelling Railway Interlocking Systems

    DEFF Research Database (Denmark)

    Lindegaard, Morten Peter; Viuf, P.; Haxthausen, Anne Elisabeth

    2000-01-01

    In this report we present a model of interlocking systems, and describe how the model may be validated by simulation. Station topologies are modelled by graphs in which the nodes denote track segments, and the edges denote connectivity for train traÆc. Points and signals are modelled by annotatio...

  14. Reproducing the observed energy-dependent structure of Earth's electron radiation belts during storm recovery with an event-specific diffusion model

    Science.gov (United States)

    Ripoll, J.-F.; Reeves, G. D.; Cunningham, G. S.; Loridan, V.; Denton, M.; Santolík, O.; Kurth, W. S.; Kletzing, C. A.; Turner, D. L.; Henderson, M. G.; Ukhorskiy, A. Y.

    2016-06-01

    We present dynamic simulations of energy-dependent losses in the radiation belt "slot region" and the formation of the two-belt structure for the quiet days after the 1 March storm. The simulations combine radial diffusion with a realistic scattering model, based data-driven spatially and temporally resolved whistler-mode hiss wave observations from the Van Allen Probes satellites. The simulations reproduce Van Allen Probes observations for all energies and L shells (2-6) including (a) the strong energy dependence to the radiation belt dynamics (b) an energy-dependent outer boundary to the inner zone that extends to higher L shells at lower energies and (c) an "S-shaped" energy-dependent inner boundary to the outer zone that results from the competition between diffusive radial transport and losses. We find that the characteristic energy-dependent structure of the radiation belts and slot region is dynamic and can be formed gradually in ~15 days, although the "S shape" can also be reproduced by assuming equilibrium conditions. The highest-energy electrons (E > 300 keV) of the inner region of the outer belt (L ~ 4-5) also constantly decay, demonstrating that hiss wave scattering affects the outer belt during times of extended plasmasphere. Through these simulations, we explain the full structure in energy and L shell of the belts and the slot formation by hiss scattering during storm recovery. We show the power and complexity of looking dynamically at the effects over all energies and L shells and the need for using data-driven and event-specific conditions.

  15. SU-E-J-171: Evaluation of Cervical Spine and Mandible Reproducibility of the CDR Mayo Mold and Civco Type-S Head and Neck Immobilization Systems.

    Science.gov (United States)

    Chungbin, S

    2012-06-01

    To evaluate the cervical spine (c-spine) and mandible reproducibility of the CDR Mayo Mold and Civco Type-S head and neck immobilization system using Mosaiq Setup Intelligence Curve Image Registration Methods: Patients were immobilized with either the Mayo Mold or Civco Type-S head and neck immobilization systems. Using curve image registration tools in Mosaiq, the c-spine and mandible were outlined. For each lateral image, two separate image registrations were performed using an initial kV image as reference - 1) c-spine only 2) mandible only. To evaluate the relative difference between the c-spine and mandible position, the mandible image registration results were subtracted from the c-spine image registration results. To evaluate whether the initial difference between the planning CT and the first kV setup image is larger than subsequent daily imaging variations, the difference in the image registration of the DRR was compared to the variation in subsequent image registrations. The degree of neck flexion was determined by observing the amount of mismatch between the upper and lower cervical spine after the pitch correction. During the first weeks of treatment, there was minimal difference in the image registration results for both the c-spine and mandible individually, and in the relative difference between them. For neck flexion, the Mayo Mold system demonstrated 82.6% minimal difference and 3.8% significant difference between the alignment of upper and lower c spine, vs. 84% and 5.2% for the S frame. For some patients, there is a greater difference between the DRR and the initial kV image registration than the variation in registrations for subsequent daily imaging. Preliminary results indicate minimal difference in the c-spine and mandible reproducibility between the two immobilization systems during the first weeks of treatment. Further analysis of whether this minimal difference remains consistent throughout the entire course and treatment and with greater

  16. Reproducible research in vadose zone sciences

    Science.gov (United States)

    A significant portion of present-day soil and Earth science research is computational, involving complex data analysis pipelines, advanced mathematical and statistical models, and sophisticated computer codes. Opportunities for scientific progress are greatly diminished if reproducing and building o...

  17. Modelling the evolution of human trail systems

    Science.gov (United States)

    Helbing, Dirk; Keltsch, Joachim; Molnár, Péter

    1997-07-01

    Many human social phenomena, such as cooperation, the growth of settlements, traffic dynamics and pedestrian movement, appear to be accessible to mathematical descriptions that invoke self-organization. Here we develop a model of pedestrian motion to explore the evolution of trails in urban green spaces such as parks. Our aim is to address such questions as what the topological structures of these trail systems are, and whether optimal path systems can be predicted for urban planning. We use an `active walker' model that takes into account pedestrian motion and orientation and the concomitant feedbacks with the surrounding environment. Such models have previously been applied to the study of complex structure formation in physical, chemical and biological systems. We find that our model is able to reproduce many of the observed large-scale spatial features of trail systems.

  18. Reproducible statistical analysis with multiple languages

    DEFF Research Database (Denmark)

    Lenth, Russell; Højsgaard, Søren

    2011-01-01

    This paper describes the system for making reproducible statistical analyses. differs from other systems for reproducible analysis in several ways. The two main differences are: (1) Several statistics programs can be in used in the same document. (2) Documents can be prepared using OpenOffice or ......This paper describes the system for making reproducible statistical analyses. differs from other systems for reproducible analysis in several ways. The two main differences are: (1) Several statistics programs can be in used in the same document. (2) Documents can be prepared using Open......Office or \\LaTeX. The main part of this paper is an example showing how to use and together in an OpenOffice text document. The paper also contains some practical considerations on the use of literate programming in statistics....

  19. Roles of Chemical Complexity and Evolutionary Theory in Some Hepatic and Intestinal Enzymatic Systems in Chemical Reproducibility and Clinical Efficiency of Herbal Derivatives

    Directory of Open Access Journals (Sweden)

    Francesco Di Pierro

    2014-01-01

    Full Text Available Despite the great marketing success, most physicians attribute poor efficacy to herbals. This perception is due to two situations that are an integral part of the herbal topic. The first is the poor phytochemical reproducibility obtained during the production process of herbal extracts, as herbal extracts are not always standardized in the whole manufacturing process, but only in their titer. The second problem is linked to the evolution of important enzymatic systems: cytochromes and ABC proteins. They are both enzyme classes with detoxifying properties and seem to have evolved from the molecular mould provided by active plant substances. During the evolution, as still happens today, polyphenols, saponins, terpenes, and alkaloids were ingested together with food. They do not possess any nutritional value but seem to be provided with a potential pharmacological activity. Cytochromes and ABC proteins, which evolved over time to detoxify food from vegetable chemical “actives,” now seem to limit the action of herbal derivatives. The comprehension of these 2 events may explain the origin of the widespread scepticism of physicians about herbal medicine and suggests that, after correct herbal standardization, use of antagonists of cytochromes and ABC systems will make it possible to recover their pharmacological potential.

  20. Selected System Models

    Science.gov (United States)

    Schmidt-Eisenlohr, F.; Puñal, O.; Klagges, K.; Kirsche, M.

    Apart from the general issue of modeling the channel, the PHY and the MAC of wireless networks, there are specific modeling assumptions that are considered for different systems. In this chapter we consider three specific wireless standards and highlight modeling options for them. These are IEEE 802.11 (as example for wireless local area networks), IEEE 802.16 (as example for wireless metropolitan networks) and IEEE 802.15 (as example for body area networks). Each section on these three systems discusses also at the end a set of model implementations that are available today.

  1. Modeling cellular systems

    CERN Document Server

    Matthäus, Franziska; Pahle, Jürgen

    2017-01-01

    This contributed volume comprises research articles and reviews on topics connected to the mathematical modeling of cellular systems. These contributions cover signaling pathways, stochastic effects, cell motility and mechanics, pattern formation processes, as well as multi-scale approaches. All authors attended the workshop on "Modeling Cellular Systems" which took place in Heidelberg in October 2014. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.

  2. Multiscale Cloud System Modeling

    Science.gov (United States)

    Tao, Wei-Kuo; Moncrieff, Mitchell W.

    2009-01-01

    The central theme of this paper is to describe how cloud system resolving models (CRMs) of grid spacing approximately 1 km have been applied to various important problems in atmospheric science across a wide range of spatial and temporal scales and how these applications relate to other modeling approaches. A long-standing problem concerns the representation of organized precipitating convective cloud systems in weather and climate models. Since CRMs resolve the mesoscale to large scales of motion (i.e., 10 km to global) they explicitly address the cloud system problem. By explicitly representing organized convection, CRMs bypass restrictive assumptions associated with convective parameterization such as the scale gap between cumulus and large-scale motion. Dynamical models provide insight into the physical mechanisms involved with scale interaction and convective organization. Multiscale CRMs simulate convective cloud systems in computational domains up to global and have been applied in place of contemporary convective parameterizations in global models. Multiscale CRMs pose a new challenge for model validation, which is met in an integrated approach involving CRMs, operational prediction systems, observational measurements, and dynamical models in a new international project: the Year of Tropical Convection, which has an emphasis on organized tropical convection and its global effects.

  3. Dynamic Systems Modeling

    Directory of Open Access Journals (Sweden)

    Sorin Dan ŞANDOR

    2003-01-01

    Full Text Available System Dynamics was introduced by Jay W. Forrester in the 1960s. Since then the methodology was adopted in many areas of natural or social sciences. This article tries to present briefly how this methodology works, both as Systems Thinking and as Modelling with Vensim computer software.

  4. Modeling Sustainable Food Systems

    Science.gov (United States)

    Allen, Thomas; Prosperi, Paolo

    2016-05-01

    The processes underlying environmental, economic, and social unsustainability derive in part from the food system. Building sustainable food systems has become a predominating endeavor aiming to redirect our food systems and policies towards better-adjusted goals and improved societal welfare. Food systems are complex social-ecological systems involving multiple interactions between human and natural components. Policy needs to encourage public perception of humanity and nature as interdependent and interacting. The systemic nature of these interdependencies and interactions calls for systems approaches and integrated assessment tools. Identifying and modeling the intrinsic properties of the food system that will ensure its essential outcomes are maintained or enhanced over time and across generations, will help organizations and governmental institutions to track progress towards sustainability, and set policies that encourage positive transformations. This paper proposes a conceptual model that articulates crucial vulnerability and resilience factors to global environmental and socio-economic changes, postulating specific food and nutrition security issues as priority outcomes of food systems. By acknowledging the systemic nature of sustainability, this approach allows consideration of causal factor dynamics. In a stepwise approach, a logical application is schematized for three Mediterranean countries, namely Spain, France, and Italy.

  5. Modeling noisy resonant system response

    Science.gov (United States)

    Weber, Patrick Thomas; Walrath, David Edwin

    2017-02-01

    In this paper, a theory-based model replicating empirical acoustic resonant signals is presented and studied to understand sources of noise present in acoustic signals. Statistical properties of empirical signals are quantified and a noise amplitude parameter, which models frequency and amplitude-based noise, is created, defined, and presented. This theory-driven model isolates each phenomenon and allows for parameters to be independently studied. Using seven independent degrees of freedom, this model will accurately reproduce qualitative and quantitative properties measured from laboratory data. Results are presented and demonstrate success in replicating qualitative and quantitative properties of experimental data.

  6. Modeling Complex Systems

    CERN Document Server

    Boccara, Nino

    2010-01-01

    Modeling Complex Systems, 2nd Edition, explores the process of modeling complex systems, providing examples from such diverse fields as ecology, epidemiology, sociology, seismology, and economics. It illustrates how models of complex systems are built and provides indispensable mathematical tools for studying their dynamics. This vital introductory text is useful for advanced undergraduate students in various scientific disciplines, and serves as an important reference book for graduate students and young researchers. This enhanced second edition includes: . -recent research results and bibliographic references -extra footnotes which provide biographical information on cited scientists who have made significant contributions to the field -new and improved worked-out examples to aid a student’s comprehension of the content -exercises to challenge the reader and complement the material Nino Boccara is also the author of Essentials of Mathematica: With Applications to Mathematics and Physics (Springer, 2007).

  7. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods.

    Science.gov (United States)

    Evans, H R; Karmakharm, T; Lawson, M A; Walker, R E; Harris, W; Fellows, C; Huggins, I D; Richmond, P; Chantry, A D

    2016-02-01

    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (±19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (±0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images), it

  8. Distributed generation systems model

    Energy Technology Data Exchange (ETDEWEB)

    Barklund, C.R.

    1994-12-31

    A slide presentation is given on a distributed generation systems model developed at the Idaho National Engineering Laboratory, and its application to a situation within the Idaho Power Company`s service territory. The objectives of the work were to develop a screening model for distributed generation alternatives, to develop a better understanding of distributed generation as a utility resource, and to further INEL`s understanding of utility concerns in implementing technological change.

  9. Modeling the earth system

    Energy Technology Data Exchange (ETDEWEB)

    Ojima, D. [ed.

    1992-12-31

    The 1990 Global Change Institute (GCI) on Earth System Modeling is the third of a series organized by the Office for Interdisciplinary Earth Studies to look in depth at particular issues critical to developing a better understanding of the earth system. The 1990 GCI on Earth System Modeling was organized around three themes: defining critical gaps in the knowledge of the earth system, developing simplified working models, and validating comprehensive system models. This book is divided into three sections that reflect these themes. Each section begins with a set of background papers offering a brief tutorial on the subject, followed by working group reports developed during the institute. These reports summarize the joint ideas and recommendations of the participants and bring to bear the interdisciplinary perspective that imbued the institute. Since the conclusion of the 1990 Global Change Institute, research programs, nationally and internationally, have moved forward to implement a number of the recommendations made at the institute, and many of the participants have maintained collegial interactions to develop research projects addressing the needs identified during the two weeks in Snowmass.

  10. Evaluation of guidewire path reproducibility.

    Science.gov (United States)

    Schafer, Sebastian; Hoffmann, Kenneth R; Noël, Peter B; Ionita, Ciprian N; Dmochowski, Jacek

    2008-05-01

    The number of minimally invasive vascular interventions is increasing. In these interventions, a variety of devices are directed to and placed at the site of intervention. The device used in almost all of these interventions is the guidewire, acting as a monorail for all devices which are delivered to the intervention site. However, even with the guidewire in place, clinicians still experience difficulties during the interventions. As a first step toward understanding these difficulties and facilitating guidewire and device guidance, we have investigated the reproducibility of the final paths of the guidewire in vessel phantom models on different factors: user, materials and geometry. Three vessel phantoms (vessel diameters approximately 4 mm) were constructed having tortuousity similar to the internal carotid artery from silicon tubing and encased in Sylgard elastomer. Several trained users repeatedly passed two guidewires of different flexibility through the phantoms under pulsatile flow conditions. After the guidewire had been placed, rotational c-arm image sequences were acquired (9 in. II mode, 0.185 mm pixel size), and the phantom and guidewire were reconstructed (512(3), 0.288 mm voxel size). The reconstructed volumes were aligned. The centerlines of the guidewire and the phantom vessel were then determined using region-growing techniques. Guidewire paths appear similar across users but not across materials. The average root mean square difference of the repeated placement was 0.17 +/- 0.02 mm (plastic-coated guidewire), 0.73 +/- 0.55 mm (steel guidewire) and 1.15 +/- 0.65 mm (steel versus plastic-coated). For a given guidewire, these results indicate that the guidewire path is relatively reproducible in shape and position.

  11. Representing plant hydraulics in a global Earth system model.

    Science.gov (United States)

    Kennedy, D.; Gentine, P.

    2015-12-01

    Earth system models need improvement to reproduce observed seasonal and diurnal cycles of photosynthesis and respiration. Model water stress parameterizations lag behind the plant physiology literature. A plant hydraulics model is developed and deployed in a global Earth system model (NCAR CESM 1.2.2 with CLM 4.5). Assimilation and transpiration are attenuated according to literature cavitation curves. Water stress is evaluated based on plant functional type hydraulic parameters forced by soil moisture and atmospheric conditions. Resolving the plant water status allows for modelling divergent strategies for water stress. The case of isohydric versus anisohydric species is presented, showing that including plant hydraulic traits alter modelled photosynthesis and transpiration.

  12. Mechanical Systems, Classical Models

    CERN Document Server

    Teodorescu, Petre P

    2009-01-01

    This third volume completes the Work Mechanical Systems, Classical Models. The first two volumes dealt with particle dynamics and with discrete and continuous mechanical systems. The present volume studies analytical mechanics. Topics like Lagrangian and Hamiltonian mechanics, the Hamilton-Jacobi method, and a study of systems with separate variables are thoroughly discussed. Also included are variational principles and canonical transformations, integral invariants and exterior differential calculus, and particular attention is given to non-holonomic mechanical systems. The author explains in detail all important aspects of the science of mechanics, regarded as a natural science, and shows how they are useful in understanding important natural phenomena and solving problems of interest in applied and engineering sciences. Professor Teodorescu has spent more than fifty years as a Professor of Mechanics at the University of Bucharest and this book relies on the extensive literature on the subject as well as th...

  13. Production process reproducibility and product quality consistency of transient gene expression in HEK293 cells with anti-PD1 antibody as the model protein.

    Science.gov (United States)

    Ding, Kai; Han, Lei; Zong, Huifang; Chen, Junsheng; Zhang, Baohong; Zhu, Jianwei

    2017-03-01

    Demonstration of reproducibility and consistency of process and product quality is one of the most crucial issues in using transient gene expression (TGE) technology for biopharmaceutical development. In this study, we challenged the production consistency of TGE by expressing nine batches of recombinant IgG antibody in human embryonic kidney 293 cells to evaluate reproducibility including viable cell density, viability, apoptotic status, and antibody yield in cell culture supernatant. Product quality including isoelectric point, binding affinity, secondary structure, and thermal stability was assessed as well. In addition, major glycan forms of antibody from different batches of production were compared to demonstrate glycosylation consistency. Glycan compositions of the antibody harvested at different time periods were also measured to illustrate N-glycan distribution over the culture time. From the results, it has been demonstrated that different TGE batches are reproducible from lot to lot in overall cell growth, product yield, and product qualities including isoelectric point, binding affinity, secondary structure, and thermal stability. Furthermore, major N-glycan compositions are consistent among different TGE batches and conserved during cell culture time.

  14. Isolated heart models: cardiovascular system studies and technological advances.

    Science.gov (United States)

    Olejnickova, Veronika; Novakova, Marie; Provaznik, Ivo

    2015-07-01

    Isolated heart model is a relevant tool for cardiovascular system studies. It represents a highly reproducible model for studying broad spectrum of biochemical, physiological, morphological, and pharmaceutical parameters, including analysis of intrinsic heart mechanics, metabolism, and coronary vascular response. Results obtained in this model are under no influence of other organ systems, plasma concentration of hormones or ions and influence of autonomic nervous system. The review describes various isolated heart models, the modes of heart perfusion, and advantages and limitations of various experimental setups. It reports the improvements of perfusion setup according to Langendorff introduced by the authors.

  15. Contextual sensitivity in scientific reproducibility.

    Science.gov (United States)

    Van Bavel, Jay J; Mende-Siedlecki, Peter; Brady, William J; Reinero, Diego A

    2016-06-07

    In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher's degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed "hidden moderators") between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility.

  16. NEP systems model

    Science.gov (United States)

    George, Jeffrey A.

    A new nuclear electric propulsion (NEP) systems analysis code is discussed. The new code is modular and consists of a driver code and various subsystem models. The code models five different subsystems: (1) reactor/shield; (2) power conversion; (3) heat rejection; (4) power management and distribution (PMAD); and (5) thrusters. The code optimizes for the following design criteria: minimum mass; minimum radiator area; and low mass/low area. The code also optimizes the following parameters: separation distance; temperature ratio; pressure ratio; and transmission frequency. The discussion is presented in vugraph form.

  17. Spectral modelling of massive binary systems

    CERN Document Server

    Palate, Matthieu; Koenigsberger, Gloria; Moreno, Edmundo

    2013-01-01

    Aims: We simulate the spectra of massive binaries at different phases of the orbital cycle, accounting for the gravitational influence of the companion star on the shape and physical properties of the stellar surface. Methods: We used the Roche potential modified to account for radiation pressure to compute the stellar surface of close circular systems and we used the TIDES code for surface computation of eccentric systems. In both cases, we accounted for gravity darkening and mutual heating generated by irradiation to compute the surface temperature. We then interpolated NLTE plane-parallel atmosphere model spectra in a grid to obtain the local spectrum at each surface point. We finally summed all contributions, accounting for the Doppler shift, limb-darkening, and visibility to obtain the total synthetic spectrum. We computed different orbital phases and sets of physical and orbital parameters. Results: Our models predict line strength variations through the orbital cycle, but fail to completely reproduce t...

  18. National Energy Modeling System

    Energy Technology Data Exchange (ETDEWEB)

    Skinner, C.W. (Energy Information Administration, Washington, DC (United States))

    1993-01-01

    The Energy Information Administration is developing a new National Energy Modeling System to provide annual forecasts of energy supply, demand, and prices on a regional basis in the United States and, to a limited extent, in the rest of the world. The design for the system was based on a requirements analysis, a comparison of requirements with existing modeling capabilities, and a series of widely circulated issue papers defining the choices and tradeoffs for 13 key design decisions. An initial prototpye of the new NEMS was implemented in late 1992, with a more complete, operational version in 1993. NEMS is expected to provide EIA and other users with a greatly enhanced ability to illustrate quickly and effectively the effects of a wide range of energy policy proposals.

  19. Modeling Novo Nordisk Production Systems

    DEFF Research Database (Denmark)

    Miller, Thomas Dedenroth

    1997-01-01

    This report describes attributes of models and systems, and how models can be used for description of production systems. There are special attention on the 'Theory of Domains'.......This report describes attributes of models and systems, and how models can be used for description of production systems. There are special attention on the 'Theory of Domains'....

  20. Hyperbolic L2-modules with Reproducing Kernels

    Institute of Scientific and Technical Information of China (English)

    David EELPODE; Frank SOMMEN

    2006-01-01

    Abstract In this paper, the Dirac operator on the Klein model for the hyperbolic space is considered. A function space containing L2-functions on the sphere Sm-1 in (R)m, which are boundary values of solutions for this operator, is defined, and it is proved that this gives rise to a Hilbert module with a reproducing kernel.

  1. Measurement of Liver Iron Concentration by MRI Is Reproducible

    Directory of Open Access Journals (Sweden)

    José María Alústiza

    2015-01-01

    Full Text Available Purpose. The objectives were (i construction of a phantom to reproduce the behavior of iron overload in the liver by MRI and (ii assessment of the variability of a previously validated method to quantify liver iron concentration between different MRI devices using the phantom and patients. Materials and Methods. A phantom reproducing the liver/muscle ratios of two patients with intermediate and high iron overload. Nine patients with different levels of iron overload were studied in 4 multivendor devices and 8 of them were studied twice in the machine where the model was developed. The phantom was analysed in the same equipment and 14 times in the reference machine. Results. FeCl3 solutions containing 0.3, 0.5, 0.6, and 1.2 mg Fe/mL were chosen to generate the phantom. The average of the intramachine variability for patients was 10% and for the intermachines 8%. For the phantom the intramachine coefficient of variation was always below 0.1 and the average of intermachine variability was 10% for moderate and 5% for high iron overload. Conclusion. The phantom reproduces the behavior of patients with moderate or high iron overload. The proposed method of calculating liver iron concentration is reproducible in several different 1.5 T systems.

  2. Simulation of the hydrodynamic conditions of the eye to better reproduce the drug release from hydrogel contact lenses: experiments and modeling.

    Science.gov (United States)

    Pimenta, A F R; Valente, A; Pereira, J M C; Pereira, J C F; Filipe, H P; Mata, J L G; Colaço, R; Saramago, B; Serro, A P

    2016-12-01

    Currently, most in vitro drug release studies for ophthalmic applications are carried out in static sink conditions. Although this procedure is simple and useful to make comparative studies, it does not describe adequately the drug release kinetics in the eye, considering the small tear volume and flow rates found in vivo. In this work, a microfluidic cell was designed and used to mimic the continuous, volumetric flow rate of tear fluid and its low volume. The suitable operation of the cell, in terms of uniformity and symmetry of flux, was proved using a numerical model based in the Navier-Stokes and continuity equations. The release profile of a model system (a hydroxyethyl methacrylate-based hydrogel (HEMA/PVP) for soft contact lenses (SCLs) loaded with diclofenac) obtained with the microfluidic cell was compared with that obtained in static conditions, showing that the kinetics of release in dynamic conditions is slower. The application of the numerical model demonstrated that the designed cell can be used to simulate the drug release in the whole range of the human eye tear film volume and allowed to estimate the drug concentration in the volume of liquid in direct contact with the hydrogel. The knowledge of this concentration, which is significantly different from that measured in the experimental tests during the first hours of release, is critical to predict the toxicity of the drug release system and its in vivo efficacy. In conclusion, the use of the microfluidic cell in conjunction with the numerical model shall be a valuable tool to design and optimize new therapeutic drug-loaded SCLs.

  3. System of systems modeling and analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, James E.; Anderson, Dennis James; Longsine, Dennis E. (Intera, Inc., Austin, TX); Shirah, Donald N.

    2005-01-01

    This report documents the results of an LDRD program entitled 'System of Systems Modeling and Analysis' that was conducted during FY 2003 and FY 2004. Systems that themselves consist of multiple systems (referred to here as System of Systems or SoS) introduce a level of complexity to systems performance analysis and optimization that is not readily addressable by existing capabilities. The objective of the 'System of Systems Modeling and Analysis' project was to develop an integrated modeling and simulation environment that addresses the complex SoS modeling and analysis needs. The approach to meeting this objective involved two key efforts. First, a static analysis approach, called state modeling, has been developed that is useful for analyzing the average performance of systems over defined use conditions. The state modeling capability supports analysis and optimization of multiple systems and multiple performance measures or measures of effectiveness. The second effort involves time simulation which represents every system in the simulation using an encapsulated state model (State Model Object or SMO). The time simulation can analyze any number of systems including cross-platform dependencies and a detailed treatment of the logistics required to support the systems in a defined mission.

  4. Large barrier, highly uniform and reproducible Ni-Si/4H-SiC forward Schottky diode characteristics: testing the limits of Tung's model

    Science.gov (United States)

    Omar, Sabih U.; Sudarshan, Tangali S.; Rana, Tawhid A.; Song, Haizheng; Chandrashekhar, M. V. S.

    2014-07-01

    We report highly ideal (n < 1.1), uniform nickel silicide (Ni-Si)/SiC Schottky barrier (1.60-1.67 eV with a standard deviation <2.8%) diodes, fabricated on 4H-SiC epitaxial layers grown by chemical vapour deposition. The barrier height was constant over a wide epilayer doping range of 1014-1016 cm-3, apart from a slight decrease consistent with image force lowering. This remarkable uniformity was achieved by careful optimization of the annealing of the Schottky interface to minimize non-idealities that could lead to inhomogeneity. Tung's barrier inhomogeneity model was used to quantify the level of inhomogeneity in the optimized annealed diodes. The estimated ‘bulk’ barrier height (1.75 eV) was consistent with the Shockley-Mott limit for the Ni-Si/4H-SiC interface, implying an unpinned Fermi level. But the model was not useful to explain the poor ideality in unoptimized, as-deposited Schottky contacts (n = 1.6 - 2.5). We show analytically and numerically that only idealities n < 1.21 can be explained using Tung's model, irrespective of material system, indicating that the barrier height inhomogeneity is not the only cause of poor ideality in Schottky diodes. For explaining this highly non-ideal behaviour, other factors (e.g. interface traps, morphological defects, extrinsic impurities, etc) need to be considered.

  5. Three-feature model to reproduce the topology of citation networks and the effects from authors' visibility on their h-index

    CERN Document Server

    Amancio, Diego R; Costa, Luciano da F; 10.1016/j.joi.2012.02.005

    2013-01-01

    Various factors are believed to govern the selection of references in citation networks, but a precise, quantitative determination of their importance has remained elusive. In this paper, we show that three factors can account for the referencing pattern of citation networks for two topics, namely "graphenes" and "complex networks", thus allowing one to reproduce the topological features of the networks built with papers being the nodes and the edges established by citations. The most relevant factor was content similarity, while the other two - in-degree (i.e. citation counts) and {age of publication} had varying importance depending on the topic studied. This dependence indicates that additional factors could play a role. Indeed, by intuition one should expect the reputation (or visibility) of authors and/or institutions to affect the referencing pattern, and this is only indirectly considered via the in-degree that should correlate with such reputation. Because information on reputation is not readily avai...

  6. The Vienna LTE simulators - Enabling reproducibility in wireless communications research

    Directory of Open Access Journals (Sweden)

    Mehlführer Christian

    2011-01-01

    Full Text Available Abstract In this article, we introduce MATLAB-based link and system level simulation environments for UMTS Long-Term Evolution (LTE. The source codes of both simulators are available under an academic non-commercial use license, allowing researchers full access to standard-compliant simulation environments. Owing to the open source availability, the simulators enable reproducible research in wireless communications and comparison of novel algorithms. In this study, we explain how link and system level simulations are connected and show how the link level simulator serves as a reference to design the system level simulator. We compare the accuracy of the PHY modeling at system level by means of simulations performed both with bit-accurate link level simulations and PHY-model-based system level simulations. We highlight some of the currently most interesting research questions for LTE, and explain by some research examples how our simulators can be applied.

  7. A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model.

    Science.gov (United States)

    Rouger, Amélie; Remenant, Benoit; Prévost, Hervé; Zagorec, Monique

    2017-04-17

    Influenced by production and storage processes and by seasonal changes the diversity of meat products microbiota can be very variable. Because microbiotas influence meat quality and safety, characterizing and understanding their dynamics during processing and storage is important for proposing innovative and efficient storage conditions. Challenge tests are usually performed using meat from the same batch, inoculated at high levels with one or few strains. Such experiments do not reflect the true microbial situation, and the global ecosystem is not taken into account. Our purpose was to constitute live stocks of chicken meat microbiotas to create standard and reproducible ecosystems. We searched for the best method to collect contaminating bacterial communities from chicken cuts to store as frozen aliquots. We tested several methods to extract DNA of these stored communities for subsequent PCR amplification. We determined the best moment to collect bacteria in sufficient amounts during the product shelf life. Results showed that the rinsing method associated to the use of Mobio DNA extraction kit was the most reliable method to collect bacteria and obtain DNA for subsequent PCR amplification. Then, 23 different chicken meat microbiotas were collected using this procedure. Microbiota aliquots were stored at -80°C without important loss of viability. Their characterization by cultural methods confirmed the large variability (richness and abundance) of bacterial communities present on chicken cuts. Four of these bacterial communities were used to estimate their ability to regrow on meat matrices. Challenge tests performed on sterile matrices showed that these microbiotas were successfully inoculated and could overgrow the natural microbiota of chicken meat. They can therefore be used for performing reproducible challenge tests mimicking a true meat ecosystem and enabling the possibility to test the influence of various processing or storage conditions on complex meat

  8. Energy-dissipation-model for metallurgical multi-phase-systems

    Energy Technology Data Exchange (ETDEWEB)

    Mavrommatis, K.T. [Rheinisch-Westfaelische Technische Hochschule Aachen, Aachen (Germany)

    1996-12-31

    Entropy production in real processes is directly associated with the dissipation of energy. Both are potential measures for the proceed of irreversible processes taking place in metallurgical systems. Many of these processes in multi-phase-systems could then be modelled on the basis of the energy-dissipation associated with. As this entity can often be estimated using very simple assumptions from first principles, the evolution of an overall measure of systems behaviour can be studied constructing an energy-dissipation -based model of the system. In this work a formulation of this concept, the Energy-Dissipation-Model (EDM), for metallurgical multi-phase-systems is given. Special examples are studied to illustrate the concept, and benefits as well as the range of validity are shown. This concept might be understood as complement to usual CFD-modelling of complex systems on a more abstract level but reproducing essential attributes of complex metallurgical systems. (author)

  9. Modelling the Milky Way's globular cluster system

    Science.gov (United States)

    Binney, James; Wong, Leong Khim

    2017-05-01

    We construct a model for the Galactic globular cluster system based on a realistic gravitational potential and a distribution function (DF) analytic in the action integrals. The DF comprises disc and halo components whose functional forms resemble those recently used to describe the stellar discs and stellar halo. We determine the posterior distribution of our model parameters using a Bayesian approach. This gives us an understanding of how well the globular cluster data constrain our model. The favoured parameter values of the disc and halo DFs are similar to values previously obtained from fits to the stellar disc and halo, although the cluster halo system shows clearer rotation than does the stellar halo. Our model reproduces the generic features of the globular cluster system, namely the density profile, the mean rotation velocity and the fraction of metal-rich clusters. However, the data indicate either incompatibility between catalogued cluster distances and current estimates of distance to the Galactic Centre, or failure to identify clusters behind the bulge. As the data for our Galaxy's components increase in volume and precision over the next few years, it will be rewarding to revisit the present analysis.

  10. ECO-BIOLOGICAL SYSTEM MODELING

    Directory of Open Access Journals (Sweden)

    T. I. Burak

    2015-01-01

    Full Text Available The methodology for computer modeling of complex eco-biological models is presented in this paper. It is based on system approach of J. Forrester. Developed methodology is universal for complex ecological and biological systems. Modeling algorithm considers specialties of eco-biological systems and shows adequate and accurate results in practice. 

  11. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  12. Evaluation of multichannel reproduced sound

    DEFF Research Database (Denmark)

    Choisel, Sylvain; Wickelmaier, Florian Maria

    2007-01-01

    A study was conducted with the goal of quantifying auditory attributes which underlie listener preference for multichannel reproduced sound. Short musical excerpts were presented in mono, stereo and several multichannel formats to a panel of forty selected listeners. Scaling of auditory attributes...

  13. [Reproducibility of subjective refraction measurement].

    Science.gov (United States)

    Grein, H-J; Schmidt, O; Ritsche, A

    2014-11-01

    Reproducibility of subjective refraction measurement is limited by various factors. The main factors affecting reproducibility include the characteristics of the measurement method and of the subject and the examiner. This article presents the results of a study on this topic, focusing on the reproducibility of subjective refraction measurement in healthy eyes. The results of previous studies are not all presented in the same way by the respective authors and cannot be fully standardized without consulting the original scientific data. To the extent that they are comparable, the results of our study largely correspond largely with those of previous investigations: During repeated subjective refraction measurement, 95% of the deviation from the mean value was approximately ±0.2 D to ±0.65 D for the spherical equivalent and cylindrical power. The reproducibility of subjective refraction measurement in healthy eyes is limited, even under ideal conditions. Correct assessment of refraction results is only feasible after identifying individual variability. Several measurements are required. Refraction cannot be measured without a tolerance range. The English full-text version of this article is available at SpringerLink (under supplemental).

  14. Reproducible research in computational science.

    Science.gov (United States)

    Peng, Roger D

    2011-12-02

    Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.

  15. ReproPhylo: An Environment for Reproducible Phylogenomics

    OpenAIRE

    2015-01-01

    The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user interve...

  16. Mathematical System Theory and System Modeling

    OpenAIRE

    1980-01-01

    Choosing models related effectively to the questions to be addressed is a central issue in the craft of systems analysis. Since the mathematical description the analyst chooses constrains the types of issues he candeal with, it is important for these models to be selected so as to yield limitations that are acceptable in view of the questions the systems analysis seeks to answer. In this paper, the author gives an overview of the central issues affecting the question of model choice. To ...

  17. Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.

    Directory of Open Access Journals (Sweden)

    Andrea Maesani

    2015-11-01

    Full Text Available The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior.

  18. ITK: Enabling Reproducible Research and Open Science

    Directory of Open Access Journals (Sweden)

    Matthew Michael McCormick

    2014-02-01

    Full Text Available Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature.Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification.This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

  19. Accuracy and reproducibility of patient-specific hemodynamic models of stented intracranial aneurysms: report on the Virtual Intracranial Stenting Challenge 2011.

    Science.gov (United States)

    Cito, S; Geers, A J; Arroyo, M P; Palero, V R; Pallarés, J; Vernet, A; Blasco, J; San Román, L; Fu, W; Qiao, A; Janiga, G; Miura, Y; Ohta, M; Mendina, M; Usera, G; Frangi, A F

    2015-01-01

    Validation studies are prerequisites for computational fluid dynamics (CFD) simulations to be accepted as part of clinical decision-making. This paper reports on the 2011 edition of the Virtual Intracranial Stenting Challenge. The challenge aimed to assess the reproducibility with which research groups can simulate the velocity field in an intracranial aneurysm, both untreated and treated with five different configurations of high-porosity stents. Particle imaging velocimetry (PIV) measurements were obtained to validate the untreated velocity field. Six participants, totaling three CFD solvers, were provided with surface meshes of the vascular geometry and the deployed stent geometries, and flow rate boundary conditions for all inlets and outlets. As output, they were invited to submit an abstract to the 8th International Interdisciplinary Cerebrovascular Symposium 2011 (ICS'11), outlining their methods and giving their interpretation of the performance of each stent configuration. After the challenge, all CFD solutions were collected and analyzed. To quantitatively analyze the data, we calculated the root-mean-square error (RMSE) over uniformly distributed nodes on a plane slicing the main flow jet along its axis and normalized it with the maximum velocity on the slice of the untreated case (NRMSE). Good agreement was found between CFD and PIV with a NRMSE of 7.28%. Excellent agreement was found between CFD solutions, both untreated and treated. The maximum difference between any two groups (along a line perpendicular to the main flow jet) was 4.0 mm/s, i.e. 4.1% of the maximum velocity of the untreated case, and the average NRMSE was 0.47% (range 0.28-1.03%). In conclusion, given geometry and flow rates, research groups can accurately simulate the velocity field inside an intracranial aneurysm-as assessed by comparison with in vitro measurements-and find excellent agreement on the hemodynamic effect of different stent configurations.

  20. Reproducibility of NIF hohlraum measurements

    Science.gov (United States)

    Moody, J. D.; Ralph, J. E.; Turnbull, D. P.; Casey, D. T.; Albert, F.; Bachmann, B. L.; Doeppner, T.; Divol, L.; Grim, G. P.; Hoover, M.; Landen, O. L.; MacGowan, B. J.; Michel, P. A.; Moore, A. S.; Pino, J. E.; Schneider, M. B.; Tipton, R. E.; Smalyuk, V. A.; Strozzi, D. J.; Widmann, K.; Hohenberger, M.

    2015-11-01

    The strategy of experimentally ``tuning'' the implosion in a NIF hohlraum ignition target towards increasing hot-spot pressure, areal density of compressed fuel, and neutron yield relies on a level of experimental reproducibility. We examine the reproducibility of experimental measurements for a collection of 15 identical NIF hohlraum experiments. The measurements include incident laser power, backscattered optical power, x-ray measurements, hot-electron fraction and energy, and target characteristics. We use exact statistics to set 1-sigma confidence levels on the variations in each of the measurements. Of particular interest is the backscatter and laser-induced hot-spot locations on the hohlraum wall. Hohlraum implosion designs typically include variability specifications [S. W. Haan et al., Phys. Plasmas 18, 051001 (2011)]. We describe our findings and compare with the specifications. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

  1. Model Reduction of Hybrid Systems

    DEFF Research Database (Denmark)

    Shaker, Hamid Reza

    systems are derived in this thesis. The results are used for output feedback control of switched nonlinear systems. Model reduction of piecewise affine systems is also studied in this thesis. The proposed method is based on the reduction of linear subsystems inside the polytopes. The methods which......High-Technological solutions of today are characterized by complex dynamical models. A lot of these models have inherent hybrid/switching structure. Hybrid/switched systems are powerful models for distributed embedded systems design where discrete controls are applied to continuous processes...... of hybrid systems, designing controllers and implementations is very high so that the use of these models is limited in applications where the size of the state space is large. To cope with complexity, model reduction is a powerful technique. This thesis presents methods for model reduction and stability...

  2. Modelling on fuzzy control systems

    Institute of Scientific and Technical Information of China (English)

    LI; Hongxing(李洪兴); WANG; Jiayin(王加银); MIAO; Zhihong(苗志宏)

    2002-01-01

    A kind of modelling method for fuzzy control systems is first proposed here, which is calledmodelling method based on fuzzy inference (MMFI). It should be regarded as the third modelling method thatis different from two well-known modelling methods, that is, the first modelling method, mechanism modellingmethod (MMM), and the second modelling method, system identification modelling method (SlMM). Thismethod can, based on the interpolation mechanism on fuzzy logic system, transfer a group of fuzzy inferencerules describing a practice system into a kind of nonlinear differential equation with variable coefficients, calledHX equations, so that the mathematical model of the system can be obtained. This means that we solve thedifficult problem of how to get a model represented as differential equations on a complicated or fuzzy controlsystem.

  3. Energy System Modeling with REopt

    Energy Technology Data Exchange (ETDEWEB)

    Simpkins, Travis; Anderson, Kate; Cutler, Dylan; Olis, Dan; Elgqvist, Emma; DiOrio, Nick; Walker, Andy

    2016-07-15

    This poster details how REopt - NREL's software modeling platform for energy systems integration and optimization - can help to model energy systems. Some benefits of modeling with REopt include optimizing behind the meter storage for cost and resiliency, optimizing lab testing, optimizing dispatch of utility scale storage, and quantifying renewable energy impact on outage survivability.

  4. Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae

    Science.gov (United States)

    Cabrales-Arellano, Patricia; Islas-Flores, Tania; Thomé, Patricia E.

    2017-01-01

    Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian–dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical, and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, Lugol’s iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 μM indomethacin after six days of exposure, and 10–25 μM after 7 days. Strobilation under optimal conditions reached 80–100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae. PMID:28265497

  5. Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae

    Directory of Open Access Journals (Sweden)

    Patricia Cabrales-Arellano

    2017-03-01

    Full Text Available Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian–dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical, and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, Lugol’s iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 μM indomethacin after six days of exposure, and 10–25 μM after 7 days. Strobilation under optimal conditions reached 80–100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae.

  6. Shortening the learning curve in endoscopic endonasal skull base surgery: a reproducible polymer tumor model for the trans-sphenoidal trans-tubercular approach to retro-infundibular tumors.

    Science.gov (United States)

    Berhouma, Moncef; Baidya, Nishanta B; Ismaïl, Abdelhay A; Zhang, Jun; Ammirati, Mario

    2013-09-01

    Endoscopic endonasal skull base surgery attracts an increasing number of young neurosurgeons. This recent technique requires specific technical skills for the approaches to non-pituitary tumors (expanded endoscopic endonasal surgery). Actual residents' busy schedules carry the risk of compromising their laboratory training by limiting significantly the dedicated time for dissections. To enhance and shorten the learning curve in expanded endoscopic endonasal skull base surgery, we propose a reproducible model based on the implantation of a polymer via an intracranial route to provide a pathological retro-infundibular expansive lesion accessible to a virgin expanded endoscopic endonasal route, avoiding the ethically-debatable need to hundreds of pituitary cases in live patients before acquiring the desired skills. A polymer-based tumor model was implanted in 6 embalmed human heads via a microsurgical right fronto-temporal approach through the carotido-oculomotor cistern to mimic a retro-infundibular tumor. The tumor's position was verified by CT-scan. An endoscopic endonasal trans-sphenoidal trans-tubercular trans-planum approach was then carried out on a virgin route under neuronavigation tracking. Dissection of the tumor model from displaced surrounding neurovascular structures reproduced live surgery's sensations and challenges. Post-implantation CT-scan allowed the pre-removal assessment of the tumor insertion, its relationships as well as naso-sphenoidal anatomy in preparation of the endoscopic approach. Training on easily reproducible retro-infundibular approaches in a context of pathological distorted anatomy provides a unique opportunity to avoid the need for repetitive live surgeries to acquire skills for this kind of rare tumors, and may shorten the learning curve for endoscopic endonasal surgery. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Additive Manufacturing: Reproducibility of Metallic Parts

    Directory of Open Access Journals (Sweden)

    Konda Gokuldoss Prashanth

    2017-02-01

    Full Text Available The present study deals with the properties of five different metals/alloys (Al-12Si, Cu-10Sn and 316L—face centered cubic structure, CoCrMo and commercially pure Ti (CP-Ti—hexagonal closed packed structure fabricated by selective laser melting. The room temperature tensile properties of Al-12Si samples show good consistency in results within the experimental errors. Similar reproducible results were observed for sliding wear and corrosion experiments. The other metal/alloy systems also show repeatable tensile properties, with the tensile curves overlapping until the yield point. The curves may then follow the same path or show a marginal deviation (~10 MPa until they reach the ultimate tensile strength and a negligible difference in ductility levels (of ~0.3% is observed between the samples. The results show that selective laser melting is a reliable fabrication method to produce metallic materials with consistent and reproducible properties.

  8. 46 CFR 56.30-3 - Piping joints (reproduces 110).

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 2 2010-10-01 2010-10-01 false Piping joints (reproduces 110). 56.30-3 Section 56.30-3 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PIPING SYSTEMS AND APPURTENANCES Selection and Limitations of Piping Joints § 56.30-3 Piping joints (reproduces 110). The type...

  9. Characterization and optimization of experimental variables within a reproducible bladder encrustation model and in vitro evaluation of the efficacy of urease inhibitors for the prevention of medical device-related encrustation.

    Science.gov (United States)

    Jones, David S; Djokic, Jasmina; Gorman, Sean P

    2006-01-01

    This study presents a reproducible, cost-effective in vitro encrustation model and, furthermore, describes the effects of components of the artificial urine and the presence of agents that modify the action of urease on encrustation on commercially available ureteral stents. The encrustation model involved the use of small-volume reactors (700 mL) containing artificial urine and employing an orbital incubator (at 37 degrees C) to ensure controlled stirring. The artificial urine contained sources of calcium and magnesium (both as chlorides), albumin and urease. Alteration of the ratio (% w/w) of calcium salt to magnesium salt affected the mass of encrustation, with the greatest encrustation noted whenever magnesium was excluded from the artificial urine. Increasing the concentration of albumin, designed to mimic the presence of protein in urine, significantly decreased the mass of both calcium and magnesium encrustation until a plateau was observed. Finally, exclusion of urease from the artificial urine significantly reduced encrustation due to the indirect effects of this enzyme on pH. Inclusion of the urease inhibitor, acetohydroxamic acid, or urease substrates (methylurea or ethylurea) into the artificial medium markedly reduced encrustation on ureteral stents. In conclusion, this study has described the design of a reproducible, cost-effective in vitro encrustation model. Encrustation was markedly reduced on biomaterials by the inclusion of agents that modify the action of urease. These agents may, therefore, offer a novel clinical approach to the control of encrustation on urological medical devices.

  10. Modeling soft interface dominated systems

    NARCIS (Netherlands)

    Lamorgese, A.; Mauri, R.; Sagis, L.M.C.

    2017-01-01

    The two main continuum frameworks used for modeling the dynamics of soft multiphase systems are the Gibbs dividing surface model, and the diffuse interface model. In the former the interface is modeled as a two dimensional surface, and excess properties such as a surface density, or surface energy

  11. Validation of systems biology models

    NARCIS (Netherlands)

    Hasdemir, D.

    2015-01-01

    The paradigm shift from qualitative to quantitative analysis of biological systems brought a substantial number of modeling approaches to the stage of molecular biology research. These include but certainly are not limited to nonlinear kinetic models, static network models and models obtained by the

  12. Modeling of deterministic chaotic systems

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Y. [Department of Physics and Astronomy and Department of Mathematics, The University of Kansas, Lawrence, Kansas 66045 (United States); Grebogi, C. [Institute for Plasma Research, University of Maryland, College Park, Maryland 20742 (United States); Grebogi, C.; Kurths, J. [Department of Physics and Astrophysics, Universitaet Potsdam, Postfach 601553, D-14415 Potsdam (Germany)

    1999-03-01

    The success of deterministic modeling of a physical system relies on whether the solution of the model would approximate the dynamics of the actual system. When the system is chaotic, situations can arise where periodic orbits embedded in the chaotic set have distinct number of unstable directions and, as a consequence, no model of the system produces reasonably long trajectories that are realized by nature. We argue and present physical examples indicating that, in such a case, though the model is deterministic and low dimensional, statistical quantities can still be reliably computed. {copyright} {ital 1999} {ital The American Physical Society}

  13. Modelling of wastewater systems

    DEFF Research Database (Denmark)

    Bechmann, Henrik

    In this thesis, models of pollution fluxes in the inlet to 2 Danish wastewater treatment plants (WWTPs) as well as of suspended solids (SS) concentrations in the aeration tanks of an alternating WWTP and in the effluent from the aeration tanks are developed. The latter model is furthermore used...

  14. Traffic Modelling for Moving-Block Train Control System

    Institute of Scientific and Technical Information of China (English)

    TANG Tao; LI Ke-Ping

    2007-01-01

    This paper presents a new cellular automaton (CA) model for train control system simulation.In the proposed CA model,the driver reactions to train movements are captured by some updated rules.The space-time diagram of traffic flow and the trajectory of train movement is used to obtain insight into the characteristic behavior of railway traffic flow.A number of simulation results demonstrate that the proposed CA model can be successfully used for the simulations of railway traffic.Not only the characteristic behavior of railway traffic flow can be reproduced,but also the simulation values of the minimum time headway are close to the theoretical values.

  15. How well do environmental archives of atmospheric mercury deposition in the Arctic reproduce rates and trends depicted by atmospheric models and measurements?

    Science.gov (United States)

    Goodsite, M E; Outridge, P M; Christensen, J H; Dastoor, A; Muir, D; Travnikov, O; Wilson, S

    2013-05-01

    This review compares the reconstruction of atmospheric Hg deposition rates and historical trends over recent decades in the Arctic, inferred from Hg profiles in natural archives such as lake and marine sediments, peat bogs and glacial firn (permanent snowpack), against those predicted by three state-of-the-art atmospheric models based on global Hg emission inventories from 1990 onwards. Model veracity was first tested against atmospheric Hg measurements. Most of the natural archive and atmospheric data came from the Canadian-Greenland sectors of the Arctic, whereas spatial coverage was poor in other regions. In general, for the Canadian-Greenland Arctic, models provided good agreement with atmospheric gaseous elemental Hg (GEM) concentrations and trends measured instrumentally. However, there are few instrumented deposition data with which to test the model estimates of Hg deposition, and these data suggest models over-estimated deposition fluxes under Arctic conditions. Reconstructed GEM data from glacial firn on Greenland Summit showed the best agreement with the known decline in global Hg emissions after about 1980, and were corroborated by archived aerosol filter data from Resolute, Nunavut. The relatively stable or slowly declining firn and model GEM trends after 1990 were also corroborated by real-time instrument measurements at Alert, Nunavut, after 1995. However, Hg fluxes and trends in northern Canadian lake sediments and a southern Greenland peat bog did not exhibit good agreement with model predictions of atmospheric deposition since 1990, the Greenland firn GEM record, direct GEM measurements, or trends in global emissions since 1980. Various explanations are proposed to account for these discrepancies between atmosphere and archives, including problems with the accuracy of archive chronologies, climate-driven changes in Hg transfer rates from air to catchments, waters and subsequently into sediments, and post-depositional diagenesis in peat bogs

  16. Modelling Epistemic Systems

    CERN Document Server

    Martins, Andre C R

    2012-01-01

    In this Chapter, I will explore the use of modeling in order to understand how Science works. I will discuss the modeling of scientific communities, providing a general, non-comprehensive overview of existing models, with a focus on the use of the tools of Agent-Based Modeling and Opinion Dynamics. A special attention will be paid to models inspired by a Bayesian formalism of Opinion Dynamics. The objective of this exploration is to better understand the effect that different conditions might have on the reliability of the opinions of a scientific community. We will see that, by using artificial worlds as exploring grounds, we can prevent some epistemological problems with the definition of truth and obtain insights on the conditions that might cause the quest for more reliable knowledge to fail.

  17. From Numeric Models to Granular System Modeling

    Directory of Open Access Journals (Sweden)

    Witold Pedrycz

    2015-03-01

    To make this study self-contained, we briefly recall the key concepts of granular computing and demonstrate how this conceptual framework and its algorithmic fundamentals give rise to granular models. We discuss several representative formal setups used in describing and processing information granules including fuzzy sets, rough sets, and interval calculus. Key architectures of models dwell upon relationships among information granules. We demonstrate how information granularity and its optimization can be regarded as an important design asset to be exploited in system modeling and giving rise to granular models. With this regard, an important category of rule-based models along with their granular enrichments is studied in detail.

  18. Reproducibility of a reaming test

    DEFF Research Database (Denmark)

    Pilny, Lukas; Müller, Pavel; De Chiffre, Leonardo

    2014-01-01

    The reproducibility of a reaming test was analysed to document its applicability as a performance test for cutting fluids. Reaming tests were carried out on a drilling machine using HSS reamers. Workpiece material was an austenitic stainless steel, machined using 4.75 m•min−1 cutting speed and 0...... a built–up edge occurrence hindering a robust evaluation of cutting fluid performance, if the data evaluation is based on surface finish only. Measurements of hole geometry provide documentation to recognise systematic error distorting the performance test....

  19. Reproducibility of a reaming test

    DEFF Research Database (Denmark)

    Pilny, Lukas; Müller, Pavel; De Chiffre, Leonardo

    2012-01-01

    The reproducibility of a reaming test was analysed to document its applicability as a performance test for cutting fluids. Reaming tests were carried out on a drilling machine using HSS reamers. Workpiece material was an austenitic stainless steel, machined using 4.75 m∙min-1 cutting speed and 0...... a built-up edge occurrence hindering a robust evaluation of cutting fluid performance, if the data evaluation is based on surface finish only. Measurements of hole geometry provide documentation to recognize systematic error distorting the performance test....

  20. Pluralistic Modeling of Complex Systems

    CERN Document Server

    Helbing, Dirk

    2010-01-01

    The modeling of complex systems such as ecological or socio-economic systems can be very challenging. Although various modeling approaches exist, they are generally not compatible and mutually consistent, and empirical data often do not allow one to decide what model is the right one, the best one, or most appropriate one. Moreover, as the recent financial and economic crisis shows, relying on a single, idealized model can be very costly. This contribution tries to shed new light on problems that arise when complex systems are modeled. While the arguments can be transferred to many different systems, the related scientific challenges are illustrated for social, economic, and traffic systems. The contribution discusses issues that are sometimes overlooked and tries to overcome some frequent misunderstandings and controversies of the past. At the same time, it is highlighted how some long-standing scientific puzzles may be solved by considering non-linear models of heterogeneous agents with spatio-temporal inte...

  1. Accessibility and Reproducibility of Stable High-qmin Steady-State Scenarios by q-profile+βN Model Predictive Control

    Science.gov (United States)

    Schuster, E.; Wehner, W.; Holcomb, C. T.; Victor, B.; Ferron, J. R.; Luce, T. C.

    2016-10-01

    The capability of combined q-profile and βN control to enable access to and repeatability of steady-state scenarios for qmin > 1.4 discharges has been assessed in DIII-D experiments. To steer the plasma to the desired state, model predictive control (MPC) of both the q-profile and βN numerically solves successive optimization problems in real time over a receding time horizon by exploiting efficient quadratic programming techniques. A key advantage of this control approach is that it allows for explicit incorporation of state/input constraints to prevent the controller from driving the plasma outside of stability/performance limits and obtain, as closely as possible, steady state conditions. The enabler of this feedback-control approach is a control-oriented model capturing the dominant physics of the q-profile and βN responses to the available actuators. Experiments suggest that control-oriented model-based scenario planning in combination with MPC can play a crucial role in exploring stability limits of scenarios of interest. Supported by the US DOE under DE-SC0010661.

  2. Integrated Modeling Systems

    Science.gov (United States)

    1989-01-01

    American Economic Review , 71:1 (March 1981). 181 J.M. Jones and F. Zufryden. "Adding Explanatory Variables to a Consumer Purchase Behavior Model: An...McCall. "An Operational Measure of Liquidity," The American Economic Review , 761 (March 1986). WMSI Working Paper 329. 212 Nelson, R., R. Sarin, and R

  3. Robust Disaster Recovery System Model

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Highly security-critical system should possess features of continuous service. We present a new Robust Disaster Recovery System Model (RDRSM). Through strengthening the ability of safe communications, RDRSM guarantees the secure and reliable command on disaster recovery. Its self-supervision capability can monitor the integrality and security of disaster recovery system itself. By 2D and 3D real-time visible platform provided by GIS, GPS and RS, the model makes the using, management and maintenance of disaster recovery system easier. RDRSM possesses predominant features of security, robustness and controllability. And it can be applied to highly security-critical environments such as E-government and bank. Conducted by RDRSM, an important E-government disaster recovery system has been constructed successfully. The feasibility of this model is verified by practice. We especially emphasize the significance of some components of the model, such as risk assessment, disaster recovery planning, system supervision and robust communication support.

  4. Mechanical Systems, Classical Models

    CERN Document Server

    Teodorescu, Petre P

    2007-01-01

    All phenomena in nature are characterized by motion; this is an essential property of matter, having infinitely many aspects. Motion can be mechanical, physical, chemical or biological, leading to various sciences of nature, mechanics being one of them. Mechanics deals with the objective laws of mechanical motion of bodies, the simplest form of motion. In the study of a science of nature mathematics plays an important role. Mechanics is the first science of nature which was expressed in terms of mathematics by considering various mathematical models, associated to phenomena of the surrounding nature. Thus, its development was influenced by the use of a strong mathematical tool; on the other hand, we must observe that mechanics also influenced the introduction and the development of many mathematical notions. In this respect, the guideline of the present book is precisely the mathematical model of mechanics. A special accent is put on the solving methodology as well as on the mathematical tools used; vectors, ...

  5. Open and reproducible global land use classification

    Science.gov (United States)

    Nüst, Daniel; Václavík, Tomáš; Pross, Benjamin

    2015-04-01

    Researchers led by the Helmholtz Centre for Environmental research (UFZ) developed a new world map of land use systems based on over 30 diverse indicators (http://geoportal.glues.geo.tu-dresden.de/stories/landsystemarchetypes.html) of land use intensity, climate and environmental and socioeconomic factors. They identified twelve land system archetypes (LSA) using a data-driven classification algorithm (self-organizing maps) to assess global impacts of land use on the environment, and found unexpected similarities across global regions. We present how the algorithm behind this analysis can be published as an executable web process using 52°North WPS4R (https://wiki.52north.org/bin/view/Geostatistics/WPS4R) within the GLUES project (http://modul-a.nachhaltiges-landmanagement.de/en/scientific-coordination-glues/). WPS4R is an open source collaboration platform for researchers, analysts and software developers to publish R scripts (http://www.r-project.org/) as a geo-enabled OGC Web Processing Service (WPS) process. The interoperable interface to call the geoprocess allows both reproducibility of the analysis and integration of user data without knowledge about web services or classification algorithms. The open platform allows everybody to replicate the analysis in their own environments. The LSA WPS process has several input parameters, which can be changed via a simple web interface. The input parameters are used to configure both the WPS environment and the LSA algorithm itself. The encapsulation as a web process allows integration of non-public datasets, while at the same time the publication requires a well-defined documentation of the analysis. We demonstrate this platform specifically to domain scientists and show how reproducibility and open source publication of analyses can be enhanced. We also discuss future extensions of the reproducible land use classification, such as the possibility for users to enter their own areas of interest to the system and

  6. IGSN at Work in the Land Down Under: Exploiting an International Sample Identifier System to Enhance Reproducibility of Australian Geochemcial and Geochronological Data.

    Science.gov (United States)

    Bastrakova, I.; Klump, J. F.; McInnes, B.; Wyborn, L. A.; Brown, A.

    2015-12-01

    The International Geo-Sample Number (IGSN) provides a globally unique identifier for physical samples used to generate analytical data. This unique identifier provides the ability to link each physical sample to any analytical data undertaken on that sample, as well as to any publications derived from any data derived on the sample. IGSN is particularly important for geochemical and geochronological data, where numerous analytical techniques can be undertaken at multiple analytical facilities not only on the parent rock sample itself, but also on derived sample splits and mineral separates. Australia now has three agencies implementing IGSN: Geoscience Australia, CSIRO and Curtin University. All three have now combined into a single project, funded by the Australian Research Data Services program, to better coordinate the implementation of IGSN in Australia, in particular how these agencies allocate IGSN identifiers. The project will register samples from pilot applications in each agency including the CSIRO National Collection of Mineral Spectra database, the Geoscience Australia sample collection, and the Digital Mineral Library of the John De Laeter Centre for Isotope Research at Curtin University. These local agency catalogues will then be aggregated into an Australian portal, which will ultimately be expanded for all geoscience specimens. The development of this portal will also involve developing a common core metadata schema for the description of Australian geoscience specimens, as well as formulating agreed governance models for registering Australian samples. These developments aim to enable a common approach across Australian academic, research organisations and government agencies for the unique identification of geoscience specimens and any analytical data and/or publications derived from them. The emerging pattern of governance and technical collaboration established in Australia may also serve as a blueprint for similar collaborations internationally.

  7. Identification and modeling of discoverers in online social systems

    CERN Document Server

    Medo, Matus; Zeng, An; Zhang, Yi-Cheng

    2015-01-01

    The dynamics of individuals is of essential importance for understanding the evolution of social systems. Most existing models assume that individuals in diverse systems, ranging from social networks to e-commerce, all tend to what is already popular. We develop an analytical time-aware framework which shows that when individuals make choices -- which item to buy, for example -- in online social systems, a small fraction of them is consistently successful in discovering popular items long before they actually become popular. We argue that these users, whom we refer to as discoverers, are fundamentally different from the previously known opinion leaders, influentials, and innovators. We use the proposed framework to demonstrate that discoverers are present in a wide range of systems. Once identified, they can be used to predict the future success of items. We propose a network model which reproduces the discovery patterns observed in the real data. Furthermore, data produced by the model pose a fundamental cha...

  8. Studies of Catalytic Model Systems

    DEFF Research Database (Denmark)

    Holse, Christian

    The overall topic of this thesis is within the field of catalysis, were model systems of different complexity have been studied utilizing a multipurpose Ultra High Vacuum chamber (UHV). The thesis falls in two different parts. First a simple model system in the form of a ruthenium single crystal...... is investigated. Second the development of a complex Cu/ZnO nanoparticle model system is described and gas-induced dynamical changes in the model system is investigated. The ruthenium crystal serves as an extremely simple model for studying CO dissociation which is the rate limiting step of the methanation...... process. The Ru(0 1 54) surface is studied by means of Scanning Tunneling Microscopy (STM), Temperature Programmed Desoprtion (TPD), and Oxygen Titration (OT) experiments. Real space evidence of periodic features on every second monatomic step is observed via STM when the a clean ruthenium surface...

  9. A Mouse Model That Reproduces the Developmental Pathways and Site Specificity of the Cancers Associated With the Human BRCA1 Mutation Carrier State.

    Science.gov (United States)

    Liu, Ying; Yen, Hai-Yun; Austria, Theresa; Pettersson, Jonas; Peti-Peterdi, Janos; Maxson, Robert; Widschwendter, Martin; Dubeau, Louis

    2015-10-01

    Predisposition to breast and extrauterine Müllerian carcinomas in BRCA1 mutation carriers is due to a combination of cell-autonomous consequences of BRCA1 inactivation on cell cycle homeostasis superimposed on cell-nonautonomous hormonal factors magnified by the effects of BRCA1 mutations on hormonal changes associated with the menstrual cycle. We used the Müllerian inhibiting substance type 2 receptor (Mis2r) promoter and a truncated form of the Follicle stimulating hormone receptor (Fshr) promoter to introduce conditional knockouts of Brca1 and p53 not only in mouse mammary and Müllerian epithelia, but also in organs that control the estrous cycle. Sixty percent of the double mutant mice developed invasive Müllerian and mammary carcinomas. Mice carrying heterozygous mutations in Brca1 and p53 also developed invasive tumors, albeit at a lesser (30%) rate, in which the wild type alleles were no longer present due to loss of heterozygosity. While mice carrying heterozygous mutations in both genes developed mammary tumors, none of the mice carrying only a heterozygous p53 mutation developed such tumors (P < 0.0001), attesting to a role for Brca1 mutations in tumor development. This mouse model is attractive to investigate cell-nonautonomous mechanisms associated with cancer predisposition in BRCA1 mutation carriers and to investigate the merit of chemo-preventive drugs targeting such mechanisms.

  10. A Mouse Model That Reproduces the Developmental Pathways and Site Specificity of the Cancers Associated With the Human BRCA1 Mutation Carrier State

    Directory of Open Access Journals (Sweden)

    Ying Liu

    2015-10-01

    Full Text Available Predisposition to breast and extrauterine Müllerian carcinomas in BRCA1 mutation carriers is due to a combination of cell-autonomous consequences of BRCA1 inactivation on cell cycle homeostasis superimposed on cell-nonautonomous hormonal factors magnified by the effects of BRCA1 mutations on hormonal changes associated with the menstrual cycle. We used the Müllerian inhibiting substance type 2 receptor (Mis2r promoter and a truncated form of the Follicle stimulating hormone receptor (Fshr promoter to introduce conditional knockouts of Brca1 and p53 not only in mouse mammary and Müllerian epithelia, but also in organs that control the estrous cycle. Sixty percent of the double mutant mice developed invasive Müllerian and mammary carcinomas. Mice carrying heterozygous mutations in Brca1 and p53 also developed invasive tumors, albeit at a lesser (30% rate, in which the wild type alleles were no longer present due to loss of heterozygosity. While mice carrying heterozygous mutations in both genes developed mammary tumors, none of the mice carrying only a heterozygous p53 mutation developed such tumors (P < 0.0001, attesting to a role for Brca1 mutations in tumor development. This mouse model is attractive to investigate cell-nonautonomous mechanisms associated with cancer predisposition in BRCA1 mutation carriers and to investigate the merit of chemo-preventive drugs targeting such mechanisms.

  11. Agent-based modeling of host-pathogen systems: The successes and challenges.

    Science.gov (United States)

    Bauer, Amy L; Beauchemin, Catherine A A; Perelson, Alan S

    2009-04-29

    Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based models relevant to host-pathogen systems and discuss their contributions to our understanding of biological processes. We then point out some limitations and challenges of agent-based models and encourage efforts towards reproducibility and model validation.

  12. Ultrasensitive, Specific, Recyclable, and Reproducible Detection of Lead Ions in Real Systems through a Polyadenine-Assisted, Surface-Enhanced Raman Scattering Silicon Chip.

    Science.gov (United States)

    Shi, Yu; Wang, Houyu; Jiang, Xiangxu; Sun, Bin; Song, Bin; Su, Yuanyuan; He, Yao

    2016-04-05

    It is of great significance to accurately and reliably detect trace lead(II) (Pb(2+)) ions, preferably at sub-nM level due to the possible long-term accumulation of Pb(2+) in the human body, which may cause serious threats to human health. However, a suitable Pb(2+) sensor meeting the demands is still scanty. Herein, we develop a polyadenine-assisted, surface-enhanced Raman scattering (SERS) silicon chip (0.5 cm × 0.5 cm) composed of core (Ag)-satellite (Au) nanoparticles (Ag-Au NPs)-decorated silicon wafers (Ag-Au NPs@Si) for high-performance Pb(2+) detection. Typically, strong SERS signals could be measured when DNAzyme conjugated on the SERS silicon chip is specifically activated by Pb(2+), cleaving the substrate strand into two free DNA strands. A good linearity exists between the normalized Raman intensities and the logarithmic concentrations of Pb(2+) ranging from 10 pM to 1 μM with a good correlation coefficient, R(2) of 0.997. Remarkably, Pb(2+) ions with a low concentration of 8.9 × 10(-12) M can be readily determined via the SERS silicon chip ascribed to its superior SERS enhancement, much lower than those (∼nM) reported by other SERS sensors. Additionally, the developed chip features good selectivity and recyclability (e.g., ∼11.1% loss of Raman intensity after three cycles). More importantly, the as-prepared chip can be used for accurate and reliable determination of unknown Pb(2+) ions in real systems including lake water, tap water and industrial wastewater, with the RSD value less than 12%.

  13. Relocatable Coastal Modeling System

    Science.gov (United States)

    2016-06-07

    These relationships are stored on a variable-resolution grid (illustrated in figure 1b below) with sampling of 1 degree in deep water (and in data...version is referred to as MODAS2.1, which is now operational at NAVO. The NOMADS interface is being replaced by a system-independent, web -based version...inside the user’s web browser plus Perl CGI scripts which ran on a webserver. This permitted the user to run MODAS (and POM and other modules as they are

  14. Repeatability and reproducibility of Population Viability Analysis (PVA and the implications for threatened species management

    Directory of Open Access Journals (Sweden)

    Clare Morrison

    2016-08-01

    Full Text Available Conservation triage focuses on prioritizing species, populations or habitats based on urgency, biodiversity benefits, recovery potential as well as cost. Population Viability Analysis (PVA is frequently used in population focused conservation prioritizations. The critical nature of many of these management decisions requires that PVA models are repeatable and reproducible to reliably rank species and/or populations quantitatively. This paper assessed the repeatability and reproducibility of a subset of previously published PVA models. We attempted to rerun baseline models from 90 publicly available PVA studies published between 2000-2012 using the two most common PVA modelling software programs, VORTEX and RAMAS-GIS. Forty percent (n = 36 failed, 50% (45 were both repeatable and reproducible, and 10% (9 had missing baseline models. Repeatability was not linked to taxa, IUCN category, PVA program version used, year published or the quality of publication outlet, suggesting that the problem is systemic within the discipline. Complete and systematic presentation of PVA parameters and results are needed to ensure that the scientific input into conservation planning is both robust and reliable, thereby increasing the chances of making decisions that are both beneficial and defensible. The implications for conservation triage may be far reaching if population viability models cannot be reproduced with confidence, thus undermining their intended value.

  15. Hydronic distribution system computer model

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, J.W.; Strasser, J.J.

    1994-10-01

    A computer model of a hot-water boiler and its associated hydronic thermal distribution loop has been developed at Brookhaven National Laboratory (BNL). It is intended to be incorporated as a submodel in a comprehensive model of residential-scale thermal distribution systems developed at Lawrence Berkeley. This will give the combined model the capability of modeling forced-air and hydronic distribution systems in the same house using the same supporting software. This report describes the development of the BNL hydronics model, initial results and internal consistency checks, and its intended relationship to the LBL model. A method of interacting with the LBL model that does not require physical integration of the two codes is described. This will provide capability now, with reduced up-front cost, as long as the number of runs required is not large.

  16. Data management system performance modeling

    Science.gov (United States)

    Kiser, Larry M.

    1993-01-01

    This paper discusses analytical techniques that have been used to gain a better understanding of the Space Station Freedom's (SSF's) Data Management System (DMS). The DMS is a complex, distributed, real-time computer system that has been redesigned numerous times. The implications of these redesigns have not been fully analyzed. This paper discusses the advantages and disadvantages for static analytical techniques such as Rate Monotonic Analysis (RMA) and also provides a rationale for dynamic modeling. Factors such as system architecture, processor utilization, bus architecture, queuing, etc. are well suited for analysis with a dynamic model. The significance of performance measures for a real-time system are discussed.

  17. Future Challenges of Modeling THMC Systems

    Science.gov (United States)

    Miller, S. A.; Heinze, T.; Hamidi, S.; Galvan, B.

    2014-12-01

    Fracture-fluid flow coupling is critical for understanding society-relevant energy sources such as Enhanced Geothermal Systems (EGS), hydrocarbon extraction via hydraulic fracture, and carbon capture and storage (CCS). Although fluid-rock interactions are one of the most important processes in lithospheric geodynamics, they are one of the most difficult to properly simulate because of the orders-of-magnitude changes in hydraulic properties at the onset of fracture or slip. These large-scale changes in hydraulic properties result in the locally rapid flow that is likely to react with their new surroundings. Advances in modeling these processes must properly modeling the evolution of fracture networks coupled to the hydraulic (and thermodynamic) properties within the advecting, over-pressured, and reactive system. Many THM simulators exist but with limited utility because their inherently low resolution do not allow for the development of evolving fracture networks. A promising approach to modeling is to develop algorithms written in the CUDA programming language and optimized for computations using the inherently parallel Graphics Processing Unit (GPU) computer architecture. We are developing such a model, with target resolutions on the order of 1000x1000x 500. This simulator models a pore-elastic-thermo-elastic-plastic rheology that includes hardening, softening, and damage, and coupled to a non-linear diffusion model of fluid pressure and a 2-phase fluid (water and gas). Both tensile and shear fractures evolve in response to far-field stresses, local stress perturbations associated with both shear and tensile fractures, and thermo-elastic and pore-elastic stresses. The advantage of this model over existing models is that the governing equations have been reformulated to run on a GPU cluster. Results from numerical experiments show that this approach has great potential to study fluid-rock interactions at all scales. In this talk, I summarize the progress to date

  18. National Energy Outlook Modelling System

    Energy Technology Data Exchange (ETDEWEB)

    Volkers, C.M. [ECN Policy Studies, Petten (Netherlands)

    2013-12-15

    For over 20 years, the Energy research Centre of the Netherlands (ECN) has been developing the National Energy Outlook Modelling System (NEOMS) for Energy projections and policy evaluations. NEOMS enables 12 energy models of ECN to exchange data and produce consistent and detailed results.

  19. ABSTRACT MODELS FOR SYSTEM VIRTUALIZATION

    Directory of Open Access Journals (Sweden)

    M. G. Koveshnikov

    2015-05-01

    Full Text Available The paper is dedicated to issues of system objects securing (system files and user system or application configuration files against unauthorized access including denial of service attacks. We have suggested the method and developed abstract system virtualization models, which are used toresearch attack scenarios for different virtualization modes. Estimation for system tools virtualization technology effectiveness is given. Suggested technology is based on redirection of access requests to system objects shared among access subjects. Whole and partial system virtualization modes have been modeled. The difference between them is the following: in the whole virtualization mode all copies of access system objects are created whereon subjects’ requests are redirected including corresponding application objects;in the partial virtualization mode corresponding copies are created only for part of a system, for example, only system objects for applications. Alternative solutions effectiveness is valued relating to different attack scenarios. We consider proprietary and approved technical solution which implements system virtualization method for Microsoft Windows OS family. Administrative simplicity and capabilities of correspondingly designed system objects security tools are illustrated on this example. Practical significance of the suggested security method has been confirmed.

  20. Aerodynamic and Mechanical System Modelling

    DEFF Research Database (Denmark)

    Jørgensen, Martin Felix

    This thesis deals with mechanical multibody-systems applied to the drivetrain of a 500 kW wind turbine. Particular focus has been on gearbox modelling of wind turbines. The main part of the present project involved programming multibody systems to investigate the connection between forces, moments...

  1. Experimental Modeling of Dynamic Systems

    DEFF Research Database (Denmark)

    Knudsen, Morten Haack

    2006-01-01

    An engineering course, Simulation and Experimental Modeling, has been developed that is based on a method for direct estimation of physical parameters in dynamic systems. Compared with classical system identification, the method appears to be easier to understand, apply, and combine with physical...

  2. Validation of a Perceptual Distraction Model in a Complex Personal Sound Zone System

    DEFF Research Database (Denmark)

    Rämö, Jussi; Marsh, Steven; Bech, Søren

    2016-01-01

    tested using more complex sound systems. A listening experiment was conducted to evaluate the performance of the model, using music target and speech interferer reproduced by a complex personal sound-zone system. The model was found to successfully predict the perceived distraction of a more complex......This paper evaluates a previously proposed perceptual model predicting user’s perceived distraction caused by interfering audio programmes. The distraction model was originally trained using a simple sound reproduction system for music-on-music interference situations and it has not been formally...... sound reproducing system with different target-interferer pairs than it was originally trained for. Thus, the model can be used as a tool for personal sound-zone evaluation and optimization tasks....

  3. In vivo models of multiple system atrophy.

    Science.gov (United States)

    Fernagut, Pierre-Olivier; Ghorayeb, Imad; Diguet, Elsa; Tison, François

    2005-08-01

    Multiple system atrophy (MSA) is a sporadic adult-onset neurodegenerative disorder of unknown etiology clinically characterized by a combination of parkinsonian, pyramidal, and cerebellar signs. Levodopa-unresponsive parkinsonism is present in 80% of MSA cases, and this dominant clinical presentation (MSA-P) is associated with a combined degeneration of the substantia nigra pars compacta and the striatum in anatomically related areas. The limited knowledge of the pathophysiology of MSA and the lack of therapeutic strategies prompted the development of lesion models reproducing striatonigral degeneration, the substrate of levodopa-unresponsive parkinsonism in MSA-P. This method was carried out first in rats with two different stereotaxic strategies using either two neurotoxins ("double toxin-double lesion") or a single neurotoxin ("single toxin-double lesion"). Double-lesioned rat models showed severe motor impairment compared to those with a single nigral or striatal lesion and helped to mimic different stages of the disease. Systemic models were also developed in mice and primates using the nigral toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and the striatal toxin 3-nitropropionic (3-NP). In mice, although MPTP reduced the subsequent sensitivity to 3-NP in a sequential lesion, simultaneous nigral and striatal insults were shown to exacerbate striatal damage. MPTP-treated monkeys displayed a significant worsening of parkinsonism and a loss of levodopa-responsiveness after the appearance of hindlimb dystonia and striatal lesion formation induced by subsequent 3-NP intoxication. The different species and intoxication paradigms used will be useful to investigate functional changes in substantia nigra and striatum and to define neuroprotective, neurorestorative, or symptomatic therapeutic strategies.

  4. An extensible analysable system model

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, Rene Rydhof

    2008-01-01

    , this does not hold for real physical systems. Approaches such as threat modelling try to target the formalisation of the real-world domain, but still are far from the rigid techniques available in security research. Many currently available approaches to assurance of critical infrastructure security...... allows for easy development of analyses for the abstracted systems. We briefly present one application of our approach, namely the analysis of systems for potential insider threats....

  5. A Neuron Model Based Ultralow Current Sensor System for Bioapplications

    Directory of Open Access Journals (Sweden)

    A. K. M. Arifuzzman

    2016-01-01

    Full Text Available An ultralow current sensor system based on the Izhikevich neuron model is presented in this paper. The Izhikevich neuron model has been used for its superior computational efficiency and greater biological plausibility over other well-known neuron spiking models. Of the many biological neuron spiking features, regular spiking, chattering, and neostriatal spiny projection spiking have been reproduced by adjusting the parameters associated with the model at hand. This paper also presents a modified interpretation of the regular spiking feature in which the firing pattern is similar to that of the regular spiking but with improved dynamic range offering. The sensor current ranges between 2 pA and 8 nA and exhibits linearity in the range of 0.9665 to 0.9989 for different spiking features. The efficacy of the sensor system in detecting low amount of current along with its high linearity attribute makes it very suitable for biomedical applications.

  6. Modeling Multi-Level Systems

    CERN Document Server

    Iordache, Octavian

    2011-01-01

    This book is devoted to modeling of multi-level complex systems, a challenging domain for engineers, researchers and entrepreneurs, confronted with the transition from learning and adaptability to evolvability and autonomy for technologies, devices and problem solving methods. Chapter 1 introduces the multi-scale and multi-level systems and highlights their presence in different domains of science and technology. Methodologies as, random systems, non-Archimedean analysis, category theory and specific techniques as model categorification and integrative closure, are presented in chapter 2. Chapters 3 and 4 describe polystochastic models, PSM, and their developments. Categorical formulation of integrative closure offers the general PSM framework which serves as a flexible guideline for a large variety of multi-level modeling problems. Focusing on chemical engineering, pharmaceutical and environmental case studies, the chapters 5 to 8 analyze mixing, turbulent dispersion and entropy production for multi-scale sy...

  7. A Low-Cost Anthropometric Walking Robot for Reproducing Gait Lab Data

    Directory of Open Access Journals (Sweden)

    Rogério Eduardo da Silva Santana

    2008-01-01

    Full Text Available Human gait analysis is one of the resources that may be used in the study and treatment of pathologies of the locomotive system. This paper deals with the modelling and control aspects of the design, construction and testing of a biped walking robot conceived to, in limited extents, reproduce the human gait. Robot dimensions have been chosen in order to guarantee anthropomorphic proportions and then to help health professionals in gait studies. The robot has been assembled with low-cost components and can reproduce, in an assisted way, real-gait patterns generated from data previously acquired in gait laboratories. Part of the simulated and experimental results are addressed to demonstrate the ability of the biped robot in reproducing normal and pathological human gait.

  8. Organ-on-a-Chip Technology for Reproducing Multiorgan Physiology.

    Science.gov (United States)

    Lee, Seung Hwan; Sung, Jong Hwan

    2017-09-25

    In the drug development process, the accurate prediction of drug efficacy and toxicity is important in order to reduce the cost, labor, and effort involved. For this purpose, conventional 2D cell culture models are used in the early phase of drug development. However, the differences between the in vitro and the in vivo systems have caused the failure of drugs in the later phase of the drug-development process. Therefore, there is a need for a novel in vitro model system that can provide accurate information for evaluating the drug efficacy and toxicity through a closer recapitulation of the in vivo system. Recently, the idea of using microtechnology for mimicking the microscale tissue environment has become widespread, leading to the development of "organ-on-a-chip." Furthermore, the system is further developed for realizing a multiorgan model for mimicking interactions between multiple organs. These advancements are still ongoing and are aimed at ultimately developing "body-on-a-chip" or "human-on-a-chip" devices for predicting the response of the whole body. This review summarizes recently developed organ-on-a-chip technologies, and their applications for reproducing multiorgan functions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. On The Reproducibility of Seasonal Land-surface Climate

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, T J

    2004-10-22

    The sensitivity of the continental seasonal climate to initial conditions is estimated from an ensemble of decadal simulations of an atmospheric general circulation model with the same specifications of radiative forcings and monthly ocean boundary conditions, but with different initial states of atmosphere and land. As measures of the ''reproducibility'' of continental climate for different initial conditions, spatio-temporal correlations are computed across paired realizations of eleven model land-surface variables in which the seasonal cycle is either included or excluded--the former case being pertinent to climate simulation, and the latter to seasonal anomaly prediction. It is found that the land-surface variables which include the seasonal cycle are impacted only marginally by changes in initial conditions; moreover, their seasonal climatologies exhibit high spatial reproducibility. In contrast, the reproducibility of a seasonal land-surface anomaly is generally low, although it is substantially higher in the Tropics; its spatial reproducibility also markedly fluctuates in tandem with warm and cold phases of the El Nino/Southern Oscillation. However, the overall degree of reproducibility depends strongly on the particular land-surface anomaly considered. It is also shown that the predictability of a land-surface anomaly implied by its reproducibility statistics is consistent with what is inferred from more conventional predictability metrics. Implications of these results for climate model intercomparison projects and for operational forecasts of seasonal continental climate also are elaborated.

  10. Distribution system modeling and analysis

    CERN Document Server

    Kersting, William H

    2002-01-01

    For decades, distribution engineers did not have the sophisticated tools developed for analyzing transmission systems-often they had only their instincts. Things have changed, and we now have computer programs that allow engineers to simulate, analyze, and optimize distribution systems. Powerful as these programs are, however, without a real understanding of the operating characteristics of a distribution system, engineers using the programs can easily make serious errors in their designs and operating procedures.Distribution System Modeling and Analysis helps prevent those errors. It gives re

  11. Stirling Engine Dynamic System Modeling

    Science.gov (United States)

    Nakis, Christopher G.

    2004-01-01

    The Thermo-Mechanical systems branch at the Glenn Research Center focuses a large amount time on Stirling engines. These engines will be used on missions where solar power is inefficient, especially in deep space. I work with Tim Regan and Ed Lewandowski who are currently developing and validating a mathematical model for the Stirling engines. This model incorporates all aspects of the system including, mechanical, electrical and thermodynamic components. Modeling is done through Simplorer, a program capable of running simulations of the model. Once created and then proven to be accurate, a model is used for developing new ideas for engine design. My largest specific project involves varying key parameters in the model and quantifying the results. This can all be done relatively trouble-free with the help of Simplorer. Once the model is complete, Simplorer will do all the necessary calculations. The more complicated part of this project is determining which parameters to vary. Finding key parameters depends on the potential for a value to be independently altered in the design. For example, a change in one dimension may lead to a proportional change to the rest of the model, and no real progress is made. Also, the ability for a changed value to have a substantial impact on the outputs of the system is important. Results will be condensed into graphs and tables with the purpose of better communication and understanding of the data. With the changing of these parameters, a more optimal design can be created without having to purchase or build any models. Also, hours and hours of results can be simulated in minutes. In the long run, using mathematical models can save time and money. Along with this project, I have many other smaller assignments throughout the summer. My main goal is to assist in the processes of model development, validation and testing.

  12. Prion pathogenesis is faithfully reproduced in cerebellar organotypic slice cultures.

    Directory of Open Access Journals (Sweden)

    Jeppe Falsig

    Full Text Available Prions cause neurodegeneration in vivo, yet prion-infected cultured cells do not show cytotoxicity. This has hampered mechanistic studies of prion-induced neurodegeneration. Here we report that prion-infected cultured organotypic cerebellar slices (COCS experienced progressive spongiform neurodegeneration closely reproducing prion disease, with three different prion strains giving rise to three distinct patterns of prion protein deposition. Neurodegeneration did not occur when PrP was genetically removed from neurons, and a comprehensive pharmacological screen indicated that neurodegeneration was abrogated by compounds known to antagonize prion replication. Prion infection of COCS and mice led to enhanced fodrin cleavage, suggesting the involvement of calpains or caspases in pathogenesis. Accordingly, neurotoxicity and fodrin cleavage were prevented by calpain inhibitors but not by caspase inhibitors, whereas prion replication proceeded unimpeded. Hence calpain inhibition can uncouple prion replication from its neurotoxic sequelae. These data validate COCS as a powerful model system that faithfully reproduces most morphological hallmarks of prion infections. The exquisite accessibility of COCS to pharmacological manipulations was instrumental in recognizing the role of calpains in neurotoxicity, and significantly extends the collection of tools necessary for rigorously dissecting prion pathogenesis.

  13. Kinetic Modeling of Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Petzold, Linda; Pettigrew, Michel F.

    2009-04-21

    The dynamics of how its constituent components interact define the spatio-temporal response of a natural system to stimuli. Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multiscale problems, and possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods, and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided.

  14. Collecting highly reproducible images to support dermatological medical diagnosis

    DEFF Research Database (Denmark)

    Gomez, David Delgado; Carstensen, Jens Michael; Ersbøll, Bjarne Kjær

    2006-01-01

    In this article, an integrated imaging system for acquisition of accurate standardized images is proposed. The system also aims at making highly reproducible images over time, so images taken at different times can be compared. The system is made up of an integrating intensity sphere illumination...

  15. Executive Information Systems' Multidimensional Models

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Executive Information Systems are design to improve the quality of strategic level of management in organization through a new type of technology and several techniques for extracting, transforming, processing, integrating and presenting data in such a way that the organizational knowledge filters can easily associate with this data and turn it into information for the organization. These technologies are known as Business Intelligence Tools. But in order to build analytic reports for Executive Information Systems (EIS in an organization we need to design a multidimensional model based on the business model from the organization. This paper presents some multidimensional models that can be used in EIS development and propose a new model that is suitable for strategic business requests.

  16. Numerical Modeling of Microelectrochemical Systems

    DEFF Research Database (Denmark)

    Adesokan, Bolaji James

    for the reactants in the bulk electrolyte that are traveling waves. The first paper presents the mathematical model which describes an electrochemical system and simulates an electroanalytical technique called cyclic voltammetry. The model is governed by a system of advection–diffusion equations with a nonlinear...... reaction term at the boundary. We investigate the effect of flow rates, scan rates, and concentration on the cyclic voltammetry. We establish that high flow rates lead to the reduced hysteresis in the cyclic voltammetry curves and increasing scan rates lead to more pronounced current peaks. The final part...... of the paper shows that the response current in a cyclic voltammetry increases proportionally to the electrolyte concentration. In the second paper we present an experiment of an electrochemical system in a microfluidc system and compare the result to the numerical solutions. We investigate how the position...

  17. The ternary sorption system U(VI)-phosphate-silica explained by spectroscopy and thermodynamic modelling

    Energy Technology Data Exchange (ETDEWEB)

    Foerstendorf, Harald; Stockmann, Madlen; Heim, Karsten; Mueller, Katharina; Brendler, Vinzenz [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Surface Processes; Comarmond, M.J.; Payne, T.E. [Australian Nuclear Science and Technology Organisation, Lucas Heights (Australia); Steudtner, Robin [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Inst. of Resource Ecology

    2017-06-01

    Spectroscopic data of sorption processes potentially provide direct impact on Surface Complexation Modelling (SCM) approaches. Based on spectroscopic data of the ternary sorption system U(VI)/phosphate/silica strongly suggesting the formation of a precipitate as the predominant surface process, SCM calculations accurately reproduced results from classical batch experiments.

  18. Remote sensing and simulation modelling for on-demand irrigation systems management

    NARCIS (Netherlands)

    D'Urso, G.; Menenti, M.; Santini, A.

    1996-01-01

    This paper describes a procedure for monitoring and improving the performance of on-demand irrigation networks, based on the integration of remote sensing techniques and simulation modelling of water flow in each component of the system. In order to adequately reproduce the actual operation of an on

  19. CFD Modeling of Flow and Ion Exchange Kinetics in a Rotating Bed Reactor System

    DEFF Research Database (Denmark)

    Larsson, Hilde Kristina; Schjøtt Andersen, Patrick Alexander; Byström, Emil

    2017-01-01

    be achieved by making the baffles deeper. Two-phase simulations were performed, which managed to reproduce the deflection of the gas–liquid interface in an unbaffled system. A chemical reaction was implemented in the model, describing the ion-exchange phenomena in the porous material using four different...

  20. Quark/gluon jet discrimination: a reproducible analysis using R

    CERN Document Server

    CERN. Geneva

    2017-01-01

    The power to discriminate between light-quark jets and gluon jets would have a huge impact on many searches for new physics at CERN and beyond. This talk will present a walk-through of the development of a prototype machine learning classifier for differentiating between quark and gluon jets at experiments like those at the Large Hadron Collider at CERN. A new fast feature selection method that combines information theory and graph analytics will be outlined. This method has found new variables that promise significant improvements in discrimination power. The prototype jet tagger is simple, interpretable, parsimonious, and computationally extremely cheap, and therefore might be suitable for use in trigger systems for real-time data processing. Nested stratified k-fold cross validation was used to generate robust estimates of model performance. The data analysis was performed entirely in the R statistical programming language, and is fully reproducible. The entire analysis workflow is data-driven, automated a...

  1. Reproducibility and reusability of scientific software

    Science.gov (United States)

    Shamir, Lior

    2017-01-01

    Information science and technology has been becoming an integral part of astronomy research, and due to the consistent growth in the size and impact of astronomical databases, that trend is bound to continue. While software is a vital part information systems and data analysis processes, in many cases the importance of the software and the standards of reporting on the use of source code has not yet elevated in the scientific communication process to the same level as other parts of the research. The purpose of the discussion is to examine the role of software in the scientific communication process in the light of transparency, reproducibility, and reusability of the research, as well as discussing software in astronomy in comparison to other disciplines.

  2. Methodological and musicological investigation of the System & Contrast model for musical form description

    OpenAIRE

    Deruty, Emmanuel; Bimbot, Frédéric; Van Wymeersch, Brigitte

    2013-01-01

    The semiotic description of music structure aims at representing the high-level organization of music pieces in a concise, generic and reproducible way as a low-rate stream of arbitrary symbols from a limited alphabet, which results into a sequence of " semiotic units ". In this context, the purpose of the System & Contrast model is to address the internal organization of the semiotic units. In this report, the System & Contrast model is approached from different angles in relation to varied ...

  3. Quark Model and multiquark system

    CERN Document Server

    da Silva, Cristiane Oldoni

    2010-01-01

    The discovery of many particles, especially in the 50's, when the firsts accelerators appeared, caused the searching for a model that would describe in a simple form the whole of known particles. The Quark Model, based in the mathematical structures of group theory, provided in the beginning of the 60's a simplified description of hadronic matter already known, proposing that three particles, called quarks, would originate all the observed hadrons. This model was able to preview the existence of particles that were later detected, confirming its consistency. Extensions of the Quark Model were made in the beginning of the 70's, focusing in describing observed particles that were excited states of the fundamental particles and others that presented new quantum numbers (flavors). Recently, exotic states as tetraquarks and pentaquarks types, also called multiquarks systems, previewed by the model, were observed, what renewed the interest in the way as quarks are confined inside the hadrons. In this article we pre...

  4. Evaluation of multichannel reproduced sound

    DEFF Research Database (Denmark)

    Choisel, Sylvain; Wickelmaier, Florian Maria

    2007-01-01

    , as well as overall preference, was based on consistency tests of binary paired-comparison judgments and on modeling the choice frequencies using probabilistic choice models. As a result, the preferences of non-expert listeners could be measured reliably at a ratio scale level. Principal components derived...... from the quantified attributes predict overall preference well. The findings allow for some generalizations within musical program genres regarding the perception of and preference for certain spatial reproduction modes, but for limited generalizations across selections from different musical genres....

  5. Theory of reproducing kernels and applications

    CERN Document Server

    Saitoh, Saburou

    2016-01-01

    This book provides a large extension of the general theory of reproducing kernels published by N. Aronszajn in 1950, with many concrete applications. In Chapter 1, many concrete reproducing kernels are first introduced with detailed information. Chapter 2 presents a general and global theory of reproducing kernels with basic applications in a self-contained way. Many fundamental operations among reproducing kernel Hilbert spaces are dealt with. Chapter 2 is the heart of this book. Chapter 3 is devoted to the Tikhonov regularization using the theory of reproducing kernels with applications to numerical and practical solutions of bounded linear operator equations. In Chapter 4, the numerical real inversion formulas of the Laplace transform are presented by applying the Tikhonov regularization, where the reproducing kernels play a key role in the results. Chapter 5 deals with ordinary differential equations; Chapter 6 includes many concrete results for various fundamental partial differential equations. In Chapt...

  6. Filters, reproducing kernel, and adaptive meshfree method

    Science.gov (United States)

    You, Y.; Chen, J.-S.; Lu, H.

    Reproducing kernel, with its intrinsic feature of moving averaging, can be utilized as a low-pass filter with scale decomposition capability. The discrete convolution of two nth order reproducing kernels with arbitrary support size in each kernel results in a filtered reproducing kernel function that has the same reproducing order. This property is utilized to separate the numerical solution into an unfiltered lower order portion and a filtered higher order portion. As such, the corresponding high-pass filter of this reproducing kernel filter can be used to identify the locations of high gradient, and consequently serves as an operator for error indication in meshfree analysis. In conjunction with the naturally conforming property of the reproducing kernel approximation, a meshfree adaptivity method is also proposed.

  7. Model selection in systems biology depends on experimental design.

    Science.gov (United States)

    Silk, Daniel; Kirk, Paul D W; Barnes, Chris P; Toni, Tina; Stumpf, Michael P H

    2014-06-01

    Experimental design attempts to maximise the information available for modelling tasks. An optimal experiment allows the inferred models or parameters to be chosen with the highest expected degree of confidence. If the true system is faithfully reproduced by one of the models, the merit of this approach is clear - we simply wish to identify it and the true parameters with the most certainty. However, in the more realistic situation where all models are incorrect or incomplete, the interpretation of model selection outcomes and the role of experimental design needs to be examined more carefully. Using a novel experimental design and model selection framework for stochastic state-space models, we perform high-throughput in-silico analyses on families of gene regulatory cascade models, to show that the selected model can depend on the experiment performed. We observe that experimental design thus makes confidence a criterion for model choice, but that this does not necessarily correlate with a model's predictive power or correctness. Finally, in the special case of linear ordinary differential equation (ODE) models, we explore how wrong a model has to be before it influences the conclusions of a model selection analysis.

  8. GENERIC model for multiphase systems

    NARCIS (Netherlands)

    Sagis, L.M.C.

    2010-01-01

    GENERIC is a nonequilibrium thermodynamic formalism in which the dynamic behavior of a system is described by a single compact equation involving two types of brackets: a Poisson bracket and a dissipative bracket. This formalism has proved to be a very powerful instrument to model the dynamic behavi

  9. Examination of reproducibility in microbiological degredation experiments

    DEFF Research Database (Denmark)

    Sommer, Helle Mølgaard; Spliid, Henrik; Holst, Helle

    1998-01-01

    Experimental data indicate that certain microbiological degradation experiments have a limited reproducibility. Nine identical batch experiments were carried out on 3 different days to examine reproducibility. A pure culture, isolated from soil, grew with toluene as the only carbon and energy sou....... The limited reproducibility may be caused by variability in the preculture, or more precisely, variations in the physiological state of the bacteria in the precultures just before used as inoculum....

  10. Thermodynamic modeling of the Au-Sb-Si ternary system

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J., E-mail: jiang.wang@empa.ch [School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin, Guangxi 541004 (China); Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Joining and Interface Technology, Uberlandstrasse 129, Duebendorf, Zuerich CH-8600 (Switzerland); Liu, Y.J. [Western Transportation Institute, Montana State University, Bozeman, MT 59715 (United States); Liu, L.B. [School of Materials Science and Engineering, Central South University, Changsha, Hunan 410083 (China); Zhou, H.Y. [School of Materials Science and Engineering, Guilin University of Electronic Technology, Guilin, Guangxi 541004 (China); Jin, Z.P. [School of Materials Science and Engineering, Central South University, Changsha, Hunan 410083 (China)

    2011-02-10

    Research highlights: > Thermodynamic optimization of the Au-Sb binary system was updated. > The Si-Sb binary system was assessed from critical review of experimental information. > Thermodynamic modeling of the Au-Sb-Si ternary system was performed. > The phase relations of this ternary system are useful to design Au-based solders. - Abstract: Thermodynamic optimization of the Au-Sb binary system was updated as well as the Si-Sb binary system was assessed thermodynamically using the CALPHAD method based on the critical review of the available experimental information from the published literature. The solution phases including liquid, fcc{sub A}1(Au), diamond{sub A}4(Si) and rhombohedral{sub A}7(Sb), are modeled as substitutional solutions and their excess Gibbs energies are expressed by a Redlich-Kister polynomial. The solubility of Si in the intermetallic compound AuSb{sub 2} is not taken into account because of the lack of experimental information. Combined with previous assessment of the Au-Si binary system, thermodynamic modeling of the Au-Sb-Si ternary system was performed to reproduce well the measured phase equilibria. The liquidus projection and several vertical sections of this ternary system were calculated, which are in reasonable agreement with the reported experimental data.

  11. Cotangent Models for Integrable Systems

    Science.gov (United States)

    Kiesenhofer, Anna; Miranda, Eva

    2017-03-01

    We associate cotangent models to a neighbourhood of a Liouville torus in symplectic and Poisson manifolds focusing on b-Poisson/ b-symplectic manifolds. The semilocal equivalence with such models uses the corresponding action-angle theorems in these settings: the theorem of Liouville-Mineur-Arnold for symplectic manifolds and an action-angle theorem for regular Liouville tori in Poisson manifolds (Laurent- Gengoux et al., IntMath Res Notices IMRN 8: 1839-1869, 2011). Our models comprise regular Liouville tori of Poisson manifolds but also consider the Liouville tori on the singular locus of a b-Poisson manifold. For this latter class of Poisson structures we define a twisted cotangent model. The equivalence with this twisted cotangent model is given by an action-angle theorem recently proved by the authors and Scott (Math. Pures Appl. (9) 105(1):66-85, 2016). This viewpoint of cotangent models provides a new machinery to construct examples of integrable systems, which are especially valuable in the b-symplectic case where not many sources of examples are known. At the end of the paper we introduce non-degenerate singularities as lifted cotangent models on b-symplectic manifolds and discuss some generalizations of these models to general Poisson manifolds.

  12. INTEGRATED HYDROGEN STORAGE SYSTEM MODEL

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, B

    2007-11-16

    Hydrogen storage is recognized as a key technical hurdle that must be overcome for the realization of hydrogen powered vehicles. Metal hydrides and their doped variants have shown great promise as a storage material and significant advances have been made with this technology. In any practical storage system the rate of H2 uptake will be governed by all processes that affect the rate of mass transport through the bed and into the particles. These coupled processes include heat and mass transfer as well as chemical kinetics and equilibrium. However, with few exceptions, studies of metal hydrides have focused primarily on fundamental properties associated with hydrogen storage capacity and kinetics. A full understanding of the complex interplay of physical processes that occur during the charging and discharging of a practical storage system requires models that integrate the salient phenomena. For example, in the case of sodium alanate, the size of NaAlH4 crystals is on the order of 300nm and the size of polycrystalline particles may be approximately 10 times larger ({approx}3,000nm). For the bed volume to be as small as possible, it is necessary to densely pack the hydride particles. Even so, in packed beds composed of NaAlH{sub 4} particles alone, it has been observed that the void fraction is still approximately 50-60%. Because of the large void fraction and particle to particle thermal contact resistance, the thermal conductivity of the hydride is very low, on the order of 0.2 W/m-{sup o}C, Gross, Majzoub, Thomas and Sandrock [2002]. The chemical reaction for hydrogen loading is exothermic. Based on the data in Gross [2003], on the order of 10{sup 8}J of heat of is released for the uptake of 5 kg of H{sub 2}2 and complete conversion of NaH to NaAlH{sub 4}. Since the hydride reaction transitions from hydrogen loading to discharge at elevated temperatures, it is essential to control the temperature of the bed. However, the low thermal conductivity of the hydride

  13. On the ternary Ag – Cu – Ga system: Electromotive force measurement and thermodynamic modeling

    Energy Technology Data Exchange (ETDEWEB)

    Gierlotka, Wojciech, E-mail: wojtek@mail.ndhu.edu.tw [Materials Science and Engineering Department, National Dong Hwa University, Hualien, Taiwan (China); Jendrzejczyk-Handzlik, Dominika; Fitzner, Krzysztof; Handzlik, Piotr [Non-Ferrous Metals Department, AGH University of Science and Technology, Krakow (Poland)

    2015-10-15

    The ternary silver–copper–gallium system found application as a solder material in jewel crafting and electronics, thus a phase diagram of this system seems to be important tool, which is necessary for a proper application of different alloys. The activity of gallium in liquid phase was determined by electromotive measurement technique and after that the equilibrium diagram of Ag – Cu – Ga was modeled based on available experimental data using Calphad approach. A set of Gibbs energies was found and used for calculation a phase diagram and thermodynamic properties of liquid phase. The experimental data was reproduced well by calculation. - Highlights: • For the first time activity of Ga in liquid Ag – Cu – Ga alloys was measured. • For the first time the ternary Ag – Cu – Ga system was thermodynamically modeled. • Modeled Ag – Cu – Ga system reproduces experimental data well.

  14. Probabilistic models for feedback systems.

    Energy Technology Data Exchange (ETDEWEB)

    Grace, Matthew D.; Boggs, Paul T.

    2011-02-01

    In previous work, we developed a Bayesian-based methodology to analyze the reliability of hierarchical systems. The output of the procedure is a statistical distribution of the reliability, thus allowing many questions to be answered. The principal advantage of the approach is that along with an estimate of the reliability, we also can provide statements of confidence in the results. The model is quite general in that it allows general representations of all of the distributions involved, it incorporates prior knowledge into the models, it allows errors in the 'engineered' nodes of a system to be determined by the data, and leads to the ability to determine optimal testing strategies. In this report, we provide the preliminary steps necessary to extend this approach to systems with feedback. Feedback is an essential component of 'complexity' and provides interesting challenges in modeling the time-dependent action of a feedback loop. We provide a mechanism for doing this and analyze a simple case. We then consider some extensions to more interesting examples with local control affecting the entire system. Finally, a discussion of the status of the research is also included.

  15. Modeling Advance Life Support Systems

    Science.gov (United States)

    Pitts, Marvin; Sager, John; Loader, Coleen; Drysdale, Alan

    1996-01-01

    Activities this summer consisted of two projects that involved computer simulation of bioregenerative life support systems for space habitats. Students in the Space Life Science Training Program (SLSTP) used the simulation, space station, to learn about relationships between humans, fish, plants, and microorganisms in a closed environment. One student complete a six week project to modify the simulation by converting the microbes from anaerobic to aerobic, and then balancing the simulation's life support system. A detailed computer simulation of a closed lunar station using bioregenerative life support was attempted, but there was not enough known about system restraints and constants in plant growth, bioreactor design for space habitats and food preparation to develop an integrated model with any confidence. Instead of a completed detailed model with broad assumptions concerning the unknown system parameters, a framework for an integrated model was outlined and work begun on plant and bioreactor simulations. The NASA sponsors and the summer Fell were satisfied with the progress made during the 10 weeks, and we have planned future cooperative work.

  16. Minisuperspace models of discrete systems

    CERN Document Server

    Baytaş, Bekir

    2016-01-01

    A discrete quantum spin system is presented in which several modern methods of canonical quantum gravity can be tested with promising results. In particular, features of interacting dynamics are analyzed with an emphasis on homogeneous configurations and the dynamical building-up and stability of long-range correlations. Different types of homogeneous minisuperspace models are introduced for the system, including one based on condensate states, and shown to capture different aspects of the discrete system. They are evaluated with effective methods and by means of continuum limits, showing good agreement with operator calculations whenever the latter are available. As a possibly quite general result, it is concluded that an analysis of the building-up of long-range correlations in discrete systems requires non-perturbative solutions of the dynamical equations. Some questions related to stability can be analyzed perturbatively, but suggest that matter couplings may be relevant for this question in the context o...

  17. Are classifications of proximal radius fractures reproducible?

    Directory of Open Access Journals (Sweden)

    dos Santos João BG

    2009-10-01

    Full Text Available Abstract Background Fractures of the proximal radius need to be classified in an appropriate and reproducible manner. The aim of this study was to assess the reliability of the three most widely used classification systems. Methods Elbow radiographs images of patients with proximal radius fractures were classified according to Mason, Morrey, and Arbeitsgemeinschaft für osteosynthesefragen/Association for the Study of Internal Fixation (AO/ASIF classifications by four observers with different experience with this subject to assess their intra- and inter-observer agreement. Each observer analyzed the images on three different occasions on a computer with numerical sequence randomly altered. Results We found that intra-observer agreement of Mason and Morrey classifications were satisfactory (κ = 0.582 and 0.554, respectively, while the AO/ASIF classification had poor intra-observer agreement (κ = 0.483. Inter-observer agreement was higher in the Mason (κ = 0.429-0.560 and Morrey (κ = 0.319-0.487 classifications than in the AO/ASIF classification (κ = 0.250-0.478, which showed poor reliability. Conclusion Inter- and intra-observer agreement of the Mason and Morey classifications showed overall satisfactory reliability when compared to the AO/ASIF system. The Mason classification is the most reliable system.

  18. The reproducible radio outbursts of SS Cygni

    Science.gov (United States)

    Russell, T. D.; Miller-Jones, J. C. A.; Sivakoff, G. R.; Altamirano, D.; O'Brien, T. J.; Page, K. L.; Templeton, M. R.; Körding, E. G.; Knigge, C.; Rupen, M. P.; Fender, R. P.; Heinz, S.; Maitra, D.; Markoff, S.; Migliari, S.; Remillard, R. A.; Russell, D. M.; Sarazin, C. L.; Waagen, E. O.

    2016-08-01

    We present the results of our intensive radio observing campaign of the dwarf nova SS Cyg during its 2010 April outburst. We argue that the observed radio emission was produced by synchrotron emission from a transient radio jet. Comparing the radio light curves from previous and subsequent outbursts of this system (including high-resolution observations from outbursts in 2011 and 2012) shows that the typical long and short outbursts of this system exhibit reproducible radio outbursts that do not vary significantly between outbursts, which is consistent with the similarity of the observed optical, ultraviolet and X-ray light curves. Contemporaneous optical and X-ray observations show that the radio emission appears to have been triggered at the same time as the initial X-ray flare, which occurs as disc material first reaches the boundary layer. This raises the possibility that the boundary region may be involved in jet production in accreting white dwarf systems. Our high spatial resolution monitoring shows that the compact jet remained active throughout the outburst with no radio quenching.

  19. The reproducible radio outbursts of SS Cygni

    CERN Document Server

    Russell, T D; Sivakoff, G R; Altamirano, D; O'Brien, T J; Page, K L; Templeton, M R; Koerding, E G; Knigge, C; Rupen, M P; Fender, R P; Heinz, S; Maitra, D; Markoff, S; Migliari, S; Remillard, R A; Russell, D M; Sarazin, C L; Waagen, E O

    2016-01-01

    We present the results of our intensive radio observing campaign of the dwarf nova SS Cyg during its 2010 April outburst. We argue that the observed radio emission was produced by synchrotron emission from a transient radio jet. Comparing the radio light curves from previous and subsequent outbursts of this system (including high-resolution observations from outbursts in 2011 and 2012) shows that the typical long and short outbursts of this system exhibit reproducible radio outbursts that do not vary significantly between outbursts, which is consistent with the similarity of the observed optical, ultraviolet and X-ray light curves. Contemporaneous optical and X-ray observations show that the radio emission appears to have been triggered at the same time as the initial X-ray flare, which occurs as disk material first reaches the boundary layer. This raises the possibility that the boundary region may be involved in jet production in accreting white dwarf systems. Our high spatial resolution monitoring shows th...

  20. Modeling belief systems with scale-free networks

    CERN Document Server

    Antal, Miklos

    2008-01-01

    Evolution of belief systems has always been in focus of cognitive research. In this paper we delineate a new model describing belief systems as a network of statements considered true. Testing the model a small number of parameters enabled us to reproduce a variety of well-known mechanisms ranging from opinion changes to development of psychological problems. The self-organizing opinion structure showed a scale-free degree distribution. The novelty of our work lies in applying a convenient set of definitions allowing us to depict opinion network dynamics in a highly favorable way, which resulted in a scale-free belief network. As an additional benefit, we listed several conjectural consequences in a number of areas related to thinking and reasoning.

  1. Reproducing Kernel Particle Method for Non-Linear Fracture Analysis

    Institute of Scientific and Technical Information of China (English)

    Cao Zhongqing; Zhou Benkuan; Chen Dapeng

    2006-01-01

    To study the non-linear fracture, a non-linear constitutive model for piezoelectric ceramics was proposed, in which the polarization switching and saturation were taken into account. Based on the model, the non-linear fracture analysis was implemented using reproducing kernel particle method (RKPM). Using local J-integral as a fracture criterion, a relation curve of fracture loads against electric fields was obtained. Qualitatively, the curve is in agreement with the experimental observations reported in literature. The reproducing equation, the shape function of RKPM, and the transformation method to impose essential boundary conditions for meshless methods were also introduced. The computation was implemented using object-oriented programming method.

  2. The Control System Modeling Language

    CERN Document Server

    Zagar, K; Sekoranja, M; Tkacik, G; Vodovnik, A; Zagar, Klemen; Plesko, Mark; Sekoranja, Matej; Tkacik, Gasper; Vodovnik, Anze

    2001-01-01

    The well-known Unified Modeling Language (UML) describes software entities, such as interfaces, classes, operations and attributes, as well as relationships among them, e.g. inheritance, containment and dependency. The power of UML lies in Computer Aided Software Engineering (CASE) tools such as Rational Rose, which are also capable of generating software structures from visual object definitions and relations. UML also allows add-ons that define specific structures and patterns in order to steer and automate the design process. We have developed an add-on called Control System Modeling Language (CSML). It introduces entities and relationships that we know from control systems, such as "property" representing a single controllable point/channel, or an "event" specifying that a device is capable of notifying its clients through events. Entities can also possess CSML-specific characteristics, such as physical units and valid ranges for input parameters. CSML is independent of any specific language or technology...

  3. Contextual Modelling of Collaboration System

    Directory of Open Access Journals (Sweden)

    Wafaa DACHRY

    2012-03-01

    Full Text Available Faced with new environmental constraints, firms decide to collaborate in collective entities and adopt new patterns of behavior. So, this firms’ collaboration becomes an unavoidable approach. Indeed, our aim interest in our study is to propose a collaborative information system for supply chain. Our proposed platform ensures cooperation and information sharing between partners in real time. In fact, several questions have to be asked: What is the information nature may be shared between partners? What processes are implemented between actors? What functional services are supported by the platform? In order to answer these questions, we present, in this article, our methodological approach of modelling, called CMCS (Contextual Modelling of Collaborative System

  4. Reproducibility principles, problems, practices, and prospects

    CERN Document Server

    Maasen, Sabine

    2016-01-01

    Featuring peer-reviewed contributions from noted experts in their fields of research, Reproducibility: Principles, Problems, Practices, and Prospects presents state-of-the-art approaches to reproducibility, the gold standard sound science, from multi- and interdisciplinary perspectives. Including comprehensive coverage for implementing and reflecting the norm of reproducibility in various pertinent fields of research, the book focuses on how the reproducibility of results is applied, how it may be limited, and how such limitations can be understood or even controlled in the natural sciences, computational sciences, life sciences, social sciences, and studies of science and technology. The book presents many chapters devoted to a variety of methods and techniques, as well as their epistemic and ontological underpinnings, which have been developed to safeguard reproducible research and curtail deficits and failures. The book also investigates the political, historical, and social practices that underlie repro...

  5. Explorations in statistics: statistical facets of reproducibility.

    Science.gov (United States)

    Curran-Everett, Douglas

    2016-06-01

    Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This eleventh installment of Explorations in Statistics explores statistical facets of reproducibility. If we obtain an experimental result that is scientifically meaningful and statistically unusual, we would like to know that our result reflects a general biological phenomenon that another researcher could reproduce if (s)he repeated our experiment. But more often than not, we may learn this researcher cannot replicate our result. The National Institutes of Health and the Federation of American Societies for Experimental Biology have created training modules and outlined strategies to help improve the reproducibility of research. These particular approaches are necessary, but they are not sufficient. The principles of hypothesis testing and estimation are inherent to the notion of reproducibility in science. If we want to improve the reproducibility of our research, then we need to rethink how we apply fundamental concepts of statistics to our science.

  6. JSim, an open-source modeling system for data analysis.

    Science.gov (United States)

    Butterworth, Erik; Jardine, Bartholomew E; Raymond, Gary M; Neal, Maxwell L; Bassingthwaighte, James B

    2013-01-01

    JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it

  7. Stochastic Models of Polymer Systems

    Science.gov (United States)

    2016-01-01

    field limit of a dynamical model for polymer systems, Science China Mathematics , (11 2012): 0. doi: TOTAL: 1 Number of Non Peer-Reviewed Conference...4.0 (4.0 max scale): Number of graduating undergraduates funded by a DoD funded Center of Excellence grant for Education , Research and Engineering...undergraduates funded by your agreement who graduated during this period and will receive scholarships or fellowships for further studies in science

  8. Model reduction of parametrized systems

    CERN Document Server

    Ohlberger, Mario; Patera, Anthony; Rozza, Gianluigi; Urban, Karsten

    2017-01-01

    The special volume offers a global guide to new concepts and approaches concerning the following topics: reduced basis methods, proper orthogonal decomposition, proper generalized decomposition, approximation theory related to model reduction, learning theory and compressed sensing, stochastic and high-dimensional problems, system-theoretic methods, nonlinear model reduction, reduction of coupled problems/multiphysics, optimization and optimal control, state estimation and control, reduced order models and domain decomposition methods, Krylov-subspace and interpolatory methods, and applications to real industrial and complex problems. The book represents the state of the art in the development of reduced order methods. It contains contributions from internationally respected experts, guaranteeing a wide range of expertise and topics. Further, it reflects an important effor t, carried out over the last 12 years, to build a growing research community in this field. Though not a textbook, some of the chapters ca...

  9. Computational models of complex systems

    CERN Document Server

    Dabbaghian, Vahid

    2014-01-01

    Computational and mathematical models provide us with the opportunities to investigate the complexities of real world problems. They allow us to apply our best analytical methods to define problems in a clearly mathematical manner and exhaustively test our solutions before committing expensive resources. This is made possible by assuming parameter(s) in a bounded environment, allowing for controllable experimentation, not always possible in live scenarios. For example, simulation of computational models allows the testing of theories in a manner that is both fundamentally deductive and experimental in nature. The main ingredients for such research ideas come from multiple disciplines and the importance of interdisciplinary research is well recognized by the scientific community. This book provides a window to the novel endeavours of the research communities to present their works by highlighting the value of computational modelling as a research tool when investigating complex systems. We hope that the reader...

  10. A comprehensive benchmarking system for evaluating global vegetation models

    Directory of Open Access Journals (Sweden)

    D. I. Kelley

    2012-11-01

    Full Text Available We present a benchmark system for global vegetation models. This system provides a quantitative evaluation of multiple simulated vegetation properties, including primary production; seasonal net ecosystem production; vegetation cover, composition and height; fire regime; and runoff. The benchmarks are derived from remotely sensed gridded datasets and site-based observations. The datasets allow comparisons of annual average conditions and seasonal and inter-annual variability, and they allow the impact of spatial and temporal biases in means and variability to be assessed separately. Specifically designed metrics quantify model performance for each process, and are compared to scores based on the temporal or spatial mean value of the observations and a "random" model produced by bootstrap resampling of the observations. The benchmark system is applied to three models: a simple light-use efficiency and water-balance model (the Simple Diagnostic Biosphere Model: SDBM, and the Lund-Potsdam-Jena (LPJ and Land Processes and eXchanges (LPX dynamic global vegetation models (DGVMs. SDBM reproduces observed CO2 seasonal cycles, but its simulation of independent measurements of net primary production (NPP is too high. The two DGVMs show little difference for most benchmarks (including the inter-annual variability in the growth rate and seasonal cycle of atmospheric CO2, but LPX represents burnt fraction demonstrably more accurately. Benchmarking also identified several weaknesses common to both DGVMs. The benchmarking system provides a quantitative approach for evaluating how adequately processes are represented in a model, identifying errors and biases, tracking improvements in performance through model development, and discriminating among models. Adoption of such a system would do much to improve confidence in terrestrial model predictions of climate change impacts and feedbacks.

  11. Model Reduction of Nonlinear Aeroelastic Systems Experiencing Hopf Bifurcation

    KAUST Repository

    Abdelkefi, Abdessattar

    2013-06-18

    In this paper, we employ the normal form to derive a reduced - order model that reproduces nonlinear dynamical behavior of aeroelastic systems that undergo Hopf bifurcation. As an example, we consider a rigid two - dimensional airfoil that is supported by nonlinear springs in the pitch and plunge directions and subjected to nonlinear aerodynamic loads. We apply the center manifold theorem on the governing equations to derive its normal form that constitutes a simplified representation of the aeroelastic sys tem near flutter onset (manifestation of Hopf bifurcation). Then, we use the normal form to identify a self - excited oscillator governed by a time - delay ordinary differential equation that approximates the dynamical behavior while reducing the dimension of the original system. Results obtained from this oscillator show a great capability to predict properly limit cycle oscillations that take place beyond and above flutter as compared with the original aeroelastic system.

  12. Genome Modeling System: A Knowledge Management Platform for Genomics.

    Directory of Open Access Journals (Sweden)

    Malachi Griffith

    2015-07-01

    Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

  13. Identification and Modelling of Linear Dynamic Systems

    Directory of Open Access Journals (Sweden)

    Stanislav Kocur

    2006-01-01

    Full Text Available System identification and modelling are very important parts of system control theory. System control is only as good as good is created model of system. So this article deals with identification and modelling problems. There are simple classification and evolution of identification methods, and then the modelling problem is described. Rest of paper is devoted to two most known and used models of linear dynamic systems.

  14. ISSM: Ice Sheet System Model

    Science.gov (United States)

    Larour, Eric; Schiermeier, John E.; Seroussi, Helene; Morlinghem, Mathieu

    2013-01-01

    In order to have the capability to use satellite data from its own missions to inform future sea-level rise projections, JPL needed a full-fledged ice-sheet/iceshelf flow model, capable of modeling the mass balance of Antarctica and Greenland into the near future. ISSM was developed with such a goal in mind, as a massively parallelized, multi-purpose finite-element framework dedicated to ice-sheet modeling. ISSM features unstructured meshes (Tria in 2D, and Penta in 3D) along with corresponding finite elements for both types of meshes. Each finite element can carry out diagnostic, prognostic, transient, thermal 3D, surface, and bed slope simulations. Anisotropic meshing enables adaptation of meshes to a certain metric, and the 2D Shelfy-Stream, 3D Blatter/Pattyn, and 3D Full-Stokes formulations capture the bulk of the ice-flow physics. These elements can be coupled together, based on the Arlequin method, so that on a large scale model such as Antarctica, each type of finite element is used in the most efficient manner. For each finite element referenced above, ISSM implements an adjoint. This adjoint can be used to carry out model inversions of unknown model parameters, typically ice rheology and basal drag at the ice/bedrock interface, using a metric such as the observed InSAR surface velocity. This data assimilation capability is crucial to allow spinning up of ice flow models using available satellite data. ISSM relies on the PETSc library for its vectors, matrices, and solvers. This allows ISSM to run efficiently on any parallel platform, whether shared or distrib- ISSM: Ice Sheet System Model NASA's Jet Propulsion Laboratory, Pasadena, California uted. It can run on the largest clusters, and is fully scalable. This allows ISSM to tackle models the size of continents. ISSM is embedded into MATLAB and Python, both open scientific platforms. This improves its outreach within the science community. It is entirely written in C/C++, which gives it flexibility in its

  15. Integrated Modeling for Flood Hazard Mapping Using Watershed Modeling System

    National Research Council Canada - National Science Library

    Seyedeh S. Sadrolashrafi; Thamer A. Mohamed; Ahmad R.B. Mahmud; Majid K. Kholghi; Amir Samadi

    2008-01-01

    ...) with the Watershed Modeling System (WMS) for flood modeling is developed. It also interconnects the terrain models and the GIS software, with commercial standard hydrological and hydraulic models, including HEC-1, HEC-RAS, etc...

  16. Learning Reproducibility with a Yearly Networking Contest

    KAUST Repository

    Canini, Marco

    2017-08-10

    Better reproducibility of networking research results is currently a major goal that the academic community is striving towards. This position paper makes the case that improving the extent and pervasiveness of reproducible research can be greatly fostered by organizing a yearly international contest. We argue that holding a contest undertaken by a plurality of students will have benefits that are two-fold. First, it will promote hands-on learning of skills that are helpful in producing artifacts at the replicable-research level. Second, it will advance the best practices regarding environments, testbeds, and tools that will aid the tasks of reproducibility evaluation committees by and large.

  17. Thou Shalt Be Reproducible! A Technology Perspective

    Directory of Open Access Journals (Sweden)

    Patrick Mair

    2016-07-01

    Full Text Available This article elaborates on reproducibility in psychology from a technological viewpoint. Modernopen source computational environments are shown and explained that foster reproducibilitythroughout the whole research life cycle, and to which emerging psychology researchers shouldbe sensitized, are shown and explained. First, data archiving platforms that make datasets publiclyavailable are presented. Second, R is advocated as the data-analytic lingua franca in psychologyfor achieving reproducible statistical analysis. Third, dynamic report generation environments forwriting reproducible manuscripts that integrate text, data analysis, and statistical outputs such asfigures and tables in a single document are described. Supplementary materials are provided inorder to get the reader started with these technologies.

  18. The Economics of Reproducibility in Preclinical Research.

    Directory of Open Access Journals (Sweden)

    Leonard P Freedman

    2015-06-01

    Full Text Available Low reproducibility rates within life science research undermine cumulative knowledge production and contribute to both delays and costs of therapeutic drug development. An analysis of past studies indicates that the cumulative (total prevalence of irreproducible preclinical research exceeds 50%, resulting in approximately US$28,000,000,000 (US$28B/year spent on preclinical research that is not reproducible-in the United States alone. We outline a framework for solutions and a plan for long-term improvements in reproducibility rates that will help to accelerate the discovery of life-saving therapies and cures.

  19. Reproducibility of atypia of undetermined significance/follicular lesion of undetermined significance category using the bethesda system for reporting thyroid cytology when reviewing slides from different institutions: A study of interobserver variability among cytopathologists.

    Science.gov (United States)

    Padmanabhan, Vijayalakshmi; Marshall, Carrie B; Akdas Barkan, Guliz; Ghofrani, Mohiedean; Laser, Alice; Tolgay Ocal, Idris; David Sturgis, Charles; Souers, Rhona; Kurtycz, Daniel F I

    2017-05-01

    The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) offers a six-tiered diagnostic scheme for thyroid Fine Needle Aspiration (FNA): Benign, Atypia of Undetermined Significance/Follicular Lesion of Undetermined Significance (AUS/FLUS), suspicious for follicular neoplasm, suspicious for malignancy, malignant, and unsatisfactory with an aim to standardize diagnostic criteria. Reported rate of AUS/FLUS category in the literature has varied from 3% to 20.5%. The aim of this study was to assess interobserver variability among cytopathologists to assess reproducibility of the AUS/FLUS category. Seven cytopathologists brought FNA cases (a mixture of atypical and non-atypical FNA diagnosis) diagnosed using TBSRTC from their respective institutions which were reviewed and diagnosed by the participants. The analysis assessed interobserver variability among 7 cytopathologists and determined characteristics on the slides which were associated with concordance to the institutional diagnosis. Seventy eight of 125 (62.4%) benign cases were classified as benign by the reviewers and 26 (21%) were called AUS/FLUS on review. A third of the AUS/FLUS cases were called benign on review and 28.2% were classified as suspicious for neoplasia/malignancy. Roughly a third each of the suspicious for follicular neoplasm/suspicious for malignancy cases were classified as AUS/FLUS. When pathologists from different institutions shared their slides, concordance was high for specimens with adequate cellularity and those that were clearly benign but thresholds varied for the other indeterminate categories. Most definite categorization of the AUS/FLUS category was seen on review. Diagn. Cytopathol. 2017;45:399-405. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. Experimental System Identification and Black Box Modeling of Hydraulic Directional Control Valve

    Directory of Open Access Journals (Sweden)

    Sondre Sanden Tørdal

    2015-10-01

    Full Text Available Directional control valves play a large role in most hydraulic systems. When modeling the hydraulic systems, it is important that both the steady state and dynamic characteristics of the valves are modeled correctly to reproduce the dynamic characteristics of the entire system. In this paper, a proportional valve (Brevini HPV 41 is investigated to identify its dynamic and steady state characteristics. The steady state characteristics are identified by experimental flow curves. The dynamics are determined through frequency response analysis and identified using several transfer functions. The paper also presents a simulation model of the valve describing both steady state and dynamic characteristics. The simulation results are verified through several experiments.

  1. Network models in anatomical systems.

    Science.gov (United States)

    Esteve-Altava, Borja; Marugán-Lobón, Jesús; Botella, Héctor; Rasskin-Gutman, Diego

    2011-01-01

    Network theory has been extensively used to model the underlying structure of biological processes. From genetics to ecology, network thinking is changing our understanding of complex systems, specifically how their internal structure determines their overall behavior. Concepts such as hubs, scale-free or small-world networks, common in the complexity literature, are now used more and more in sociology, neurosciences, as well as other anthropological fields. Even though the use of network models is nowadays so widely applied, few attempts have been carried out to enrich our understanding in the classical morphological sciences such as in comparative anatomy or physical anthropology. The purpose of this article is to introduce the usage of network tools in morphology; specifically by building anatomical networks, dealing with the most common analyses and problems, and interpreting their outcome.

  2. Thermodynamic modeling of complex systems

    DEFF Research Database (Denmark)

    Liang, Xiaodong

    Offshore reservoirs represent one of the major growth areas of the oil and gas industry, and environmental safety is one of the biggest challenges for the offshore exploration and production. The oil accidents in the Gulf of Mexico in 1979 and 2010 were two of the biggest disasters in history...... after an oil spill. Engineering thermodynamics could be applied in the state-of-the-art sonar products through advanced artificial technology, if the speed of sound, solubility and density of oil-seawater systems could be satisfactorily modelled. The addition of methanol or glycols into unprocessed well...

  3. Models for Gaze Tracking Systems

    Directory of Open Access Journals (Sweden)

    Villanueva Arantxa

    2007-01-01

    Full Text Available One of the most confusing aspects that one meets when introducing oneself into gaze tracking technology is the wide variety, in terms of hardware equipment, of available systems that provide solutions to the same matter, that is, determining the point the subject is looking at. The calibration process permits generally adjusting nonintrusive trackers based on quite different hardware and image features to the subject. The negative aspect of this simple procedure is that it permits the system to work properly but at the expense of a lack of control over the intrinsic behavior of the tracker. The objective of the presented article is to overcome this obstacle to explore more deeply the elements of a video-oculographic system, that is, eye, camera, lighting, and so forth, from a purely mathematical and geometrical point of view. The main contribution is to find out the minimum number of hardware elements and image features that are needed to determine the point the subject is looking at. A model has been constructed based on pupil contour and multiple lighting, and successfully tested with real subjects. On the other hand, theoretical aspects of video-oculographic systems have been thoroughly reviewed in order to build a theoretical basis for further studies.

  4. Models for Gaze Tracking Systems

    Directory of Open Access Journals (Sweden)

    Arantxa Villanueva

    2007-10-01

    Full Text Available One of the most confusing aspects that one meets when introducing oneself into gaze tracking technology is the wide variety, in terms of hardware equipment, of available systems that provide solutions to the same matter, that is, determining the point the subject is looking at. The calibration process permits generally adjusting nonintrusive trackers based on quite different hardware and image features to the subject. The negative aspect of this simple procedure is that it permits the system to work properly but at the expense of a lack of control over the intrinsic behavior of the tracker. The objective of the presented article is to overcome this obstacle to explore more deeply the elements of a video-oculographic system, that is, eye, camera, lighting, and so forth, from a purely mathematical and geometrical point of view. The main contribution is to find out the minimum number of hardware elements and image features that are needed to determine the point the subject is looking at. A model has been constructed based on pupil contour and multiple lighting, and successfully tested with real subjects. On the other hand, theoretical aspects of video-oculographic systems have been thoroughly reviewed in order to build a theoretical basis for further studies.

  5. Reproducibility Experiment of OSL and TL Dosimeter

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>Reproducibility is an important property of personal dosimeter. It not only can indicate the stability of dosimeter, appraise the precision and accuracy of measured value, but also can evaluate the

  6. Area Logistics System Based on System Dynamics Model

    Institute of Scientific and Technical Information of China (English)

    GUI Shouping; ZHU Qiang; LU Lifang

    2005-01-01

    At present, there are few effective ways to analyze area logistics systems. This paper uses system dynamics to analyze the area logistics system and establishes a system dynamics model for the area logistics system based on the characteristics of the area logistics system and system dynamics. Numerical simulations with the system dynamic model were used to analyze a logistic system. Analysis of the Guangzhou economy shows that the model can reflect the actual state of the system objectively and can be used to make policy and harmonize environment.

  7. A user-friendly earth system model of low complexity: the ESCIMO system dynamics model of global warming towards 2100

    Science.gov (United States)

    Randers, Jorgen; Golüke, Ulrich; Wenstøp, Fred; Wenstøp, Søren

    2016-11-01

    We have made a simple system dynamics model, ESCIMO (Earth System Climate Interpretable Model), which runs on a desktop computer in seconds and is able to reproduce the main output from more complex climate models. ESCIMO represents the main causal mechanisms at work in the Earth system and is able to reproduce the broad outline of climate history from 1850 to 2015. We have run many simulations with ESCIMO to 2100 and beyond. In this paper we present the effects of introducing in 2015 six possible global policy interventions that cost around USD 1000 billion per year - around 1 % of world GDP. We tentatively conclude (a) that these policy interventions can at most reduce the global mean surface temperature - GMST - by up to 0.5 °C in 2050 and up to 1.0 °C in 2100 relative to no intervention. The exception is injection of aerosols into the stratosphere, which can reduce the GMST by more than 1.0 °C in a decade but creates other serious problems. We also conclude (b) that relatively cheap human intervention can keep global warming in this century below +2 °C relative to preindustrial times. Finally, we conclude (c) that run-away warming is unlikely to occur in this century but is likely to occur in the longer run. The ensuing warming is slow, however. In ESCIMO, it takes several hundred years to lift the GMST to +3 °C above preindustrial times through gradual self-reinforcing melting of the permafrost. We call for research to test whether more complex climate models support our tentative conclusions from ESCIMO.

  8. Reproducibility of AMPLICOR enterovirus PCR test results.

    OpenAIRE

    1997-01-01

    The reproducibility of AMPLICOR enterovirus PCR test results was determined with clinical samples of cerebrospinal fluid, serum, urine, and throat and rectal swabs. Among 608 samples from which duplicate aliquots were run simultaneously, only seven pairs gave discordant results. Among 104 samples from which duplicate aliquots were run in separate assays, no discordance was seen. Overall, the reproducibility of test kit results was 99% (705 of 712).

  9. Relevant principal factors affecting the reproducibility of insect primary culture.

    Science.gov (United States)

    Ogata, Norichika; Iwabuchi, Kikuo

    2017-06-01

    The primary culture of insect cells often suffers from problems with poor reproducibility in the quality of the final cell preparations. The cellular composition of the explants (cell number and cell types), surgical methods (surgical duration and surgical isolation), and physiological and genetic differences between donors may be critical factors affecting the reproducibility of culture. However, little is known about where biological variation (interindividual differences between donors) ends and technical variation (variance in replication of culture conditions) begins. In this study, we cultured larval fat bodies from the Japanese rhinoceros beetle, Allomyrina dichotoma, and evaluated, using linear mixed models, the effect of interindividual variation between donors on the reproducibility of the culture. We also performed transcriptome analysis of the hemocyte-like cells mainly seen in the cultures using RNA sequencing and ultrastructural analyses of hemocytes using a transmission electron microscope, revealing that the cultured cells have many characteristics of insect hemocytes.

  10. Enterprise Modelling supported by Manufacturing Systems Theory

    OpenAIRE

    MYKLEBUST, Odd

    2002-01-01

    There exist today a large number of enterprise models or enterprise modelling approaches. In a study of standards and project developed models there are two approaches: CIMOSA “The Open Systems Architecture for CIM” and GERAM, “Generalised Enterprise Reference Architecture”, which show a system orientation that can be further followed as interesting research topics for a system theory oriented approach for enterprise models. In the selection of system theories, manufacturing system theory...

  11. Modeling integrated water user decisions in intermittent supply systems

    Science.gov (United States)

    Rosenberg, David E.; Tarawneh, Tarek; Abdel-Khaleq, Rania; Lund, Jay R.

    2007-07-01

    We apply systems analysis to estimate household water use in an intermittent supply system considering numerous interdependent water user behaviors. Some 39 household actions include conservation; improving local storage or water quality; and accessing sources having variable costs, availabilities, reliabilities, and qualities. A stochastic optimization program with recourse decisions identifies the infrastructure investments and short-term coping actions a customer can adopt to cost-effectively respond to a probability distribution of piped water availability. Monte Carlo simulations show effects for a population of customers. Model calibration reproduces the distribution of billed residential water use in Amman, Jordan. Parametric analyses suggest economic and demand responses to increased availability and alternative pricing. It also suggests potential market penetration for conservation actions, associated water savings, and subsidies to entice further adoption. We discuss new insights to size, target, and finance conservation.

  12. Modeling learning technology systems as business systems

    NARCIS (Netherlands)

    Avgeriou, Paris; Retalis, Symeon; Papaspyrou, Nikolaos

    2003-01-01

    The design of Learning Technology Systems, and the Software Systems that support them, is largely conducted on an intuitive, ad hoc basis, thus resulting in inefficient systems that defectively support the learning process. There is now justifiable, increasing effort in formalizing the engineering o

  13. Modeling learning technology systems as business systems

    NARCIS (Netherlands)

    Avgeriou, Paris; Retalis, Symeon; Papaspyrou, Nikolaos

    2003-01-01

    The design of Learning Technology Systems, and the Software Systems that support them, is largely conducted on an intuitive, ad hoc basis, thus resulting in inefficient systems that defectively support the learning process. There is now justifiable, increasing effort in formalizing the engineering

  14. A View of Earth System Model Development

    Institute of Scientific and Technical Information of China (English)

    ZHOU Tianjun; YU Yongqiang; WANG Bin

    2009-01-01

    This paper gives a definition of earth system model and shows three development phases of it, including physical climate system model, earth climate system model, and earth system model, based on an inves-tigation of climate system models in the world. It provides an expatiation on the strategic significance of future development of earth system model, an introduction of some representative scientific research plans on development of earth system model home and abroad, and a review of its status and trends based on the models of the fourth assessment report (AR4) of the Intergovernmental Panel on Climate Change (IPCC).Some suggestions on future development of earth system model in China are given, which are expected to be helpful to advance the development.

  15. Regional integrated environmental model system and its simulation of East Asia summer monsoon

    Institute of Scientific and Technical Information of China (English)

    XIONG Zhe; FU CongBin; YAN XiaoDong

    2009-01-01

    A continuous 22-year simulation in Asia for the period of 1 January 1979 to 31 December 2000 was conducted using the Regional Integrated Environmental Model System (RIEMS 2.0) with NCEP Reanalysis Ⅱ data as the driving fields.The model processes include surface physics state package (BATS le),a Grell cumulus parameterization,and a modified radiation package (CCM3) with the focus on the ability of the model to simulate the summer monsoon over East Asia.The analysis results show that (1)RIEMS reproduces well the spatial pattern and the seasonal cycle of surface temperature.When regionally averaged,the summer mean temperature biases are within 1-2℃.(2) For precipitation,the model reproduces well the spatial pattern,and temporal evolution of the East Asia summer monsoon rain belt,with steady phases separated by more rapid transitions,is reproduced.The rain belt simulated by RIEMS 2.0 is closer to observation than by RIEMS 1.0.(3) RIEMS 2.0 can reasonably reproduce the large-scale circulation.

  16. Modeling stream temperature in the Anthropocene: An earth system modeling approach

    Science.gov (United States)

    Li, Hong-Yi; Ruby Leung, L.; Tesfa, Teklu; Voisin, Nathalie; Hejazi, Mohamad; Liu, Lu; Liu, Ying; Rice, Jennie; Wu, Huan; Yang, Xiaofan

    2015-12-01

    A new large-scale stream temperature model has been developed within the Community Earth System Model (CESM) framework. The model is coupled with the Model for Scale Adaptive River Transport (MOSART) that represents river routing and a water management model (WM) that represents the effects of reservoir operations and water withdrawals on flow regulation. The coupled models allow the impacts of reservoir operations and withdrawals on stream temperature to be explicitly represented in a physically based and consistent way. The models have been applied to the Contiguous United States driven by observed meteorological forcing. Including water management in the models improves the agreement between the simulated and observed streamflow at a large number of stream gauge stations. It is then shown that the model is capable of reproducing stream temperature spatiotemporal variation satisfactorily by comparing against the observed data from over 320 USGS stations. Both climate and water management are found to have important influence on the spatiotemporal patterns of stream temperature. Furthermore, it is quantitatively estimated that reservoir operation could cool down stream temperature in the summer low-flow season (August-October) by as much as 1˜2°C due to enhanced low-flow conditions, which have important implications to aquatic ecosystems. Sensitivity of the simulated stream temperature to input data and reservoir operation rules used in the WM model motivates future directions to address some limitations in the current modeling framework.

  17. Reproducibility in Data-Scarce Environments

    Science.gov (United States)

    Darch, P. T.

    2016-12-01

    Among the usual requirements for reproducibility are large volumes of data and computationally intensive methods. Many fields within earth sciences, however, do not meet these requirements. Data are scarce and data-intensive methods are not well established. How can science be reproducible under these conditions? What changes, both infrastructural and cultural, are needed to advance reproducibility? This paper presents findings from a long-term social scientific case study of an emergent and data scarce field, the deep subseafloor biosphere. This field studies interactions between microbial communities living in the seafloor and the physical environments they inhabit. Factors such as these make reproducibility seem a distant goal for this community: - The relative newness of the field. Serious study began in the late 1990s; - The highly multidisciplinary nature of the field. Researchers come from a range of physical and life science backgrounds; - Data scarcity. Domain researchers produce much of these data in their own onshore laboratories by analyzing cores from international ocean drilling expeditions. Allocation of cores is negotiated between researchers from many fields. These factors interact in multiple ways to inhibit reproducibility: - Incentive structures emphasize producing new data and new knowledge rather than reanalysing extant data; - Only a few steps of laboratory analyses can be reproduced - such as analysis of DNA sequences, but not extraction of DNA from cores -, due to scarcity of cores; - Methodological heterogeneity is a consequence of multidisciplinarity, as researchers bring different techniques from diverse fields. - Few standards for data collection or analysis are available at this early stage of the field; - While datasets from multiple biological and physical phenomena can be integrated into a single workflow, curation tends to be divergent. Each type of dataset may be subject to different disparate policies and contributed to different

  18. System identification application using Hammerstein model

    Indian Academy of Sciences (India)

    SABAN OZER; HASAN ZORLU; SELCUK METE

    2016-06-01

    Generally, memoryless polynomial nonlinear model for nonlinear part and finite impulse response (FIR) model or infinite impulse response model for linear part are preferred in Hammerstein models in literature. In this paper, system identification applications of Hammerstein model that is cascade of nonlinear second order volterra and linear FIR model are studied. Recursive least square algorithm is used to identify the proposed Hammerstein model parameters. Furthermore, the results are compared to identify the success of proposed Hammerstein model and different types of models

  19. Modeling of economic systems with Petri nets

    Directory of Open Access Journals (Sweden)

    Pavel Valeryevich Skorodumov

    2014-09-01

    Full Text Available Modeling is one of the most important tools to study complex systems. Components of both continuous and discrete nature are present in the behavior of contemporary economic systems. The article uses formalism of nested hybrid Petri nets as a tool to study complex economic systems. The author describes basic approaches of simulation modelling, concepts of classical Petri nets, modified means of nested hybrid Petri nets, benefits of their use for systems modeling. The article presents the concept of a universal system of simulation modeling. On the basis of considered approaches the article proposes to develop a universal system of simulation modeling on the basis of the modified machine Petri nets

  20. Data Science Innovations That Streamline Development, Documentation, Reproducibility, and Dissemination of Models in Computational Thermodynamics: An Application of Image Processing Techniques for Rapid Computation, Parameterization and Modeling of Phase Diagrams

    Science.gov (United States)

    Ghiorso, M. S.

    2014-12-01

    Computational thermodynamics (CT) represents a collection of numerical techniques that are used to calculate quantitative results from thermodynamic theory. In the Earth sciences, CT is most often applied to estimate the equilibrium properties of solutions, to calculate phase equilibria from models of the thermodynamic properties of materials, and to approximate irreversible reaction pathways by modeling these as a series of local equilibrium steps. The thermodynamic models that underlie CT calculations relate the energy of a phase to temperature, pressure and composition. These relationships are not intuitive and they are seldom well constrained by experimental data; often, intuition must be applied to generate a robust model that satisfies the expectations of use. As a consequence of this situation, the models and databases the support CT applications in geochemistry and petrology are tedious to maintain as new data and observations arise. What is required to make the process more streamlined and responsive is a computational framework that permits the rapid generation of observable outcomes from the underlying data/model collections, and importantly, the ability to update and re-parameterize the constitutive models through direct manipulation of those outcomes. CT procedures that take models/data to the experiential reference frame of phase equilibria involve function minimization, gradient evaluation, the calculation of implicit lines, curves and surfaces, contour extraction, and other related geometrical measures. All these procedures are the mainstay of image processing analysis. Since the commercial escalation of video game technology, open source image processing libraries have emerged (e.g., VTK) that permit real time manipulation and analysis of images. These tools find immediate application to CT calculations of phase equilibria by permitting rapid calculation and real time feedback between model outcome and the underlying model parameters.

  1. Precision and reproducibility in AMS radiocarbon measurements.

    Energy Technology Data Exchange (ETDEWEB)

    Hotchkis, M.A.; Fink, D.; Hua, Q.; Jacobsen, G.E.; Lawson, E. M.; Smith, A.M.; Tuniz, C. [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)

    1996-12-31

    Accelerator Mass Spectrometry (AMS) is a technique by which rare radioisotopes such as {sup 14}C can be measured at environmental levels with high efficiency. Instead of detecting radioactivity, which is very weak for long-lived environmental radioisotopes, atoms are counted directly. The sample is placed in an ion source, from which a negative ion beam of the atoms of interest is extracted, mass analysed, and injected into a tandem accelerator. After stripping to positive charge states in the accelerator HV terminal, the ions are further accelerated, analysed with magnetic and electrostatic devices and counted in a detector. An isotopic ratio is derived from the number of radioisotope atoms counted in a given time and the beam current of a stable isotope of the same element, measured after the accelerator. For radiocarbon, {sup 14}C/{sup 13}C ratios are usually measured, and the ratio of an unknown sample is compared to that of a standard. The achievable precision for such ratio measurements is limited primarily by {sup 14}C counting statistics and also by a variety of factors related to accelerator and ion source stability. At the ANTARES AMS facility at Lucas Heights Research Laboratories we are currently able to measure {sup 14}C with 0.5% precision. In the two years since becoming operational, more than 1000 {sup 14}C samples have been measured. Recent improvements in precision for {sup 14}C have been achieved with the commissioning of a 59 sample ion source. The measurement system, from sample changing to data acquisition, is under common computer control. These developments have allowed a new regime of automated multi-sample processing which has impacted both on the system throughput and the measurement precision. We have developed data evaluation methods at ANTARES which cross-check the self-consistency of the statistical analysis of our data. Rigorous data evaluation is invaluable in assessing the true reproducibility of the measurement system and aids in

  2. Modeling Power Systems as Complex Adaptive Systems

    Energy Technology Data Exchange (ETDEWEB)

    Chassin, David P.; Malard, Joel M.; Posse, Christian; Gangopadhyaya, Asim; Lu, Ning; Katipamula, Srinivas; Mallow, J V.

    2004-12-30

    Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today's most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This report explores the state-of-the-art physical analogs for understanding the behavior of some econophysical systems and deriving stable and robust control strategies for using them. We review and discuss applications of some analytic methods based on a thermodynamic metaphor, according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood. We apply these methods to the question of how power markets can be expected to behave under a variety of conditions.

  3. Neuman systems model in holland: an update.

    Science.gov (United States)

    Merks, André; Verberk, Frans; de Kuiper, Marlou; Lowry, Lois W

    2012-10-01

    The authors of this column, leading members of the International Neuman Systems Model Association, provide an update on the use of Neuman systems model in Holland and document the various changes in The Netherlands that have influenced the use of the model in that country. The model's link to systems theory and stress theory are discussed, as well as a shift to greater emphasis on patient self-management. The model is also linked to healthcare quality improvement and interprofessional collaboration in Holland.

  4. Reproducibility of psychophysics and electroencephalography during offset analgesia.

    Science.gov (United States)

    Nilsson, M; Piasco, A; Nissen, T D; Graversen, C; Gazerani, P; Lucas, M-F; Dahan, A; Drewes, A M; Brock, C

    2014-07-01

    Offset analgesia (OA) is a pain-inhibiting mechanism, defined as a disproportionately large decrease in pain perception in response to a discrete decrease in noxious stimulus intensity. Hence, the aims were (1) to investigate whether psychophysics and electroencephalography (EEG) can be assessed simultaneously during OA and (2) to assess whether OA is reproducible within the same day as well as between different days. Two separate studies investigated OA: Study I (13 healthy volunteers; seven men; 25.5 ± 0.65 years) aimed at determining the feasibility of recording psychophysics and EEG simultaneously during OA. Study II (18 healthy volunteers; 12 men; 34 ± 3.15 years) assessed reproducibility of OA in terms of psychophysics and EEG. Subjects were presented to a 30-s OA heat stimulus paradigm on the volar forearm and psychophysics, and EEG recordings were obtained throughout the procedure. Reproducibility was assessed within the same day and between different days, using intraclass correlation coefficients (ICCs). Additionally, the reproducible psychophysical parameters were correlated to relevant EEG frequency bands. Simultaneous recording of psychophysics and EEG affects the frequency distribution in terms of alpha suppression. Reproducibility was proven for the psychophysics and EEG frequency bands both within the same day (all ICCs > 0.62) and between different days (all ICCs > 0.66, except for the delta band). Correlations between psychophysics and EEG were found in the theta (4-8 Hz), alpha (8-12 Hz) and gamma (32-80 Hz) bands (all p < 0.01). OA is a robust and reproducible model for experimental pain research, making it suitable for future research. © 2013 European Pain Federation - EFIC®

  5. New model systems for experimental evolution.

    Science.gov (United States)

    Collins, Sinéad

    2013-07-01

    Microbial experimental evolution uses a few well-characterized model systems to answer fundamental questions about how evolution works. This special section highlights novel model systems for experimental evolution, with a focus on marine model systems that can be used to understand evolutionary responses to global change in the oceans.

  6. Performance modeling of automated manufacturing systems

    Science.gov (United States)

    Viswanadham, N.; Narahari, Y.

    A unified and systematic treatment is presented of modeling methodologies and analysis techniques for performance evaluation of automated manufacturing systems. The book is the first treatment of the mathematical modeling of manufacturing systems. Automated manufacturing systems are surveyed and three principal analytical modeling paradigms are discussed: Markov chains, queues and queueing networks, and Petri nets.

  7. Modeling human operator involvement in robotic systems

    NARCIS (Netherlands)

    Wewerinke, P.H.

    1991-01-01

    A modeling approach is presented to describe complex manned robotic systems. The robotic system is modeled as a (highly) nonlinear, possibly time-varying dynamic system including any time delays in terms of optimal estimation, control and decision theory. The role of the human operator(s) is modeled

  8. Visual computing model for immune system and medical system.

    Science.gov (United States)

    Gong, Tao; Cao, Xinxue; Xiong, Qin

    2015-01-01

    Natural immune system is an intelligent self-organizing and adaptive system, which has a variety of immune cells with different types of immune mechanisms. The mutual cooperation between the immune cells shows the intelligence of this immune system, and modeling this immune system has an important significance in medical science and engineering. In order to build a comprehensible model of this immune system for better understanding with the visualization method than the traditional mathematic model, a visual computing model of this immune system was proposed and also used to design a medical system with the immune system, in this paper. Some visual simulations of the immune system were made to test the visual effect. The experimental results of the simulations show that the visual modeling approach can provide a more effective way for analyzing this immune system than only the traditional mathematic equations.

  9. Reversible and Reproducible Giant Universal Electroresistance Effect

    Institute of Scientific and Technical Information of China (English)

    SYED Rizwan; ZHANG Sen; YU Tian; ZHAO Yong-Gang; ZHANG Shu-Feng; HAN Xiu-Feng

    2011-01-01

    After the prediction of the giant electroresistance effect, much work has been carried out to find this effect in practical devices. We demonstrate a novel way to obtain a large electroresistance (ER) effect in the multilayer system at room temperature. The current-in-plane (CIP) electric transport measurement is performed on the multilayer structure consisting of (011)-Pb(Mg1/3Nb2/3)O3-PbTiO3(PMN-PT)/Ta/Al-O/metal. It is found that the resistance of the top metallic layer shows a hysteretic behavior as a function electric field, which corresponds well with the substrate polarization versus electric Reid (P-E) loop. This reversible hysteretic R-E behavior is independent of the applied magnetic field as well as the magnetic structure of the top metallic layer and keeps its memory state. This novel memory effect is attributed to the polarization reversal induced electrostatic potential, which is felt throughout the multilayer stack and is enhanced by the dielectric Al-O layer producing unique hysteretic, reversible, and reproducible resistance switching behavior. This novel universal electroresistance effect will open a new gateway to the development of future multiferroic memory devices operating at room temperature.%After the prediction of the giant electroresistance effect,much work has been carried out to find this effect in practical devices.We demonstrate a novel way to obtain a large electroresistance (ER) effect in the multilayer system at room temperature.The current-in-plane (CIP) electric transport measurement is performed on the multilayer structure consisting of (011)-Pb(Mg1/3 Nb2/3) O3-PbTiO3 (PMN-PT)/Ta/Al-O/metal.It is found that the resistance of the top metallic layer shows a hysteretic behavior as a function electric field,which corresponds well with the substrate polarization versus electric field (P-E) loop.This reversible hysteretic R-E behavior is independent of the applied magnetic field as well as the magnetic structure of the top metallic

  10. A discrete model to study reaction-diffusion-mechanics systems.

    Science.gov (United States)

    Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  11. A discrete model to study reaction-diffusion-mechanics systems.

    Directory of Open Access Journals (Sweden)

    Louis D Weise

    Full Text Available This article introduces a discrete reaction-diffusion-mechanics (dRDM model to study the effects of deformation on reaction-diffusion (RD processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material. Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  12. Externalizing Behaviour for Analysing System Models

    NARCIS (Netherlands)

    Ivanova, Marieta Georgieva; Probst, Christian W.; Hansen, René Rydhof; Kammüller, Florian

    Systems models have recently been introduced to model organisationsandevaluate their vulnerability to threats and especially insiderthreats. Especially for the latter these models are very suitable, since insiders can be assumed to have more knowledge about the attacked organisation than outside

  13. ReproPhylo: An Environment for Reproducible Phylogenomics.

    Science.gov (United States)

    Szitenberg, Amir; John, Max; Blaxter, Mark L; Lunt, David H

    2015-09-01

    The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This 'single file' approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.

  14. ReproPhylo: An Environment for Reproducible Phylogenomics.

    Directory of Open Access Journals (Sweden)

    Amir Szitenberg

    2015-09-01

    Full Text Available The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This 'single file' approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.

  15. CONTROL SYSTEM IDENTIFICATION THROUGH MODEL MODULATION METHODS

    Science.gov (United States)

    identification has been achieved by using model modulation techniques to drive dynamic models into correspondence with operating control systems. The system ... identification then proceeded from examination of the model and the adaptive loop. The model modulation techniques applied to adaptive control

  16. Applying Geospatial Semantic Array Programming for a Reproducible Set of Bioclimatic Indices in Europe

    CERN Document Server

    Caudullo, Giovanni

    2014-01-01

    Bioclimate-driven regression analysis is a widely used approach for modelling ecological niches and zonation. Although the bioclimatic complexity of the European continent is high, a particular combination of 12 climatic and topographic covariates was recently found able to reliably reproduce the ecological zoning of the Food and Agriculture Organization of the United Nations (FAO) for forest resources assessment at pan-European scale, generating the first fuzzy similarity map of FAO ecozones in Europe. The reproducible procedure followed to derive this collection of bioclimatic indices is now presented. It required an integration of data-transformation modules (D-TM) using geospatial tools such as Geographic Information System (GIS) software, and array-based mathematical implementation such as semantic array programming (SemAP). Base variables, intermediate and final covariates are described and semantically defined by providing the workflow of D-TMs and the mathematical formulation following the SemAP notat...

  17. Reproducing Kernel for D2(Ω, ρ) and Metric Induced by Reproducing Kernel

    Institute of Scientific and Technical Information of China (English)

    ZHAO Zhen Gang

    2009-01-01

    An important property of the reproducing kernel of D2(Ω, ρ) is obtained and the reproducing kernels for D2(Ω, ρ) are calculated when Ω = Bn × Bn and ρ are some special functions. A reproducing kernel is used to construct a semi-positive definite matrix and a distance function defined on Ω×Ω. An inequality is obtained about the distance function and the pseudodistance induced by the matrix.

  18. Reproducibility, controllability, and optimization of LENR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Nagel, David J. [The George Washington University, Washington DC 20052 (United States)

    2006-07-01

    Low-energy nuclear reaction (LENR) measurements are significantly, and increasingly reproducible. Practical control of the production of energy or materials by LENR has yet to be demonstrated. Minimization of costly inputs and maximization of desired outputs of LENR remain for future developments. The paper concludes by underlying that it is now clearly that demands for reproducible experiments in the early years of LENR experiments were premature. In fact, one can argue that irreproducibility should be expected for early experiments in a complex new field. As emphasized in the paper and as often happened in the history of science, experimental and theoretical progress can take even decades. It is likely to be many years before investments in LENR experiments will yield significant returns, even for successful research programs. However, it is clearly that a fundamental understanding of the anomalous effects observed in numerous experiments will significantly increase reproducibility, improve controllability, enable optimization of processes, and accelerate the economic viability of LENR.

  19. Reproducibility of surface roughness in reaming

    DEFF Research Database (Denmark)

    Müller, Pavel; De Chiffre, Leonardo

    concentration of the oil in water-based cutting fluid (or when using a straight mineral oil) results in surface profiles that are more reproducible at higher cutting speed. Moreover, it can be seen that three cutting fluids (two water-based cutting fluids with different oil concentration and a straight mineral......An investigation on the reproducibility of surface roughness in reaming was performed to document the applicability of this approach for testing cutting fluids. Austenitic stainless steel was used as a workpiece material and HSS reamers as cutting tools. Reproducibility of the results was evaluated...... oil) used in connection with a low cutting speed result in "identical" surface profiles. Biggest uncertainty contributors were due to the process repeatability and repeatability around the hole circumference. This was however only in the case of high cutting speeds and low degree of oil concentration...

  20. Two sustainable energy system analysis models

    DEFF Research Database (Denmark)

    Lund, Henrik; Goran Krajacic, Neven Duic; da Graca Carvalho, Maria

    2005-01-01

    This paper presents a comparative study of two energy system analysis models both designed with the purpose of analysing electricity systems with a substantial share of fluctuating renewable energy.......This paper presents a comparative study of two energy system analysis models both designed with the purpose of analysing electricity systems with a substantial share of fluctuating renewable energy....

  1. PLATO: data-oriented approach to collaborative large-scale brain system modeling.

    Science.gov (United States)

    Kannon, Takayuki; Inagaki, Keiichiro; Kamiji, Nilton L; Makimura, Kouji; Usui, Shiro

    2011-11-01

    The brain is a complex information processing system, which can be divided into sub-systems, such as the sensory organs, functional areas in the cortex, and motor control systems. In this sense, most of the mathematical models developed in the field of neuroscience have mainly targeted a specific sub-system. In order to understand the details of the brain as a whole, such sub-system models need to be integrated toward the development of a neurophysiologically plausible large-scale system model. In the present work, we propose a model integration library where models can be connected by means of a common data format. Here, the common data format should be portable so that models written in any programming language, computer architecture, and operating system can be connected. Moreover, the library should be simple so that models can be adapted to use the common data format without requiring any detailed knowledge on its use. Using this library, we have successfully connected existing models reproducing certain features of the visual system, toward the development of a large-scale visual system model. This library will enable users to reuse and integrate existing and newly developed models toward the development and simulation of a large-scale brain system model. The resulting model can also be executed on high performance computers using Message Passing Interface (MPI).

  2. Reproducibility of operator processing for radiation dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Sui Shen; DeNardo, Gerald L.; DeNardo, Sally J.; Aina, Yuan; DeNardo, Diane A.; Lamborn, Kathleen R

    1997-01-01

    Reproducibility of operator processing for radiation dose and biological half-life was assessed for radioimmunotherapy. Mean coefficient of variation for intra-operator consecutive processing and for inter-operator processing was less than 15% for all tissues. The mean coefficient of variation for intra-operator processing over 2 wk or inter-operator processing comparing an experienced and less experienced operator was generally greater, and particularly so for tumors. Satisfactory reproducibility was achievable using visual determination of regions of interests after 80 h of training.

  3. Archiving Reproducible Research with R and Dataverse

    DEFF Research Database (Denmark)

    Leeper, Thomas

    2014-01-01

    Reproducible research and data archiving are increasingly important issues in research involving statistical analyses of quantitative data. This article introduces the dvn package, which allows R users to publicly archive datasets, analysis files, codebooks, and associated metadata in Dataverse...... Network online repositories, an open-source data archiving project sponsored by Harvard University. In this article I review the importance of data archiving in the context of reproducible research, introduce the Dataverse Network, explain the implementation of the dvn package, and provide example code...... for archiving and releasing data using the package....

  4. Archiving Reproducible Research with R and Dataverse

    DEFF Research Database (Denmark)

    Leeper, Thomas

    2014-01-01

    Reproducible research and data archiving are increasingly important issues in research involving statistical analyses of quantitative data. This article introduces the dvn package, which allows R users to publicly archive datasets, analysis files, codebooks, and associated metadata in Dataverse...... Network online repositories, an open-source data archiving project sponsored by Harvard University. In this article I review the importance of data archiving in the context of reproducible research, introduce the Dataverse Network, explain the implementation of the dvn package, and provide example code...

  5. Audiovisual biofeedback improves diaphragm motion reproducibility in MRI

    Science.gov (United States)

    Kim, Taeho; Pollock, Sean; Lee, Danny; O’Brien, Ricky; Keall, Paul

    2012-01-01

    Purpose: In lung radiotherapy, variations in cycle-to-cycle breathing results in four-dimensional computed tomography imaging artifacts, leading to inaccurate beam coverage and tumor targeting. In previous studies, the effect of audiovisual (AV) biofeedback on the external respiratory signal reproducibility has been investigated but the internal anatomy motion has not been fully studied. The aim of this study is to test the hypothesis that AV biofeedback improves diaphragm motion reproducibility of internal anatomy using magnetic resonance imaging (MRI). Methods: To test the hypothesis 15 healthy human subjects were enrolled in an ethics-approved AV biofeedback study consisting of two imaging sessions spaced ∼1 week apart. Within each session MR images were acquired under free breathing and AV biofeedback conditions. The respiratory signal to the AV biofeedback system utilized optical monitoring of an external marker placed on the abdomen. Synchronously, serial thoracic 2D MR images were obtained to measure the diaphragm motion using a fast gradient-recalled-echo MR pulse sequence in both coronal and sagittal planes. The improvement in the diaphragm motion reproducibility using the AV biofeedback system was quantified by comparing cycle-to-cycle variability in displacement, respiratory period, and baseline drift. Additionally, the variation in improvement between the two sessions was also quantified. Results: The average root mean square error (RMSE) of diaphragm cycle-to-cycle displacement was reduced from 2.6 mm with free breathing to 1.6 mm (38% reduction) with the implementation of AV biofeedback (p-value biofeedback (p-value biofeedback (p-value = 0.012). The diaphragm motion reproducibility improvements with AV biofeedback were consistent with the abdominal motion reproducibility that was observed from the external marker motion variation. Conclusions: This study was the first to investigate the potential of AV biofeedback to improve the motion

  6. Graphical Model Debugger Framework for Embedded Systems

    DEFF Research Database (Denmark)

    Zeng, Kebin; Guo, Yu; Angelov, Christo K.

    2010-01-01

    Model Driven Software Development has offered a faster way to design and implement embedded real-time software by moving the design to a model level, and by transforming models to code. However, the testing of embedded systems has remained at the code level. This paper presents a Graphical Model...... Debugger Framework, providing an auxiliary avenue of analysis of system models at runtime by executing generated code and updating models synchronously, which allows embedded developers to focus on the model level. With the model debugger, embedded developers can graphically test their design model...

  7. Particle Tracking Model (PTM) with Coastal Modeling System (CMS)

    Science.gov (United States)

    2014-10-31

    System ( CMS ) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER...www.erdc.usace.army.mil/Missions/WaterResources/CIRP.aspx Coastal Inlets Research Program Particle Tracking Model (PTM) with Coastal Modeling System ( CMS ) The...System ( CMS ), which provides coupled wave and current forcing for PTM simulations. CMS -PTM is implemented in the Surface-water Modeling System, a

  8. An information theory model for dissipation in open quantum systems

    Science.gov (United States)

    Rogers, David M.

    2017-08-01

    This work presents a general model for open quantum systems using an information game along the lines of Jaynes’ original work. It is shown how an energy based reweighting of propagators provides a novel moment generating function at each time point in the process. Derivatives of the generating function give moments of the time derivatives of observables. Aside from the mathematically helpful properties, the ansatz reproduces key physics of stochastic quantum processes. At high temperature, the average density matrix follows the Caldeira-Leggett equation. Its associated Langevin equation clearly demonstrates the emergence of dissipation and decoherence time scales, as well as an additional diffusion due to quantum confinement. A consistent interpretation of these results is that decoherence and wavefunction collapse during measurement are directly related to the degree of environmental noise, and thus occur because of subjective uncertainty of an observer.

  9. Atomistic modelling of the Fe-Cr-C system

    Science.gov (United States)

    Wallenius, Janne; Sandberg, Nils; Henriksson, Krister

    2011-08-01

    For the purpose of modelling the impact of carbon on radiation damage phenomena in steels, we have performed an extensive set of first principle calculations on the Fe-Cr-C system. The calculated solution and diffusion enthalpies of carbon in iron and in chromium agree well with experimental data, as do the relative formation energies of mono-carbides, cementite, Hägg and M 23C 6 carbides. Our data further indicate that interstitial carbon is attracted to a solute iron atom in bcc chromium, while the reaction between carbon and a solute chromium atom in bcc iron is repulsive. An empirical potential fitted to data for iron carbides is capable of reproducing melting behaviour of cementite, while the predicted interaction with point defects agrees less well with DFT data than a potential recently published by Hepburn and Ackland.

  10. Analysis hierarchical model for discrete event systems

    Science.gov (United States)

    Ciortea, E. M.

    2015-11-01

    The This paper presents the hierarchical model based on discrete event network for robotic systems. Based on the hierarchical approach, Petri network is analysed as a network of the highest conceptual level and the lowest level of local control. For modelling and control of complex robotic systems using extended Petri nets. Such a system is structured, controlled and analysed in this paper by using Visual Object Net ++ package that is relatively simple and easy to use, and the results are shown as representations easy to interpret. The hierarchical structure of the robotic system is implemented on computers analysed using specialized programs. Implementation of hierarchical model discrete event systems, as a real-time operating system on a computer network connected via a serial bus is possible, where each computer is dedicated to local and Petri model of a subsystem global robotic system. Since Petri models are simplified to apply general computers, analysis, modelling, complex manufacturing systems control can be achieved using Petri nets. Discrete event systems is a pragmatic tool for modelling industrial systems. For system modelling using Petri nets because we have our system where discrete event. To highlight the auxiliary time Petri model using transport stream divided into hierarchical levels and sections are analysed successively. Proposed robotic system simulation using timed Petri, offers the opportunity to view the robotic time. Application of goods or robotic and transmission times obtained by measuring spot is obtained graphics showing the average time for transport activity, using the parameters sets of finished products. individually.

  11. Extensions in model-based system analysis

    OpenAIRE

    Graham, Matthew R.

    2007-01-01

    Model-based system analysis techniques provide a means for determining desired system performance prior to actual implementation. In addition to specifying desired performance, model-based analysis techniques require mathematical descriptions that characterize relevant behavior of the system. The developments of this dissertation give ex. tended formulations for control- relevant model estimation as well as model-based analysis conditions for performance requirements specified as frequency do...

  12. Spatial characteristics of the tropical cloud systems: comparison between model simulation and satellite observations

    OpenAIRE

    Guang J. Zhang; Zurovac-Jevtic, Dance; Erwin R Boer

    2011-01-01

    A Lagrangian cloud classification algorithm is applied to the cloud fields in the tropical Pacificsimulated by a high-resolution regional atmospheric model. The purpose of this work is toassess the model’s ability to reproduce the observed spatial characteristics of the tropical cloudsystems. The cloud systems are broadly grouped into three categories: deep clouds, mid-levelclouds and low clouds. The deep clouds are further divided into mesoscale convective systemsand non-mesoscale convective...

  13. Inductive modelling of an entrepreneurial system

    OpenAIRE

    Yearworth, M

    2010-01-01

    We describe the development of a novel approach to generating theory about the behaviour of an entrepreneurial or start-up system. The new technology business creation system in and around the cities of Bath and Bristol in the UK was analysed using an inductive modelling approach that hybridises grounded theory with system dynamics, a technique we have called grounded systems modelling. Three models that represent the stages of development of an idea through to successful exploitation have be...

  14. Control model for reconfigurable assembly systems

    Institute of Scientific and Technical Information of China (English)

    Yu Jianfeng; Yin Yuehong; Chen Zhaoneng

    2005-01-01

    This paper proposes knowledge based object-oriented timed colored Petri net, a modeling method for reconfigurable assembly systems. Combining knowledge and object-oriented method into timed colored Petri net, a comprehensive and powerful representation model for control of RAS is obtained. With object-oriented method the whole system can be decomposed into concrete objects explicitly, and their relationships are constructed according to the system assembly requirements. Finally, a simple assembly system modeled by the KTCOPN is presented.

  15. Evaluation of AirGIS: a GIS-based air pollution and human exposure modelling system

    DEFF Research Database (Denmark)

    Ketzel, Matthias; Berkowicz, Ruwim; Hvidberg, Martin

    2011-01-01

    This study describes in brief the latest extensions of the Danish Geographic Information System (GIS)-based air pollution and human exposure modelling system (AirGIS), which has been developed in Denmark since 2001 and gives results of an evaluation with measured air pollution data. The system...... shows, in general, a good performance for both long-term averages (annual and monthly averages), short-term averages (hourly and daily) as well as when reproducing spatial variation in air pollution concentrations. Some shortcomings and future perspectives of the system are discussed too....

  16. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Anderson, Joanna E.; Aarts, Alexander A.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahník, Štěpán; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Brüning, Jovita; Calhoun-Sauls, Ann; Callahan, Shannon P.; Chagnon, Elizabeth; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Christopherson, Cody D.; Cillessen, Linda; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Conn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Penna, Nicolás Delia; Den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernández-Castilla, Belén; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Glöckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O Y; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jäkel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knežević, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniël|info:eu-repo/dai/nl/298811855; Lane, Kristin A.; Lassetter, Bethany; Lazarević, Ljiljana B.; Le Bel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, Melissa; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; MacKinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Möschl, Marcus; Motyl, Matt; Müller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michèle B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schlegelmilch, René; Schmidt, Kathleen; Scholz, Sabine; Seibel, Larissa; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L M; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; Te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valášek, Milan; Van't Veer, Anna E.; Van Aert, Robbie; Van Assen, Marcel|info:eu-repo/dai/nl/407629971; Van Bork, Riet; Van De Ven, Mathijs; Van Den Bergh, Don; Van Der Hulst, Marije; Van Dooren, Roel; Van Doorn, Johnny; Van Renswoude, Daan R.; Van Rijn, Hedderik; Vanpaemel, Wolf; Echeverría, Alejandro Vásquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark; Vianello, Michelangelo; Voracek, Martin; Vuu, Gina; Wagenmakers, Eric Jan; Weerdmeester, Joanneke; Welsh, Ashlee; Westgate, Erin C.; Wissink, Joeri; Wood, Michael; Woods, Andy; Wright, Emily; Wu, Sining; Zeelenberg, Marcel; Zuni, Kellylynn

    2015-01-01

    Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Rep

  17. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Anderson, Joanna E.; Aarts, Alexander A.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahník, Štěpán; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Brüning, Jovita; Calhoun-Sauls, Ann; Callahan, Shannon P.; Chagnon, Elizabeth; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Christopherson, Cody D.; Cillessen, Linda; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Conn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Penna, Nicolás Delia; Den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernández-Castilla, Belén; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Glöckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O Y; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jäkel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knežević, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniël|info:eu-repo/dai/nl/298811855; Lane, Kristin A.; Lassetter, Bethany; Lazarević, Ljiljana B.; Le Bel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, Melissa; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; MacKinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Möschl, Marcus; Motyl, Matt; Müller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michèle B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schlegelmilch, René; Schmidt, Kathleen; Scholz, Sabine; Seibel, Larissa; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L M; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; Te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valášek, Milan; Van't Veer, Anna E.; Van Aert, Robbie; Van Assen, Marcel|info:eu-repo/dai/nl/407629971; Van Bork, Riet; Van De Ven, Mathijs; Van Den Bergh, Don; Van Der Hulst, Marije; Van Dooren, Roel; Van Doorn, Johnny; Van Renswoude, Daan R.; Van Rijn, Hedderik; Vanpaemel, Wolf

    2015-01-01

    Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available.

  18. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Aarts, Alexander A.; Anderson, Joanna E.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahnik, Stepan; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Bruening, Jovita; Calhoun-Sauls, Ann; Chagnon, Elizabeth; Callahan, Shannon P.; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Cillessen, Linda; Christopherson, Cody D.; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Cohn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D. Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Della Penna, Nicolas; den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernandez-Castilla, Belen; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Gloeckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O. -Y.; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jaekel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knezevic, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniel; Lane, Kristin A.; Lassetter, Bethany; Lazarevic, Ljiljana B.; LeBel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, M.; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; Mackinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Moeschl, Marcus; Motyl, Matt; Mueller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michele B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima-Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schmidt, Kathleen; Schlegelmilch, Rene; Seibel, Larissa; Scholz, Sabine; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L. M.; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valasek, Milan; van 't Veer, Anna E.; Van Aert, Robbie; van Assen, M.A.L.M.; van Bork, Riet; van de Ven, Mathijs; van den Bergh, Don; van der Hulst, Marije; van Dooren, Roel; van Doorn, Johnny; van Renswoude, Daan R.; van Rijn, Hedderik; Vanpaemel, Wolf; Echeverria, Alejandro Vasquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark

    2015-01-01

    INTRODUCTION Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research

  19. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Anderson, Joanna E.; Aarts, Alexander A.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahník, Štěpán; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Brüning, Jovita; Calhoun-Sauls, Ann; Callahan, Shannon P.; Chagnon, Elizabeth; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Christopherson, Cody D.; Cillessen, Linda; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Conn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Penna, Nicolás Delia; Den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernández-Castilla, Belén; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Glöckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O Y; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jäkel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knežević, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniël; Lane, Kristin A.; Lassetter, Bethany; Lazarević, Ljiljana B.; Le Bel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, Melissa; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; MacKinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Möschl, Marcus; Motyl, Matt; Müller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michèle B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schlegelmilch, René; Schmidt, Kathleen; Scholz, Sabine; Seibel, Larissa; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L M; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; Te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valášek, Milan; Van't Veer, Anna E.; Van Aert, Robbie; Van Assen, Marcel; Van Bork, Riet; Van De Ven, Mathijs; Van Den Bergh, Don; Van Der Hulst, Marije; Van Dooren, Roel; Van Doorn, Johnny; Van Renswoude, Daan R.; Van Rijn, Hedderik; Vanpaemel, Wolf; Echeverría, Alejandro Vásquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark; Vianello, Michelangelo; Voracek, Martin; Vuu, Gina; Wagenmakers, Eric Jan; Weerdmeester, Joanneke; Welsh, Ashlee; Westgate, Erin C.; Wissink, Joeri; Wood, Michael; Woods, Andy; Wright, Emily; Wu, Sining; Zeelenberg, Marcel; Zuni, Kellylynn

    2015-01-01

    Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Rep

  20. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Aarts, Alexander A.; Anderson, Joanna E.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahnik, Stepan; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Bruening, Jovita; Calhoun-Sauls, Ann; Chagnon, Elizabeth; Callahan, Shannon P.; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Cillessen, Linda; Christopherson, Cody D.; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Cohn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D. Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Della Penna, Nicolas; den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernandez-Castilla, Belen; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Gloeckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O. -Y.; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jaekel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knezevic, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniel; Lane, Kristin A.; Lassetter, Bethany; Lazarevic, Ljiljana B.; LeBel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, M.; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; Mackinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Moeschl, Marcus; Motyl, Matt; Mueller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michele B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima-Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schmidt, Kathleen; Schlegelmilch, Rene; Seibel, Larissa; Scholz, Sabine; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L. M.; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valasek, Milan; van 't Veer, Anna E.; Van Aert, Robbie; van Assen, M.A.L.M.; van Bork, Riet; van de Ven, Mathijs; van den Bergh, Don; van der Hulst, Marije; van Dooren, Roel; van Doorn, Johnny; van Renswoude, Daan R.; van Rijn, Hedderik; Vanpaemel, Wolf; Echeverria, Alejandro Vasquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark; Vianello, Michelangelo; Voracek, Martin; Vuu, Gina; Wagenmakers, Eric-Jan; Weerdmeester, Joanneke; Welsh, Ashlee; Westgate, Erin C.; Wissink, Joeri; Wood, Michael; Woods, Andy; Wright, Emily; Wu, Sining; Zeelenberg, Marcel; Zuni, Kellylynn

    2015-01-01

    INTRODUCTION Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research

  1. Modelling Immune System: Principles, Models,Analysis and Perspectives

    Institute of Scientific and Technical Information of China (English)

    Xiang-hua Li; Zheng-xuan Wang; Tian-yang Lu; Xiang-jiu Che

    2009-01-01

    The biological immune system is a complex adaptive system. There are lots of benefits for building the model of the immune system. For biological researchers, they can test some hypotheses about the infection process or simulate the responses of some drugs. For computer researchers, they can build distributed, robust and fault tolerant networks inspired by the functions of the immune system. This paper provides a comprehensive survey of the literatures on modelling the immune system. From the methodology perspective, the paper compares and analyzes the existing approaches and models, and also demonstrates the focusing research effort on the future immune models in the next few years.

  2. Comparison of Photovoltaic Models in the System Advisor Model: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Blair, N. J.; Dobos, A. P.; Gilman, P.

    2013-08-01

    The System Advisor Model (SAM) is free software developed by the National Renewable Energy Laboratory (NREL) for predicting the performance of renewable energy systems and analyzing the financial feasibility of residential, commercial, and utility-scale grid-connected projects. SAM offers several options for predicting the performance of photovoltaic (PV) systems. The model requires that the analyst choose from three PV system models, and depending on that choice, possibly choose from three module and two inverter component models. To obtain meaningful results from SAM, the analyst must be aware of the differences between the model options and their applicability to different modeling scenarios. This paper presents an overview the different PV model options and presents a comparison of results for a 200-kW system using different model options.

  3. Graphical Model Debugger Framework for Embedded Systems

    DEFF Research Database (Denmark)

    Zeng, Kebin

    2010-01-01

    Debugger Framework, providing an auxiliary avenue of analysis of system models at runtime by executing generated code and updating models synchronously, which allows embedded developers to focus on the model level. With the model debugger, embedded developers can graphically test their design model......Model Driven Software Development has offered a faster way to design and implement embedded real-time software by moving the design to a model level, and by transforming models to code. However, the testing of embedded systems has remained at the code level. This paper presents a Graphical Model...... and check the running status of the system, which offers a debugging capability on a higher level of abstraction. The framework intends to contribute a tool to the Eclipse society, especially suitable for model-driven development of embedded systems....

  4. Validation of newly designed regional earth system model (RegESM) for Mediterranean Basin

    Science.gov (United States)

    Turuncoglu, Ufuk Utku; Sannino, Gianmaria

    2017-05-01

    We present a validation analysis of a regional earth system model system (RegESM) for the Mediterranean Basin. The used configuration of the modeling system includes two active components: a regional climate model (RegCM4) and an ocean modeling system (ROMS). To assess the performance of the coupled modeling system in representing the climate of the basin, the results of the coupled simulation (C50E) are compared to the results obtained by a standalone atmospheric simulation (R50E) as well as several observation datasets. Although there is persistent cold bias in fall and winter, which is also seen in previous studies, the model reproduces the inter-annual variability and the seasonal cycles of sea surface temperature (SST) in a general good agreement with the available observations. The analysis of the near-surface wind distribution and the main circulation of the sea indicates that the coupled model can reproduce the main characteristics of the Mediterranean Sea surface and intermediate layer circulation as well as the seasonal variability of wind speed and direction when it is compared with the available observational datasets. The results also reveal that the simulated near-surface wind speed and direction have poor performance in the Gulf of Lion and surrounding regions that also affects the large positive SST bias in the region due to the insufficient horizontal resolution of the atmospheric component of the coupled modeling system. The simulated seasonal climatologies of the surface heat flux components are also consistent with the CORE.2 and NOCS datasets along with the overestimation in net long-wave radiation and latent heat flux (or evaporation, E), although a large observational uncertainty is found in these variables. Also, the coupled model tends to improve the latent heat flux by providing a better representation of the air-sea interaction as well as total heat flux budget over the sea. Both models are also able to reproduce the temporal evolution of

  5. Validation of newly designed regional earth system model (RegESM) for Mediterranean Basin

    Science.gov (United States)

    Turuncoglu, Ufuk Utku; Sannino, Gianmaria

    2016-06-01

    We present a validation analysis of a regional earth system model system (RegESM) for the Mediterranean Basin. The used configuration of the modeling system includes two active components: a regional climate model (RegCM4) and an ocean modeling system (ROMS). To assess the performance of the coupled modeling system in representing the climate of the basin, the results of the coupled simulation (C50E) are compared to the results obtained by a standalone atmospheric simulation (R50E) as well as several observation datasets. Although there is persistent cold bias in fall and winter, which is also seen in previous studies, the model reproduces the inter-annual variability and the seasonal cycles of sea surface temperature (SST) in a general good agreement with the available observations. The analysis of the near-surface wind distribution and the main circulation of the sea indicates that the coupled model can reproduce the main characteristics of the Mediterranean Sea surface and intermediate layer circulation as well as the seasonal variability of wind speed and direction when it is compared with the available observational datasets. The results also reveal that the simulated near-surface wind speed and direction have poor performance in the Gulf of Lion and surrounding regions that also affects the large positive SST bias in the region due to the insufficient horizontal resolution of the atmospheric component of the coupled modeling system. The simulated seasonal climatologies of the surface heat flux components are also consistent with the CORE.2 and NOCS datasets along with the overestimation in net long-wave radiation and latent heat flux (or evaporation, E), although a large observational uncertainty is found in these variables. Also, the coupled model tends to improve the latent heat flux by providing a better representation of the air-sea interaction as well as total heat flux budget over the sea. Both models are also able to reproduce the temporal evolution of

  6. Modeling and Identification of Multirate Systems

    Institute of Scientific and Technical Information of China (English)

    Feng DING; Tongwen CHEN

    2005-01-01

    Multirate systems are abundant in industry; for example, many soft-sensor design problems are related to modeling, parameter identification, or state estimation involving multirate systems. The study of multirate systems goes back to the early 1950's, and has become an active research area in systems and control. This paper briefly surveys the history of development in the area of multirate systems, and introduces some basic concepts and latest results on multirate systems, including a polynomial transformation technique and the lifting technique as tools for handling multirate systems, lifted state space models, parameter identification of dual-rate systems, how to determine fast single-rate models from dual-rate models and directly from dual-rate data, and a hierarchical identification method for general multirate systems. Finally, some further research topics for multirate systems are given.

  7. On Problems of Multicomponent System Maintenance Modelling

    Institute of Scientific and Technical Information of China (English)

    Tomasz Nowakowski; Sylwia Werbinka

    2009-01-01

    We present an overview of some recent developments in the area of mathematical modeling of maintenance decisions for multi-unit systems. The emphasis is on three main groups of multicomponent maintenance optimization models: the block replacement models, group maintenance models, and opportunistic maintenance models. Moreover, an example of a two-unit system maintenance process is provided in order to compare various maintenance policies.

  8. A PHYSICAL ACTIVITY QUESTIONNAIRE: REPRODUCIBILITY AND VALIDITY

    Directory of Open Access Journals (Sweden)

    Nicolas Barbosa

    2007-12-01

    Full Text Available This study evaluates the Quantification de L'Activite Physique en Altitude chez les Enfants (QAPACE supervised self-administered questionnaire reproducibility and validity on the estimation of the mean daily energy expenditure (DEE on Bogotá's schoolchildren. The comprehension was assessed on 324 students, whereas the reproducibility was studied on a different random sample of 162 who were exposed twice to it. Reproducibility was assessed using both the Bland-Altman plot and the intra-class correlation coefficient (ICC. The validity was studied in a sample of 18 girls and 18 boys randomly selected, which completed the test - re-test study. The DEE derived from the questionnaire was compared with the laboratory measurement results of the peak oxygen uptake (Peak VO2 from ergo-spirometry and Leger Test. The reproducibility ICC was 0.96 (95% C.I. 0.95-0.97; by age categories 8-10, 0.94 (0.89-0. 97; 11-13, 0.98 (0.96- 0.99; 14-16, 0.95 (0.91-0.98. The ICC between mean TEE as estimated by the questionnaire and the direct and indirect Peak VO2 was 0.76 (0.66 (p<0.01; by age categories, 8-10, 11-13, and 14-16 were 0.89 (0.87, 0.76 (0.78 and 0.88 (0.80 respectively. The QAPACE questionnaire is reproducible and valid for estimating PA and showed a high correlation with the Peak VO2 uptake

  9. Traffic Modeling in WCDMA System Level Simulations

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Traffic modeling is a crucial element in WCDMA system level simulations. A clear understanding of the nature of traffic in the WCDMA system and subsequent selection of an appropriate random traffic model are critical to the success of the modeling enterprise. The resultant performances will evidently be of a function that our design has been well adapted to the traffic, channel and user mobility models, and these models are also accurate. In this article, our attention will be focused on modeling voice and WWW data traffic with the SBBP model and Victor model respectively.

  10. Towards Modelling of Hybrid Systems

    DEFF Research Database (Denmark)

    Wisniewski, Rafal

    2006-01-01

    The article is an attempt to use methods of category theory and topology for analysis of hybrid systems. We use the notion of a directed topological space; it is a topological space together with a set of privileged paths. Dynamical systems are examples of directed topological spaces. A hybrid...... system consists of a number of dynamical systems that are glued together according to information encoded in the discrete part of the system. We develop a definition of a hybrid system as a functor from the category generated by a transition system to the category of directed topological spaces. Its...... directed homotopy colimit (geometric realization) is a single directed topological space. The behavior of hybrid systems can be then understood in terms of the behavior of dynamical systems through the directed homotopy colimit....

  11. Reproducing entanglement through local classical resources with no communication

    CERN Document Server

    Di Lorenzo, Antonio

    2011-01-01

    Entanglement is one of the most intriguing features of quantum mechanics. It gives rise to peculiar correlations which cannot be reproduced by a large class of alternative theories, the so-called hidden-variable models, that use parameters in addition to the wave-function. This incompatibility was quantified through the celebrated Bell inequalities, and more recently through new inequalities due to Leggett. Experiments confirm the predictions of quantum mechanics. However, this does not imply that quantum mechanics is the ultimate theory, unsusceptible of improvement, nor that quantum mechanics is essentially non-local. The theories ruled out by Bell and Leggett inequalities are required to satisfy some hypotheses, none of which is implied by locality alone. By dropping one or more hypotheses, it is possible not only to violate said inequalities, but to reproduce the quantum mechanical predictions altogether. So far, the models proposed were only mathematical constructs. In this paper we provide a classical r...

  12. Service systems concepts, modeling, and programming

    CERN Document Server

    Cardoso, Jorge; Poels, Geert

    2014-01-01

    This SpringerBrief explores the internal workings of service systems. The authors propose a lightweight semantic model for an effective representation to capture the essence of service systems. Key topics include modeling frameworks, service descriptions and linked data, creating service instances, tool support, and applications in enterprises.Previous books on service system modeling and various streams of scientific developments used an external perspective to describe how systems can be integrated. This brief introduces the concept of white-box service system modeling as an approach to mo

  13. Hydrological modelling in forested systems

    Science.gov (United States)

    This chapter provides a brief overview of forest hydrology modelling approaches for answering important global research and management questions. Many hundreds of hydrological models have been applied globally across multiple decades to represent and predict forest hydrological p...

  14. Survey of Channel and Radio Propagation Models for Wireless MIMO Systems

    Directory of Open Access Journals (Sweden)

    A. Burr

    2007-02-01

    Full Text Available This paper provides an overview of the state-of-the-art radio propagation and channel models for wireless multiple-input multiple-output (MIMO systems. We distinguish between physical models and analytical models and discuss popular examples from both model types. Physical models focus on the double-directional propagation mechanisms between the location of transmitter and receiver without taking the antenna configuration into account. Analytical models capture physical wave propagation and antenna configuration simultaneously by describing the impulse response (equivalently, the transfer function between the antenna arrays at both link ends. We also review some MIMO models that are included in current standardization activities for the purpose of reproducible and comparable MIMO system evaluations. Finally, we describe a couple of key features of channels and radio propagation which are not sufficiently included in current MIMO models.

  15. Survey of Channel and Radio Propagation Models for Wireless MIMO Systems

    Directory of Open Access Journals (Sweden)

    Kyösti P

    2007-01-01

    Full Text Available This paper provides an overview of the state-of-the-art radio propagation and channel models for wireless multiple-input multiple-output (MIMO systems. We distinguish between physical models and analytical models and discuss popular examples from both model types. Physical models focus on the double-directional propagation mechanisms between the location of transmitter and receiver without taking the antenna configuration into account. Analytical models capture physical wave propagation and antenna configuration simultaneously by describing the impulse response (equivalently, the transfer function between the antenna arrays at both link ends. We also review some MIMO models that are included in current standardization activities for the purpose of reproducible and comparable MIMO system evaluations. Finally, we describe a couple of key features of channels and radio propagation which are not sufficiently included in current MIMO models.

  16. Modeling, Control and Coordination of Helicopter Systems

    CERN Document Server

    Ren, Beibei; Chen, Chang; Fua, Cheng-Heng; Lee, Tong Heng

    2012-01-01

    Modeling, Control and Coordination of Helicopter Systems provides a comprehensive treatment of helicopter systems, ranging from related nonlinear flight dynamic modeling and stability analysis to advanced control design for single helicopter systems, and also covers issues related to the coordination and formation control of multiple helicopter systems to achieve high performance tasks. Ensuring stability in helicopter flight is a challenging problem for nonlinear control design and development. This book is a valuable reference on modeling, control and coordination of helicopter systems,providing readers with practical solutions for the problems that still plague helicopter system design and implementation. Readers will gain a complete picture of helicopters at the systems level, as well as a better understanding of the technical intricacies involved. This book also: Presents a complete picture of modeling, control and coordination for helicopter systems Provides a modeling platform for a general class of ro...

  17. Electronic Education System Model-2

    Science.gov (United States)

    Güllü, Fatih; Kuusik, Rein; Laanpere, Mart

    2015-01-01

    In this study we presented new EES Model-2 extended from EES model for more productive implementation in e-learning process design and modelling in higher education. The most updates were related to uppermost instructional layer. We updated learning processes object of the layer for adaptation of educational process for young and old people,…

  18. Network and adaptive system of systems modeling and analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Lawton, Craig R.; Campbell, James E. Dr. (.; .); Anderson, Dennis James; Eddy, John P.

    2007-05-01

    This report documents the results of an LDRD program entitled ''Network and Adaptive System of Systems Modeling and Analysis'' that was conducted during FY 2005 and FY 2006. The purpose of this study was to determine and implement ways to incorporate network communications modeling into existing System of Systems (SoS) modeling capabilities. Current SoS modeling, particularly for the Future Combat Systems (FCS) program, is conducted under the assumption that communication between the various systems is always possible and occurs instantaneously. A more realistic representation of these communications allows for better, more accurate simulation results. The current approach to meeting this objective has been to use existing capabilities to model network hardware reliability and adding capabilities to use that information to model the impact on the sustainment supply chain and operational availability.

  19. On Verification Modelling of Embedded Systems

    NARCIS (Netherlands)

    Brinksma, Ed; Mader, Angelika

    2004-01-01

    Computer-aided verification of embedded systems hinges on the availability of good verification models of the systems at hand. Such models must be much simpler than full design models or specifications to be of practical value, because of the unavoidable combinatorial complexities in the verificatio

  20. Applying Modeling Tools to Ground System Procedures

    Science.gov (United States)

    Di Pasquale, Peter

    2012-01-01

    As part of a long-term effort to revitalize the Ground Systems (GS) Engineering Section practices, Systems Modeling Language (SysML) and Business Process Model and Notation (BPMN) have been used to model existing GS products and the procedures GS engineers use to produce them.

  1. System Level Modelling and Performance Estimation of Embedded Systems

    DEFF Research Database (Denmark)

    Tranberg-Hansen, Anders Sejer

    is simulation based and allows performance estimation to be carried out throughout all design phases ranging from early functional to cycle accurate and bit true descriptions of the system, modelling both hardware and software components in a unied way. Design space exploration and performance estimation...... an efficient system level design methodology, a modelling framework for performance estimation and design space exploration at the system level is required. This thesis presents a novel component based modelling framework for system level modelling and performance estimation of embedded systems. The framework...... is performed by having the framework produce detailed quantitative information about the system model under investigation. The project is part of the national Danish research project, Danish Network of Embedded Systems (DaNES), which is funded by the Danish National Advanced Technology Foundation. The project...

  2. EXPOSURE ANALYSIS MODELING SYSTEM (EXAMS): USER MANUAL AND SYSTEM DOCUMENTATION

    Science.gov (United States)

    The Exposure Analysis Modeling System, first published in 1982 (EPA-600/3-82-023), provides interactive computer software for formulating aquatic ecosystem models and rapidly evaluating the fate, transport, and exposure concentrations of synthetic organic chemicals - pesticides, ...

  3. Reply to the comment of S. Rayne on "QSAR model reproducibility and applicability: A case study of rate constants of hydroxyl radical reaction models applied to polybrominated diphenyl ethers and (benzo-)triazoles".

    Science.gov (United States)

    Gramatica, Paola; Kovarich, Simona; Roy, Partha Pratim

    2013-07-30

    We appreciate the interest of Dr. Rayne on our article and we completely agree that the dataset of (benzo-)triazoles, which were screened by the hydroxyl radical reaction quantitative structure-activity relationship (QSAR) model, was not only composed of benzo-triazoles but also included some simpler triazoles (without the condensed benzene ring), such as the chemicals listed by Dr. Rayne, as well as some related heterocycles (also few not aromatic). We want to clarify that in this article (as well as in other articles in which the same dataset was screened), for conciseness, the abbreviations (B)TAZs and BTAZs were used as general (and certainly too simplified) notations meaning an extended dataset of benzo-triazoles, triazoles, and related compounds. Copyright © 2013 Wiley Periodicals, Inc.

  4. Effective Reproducible Research with Org-Mode and Git

    OpenAIRE

    Stanisic, Luka; Legrand, Arnaud

    2014-01-01

    International audience; In this article we address the question of developing a lightweight and effective workflow for conducting experimental research on modern parallel computer systems in a reproducible way. Our workflowsimply builds on two well-known tools (Org-mode and Git) and enablesto address issues such as provenance tracking, experimental setup reconstruction, replicable analysis. Although this workflow is perfectible and cannot be seen as a final solution, we have been usingit for ...

  5. Pǎun's systems as models of economic systems

    Institute of Scientific and Technical Information of China (English)

    Waldemar Korczynski

    2007-01-01

    In the paper a concept for modeling the economic systems by the formalism of Pǎun's systems is proposed. The main idea is to represent economic systems as homomorphic images of Petri nets corresponding to the (super) cells of Pǎun's systems.

  6. Data Processing Workflows to Support Reproducible Data-driven Research in Hydrology

    Science.gov (United States)

    Goodall, J. L.; Essawy, B.; Xu, H.; Rajasekar, A.; Moore, R. W.

    2015-12-01

    Geoscience analyses often require the use of existing data sets that are large, heterogeneous, and maintained by different organizations. A particular challenge in creating reproducible analyses using these data sets is automating the workflows required to transform raw datasets into model specific input files and finally into publication ready visualizations. Data grids, such as the Integrated Rule-Oriented Data System (iRODS), are architectures that allow scientists to access and share large data sets that are geographically distributed on the Internet, but appear to the scientist as a single file management system. The DataNet Federation Consortium (DFC) project is built on iRODS and aims to demonstrate data and computational interoperability across scientific communities. This paper leverages iRODS and the DFC to demonstrate how hydrological modeling workflows can be encapsulated as workflows using the iRODS concept of Workflow Structured Objects (WSO). An example use case is presented for automating hydrologic model post-processing routines that demonstrates how WSOs can be created and used within the DFC to automate the creation of data visualizations from large model output collections. By co-locating the workflow used to create the visualization with the data collection, the use case demonstrates how data grid technology aids in reuse, reproducibility, and sharing of workflows within scientific communities.

  7. Modeling Control Situations in Power System Operations

    DEFF Research Database (Denmark)

    Saleem, Arshad; Lind, Morten; Singh, Sri Niwas

    2010-01-01

    Increased interconnection and loading of the power system along with deregulation has brought new challenges for electric power system operation, control and automation. Traditional power system models used in intelligent operation and control are highly dependent on the task purpose. Thus, a model...... for intelligent operation and control must represent system features, so that information from measurements can be related to possible system states and to control actions. These general modeling requirements are well understood, but it is, in general, difficult to translate them into a model because of the lack...... of explicit principles for model construction. This paper presents a work on using explicit means-ends model based reasoning about complex control situations which results in maintaining consistent perspectives and selecting appropriate control action for goal driven agents. An example of power system...

  8. Modeling Control Situations in Power System Operations

    DEFF Research Database (Denmark)

    Saleem, Arshad; Lind, Morten; Singh, Sri Niwas

    2010-01-01

    Increased interconnection and loading of the power system along with deregulation has brought new challenges for electric power system operation, control and automation. Traditional power system models used in intelligent operation and control are highly dependent on the task purpose. Thus, a model...... for intelligent operation and control must represent system features, so that information from measurements can be related to possible system states and to control actions. These general modeling requirements are well understood, but it is, in general, difficult to translate them into a model because of the lack...... of explicit principles for model construction. This paper presents a work on using explicit means-ends model based reasoning about complex control situations which results in maintaining consistent perspectives and selecting appropriate control action for goal driven agents. An example of power system...

  9. Second Order Kinetic Modeling of Headspace Solid Phase Microextraction of Flavors Released from Selected Food Model Systems

    Directory of Open Access Journals (Sweden)

    Jiyuan Zhang

    2014-09-01

    Full Text Available The application of headspace-solid phase microextraction (HS-SPME has been widely used in various fields as a simple and versatile method, yet challenging in quantification. In order to improve the reproducibility in quantification, a mathematical model with its root in psychological modeling and chemical reactor modeling was developed, describing the kinetic behavior of aroma active compounds extracted by SPME from two different food model systems, i.e., a semi-solid food and a liquid food. The model accounted for both adsorption and release of the analytes from SPME fiber, which occurred simultaneously but were counter-directed. The model had four parameters and their estimated values were found to be more reproducible than the direct measurement of the compounds themselves by instrumental analysis. With the relative standard deviations (RSD of each parameter less than 5% and root mean square error (RMSE less than 0.15, the model was proved to be a robust one in estimating the release of a wide range of low molecular weight acetates at three environmental temperatures i.e., 30, 40 and 60 °C. More insights of SPME behavior regarding the small molecule analytes were also obtained through the kinetic parameters and the model itself.

  10. Generic Model Host System Design

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Chungming; /SLAC; Wu, Juhao; /SLAC; Qiang, Ji; /LBL, Berkeley; Shen, Guobao; /Brookhaven

    2012-06-22

    There are many simulation codes for accelerator modelling; each one has some strength but not all. A platform which can host multiple modelling tools would be ideal for various purposes. The model platform along with infrastructure support can be used not only for online applications but also for offline purposes. Collaboration is formed for the effort of providing such a platform. In order to achieve such a platform, a set of common physics data structure has to be set. Application Programming Interface (API) for physics applications should also be defined within a model data provider. A preliminary platform design and prototype is discussed.

  11. Four MATLAB-Simulink models ofphotovoltaic system

    Directory of Open Access Journals (Sweden)

    Jawad Radhi Mahmood, Nasir Hussein Selman

    2016-01-01

    Full Text Available This paper presents four different MATLAB models to simulate the output I-V and P-V characteristics of photovoltaic (PV cells or systems. All of the models are implemented with Matlab-Simulink. Detailed modeling procedure for one-diode equivalent circuit model with all equations and numerical values is presented. The parameters required for the modeling have been taken from manufacturer's datasheet for 240W SOLIMPEKS solar panel. I-V and P-V characteristics of a typical 1.92 kW PV system have been simulated using the proposed models. The simulation took into account the sunlight insolation and temperature effect. Results of the models are validated with I-V and P-V curves provided by the manufacturer(s. The proposed models are very useful for those interested in working in the field of solar systems because they emulate and analyze the characteristics of all the solar systems easily.

  12. CTL Model Update for System Modifications

    CERN Document Server

    Ding, Yulin; Zhang, Yan; Zhang, Y; 10.1613/jair.2420

    2011-01-01

    Model checking is a promising technology, which has been applied for verification of many hardware and software systems. In this paper, we introduce the concept of model update towards the development of an automatic system modification tool that extends model checking functions. We define primitive update operations on the models of Computation Tree Logic (CTL) and formalize the principle of minimal change for CTL model update. These primitive update operations, together with the underlying minimal change principle, serve as the foundation for CTL model update. Essential semantic and computational characterizations are provided for our CTL model update approach. We then describe a formal algorithm that implements this approach. We also illustrate two case studies of CTL model updates for the well-known microwave oven example and the Andrew File System 1, from which we further propose a method to optimize the update results in complex system modifications.

  13. Reproducibility of scoring emphysema by HRCT

    Energy Technology Data Exchange (ETDEWEB)

    Malinen, A.; Partanen, K.; Rytkoenen, H.; Vanninen, R. [Kuopio Univ. Hospital (Finland). Dept. of Clinical Radiology; Erkinjuntti-Pekkanen, R. [Kuopio Univ. Hospital (Finland). Dept. of Pulmonary Diseases

    2002-04-01

    Purpose: We evaluated the reproducibility of three visual scoring methods of emphysema and compared these methods with pulmonary function tests (VC, DLCO, FEV1 and FEV%) among farmer's lung patients and farmers. Material and Methods: Three radiologists examined high-resolution CT images of farmer's lung patients and their matched controls (n=70) for chronic interstitial lung diseases. Intraobserver reproducibility and interobserver variability were assessed for three methods: severity, Sanders' (extent) and Sakai. Pulmonary function tests as spirometry and diffusing capacity were measured. Results: Intraobserver -values for all three methods were good (0.51-0.74). Interobserver varied from 0.35 to 0.72. The Sanders' and the severity methods correlated strongly with pulmonary function tests, especially DLCO and FEV1. Conclusion: The Sanders' method proved to be reliable in evaluating emphysema, in terms of good consistency of interpretation and good correlation with pulmonary function tests.

  14. Reproducibility of electroretinograms recorded with DTL electrodes.

    Science.gov (United States)

    Hébert, M; Lachapelle, P; Dumont, M

    The purpose of this study was to examine whether the use of the DTL fiber electrode yields stable and reproducible electroretinographic recordings. To do so, luminance response function, derived from dark-adapted electroretinograms, was obtained from both eyes of 10 normal subjects at two recording sessions spaced by 7-14 days. The data thus generated was used to calculate Naka-Rushton Vmax and k parameters and values obtained at the two recording sessions were compared. Our results showed that there was no significant difference in the values of Vmax and k calculated from the data generated at the two recording sessions. The above clearly demonstrate that the use of the DTL fiber electrode does not jeopardize, in any way, the stability and reproducibility of ERG responses.

  15. Repeatability and Reproducibility of Virtual Subjective Refraction.

    Science.gov (United States)

    Perches, Sara; Collados, M Victoria; Ares, Jorge

    2016-10-01

    To establish the repeatability and reproducibility of a virtual refraction process using simulated retinal images. With simulation software, aberrated images corresponding with each step of the refraction process were calculated following the typical protocol of conventional subjective refraction. Fifty external examiners judged simulated retinal images until the best sphero-cylindrical refraction and the best visual acuity were achieved starting from the aberrometry data of three patients. Data analyses were performed to assess repeatability and reproducibility of the virtual refraction as a function of pupil size and aberrometric profile of different patients. SD values achieved in three components of refraction (M, J0, and J45) are lower than 0.25D in repeatability analysis. Regarding reproducibility, we found SD values lower than 0.25D in the most cases. When the results of virtual refraction with different pupil diameters (4 and 6 mm) were compared, the mean of differences (MoD) obtained were not clinically significant (less than 0.25D). Only one of the aberrometry profiles with high uncorrected astigmatism shows poor results for the M component in reproducibility and pupil size dependence analysis. In all cases, vision achieved was better than 0 logMAR. A comparison between the compensation obtained with virtual and conventional subjective refraction was made as an example of this application, showing good quality retinal images in both processes. The present study shows that virtual refraction has similar levels of precision as conventional subjective refraction. Moreover, virtual refraction has also shown that when high low order astigmatism is present, the refraction result is less precise and highly dependent on pupil size.

  16. Data Identifiers and Citations Enable Reproducible Science

    Science.gov (United States)

    Tilmes, C.

    2011-12-01

    Modern science often involves data processing with tremendous volumes of data. Keeping track of that data has been a growing challenge for data center. Researchers who access and use that data don't always reference and cite their data sources adequately for consumers of their research to follow their methodology or reproduce their analyses or experiments. Recent research has led to recommendations for good identifiers and citations that can help address this problem. This paper will describe some of the best practices in data identifiers, reference and citation. Using a simplified example scenario based on a long term remote sensing satellite mission, it will explore issues in identifying dynamic data sets and the importance of good data citations for reproducibility. It will describe the difference between granule and collection level identifiers, using UUIDs and DOIs to illustrate some recommendations for developing identifiers and assigning them during data processing. As data processors create data products, the provenance of the input products and precise steps that led to their creation are recorded and published for users of the data to see. As researchers access the data from an archive, they can use the provenance to help understand the genesis of the data, which could have effects on their usage of the data. By citing the data on publishing their research, others can retrieve the precise data used in their research and reproduce the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to reproduce the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.

  17. Computational Models for Nonlinear Aeroelastic Systems Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Clear Science Corp. and Duke University propose to develop and demonstrate new and efficient computational methods of modeling nonlinear aeroelastic systems. The...

  18. Model Updating Nonlinear System Identification Toolbox Project

    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...

  19. Modeling and analysis of biomass production systems

    Energy Technology Data Exchange (ETDEWEB)

    Mishoe, J.W.; Lorber, M.N.; Peart, R.M.; Fluck, R.C.; Jones, J.W.

    1984-01-01

    BIOMET is an interactive simulation model that is used to analyze specific biomass and methane production systems. The system model is composed of crop growth models, harvesting, transportation, conversion and economic submodels. By use of menus the users can configure the structure and set selected parameters of the system to analyze the effects of variables within the component models. For example, simulations of a water hyacinth system resulted in yields of 63, 48 and 37 mg/ha/year for different harvest schedules. For napier grass, unit methane costs were $3.04, $2.86 and $2.98 for various yields of biomass. 10 references.

  20. Error Propagation in a System Model

    Science.gov (United States)

    Schloegel, Kirk (Inventor); Bhatt, Devesh (Inventor); Oglesby, David V. (Inventor); Madl, Gabor (Inventor)

    2015-01-01

    Embodiments of the present subject matter can enable the analysis of signal value errors for system models. In an example, signal value errors can be propagated through the functional blocks of a system model to analyze possible effects as the signal value errors impact incident functional blocks. This propagation of the errors can be applicable to many models of computation including avionics models, synchronous data flow, and Kahn process networks.

  1. Hydrological modeling in forested systems

    Science.gov (United States)

    H.E. Golden; G.R. Evenson; S. Tian; Devendra Amatya; Ge Sun

    2015-01-01

    Characterizing and quantifying interactions among components of the forest hydrological cycle is complex and usually requires a combination of field monitoring and modelling approaches (Weiler and McDonnell, 2004; National Research Council, 2008). Models are important tools for testing hypotheses, understanding hydrological processes and synthesizing experimental data...

  2. Stochastic Modelling of Energy Systems

    DEFF Research Database (Denmark)

    Andersen, Klaus Kaae

    2001-01-01

    equations are expressed in terms of stochastic differential equations. From a theoretical viewpoint the techniques for experimental design, parameter estimation and model validation are considered. From the practical viewpoint emphasis is put on how this methods can be used to construct models adequate...

  3. Dynamic modelling of nitrous oxide emissions from three Swedish sludge liquor treatment systems

    DEFF Research Database (Denmark)

    Lindblom, E.; Arnell, M.; Flores-Alsina, X.

    2014-01-01

    The objective of this paper is to model the dynamics and validate the results of nitrous oxide (N2O)emissions from three Swedish nitrifying/denitrifying, nitritation and anammox systems treating real anaerobic digester sludge liquor. The Activated Sludge Model No. 1 is extended to describe N2O......) a moving-bed biofilm reactor. Results show that the calibrated model is partly capable of reproducing the behaviour of N2O as well as the nitritation/nitrification/denitrification dynamics. However, the results emphasize that additional work is required before N2O emissions from sludge liquor treatment...

  4. Dynamic modelling of nitrous oxide emissions from three Swedish sludge liquor treatment systems

    DEFF Research Database (Denmark)

    Lindblom, E.; Arnell, M.; Flores-Alsina, X.

    2016-01-01

    The objective of this paper is to model the dynamics and validate the results of nitrous oxide (N2O)emissions from three Swedish nitrifying/denitrifying, nitritation and anammox systems treating real anaerobic digester sludge liquor. The Activated Sludge Model No. 1 is extended to describe N2O......) a moving-bed biofilm reactor. Results show that the calibrated model is partly capable of reproducing the behaviour of N2O as well as the nitritation/nitrification/denitrification dynamics. However, the results emphasize that additional work is required before N2O emissions from sludge liquor treatment...

  5. Tissue Doppler imaging reproducibility during exercise.

    Science.gov (United States)

    Bougault, V; Nottin, S; Noltin, S; Doucende, G; Obert, P

    2008-05-01

    Tissue Doppler imaging (TDI) is an echocardiographic technique used during exercising to improve the accuracy of a cardiovascular diagnostic. The validity of TDI requires its reproducibility, which has never been challenged during moderate to maximal intensity exercising. The present study was specifically designed to assess the transmitral Doppler and pulsed TDI reproducibility in 19 healthy men, who had undergone two identical semi-supine maximal exercise tests on a cycle ergometer. Systolic (S') and diastolic (E') tissue velocities at the septal and lateral walls as well as early transmitral velocities (E) were assessed during exercise up to maximal effort. The data were compared between the two tests at 40 %, 60 %, 80 % and 100 % of maximal aerobic power. Despite upper body movements and hyperventilation, good quality echocardiographic images were obtained in each case. Regardless of exercise intensity, no differences were noticed between the two tests for all measurements. The variation coefficients for Doppler variables ranged from 3 % to 9 % over the transition from rest to maximal exercise. The random measurement error was, on average, 5.8 cm/s for E' and 4.4 cm/s for S'. Overall, the reproducibility of TDI was acceptable. Tissue Doppler imaging can be used to accurately evaluate LV diastolic and/or systolic function for this range of exercise intensity.

  6. How to Write a Reproducible Paper

    Science.gov (United States)

    Irving, D. B.

    2016-12-01

    The geosciences have undergone a computational revolution in recent decades, to the point where almost all modern research relies heavily on software and code. Despite this profound change in the research methods employed by geoscientists, the reporting of computational results has changed very little in academic journals. This lag has led to something of a reproducibility crisis, whereby it is impossible to replicate and verify most of today's published computational results. While it is tempting to decry the slow response of journals and funding agencies in the face of this crisis, there are very few examples of reproducible research upon which to base new communication standards. In an attempt to address this deficiency, this presentation will describe a procedure for reporting computational results that was employed in a recent Journal of Climate paper. The procedure was developed to be consistent with recommended computational best practices and seeks to minimize the time burden on authors, which has been identified as the most important barrier to publishing code. It should provide a starting point for geoscientists looking to publish reproducible research, and could be adopted by journals as a formal minimum communication standard.

  7. Tools and techniques for computational reproducibility.

    Science.gov (United States)

    Piccolo, Stephen R; Frampton, Michael B

    2016-07-11

    When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced because of complexities in how software is packaged, installed, and executed-and because of limitations associated with how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges; here we describe seven such strategies. With a broad scientific audience in mind, we describe the strengths and limitations of each approach, as well as the circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.

  8. Stochastic Modelling of Hydrologic Systems

    DEFF Research Database (Denmark)

    Jonsdottir, Harpa

    2007-01-01

    In this PhD project several stochastic modelling methods are studied and applied on various subjects in hydrology. The research was prepared at Informatics and Mathematical Modelling at the Technical University of Denmark. The thesis is divided into two parts. The first part contains an introduct......In this PhD project several stochastic modelling methods are studied and applied on various subjects in hydrology. The research was prepared at Informatics and Mathematical Modelling at the Technical University of Denmark. The thesis is divided into two parts. The first part contains...... an introduction and an overview of the papers published. Then an introduction to basic concepts in hydrology along with a description of hydrological data is given. Finally an introduction to stochastic modelling is given. The second part contains the research papers. In the research papers the stochastic methods...

  9. Hypervirial Models of Stellar Systems

    CERN Document Server

    Evans, N W

    2005-01-01

    A family of cusped potential-density pairs is introduced for modelling galaxies and dark haloes. The density profile is cusped like 1/r^(2-p) at small radii. The distribution function takes the simple form L^(p-2) E^([3p+1]/2) (where E is the binding energy and L is the angular momentum). The models all possess the remarkable property that the virial theorem holds locally, from which they earn their name as the hypervirial family. Famously, this property was first discovered by Eddington to hold for the Plummer model in 1916. In fact, the seductive properties of the Plummer model extend to the whole hypervirial family, including the members possessing the cosmologically important cusps with density behaving like 1/r or 1/r^1.5 or 1/r^1.33. The intrinsic and projected properties of the family of models are discussed in some detail.

  10. Semantic models for adaptive interactive systems

    CERN Document Server

    Hussein, Tim; Lukosch, Stephan; Ziegler, Jürgen; Calvary, Gaëlle

    2013-01-01

    Providing insights into methodologies for designing adaptive systems based on semantic data, and introducing semantic models that can be used for building interactive systems, this book showcases many of the applications made possible by the use of semantic models.Ontologies may enhance the functional coverage of an interactive system as well as its visualization and interaction capabilities in various ways. Semantic models can also contribute to bridging gaps; for example, between user models, context-aware interfaces, and model-driven UI generation. There is considerable potential for using

  11. Model reduction of linear conservative mechanical systems

    NARCIS (Netherlands)

    Schaft, van der A.J.; Oeloff, J.E.

    1990-01-01

    An approach for model reduction of linear conservative or weakly damped mechanical systems is proposed. It is based on the balancing of an associated gradient system. It uses the joint knowledge of the system matrix and the input and output matrices of the Hamiltonian system. The key idea is to asso

  12. Modeling complex work systems - method meets reality

    OpenAIRE

    Veer, van der, C.G.; Hoeve, Machteld; Lenting, Bert F.

    1996-01-01

    Modeling an existing task situation is often a first phase in the (re)design of information systems. For complex systems design, this model should consider both the people and the organization involved, the work, and situational aspects. Groupware Task Analysis (GTA) as part of a method for the design of complex systems, has been applied in a situation of redesign of a Dutch public administration system. The most feasible method to collect information in this case was ethnography, the resulti...

  13. Digital clocks: simple Boolean models can quantitatively describe circadian systems.

    Science.gov (United States)

    Akman, Ozgur E; Watterson, Steven; Parton, Andrew; Binns, Nigel; Millar, Andrew J; Ghazal, Peter

    2012-09-07

    The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be entrained to the external 24-h day-night cycle, enabling organisms to optimally time biochemical processes relative to dawn and dusk. In recent years, computational models based on differential equations have become useful tools for dissecting and quantifying the complex regulatory relationships underlying the clock's oscillatory dynamics. However, optimizing the large parameter sets characteristic of these models places intense demands on both computational and experimental resources, limiting the scope of in silico studies. Here, we develop an approach based on Boolean logic that dramatically reduces the parametrization, making the state and parameter spaces finite and tractable. We introduce efficient methods for fitting Boolean models to molecular data, successfully demonstrating their application to synthetic time courses generated by a number of established clock models, as well as experimental expression levels measured using luciferase imaging. Our results indicate that despite their relative simplicity, logic models can (i) simulate circadian oscillations with the correct, experimentally observed phase relationships among genes and (ii) flexibly entrain to light stimuli, reproducing the complex responses to variations in daylength generated by more detailed differential equation formulations. Our work also demonstrates that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data. By presenting the first Boolean models of circadian circuits together with general techniques for their optimization, we hope to establish a new framework for the systematic modelling of more complex clocks, as well as other circuits with different qualitative dynamics. In particular, we anticipate

  14. Modeling of power electronic systems with EMTP

    Science.gov (United States)

    Tam, Kwa-Sur; Dravid, Narayan V.

    1989-01-01

    In view of the potential impact of power electronics on power systems, there is need for a computer modeling/analysis tool to perform simulation studies on power systems with power electronic components as well as to educate engineering students about such systems. The modeling of the major power electronic components of the NASA Space Station Freedom Electric Power System is described along with ElectroMagnetic Transients Program (EMTP) and it is demonstrated that EMTP can serve as a very useful tool for teaching, design, analysis, and research in the area of power systems with power electronic components. EMTP modeling of power electronic circuits is described and simulation results are presented.

  15. Models of the venous system

    DEFF Research Database (Denmark)

    Mehlsen, J

    2000-01-01

    of the venous system require at least three elements: a resistor, a capacitor and an inductor, with the latter being of more importance in the venous than in the arterial system. Non-linearities must be considered in pressure/flow relations in the small venules, during venous collapse, or low flow conditions...

  16. Hybrid Model for Cascading Outage in a Power System: A Numerical Study

    Science.gov (United States)

    Susuki, Yoshihiko; Takatsuji, Yu; Hikihara, Takashi

    Analysis of cascading outages in power systems is important for understanding why large blackouts emerge and how to prevent them. Cascading outages are complex dynamics of power systems, and one cause of them is the interaction between swing dynamics of synchronous machines and protection operation of relays and circuit breakers. This paper uses hybrid dynamical systems as a mathematical model for cascading outages caused by the interaction. Hybrid dynamical systems can combine families of flows describing swing dynamics with switching rules that are based on protection operation. This paper refers to data on a cascading outage in the September 2003 blackout in Italy and shows a hybrid dynamical system by which propagation of outages reproduced is consistent with the data. This result suggests that hybrid dynamical systems can provide an effective model for the analysis of cascading outages in power systems.

  17. Reproducibility of magnetic resonance perfusion imaging.

    Directory of Open Access Journals (Sweden)

    Xiaomeng Zhang

    Full Text Available Dynamic MR biomarkers (T2*-weighted or susceptibility-based and T1-weighted or relaxivity-enhanced have been applied to assess tumor perfusion and its response to therapies. A significant challenge in the development of reliable biomarkers is a rigorous assessment and optimization of reproducibility. The purpose of this study was to determine the measurement reproducibility of T1-weighted dynamic contrast-enhanced (DCE-MRI and T2*-weighted dynamic susceptibility contrast (DSC-MRI with two contrast agents (CA of different molecular weight (MW: gadopentetate (Gd-DTPA, 0.5 kDa and Gadomelitol (P792, 6.5 kDa. Each contrast agent was tested with eight mice that had subcutaneous MDA-MB-231 breast xenograft tumors. Each mouse was imaged with a combined DSC-DCE protocol three times within one week to achieve measures of reproducibility. DSC-MRI results were evaluated with a contrast to noise ratio (CNR efficiency threshold. There was a clear signal drop (>95% probability threshold in the DSC of normal tissue, while signal changes were minimal or non-existent (<95% probability threshold in tumors. Mean within-subject coefficient of variation (wCV of relative blood volume (rBV in normal tissue was 11.78% for Gd-DTPA and 6.64% for P792. The intra-class correlation coefficient (ICC of rBV in normal tissue was 0.940 for Gd-DTPA and 0.978 for P792. The inter-subject correlation coefficient was 0.092. Calculated K(trans from DCE-MRI showed comparable reproducibility (mean wCV, 5.13% for Gd-DTPA, 8.06% for P792. ICC of K(trans showed high intra-subject reproducibility (ICC = 0.999/0.995 and inter-subject heterogeneity (ICC = 0.774. Histograms of K(trans distributions for three measurements had high degrees of overlap (sum of difference of the normalized histograms <0.01. These results represent homogeneous intra-subject measurement and heterogeneous inter-subject character of biological population, suggesting that perfusion MRI could be an imaging biomarker to

  18. Learning Markov models for stationary system behaviors

    DEFF Research Database (Denmark)

    Chen, Yingke; Mao, Hua; Jaeger, Manfred

    2012-01-01

    Establishing an accurate model for formal verification of an existing hardware or software system is often a manual process that is both time consuming and resource demanding. In order to ease the model construction phase, methods have recently been proposed for automatically learning accurate...... system models from data in the form of observations of the target system. Common for these approaches is that they assume the data to consist of multiple independent observation sequences. However, for certain types of systems, in particular many running embedded systems, one would only have access...... the learned model. Experiments demonstrate that system properties (formulated as stationary probabilities of LTL formulas) can be reliably identified using the learned model....

  19. Refining the Ciona intestinalis model of central nervous system regeneration.