WorldWideScience

Sample records for models reproduce observed

  1. Dysplastic naevus: histological criteria and their inter-observer reproducibility.

    Science.gov (United States)

    Hastrup, N; Clemmensen, O J; Spaun, E; Søndergaard, K

    1994-06-01

    Forty melanocytic lesions were examined in a pilot study, which was followed by a final series of 100 consecutive melanocytic lesions, in order to evaluate the inter-observer reproducibility of the histological criteria proposed for the dysplastic naevus. The specimens were examined in a blind fashion by four observers. Analysis by kappa statistics showed poor reproducibility of nuclear features, while reproducibility of architectural features was acceptable, improving in the final series. Consequently, we cannot apply the combined criteria of cytological and architectural features with any confidence in the diagnosis of dysplastic naevus, and, until further studies have documented that architectural criteria alone will suffice in the diagnosis of dysplastic naevus, we, as pathologists, shall avoid this term.

  2. Evaluation of Oceanic Surface Observation for Reproducing the Upper Ocean Structure in ECHAM5/MPI-OM

    Science.gov (United States)

    Luo, Hao; Zheng, Fei; Zhu, Jiang

    2017-12-01

    Better constraints of initial conditions from data assimilation are necessary for climate simulations and predictions, and they are particularly important for the ocean due to its long climate memory; as such, ocean data assimilation (ODA) is regarded as an effective tool for seasonal to decadal predictions. In this work, an ODA system is established for a coupled climate model (ECHAM5/MPI-OM), which can assimilate all available oceanic observations using an ensemble optimal interpolation approach. To validate and isolate the performance of different surface observations in reproducing air-sea climate variations in the model, a set of observing system simulation experiments (OSSEs) was performed over 150 model years. Generally, assimilating sea surface temperature, sea surface salinity, and sea surface height (SSH) can reasonably reproduce the climate variability and vertical structure of the upper ocean, and assimilating SSH achieves the best results compared to the true states. For the El Niño-Southern Oscillation (ENSO), assimilating different surface observations captures true aspects of ENSO well, but assimilating SSH can further enhance the accuracy of ENSO-related feedback processes in the coupled model, leading to a more reasonable ENSO evolution and air-sea interaction over the tropical Pacific. For ocean heat content, there are still limitations in reproducing the long time-scale variability in the North Atlantic, even if SSH has been taken into consideration. These results demonstrate the effectiveness of assimilating surface observations in capturing the interannual signal and, to some extent, the decadal signal but still highlight the necessity of assimilating profile data to reproduce specific decadal variability.

  3. Guidelines for Reproducibly Building and Simulating Systems Biology Models.

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    Medley, J Kyle; Goldberg, Arthur P; Karr, Jonathan R

    2016-10-01

    Reproducibility is the cornerstone of the scientific method. However, currently, many systems biology models cannot easily be reproduced. This paper presents methods that address this problem. We analyzed the recent Mycoplasma genitalium whole-cell (WC) model to determine the requirements for reproducible modeling. We determined that reproducible modeling requires both repeatable model building and repeatable simulation. New standards and simulation software tools are needed to enhance and verify the reproducibility of modeling. New standards are needed to explicitly document every data source and assumption, and new deterministic parallel simulation tools are needed to quickly simulate large, complex models. We anticipate that these new standards and software will enable researchers to reproducibly build and simulate more complex models, including WC models.

  4. Reproducibility in Computational Neuroscience Models and Simulations

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    McDougal, Robert A.; Bulanova, Anna S.; Lytton, William W.

    2016-01-01

    Objective Like all scientific research, computational neuroscience research must be reproducible. Big data science, including simulation research, cannot depend exclusively on journal articles as the method to provide the sharing and transparency required for reproducibility. Methods Ensuring model reproducibility requires the use of multiple standard software practices and tools, including version control, strong commenting and documentation, and code modularity. Results Building on these standard practices, model sharing sites and tools have been developed that fit into several categories: 1. standardized neural simulators, 2. shared computational resources, 3. declarative model descriptors, ontologies and standardized annotations; 4. model sharing repositories and sharing standards. Conclusion A number of complementary innovations have been proposed to enhance sharing, transparency and reproducibility. The individual user can be encouraged to make use of version control, commenting, documentation and modularity in development of models. The community can help by requiring model sharing as a condition of publication and funding. Significance Model management will become increasingly important as multiscale models become larger, more detailed and correspondingly more difficult to manage by any single investigator or single laboratory. Additional big data management complexity will come as the models become more useful in interpreting experiments, thus increasing the need to ensure clear alignment between modeling data, both parameters and results, and experiment. PMID:27046845

  5. Intra-observer reproducibility and diagnostic performance of breast shear-wave elastography in Asian women.

    Science.gov (United States)

    Park, Hye Young; Han, Kyung Hwa; Yoon, Jung Hyun; Moon, Hee Jung; Kim, Min Jung; Kim, Eun-Kyung

    2014-06-01

    Our aim was to evaluate intra-observer reproducibility of shear-wave elastography (SWE) in Asian women. Sixty-four breast masses (24 malignant, 40 benign) were examined with SWE in 53 consecutive Asian women (mean age, 44.9 y old). Two SWE images were obtained for each of the lesions. The intra-observer reproducibility was assessed by intra-class correlation coefficients (ICC). We also evaluated various clinicoradiologic factors that can influence reproducibility in SWE. The ICC of intra-observer reproducibility was 0.789. In clinicoradiologic factor evaluation, masses surrounded by mixed fatty and glandular tissue (ICC: 0.619) showed lower intra-observer reproducibility compared with lesions that were surrounded by glandular tissue alone (ICC: 0.937; p breast SWE was excellent in Asian women. However, it may decrease when breast tissue is in a heterogeneous background. Therefore, SWE should be performed carefully in these cases. Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  6. NRFixer: Sentiment Based Model for Predicting the Fixability of Non-Reproducible Bugs

    Directory of Open Access Journals (Sweden)

    Anjali Goyal

    2017-08-01

    Full Text Available Software maintenance is an essential step in software development life cycle. Nowadays, software companies spend approximately 45\\% of total cost in maintenance activities. Large software projects maintain bug repositories to collect, organize and resolve bug reports. Sometimes it is difficult to reproduce the reported bug with the information present in a bug report and thus this bug is marked with resolution non-reproducible (NR. When NR bugs are reconsidered, a few of them might get fixed (NR-to-fix leaving the others with the same resolution (NR. To analyse the behaviour of developers towards NR-to-fix and NR bugs, the sentiment analysis of NR bug report textual contents has been conducted. The sentiment analysis of bug reports shows that NR bugs' sentiments incline towards more negativity than reproducible bugs. Also, there is a noticeable opinion drift found in the sentiments of NR-to-fix bug reports. Observations driven from this analysis were an inspiration to develop a model that can judge the fixability of NR bugs. Thus a framework, {NRFixer,} which predicts the probability of NR bug fixation, is proposed. {NRFixer} was evaluated with two dimensions. The first dimension considers meta-fields of bug reports (model-1 and the other dimension additionally incorporates the sentiments (model-2 of developers for prediction. Both models were compared using various machine learning classifiers (Zero-R, naive Bayes, J48, random tree and random forest. The bug reports of Firefox and Eclipse projects were used to test {NRFixer}. In Firefox and Eclipse projects, J48 and Naive Bayes classifiers achieve the best prediction accuracy, respectively. It was observed that the inclusion of sentiments in the prediction model shows a rise in the prediction accuracy ranging from 2 to 5\\% for various classifiers.

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

    International Nuclear Information System (INIS)

    Kornaat, Peter R.; Ceulemans, Ruth Y.T.; Kroon, Herman M.; Bloem, Johan L.; Riyazi, Naghmeh; Kloppenburg, Margreet; Carter, Wayne O.; Woodworth, Thasia G.

    2005-01-01

    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.)

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

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    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

  9. 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.

  10. Cyberinfrastructure to Support Collaborative and Reproducible Computational Hydrologic Modeling

    Science.gov (United States)

    Goodall, J. L.; Castronova, A. M.; Bandaragoda, C.; Morsy, M. M.; Sadler, J. M.; Essawy, B.; Tarboton, D. G.; Malik, T.; Nijssen, B.; Clark, M. P.; Liu, Y.; Wang, S. W.

    2017-12-01

    Creating cyberinfrastructure to support reproducibility of computational hydrologic models is an important research challenge. Addressing this challenge requires open and reusable code and data with machine and human readable metadata, organized in ways that allow others to replicate results and verify published findings. Specific digital objects that must be tracked for reproducible computational hydrologic modeling include (1) raw initial datasets, (2) data processing scripts used to clean and organize the data, (3) processed model inputs, (4) model results, and (5) the model code with an itemization of all software dependencies and computational requirements. HydroShare is a cyberinfrastructure under active development designed to help users store, share, and publish digital research products in order to improve reproducibility in computational hydrology, with an architecture supporting hydrologic-specific resource metadata. Researchers can upload data required for modeling, add hydrology-specific metadata to these resources, and use the data directly within HydroShare.org for collaborative modeling using tools like CyberGIS, Sciunit-CLI, and JupyterHub that have been integrated with HydroShare to run models using notebooks, Docker containers, and cloud resources. Current research aims to implement the Structure For Unifying Multiple Modeling Alternatives (SUMMA) hydrologic model within HydroShare to support hypothesis-driven hydrologic modeling while also taking advantage of the HydroShare cyberinfrastructure. The goal of this integration is to create the cyberinfrastructure that supports hypothesis-driven model experimentation, education, and training efforts by lowering barriers to entry, reducing the time spent on informatics technology and software development, and supporting collaborative research within and across research groups.

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

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    Wang, Fang; Yang, Song

    2018-02-01

    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

  12. Do detailed simulations with size-resolved microphysics reproduce basic features of observed cirrus ice size distributions?

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    Fridlind, A. M.; Atlas, R.; van Diedenhoven, B.; Ackerman, A. S.; Rind, D. H.; Harrington, J. Y.; McFarquhar, G. M.; Um, J.; Jackson, R.; Lawson, P.

    2017-12-01

    It has recently been suggested that seeding synoptic cirrus could have desirable characteristics as a geoengineering approach, but surprisingly large uncertainties remain in the fundamental parameters that govern cirrus properties, such as mass accommodation coefficient, ice crystal physical properties, aggregation efficiency, and ice nucleation rate from typical upper tropospheric aerosol. Only one synoptic cirrus model intercomparison study has been published to date, and studies that compare the shapes of observed and simulated ice size distributions remain sparse. Here we amend a recent model intercomparison setup using observations during two 2010 SPARTICUS campaign flights. We take a quasi-Lagrangian column approach and introduce an ensemble of gravity wave scenarios derived from collocated Doppler cloud radar retrievals of vertical wind speed. We use ice crystal properties derived from in situ cloud particle images, for the first time allowing smoothly varying and internally consistent treatments of nonspherical ice capacitance, fall speed, gravitational collection, and optical properties over all particle sizes in our model. We test two new parameterizations for mass accommodation coefficient as a function of size, temperature and water vapor supersaturation, and several ice nucleation scenarios. Comparison of results with in situ ice particle size distribution data, corrected using state-of-the-art algorithms to remove shattering artifacts, indicate that poorly constrained uncertainties in the number concentration of crystals smaller than 100 µm in maximum dimension still prohibit distinguishing which parameter combinations are more realistic. When projected area is concentrated at such sizes, the only parameter combination that reproduces observed size distribution properties uses a fixed mass accommodation coefficient of 0.01, on the low end of recently reported values. No simulations reproduce the observed abundance of such small crystals when the

  13. Stratospheric dryness: model simulations and satellite observations

    Directory of Open Access Journals (Sweden)

    J. Lelieveld

    2007-01-01

    Full Text Available The mechanisms responsible for the extreme dryness of the stratosphere have been debated for decades. A key difficulty has been the lack of comprehensive models which are able to reproduce the observations. Here we examine results from the coupled lower-middle atmosphere chemistry general circulation model ECHAM5/MESSy1 together with satellite observations. Our model results match observed temperatures in the tropical lower stratosphere and realistically represent the seasonal and inter-annual variability of water vapor. The model reproduces the very low water vapor mixing ratios (below 2 ppmv periodically observed at the tropical tropopause near 100 hPa, as well as the characteristic tape recorder signal up to about 10 hPa, providing evidence that the dehydration mechanism is well-captured. Our results confirm that the entry of tropospheric air into the tropical stratosphere is forced by large-scale wave dynamics, whereas radiative cooling regionally decelerates upwelling and can even cause downwelling. Thin cirrus forms in the cold air above cumulonimbus clouds, and the associated sedimentation of ice particles between 100 and 200 hPa reduces water mass fluxes by nearly two orders of magnitude compared to air mass fluxes. Transport into the stratosphere is supported by regional net radiative heating, to a large extent in the outer tropics. During summer very deep monsoon convection over Southeast Asia, centered over Tibet, moistens the stratosphere.

  14. Modeling reproducibility of porescale multiphase flow experiments

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    Ling, B.; Tartakovsky, A. M.; Bao, J.; Oostrom, M.; Battiato, I.

    2017-12-01

    Multi-phase flow in porous media is widely encountered in geological systems. Understanding immiscible fluid displacement is crucial for processes including, but not limited to, CO2 sequestration, non-aqueous phase liquid contamination and oil recovery. Microfluidic devices and porescale numerical models are commonly used to study multiphase flow in biological, geological, and engineered porous materials. In this work, we perform a set of drainage and imbibition experiments in six identical microfluidic cells to study the reproducibility of multiphase flow experiments. We observe significant variations in the experimental results, which are smaller during the drainage stage and larger during the imbibition stage. We demonstrate that these variations are due to sub-porescale geometry differences in microcells (because of manufacturing defects) and variations in the boundary condition (i.e.,fluctuations in the injection rate inherent to syringe pumps). Computational simulations are conducted using commercial software STAR-CCM+, both with constant and randomly varying injection rate. Stochastic simulations are able to capture variability in the experiments associated with the varying pump injection rate.

  15. Verification of land-atmosphere coupling in forecast models, reanalyses and land surface models using flux site observations.

    Science.gov (United States)

    Dirmeyer, Paul A; Chen, Liang; Wu, Jiexia; Shin, Chul-Su; Huang, Bohua; Cash, Benjamin A; Bosilovich, Michael G; Mahanama, Sarith; Koster, Randal D; Santanello, Joseph A; Ek, Michael B; Balsamo, Gianpaolo; Dutra, Emanuel; Lawrence, D M

    2018-02-01

    We confront four model systems in three configurations (LSM, LSM+GCM, and reanalysis) with global flux tower observations to validate states, surface fluxes, and coupling indices between land and atmosphere. Models clearly under-represent the feedback of surface fluxes on boundary layer properties (the atmospheric leg of land-atmosphere coupling), and may over-represent the connection between soil moisture and surface fluxes (the terrestrial leg). Models generally under-represent spatial and temporal variability relative to observations, which is at least partially an artifact of the differences in spatial scale between model grid boxes and flux tower footprints. All models bias high in near-surface humidity and downward shortwave radiation, struggle to represent precipitation accurately, and show serious problems in reproducing surface albedos. These errors create challenges for models to partition surface energy properly and errors are traceable through the surface energy and water cycles. The spatial distribution of the amplitude and phase of annual cycles (first harmonic) are generally well reproduced, but the biases in means tend to reflect in these amplitudes. Interannual variability is also a challenge for models to reproduce. Our analysis illuminates targets for coupled land-atmosphere model development, as well as the value of long-term globally-distributed observational monitoring.

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

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    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 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.

  17. Intra- and inter-observer reproducibility of global and regional magnetic resonance feature tracking derived strain parameters of the left and right ventricle

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Björn, E-mail: bjoernschmidt1989@gmx.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Dick, Anastasia, E-mail: anastasia-dick@web.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Treutlein, Melanie, E-mail: melanie-treutlein@web.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Schiller, Petra, E-mail: petra.schiller@uni-koeln.de [Institute of Medical Statistics, Informatics and Epidemiology, University of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Bunck, Alexander C., E-mail: alexander.bunck@uk-koeln.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Maintz, David, E-mail: david.maintz@uk-koeln.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Baeßler, Bettina, E-mail: bettina.baessler@uk-koeln.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany)

    2017-04-15

    Highlights: • Left and right ventricular CMR feature tracking is highly reproducible. • The only exception is radial strain and strain rate. • Sample size estimations are presented as a practical reference for future studies. - Abstract: Objectives: To investigate the reproducibility of regional and global strain and strain rate (SR) parameters of both ventricles and to determine sample sizes for all investigated strain and SR parameters in order to generate a practical reference for future studies. Materials and methods: The study population consisted of 20 healthy individuals and 20 patients with acute myocarditis. Cine sequences in three horizontal long axis views and a stack of short axis views covering the entire left and right ventricle (LV, RV) were retrospectively analysed using a dedicated feature tracking (FT) software algorithm (TOMTEC). For intra-observer analysis, one observer analysed CMR images of all patients and volunteers twice. For inter-observer analysis, three additional blinded observers analysed the same datasets once. Intra- and inter-observer reproducibility were tested in all patients and controls using Bland-Altman analyses, intra-class correlation coefficients (ICCs) and coefficients of variation. Results: Intra-observer reproducibility of global LV strain and SR parameters was excellent (range of ICCs: 0.81–1.00), the only exception being global radial SR with a poor reproducibility (ICC 0.23). On a regional level, basal and midventricular strain and SR parameters were more reproducible when compared to apical parameters. Inter-observer reproducibility of all LV parameters was slightly lower than intra-observer reproducibility, yet still good to excellent for all global and regional longitudinal and circumferential strain and SR parameters (range of ICCs: 0.66–0.93). Similar to the LV, all global RV longitudinal and circumferential strain and SR parameters showed an excellent reproducibility, (range of ICCs: 0.75–0

  18. Intra- and inter-observer reproducibility of global and regional magnetic resonance feature tracking derived strain parameters of the left and right ventricle

    International Nuclear Information System (INIS)

    Schmidt, Björn; Dick, Anastasia; Treutlein, Melanie; Schiller, Petra; Bunck, Alexander C.; Maintz, David; Baeßler, Bettina

    2017-01-01

    Highlights: • Left and right ventricular CMR feature tracking is highly reproducible. • The only exception is radial strain and strain rate. • Sample size estimations are presented as a practical reference for future studies. - Abstract: Objectives: To investigate the reproducibility of regional and global strain and strain rate (SR) parameters of both ventricles and to determine sample sizes for all investigated strain and SR parameters in order to generate a practical reference for future studies. Materials and methods: The study population consisted of 20 healthy individuals and 20 patients with acute myocarditis. Cine sequences in three horizontal long axis views and a stack of short axis views covering the entire left and right ventricle (LV, RV) were retrospectively analysed using a dedicated feature tracking (FT) software algorithm (TOMTEC). For intra-observer analysis, one observer analysed CMR images of all patients and volunteers twice. For inter-observer analysis, three additional blinded observers analysed the same datasets once. Intra- and inter-observer reproducibility were tested in all patients and controls using Bland-Altman analyses, intra-class correlation coefficients (ICCs) and coefficients of variation. Results: Intra-observer reproducibility of global LV strain and SR parameters was excellent (range of ICCs: 0.81–1.00), the only exception being global radial SR with a poor reproducibility (ICC 0.23). On a regional level, basal and midventricular strain and SR parameters were more reproducible when compared to apical parameters. Inter-observer reproducibility of all LV parameters was slightly lower than intra-observer reproducibility, yet still good to excellent for all global and regional longitudinal and circumferential strain and SR parameters (range of ICCs: 0.66–0.93). Similar to the LV, all global RV longitudinal and circumferential strain and SR parameters showed an excellent reproducibility, (range of ICCs: 0.75–0

  19. Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

    Science.gov (United States)

    Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

    2015-03-01

    A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

  20. Observational Constraints for Modeling Diffuse Molecular Clouds

    Science.gov (United States)

    Federman, S. R.

    2014-02-01

    Ground-based and space-borne observations of diffuse molecular clouds suggest a number of areas where further improvements to modeling efforts is warranted. I will highlight those that have the widest applicability. The range in CO fractionation caused by selective isotope photodissociation, in particular the large 12C16O/13C16O ratios observed toward stars in Ophiuchus, is not reproduced well by current models. Our ongoing laboratory measurements of oscillator strengths and predissociation rates for Rydberg transitions in CO isotopologues may help clarify the situtation. The CH+ abundance continues to draw attention. Small scale structure seen toward ζ Per may provide additional constraints on the possible synthesis routes. The connection between results from optical transitions and those from radio and sub-millimeter wave transitions requires further effort. A study of OH+ and OH toward background stars reveals that these species favor different environments. This brings to focus the need to model each cloud along the line of sight separately, and to allow the physical conditions to vary within an individual cloud, in order to gain further insight into the chemistry. Now that an extensive set of data on molecular excitation is available, the models should seek to reproduce these data to place further constraints on the modeling results.

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

    Directory of Open Access Journals (Sweden)

    N. Candogan Yossef

    2012-11-01

    Full Text Available 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 PCR-GLOBWB in reproducing the occurrence of past extremes in monthly discharge on a global scale. Global terrestrial hydrology from 1958 until 2001 is simulated by forcing PCR-GLOBWB with daily meteorological data obtained by downscaling the CRU dataset to daily fields using the ERA-40 reanalysis. Simulated discharge values are compared with observed monthly streamflow records for a selection of 20 large river basins that represent all continents and a wide range of climatic zones.

    We assess model skill in three ways all of which contribute different information on the potential forecasting skill of a GHM. First, the general skill of the model in reproducing hydrographs is evaluated. Second, model skill in reproducing significantly higher and lower flows than the monthly normals is assessed in terms of skill scores used for forecasts of categorical events. Third, model skill in reproducing flood and drought events is assessed by constructing binary contingency tables for floods and droughts for each basin. The skill is then compared to that of a simple estimation of discharge from the water balance (PE.

    The results show that the model has skill in all three types of assessments. After bias correction the model skill in simulating hydrographs is improved considerably. For most basins it is higher than that of the climatology. The skill is highest in reproducing monthly anomalies. The model also has skill in reproducing floods and droughts, with a markedly higher skill in floods. The model skill far exceeds that of the water balance estimate. We conclude that the prospect for using PCR-GLOBWB for monthly and seasonal forecasting of the occurrence of hydrological extremes is positive. We argue that this conclusion applies equally to other similar GHMs and

  2. 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

  3. Assessing trends in observed and modelled climate extremes over Australia in relation to future projections

    International Nuclear Information System (INIS)

    Alexander, Lisa

    2007-01-01

    Full text: Nine global coupled climate models were assessed for their ability to reproduce observed trends in a set of indices representing temperature and precipitation extremes over Australia. Observed trends for 1957-1999 were compared with individual and multi-modelled trends calculated over the same period. When averaged across Australia the magnitude of trends and interannual variability of temperature extremes were well simulated by most models, particularly for the warm nights index. Except for consecutive dry days, the majority of models also reproduced the correct sign of trend for precipitation extremes. A bootstrapping technique was used to show that most models produce plausible trends when averaged over Australia, although only heavy precipitation days simulated from the multi-model ensemble showed significant skill at reproducing the observed spatial pattern of trends. Two of the models with output from different forcings showed that only with anthropogenic forcing included could the models capture the observed areally averaged trend for some of the temperature indices, but the forcing made little difference to the models' ability to reproduce the spatial pattern of trends over Australia. Future projected changes in extremes using three emissions scenarios were also analysed. Australia shows a shift towards significant warming of temperature extremes with much longer dry spells interspersed with periods of increased extreme precipitation irrespective of the scenario used. More work is required to determine whether regional projected changes over Australia are robust

  4. Modeling and evaluating repeatability and reproducibility of ordinal classifications

    NARCIS (Netherlands)

    de Mast, J.; van Wieringen, W.N.

    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

  5. From alginate impressions to digital virtual models: accuracy and reproducibility.

    Science.gov (United States)

    Dalstra, Michel; Melsen, Birte

    2009-03-01

    To compare the accuracy and reproducibility of measurements performed on digital virtual models with those taken on plaster casts from models poured immediately after the impression was taken, the 'gold standard', and from plaster models poured following a 3-5 day shipping procedure of the alginate impression. Direct comparison of two measuring techniques. The study was conducted at the Department of Orthodontics, School of Dentistry, University of Aarhus, Denmark in 2006/2007. Twelve randomly selected orthodontic graduate students with informed consent. Three sets of alginate impressions were taken from the participants within 1 hour. Plaster models were poured immediately from two of the sets, while the third set was kept in transit in the mail for 3-5 days. Upon return a plaster model was poured as well. Finally digital models were made from the plaster models. A number of measurements were performed on the plaster casts with a digital calliper and on the corresponding digital models using the virtual measuring tool of the accompanying software. Afterwards these measurements were compared statistically. No statistical differences were found between the three sets of plaster models. The intra- and inter-observer variability are smaller for the measurements performed on the digital models. Sending alginate impressions by mail does not affect the quality and accuracy of plaster casts poured from them afterwards. Virtual measurements performed on digital models display less variability than the corresponding measurements performed with a calliper on the actual models.

  6. The construction of a two-dimensional reproducing kernel function and its application in a biomedical model.

    Science.gov (United States)

    Guo, Qi; Shen, Shu-Ting

    2016-04-29

    There are two major classes of cardiac tissue models: the ionic model and the FitzHugh-Nagumo model. During computer simulation, each model entails solving a system of complex ordinary differential equations and a partial differential equation with non-flux boundary conditions. The reproducing kernel method possesses significant applications in solving partial differential equations. The derivative of the reproducing kernel function is a wavelet function, which has local properties and sensitivities to singularity. Therefore, study on the application of reproducing kernel would be advantageous. Applying new mathematical theory to the numerical solution of the ventricular muscle model so as to improve its precision in comparison with other methods at present. A two-dimensional reproducing kernel function inspace is constructed and applied in computing the solution of two-dimensional cardiac tissue model by means of the difference method through time and the reproducing kernel method through space. Compared with other methods, this method holds several advantages such as high accuracy in computing solutions, insensitivity to different time steps and a slow propagation speed of error. It is suitable for disorderly scattered node systems without meshing, and can arbitrarily change the location and density of the solution on different time layers. The reproducing kernel method has higher solution accuracy and stability in the solutions of the two-dimensional cardiac tissue model.

  7. 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.

  8. Pharmacokinetic Modelling to Predict FVIII:C Response to Desmopressin and Its Reproducibility in Nonsevere Haemophilia A Patients.

    Science.gov (United States)

    Schütte, Lisette M; van Hest, Reinier M; Stoof, Sara C M; Leebeek, Frank W G; Cnossen, Marjon H; Kruip, Marieke J H A; Mathôt, Ron A A

    2018-04-01

     Nonsevere haemophilia A (HA) patients can be treated with desmopressin. Response of factor VIII activity (FVIII:C) differs between patients and is difficult to predict.  Our aims were to describe FVIII:C response after desmopressin and its reproducibility by population pharmacokinetic (PK) modelling.  Retrospective data of 128 nonsevere HA patients (age 7-75 years) receiving an intravenous or intranasal dose of desmopressin were used. PK modelling of FVIII:C was performed by nonlinear mixed effect modelling. Reproducibility of FVIII:C response was defined as less than 25% difference in peak FVIII:C between administrations.  A total of 623 FVIII:C measurements from 142 desmopressin administrations were available; 14 patients had received two administrations at different occasions. The FVIII:C time profile was best described by a two-compartment model with first-order absorption and elimination. Interindividual variability of the estimated baseline FVIII:C, central volume of distribution and clearance were 37, 43 and 50%, respectively. The most recently measured FVIII:C (FVIII-recent) was significantly associated with FVIII:C response to desmopressin ( p  C increase of 0.47 IU/mL (median, interquartile range: 0.32-0.65 IU/mL, n  = 142). C response was reproducible in 6 out of 14 patients receiving two desmopressin administrations.  FVIII:C response to desmopressin in nonsevere HA patients was adequately described by a population PK model. Large variability in FVIII:C response was observed, which could only partially be explained by FVIII-recent. C response was not reproducible in a small subset of patients. Therefore, monitoring FVIII:C around surgeries or bleeding might be considered. Research is needed to study this further. Schattauer Stuttgart.

  9. Prospective validation of pathologic complete response models in rectal cancer: Transferability and reproducibility.

    Science.gov (United States)

    van Soest, Johan; Meldolesi, Elisa; van Stiphout, Ruud; Gatta, Roberto; Damiani, Andrea; Valentini, Vincenzo; Lambin, Philippe; Dekker, Andre

    2017-09-01

    Multiple models have been developed to predict pathologic complete response (pCR) in locally advanced rectal cancer patients. Unfortunately, validation of these models normally omit the implications of cohort differences on prediction model performance. In this work, we will perform a prospective validation of three pCR models, including information whether this validation will target transferability or reproducibility (cohort differences) of the given models. We applied a novel methodology, the cohort differences model, to predict whether a patient belongs to the training or to the validation cohort. If the cohort differences model performs well, it would suggest a large difference in cohort characteristics meaning we would validate the transferability of the model rather than reproducibility. We tested our method in a prospective validation of three existing models for pCR prediction in 154 patients. Our results showed a large difference between training and validation cohort for one of the three tested models [Area under the Receiver Operating Curve (AUC) cohort differences model: 0.85], signaling the validation leans towards transferability. Two out of three models had a lower AUC for validation (0.66 and 0.58), one model showed a higher AUC in the validation cohort (0.70). We have successfully applied a new methodology in the validation of three prediction models, which allows us to indicate if a validation targeted transferability (large differences between training/validation cohort) or reproducibility (small cohort differences). © 2017 American Association of Physicists in Medicine.

  10. Inter-observer reproducibility in reporting on renal drainage in children with hydronephrosis: a large collaborative study

    International Nuclear Information System (INIS)

    Tondeur, Marianne; Piepsz, Amy; De Palma, Diego; Roca, Isabel; Ham, Hamphrey

    2008-01-01

    The goal of this study was to evaluate the inter-observer reproducibility in reporting on renal drainage obtained during 99m Tc MAG3 renography in children, when already processed data are offered to the observers. Because web site facilities were used for communication, 57 observers from five continents participated in the study. Twenty-three renograms, including furosemide stimulation and posterect postmicturition views, covering various patterns of drainage, were submitted to the observers. Images, curves and quantitative parameters were provided. Good or almost good drainage, partial drainage and poor or no drainage were the three possible responses for each kidney. An important bias was observed among the observers, some of them more systematically reporting the drainage as being good, while others had a general tendency to consider the drainage as poor. This resulted in rather poor inter-observer reproducibility, as for more than half of the kidneys, less than 80% of the observers agreed on one of the three responses. Analysis of the individual cases identified some obvious causes of discrepancy: the absence of a clear limit between partial and good or almost good drainage, the fact of including or neglecting the effect of micturition and change of patient's position, the underestimation of drainage in the case of a flat renographic curve, and the difficulties of interpretation in the case of a small, not well functioning kidney. There is an urgent need for better standardisation in estimating the quality of drainage. (orig.)

  11. Inter-observer reproducibility in reporting on renal drainage in children with hydronephrosis: a large collaborative study

    Energy Technology Data Exchange (ETDEWEB)

    Tondeur, Marianne; Piepsz, Amy [CHU Saint-Pierre, Departement des Radio-Isotopes, Brussels (Belgium); De Palma, Diego [Ospedale di Circolo, Nuclear Medicine, Varese (Italy); Roca, Isabel [Vall d' Hebron Hospital, Nuclear Medicine, Barcelona (Spain); Ham, Hamphrey [University Hospital, Department Nuclear Medicine, Ghent (Belgium)

    2008-03-15

    The goal of this study was to evaluate the inter-observer reproducibility in reporting on renal drainage obtained during {sup 99m}Tc MAG3 renography in children, when already processed data are offered to the observers. Because web site facilities were used for communication, 57 observers from five continents participated in the study. Twenty-three renograms, including furosemide stimulation and posterect postmicturition views, covering various patterns of drainage, were submitted to the observers. Images, curves and quantitative parameters were provided. Good or almost good drainage, partial drainage and poor or no drainage were the three possible responses for each kidney. An important bias was observed among the observers, some of them more systematically reporting the drainage as being good, while others had a general tendency to consider the drainage as poor. This resulted in rather poor inter-observer reproducibility, as for more than half of the kidneys, less than 80% of the observers agreed on one of the three responses. Analysis of the individual cases identified some obvious causes of discrepancy: the absence of a clear limit between partial and good or almost good drainage, the fact of including or neglecting the effect of micturition and change of patient's position, the underestimation of drainage in the case of a flat renographic curve, and the difficulties of interpretation in the case of a small, not well functioning kidney. There is an urgent need for better standardisation in estimating the quality of drainage. (orig.)

  12. The intra-observer reproducibility of cardiovascular magnetic resonance myocardial feature tracking strain assessment is independent of field strength

    International Nuclear Information System (INIS)

    Schuster, Andreas; Morton, Geraint; Hussain, Shazia T.

    2013-01-01

    Background: Cardiovascular magnetic resonance myocardial feature tracking (CMR-FT) is a promising novel method for quantification of myocardial wall mechanics from standard steady-state free precession (SSFP) images. We sought to determine whether magnetic field strength affects the intra-observer reproducibility of CMR-FT strain analysis. Methods: We studied 2 groups, each consisting of 10 healthy subjects, at 1.5 T or 3 T Analysis was performed at baseline and after 4 weeks using dedicated CMR-FT prototype software (Tomtec, Germany) to analyze standard SSFP cine images. Right ventricular (RV) and left ventricular (LV) longitudinal strain (Ell RV and Ell LV ) and LV long-axis radial strain (Err LAX ) were derived from the 4-chamber cine, and LV short-axis circumferential and radial strains (Ecc SAX , Err SAX ) from the short-axis orientation. Strain parameters were assessed together with LV ejection fraction (EF) and volumes. Intra-observer reproducibility was determined by comparing the first and the second analysis in both groups. Results: In all volunteers resting strain parameters were successfully derived from the SSFP images. There was no difference in strain parameters, volumes and EF between field strengths (p > 0.05). In general Ecc SAX was the most reproducible strain parameter as determined by the coefficient of variation (CV) at 1.5 T (CV 13.3% and 46% global and segmental respectively) and 3 T (CV 17.2% and 31.1% global and segmental respectively). The least reproducible parameter was Ell RV (CV 1.5 T 28.7% and 53.2%; 3 T 43.5% and 63.3% global and segmental respectively). Conclusions: CMR-FT results are similar with reasonable intra-observer reproducibility in different groups of volunteers at 1.5 T and 3 T. CMR-FT is a promising novel technique and our data indicate that results might be transferable between field strengths. However there is a considerable amount of segmental variability indicating that further refinements are needed before CMR

  13. 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

  14. Paleomagnetic analysis of curved thrust belts reproduced by physical models

    Science.gov (United States)

    Costa, Elisabetta; Speranza, Fabio

    2003-12-01

    This paper presents a new methodology for studying the evolution of curved mountain belts by means of paleomagnetic analyses performed on analogue models. Eleven models were designed aimed at reproducing various tectonic settings in thin-skinned tectonics. Our models analyze in particular those features reported in the literature as possible causes for peculiar rotational patterns in the outermost as well as in the more internal fronts. In all the models the sedimentary cover was reproduced by frictional low-cohesion materials (sand and glass micro-beads), which detached either on frictional or on viscous layers. These latter were reproduced in the models by silicone. The sand forming the models has been previously mixed with magnetite-dominated powder. Before deformation, the models were magnetized by means of two permanent magnets generating within each model a quasi-linear magnetic field of intensity variable between 20 and 100 mT. After deformation, the models were cut into closely spaced vertical sections and sampled by means of 1×1-cm Plexiglas cylinders at several locations along curved fronts. Care was taken to collect paleomagnetic samples only within virtually undeformed thrust sheets, avoiding zones affected by pervasive shear. Afterwards, the natural remanent magnetization of these samples was measured, and alternating field demagnetization was used to isolate the principal components. The characteristic components of magnetization isolated were used to estimate the vertical-axis rotations occurring during model deformation. We find that indenters pushing into deforming belts from behind form non-rotational curved outer fronts. The more internal fronts show oroclinal-type rotations of a smaller magnitude than that expected for a perfect orocline. Lateral symmetrical obstacles in the foreland colliding with forward propagating belts produce non-rotational outer curved fronts as well, whereas in between and inside the obstacles a perfect orocline forms

  15. Intra- and inter-observer reproducibility and generalizability of first trimester uterine artery pulsatility index by transabdominal and transvaginal ultrasound

    NARCIS (Netherlands)

    Marchi, Laura; Zwertbroek, Eva; Snelder, Judith; Kloosterman, Maaike; Bilardo, Caterina Maddalena

    2016-01-01

    Objectives The primary aim of the study was to assess intra-observer and inter-observer reproducibility and generalizability (general reliability) of first trimester Doppler measurements of uterine arteries (UtA) performed both transabdominally (TA) and transvaginally (TV). Secondary aims were to

  16. Can Computational Sediment Transport Models Reproduce the Observed Variability of Channel Networks in Modern Deltas?

    Science.gov (United States)

    Nesvold, E.; Mukerji, T.

    2017-12-01

    River deltas display complex channel networks that can be characterized through the framework of graph theory, as shown by Tejedor et al. (2015). Deltaic patterns may also be useful in a Bayesian approach to uncertainty quantification of the subsurface, but this requires a prior distribution of the networks of ancient deltas. By considering subaerial deltas, one can at least obtain a snapshot in time of the channel network spectrum across deltas. In this study, the directed graph structure is semi-automatically extracted from satellite imagery using techniques from statistical processing and machine learning. Once the network is labeled with vertices and edges, spatial trends and width and sinuosity distributions can also be found easily. Since imagery is inherently 2D, computational sediment transport models can serve as a link between 2D network structure and 3D depositional elements; the numerous empirical rules and parameters built into such models makes it necessary to validate the output with field data. For this purpose we have used a set of 110 modern deltas, with average water discharge ranging from 10 - 200,000 m3/s, as a benchmark for natural variability. Both graph theoretic and more general distributions are established. A key question is whether it is possible to reproduce this deltaic network spectrum with computational models. Delft3D was used to solve the shallow water equations coupled with sediment transport. The experimental setup was relatively simple; incoming channelized flow onto a tilted plane, with varying wave and tidal energy, sediment types and grain size distributions, river discharge and a few other input parameters. Each realization was run until a delta had fully developed: between 50 and 500 years (with a morphology acceleration factor). It is shown that input parameters should not be sampled independently from the natural ranges, since this may result in deltaic output that falls well outside the natural spectrum. Since we are

  17. The Accuracy and Reproducibility of Linear Measurements Made on CBCT-derived Digital Models.

    Science.gov (United States)

    Maroua, Ahmad L; Ajaj, Mowaffak; Hajeer, Mohammad Y

    2016-04-01

    To evaluate the accuracy and reproducibility of linear measurements made on cone-beam computed tomography (CBCT)-derived digital models. A total of 25 patients (44% female, 18.7 ± 4 years) who had CBCT images for diagnostic purposes were included. Plaster models were obtained and digital models were extracted from CBCT scans. Seven linear measurements from predetermined landmarks were measured and analyzed on plaster models and the corresponding digital models. The measurements included arch length and width at different sites. Paired t test and Bland-Altman analysis were used to evaluate the accuracy of measurements on digital models compared to the plaster models. Also, intraclass correlation coefficients (ICCs) were used to evaluate the reproducibility of the measurements in order to assess the intraobserver reliability. The statistical analysis showed significant differences on 5 out of 14 variables, and the mean differences ranged from -0.48 to 0.51 mm. The Bland-Altman analysis revealed that the mean difference between variables was (0.14 ± 0.56) and (0.05 ± 0.96) mm and limits of agreement between the two methods ranged from -1.2 to 0.96 and from -1.8 to 1.9 mm in the maxilla and the mandible, respectively. The intraobserver reliability values were determined for all 14 variables of two types of models separately. The mean ICC value for the plaster models was 0.984 (0.924-0.999), while it was 0.946 for the CBCT models (range from 0.850 to 0.985). Linear measurements obtained from the CBCT-derived models appeared to have a high level of accuracy and reproducibility.

  18. 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...... source. Toluene was degraded under aerobic conditions at a constant temperature of 28 degreesC. The experiments were modelled by a Monod model - extended to meet the air/liquid system, and the parameter values were estimated using a statistical nonlinear estimation procedure. Model reduction analysis...... resulted in a simpler model without the biomass decay term. In order to test for model reduction and reproducibility of parameter estimates, a likelihood ratio test was employed. The limited reproducibility for these experiments implied that all 9 batch experiments could not be described by the same set...

  19. GeoTrust Hub: A Platform For Sharing And Reproducing Geoscience Applications

    Science.gov (United States)

    Malik, T.; Tarboton, D. G.; Goodall, J. L.; Choi, E.; Bhatt, A.; Peckham, S. D.; Foster, I.; Ton That, D. H.; Essawy, B.; Yuan, Z.; Dash, P. K.; Fils, G.; Gan, T.; Fadugba, O. I.; Saxena, A.; Valentic, T. A.

    2017-12-01

    Recent requirements of scholarly communication emphasize the reproducibility of scientific claims. Text-based research papers are considered poor mediums to establish reproducibility. Papers must be accompanied by "research objects", aggregation of digital artifacts that together with the paper provide an authoritative record of a piece of research. We will present GeoTrust Hub (http://geotrusthub.org), a platform for creating, sharing, and reproducing reusable research objects. GeoTrust Hub provides tools for scientists to create `geounits'--reusable research objects. Geounits are self-contained, annotated, and versioned containers that describe and package computational experiments in an efficient and light-weight manner. Geounits can be shared on public repositories such as HydroShare and FigShare, and also using their respective APIs reproduced on provisioned clouds. The latter feature enables science applications to have a lifetime beyond sharing, wherein they can be independently verified and trust be established as they are repeatedly reused. Through research use cases from several geoscience laboratories across the United States, we will demonstrate how tools provided from GeoTrust Hub along with Hydroshare as its public repository for geounits is advancing the state of reproducible research in the geosciences. For each use case, we will address different computational reproducibility requirements. Our first use case will be an example of setup reproducibility which enables a scientist to set up and reproduce an output from a model with complex configuration and development environments. Our second use case will be an example of algorithm/data reproducibility, where in a shared data science model/dataset can be substituted with an alternate one to verify model output results, and finally an example of interactive reproducibility, in which an experiment is dependent on specific versions of data to produce the result. Toward this we will use software and data

  20. Reproducing tailing in breakthrough curves: Are statistical models equally representative and predictive?

    Science.gov (United States)

    Pedretti, Daniele; Bianchi, Marco

    2018-03-01

    Breakthrough curves (BTCs) observed during tracer tests in highly heterogeneous aquifers display strong tailing. Power laws are popular models for both the empirical fitting of these curves, and the prediction of transport using upscaling models based on best-fitted estimated parameters (e.g. the power law slope or exponent). The predictive capacity of power law based upscaling models can be however questioned due to the difficulties to link model parameters with the aquifers' physical properties. This work analyzes two aspects that can limit the use of power laws as effective predictive tools: (a) the implication of statistical subsampling, which often renders power laws undistinguishable from other heavily tailed distributions, such as the logarithmic (LOG); (b) the difficulties to reconcile fitting parameters obtained from models with different formulations, such as the presence of a late-time cutoff in the power law model. Two rigorous and systematic stochastic analyses, one based on benchmark distributions and the other on BTCs obtained from transport simulations, are considered. It is found that a power law model without cutoff (PL) results in best-fitted exponents (αPL) falling in the range of typical experimental values reported in the literature (1.5 tailing becomes heavier. Strong fluctuations occur when the number of samples is limited, due to the effects of subsampling. On the other hand, when the power law model embeds a cutoff (PLCO), the best-fitted exponent (αCO) is insensitive to the degree of tailing and to the effects of subsampling and tends to a constant αCO ≈ 1. In the PLCO model, the cutoff rate (λ) is the parameter that fully reproduces the persistence of the tailing and is shown to be inversely correlated to the LOG scale parameter (i.e. with the skewness of the distribution). The theoretical results are consistent with the fitting analysis of a tracer test performed during the MADE-5 experiment. It is shown that a simple

  1. REPRODUCING THE OBSERVED ABUNDANCES IN RCB AND HdC STARS WITH POST-DOUBLE-DEGENERATE MERGER MODELS-CONSTRAINTS ON MERGER AND POST-MERGER SIMULATIONS AND PHYSICS PROCESSES

    Energy Technology Data Exchange (ETDEWEB)

    Menon, Athira; Herwig, Falk; Denissenkov, Pavel A. [Department of Physics and Astronomy, University of Victoria, Victoria, BC V8P5C2 (Canada); Clayton, Geoffrey C.; Staff, Jan [Department of Physics and Astronomy, Louisiana State University, 202 Nicholson Hall, Tower Dr., Baton Rouge, LA 70803-4001 (United States); Pignatari, Marco [Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland); Paxton, Bill [Kavli Institute for Theoretical Physics and Department of Physics, Kohn Hall, University of California, Santa Barbara, CA 93106 (United States)

    2013-07-20

    The R Coronae Borealis (RCB) stars are hydrogen-deficient, variable stars that are most likely the result of He-CO WD mergers. They display extremely low oxygen isotopic ratios, {sup 16}O/{sup 18}O {approx_equal} 1-10, {sup 12}C/{sup 13}C {>=} 100, and enhancements up to 2.6 dex in F and in s-process elements from Zn to La, compared to solar. These abundances provide stringent constraints on the physical processes during and after the double-degenerate merger. As shown previously, O-isotopic ratios observed in RCB stars cannot result from the dynamic double-degenerate merger phase, and we now investigate the role of the long-term one-dimensional spherical post-merger evolution and nucleosynthesis based on realistic hydrodynamic merger progenitor models. We adopt a model for extra envelope mixing to represent processes driven by rotation originating in the dynamical merger. Comprehensive nucleosynthesis post-processing simulations for these stellar evolution models reproduce, for the first time, the full range of the observed abundances for almost all the elements measured in RCB stars: {sup 16}O/{sup 18}O ratios between 9 and 15, C-isotopic ratios above 100, and {approx}1.4-2.35 dex F enhancements, along with enrichments in s-process elements. The nucleosynthesis processes in our models constrain the length and temperature in the dynamic merger shell-of-fire feature as well as the envelope mixing in the post-merger phase. s-process elements originate either in the shell-of-fire merger feature or during the post-merger evolution, but the contribution from the asymptotic giant branch progenitors is negligible. The post-merger envelope mixing must eventually cease {approx}10{sup 6} yr after the dynamic merger phase before the star enters the RCB phase.

  2. Intra-observer reproducibility and interobserver reliability of the radiographic parameters in the Spinal Deformity Study Group's AIS Radiographic Measurement Manual.

    Science.gov (United States)

    Dang, Natasha Radhika; Moreau, Marc J; Hill, Douglas L; Mahood, James K; Raso, James

    2005-05-01

    Retrospective cross-sectional assessment of the reproducibility and reliability of radiographic parameters. To measure the intra-examiner and interexaminer reproducibility and reliability of salient radiographic features. The management and treatment of adolescent idiopathic scoliosis (AIS) depends on accurate and reproducible radiographic measurements of the deformity. Ten sets of radiographs were randomly selected from a sample of patients with AIS, with initial curves between 20 degrees and 45 degrees. Fourteen measures of the deformity were measured from posteroanterior and lateral radiographs by 2 examiners, and were repeated 5 times at intervals of 3-5 days. Intra-examiner and interexaminer differences were examined. The parameters include measures of curve size, spinal imbalance, sagittal kyphosis and alignment, maximum apical vertebral rotation, T1 tilt, spondylolysis/spondylolisthesis, and skeletal age. Intra-examiner reproducibility was generally excellent for parameters measured from the posteroanterior radiographs but only fair to good for parameters from the lateral radiographs, in which some landmarks were not clearly visible. Of the 13 parameters observed, 7 had excellent interobserver reliability. The measurements from the lateral radiograph were less reproducible and reliable and, thus, may not add value to the assessment of AIS. Taking additional measures encourages a systematic and comprehensive assessment of spinal radiographs.

  3. Characterization of the Sahelian-Sudan rainfall based on observations and regional climate models

    Science.gov (United States)

    Salih, Abubakr A. M.; Elagib, Nadir Ahmed; Tjernström, Michael; Zhang, Qiong

    2018-04-01

    The African Sahel region is known to be highly vulnerable to climate variability and change. We analyze rainfall in the Sahelian Sudan in terms of distribution of rain-days and amounts, and examine whether regional climate models can capture these rainfall features. Three regional models namely, Regional Model (REMO), Rossby Center Atmospheric Model (RCA) and Regional Climate Model (RegCM4), are evaluated against gridded observations (Climate Research Unit, Tropical Rainfall Measuring Mission, and ERA-interim reanalysis) and rain-gauge data from six arid and semi-arid weather stations across Sahelian Sudan over the period 1989 to 2008. Most of the observed rain-days are characterized by weak (0.1-1.0 mm/day) to moderate (> 1.0-10.0 mm/day) rainfall, with average frequencies of 18.5% and 48.0% of the total annual rain-days, respectively. Although very strong rainfall events (> 30.0 mm/day) occur rarely, they account for a large fraction of the total annual rainfall (28-42% across the stations). The performance of the models varies both spatially and temporally. RegCM4 most closely reproduces the observed annual rainfall cycle, especially for the more arid locations, but all of the three models fail to capture the strong rainfall events and hence underestimate its contribution to the total annual number of rain-days and rainfall amount. However, excessive moderate rainfall compensates this underestimation in the models in an annual average sense. The present study uncovers some of the models' limitations in skillfully reproducing the observed climate over dry regions, will aid model users in recognizing the uncertainties in the model output and will help climate and hydrological modeling communities in improving models.

  4. 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.

  5. The Seasonal cycle of the Tropical Lower Stratospheric Water Vapor in Chemistry-Climate Models in Comparison with Observations

    Science.gov (United States)

    Wang, X.; Dessler, A. E.

    2017-12-01

    The seasonal cycle is one of the key features of the tropical lower stratospheric water vapor, so it is important that the climate models reproduce it. In this analysis, we evaluate how well the Goddard Earth Observing System Chemistry Climate Model (GEOSCCM) and the Whole Atmosphere Community Climate Model (WACCM) reproduce the seasonal cycle of tropical lower stratospheric water vapor. We do this by comparing the models to observations from the Microwave Limb Sounder (MLS) and the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA-Interim (ERAi). We also evaluate if the chemistry-climate models (CCMs) reproduce the key transport and dehydration processes that regulate the seasonal cycle using a forward, domain filling, diabatic trajectory model. Finally, we explore the changes of the seasonal cycle during the 21st century in the two CCMs. Our results show general agreement in the seasonal cycles from the MLS, the ERAi, and the CCMs. Despite this agreement, there are some clear disagreements between the models and the observations on the details of transport and dehydration in the TTL. Finally, both the CCMs predict a moister seasonal cycle by the end of the 21st century. But they disagree on the changes of the seasonal amplitude, which is predicted to increase in the GEOSCCM and decrease in the WACCM.

  6. 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

  7. Reproducibility in the analysis of multigated radionuclide studies of left ventricular ejection fraction

    International Nuclear Information System (INIS)

    Gjorup, T.; Kelbaek, H.; Vestergaard, B.; Fogh, J.; Munck, O.; Jensen, A.M.

    1989-01-01

    The authors determined the reproducibility (the standard deviation [SD]) in the analysis of multigated radionuclide studies of left ventricular ejection fraction (LVEF). Radionuclide studies from a consecutive series of 38 patients suspected of ischemic heart disease were analyzed independently by four nuclear medicine physiologists and four laboratory technicians. Each study was analyzed three times by each of the observers. Based on the analyses of the eight observers, the SD could be estimated by the use of a variance component model for LVEF determinations calculated as the average of the analyses of an arbitrary number of observers making an arbitrary number of analyses. This study presents the SDs for LVEF determinations based on the analyses of one to five observers making one to five analyses each. The SD of a LVEF determination decreased from 3.96% to 2.98% when an observer increased his number of analyses from one to five. A more pronounced decrease in the SD from 3.96% to 1.77% was obtained when the LVEF determinations were based on the average of a single analysis made by one to five observers. However, when dealing with the difference between LVEF determinations from two studies, the highest reproducibility was obtained if the LVEF determinations at both studies were based on the analyses made by the same observer. No significant difference was found in the reproducibility of analyses made by nuclear medicine physicians and laboratory technicians. Our study revealed that to increase the reproducibility of LVEF determinations, special efforts should be made to standardize the outlining of the end-systolic region interest

  8. Reproducibility of precipitation distributions over extratropical continental regions in the CMIP5

    Science.gov (United States)

    Hirota, Nagio; Takayabu, Yukari

    2013-04-01

    Reproducibility of precipitation distributions over extratropical continental regions in the CMIP5 Nagio Hirota1,2 and Yukari N. Takayabu2 (1) National Institute of Polar Research (NIPR) (2) Atmosphere and Ocean Research Institute (AORI), the University of Tokyo Reproducibility of precipitation distributions over extratropical continental regions by CMIP5 climate models in their historical runs are evaluated, in comparison with GPCP(V2.2), CMAP(V0911), daily gridded gauge data APHRODITE. Surface temperature, cloud radiative forcing, and atmospheric circulations are also compared with observations of CRU-UEA, CERES, and ERA-interim/ERA40/JRA reanalysis data. It is shown that many CMIP5 models underestimate and overestimate summer precipitation over West and East Eurasia, respectively. These precipitation biases correspond to moisture transport associated with a cyclonic circulation bias over the whole continent of Eurasia. Meanwhile, many models underestimate cloud over the Eurasian continent, and associated shortwave cloud radiative forcing result in a significant warm bias. Evaporation feedback amplify the warm bias over West Eurasia. These processes consistently explain the precipitation biases over the Erasian continent in summer. We also examined reproducibility of winter precipitation, but robust results are not obtained yet due to the large uncertainty in observation associated with the adjustment of snow measurement in windy condition. Better observational data sets are necessary for further model validation. Acknowledgment: This study is supported by the PMM RA of JAXA, Green Network of Excellence (GRENE) Program by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and Environment Research and Technology Development Fund (A-1201) of the Ministry of the Environment, Japan.

  9. Properties of galaxies reproduced by a hydrodynamic simulation

    Science.gov (United States)

    Vogelsberger, M.; Genel, S.; Springel, V.; Torrey, P.; Sijacki, D.; Xu, D.; Snyder, G.; Bird, S.; Nelson, D.; Hernquist, L.

    2014-05-01

    Previous simulations of the growth of cosmic structures have broadly reproduced the `cosmic web' of galaxies that we see in the Universe, but failed to create a mixed population of elliptical and spiral galaxies, because of numerical inaccuracies and incomplete physical models. Moreover, they were unable to track the small-scale evolution of gas and stars to the present epoch within a representative portion of the Universe. Here we report a simulation that starts 12 million years after the Big Bang, and traces 13 billion years of cosmic evolution with 12 billion resolution elements in a cube of 106.5 megaparsecs a side. It yields a reasonable population of ellipticals and spirals, reproduces the observed distribution of galaxies in clusters and characteristics of hydrogen on large scales, and at the same time matches the `metal' and hydrogen content of galaxies on small scales.

  10. Why are models unable to reproduce multi-decadal trends in lower tropospheric baseline ozone levels?

    Science.gov (United States)

    Hu, L.; Liu, J.; Mickley, L. J.; Strahan, S. E.; Steenrod, S.

    2017-12-01

    Assessments of tropospheric ozone radiative forcing rely on accurate model simulations. Parrish et al (2014) found that three chemistry-climate models (CCMs) overestimate present-day O3 mixing ratios and capture only 50% of the observed O3 increase over the last five decades at 12 baseline sites in the northern mid-latitudes, indicating large uncertainties in our understanding of the ozone trends and their implications for radiative forcing. Here we present comparisons of outputs from two chemical transport models (CTMs) - GEOS-Chem and the Global Modeling Initiative model - with O3 observations from the same sites and from the global ozonesonde network. Both CTMs are driven by reanalysis meteorological data (MERRA or MERRA2) and thus are expected to be different in atmospheric transport processes relative to those freely running CCMs. We test whether recent model developments leading to more active ozone chemistry affect the computed ozone sensitivity to perturbations in emissions. Preliminary results suggest these CTMs can reproduce present-day ozone levels but fail to capture the multi-decadal trend since 1980. Both models yield widespread overpredictions of free tropospheric ozone in the 1980s. Sensitivity studies in GEOS-Chem suggest that the model estimate of natural background ozone is too high. We discuss factors that contribute to the variability and trends of tropospheric ozone over the last 30 years, with a focus on intermodel differences in spatial resolution and in the representation of stratospheric chemistry, stratosphere-troposphere exchange, halogen chemistry, and biogenic VOC emissions and chemistry. We also discuss uncertainty in the historical emission inventories used in models, and how these affect the simulated ozone trends.

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

    International Nuclear Information System (INIS)

    Tian, Jun-fang; Yuan, Zhen-zhou; Jia, Bin; Fan, Hong-qiang; Wang, Tao

    2012-01-01

    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.

  12. Shear wave elastography for breast masses is highly reproducible.

    Science.gov (United States)

    Cosgrove, David O; Berg, Wendie A; Doré, Caroline J; Skyba, Danny M; Henry, Jean-Pierre; Gay, Joel; Cohen-Bacrie, Claude

    2012-05-01

    To evaluate intra- and interobserver reproducibility of shear wave elastography (SWE) for breast masses. For intraobserver reproducibility, each observer obtained three consecutive SWE images of 758 masses that were visible on ultrasound. 144 (19%) were malignant. Weighted kappa was used to assess the agreement of qualitative elastographic features; the reliability of quantitative measurements was assessed by intraclass correlation coefficients (ICC). For the interobserver reproducibility, a blinded observer reviewed images and agreement on features was determined. Mean age was 50 years; mean mass size was 13 mm. Qualitatively, SWE images were at least reasonably similar for 666/758 (87.9%). Intraclass correlation for SWE diameter, area and perimeter was almost perfect (ICC ≥ 0.94). Intraobserver reliability for maximum and mean elasticity was almost perfect (ICC = 0.84 and 0.87) and was substantial for the ratio of mass-to-fat elasticity (ICC = 0.77). Interobserver agreement was moderate for SWE homogeneity (κ = 0.57), substantial for qualitative colour assessment of maximum elasticity (κ = 0.66), fair for SWE shape (κ = 0.40), fair for B-mode mass margins (κ = 0.38), and moderate for B-mode mass shape (κ = 0.58), orientation (κ = 0.53) and BI-RADS assessment (κ = 0.59). SWE is highly reproducible for assessing elastographic features of breast masses within and across observers. SWE interpretation is at least as consistent as that of BI-RADS ultrasound B-mode features. • Shear wave ultrasound elastography can measure the stiffness of breast tissue • It provides a qualitatively and quantitatively interpretable colour-coded map of tissue stiffness • Intraobserver reproducibility of SWE is almost perfect while intraobserver reproducibility of SWE proved to be moderate to substantial • The most reproducible SWE features between observers were SWE image homogeneity and maximum elasticity.

  13. COMBINE archive and OMEX format : One file to share all information to reproduce a modeling project

    NARCIS (Netherlands)

    Bergmann, Frank T.; Olivier, Brett G.; Soiland-Reyes, Stian

    2014-01-01

    Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models,

  14. Investigation of dimensional variation in parts manufactured by fused deposition modeling using Gauge Repeatability and Reproducibility

    Science.gov (United States)

    Mohamed, Omar Ahmed; Hasan Masood, Syed; Lal Bhowmik, Jahar

    2018-02-01

    In the additive manufacturing (AM) market, the question is raised by industry and AM users on how reproducible and repeatable the fused deposition modeling (FDM) process is in providing good dimensional accuracy. This paper aims to investigate and evaluate the repeatability and reproducibility of the FDM process through a systematic approach to answer this frequently asked question. A case study based on the statistical gage repeatability and reproducibility (gage R&R) technique is proposed to investigate the dimensional variations in the printed parts of the FDM process. After running the simulation and analysis of the data, the FDM process capability is evaluated, which would help the industry for better understanding the performance of FDM technology.

  15. Mesoscale influence on long-range transport — evidence from ETEX modelling and observations

    Science.gov (United States)

    Sørensen, Jens Havskov; Rasmussen, Alix; Ellermann, Thomas; Lyck, Erik

    During the first European Tracer Experiment (ETEX) tracer gas was released from a site in Brittany, France, and subsequently observed over a range of 2000 km. Hourly measurements were taken at the National Environmental Research Institute (NERI) located at Risø, Denmark, using two measurement techniques. At this location, the observed concentration time series shows a double-peak structure occurring between two and three days after the release. By using the Danish Emergency Response Model of the Atmosphere (DERMA), which is developed at the Danish Meteorological Institute (DMI), simulations of the dispersion of the tracer gas have been performed. Using numerical weather-prediction data from the European Centre for Medium-Range Weather Forecast (ECMWF) by DERMA, the arrival time of the tracer is quite well predicted, so also is the duration of the passage of the plume, but the double-peak structure is not reproduced. However, using higher-resolution data from the DMI version of the HIgh Resolution Limited Area Model (DMI-HIRLAM), DERMA reproduces the observed structure very well. The double-peak structure is caused by the influence of a mesoscale anti-cyclonic eddy on the tracer gas plume about one day earlier.

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

    International Nuclear Information System (INIS)

    Pittayapat, Pisha; Jacobs, Reinhilde; Odri, Guillaume A.; De Faria Vasconcelos, Karla; Willems, Guy; Olszewski, Raphael

    2015-01-01

    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.

  17. 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.

  18. Interannual Rainfall Variability in North-East Brazil: Observation and Model Simulation

    Science.gov (United States)

    Harzallah, A.; Rocha de Aragão, J. O.; Sadourny, R.

    1996-08-01

    The relationship between interannual variability of rainfall in north-east Brazil and tropical sea-surface temperature is studied using observations and model simulations. The simulated precipitation is the average of seven independent realizations performed using the Laboratoire de Météorologie Dynamique atmospheric general model forced by the 1970-1988 observed sea-surface temperature. The model reproduces very well the rainfall anomalies (correlation of 091 between observed and modelled anomalies). The study confirms that precipitation in north-east Brazil is highly correlated to the sea-surface temperature in the tropical Atlantic and Pacific oceans. Using the singular value decomposition method, we find that Nordeste rainfall is modulated by two independent oscillations, both governed by the Atlantic dipole, but one involving only the Pacific, the other one having a period of about 10 years. Correlations between precipitation in north-east Brazil during February-May and the sea-surface temperature 6 months earlier indicate that both modes are essential to estimate the quality of the rainy season.

  19. Observation and modelling of the Fe XXI line profile observed by IRIS during the impulsive phase of flares

    Science.gov (United States)

    Polito, V.; Testa, P.; De Pontieu, B.; Allred, J. C.

    2017-12-01

    The observation of the high temperature (above 10 MK) Fe XXI 1354.1 A line with the Interface Region Imaging Spectrograph (IRIS) has provided significant insights into the chromospheric evaporation process in flares. In particular, the line is often observed to be completely blueshifted, in contrast to previous observations at lower spatial and spectral resolution, and in agreement with predictions from theoretical models. Interestingly, the line is also observed to be mostly symmetric and with a large excess above the thermal width. One popular interpretation for the excess broadening is given by assuming a superposition of flows from different loop strands. In this work, we perform a statistical analysis of Fe XXI line profiles observed by IRIS during the impulsive phase of flares and compare our results with hydrodynamic simulations of multi-thread flare loops performed with the 1D RADYN code. Our results indicate that the multi-thread models cannot easily reproduce the symmetry of the line and that some other physical process might need to be invoked in order to explain the observed profiles.

  20. Hyper-Resolution Global Land Surface Model at Regional-to-Local Scales with observed Groundwater data assimilation

    OpenAIRE

    Singh, Raj Shekhar

    2014-01-01

    Modeling groundwater is challenging: it is not readily visible and is difficult to measure, with limited sets of observations available. Even though groundwater models can reproduce water table and head variations, considerable drift in modeled land surface states can nonetheless result from partially known geologic structure, errors in the input forcing fields, and imperfect Land Surface Model (LSM) parameterizations. These models frequently have biased results that are very different from o...

  1. 4-D modeling of CME expansion and EUV dimming observed with STEREO/EUVI

    Directory of Open Access Journals (Sweden)

    M. J. Aschwanden

    2009-08-01

    Full Text Available This is the first attempt to model the kinematics of a CME launch and the resulting EUV dimming quantitatively with a self-consistent model. Our 4-D-model assumes self-similar expansion of a spherical CME geometry that consists of a CME front with density compression and a cavity with density rarefaction, satisfying mass conservation of the total CME and swept-up corona. The model contains 14 free parameters and is fitted to the 25 March 2008 CME event observed with STEREO/A and B. Our model is able to reproduce the observed CME expansion and related EUV dimming during the initial phase from 18:30 UT to 19:00 UT. The CME kinematics can be characterized by a constant acceleration (i.e., a constant magnetic driving force. While the observations of EUVI/A are consistent with a spherical bubble geometry, we detect significant asymmetries and density inhomogeneities with EUVI/B. This new forward-modeling method demonstrates how the observed EUV dimming can be used to model physical parameters of the CME source region, the CME geometry, and CME kinematics.

  2. Effect of Initial Conditions on Reproducibility of Scientific Research

    Science.gov (United States)

    Djulbegovic, Benjamin; Hozo, Iztok

    2014-01-01

    Background: It is estimated that about half of currently published research cannot be reproduced. Many reasons have been offered as explanations for failure to reproduce scientific research findings- from fraud to the issues related to design, conduct, analysis, or publishing scientific research. We also postulate a sensitive dependency on initial conditions by which small changes can result in the large differences in the research findings when attempted to be reproduced at later times. Methods: We employed a simple logistic regression equation to model the effect of covariates on the initial study findings. We then fed the input from the logistic equation into a logistic map function to model stability of the results in repeated experiments over time. We illustrate the approach by modeling effects of different factors on the choice of correct treatment. Results: We found that reproducibility of the study findings depended both on the initial values of all independent variables and the rate of change in the baseline conditions, the latter being more important. When the changes in the baseline conditions vary by about 3.5 to about 4 in between experiments, no research findings could be reproduced. However, when the rate of change between the experiments is ≤2.5 the results become highly predictable between the experiments. Conclusions: Many results cannot be reproduced because of the changes in the initial conditions between the experiments. Better control of the baseline conditions in-between the experiments may help improve reproducibility of scientific findings. PMID:25132705

  3. Accuracy, reproducibility, and time efficiency of dental measurements using different technologies.

    Science.gov (United States)

    Grünheid, Thorsten; Patel, Nishant; De Felippe, Nanci L; Wey, Andrew; Gaillard, Philippe R; Larson, Brent E

    2014-02-01

    Historically, orthodontists have taken dental measurements on plaster models. Technological advances now allow orthodontists to take these measurements on digital models. In this study, we aimed to assess the accuracy, reproducibility, and time efficiency of dental measurements taken on 3 types of digital models. emodels (GeoDigm, Falcon Heights, Minn), SureSmile models (OraMetrix, Richardson, Tex), and AnatoModels (Anatomage, San Jose, Calif) were made for 30 patients. Mesiodistal tooth-width measurements taken on these digital models were timed and compared with those on the corresponding plaster models, which were used as the gold standard. Accuracy and reproducibility were assessed using the Bland-Altman method. Differences in time efficiency were tested for statistical significance with 1-way analysis of variance. Measurements on SureSmile models were the most accurate, followed by those on emodels and AnatoModels. Measurements taken on SureSmile models were also the most reproducible. Measurements taken on SureSmile models and emodels were significantly faster than those taken on AnatoModels and plaster models. Tooth-width measurements on digital models can be as accurate as, and might be more reproducible and significantly faster than, those taken on plaster models. Of the models studied, the SureSmile models provided the best combination of accuracy, reproducibility, and time efficiency of measurement. Copyright © 2014 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

  4. Intra- and inter-observer reproducibility study of gestational age estimation using three common foetal biometric parameters: Experienced versus inexperienced sonographer

    International Nuclear Information System (INIS)

    Ohagwu, C.C.; Onoduagu, H.I.; Eze, C.U.; Ochie, K.; Ohagwu, C.I.

    2015-01-01

    Aim: To assess reproducibility of estimating gestational age (GA) of foetus using femur length (FL), biparietal diameter (BPD) and abdominal circumference (AC) within experienced and inexperienced sonographers and between the two. Patients and methods: Two sets of GA estimates each were obtained for FL, BPD and AC by the two observers in 20 normal singleton foetuses. The first estimates for the three biometric parameters were made by the experienced sonographer. Subsequently, the inexperienced sonographer, blind to the estimates of the first observer obtained his own estimates for the same biometric parameters. After a time interval of ten minutes the process was repeated for the second set of GA estimates. All the gestational age estimates were made following standard protocol. Statistical analysis was performed by Pearson's and intraclass correlations, coefficient of variation and Bland–Altman plots. Statistical inferences were drawn at p < 0.05. Results: The Pearson's and intraclass correlations of between GA estimates within and between both observers from measurement of FL, BPD and AC were very high and statistically significant (p < 0.05). Coefficient of variation for duplicate measurements for GA estimates within observers and between observers were quite negligible. Between observers, the first and second GA estimates from FL measurements showed the least variation. Estimates from BPD and AC measurements showed greater degree of variation between the observers. Conclusion: Reproducibility of GA estimation using FL, BPD and AC within experienced and inexperienced sonographers and between the two was excellent. Therefore, a fresh Nigerian radiography graduate with adequate exposure in obstetric ultrasound can correctly determine the gestational age of foetus in routine obstetric ultrasound without supervision

  5. Intra-and interobserver reproducibility of shear wave elastography for evaluation of the breast lesions

    International Nuclear Information System (INIS)

    Hong, Min Ji; Kim, Hak Hee

    2017-01-01

    To evaluate reproducibility of shear wave elastography (SWE) for breast lesions within and between observers and compare the reproducibility of SWE features. For intraobserver reproducibility, 225 masses with 208 patients were included; and two consecutive SWE images were acquired by each observer. For interobserver reproducibility, SWE images of the same mass were obtained by another observer before surgery in 40 patients. Intraclass correlation coefficients (ICC) were used to determine intra- and interobserver reproducibility. Intraobserver reliability for mean elasticity (Emean) and maximum elasticity (Emax) were excellent (ICC = 0.803, 0.799). ICC for SWE ratio and minimum elasticity (Emin) were fair to good (ICC = 0.703, 0.539). Emean showed excellent ICC regardless of histopathologic type and tumor size. Emax, SWE ratio and Emin represented excellent or fair to good reproducibility based on histopathologic type and tumor size. In interobserver study, ICC for Emean, Emax and SWE ratio were excellent. Emean, Emax and SWE ratio represented excellent ICC irrespective of histopathologic type. ICC for Emean was excellent regardless of tumor size. SWE ratio and Emax showed fair to good interobserver reproducibility based on tumor size. Emin represented poor interobserver reliability. Emean in SWE was highly reproducible within and between observers

  6. Intra-and interobserver reproducibility of shear wave elastography for evaluation of the breast lesions

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Min Ji [Dept. of Radiology, Gil Hospital, Gachon University of Medicine and Science, Incheon (Korea, Republic of); Kim, Hak Hee [Dept. of Radiology, and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of)

    2017-03-15

    To evaluate reproducibility of shear wave elastography (SWE) for breast lesions within and between observers and compare the reproducibility of SWE features. For intraobserver reproducibility, 225 masses with 208 patients were included; and two consecutive SWE images were acquired by each observer. For interobserver reproducibility, SWE images of the same mass were obtained by another observer before surgery in 40 patients. Intraclass correlation coefficients (ICC) were used to determine intra- and interobserver reproducibility. Intraobserver reliability for mean elasticity (Emean) and maximum elasticity (Emax) were excellent (ICC = 0.803, 0.799). ICC for SWE ratio and minimum elasticity (Emin) were fair to good (ICC = 0.703, 0.539). Emean showed excellent ICC regardless of histopathologic type and tumor size. Emax, SWE ratio and Emin represented excellent or fair to good reproducibility based on histopathologic type and tumor size. In interobserver study, ICC for Emean, Emax and SWE ratio were excellent. Emean, Emax and SWE ratio represented excellent ICC irrespective of histopathologic type. ICC for Emean was excellent regardless of tumor size. SWE ratio and Emax showed fair to good interobserver reproducibility based on tumor size. Emin represented poor interobserver reliability. Emean in SWE was highly reproducible within and between observers.

  7. Results of an interactively coupled atmospheric chemistry - general circulation model. Comparison with observations

    Energy Technology Data Exchange (ETDEWEB)

    Hein, R.; Dameris, M.; Schnadt, C. [and others

    2000-01-01

    An interactively coupled climate-chemistry model which enables a simultaneous treatment of meteorology and atmospheric chemistry and their feedbacks is presented. This is the first model, which interactively combines a general circulation model based on primitive equations with a rather complex model of stratospheric and tropospheric chemistry, and which is computational efficient enough to allow long-term integrations with currently available computer resources. The applied model version extends from the Earth's surface up to 10 hPa with a relatively high number (39) of vertical levels. We present the results of a present-day (1990) simulation and compare it to available observations. We focus on stratospheric dynamics and chemistry relevant to describe the stratospheric ozone layer. The current model version ECHAM4.L39(DLR)/CHEM can realistically reproduce stratospheric dynamics in the Arctic vortex region, including stratospheric warming events. This constitutes a major improvement compared to formerly applied model versions. However, apparent shortcomings in Antarctic circulation and temperatures persist. The seasonal and interannual variability of the ozone layer is simulated in accordance with observations. Activation and deactivation of chlorine in the polar stratospheric vortices and their interhemispheric differences are reproduced. The consideration of the chemistry feedback on dynamics results in an improved representation of the spatial distribution of stratospheric water vapor concentrations, i.e., the simulated meriodional water vapor gradient in the stratosphere is realistic. The present model version constitutes a powerful tool to investigate, for instance, the combined direct and indirect effects of anthropogenic trace gas emissions, and the future evolution of the ozone layer. (orig.)

  8. 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 (free flap 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.

  9. 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.

  10. Interpretative intra- and interobserver reproducibility of Stress/Rest 99m Tc-steamboat's myocardial perfusion SPECT using semi quantitative 20-segment model

    International Nuclear Information System (INIS)

    Fazeli, M.; Firoozi, F.

    2002-01-01

    It well established that myocardial perfusion SPECT with 201 T L or 99 mTc-se sta mi bi play an important role diagnosis and risk assessment in patients with known or suspected coronary artery disease. Both quantitative and qualitative methods are available for interpretation of images. The use of a semi quantitative scoring system in which each of 20 segments is scored according to a five-point scheme provides an approach to interpretation that is more systematic and reproducible than simple qualitative evaluation. Only a limited number of studies have dealt with the interpretive observer reproducibility of 99 mTc-steamboat's myocardial perfusion imaging. The aim of this study was to assess the intra-and inter observer variability of semi quantitative SPECT performed with this technique. Among 789 patients that underwent myocardial perfusion SPECT during last year 80 patients finally need to coronary angiography as gold standard. In this group of patients a semi quantitative visual interpretation was carried out using short axis and vertical long-axis myocardial tomograms and a 20-segments model. These segments we reassigned on six evenly spaced regions in the apical, mid-ventricular, and basal short-axis view and two apical segments on the mid-ventricular long-axis slice. Uptake in each segment was graded on a 5-point scale (0=normal, 1=equivocal, 2=moderate, 3=severe, 4=absence of uptake). The steamboat's images was interpreted separately w ice by two observers without knowledge of each other's findings or results of angiography. A SPECT study was judged abnormal if there were two or more segments with a stress score equal or more than 2. We con eluded that semi-quantitative visual analysis is a simple and reproducible method of interpretation

  11. A NANOFLARE-BASED CELLULAR AUTOMATON MODEL AND THE OBSERVED PROPERTIES OF THE CORONAL PLASMA

    Energy Technology Data Exchange (ETDEWEB)

    Fuentes, Marcelo López [Instituto de Astronomía y Física del Espacio, CONICET-UBA, CC. 67, Suc. 28, 1428 Buenos Aires (Argentina); Klimchuk, James A., E-mail: lopezf@iafe.uba.ar [NASA Goddard Space Flight Center, Code 671, Greenbelt, MD 20771 (United States)

    2016-09-10

    We use the cellular automaton model described in López Fuentes and Klimchuk to study the evolution of coronal loop plasmas. The model, based on the idea of a critical misalignment angle in tangled magnetic fields, produces nanoflares of varying frequency with respect to the plasma cooling time. We compare the results of the model with active region (AR) observations obtained with the Hinode /XRT and SDO /AIA instruments. The comparison is based on the statistical properties of synthetic and observed loop light curves. Our results show that the model reproduces the main observational characteristics of the evolution of the plasma in AR coronal loops. The typical intensity fluctuations have amplitudes of 10%–15% both for the model and the observations. The sign of the skewness of the intensity distributions indicates the presence of cooling plasma in the loops. We also study the emission measure (EM) distribution predicted by the model and obtain slopes in log(EM) versus log(T) between 2.7 and 4.3, in agreement with published observational values.

  12. A Nanoflare-Based Cellular Automaton Model and the Observed Properties of the Coronal Plasma

    Science.gov (United States)

    Lopez-Fuentes, Marcelo; Klimchuk, James Andrew

    2016-01-01

    We use the cellular automaton model described in Lopez Fuentes and Klimchuk to study the evolution of coronal loop plasmas. The model, based on the idea of a critical misalignment angle in tangled magnetic fields, produces nanoflares of varying frequency with respect to the plasma cooling time. We compare the results of the model with active region (AR) observations obtained with the Hinode/XRT and SDOAIA instruments. The comparison is based on the statistical properties of synthetic and observed loop light curves. Our results show that the model reproduces the main observational characteristics of the evolution of the plasma in AR coronal loops. The typical intensity fluctuations have amplitudes of 10 percent - 15 percent both for the model and the observations. The sign of the skewness of the intensity distributions indicates the presence of cooling plasma in the loops. We also study the emission measure (EM) distribution predicted by the model and obtain slopes in log(EM) versus log(T) between 2.7 and 4.3, in agreement with published observational values.

  13. Reproducibility of brain ADC histograms

    International Nuclear Information System (INIS)

    Steens, S.C.A.; Buchem, M.A. van; Admiraal-Behloul, F.; Schaap, J.A.; Hoogenraad, F.G.C.; Wheeler-Kingshott, C.A.M.; Tofts, P.S.; Cessie, S. le

    2004-01-01

    The aim of this study was to assess the effect of differences in acquisition technique on whole-brain apparent diffusion coefficient (ADC) histogram parameters, as well as to assess scan-rescan reproducibility. Diffusion-weighted imaging (DWI) was performed in 7 healthy subjects with b-values 0-800, 0-1000, and 0-1500 s/mm 2 and fluid-attenuated inversion recovery (FLAIR) DWI with b-values 0-1000 s/mm 2 . All sequences were repeated with and without repositioning. The peak location, peak height, and mean ADC of the ADC histograms and mean ADC of a region of interest (ROI) in the white matter were compared using paired-sample t tests. Scan-rescan reproducibility was assessed using paired-sample t tests, and repeatability coefficients were reported. With increasing maximum b-values, ADC histograms shifted to lower values, with an increase in peak height (p<0.01). With FLAIR DWI, the ADC histogram shifted to lower values with a significantly higher, narrower peak (p<0.01), although the ROI mean ADC showed no significant differences. For scan-rescan reproducibility, no significant differences were observed. Different DWI pulse sequences give rise to different ADC histograms. With a given pulse sequence, however, ADC histogram analysis is a robust and reproducible technique. Using FLAIR DWI, the partial-voluming effect of cerebrospinal fluid, and thus its confounding effect on histogram analyses, can be reduced

  14. Evaluation of NASA's MERRA Precipitation Product in Reproducing the Observed Trend and Distribution of Extreme Precipitation Events in the United States

    Science.gov (United States)

    Ashouri, Hamed; Sorooshian, Soroosh; Hsu, Kuo-Lin; Bosilovich, Michael G.; Lee, Jaechoul; Wehner, Michael F.; Collow, Allison

    2016-01-01

    This study evaluates the performance of NASA's Modern-Era Retrospective Analysis for Research and Applications (MERRA) precipitation product in reproducing the trend and distribution of extreme precipitation events. Utilizing the extreme value theory, time-invariant and time-variant extreme value distributions are developed to model the trends and changes in the patterns of extreme precipitation events over the contiguous United States during 1979-2010. The Climate Prediction Center (CPC) U.S.Unified gridded observation data are used as the observational dataset. The CPC analysis shows that the eastern and western parts of the United States are experiencing positive and negative trends in annual maxima, respectively. The continental-scale patterns of change found in MERRA seem to reasonably mirror the observed patterns of change found in CPC. This is not previously expected, given the difficulty in constraining precipitation in reanalysis products. MERRA tends to overestimate the frequency at which the 99th percentile of precipitation is exceeded because this threshold tends to be lower in MERRA, making it easier to be exceeded. This feature is dominant during the summer months. MERRA tends to reproduce spatial patterns of the scale and location parameters of the generalized extreme value and generalized Pareto distributions. However, MERRA underestimates these parameters, particularly over the Gulf Coast states, leading to lower magnitudes in extreme precipitation events. Two issues in MERRA are identified: 1) MERRA shows a spurious negative trend in Nebraska and Kansas, which is most likely related to the changes in the satellite observing system over time that has apparently affected the water cycle in the central United States, and 2) the patterns of positive trend over the Gulf Coast states and along the East Coast seem to be correlated with the tropical cyclones in these regions. The analysis of the trends in the seasonal precipitation extremes indicates that

  15. Ability of an ensemble of regional climate models to reproduce weather regimes over Europe-Atlantic during the period 1961-2000

    Science.gov (United States)

    Sanchez-Gomez, Emilia; Somot, S.; Déqué, M.

    2009-10-01

    One of the main concerns in regional climate modeling is to which extent limited-area regional climate models (RCM) reproduce the large-scale atmospheric conditions of their driving general circulation model (GCM). In this work we investigate the ability of a multi-model ensemble of regional climate simulations to reproduce the large-scale weather regimes of the driving conditions. The ensemble consists of a set of 13 RCMs on a European domain, driven at their lateral boundaries by the ERA40 reanalysis for the time period 1961-2000. Two sets of experiments have been completed with horizontal resolutions of 50 and 25 km, respectively. The spectral nudging technique has been applied to one of the models within the ensemble. The RCMs reproduce the weather regimes behavior in terms of composite pattern, mean frequency of occurrence and persistence reasonably well. The models also simulate well the long-term trends and the inter-annual variability of the frequency of occurrence. However, there is a non-negligible spread among the models which is stronger in summer than in winter. This spread is due to two reasons: (1) we are dealing with different models and (2) each RCM produces an internal variability. As far as the day-to-day weather regime history is concerned, the ensemble shows large discrepancies. At daily time scale, the model spread has also a seasonal dependence, being stronger in summer than in winter. Results also show that the spectral nudging technique improves the model performance in reproducing the large-scale of the driving field. In addition, the impact of increasing the number of grid points has been addressed by comparing the 25 and 50 km experiments. We show that the horizontal resolution does not affect significantly the model performance for large-scale circulation.

  16. Ability of an ensemble of regional climate models to reproduce weather regimes over Europe-Atlantic during the period 1961-2000

    Energy Technology Data Exchange (ETDEWEB)

    Somot, S.; Deque, M. [Meteo-France CNRM/GMGEC CNRS/GAME, Toulouse (France); Sanchez-Gomez, Emilia

    2009-10-15

    One of the main concerns in regional climate modeling is to which extent limited-area regional climate models (RCM) reproduce the large-scale atmospheric conditions of their driving general circulation model (GCM). In this work we investigate the ability of a multi-model ensemble of regional climate simulations to reproduce the large-scale weather regimes of the driving conditions. The ensemble consists of a set of 13 RCMs on a European domain, driven at their lateral boundaries by the ERA40 reanalysis for the time period 1961-2000. Two sets of experiments have been completed with horizontal resolutions of 50 and 25 km, respectively. The spectral nudging technique has been applied to one of the models within the ensemble. The RCMs reproduce the weather regimes behavior in terms of composite pattern, mean frequency of occurrence and persistence reasonably well. The models also simulate well the long-term trends and the inter-annual variability of the frequency of occurrence. However, there is a non-negligible spread among the models which is stronger in summer than in winter. This spread is due to two reasons: (1) we are dealing with different models and (2) each RCM produces an internal variability. As far as the day-to-day weather regime history is concerned, the ensemble shows large discrepancies. At daily time scale, the model spread has also a seasonal dependence, being stronger in summer than in winter. Results also show that the spectral nudging technique improves the model performance in reproducing the large-scale of the driving field. In addition, the impact of increasing the number of grid points has been addressed by comparing the 25 and 50 km experiments. We show that the horizontal resolution does not affect significantly the model performance for large-scale circulation. (orig.)

  17. Reliability versus reproducibility

    International Nuclear Information System (INIS)

    Lautzenheiser, C.E.

    1976-01-01

    Defect detection and reproducibility of results are two separate but closely related subjects. It is axiomatic that a defect must be detected from examination to examination or reproducibility of results is very poor. On the other hand, a defect can be detected on each of subsequent examinations for higher reliability and still have poor reproducibility of results

  18. 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.

  19. 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.

  20. 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.

  1. Combined constraints on global ocean primary production using observations and models

    Science.gov (United States)

    Buitenhuis, Erik T.; Hashioka, Taketo; Quéré, Corinne Le

    2013-09-01

    production is at the base of the marine food web and plays a central role for global biogeochemical cycles. Yet global ocean primary production is known to only a factor of 2, with previous estimates ranging from 38 to 65 Pg C yr-1 and no formal uncertainty analysis. Here, we present an improved global ocean biogeochemistry model that includes a mechanistic representation of photosynthesis and a new observational database of net primary production (NPP) in the ocean. We combine the model and observations to constrain particulate NPP in the ocean with statistical metrics. The PlankTOM5.3 model includes a new photosynthesis formulation with a dynamic representation of iron-light colimitation, which leads to a considerable improvement of the interannual variability of surface chlorophyll. The database includes a consistent set of 50,050 measurements of 14C primary production. The model best reproduces observations when global NPP is 58 ± 7 Pg C yr-1, with a most probable value of 56 Pg C yr-1. The most probable value is robust to the model used. The uncertainty represents 95% confidence intervals. It considers all random errors in the model and observations, but not potential biases in the observations. We show that tropical regions (23°S-23°N) contribute half of the global NPP, while NPPs in the Northern and Southern Hemispheres are approximately equal in spite of the larger ocean area in the South.

  2. Reproducing an extreme flood with uncertain post-event information

    Directory of Open Access Journals (Sweden)

    D. Fuentes-Andino

    2017-07-01

    Full Text Available Studies for the prevention and mitigation of floods require information on discharge and extent of inundation, commonly unavailable or uncertain, especially during extreme events. This study was initiated by the devastating flood in Tegucigalpa, the capital of Honduras, when Hurricane Mitch struck the city. In this study we hypothesized that it is possible to estimate, in a trustworthy way considering large data uncertainties, this extreme 1998 flood discharge and the extent of the inundations that followed from a combination of models and post-event measured data. Post-event data collected in 2000 and 2001 were used to estimate discharge peaks, times of peak, and high-water marks. These data were used in combination with rain data from two gauges to drive and constrain a combination of well-known modelling tools: TOPMODEL, Muskingum–Cunge–Todini routing, and the LISFLOOD-FP hydraulic model. Simulations were performed within the generalized likelihood uncertainty estimation (GLUE uncertainty-analysis framework. The model combination predicted peak discharge, times of peaks, and more than 90 % of the observed high-water marks within the uncertainty bounds of the evaluation data. This allowed an inundation likelihood map to be produced. Observed high-water marks could not be reproduced at a few locations on the floodplain. Identifications of these locations are useful to improve model set-up, model structure, or post-event data-estimation methods. Rainfall data were of central importance in simulating the times of peak and results would be improved by a better spatial assessment of rainfall, e.g. from radar data or a denser rain-gauge network. Our study demonstrated that it was possible, considering the uncertainty in the post-event data, to reasonably reproduce the extreme Mitch flood in Tegucigalpa in spite of no hydrometric gauging during the event. The method proposed here can be part of a Bayesian framework in which more events

  3. 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.

  4. Modeling active region transient brightenings observed with X-ray telescope as multi-stranded loops

    Energy Technology Data Exchange (ETDEWEB)

    Kobelski, Adam R.; McKenzie, David E. [Department of Physics, P.O. Box 173840, Montana State University, Bozeman, MT 59717-3840 (United States); Donachie, Martin, E-mail: kobelski@solar.physics.montana.edu [University of Glasgow, Glasgow, G128QQ, Scotland (United Kingdom)

    2014-05-10

    Strong evidence exists that coronal loops as observed in extreme ultraviolet and soft X-rays may not be monolithic isotropic structures, but can often be more accurately modeled as bundles of independent strands. Modeling the observed active region transient brightenings (ARTBs) within this framework allows for the exploration of the energetic ramifications and characteristics of these stratified structures. Here we present a simple method of detecting and modeling ARTBs observed with the Hinode X-Ray Telescope (XRT) as groups of zero-dimensional strands, which allows us to probe parameter space to better understand the spatial and temporal dependence of strand heating in impulsively heated loops. This partially automated method can be used to analyze a large number of observations to gain a statistical insight into the parameters of coronal structures, including the number of heating events required in a given model to fit the observations. In this article, we present the methodology and demonstrate its use in detecting and modeling ARTBs in a sample data set from Hinode/XRT. These initial results show that, in general, multiple heating events are necessary to reproduce observed ARTBs, but the spatial dependence of these heating events cannot yet be established.

  5. Modeling active region transient brightenings observed with X-ray telescope as multi-stranded loops

    International Nuclear Information System (INIS)

    Kobelski, Adam R.; McKenzie, David E.; Donachie, Martin

    2014-01-01

    Strong evidence exists that coronal loops as observed in extreme ultraviolet and soft X-rays may not be monolithic isotropic structures, but can often be more accurately modeled as bundles of independent strands. Modeling the observed active region transient brightenings (ARTBs) within this framework allows for the exploration of the energetic ramifications and characteristics of these stratified structures. Here we present a simple method of detecting and modeling ARTBs observed with the Hinode X-Ray Telescope (XRT) as groups of zero-dimensional strands, which allows us to probe parameter space to better understand the spatial and temporal dependence of strand heating in impulsively heated loops. This partially automated method can be used to analyze a large number of observations to gain a statistical insight into the parameters of coronal structures, including the number of heating events required in a given model to fit the observations. In this article, we present the methodology and demonstrate its use in detecting and modeling ARTBs in a sample data set from Hinode/XRT. These initial results show that, in general, multiple heating events are necessary to reproduce observed ARTBs, but the spatial dependence of these heating events cannot yet be established.

  6. 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.

  7. Reproducibility of somatosensory spatial perceptual maps.

    Science.gov (United States)

    Steenbergen, Peter; Buitenweg, Jan R; Trojan, Jörg; Veltink, Peter H

    2013-02-01

    Various studies have shown subjects to mislocalize cutaneous stimuli in an idiosyncratic manner. Spatial properties of individual localization behavior can be represented in the form of perceptual maps. Individual differences in these maps may reflect properties of internal body representations, and perceptual maps may therefore be a useful method for studying these representations. For this to be the case, individual perceptual maps need to be reproducible, which has not yet been demonstrated. We assessed the reproducibility of localizations measured twice on subsequent days. Ten subjects participated in the experiments. Non-painful electrocutaneous stimuli were applied at seven sites on the lower arm. Subjects localized the stimuli on a photograph of their own arm, which was presented on a tablet screen overlaying the real arm. Reproducibility was assessed by calculating intraclass correlation coefficients (ICC) for the mean localizations of each electrode site and the slope and offset of regression models of the localizations, which represent scaling and displacement of perceptual maps relative to the stimulated sites. The ICCs of the mean localizations ranged from 0.68 to 0.93; the ICCs of the regression parameters were 0.88 for the intercept and 0.92 for the slope. These results indicate a high degree of reproducibility. We conclude that localization patterns of non-painful electrocutaneous stimuli on the arm are reproducible on subsequent days. Reproducibility is a necessary property of perceptual maps for these to reflect properties of a subject's internal body representations. Perceptual maps are therefore a promising method for studying body representations.

  8. An empirical model of the topside plasma density around 600 km based on ROCSAT-1 and Hinotori observations

    Science.gov (United States)

    Huang, He; Chen, Yiding; Liu, Libo; Le, Huijun; Wan, Weixing

    2015-05-01

    It is an urgent task to improve the ability of ionospheric empirical models to more precisely reproduce the plasma density variations in the topside ionosphere. Based on the Republic of China Satellite 1 (ROCSAT-1) observations, we developed a new empirical model of topside plasma density around 600 km under relatively quiet geomagnetic conditions. The model reproduces the ROCSAT-1 plasma density observations with a root-mean-square-error of 0.125 in units of lg(Ni(cm-3)) and reasonably describes the temporal and spatial variations of plasma density at altitudes in the range from 550 to 660 km. The model results are also in good agreement with observations from Hinotori, Coupled Ion-Neutral Dynamics Investigations/Communications/Navigation Outage Forecasting System satellites and the incoherent scatter radar at Arecibo. Further, we combined ROCSAT-1 and Hinotori data to improve the ROCSAT-1 model and built a new model (R&H model) after the consistency between the two data sets had been confirmed with the original ROCSAT-1 model. In particular, we studied the solar activity dependence of topside plasma density at a fixed altitude by R&H model and find that its feature slightly differs from the case when the orbit altitude evolution is ignored. In addition, the R&H model shows the merging of the two crests of equatorial ionization anomaly above the F2 peak, while the IRI_Nq topside option always produces two separate crests in this range of altitudes.

  9. Planck intermediate results XXIX. All-sky dust modelling with Planck, IRAS, and WISE observations

    DEFF Research Database (Denmark)

    Ade, P. A. R.; Aghanim, N.; Alves, M. I. R.

    2016-01-01

    We present all-sky modelling of the high resolution Planck, IRAS, andWISE infrared (IR) observations using the physical dust model presented by Draine & Li in 2007 (DL, ApJ, 657, 810). We study the performance and results of this model, and discuss implications for future dust modelling....... The present work extends the DL dust modelling carried out on nearby galaxies using Herschel and Spitzer data to Galactic dust emission. We employ the DL dust model to generate maps of the dust mass surface density Sigma(Md), the dust optical extinction A(V), and the starlight intensity heating the bulk...... of the dust, parametrized by U-min. The DL model reproduces the observed spectral energy distribution (SED) satisfactorily over most of the sky, with small deviations in the inner Galactic disk and in low ecliptic latitude areas, presumably due to zodiacal light contamination. In the Andromeda galaxy (M31...

  10. Modelling soil erosion at European scale: towards harmonization and reproducibility

    Science.gov (United States)

    Bosco, C.; de Rigo, D.; Dewitte, O.; Poesen, J.; Panagos, P.

    2015-02-01

    Soil erosion by water is one of the most widespread forms of soil degradation. The loss of soil as a result of erosion can lead to decline in organic matter and nutrient contents, breakdown of soil structure and reduction of the water-holding capacity. Measuring soil loss across the whole landscape is impractical and thus research is needed to improve methods of estimating soil erosion with computational modelling, upon which integrated assessment and mitigation strategies may be based. Despite the efforts, the prediction value of existing models is still limited, especially at regional and continental scale, because a systematic knowledge of local climatological and soil parameters is often unavailable. A new approach for modelling soil erosion at regional scale is here proposed. It is based on the joint use of low-data-demanding models and innovative techniques for better estimating model inputs. The proposed modelling architecture has at its basis the semantic array programming paradigm and a strong effort towards computational reproducibility. An extended version of the Revised Universal Soil Loss Equation (RUSLE) has been implemented merging different empirical rainfall-erosivity equations within a climatic ensemble model and adding a new factor for a better consideration of soil stoniness within the model. Pan-European soil erosion rates by water have been estimated through the use of publicly available data sets and locally reliable empirical relationships. The accuracy of the results is corroborated by a visual plausibility check (63% of a random sample of grid cells are accurate, 83% at least moderately accurate, bootstrap p ≤ 0.05). A comparison with country-level statistics of pre-existing European soil erosion maps is also provided.

  11. Towards interoperable and reproducible QSAR analyses: Exchange of datasets.

    Science.gov (United States)

    Spjuth, Ola; Willighagen, Egon L; Guha, Rajarshi; Eklund, Martin; Wikberg, Jarl Es

    2010-06-30

    QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but

  12. Towards interoperable and reproducible QSAR analyses: Exchange of datasets

    Directory of Open Access Journals (Sweden)

    Spjuth Ola

    2010-06-01

    Full Text Available Abstract Background QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. Results We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Conclusions Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join

  13. Inter- and intra-laboratory study to determine the reproducibility of toxicogenomics datasets.

    Science.gov (United States)

    Scott, D J; Devonshire, A S; Adeleye, Y A; Schutte, M E; Rodrigues, M R; Wilkes, T M; Sacco, M G; Gribaldo, L; Fabbri, M; Coecke, S; Whelan, M; Skinner, N; Bennett, A; White, A; Foy, C A

    2011-11-28

    The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, it predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we assessed whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories. All test centres (TCs) adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen benzo[a]pyrene (B[a]P) and the human hepatoma cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were observed between the TCs, a common subset of B[a]P responsive genes (n=400 gene probes) was identified at all TCs which included many genes previously reported in the literature as B[a]P responsive. These data show promise that the current generation of microarray technology, in combination with a standard in vitro experimental design, can produce robust data that can be generated reproducibly in independent laboratories. Future work will need to determine whether such reproducible in vitro model(s) can be predictive for a range of toxic chemicals with different mechanisms of action and thus be considered as part of future testing regimes for regulatory risk assessment. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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

    International Nuclear Information System (INIS)

    Wang, Jian; Chekenya, Martha; Bjerkvig, Rolf; Enger, Per Ø; Miletic, Hrvoje; Sakariassen, Per Ø; Huszthy, Peter C; Jacobsen, Hege; Brekkå, Narve; Li, Xingang; Zhao, Peng; Mørk, Sverre

    2009-01-01

    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. 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. 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. 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

  15. 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.

  16. 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?

  17. Global assessment of ocean carbon export by combining satellite observations and food-web models

    Science.gov (United States)

    Siegel, D. A.; Buesseler, K. O.; Doney, S. C.; Sailley, S. F.; Behrenfeld, M. J.; Boyd, P. W.

    2014-03-01

    The export of organic carbon from the surface ocean by sinking particles is an important, yet highly uncertain, component of the global carbon cycle. Here we introduce a mechanistic assessment of the global ocean carbon export using satellite observations, including determinations of net primary production and the slope of the particle size spectrum, to drive a food-web model that estimates the production of sinking zooplankton feces and algal aggregates comprising the sinking particle flux at the base of the euphotic zone. The synthesis of observations and models reveals fundamentally different and ecologically consistent regional-scale patterns in export and export efficiency not found in previous global carbon export assessments. The model reproduces regional-scale particle export field observations and predicts a climatological mean global carbon export from the euphotic zone of 6 Pg C yr-1. Global export estimates show small variation (typically model parameter values. The model is also robust to the choices of the satellite data products used and enables interannual changes to be quantified. The present synthesis of observations and models provides a path for quantifying the ocean's biological pump.

  18. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

    Science.gov (United States)

    Bergmann, Frank T; Adams, Richard; Moodie, Stuart; Cooper, Jonathan; Glont, Mihai; Golebiewski, Martin; Hucka, Michael; Laibe, Camille; Miller, Andrew K; Nickerson, David P; Olivier, Brett G; Rodriguez, Nicolas; Sauro, Herbert M; Scharm, Martin; Soiland-Reyes, Stian; Waltemath, Dagmar; Yvon, Florent; Le Novère, Nicolas

    2014-12-14

    With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.

  19. Dynamic Contrast-enhanced MR Imaging in Renal Cell Carcinoma: Reproducibility of Histogram Analysis on Pharmacokinetic Parameters

    Science.gov (United States)

    Wang, Hai-yi; Su, Zi-hua; Xu, Xiao; Sun, Zhi-peng; Duan, Fei-xue; Song, Yuan-yuan; Li, Lu; Wang, Ying-wei; Ma, Xin; Guo, Ai-tao; Ma, Lin; Ye, Hui-yi

    2016-01-01

    Pharmacokinetic parameters derived from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) have been increasingly used to evaluate the permeability of tumor vessel. Histogram metrics are a recognized promising method of quantitative MR imaging that has been recently introduced in analysis of DCE-MRI pharmacokinetic parameters in oncology due to tumor heterogeneity. In this study, 21 patients with renal cell carcinoma (RCC) underwent paired DCE-MRI studies on a 3.0 T MR system. Extended Tofts model and population-based arterial input function were used to calculate kinetic parameters of RCC tumors. Mean value and histogram metrics (Mode, Skewness and Kurtosis) of each pharmacokinetic parameter were generated automatically using ImageJ software. Intra- and inter-observer reproducibility and scan–rescan reproducibility were evaluated using intra-class correlation coefficients (ICCs) and coefficient of variation (CoV). Our results demonstrated that the histogram method (Mode, Skewness and Kurtosis) was not superior to the conventional Mean value method in reproducibility evaluation on DCE-MRI pharmacokinetic parameters (K trans & Ve) in renal cell carcinoma, especially for Skewness and Kurtosis which showed lower intra-, inter-observer and scan-rescan reproducibility than Mean value. Our findings suggest that additional studies are necessary before wide incorporation of histogram metrics in quantitative analysis of DCE-MRI pharmacokinetic parameters. PMID:27380733

  20. Improving the Pattern Reproducibility of Multiple-Point-Based Prior Models Using Frequency Matching

    DEFF Research Database (Denmark)

    Cordua, Knud Skou; Hansen, Thomas Mejer; Mosegaard, Klaus

    2014-01-01

    Some multiple-point-based sampling algorithms, such as the snesim algorithm, rely on sequential simulation. The conditional probability distributions that are used for the simulation are based on statistics of multiple-point data events obtained from a training image. During the simulation, data...... events with zero probability in the training image statistics may occur. This is handled by pruning the set of conditioning data until an event with non-zero probability is found. The resulting probability distribution sampled by such algorithms is a pruned mixture model. The pruning strategy leads...... to a probability distribution that lacks some of the information provided by the multiple-point statistics from the training image, which reduces the reproducibility of the training image patterns in the outcome realizations. When pruned mixture models are used as prior models for inverse problems, local re...

  1. Acute multi-sgRNA knockdown of KEOPS complex genes reproduces the microcephaly phenotype of the stable knockout zebrafish model.

    Directory of Open Access Journals (Sweden)

    Tilman Jobst-Schwan

    Full Text Available Until recently, morpholino oligonucleotides have been widely employed in zebrafish as an acute and efficient loss-of-function assay. However, off-target effects and reproducibility issues when compared to stable knockout lines have compromised their further use. Here we employed an acute CRISPR/Cas approach using multiple single guide RNAs targeting simultaneously different positions in two exemplar genes (osgep or tprkb to increase the likelihood of generating mutations on both alleles in the injected F0 generation and to achieve a similar effect as morpholinos but with the reproducibility of stable lines. This multi single guide RNA approach resulted in median likelihoods for at least one mutation on each allele of >99% and sgRNA specific insertion/deletion profiles as revealed by deep-sequencing. Immunoblot showed a significant reduction for Osgep and Tprkb proteins. For both genes, the acute multi-sgRNA knockout recapitulated the microcephaly phenotype and reduction in survival that we observed previously in stable knockout lines, though milder in the acute multi-sgRNA knockout. Finally, we quantify the degree of mutagenesis by deep sequencing, and provide a mathematical model to quantitate the chance for a biallelic loss-of-function mutation. Our findings can be generalized to acute and stable CRISPR/Cas targeting for any zebrafish gene of interest.

  2. Reproducing the nonlinear dynamic behavior of a structured beam with a generalized continuum model

    Science.gov (United States)

    Vila, J.; Fernández-Sáez, J.; Zaera, R.

    2018-04-01

    In this paper we study the coupled axial-transverse nonlinear vibrations of a kind of one dimensional structured solids by application of the so called Inertia Gradient Nonlinear continuum model. To show the accuracy of this axiomatic model, previously proposed by the authors, its predictions are compared with numeric results from a previously defined finite discrete chain of lumped masses and springs, for several number of particles. A continualization of the discrete model equations based on Taylor series allowed us to set equivalent values of the mechanical properties in both discrete and axiomatic continuum models. Contrary to the classical continuum model, the inertia gradient nonlinear continuum model used herein is able to capture scale effects, which arise for modes in which the wavelength is comparable to the characteristic distance of the structured solid. The main conclusion of the work is that the proposed generalized continuum model captures the scale effects in both linear and nonlinear regimes, reproducing the behavior of the 1D nonlinear discrete model adequately.

  3. Towards Reproducibility in Computational Hydrology

    Science.gov (United States)

    Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

    2017-04-01

    Reproducibility is a foundational principle in scientific research. The ability to independently re-run an experiment helps to verify the legitimacy of individual findings, and evolve (or reject) hypotheses and models of how environmental systems function, and move them from specific circumstances to more general theory. Yet in computational hydrology (and in environmental science more widely) the code and data that produces published results are not regularly made available, and even if they are made available, there remains a multitude of generally unreported choices that an individual scientist may have made that impact the study result. This situation strongly inhibits the ability of our community to reproduce and verify previous findings, as all the information and boundary conditions required to set up a computational experiment simply cannot be reported in an article's text alone. In Hutton et al 2016 [1], we argue that a cultural change is required in the computational hydrological community, in order to advance and make more robust the process of knowledge creation and hypothesis testing. We need to adopt common standards and infrastructures to: (1) make code readable and re-useable; (2) create well-documented workflows that combine re-useable code together with data to enable published scientific findings to be reproduced; (3) make code and workflows available, easy to find, and easy to interpret, using code and code metadata repositories. To create change we argue for improved graduate training in these areas. In this talk we reflect on our progress in achieving reproducible, open science in computational hydrology, which are relevant to the broader computational geoscience community. In particular, we draw on our experience in the Switch-On (EU funded) virtual water science laboratory (http://www.switch-on-vwsl.eu/participate/), which is an open platform for collaboration in hydrological experiments (e.g. [2]). While we use computational hydrology as

  4. 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.

  5. Reproducibility, controllability, and optimization of LENR experiments

    International Nuclear Information System (INIS)

    Nagel, David J.

    2006-01-01

    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

  6. Charge state evolution in the solar wind. III. Model comparison with observations

    Energy Technology Data Exchange (ETDEWEB)

    Landi, E.; Oran, R.; Lepri, S. T.; Zurbuchen, T. H.; Fisk, L. A.; Van der Holst, B. [Department of Atmospheric, Oceanic and Space Sciences, University of Michigan, Ann Arbor, MI 48109 (United States)

    2014-08-01

    We test three theoretical models of the fast solar wind with a set of remote sensing observations and in-situ measurements taken during the minimum of solar cycle 23. First, the model electron density and temperature are compared to SOHO/SUMER spectroscopic measurements. Second, the model electron density, temperature, and wind speed are used to predict the charge state evolution of the wind plasma from the source regions to the freeze-in point. Frozen-in charge states are compared with Ulysses/SWICS measurements at 1 AU, while charge states close to the Sun are combined with the CHIANTI spectral code to calculate the intensities of selected spectral lines, to be compared with SOHO/SUMER observations in the north polar coronal hole. We find that none of the theoretical models are able to completely reproduce all observations; namely, all of them underestimate the charge state distribution of the solar wind everywhere, although the levels of disagreement vary from model to model. We discuss possible causes of the disagreement, namely, uncertainties in the calculation of the charge state evolution and of line intensities, in the atomic data, and in the assumptions on the wind plasma conditions. Last, we discuss the scenario where the wind is accelerated from a region located in the solar corona rather than in the chromosphere as assumed in the three theoretical models, and find that a wind originating from the corona is in much closer agreement with observations.

  7. Charge state evolution in the solar wind. III. Model comparison with observations

    International Nuclear Information System (INIS)

    Landi, E.; Oran, R.; Lepri, S. T.; Zurbuchen, T. H.; Fisk, L. A.; Van der Holst, B.

    2014-01-01

    We test three theoretical models of the fast solar wind with a set of remote sensing observations and in-situ measurements taken during the minimum of solar cycle 23. First, the model electron density and temperature are compared to SOHO/SUMER spectroscopic measurements. Second, the model electron density, temperature, and wind speed are used to predict the charge state evolution of the wind plasma from the source regions to the freeze-in point. Frozen-in charge states are compared with Ulysses/SWICS measurements at 1 AU, while charge states close to the Sun are combined with the CHIANTI spectral code to calculate the intensities of selected spectral lines, to be compared with SOHO/SUMER observations in the north polar coronal hole. We find that none of the theoretical models are able to completely reproduce all observations; namely, all of them underestimate the charge state distribution of the solar wind everywhere, although the levels of disagreement vary from model to model. We discuss possible causes of the disagreement, namely, uncertainties in the calculation of the charge state evolution and of line intensities, in the atomic data, and in the assumptions on the wind plasma conditions. Last, we discuss the scenario where the wind is accelerated from a region located in the solar corona rather than in the chromosphere as assumed in the three theoretical models, and find that a wind originating from the corona is in much closer agreement with observations.

  8. THE STELLAR MASS COMPONENTS OF GALAXIES: COMPARING SEMI-ANALYTICAL MODELS WITH OBSERVATION

    International Nuclear Information System (INIS)

    Liu Lei; Yang Xiaohu; Mo, H. J.; Van den Bosch, Frank C.; Springel, Volker

    2010-01-01

    We compare the stellar masses of central and satellite galaxies predicted by three independent semi-analytical models (SAMs) with observational results obtained from a large galaxy group catalog constructed from the Sloan Digital Sky Survey. In particular, we compare the stellar mass functions of centrals and satellites, the relation between total stellar mass and halo mass, and the conditional stellar mass functions, Φ(M * |M h ), which specify the average number of galaxies of stellar mass M * that reside in a halo of mass M h . The SAMs only predict the correct stellar masses of central galaxies within a limited mass range and all models fail to reproduce the sharp decline of stellar mass with decreasing halo mass observed at the low mass end. In addition, all models over-predict the number of satellite galaxies by roughly a factor of 2. The predicted stellar mass in satellite galaxies can be made to match the data by assuming that a significant fraction of satellite galaxies are tidally stripped and disrupted, giving rise to a population of intra-cluster stars (ICS) in their host halos. However, the amount of ICS thus predicted is too large compared to observation. This suggests that current galaxy formation models still have serious problems in modeling star formation in low-mass halos.

  9. Comparing soil moisture memory in satellite observations and models

    Science.gov (United States)

    Stacke, Tobias; Hagemann, Stefan; Loew, Alexander

    2013-04-01

    A major obstacle to a correct parametrization of soil processes in large scale global land surface models is the lack of long term soil moisture observations for large parts of the globe. Currently, a compilation of soil moisture data derived from a range of satellites is released by the ESA Climate Change Initiative (ECV_SM). Comprising the period from 1978 until 2010, it provides the opportunity to compute climatological relevant statistics on a quasi-global scale and to compare these to the output of climate models. Our study is focused on the investigation of soil moisture memory in satellite observations and models. As a proxy for memory we compute the autocorrelation length (ACL) of the available satellite data and the uppermost soil layer of the models. Additional to the ECV_SM data, AMSR-E soil moisture is used as observational estimate. Simulated soil moisture fields are taken from ERA-Interim reanalysis and generated with the land surface model JSBACH, which was driven with quasi-observational meteorological forcing data. The satellite data show ACLs between one week and one month for the greater part of the land surface while the models simulate a longer memory of up to two months. Some pattern are similar in models and observations, e.g. a longer memory in the Sahel Zone and the Arabian Peninsula, but the models are not able to reproduce regions with a very short ACL of just a few days. If the long term seasonality is subtracted from the data the memory is strongly shortened, indicating the importance of seasonal variations for the memory in most regions. Furthermore, we analyze the change of soil moisture memory in the different soil layers of the models to investigate to which extent the surface soil moisture includes information about the whole soil column. A first analysis reveals that the ACL is increasing for deeper layers. However, its increase is stronger in the soil moisture anomaly than in its absolute values and the first even exceeds the

  10. Magnet stability and reproducibility

    CERN Document Server

    Marks, N

    2010-01-01

    Magnet stability and reproducibility have become increasingly important as greater precision and beams with smaller dimension are required for research, medical and other purpose. The observed causes of mechanical and electrical instability are introduced and the engineering arrangements needed to minimize these problems discussed; the resulting performance of a state-of-the-art synchrotron source (Diamond) is then presented. The need for orbit feedback to obtain best possible beam stability is briefly introduced, but omitting any details of the necessary technical equipment, which is outside the scope of the presentation.

  11. Contrasting spatial structures of Atlantic Multidecadal Oscillation between observations and slab ocean model simulations

    Science.gov (United States)

    Sun, Cheng; Li, Jianping; Kucharski, Fred; Xue, Jiaqing; Li, Xiang

    2018-04-01

    The spatial structure of Atlantic multidecadal oscillation (AMO) is analyzed and compared between the observations and simulations from slab ocean models (SOMs) and fully coupled models. The observed sea surface temperature (SST) pattern of AMO is characterized by a basin-wide monopole structure, and there is a significantly high degree of spatial coherence of decadal SST variations across the entire North Atlantic basin. The observed SST anomalies share a common decadal-scale signal, corresponding to the basin-wide average (i. e., the AMO). In contrast, the simulated AMO in SOMs (AMOs) exhibits a tripole-like structure, with the mid-latitude North Atlantic SST showing an inverse relationship with other parts of the basin, and the SOMs fail to reproduce the observed strong spatial coherence of decadal SST variations associated with the AMO. The observed spatial coherence of AMO SST anomalies is identified as a key feature that can be used to distinguish the AMO mechanism. The tripole-like SST pattern of AMOs in SOMs can be largely explained by the atmosphere-forced thermodynamics mechanism due to the surface heat flux changes associated with the North Atlantic Oscillation (NAO). The thermodynamic forcing of AMOs by the NAO gives rise to a simultaneous inverse NAO-AMOs relationship at both interannual and decadal timescales and a seasonal phase locking of the AMOs variability to the cold season. However, the NAO-forced thermodynamics mechanism cannot explain the observed NAO-AMO relationship and the seasonal phase locking of observed AMO variability to the warm season. At decadal timescales, a strong lagged relationship between NAO and AMO is observed, with the NAO leading by up to two decades, while the simultaneous correlation of NAO with AMO is weak. This lagged relationship and the spatial coherence of AMO can be well understood from the view point of ocean dynamics. A time-integrated NAO index, which reflects the variations in Atlantic meridional overturning

  12. Development of a Consistent and Reproducible Porcine Scald Burn Model

    Science.gov (United States)

    Kempf, Margit; Kimble, Roy; Cuttle, Leila

    2016-01-01

    There are very few porcine burn models that replicate scald injuries similar to those encountered by children. We have developed a robust porcine burn model capable of creating reproducible scald burns for a wide range of burn conditions. The study was conducted with juvenile Large White pigs, creating replicates of burn combinations; 50°C for 1, 2, 5 and 10 minutes and 60°C, 70°C, 80°C and 90°C for 5 seconds. Visual wound examination, biopsies and Laser Doppler Imaging were performed at 1, 24 hours and at 3 and 7 days post-burn. A consistent water temperature was maintained within the scald device for long durations (49.8 ± 0.1°C when set at 50°C). The macroscopic and histologic appearance was consistent between replicates of burn conditions. For 50°C water, 10 minute duration burns showed significantly deeper tissue injury than all shorter durations at 24 hours post-burn (p ≤ 0.0001), with damage seen to increase until day 3 post-burn. For 5 second duration burns, by day 7 post-burn the 80°C and 90°C scalds had damage detected significantly deeper in the tissue than the 70°C scalds (p ≤ 0.001). A reliable and safe model of porcine scald burn injury has been successfully developed. The novel apparatus with continually refreshed water improves consistency of scald creation for long exposure times. This model allows the pathophysiology of scald burn wound creation and progression to be examined. PMID:27612153

  13. A catalyzing phantom for reproducible dynamic conversion of hyperpolarized [1-¹³C]-pyruvate.

    Science.gov (United States)

    Walker, Christopher M; Lee, Jaehyuk; Ramirez, Marc S; Schellingerhout, Dawid; Millward, Steven; Bankson, James A

    2013-01-01

    In vivo real time spectroscopic imaging of hyperpolarized ¹³C labeled metabolites shows substantial promise for the assessment of physiological processes that were previously inaccessible. However, reliable and reproducible methods of measurement are necessary to maximize the effectiveness of imaging biomarkers that may one day guide personalized care for diseases such as cancer. Animal models of human disease serve as poor reference standards due to the complexity, heterogeneity, and transient nature of advancing disease. In this study, we describe the reproducible conversion of hyperpolarized [1-¹³C]-pyruvate to [1-¹³C]-lactate using a novel synthetic enzyme phantom system. The rate of reaction can be controlled and tuned to mimic normal or pathologic conditions of varying degree. Variations observed in the use of this phantom compare favorably against within-group variations observed in recent animal studies. This novel phantom system provides crucial capabilities as a reference standard for the optimization, comparison, and certification of quantitative imaging strategies for hyperpolarized tracers.

  14. A catalyzing phantom for reproducible dynamic conversion of hyperpolarized [1-¹³C]-pyruvate.

    Directory of Open Access Journals (Sweden)

    Christopher M Walker

    Full Text Available In vivo real time spectroscopic imaging of hyperpolarized ¹³C labeled metabolites shows substantial promise for the assessment of physiological processes that were previously inaccessible. However, reliable and reproducible methods of measurement are necessary to maximize the effectiveness of imaging biomarkers that may one day guide personalized care for diseases such as cancer. Animal models of human disease serve as poor reference standards due to the complexity, heterogeneity, and transient nature of advancing disease. In this study, we describe the reproducible conversion of hyperpolarized [1-¹³C]-pyruvate to [1-¹³C]-lactate using a novel synthetic enzyme phantom system. The rate of reaction can be controlled and tuned to mimic normal or pathologic conditions of varying degree. Variations observed in the use of this phantom compare favorably against within-group variations observed in recent animal studies. This novel phantom system provides crucial capabilities as a reference standard for the optimization, comparison, and certification of quantitative imaging strategies for hyperpolarized tracers.

  15. Apparent diffusion coefficient measurements in diffusion-weighted magnetic resonance imaging of the anterior mediastinum: inter-observer reproducibility of five different methods of region-of-interest positioning

    Energy Technology Data Exchange (ETDEWEB)

    Priola, Adriano Massimiliano; Priola, Sandro Massimo; Parlatano, Daniela; Gned, Dario; Veltri, Andrea [San Luigi Gonzaga University Hospital, Department of Diagnostic Imaging, Regione Gonzole 10, Orbassano, Torino (Italy); Giraudo, Maria Teresa [University of Torino, Department of Mathematics ' ' Giuseppe Peano' ' , Torino (Italy); Giardino, Roberto; Ardissone, Francesco [San Luigi Gonzaga University Hospital, Department of Thoracic Surgery, Regione Gonzole 10, Orbassano, Torino (Italy); Ferrero, Bruno [San Luigi Gonzaga University Hospital, Department of Neurology, Regione Gonzole 10, Orbassano, Torino (Italy)

    2017-04-15

    To investigate inter-reader reproducibility of five different region-of-interest (ROI) protocols for apparent diffusion coefficient (ADC) measurements in the anterior mediastinum. In eighty-one subjects, on ADC mapping, two readers measured the ADC using five methods of ROI positioning that encompassed the entire tissue (whole tissue volume [WTV], three slices observer-defined [TSOD], single-slice [SS]) or the more restricted areas (one small round ROI [OSR], multiple small round ROI [MSR]). Inter-observer variability was assessed with interclass correlation coefficient (ICC), coefficient of variation (CoV), and Bland-Altman analysis. Nonparametric tests were performed to compare the ADC between ROI methods. The measurement time was recorded and compared between ROI methods. All methods showed excellent inter-reader agreement with best and worst reproducibility in WTV and OSR, respectively (ICC, 0.937/0.874; CoV, 7.3 %/16.8 %; limits of agreement, ±0.44/±0.77 x 10{sup -3} mm{sup 2}/s). ADC values of OSR and MSR were significantly lower compared to the other methods in both readers (p < 0.001). The SS and OSR methods required less measurement time (14 ± 2 s) compared to the others (p < 0.0001), while the WTV method required the longest measurement time (90 ± 56 and 77 ± 49 s for each reader) (p < 0.0001). All methods demonstrate excellent inter-observer reproducibility with the best agreement in WTV, although it requires the longest measurement time. (orig.)

  16. A UNIFIED EMPIRICAL MODEL FOR INFRARED GALAXY COUNTS BASED ON THE OBSERVED PHYSICAL EVOLUTION OF DISTANT GALAXIES

    International Nuclear Information System (INIS)

    Béthermin, Matthieu; Daddi, Emanuele; Sargent, Mark T.; Elbaz, David; Mullaney, James; Pannella, Maurilio; Magdis, Georgios; Hezaveh, Yashar; Le Borgne, Damien; Buat, Véronique; Charmandaris, Vassilis; Lagache, Guilaine; Scott, Douglas

    2012-01-01

    We reproduce the mid-infrared to radio galaxy counts with a new empirical model based on our current understanding of the evolution of main-sequence (MS) and starburst (SB) galaxies. We rely on a simple spectral energy distribution (SED) library based on Herschel observations: a single SED for the MS and another one for SB, getting warmer with redshift. Our model is able to reproduce recent measurements of galaxy counts performed with Herschel, including counts per redshift slice. This agreement demonstrates the power of our 2-Star-Formation Modes (2SFM) decomposition in describing the statistical properties of infrared sources and their evolution with cosmic time. We discuss the relative contribution of MS and SB galaxies to the number counts at various wavelengths and flux densities. We also show that MS galaxies are responsible for a bump in the 1.4 GHz radio counts around 50 μJy. Material of the model (predictions, SED library, mock catalogs, etc.) is available online.

  17. Observations and Numerical Modeling of the Jovian Ribbon

    Science.gov (United States)

    Cosentino, R. G.; Simon, A.; Morales-Juberias, R.; Sayanagi, K. M.

    2015-01-01

    Multiple wavelength observations made by the Hubble Space Telescope in early 2007 show the presence of a wavy, high-contrast feature in Jupiter's atmosphere near 30 degrees North. The "Jovian Ribbon," best seen at 410 nanometers, irregularly undulates in latitude and is time-variable in appearance. A meridional intensity gradient algorithm was applied to the observations to track the Ribbon's contour. Spectral analysis of the contour revealed that the Ribbon's structure is a combination of several wavenumbers ranging from k equals 8-40. The Ribbon is a dynamic structure that has been observed to have spectral power for dominant wavenumbers which vary over a time period of one month. The presence of the Ribbon correlates with periods when the velocity of the westward jet at the same location is highest. We conducted numerical simulations to investigate the stability of westward jets of varying speed, vertical shear, and background static stability to different perturbations. A Ribbon-like morphology was best reproduced with a 35 per millisecond westward jet that decreases in amplitude for pressures greater than 700 hectopascals and a background static stability of N equals 0.005 per second perturbed by heat pulses constrained to latitudes south of 30 degrees North. Additionally, the simulated feature had wavenumbers that qualitatively matched observations and evolved throughout the simulation reproducing the Jovian Ribbon's dynamic structure.

  18. 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....

  19. 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......, 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...

  20. Evaluation of CMIP5 Ability to Reproduce 20th Century Regional Trends in Surface Air Temperature and Precipitation over CONUS

    Science.gov (United States)

    Lee, J.; Waliser, D. E.; Lee, H.; Loikith, P. C.; Kunkel, K.

    2017-12-01

    Monitoring temporal changes in key climate variables, such as surface air temperature and precipitation, is an integral part of the ongoing efforts of the United States National Climate Assessment (NCA). Climate models participating in CMIP5 provide future trends for four different emissions scenarios. In order to have confidence in the future projections of surface air temperature and precipitation, it is crucial to evaluate the ability of CMIP5 models to reproduce observed trends for three different time periods (1895-1939, 1940-1979, and 1980-2005). Towards this goal, trends in surface air temperature and precipitation obtained from the NOAA nClimGrid 5 km gridded station observation-based product are compared during all three time periods to the 206 CMIP5 historical simulations from 48 unique GCMs and their multi-model ensemble (MME) for NCA-defined climate regions during summer (JJA) and winter (DJF). This evaluation quantitatively examines the biases of simulated trends of the spatially averaged temperature and precipitation in the NCA climate regions. The CMIP5 MME reproduces historical surface air temperature trends for JJA for all time period and all regions, except the Northern Great Plains from 1895-1939 and Southeast during 1980-2005. Likewise, for DJF, the MME reproduces historical surface air temperature trends across all time periods over all regions except the Southeast from 1895-1939 and the Midwest during 1940-1979. The Regional Climate Model Evaluation System (RCMES), an analysis tool which supports the NCA by providing access to data and tools for regional climate model validation, facilitates the comparisons between the models and observation. The RCMES Toolkit is designed to assist in the analysis of climate variables and the procedure of the evaluation of climate projection models to support the decision-making processes. This tool is used in conjunction with the above analysis and results will be presented to demonstrate its capability to

  1. Reproducibility of Ultrasound and Magnetic Resonance Imaging Measurements of Tendon Size

    International Nuclear Information System (INIS)

    Brushoej, C.; Henriksen, B.M.; Albrecht-Beste, E.; Hoelmich, P.; Larsen, K.; Bachmann Nielsen, M.

    2006-01-01

    Purpose: To investigate the intra- and inter-tester reproducibility of measurements of the Achilles tendon, tibialis anterior tendon, and the tibialis posterior tendon in football players using ultrasound (US) and magnetic resonance imaging (MRI). Material and Methods: Eleven asymptomatic football players were examined. Using a standardized US scanning protocol, the tendons were examined by two observers with US for thickness, width, and cross-sectional area. One observer conducted the procedure twice. The subjects also underwent an MRI examination, and the assessment of tendon size was conducted twice by two observers. Results: The best reproducibility judged by coefficient of variation (CV) and 95% confidence interval was determined for the Achilles tendon on both US and MRI. The variability of US on measurements on the tibialis anterior and tibialis posterior tendons was less than that when using MRI. In 12 out of 18 measurements, there were systematic differences between observers as judged by one-sided F-test. Conclusion: The reproducibility of the three tendons was limited. Precaution should be taken when looking for minor quantitative changes, i.e., training-induced hypertrophy, and when doing so, the Achilles tendon should be used

  2. 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.

  3. How well do CMIP5 Climate Models Reproduce the Hydrologic Cycle of the Colorado River Basin?

    Science.gov (United States)

    Gautam, J.; Mascaro, G.

    2017-12-01

    The Colorado River, which is the primary source of water for nearly 40 million people in the arid Southwestern states of the United States, has been experiencing an extended drought since 2000, which has led to a significant reduction in water supply. As the water demands increase, one of the major challenges for water management in the region has been the quantification of uncertainties associated with streamflow predictions in the Colorado River Basin (CRB) under potential changes of future climate. Hence, testing the reliability of model predictions in the CRB is critical in addressing this challenge. In this study, we evaluated the performances of 17 General Circulation Models (GCMs) from the Coupled Model Intercomparison Project Phase Five (CMIP5) and 4 Regional Climate Models (RCMs) in reproducing the statistical properties of the hydrologic cycle in the CRB. We evaluated the water balance components at four nested sub-basins along with the inter-annual and intra-annual changes of precipitation (P), evaporation (E), runoff (R) and temperature (T) from 1979 to 2005. Most of the models captured the net water balance fairly well in the most-upstream basin but simulated a weak hydrological cycle in the evaporation channel at the downstream locations. The simulated monthly variability of P had different patterns, with correlation coefficients ranging from -0.6 to 0.8 depending on the sub-basin and the models from same parent institution clustering together. Apart from the most-upstream sub-basin where the models were mainly characterized by a negative seasonal bias in SON (of up to -50%), most of them had a positive bias in all seasons (of up to +260%) in the other three sub-basins. The models, however, captured the monthly variability of T well at all sites with small inter-model variabilities and a relatively similar range of bias (-7 °C to +5 °C) across all seasons. Mann-Kendall test was applied to the annual P and T time-series where majority of the models

  4. 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

  5. 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

  6. Reproducibility analysis of measurements with a mechanical semiautomatic eye model for evaluation of intraocular lenses

    Science.gov (United States)

    Rank, Elisabet; Traxler, Lukas; Bayer, Natascha; Reutterer, Bernd; Lux, Kirsten; Drauschke, Andreas

    2014-03-01

    Mechanical eye models are used to validate ex vivo the optical quality of intraocular lenses (IOLs). The quality measurement and test instructions for IOLs are defined in the ISO 11979-2. However, it was mentioned in literature that these test instructions could lead to inaccurate measurements in case of some modern IOL designs. Reproducibility of alignment and measurement processes are presented, performed with a semiautomatic mechanical ex vivo eye model based on optical properties published by Liou and Brennan in the scale 1:1. The cornea, the iris aperture and the IOL itself are separately changeable within the eye model. The adjustment of the IOL can be manipulated by automatic decentration and tilt of the IOL in reference to the optical axis of the whole system, which is defined by the connection line of the central point of the artificial cornea and the iris aperture. With the presented measurement setup two quality criteria are measurable: the modulation transfer function (MTF) and the Strehl ratio. First the reproducibility of the alignment process for definition of initial conditions of the lateral position and tilt in reference to the optical axis of the system is investigated. Furthermore, different IOL holders are tested related to the stable holding of the IOL. The measurement is performed by a before-after comparison of the lens position using a typical decentration and tilt tolerance analysis path. Modulation transfer function MTF and Strehl ratio S before and after this tolerance analysis are compared and requirements for lens holder construction are deduced from the presented results.

  7. WRF-Chem model simulations of a dust outbreak over the central Mediterranean and comparison with multi-sensor desert dust observations

    Science.gov (United States)

    Rizza, Umberto; Barnaba, Francesca; Marcello Miglietta, Mario; Mangia, Cristina; Di Liberto, Luca; Dionisi, Davide; Costabile, Francesca; Grasso, Fabio; Gobbi, Gian Paolo

    2017-01-01

    In this study, the Weather Research and Forecasting model with online coupled chemistry (WRF-Chem) is applied to simulate an intense Saharan dust outbreak event that took place over the Mediterranean in May 2014. Comparison of a simulation using a physics-based desert dust emission scheme with a numerical experiment using a simplified (minimal) emission scheme is included to highlight the advantages of the former. The model was found to reproduce well the synoptic meteorological conditions driving the dust outbreak: an omega-like pressure configuration associated with a cyclogenesis in the Atlantic coasts of Spain. The model performances in reproducing the atmospheric desert dust load were evaluated using a multi-platform observational dataset of aerosol and desert dust properties, including optical properties from satellite and ground-based sun photometers and lidars, plus in situ particulate matter mass concentration (PM) data. This comparison allowed us to investigate the model ability in reproducing both the horizontal and the vertical displacement of the dust plume, as well as its evolution in time. The comparison with satellite (MODIS-Terra) and sun photometers (AERONET) showed that the model is able to reproduce well the horizontal field of the aerosol optical depth (AOD) and its evolution in time (temporal correlation coefficient with AERONET of 0.85). On the vertical scale, the comparison with lidar data at a single site (Rome, Italy) confirms that the desert dust advection occurs in several, superimposed "pulses" as simulated by the model. Cross-analysis of the modeled AOD and desert dust emission fluxes further allowed for the source regions of the observed plumes to be inferred. The vertical displacement of the modeled dust plume was in rather good agreement with the lidar soundings, with correlation coefficients among aerosol extinction profiles up to 1 and mean discrepancy of about 50 %. The model-measurement comparison for PM10 and PM2.5 showed a

  8. Reproducibility of temporomandibular joint tomography. Influence of shifted X-ray beam and tomographic focal plane on reproducibility

    International Nuclear Information System (INIS)

    Saito, Masashi

    1999-01-01

    Proper tomographic focal plane and x-ray beam direction are the most important factors to obtain accurate images of the temporomandibular joint (TMJ). In this study, to clarify the magnitude of effect of these two factors on the image quality. We evaluated the reproducibility of tomograms by measuring the distortion when the x-ray beam was shifted from the correct center of the object. The effects of the deviation of the tomographic focal plane on image quality were evaluated by the MTF (Modulation Transfer Function). Two types of tomograms, one the plane type, the other the rotational type were used in this study. A TMJ model was made from Teflon for the purpose of evaluation by shifting the x-ray beam. The x-ray images were obtained by tilting the model from 0 to 10 degrees 2-degree increments. These x-ray images were processed for computer image analysis, and then the distance between condyle and the joint space was measured. To evaluate the influence of the shifted tomographic focal plane on image sharpness, the x-ray images from each setting were analyzed by MTF. To obtain the MTF, ''knife-edge'' made from Pb was used. The images were scanned with a microdensitometer at the central focal plane, and 0, 0.5, 1 mm away respectively. The density curves were analyzed by Fourier analysis and the MTF was calculated. The reproducibility of images became worse by shifting the x-ray beam. This tendency was similar for both tomograms. Object characteristics such as anterior and posterior portion of the joint space affected the deterioration of reproducibility of the tomography. The deviation of the tomographic focal plane also decreased the reproducibility of the x-ray images. The rotational type showed a better MTF, but it became seriously unfavorable with slight changes of the tomographic focal plane. Contrarily, the plane type showed a lower MTF, but the image was stable with shifting of the tomographic focal plane. (author)

  9. REPRODUCING THE CORRELATIONS OF TYPE C LOW-FREQUENCY QUASI-PERIODIC OSCILLATION PARAMETERS IN XTE J1550–564 WITH A SPIRAL STRUCTURE

    Energy Technology Data Exchange (ETDEWEB)

    Varniere, Peggy [APC, AstroParticule et Cosmologie, Universite Paris Diderot, CNRS/IN2P3, CEA/Irfu, Observatoire de Paris, Sorbonne Paris Cité, 10, rue Alice Domon et Lonie Duquet, F-75205 Paris Cedex 13 (France); Vincent, Frederic H., E-mail: varniere@apc.univ-paris7.fr [Observatoire de Paris/LESIA, 5, place Jules Janssen, F-92195 Meudon Cedex (France)

    2017-01-10

    While it has been observed that the parameters intrinsic to the type C low-frequency quasi-periodic oscillations are related in a nonlinear manner among themselves, there has been, up to now, no model to explain or reproduce how the frequency, the FWHM, and the rms amplitude of the type C low-frequency quasi-periodic oscillations behave with respect to one another. Here we are using a simple toy model representing the emission from a standard disk and a spiral such as that caused by the accretion–ejection instability to reproduce the overall observed behavior and shed some light on its origin. This allows us to prove the ability of such a spiral structure to be at the origin of flux modulation over more than an order of magnitude in frequency.

  10. Personalized, Shareable Geoscience Dataspaces For Simplifying Data Management and Improving Reproducibility

    Science.gov (United States)

    Malik, T.; Foster, I.; Goodall, J. L.; Peckham, S. D.; Baker, J. B. H.; Gurnis, M.

    2015-12-01

    Research activities are iterative, collaborative, and now data- and compute-intensive. Such research activities mean that even the many researchers who work in small laboratories must often create, acquire, manage, and manipulate much diverse data and keep track of complex software. They face difficult data and software management challenges, and data sharing and reproducibility are neglected. There is signficant federal investment in powerful cyberinfrastructure, in part to lesson the burden associated with modern data- and compute-intensive research. Similarly, geoscience communities are establishing research repositories to facilitate data preservation. Yet we observe a large fraction of the geoscience community continues to struggle with data and software management. The reason, studies suggest, is not lack of awareness but rather that tools do not adequately support time-consuming data life cycle activities. Through NSF/EarthCube-funded GeoDataspace project, we are building personalized, shareable dataspaces that help scientists connect their individual or research group efforts with the community at large. The dataspaces provide a light-weight multiplatform research data management system with tools for recording research activities in what we call geounits, so that a geoscientist can at any time snapshot and preserve, both for their own use and to share with the community, all data and code required to understand and reproduce a study. A software-as-a-service (SaaS) deployment model enhances usability of core components, and integration with widely used software systems. In this talk we will present the open-source GeoDataspace project and demonstrate how it is enabling reproducibility across geoscience domains of hydrology, space science, and modeling toolkits.

  11. Reproducibility in the assessment of acute pancreatitis with computed tomography

    International Nuclear Information System (INIS)

    Freire Filho, Edison de Oliveira; Vieira, Renata La Rocca; Yamada, Andre Fukunishi; Shigueoka, David Carlos; Bekhor, Daniel; Freire, Maxime Figueiredo de Oliveira; Ajzen, Sergio; D'Ippolito, Giuseppe

    2007-01-01

    Objective: To evaluate the reproducibility of unenhanced and contrast-enhanced computed tomography in the assessment of patients with acute pancreatitis. Materials and methods: Fifty-one unenhanced and contrast-enhanced abdominal computed tomography studies of patients with acute pancreatitis were blindly reviewed by two radiologists (observers 1 and 2). The morphological index was separately calculated for unenhanced and contrast-enhanced computed tomography and the disease severity index was established. Intraobserver and interobserver reproducibility of computed tomography was measured by means of the kappa index (κ). Results: Interobserver agreement was κ 0.666, 0.705, 0.648, 0.547 and 0.631, respectively for unenhanced and contrast-enhanced morphological index, presence of pancreatic necrosis, pancreatic necrosis extension, and disease severity index. Intraobserver agreement (observers 1 and 2, respectively) was κ = 0.796 and 0.732 for unenhanced morphological index; κ 0.725 and 0.802 for contrast- enhanced morphological index; κ = 0.674 and 0.849 for presence of pancreatic necrosis; κ = 0.606 and 0.770 for pancreatic necrosis extension; and κ = 0.801 and 0.687 for disease severity index at computed tomography. Conclusion: Computed tomography for determination of morphological index and disease severity index in the staging of acute pancreatitis is a quite reproducible method. The absence of contrast- enhancement does not affect the computed tomography morphological index reproducibility. (author)

  12. Three-dimensional Kinetic Pulsar Magnetosphere Models: Connecting to Gamma-Ray Observations

    Science.gov (United States)

    Kalapotharakos, Constantinos; Brambilla, Gabriele; Timokhin, Andrey; Harding, Alice K.; Kazanas, Demosthenes

    2018-04-01

    We present three-dimensional (3D) global kinetic pulsar magnetosphere models, where the charged particle trajectories and the corresponding electromagnetic fields are treated self-consistently. For our study, we have developed a Cartesian 3D relativistic particle-in-cell code that incorporates radiation reaction forces. We describe our code and discuss the related technical issues, treatments, and assumptions. Injecting particles up to large distances in the magnetosphere, we apply arbitrarily low to high particle injection rates, and obtain an entire spectrum of solutions from close to the vacuum-retarded dipole to close to the force-free (FF) solution, respectively. For high particle injection rates (close to FF solutions), significant accelerating electric field components are confined only near the equatorial current sheet outside the light cylinder. A judicious interpretation of our models allows the particle emission to be calculated, and consequently, the corresponding realistic high-energy sky maps and spectra to be derived. Using model parameters that cover the entire range of spin-down powers of Fermi young and millisecond pulsars, we compare the corresponding model γ-ray light curves, cutoff energies, and total γ-ray luminosities with those observed by Fermi to discover a dependence of the particle injection rate, { \\mathcal F }, on the spin-down power, \\dot{{ \\mathcal E }}, indicating an increase of { \\mathcal F } with \\dot{{ \\mathcal E }}. Our models, guided by Fermi observations, provide field structures and particle distributions that are not only consistent with each other but also able to reproduce a broad range of the observed γ-ray phenomenologies of both young and millisecond pulsars.

  13. 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

  14. 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.

  15. 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...

  16. Mismatch between observed and modeled trends in dissolved upper-ocean oxygen over the last 50 yr

    Directory of Open Access Journals (Sweden)

    L. Stramma

    2012-10-01

    Full Text Available Observations and model runs indicate trends in dissolved oxygen (DO associated with current and ongoing global warming. However, a large-scale observation-to-model comparison has been missing and is presented here. This study presents a first global compilation of DO measurements covering the last 50 yr. It shows declining upper-ocean DO levels in many regions, especially the tropical oceans, whereas areas with increasing trends are found in the subtropics and in some subpolar regions. For the Atlantic Ocean south of 20° N, the DO history could even be extended back to about 70 yr, showing decreasing DO in the subtropical South Atlantic. The global mean DO trend between 50° S and 50° N at 300 dbar for the period 1960 to 2010 is –0.066 μmol kg−1 yr−1. Results of a numerical biogeochemical Earth system model reveal that the magnitude of the observed change is consistent with CO2-induced climate change. However, the pattern correlation between simulated and observed patterns of past DO change is negative, indicating that the model does not correctly reproduce the processes responsible for observed regional oxygen changes in the past 50 yr. A negative pattern correlation is also obtained for model configurations with particularly low and particularly high diapycnal mixing, for a configuration that assumes a CO2-induced enhancement of the C : N ratios of exported organic matter and irrespective of whether climatological or realistic winds from reanalysis products are used to force the model. Depending on the model configuration the 300 dbar DO trend between 50° S and 50° N is −0.027 to –0.047 μmol kg−1 yr−1 for climatological wind forcing, with a much larger range of –0.083 to +0.027 μmol kg−1 yr−1 for different initializations of sensitivity runs with reanalysis wind forcing. Although numerical models reproduce the overall sign and, to

  17. A comparison of the probability distribution of observed substorm magnitude with that predicted by a minimal substorm model

    Directory of Open Access Journals (Sweden)

    S. K. Morley

    2007-11-01

    Full Text Available We compare the probability distributions of substorm magnetic bay magnitudes from observations and a minimal substorm model. The observed distribution was derived previously and independently using the IL index from the IMAGE magnetometer network. The model distribution is derived from a synthetic AL index time series created using real solar wind data and a minimal substorm model, which was previously shown to reproduce observed substorm waiting times. There are two free parameters in the model which scale the contributions to AL from the directly-driven DP2 electrojet and loading-unloading DP1 electrojet, respectively. In a limited region of the 2-D parameter space of the model, the probability distribution of modelled substorm bay magnitudes is not significantly different to the observed distribution. The ranges of the two parameters giving acceptable (95% confidence level agreement are consistent with expectations using results from other studies. The approximately linear relationship between the two free parameters over these ranges implies that the substorm magnitude simply scales linearly with the solar wind power input at the time of substorm onset.

  18. Observations and modeling of air quality trends over 1990-2010 across the Northern Hemisphere: China, the United States and Europe

    Science.gov (United States)

    Xing, J.; Mathur, R.; Pleim, J.; Hogrefe, C.; Gan, C.-M.; Wong, D. C.; Wei, C.; Gilliam, R.; Pouliot, G.

    2015-03-01

    Trends in air quality across the Northern Hemisphere over a 21-year period (1990-2010) were simulated using the Community Multiscale Air Quality (CMAQ) multiscale chemical transport model driven by meteorology from Weather Research and Forecasting (WRF) simulations and internally consistent historical emission inventories obtained from EDGAR. Thorough comparison with several ground observation networks mostly over Europe and North America was conducted to evaluate the model performance as well as the ability of CMAQ to reproduce the observed trends in air quality over the past 2 decades in three regions: eastern China, the continental United States and Europe. The model successfully reproduced the observed decreasing trends in SO2, NO2, 8 h O3 maxima, SO42- and elemental carbon (EC) in the US and Europe. However, the model fails to reproduce the decreasing trends in NO3- in the US, potentially pointing to uncertainties of NH3 emissions. The model failed to capture the 6-year trends of SO2 and NO2 in CN-API (China - Air Pollution Index) from 2005 to 2010, but reproduced the observed pattern of O3 trends shown in three World Data Centre for Greenhouse Gases (WDCGG) sites over eastern Asia. Due to the coarse spatial resolution employed in these calculations, predicted SO2 and NO2 concentrations are underestimated relative to all urban networks, i.e., US-AQS (US - Air Quality System; normalized mean bias (NMB) = -38% and -48%), EU-AIRBASE (European Air quality data Base; NMB = -18 and -54%) and CN-API (NMB = -36 and -68%). Conversely, at the rural network EU-EMEP (European Monitoring and Evaluation Programme), SO2 is overestimated (NMB from 4 to 150%) while NO2 is simulated well (NMB within ±15%) in all seasons. Correlations between simulated and observed O3 wintertime daily 8 h maxima (DM8) are poor compared to other seasons for all networks. Better correlation between simulated and observed SO42- was found compared to that for SO2. Underestimation of summer SO42- in

  19. SU-E-J-252: Reproducibility of Radiogenomic Image Features: Comparison of Two Semi-Automated Segmentation Methods

    Energy Technology Data Exchange (ETDEWEB)

    Lee, M; Woo, B; Kim, J [Seoul National University, Seoul (Korea, Republic of); Jamshidi, N; Kuo, M [UCLA School of Medicine, Los Angeles, CA (United States)

    2015-06-15

    Purpose: Objective and reliable quantification of imaging phenotype is an essential part of radiogenomic studies. We compared the reproducibility of two semi-automatic segmentation methods for quantitative image phenotyping in magnetic resonance imaging (MRI) of glioblastoma multiforme (GBM). Methods: MRI examinations with T1 post-gadolinium and FLAIR sequences of 10 GBM patients were downloaded from the Cancer Image Archive site. Two semi-automatic segmentation tools with different algorithms (deformable model and grow cut method) were used to segment contrast enhancement, necrosis and edema regions by two independent observers. A total of 21 imaging features consisting of area and edge groups were extracted automatically from the segmented tumor. The inter-observer variability and coefficient of variation (COV) were calculated to evaluate the reproducibility. Results: Inter-observer correlations and coefficient of variation of imaging features with the deformable model ranged from 0.953 to 0.999 and 2.1% to 9.2%, respectively, and the grow cut method ranged from 0.799 to 0.976 and 3.5% to 26.6%, respectively. Coefficient of variation for especially important features which were previously reported as predictive of patient survival were: 3.4% with deformable model and 7.4% with grow cut method for the proportion of contrast enhanced tumor region; 5.5% with deformable model and 25.7% with grow cut method for the proportion of necrosis; and 2.1% with deformable model and 4.4% with grow cut method for edge sharpness of tumor on CE-T1W1. Conclusion: Comparison of two semi-automated tumor segmentation techniques shows reliable image feature extraction for radiogenomic analysis of GBM patients with multiparametric Brain MRI.

  20. SU-E-J-252: Reproducibility of Radiogenomic Image Features: Comparison of Two Semi-Automated Segmentation Methods

    International Nuclear Information System (INIS)

    Lee, M; Woo, B; Kim, J; Jamshidi, N; Kuo, M

    2015-01-01

    Purpose: Objective and reliable quantification of imaging phenotype is an essential part of radiogenomic studies. We compared the reproducibility of two semi-automatic segmentation methods for quantitative image phenotyping in magnetic resonance imaging (MRI) of glioblastoma multiforme (GBM). Methods: MRI examinations with T1 post-gadolinium and FLAIR sequences of 10 GBM patients were downloaded from the Cancer Image Archive site. Two semi-automatic segmentation tools with different algorithms (deformable model and grow cut method) were used to segment contrast enhancement, necrosis and edema regions by two independent observers. A total of 21 imaging features consisting of area and edge groups were extracted automatically from the segmented tumor. The inter-observer variability and coefficient of variation (COV) were calculated to evaluate the reproducibility. Results: Inter-observer correlations and coefficient of variation of imaging features with the deformable model ranged from 0.953 to 0.999 and 2.1% to 9.2%, respectively, and the grow cut method ranged from 0.799 to 0.976 and 3.5% to 26.6%, respectively. Coefficient of variation for especially important features which were previously reported as predictive of patient survival were: 3.4% with deformable model and 7.4% with grow cut method for the proportion of contrast enhanced tumor region; 5.5% with deformable model and 25.7% with grow cut method for the proportion of necrosis; and 2.1% with deformable model and 4.4% with grow cut method for edge sharpness of tumor on CE-T1W1. Conclusion: Comparison of two semi-automated tumor segmentation techniques shows reliable image feature extraction for radiogenomic analysis of GBM patients with multiparametric Brain MRI

  1. Results of an interactively coupled atmospheric chemistry – general circulation model: Comparison with observations

    Directory of Open Access Journals (Sweden)

    R. Hein

    Full Text Available The coupled climate-chemistry model ECHAM4.L39(DLR/CHEM is presented which enables a simultaneous treatment of meteorology and atmospheric chemistry and their feedbacks. This is the first model which interactively combines a general circulation model with a chemical model, employing most of the important reactions and species necessary to describe the stratospheric and upper tropospheric ozone chemistry, and which is computationally fast enough to allow long-term integrations with currently available computer resources. This is possible as the model time-step used for the chemistry can be chosen as large as the integration time-step for the dynamics. Vertically the atmosphere is discretized by 39 levels from the surface up to the top layer which is centred at 10 hPa, with a relatively high vertical resolution of approximately 700 m near the extra-tropical tropopause. We present the results of a control simulation representing recent conditions (1990 and compare it to available observations. The focus is on investigations of stratospheric dynamics and chemistry relevant to describe the stratospheric ozone layer. ECHAM4.L39(DLR/CHEM reproduces main features of stratospheric dynamics in the arctic vortex region, including stratospheric warming events. This constitutes a major improvement compared to earlier model versions. However, apparent shortcomings in Antarctic circulation and temperatures persist. The seasonal and interannual variability of the ozone layer is simulated in accordance with observations. Activation and deactivation of chlorine in the polar stratospheric vortices and their inter-hemispheric differences are reproduced. Considering methane oxidation as part of the dynamic-chemistry feedback results in an improved representation of the spatial distribution of stratospheric water vapour concentrations. The current model constitutes a powerful tool to investigate, for instance, the combined direct and indirect effects of anthropogenic

  2. A comparison of large scale changes in surface humidity over land in observations and CMIP3 general circulation models

    International Nuclear Information System (INIS)

    Willett, Katharine M; Thorne, Peter W; Jones, Philip D; Gillett, Nathan P

    2010-01-01

    Observed changes in the HadCRUH global land surface specific humidity and CRUTEM3 surface temperature from 1973 to 1999 are compared to CMIP3 archive climate model simulations with 20th Century forcings. Observed humidity increases are proportionately largest in the Northern Hemisphere, especially in winter. At the largest spatio-temporal scales moistening is close to the Clausius-Clapeyron scaling of the saturated specific humidity (∼7% K -1 ). At smaller scales in water-limited regions, changes in specific humidity are strongly inversely correlated with total changes in temperature. Conversely, in some regions increases are faster than implied by the Clausius-Clapeyron relation. The range of climate model specific humidity seasonal climatology and variance encompasses the observations. The models also reproduce the magnitude of observed interannual variance over all large regions. Observed and modelled trends and temperature-humidity relationships are comparable except for the extratropical Southern Hemisphere where observations exhibit no trend but models exhibit moistening. This may arise from: long-term biases remaining in the observations; the relative paucity of observational coverage; or common model errors. The overall degree of consistency of anthropogenically forced models with the observations is further evidence for anthropogenic influence on the climate of the late 20th century.

  3. Modelled radiative forcing of the direct aerosol effect with multi-observation evaluation

    Directory of Open Access Journals (Sweden)

    G. Myhre

    2009-02-01

    Full Text Available A high-resolution global aerosol model (Oslo CTM2 driven by meteorological data and allowing a comparison with a variety of aerosol observations is used to simulate radiative forcing (RF of the direct aerosol effect. The model simulates all main aerosol components, including several secondary components such as nitrate and secondary organic carbon. The model reproduces the main chemical composition and size features observed during large aerosol campaigns. Although the chemical composition compares best with ground-based measurement over land for modelled sulphate, no systematic differences are found for other compounds. The modelled aerosol optical depth (AOD is compared to remote sensed data from AERONET ground and MODIS and MISR satellite retrievals. To gain confidence in the aerosol modelling, we have tested its ability to reproduce daily variability in the aerosol content, and this is performing well in many regions; however, we also identified some locations where model improvements are needed. The annual mean regional pattern of AOD from the aerosol model is broadly similar to the AERONET and the satellite retrievals (mostly within 10–20%. We notice a significant improvement from MODIS Collection 4 to Collection 5 compared to AERONET data. Satellite derived estimates of aerosol radiative effect over ocean for clear sky conditions differs significantly on regional scales (almost up to a factor two, but also in the global mean. The Oslo CTM2 has an aerosol radiative effect close to the mean of the satellite derived estimates. We derive a radiative forcing (RF of the direct aerosol effect of −0.35 Wm−2 in our base case. Implementation of a simple approach to consider internal black carbon (BC mixture results in a total RF of −0.28 Wm−2. Our results highlight the importance of carbonaceous particles, producing stronger individual RF than considered in the recent IPCC estimate; however, net RF is less different

  4. Interpretation of TOMS Observations of Tropical Tropospheric Ozone with a Global Model and In Situ Observations

    Science.gov (United States)

    Martin, Randall V.; Jacob, Daniel J.; Logan, Jennifer A.; Bey, Isabelle; Yantosca, Robert M.; Staudt, Amanda C.; Fiore, Arlene M.; Duncan, Bryan N.; Liu, Hongyu; Ginoux, Paul

    2004-01-01

    We interpret the distribution of tropical tropospheric ozone columns (TTOCs) from the Total Ozone Mapping Spectrometer (TOMS) by using a global three-dimensional model of tropospheric chemistry (GEOS-CHEM) and additional information from in situ observations. The GEOS-CHEM TTOCs capture 44% of the variance of monthly mean TOMS TTOCs from the convective cloud differential method (CCD) with no global bias. Major discrepancies are found over northern Africa and south Asia where the TOMS TTOCs do not capture the seasonal enhancements from biomass burning found in the model and in aircraft observations. A characteristic feature of these northern topical enhancements, in contrast to southern tropical enhancements, is that they are driven by the lower troposphere where the sensitivity of TOMS is poor due to Rayleigh scattering. We develop an efficiency correction to the TOMS retrieval algorithm that accounts for the variability of ozone in the lower troposphere. This efficiency correction increases TTOC's over biomass burning regions by 3-5 Dobson units (DU) and decreases them by 2-5 DU over oceanic regions, improving the agreement between CCD TTOCs and in situ observations. Applying the correction to CCD TTOCs reduces by approximately DU the magnitude of the "tropical Atlantic paradox" [Thompson et al, 2000], i.e. the presence of a TTOC enhancement over the southern tropical Atlantic during the northern African biomass burning season in December-February. We reproduce the remainder of the paradox in the model and explain it by the combination of upper tropospheric ozone production from lightning NOx, peristent subsidence over the southern tropical Atlantic as part of the Walker circulation, and cross-equatorial transport of upper tropospheric ozone from northern midlatitudes in the African "westerly duct." These processes in the model can also account for the observed 13-17 DU persistent wave-1 pattern in TTOCs with a maximum above the tropical Atlantic and a minimum

  5. Reproducibility in a multiprocessor system

    Science.gov (United States)

    Bellofatto, Ralph A; Chen, Dong; Coteus, Paul W; Eisley, Noel A; Gara, Alan; Gooding, Thomas M; Haring, Rudolf A; Heidelberger, Philip; Kopcsay, Gerard V; Liebsch, Thomas A; Ohmacht, Martin; Reed, Don D; Senger, Robert M; Steinmacher-Burow, Burkhard; Sugawara, Yutaka

    2013-11-26

    Fixing a problem is usually greatly aided if the problem is reproducible. To ensure reproducibility of a multiprocessor system, the following aspects are proposed; a deterministic system start state, a single system clock, phase alignment of clocks in the system, system-wide synchronization events, reproducible execution of system components, deterministic chip interfaces, zero-impact communication with the system, precise stop of the system and a scan of the system state.

  6. Contextual sensitivity in scientific reproducibility

    Science.gov (United States)

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

    2016-01-01

    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. PMID:27217556

  7. 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.

  8. Reproducibility of the Portuguese version of the PEDro Scale

    Directory of Open Access Journals (Sweden)

    Silvia Regina Shiwa

    2011-10-01

    Full Text Available The objective of this study was to test the inter-rater reproducibility of the Portuguese version of the PEDro Scale. Seven physiotherapists rated the methodological quality of 50 reports of randomized controlled trials written in Portuguese indexed on the PEDro database. Each report was also rated using the English version of the PEDro Scale. Reproducibility was evaluated by comparing two separate ratings of reports written in Portuguese and comparing the Portuguese PEDro score with the English version of the scale. Kappa coefficients ranged from 0.53 to 1.00 for individual item and an intraclass correlation coefficient (ICC of 0.82 for the total PEDro score was observed. The standard error of the measurement of the scale was 0.58. The Portuguese version of the scale was comparable with the English version, with an ICC of 0.78. The inter-rater reproducibility of the Brazilian Portuguese PEDro Scale is adequate and similar to the original English version.

  9. Standing Together for Reproducibility in Large-Scale Computing: Report on reproducibility@XSEDE

    OpenAIRE

    James, Doug; Wilkins-Diehr, Nancy; Stodden, Victoria; Colbry, Dirk; Rosales, Carlos; Fahey, Mark; Shi, Justin; Silva, Rafael F.; Lee, Kyo; Roskies, Ralph; Loewe, Laurence; Lindsey, Susan; Kooper, Rob; Barba, Lorena; Bailey, David

    2014-01-01

    This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda focused on reproducibility in large-scale computational research. Two important themes capture the spirit of the workshop submissions and discussions: (1) organizational stakeholders, especially supercomputer centers, are in a unique position to promote, enab...

  10. Validity, reliability, and reproducibility of linear measurements on digital models obtained from intraoral and cone-beam computed tomography scans of alginate impressions

    NARCIS (Netherlands)

    Wiranto, Matthew G.; Engelbrecht, W. Petrie; Nolthenius, Heleen E. Tutein; van der Meer, W. Joerd; Ren, Yijin

    INTRODUCTION: Digital 3-dimensional models are widely used for orthodontic diagnosis. The aim of this study was to assess the validity, reliability, and reproducibility of digital models obtained from the Lava Chairside Oral scanner (3M ESPE, Seefeld, Germany) and cone-beam computed tomography scans

  11. 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...

  12. Observations and a linear model of water level in an interconnected inlet-bay system

    Science.gov (United States)

    Aretxabaleta, Alfredo; Ganju, Neil K.; Butman, Bradford; Signell, Richard

    2017-01-01

    A system of barrier islands and back-barrier bays occurs along southern Long Island, New York, and in many coastal areas worldwide. Characterizing the bay physical response to water level fluctuations is needed to understand flooding during extreme events and evaluate their relation to geomorphological changes. Offshore sea level is one of the main drivers of water level fluctuations in semienclosed back-barrier bays. We analyzed observed water levels (October 2007 to November 2015) and developed analytical models to better understand bay water level along southern Long Island. An increase (∼0.02 m change in 0.17 m amplitude) in the dominant M2 tidal amplitude (containing the largest fraction of the variability) was observed in Great South Bay during mid-2014. The observed changes in both tidal amplitude and bay water level transfer from offshore were related to the dredging of nearby inlets and possibly the changing size of a breach across Fire Island caused by Hurricane Sandy (after December 2012). The bay response was independent of the magnitude of the fluctuations (e.g., storms) at a specific frequency. An analytical model that incorporates bay and inlet dimensions reproduced the observed transfer function in Great South Bay and surrounding areas. The model predicts the transfer function in Moriches and Shinnecock bays where long-term observations were not available. The model is a simplified tool to investigate changes in bay water level and enables the evaluation of future conditions and alternative geomorphological settings.

  13. A MODEL OF MAGNETIC BRAKING OF SOLAR ROTATION THAT SATISFIES OBSERVATIONAL CONSTRAINTS

    International Nuclear Information System (INIS)

    Denissenkov, Pavel A.

    2010-01-01

    The model of magnetic braking of solar rotation considered by Charbonneau and MacGregor has been modified so that it is able to reproduce for the first time the rotational evolution of both the fastest and slowest rotators among solar-type stars in open clusters of different ages, without coming into conflict with other observational constraints, such as the time evolution of the atmospheric Li abundance in solar twins and the thinness of the solar tachocline. This new model assumes that rotation-driven turbulent diffusion, which is thought to amplify the viscosity and magnetic diffusivity in stellar radiative zones, is strongly anisotropic with the horizontal components of the transport coefficients strongly dominating over those in the vertical direction. Also taken into account is the poloidal field decay that helps to confine the width of the tachocline at the solar age. The model's properties are investigated by numerically solving the azimuthal components of the coupled momentum and magnetic induction equations in two dimensions using a finite element method.

  14. Observations and a model of undertow over the inner continental shelf

    Science.gov (United States)

    Lentz, Steven J.; Fewings, Melanie; Howd, Peter; Fredericks, Janet; Hathaway, Kent

    2008-01-01

    Onshore volume transport (Stokes drift) due to surface gravity waves propagating toward the beach can result in a compensating Eulerian offshore flow in the surf zone referred to as undertow. Observed offshore flows indicate that wave-driven undertow extends well offshore of the surf zone, over the inner shelves of Martha’s Vineyard, Massachusetts, and North Carolina. Theoretical estimates of the wave-driven offshore transport from linear wave theory and observed wave characteristics account for 50% or more of the observed offshore transport variance in water depths between 5 and 12 m, and reproduce the observed dependence on wave height and water depth.During weak winds, wave-driven cross-shelf velocity profiles over the inner shelf have maximum offshore flow (1–6 cm s−1) and vertical shear near the surface and weak flow and shear in the lower half of the water column. The observed offshore flow profiles do not resemble the parabolic profiles with maximum flow at middepth observed within the surf zone. Instead, the vertical structure is similar to the Stokes drift velocity profile but with the opposite direction. This vertical structure is consistent with a dynamical balance between the Coriolis force associated with the offshore flow and an along-shelf “Hasselmann wave stress” due to the influence of the earth’s rotation on surface gravity waves. The close agreement between the observed and modeled profiles provides compelling evidence for the importance of the Hasselmann wave stress in forcing oceanic flows. Summer profiles are more vertically sheared than either winter profiles or model profiles, for reasons that remain unclear.

  15. Reliability and reproducibility of disc-foveal angle measurements by non-mydriatic fundus photography.

    Science.gov (United States)

    Le Jeune, Caroline; Chebli, Fayçal; Leon, Lorette; Anthoine, Emmanuelle; Weber, Michel; Péchereau, Alain; Lebranchu, Pierre

    2018-01-01

    Abnormal torsion could be associated with cyclovertical strabismus, but torsion measurements are not reliable in children. To assess an objective fundus torsion evaluation in a paediatric population, we used Non-Mydriatic Fundus photography (NMFP) in healthy and cyclovertical strabismus patients to evaluate the disc-foveal angle over time and observers. We used a retrospective set of NMFP including 24 A or V-pattern strabismus and 27 age-matched normal children (mean age 6.4 and 6.7 years respectively), taken during 2 distinct follow-up consultations (separated by 251 and 479 days respectively). Each disc-foveal angle measurement (from which the ocular torsion can be assessed) was performed by 5 different observers, using graphical software and based on reproducible fundus anatomical marks. Statistical analysis was performed with a multivariate ANOVA using group, time and observers as factors, in addition to intraclass coefficient correlation (ICC) to assess measurement reproducibility. A significant difference of disc-foveal angle measures was observed between groups (p0,97). Abnormal amount of objective torsion could be associated with alphabet-pattern strabismus. Disc-foveal angle evaluation by NMFP in a children population appears as a non-invasive, reliable and reproducible method.

  16. Composting in small laboratory pilots: Performance and reproducibility

    International Nuclear Information System (INIS)

    Lashermes, G.; Barriuso, E.; Le Villio-Poitrenaud, M.; Houot, S.

    2012-01-01

    Highlights: ► We design an innovative small-scale composting device including six 4-l reactors. ► We investigate the performance and reproducibility of composting on a small scale. ► Thermophilic conditions are established by self-heating in all replicates. ► Biochemical transformations, organic matter losses and stabilisation are realistic. ► The organic matter evolution exhibits good reproducibility for all six replicates. - Abstract: Small-scale reactors ( 2 consumption and CO 2 emissions, and characterising the biochemical evolution of organic matter. A good reproducibility was found for the six replicates with coefficients of variation for all parameters generally lower than 19%. An intense self-heating ensured the existence of a spontaneous thermophilic phase in all reactors. The average loss of total organic matter (TOM) was 46% of the initial content. Compared to the initial mixture, the hot water soluble fraction decreased by 62%, the hemicellulose-like fraction by 68%, the cellulose-like fraction by 50% and the lignin-like fractions by 12% in the final compost. The TOM losses, compost stabilisation and evolution of the biochemical fractions were similar to observed in large reactors or on-site experiments, excluding the lignin degradation, which was less important than in full-scale systems. The reproducibility of the process and the quality of the final compost make it possible to propose the use of this experimental device for research requiring a mass reduction of the initial composted waste mixtures.

  17. Confronting Weather and Climate Models with Observational Data from Soil Moisture Networks over the United States

    Science.gov (United States)

    Dirmeyer, Paul A.; Wu, Jiexia; Norton, Holly E.; Dorigo, Wouter A.; Quiring, Steven M.; Ford, Trenton W.; Santanello, Joseph A., Jr.; Bosilovich, Michael G.; Ek, Michael B.; Koster, Randal Dean; hide

    2016-01-01

    Four land surface models in uncoupled and coupled configurations are compared to observations of daily soil moisture from 19 networks in the conterminous United States to determine the viability of such comparisons and explore the characteristics of model and observational data. First, observations are analyzed for error characteristics and representation of spatial and temporal variability. Some networks have multiple stations within an area comparable to model grid boxes; for those we find that aggregation of stations before calculation of statistics has little effect on estimates of variance, but soil moisture memory is sensitive to aggregation. Statistics for some networks stand out as unlike those of their neighbors, likely due to differences in instrumentation, calibration and maintenance. Buried sensors appear to have less random error than near-field remote sensing techniques, and heat dissipation sensors show less temporal variability than other types. Model soil moistures are evaluated using three metrics: standard deviation in time, temporal correlation (memory) and spatial correlation (length scale). Models do relatively well in capturing large-scale variability of metrics across climate regimes, but poorly reproduce observed patterns at scales of hundreds of kilometers and smaller. Uncoupled land models do no better than coupled model configurations, nor do reanalyses out perform free-running models. Spatial decorrelation scales are found to be difficult to diagnose. Using data for model validation, calibration or data assimilation from multiple soil moisture networks with different types of sensors and measurement techniques requires great caution. Data from models and observations should be put on the same spatial and temporal scales before comparison.

  18. 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...... was considerably more reproducible than CBF level. Using a single detector instead of five regional values averaged as the hemispheric flow increased standard deviation of CBF level by 10-20%, while the variation in asymmetry was doubled. In optimal measuring conditions the two models revealed no significant...... 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....

  19. AOD trends during 2001-2010 from observations and model simulations

    Science.gov (United States)

    Pozzer, Andrea; de Meij, Alexander; Yoon, Jongmin; Astitha, Marina

    2016-04-01

    The trend of aerosol optical depth (AOD) between 2001 and 2010 is estimated globally and regionally from remote sensed observations by the MODIS (Moderate Resolution Imaging Spectroradiometer), MISR (Multi-angle Imaging SpectroRadiometer) and SeaWIFS (Sea-viewing Wide Field-of-view Sensor) satellite sensor. The resulting trends have been compared to model results from the EMAC (ECHAM5/MESSy Atmospheric Chemistry {[1]}), model. Although interannual variability is applied only to anthropogenic and biomass-burning emissions, the model is able to quantitatively reproduce the AOD trends as observed by MODIS, while some discrepancies are found when compared to MISR and SeaWIFS. An additional numerical simulation with the same model was performed, neglecting any temporal change in the emissions, i.e. with no interannual variability for any emission source. It is shown that decreasing AOD trends over the US and Europe are due to the decrease in the (anthropogenic) emissions. On contrary over the Sahara Desert and the Middle East region, the meteorological/dynamical changes in the last decade play a major role in driving the AOD trends. Further, over Southeast Asia, both meteorology and emissions changes are equally important in defining AOD trends {[2]}. Finally, decomposing the regional AOD trends into individual aerosol components reveals that the soluble components are the most dominant contributors to the total AOD, as their influence on the total AOD is enhanced by the aerosol water content. {[1]}: Jöckel, P., Kerkweg, A., Pozzer, A., Sander, R., Tost, H., Riede, H., Baumgaertner, A., Gromov, S., and Kern, B.: Development cycle 2 of the Modular Earth Submodel System (MESSy2), Geosci. Model Dev., 3, 717-752, doi:10.5194/gmd-3-717-2010, 2010. {[2]}: Pozzer, A., de Meij, A., Yoon, J., Tost, H., Georgoulias, A. K., and Astitha, M.: AOD trends during 2001-2010 from observations and model simulations, Atmos. Chem. Phys., 15, 5521-5535, doi:10.5194/acp-15-5521-2015, 2015.

  20. Simulating AIA observations of a flux rope ejection

    Science.gov (United States)

    Pagano, P.; Mackay, D. H.; Poedts, S.

    2014-08-01

    Context. Coronal mass ejections (CMEs) are the most violent phenomena observed on the Sun. Currently, extreme ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) are providing new insights into the early phase of CME evolution. In particular, observations now show the ejection of magnetic flux ropes from the solar corona and how they evolve into CMEs. While this is the case, these observations are difficult to interpret in terms of basic physical mechanisms and quantities. To fully understand CMEs we need to compare equivalent quantities derived from both observations and theoretical models. This will aid in bridging the gap between observations and models. Aims: To this end, we aim to produce synthesised AIA observations from simulations of a flux rope ejection. To carry this out we include the role of thermal conduction and radiative losses, both of which are important for determining the temperature distribution of the solar corona during a CME. Methods: We perform a simulation where a flux rope is ejected from the solar corona. From the density and temperature of the plasma in the simulation we synthesise AIA observations. The emission is then integrated along the line of sight using the instrumental response function of AIA. Results: We sythesise observations of AIA in the channels at 304 Å, 171 Å, 335 Å, and 94 Å. The synthesised observations show a number of features similar to actual observations and in particular reproduce the general development of CMEs in the low corona as observed by AIA. In particular we reproduce an erupting and expanding arcade in the 304 Å and 171 Å channels with a high density core. Conclusions: The ejection of a flux rope reproduces many of the features found in the AIA observations. This work is therefore a step forward in bridging the gap between observations and models, and can lead to more direct interpretations of EUV observations in terms of flux rope

  1. Effective Form of Reproducing the Total Financial Potential of Ukraine

    Directory of Open Access Journals (Sweden)

    Portna Oksana V.

    2015-03-01

    Full Text Available Development of scientific principles of reproducing the total financial potential of the country and its effective form is an urgent problem both in theoretical and practical aspects of the study, the solution of which is intended to ensure the active mobilization and effective use of the total financial potential of Ukraine, and as a result — its expanded reproduction as well, which would contribute to realization of the internal capacities for stabilization of the national economy. The purpose of the article is disclosing the essence of the effective form of reproducing the total financial potential of the country, analyzing the results of reproducing the total financial potential of Ukraine. It has been proved that the basis for the effective form of reproducing the total financial potential of the country is the volume and flow of resources, which are associated with the «real» economy, affect the dynamics of GDP and define it, i.e. resource and process forms of reproducing the total financial potential of Ukraine (which precede the effective one. The analysis of reproducing the total financial potential of Ukraine has shown that in the analyzed period there was an increase in the financial possibilities of the country, but steady dynamics of reduction of the total financial potential was observed. If we consider the amount of resources involved in production, creating a net value added and GDP, it occurs on a restricted basis. Growth of the total financial potential of Ukraine is connected only with extensive quantitative factors rather than intensive qualitative changes.

  2. Prediction of lung tumour position based on spirometry and on abdominal displacement: Accuracy and reproducibility

    International Nuclear Information System (INIS)

    Hoisak, Jeremy D.P.; Sixel, Katharina E.; Tirona, Romeo; Cheung, Patrick C.F.; Pignol, Jean-Philippe

    2006-01-01

    Background and purpose: A simulation investigating the accuracy and reproducibility of a tumour motion prediction model over clinical time frames is presented. The model is formed from surrogate and tumour motion measurements, and used to predict the future position of the tumour from surrogate measurements alone. Patients and methods: Data were acquired from five non-small cell lung cancer patients, on 3 days. Measurements of respiratory volume by spirometry and abdominal displacement by a real-time position tracking system were acquired simultaneously with X-ray fluoroscopy measurements of superior-inferior tumour displacement. A model of tumour motion was established and used to predict future tumour position, based on surrogate input data. The calculated position was compared against true tumour motion as seen on fluoroscopy. Three different imaging strategies, pre-treatment, pre-fraction and intrafractional imaging, were employed in establishing the fitting parameters of the prediction model. The impact of each imaging strategy upon accuracy and reproducibility was quantified. Results: When establishing the predictive model using pre-treatment imaging, four of five patients exhibited poor interfractional reproducibility for either surrogate in subsequent sessions. Simulating the formulation of the predictive model prior to each fraction resulted in improved interfractional reproducibility. The accuracy of the prediction model was only improved in one of five patients when intrafractional imaging was used. Conclusions: Employing a prediction model established from measurements acquired at planning resulted in localization errors. Pre-fractional imaging improved the accuracy and reproducibility of the prediction model. Intrafractional imaging was of less value, suggesting that the accuracy limit of a surrogate-based prediction model is reached with once-daily imaging

  3. 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...

  4. 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.

  5. Reproducibility of coronary calcification detection with electron-beam computed tomography

    International Nuclear Information System (INIS)

    Hernigou, A.; Challande, P.; Boudeville, J.C.; Sene, V.; Grataloup, C.; Plainfosse, M.

    1996-01-01

    If coronary calcification scores obtained with electron-beam computed tomography (EBT) were proved to be correlated to coronary atherosclerosis, the reproducibility of the technique had to be assessed before being useed for patient follow-up. A total of 150 patients, selected as a result of a cholesterol screening programme, were studied by EBT. Twelve contiguous 3-mm-thick transverse slices beginning on the proximal coronary arteries were obtained through the base of the heart. The amount of calcium was evaluated as the calcified area weighted by a coefficient depending on the density peak level. The value was expressed as a logarithmic scale. Intra-observer, inter-observer and inter-examination reproducibilities were calculated. They were 1.9, 1.3 and 7.2%, respectively. These results were good enough to allow the use of EBT for longitudinal studies. The influence of acquisition and calculation conditions on score computation were also analysed. (orig.)

  6. 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

    Purpose Calculating the timing of bruises is crucial in forensic pathology but is a challenging discipline in both human and veterinary medicine. A mechanical device for inflicting bruises in pigs was developed and validated, and the pathological reactions in the bruises were studied over time......-dependent response. Combining these parameters, bruises could be grouped as being either less than 4 h old or between 4 and 10 h of age. Gross lesions and changes in the epidermis and dermis were inconclusive with respect to time determination. Conclusions The model was reproducible and resembled forensic cases...

  7. Evolvix BEST Names for semantic reproducibility across code2brain interfaces.

    Science.gov (United States)

    Loewe, Laurence; Scheuer, Katherine S; Keel, Seth A; Vyas, Vaibhav; Liblit, Ben; Hanlon, Bret; Ferris, Michael C; Yin, John; Dutra, Inês; Pietsch, Anthony; Javid, Christine G; Moog, Cecilia L; Meyer, Jocelyn; Dresel, Jerdon; McLoone, Brian; Loberger, Sonya; Movaghar, Arezoo; Gilchrist-Scott, Morgaine; Sabri, Yazeed; Sescleifer, Dave; Pereda-Zorrilla, Ivan; Zietlow, Andrew; Smith, Rodrigo; Pietenpol, Samantha; Goldfinger, Jacob; Atzen, Sarah L; Freiberg, Erika; Waters, Noah P; Nusbaum, Claire; Nolan, Erik; Hotz, Alyssa; Kliman, Richard M; Mentewab, Ayalew; Fregien, Nathan; Loewe, Martha

    2017-01-01

    Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general-purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality. To protect learning and coding investments, C2B interfaces require long-term backward compatibility and semantic reproducibility (accurate reproduction of computational meaning from coder-brains to reader-brains by code alone). Semantic reproducibility is often assumed until confusing synonyms degrade modeling in biology to deciphering exercises. We highlight empirical naming priorities from diverse individuals and roles of names in different modes of computing to show how naming easily becomes impossibly difficult. We present the Evolvix BEST (Brief, Explicit, Summarizing, Technical) Names concept for reducing naming priority conflicts, test it on a real challenge by naming subfolders for the Project Organization Stabilizing Tool system, and provide naming questionnaires designed to facilitate C2B debugging by improving names used as keywords in a stabilizing programming language. Our experiences inspired us to develop Evolvix using a flipped programming language design approach with some unexpected features and BEST Names at its core. © 2016 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

  8. Renormalization group running of fermion observables in an extended non-supersymmetric SO(10) model

    Energy Technology Data Exchange (ETDEWEB)

    Meloni, Davide [Dipartimento di Matematica e Fisica, Università di Roma Tre,Via della Vasca Navale 84, 00146 Rome (Italy); Ohlsson, Tommy; Riad, Stella [Department of Physics, School of Engineering Sciences,KTH Royal Institute of Technology - AlbaNova University Center,Roslagstullsbacken 21, 106 91 Stockholm (Sweden)

    2017-03-08

    We investigate the renormalization group evolution of fermion masses, mixings and quartic scalar Higgs self-couplings in an extended non-supersymmetric SO(10) model, where the Higgs sector contains the 10{sub H}, 120{sub H}, and 126{sub H} representations. The group SO(10) is spontaneously broken at the GUT scale to the Pati-Salam group and subsequently to the Standard Model (SM) at an intermediate scale M{sub I}. We explicitly take into account the effects of the change of gauge groups in the evolution. In particular, we derive the renormalization group equations for the different Yukawa couplings. We find that the computed physical fermion observables can be successfully matched to the experimental measured values at the electroweak scale. Using the same Yukawa couplings at the GUT scale, the measured values of the fermion observables cannot be reproduced with a SM-like evolution, leading to differences in the numerical values up to around 80%. Furthermore, a similar evolution can be performed for a minimal SO(10) model, where the Higgs sector consists of the 10{sub H} and 126{sub H} representations only, showing an equally good potential to describe the low-energy fermion observables. Finally, for both the extended and the minimal SO(10) models, we present predictions for the three Dirac and Majorana CP-violating phases as well as three effective neutrino mass parameters.

  9. On-line quantile regression in the RKHS (Reproducing Kernel Hilbert Space) for operational probabilistic forecasting of wind power

    International Nuclear Information System (INIS)

    Gallego-Castillo, Cristobal; Bessa, Ricardo; Cavalcante, Laura; Lopez-Garcia, Oscar

    2016-01-01

    Wind power probabilistic forecast is being used as input in several decision-making problems, such as stochastic unit commitment, operating reserve setting and electricity market bidding. This work introduces a new on-line quantile regression model based on the Reproducing Kernel Hilbert Space (RKHS) framework. Its application to the field of wind power forecasting involves a discussion on the choice of the bias term of the quantile models, and the consideration of the operational framework in order to mimic real conditions. Benchmark against linear and splines quantile regression models was performed for a real case study during a 18 months period. Model parameter selection was based on k-fold crossvalidation. Results showed a noticeable improvement in terms of calibration, a key criterion for the wind power industry. Modest improvements in terms of Continuous Ranked Probability Score (CRPS) were also observed for prediction horizons between 6 and 20 h ahead. - Highlights: • New online quantile regression model based on the Reproducing Kernel Hilbert Space. • First application to operational probabilistic wind power forecasting. • Modest improvements of CRPS for prediction horizons between 6 and 20 h ahead. • Noticeable improvements in terms of Calibration due to online learning.

  10. Reproducibility of positive results for the detection of serum galactomannan by Platelia™ aspergillus EIA.

    Science.gov (United States)

    Pedroza, Kelly C M C; de Matos, Sócrates B; de Moura, Daniel L; Oliveira, Mônica B B; Araújo, Marco A S; Nascimento, Roberto J M; Lima, Fernanda W M

    2013-10-01

    Galactomannan (GM) was recently included in consensus guidelines as an indirect mycological criterion for the diagnosis of invasive aspergillosis. Currently, there is an enzyme immunoassay available to detect GM in biological samples, the Platelia™ Aspergillus EIA. In this study, the reproducibility of positive results obtained using this assay was evaluated using serum samples from neutropenic patients. A trend toward lower values was observed, and 55 %(27/49) of positive results were negative after retesting. A low reproducibility of positive results for the detection of GM in serum was observed.

  11. Constraining the models' response of tropical low clouds to SST forcings using CALIPSO observations

    Science.gov (United States)

    Cesana, G.; Del Genio, A. D.; Ackerman, A. S.; Brient, F.; Fridlind, A. M.; Kelley, M.; Elsaesser, G.

    2017-12-01

    Low-cloud response to a warmer climate is still pointed out as being the largest source of uncertainty in the last generation of climate models. To date there is no consensus among the models on whether the tropical low cloudiness would increase or decrease in a warmer climate. In addition, it has been shown that - depending on their climate sensitivity - the models either predict deeper or shallower low clouds. Recently, several relationships between inter-model characteristics of the present-day climate and future climate changes have been highlighted. These so-called emergent constraints aim to target relevant model improvements and to constrain models' projections based on current climate observations. Here we propose to use - for the first time - 10 years of CALIPSO cloud statistics to assess the ability of the models to represent the vertical structure of tropical low clouds for abnormally warm SST. We use a simulator approach to compare observations and simulations and focus on the low-layered clouds (i.e. z fraction. Vertically, the clouds deepen namely by decreasing the cloud fraction in the lowest levels and increasing it around the top of the boundary-layer. This feature is coincident with an increase of the high-level cloud fraction (z > 6.5km). Although the models' spread is large, the multi-model mean captures the observed variations but with a smaller amplitude. We then employ the GISS model to investigate how changes in cloud parameterizations affect the response of low clouds to warmer SSTs on the one hand; and how they affect the variations of the model's cloud profiles with respect to environmental parameters on the other hand. Finally, we use CALIPSO observations to constrain the model by determining i) what set of parameters allows reproducing the observed relationships and ii) what are the consequences on the cloud feedbacks. These results point toward process-oriented constraints of low-cloud responses to surface warming and environmental

  12. Interobserver and test-retest reproducibility of T1ρ and T2 mesurements of lumber intervertebral discs by 3t magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Yeon Hwa; Yoon, Choon Sik; Eun, Na Lae; Kim, Sung Jin; Chung, Tae Sub [Dept. of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Hwang, Moon Jung [GE Health Care, Seoul (Korea, Republic of); Yoo, Hanna [Biostatistics Collaboration Lab, Yonsei University College of Medicine, Seoul (Korea, Republic of); Peter, Robert D. [GE Health Care, Milwaukee (United States); Lee, Young Han; Suh, Jin Suck [Dept. of Radiology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2016-11-15

    To investigate the interobserver and test-retest reproducibility of T1ρ and T2 measurements of lumbar intervertebral discs using 3T magnetic resonance imaging (MRI). This study included a total of 51 volunteers (female, 26; male, 25; mean age, 54 ± 16.3 years) who underwent lumbar spine MRI with a 3.0 T scanner. Amongst these subjects, 40 underwent repeat T1ρ and T2 measurement acquisitions with identical image protocol. Two observers independently performed the region of interest measurements in the nuclei pulposi of the discs from L1-2 through L5-S1 levels. Statistical analysis was performed using intraclass correlation coefficient (ICC) with a two-way random model of absolute agreement. Comparison of the ICC values was done after acquisition of ICC values using Z test. Statistical significance was defined as p value < 0.05. The ICCs of interobserver reproducibility were 0.951 and 0.672 for T1ρ and T2 mapping, respectively. The ICCs of test-retest reproducibility (40 subjects) for T1ρ and T2 measurements were 0.922 and 0.617 for observer A and 0.914 and 0.628 for observer B, respectively. In the comparison of the aforementioned ICCs, ICCs of interobserver and test-retest reproducibility for T1ρ mapping were significantly higher than T2 mapping (p < 0.001). The interobserver and test-retest reproducibility of T1ρ mapping were significantly higher than those of T2 mapping for the quantitative assessment of nuclei pulposi of lumbar intervertebral discs.

  13. 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.

  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. On the origin of reproducible sequential activity in neural circuits

    Science.gov (United States)

    Afraimovich, V. S.; Zhigulin, V. P.; Rabinovich, M. I.

    2004-12-01

    Robustness and reproducibility of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of reproducible transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and reproducible sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.

  16. Mouse Models of Diet-Induced Nonalcoholic Steatohepatitis Reproduce the Heterogeneity of the Human Disease

    Science.gov (United States)

    Machado, Mariana Verdelho; Michelotti, Gregory Alexander; Xie, Guanhua; de Almeida, Thiago Pereira; Boursier, Jerome; Bohnic, Brittany; Guy, Cynthia D.; Diehl, Anna Mae

    2015-01-01

    Background and aims Non-alcoholic steatohepatitis (NASH), the potentially progressive form of nonalcoholic fatty liver disease (NAFLD), is the pandemic liver disease of our time. Although there are several animal models of NASH, consensus regarding the optimal model is lacking. We aimed to compare features of NASH in the two most widely-used mouse models: methionine-choline deficient (MCD) diet and Western diet. Methods Mice were fed standard chow, MCD diet for 8 weeks, or Western diet (45% energy from fat, predominantly saturated fat, with 0.2% cholesterol, plus drinking water supplemented with fructose and glucose) for 16 weeks. Liver pathology and metabolic profile were compared. Results The metabolic profile associated with human NASH was better mimicked by Western diet. Although hepatic steatosis (i.e., triglyceride accumulation) was also more severe, liver non-esterified fatty acid content was lower than in the MCD diet group. NASH was also less severe and less reproducible in the Western diet model, as evidenced by less liver cell death/apoptosis, inflammation, ductular reaction, and fibrosis. Various mechanisms implicated in human NASH pathogenesis/progression were also less robust in the Western diet model, including oxidative stress, ER stress, autophagy deregulation, and hedgehog pathway activation. Conclusion Feeding mice a Western diet models metabolic perturbations that are common in humans with mild NASH, whereas administration of a MCD diet better models the pathobiological mechanisms that cause human NAFLD to progress to advanced NASH. PMID:26017539

  17. Mouse models of diet-induced nonalcoholic steatohepatitis reproduce the heterogeneity of the human disease.

    Directory of Open Access Journals (Sweden)

    Mariana Verdelho Machado

    Full Text Available Non-alcoholic steatohepatitis (NASH, the potentially progressive form of nonalcoholic fatty liver disease (NAFLD, is the pandemic liver disease of our time. Although there are several animal models of NASH, consensus regarding the optimal model is lacking. We aimed to compare features of NASH in the two most widely-used mouse models: methionine-choline deficient (MCD diet and Western diet.Mice were fed standard chow, MCD diet for 8 weeks, or Western diet (45% energy from fat, predominantly saturated fat, with 0.2% cholesterol, plus drinking water supplemented with fructose and glucose for 16 weeks. Liver pathology and metabolic profile were compared.The metabolic profile associated with human NASH was better mimicked by Western diet. Although hepatic steatosis (i.e., triglyceride accumulation was also more severe, liver non-esterified fatty acid content was lower than in the MCD diet group. NASH was also less severe and less reproducible in the Western diet model, as evidenced by less liver cell death/apoptosis, inflammation, ductular reaction, and fibrosis. Various mechanisms implicated in human NASH pathogenesis/progression were also less robust in the Western diet model, including oxidative stress, ER stress, autophagy deregulation, and hedgehog pathway activation.Feeding mice a Western diet models metabolic perturbations that are common in humans with mild NASH, whereas administration of a MCD diet better models the pathobiological mechanisms that cause human NAFLD to progress to advanced NASH.

  18. REPRODUCING THE OBSERVED ABUNDANCES IN RCB AND HdC STARS WITH POST-DOUBLE-DEGENERATE MERGER MODELS—CONSTRAINTS ON MERGER AND POST-MERGER SIMULATIONS AND PHYSICS PROCESSES

    International Nuclear Information System (INIS)

    Menon, Athira; Herwig, Falk; Denissenkov, Pavel A.; Clayton, Geoffrey C.; Staff, Jan; Pignatari, Marco; Paxton, Bill

    2013-01-01

    The R Coronae Borealis (RCB) stars are hydrogen-deficient, variable stars that are most likely the result of He-CO WD mergers. They display extremely low oxygen isotopic ratios, 16 O/ 18 O ≅ 1-10, 12 C/ 13 C ≥ 100, and enhancements up to 2.6 dex in F and in s-process elements from Zn to La, compared to solar. These abundances provide stringent constraints on the physical processes during and after the double-degenerate merger. As shown previously, O-isotopic ratios observed in RCB stars cannot result from the dynamic double-degenerate merger phase, and we now investigate the role of the long-term one-dimensional spherical post-merger evolution and nucleosynthesis based on realistic hydrodynamic merger progenitor models. We adopt a model for extra envelope mixing to represent processes driven by rotation originating in the dynamical merger. Comprehensive nucleosynthesis post-processing simulations for these stellar evolution models reproduce, for the first time, the full range of the observed abundances for almost all the elements measured in RCB stars: 16 O/ 18 O ratios between 9 and 15, C-isotopic ratios above 100, and ∼1.4-2.35 dex F enhancements, along with enrichments in s-process elements. The nucleosynthesis processes in our models constrain the length and temperature in the dynamic merger shell-of-fire feature as well as the envelope mixing in the post-merger phase. s-process elements originate either in the shell-of-fire merger feature or during the post-merger evolution, but the contribution from the asymptotic giant branch progenitors is negligible. The post-merger envelope mixing must eventually cease ∼10 6 yr after the dynamic merger phase before the star enters the RCB phase

  19. 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

    osteosarcoma model was shown to be feasible: the take rate was high, surgical mortality was 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.

  20. Reproducibility study of TLD-100 micro-cubes at radiotherapy dose level

    International Nuclear Information System (INIS)

    Rosa, Luiz Antonio R. da; Regulla, Dieter F.; Fill, Ute A.

    1999-01-01

    The precision of the thermoluminescent response of Harshaw micro-cube dosimeters (TLD-100), evaluated in both Harshaw thermoluminescent readers 5500 and 3500, for 1 Gy dose value, was investigated. The mean reproducibility for micro-cubes, pre-readout annealed at 100 deg. C for 15 min, evaluated with the manual planchet reader 3500, is 0.61% (1 standard deviation). When micro-cubes are evaluated with the automated hot-gas reader 5500, reproducibility values are undoubtedly worse, mean reproducibility for numerically stabilised dosimeters being equal to 3.27% (1 standard deviation). These results indicate that the reader model 5500, or, at least, the instrument used for the present measurements, is not adequate for micro-cube evaluation, if precise and accurate dosimetry is required. The difference in precision is apparently due to geometry inconsistencies in the orientation of the imperfect micro-cube faces during readout, requiring careful and manual reproducible arrangement of the selected micro-cube faces in contact with the manual reader planchet

  1. Improving the representation of river-groundwater interactions in land surface modeling at the regional scale: Observational evidence and parameterization applied in the Community Land Model

    KAUST Repository

    Zampieri, Matteo

    2012-02-01

    Groundwater is an important component of the hydrological cycle, included in many land surface models to provide a lower boundary condition for soil moisture, which in turn plays a key role in the land-vegetation-atmosphere interactions and the ecosystem dynamics. In regional-scale climate applications land surface models (LSMs) are commonly coupled to atmospheric models to close the surface energy, mass and carbon balance. LSMs in these applications are used to resolve the momentum, heat, water and carbon vertical fluxes, accounting for the effect of vegetation, soil type and other surface parameters, while lack of adequate resolution prevents using them to resolve horizontal sub-grid processes. Specifically, LSMs resolve the large-scale runoff production associated with infiltration excess and sub-grid groundwater convergence, but they neglect the effect from loosing streams to groundwater. Through the analysis of observed data of soil moisture obtained from the Oklahoma Mesoscale Network stations and land surface temperature derived from MODIS we provide evidence that the regional scale soil moisture and surface temperature patterns are affected by the rivers. This is demonstrated on the basis of simulations from a land surface model (i.e., Community Land Model - CLM, version 3.5). We show that the model cannot reproduce the features of the observed soil moisture and temperature spatial patterns that are related to the underlying mechanism of reinfiltration of river water to groundwater. Therefore, we implement a simple parameterization of this process in CLM showing the ability to reproduce the soil moisture and surface temperature spatial variabilities that relate to the river distribution at regional scale. The CLM with this new parameterization is used to evaluate impacts of the improved representation of river-groundwater interactions on the simulated water cycle parameters and the surface energy budget at the regional scale. © 2011 Elsevier B.V.

  2. Thermally-Driven Mantle Plumes Reconcile Hot-spot Observations

    Science.gov (United States)

    Davies, D.; Davies, J.

    2008-12-01

    Hot-spots are anomalous regions of magmatism that cannot be directly associated with plate tectonic processes (e.g. Morgan, 1972). They are widely regarded as the surface expression of upwelling mantle plumes. Hot-spots exhibit variable life-spans, magmatic productivity and fixity (e.g. Ito and van Keken, 2007). This suggests that a wide-range of upwelling structures coexist within Earth's mantle, a view supported by geochemical and seismic evidence, but, thus far, not reproduced by numerical models. Here, results from a new, global, 3-D spherical, mantle convection model are presented, which better reconcile hot-spot observations, the key modification from previous models being increased convective vigor. Model upwellings show broad-ranging dynamics; some drift slowly, while others are more mobile, displaying variable life-spans, intensities and migration velocities. Such behavior is consistent with hot-spot observations, indicating that the mantle must be simulated at the correct vigor and in the appropriate geometry to reproduce Earth-like dynamics. Thermally-driven mantle plumes can explain the principal features of hot-spot volcanism on Earth.

  3. Testing Reproducibility in Earth Sciences

    Science.gov (United States)

    Church, M. A.; Dudill, A. R.; Frey, P.; Venditti, J. G.

    2017-12-01

    Reproducibility represents how closely the results of independent tests agree when undertaken using the same materials but different conditions of measurement, such as operator, equipment or laboratory. The concept of reproducibility is fundamental to the scientific method as it prevents the persistence of incorrect or biased results. Yet currently the production of scientific knowledge emphasizes rapid publication of previously unreported findings, a culture that has emerged from pressures related to hiring, publication criteria and funding requirements. Awareness and critique of the disconnect between how scientific research should be undertaken, and how it actually is conducted, has been prominent in biomedicine for over a decade, with the fields of economics and psychology more recently joining the conversation. The purpose of this presentation is to stimulate the conversation in earth sciences where, despite implicit evidence in widely accepted classifications, formal testing of reproducibility is rare.As a formal test of reproducibility, two sets of experiments were undertaken with the same experimental procedure, at the same scale, but in different laboratories. Using narrow, steep flumes and spherical glass beads, grain size sorting was examined by introducing fine sediment of varying size and quantity into a mobile coarse bed. The general setup was identical, including flume width and slope; however, there were some variations in the materials, construction and lab environment. Comparison of the results includes examination of the infiltration profiles, sediment mobility and transport characteristics. The physical phenomena were qualitatively reproduced but not quantitatively replicated. Reproduction of results encourages more robust research and reporting, and facilitates exploration of possible variations in data in various specific contexts. Following the lead of other fields, testing of reproducibility can be incentivized through changes to journal

  4. Reproducibility analysis of the stability and treatment of vertebral metastatic lesions

    Directory of Open Access Journals (Sweden)

    Raphael de Rezende Pratali

    2014-09-01

    Full Text Available OBJECTIVES: To investigate the reproducibility among spine surgeons in defining the treatment of vertebral metastatic lesions, taking into account the mechanical stability of injuries. METHODS: Twenty cases of isolated vertebral metastatic lesions were presented to ten experts. Their opinion was then asked about the stability of the lesion, as well as their treatment option. RESULTS: The interobserver Kappa coefficient obtained both for stability analysis as to the decision of the treatment was poor (0.334 and 0.248, respectively. CONCLUSIONS: Poor interobserver reproducibility was observed in deciding the treatment of vertebral metastatic lesions when considering the stability of the lesions.

  5. Lightning NOx emissions over the USA constrained by TES ozone observations and the GEOS-Chem model

    Science.gov (United States)

    Jourdain, L.; Kulawik, S. S.; Worden, H. M.; Pickering, K. E.; Worden, J.; Thompson, A. M.

    2010-01-01

    Improved estimates of NOx from lightning sources are required to understand tropospheric NOx and ozone distributions, the oxidising capacity of the troposphere and corresponding feedbacks between chemistry and climate change. In this paper, we report new satellite ozone observations from the Tropospheric Emission Spectrometer (TES) instrument that can be used to test and constrain the parameterization of the lightning source of NOx in global models. Using the National Lightning Detection (NLDN) and the Long Range Lightning Detection Network (LRLDN) data as well as the HYPSLIT transport and dispersion model, we show that TES provides direct observations of ozone enhanced layers downwind of convective events over the USA in July 2006. We find that the GEOS-Chem global chemistry-transport model with a parameterization based on cloud top height, scaled regionally and monthly to OTD/LIS (Optical Transient Detector/Lightning Imaging Sensor) climatology, captures the ozone enhancements seen by TES. We show that the model's ability to reproduce the location of the enhancements is due to the fact that this model reproduces the pattern of the convective events occurrence on a daily basis during the summer of 2006 over the USA, even though it does not well represent the relative distribution of lightning intensities. However, this model with a value of 6 Tg N/yr for the lightning source (i.e.: with a mean production of 260 moles NO/Flash over the USA in summer) underestimates the intensities of the ozone enhancements seen by TES. By imposing a production of 520 moles NO/Flash for lightning occurring in midlatitudes, which better agrees with the values proposed by the most recent studies, we decrease the bias between TES and GEOS-Chem ozone over the USA in July 2006 by 40%. However, our conclusion on the strength of the lightning source of NOx is limited by the fact that the contribution from the stratosphere is underestimated in the GEOS-Chem simulations.

  6. Energetic protons at Mars. Interpretation of SLED/Phobos-2 observations by a kinetic model

    International Nuclear Information System (INIS)

    Kallio, E.; Alho, M.; Jarvinen, R.; Dyadechkin, S.; McKenna-Lawlor, S.; Afonin, V.V.

    2012-01-01

    Mars has neither a significant global intrinsic magnetic field nor a dense atmosphere. Therefore, solar energetic particles (SEPs) from the Sun can penetrate close to the planet (under some circumstances reaching the surface). On 13 March 1989 the SLED instrument aboard the Phobos- 2 spacecraft recorded the presence of SEPs near Mars while traversing a circular orbit (at 2.8RM). In the present study the response of the Martian plasma environment to SEP impingement on 13 March was simulated using a kinetic model. The electric and magnetic fields were derived using a 3- D self-consistent hybrid model (HYB-Mars) where ions are modelled as particles while electrons form a massless charge neutralizing fluid. The case study shows that the model successfully reproduced several of the observed features of the in situ observations: (1) a flux enhancement near the inbound bow shock, (2) the formation of a magnetic shadow where the energetic particle flux was decreased relative to its solar wind values, (3) the energy dependency of the flux enhancement near the bow shock and (4) how the size of the magnetic shadow depends on the incident particle energy. Overall, it is demonstrated that the Martian magnetic field environment resulting from the Mars-solar wind interaction significantly modulated the Martian energetic particle environment. (orig.)

  7. Energetic protons at Mars. Interpretation of SLED/Phobos-2 observations by a kinetic model

    Energy Technology Data Exchange (ETDEWEB)

    Kallio, E.; Alho, M.; Jarvinen, R.; Dyadechkin, S. [Finnish Meteorological Institute, Helsinki (Finland); McKenna-Lawlor, S. [Space Technology Ireland, Maynooth, Co. Kildare (Ireland); Afonin, V.V. [Space Research Institute, Moscow (Russian Federation)

    2012-07-01

    Mars has neither a significant global intrinsic magnetic field nor a dense atmosphere. Therefore, solar energetic particles (SEPs) from the Sun can penetrate close to the planet (under some circumstances reaching the surface). On 13 March 1989 the SLED instrument aboard the Phobos- 2 spacecraft recorded the presence of SEPs near Mars while traversing a circular orbit (at 2.8RM). In the present study the response of the Martian plasma environment to SEP impingement on 13 March was simulated using a kinetic model. The electric and magnetic fields were derived using a 3- D self-consistent hybrid model (HYB-Mars) where ions are modelled as particles while electrons form a massless charge neutralizing fluid. The case study shows that the model successfully reproduced several of the observed features of the in situ observations: (1) a flux enhancement near the inbound bow shock, (2) the formation of a magnetic shadow where the energetic particle flux was decreased relative to its solar wind values, (3) the energy dependency of the flux enhancement near the bow shock and (4) how the size of the magnetic shadow depends on the incident particle energy. Overall, it is demonstrated that the Martian magnetic field environment resulting from the Mars-solar wind interaction significantly modulated the Martian energetic particle environment. (orig.)

  8. Reproducibility of Quantitative Structural and Physiological MRI Measurements

    Science.gov (United States)

    2017-08-09

    project.org/) and SPSS (IBM Corp., Armonk, NY) for data analysis. Mean and confidence inter- vals for each measure are found in Tables 1–7. To assess...visits, and was calculated using a two- way mixed model in SPSS MCV and MRD values closer to 0 are considered to be the most reproducible, and ICC

  9. 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.

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

    Science.gov (United States)

    Goswami, Sonal; Samuel, Sherin; Sierra, Olga R; Cascardi, Michele; Paré, Denis

    2012-01-01

    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 (EPM). 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.

  11. A Study of the Oklahoma City Urban Heat Island Effect Using a WRF/Single-Layer Urban Canopy Model, a Joint Urban 2003 Field Campaign, and MODIS Satellite Observations

    Directory of Open Access Journals (Sweden)

    Hengyue Zhang

    2017-09-01

    Full Text Available The urban heat island effect (UHI for inner land regions was investigated using satellite data, ground observations, and simulations with an Single-Layer Urban Canopy Parameterization (SLUCP coupled into the regional Weather Research Forecasting model (WRF, http://wrf-model.org/index.php. Specifically, using the satellite-observed surface skin temperatures (Tskin, the intensity of the UHI was first compared for two inland cities (Xi’an City, China, and Oklahoma City (OKC, which have different city populations and building densities. The larger population density and larger building density in Xi’an lead to a stronger skin-level UHI by 2 °C. However, the ground observed 2 m surface air temperature (Tair observations showed an urban cooling island effect (UCI over the downtown region in OKC during the daytime of 19 July 2003, from a DOE field campaign (Joint Urban 2003. To understand this contrast between satellite-based Tskin and ground-based Tair, a sensitivity study using WRF/SLUCP was analyzed. The model reproduced a UCI in OKC. Furthermore, WRF/Noah/SLUCM simulations were also compared with the Joint Urban 2003 ground observations, including wind speeds, wind directions, and energy fluxes. Although the WRF/SLUCM model failed to simulate these variables accurately, it reproduced the diurnal variations of surface temperatures, wind speeds, wind directions, and energy fluxes reasonably well.

  12. Reproducibility of the pink esthetic score--rating soft tissue esthetics around single-implant restorations with regard to dental observer specialization.

    Science.gov (United States)

    Gehrke, Peter; Lobert, Markus; Dhom, Günter

    2008-01-01

    The pink esthetic score (PES) evaluates the esthetic outcome of soft tissue around implant-supported single crowns in the anterior zone by awarding seven points for the mesial and distal papilla, soft-tissue level, soft-tissue contour, soft-tissue color, soft-tissue texture, and alveolar process deficiency. The aim of this study was to measure the reproducibility of the PES and assess the influence exerted by the examiner's degree of dental specialization. Fifteen examiners (three general dentists, three oral maxillofacial surgeons, three orthodontists, three postgraduate students in implant dentistry, and three lay people) applied the PES to 30 implant-supported single restorations twice at an interval of 4 weeks. Using a 0-1-2 scoring system, 0 being the lowest, 2 being the highest value, the maximum achievable PES was 14. At the second assessment, the photographs were scored in reverse order. Differences between the two assessments were evaluated with the Spearman's rank correlation coefficient (R). The Wilcoxon signed-rank test was used for comparisons of differences between the ratings. A significance level of p esthetic restorations showed the smallest deviations. Orthodontists were found to have assigned significantly poorer ratings than any other group. The assessment of postgraduate students and laypersons were the most favorable. The PES allows for a more objective appraisal of the esthetic short- and long-term results of various surgical and prosthetic implant procedures. It reproducibly evaluates the peri-implant soft tissue around single-implant restorations and results in good intra-examiner agreement. However, an effect of observer specialization on rating soft-tissue esthetics can be shown.

  13. 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.

  14. Reproducible Hydrogeophysical Inversions through the Open-Source Library pyGIMLi

    Science.gov (United States)

    Wagner, F. M.; Rücker, C.; Günther, T.

    2017-12-01

    Many tasks in applied geosciences cannot be solved by a single measurement method and require the integration of geophysical, geotechnical and hydrological methods. In the emerging field of hydrogeophysics, researchers strive to gain quantitative information on process-relevant subsurface parameters by means of multi-physical models, which simulate the dynamic process of interest as well as its geophysical response. However, such endeavors are associated with considerable technical challenges, since they require coupling of different numerical models. This represents an obstacle for many practitioners and students. Even technically versatile users tend to build individually tailored solutions by coupling different (and potentially proprietary) forward simulators at the cost of scientific reproducibility. We argue that the reproducibility of studies in computational hydrogeophysics, and therefore the advancement of the field itself, requires versatile open-source software. To this end, we present pyGIMLi - a flexible and computationally efficient framework for modeling and inversion in geophysics. The object-oriented library provides management for structured and unstructured meshes in 2D and 3D, finite-element and finite-volume solvers, various geophysical forward operators, as well as Gauss-Newton based frameworks for constrained, joint and fully-coupled inversions with flexible regularization. In a step-by-step demonstration, it is shown how the hydrogeophysical response of a saline tracer migration can be simulated. Tracer concentration data from boreholes and measured voltages at the surface are subsequently used to estimate the hydraulic conductivity distribution of the aquifer within a single reproducible Python script.

  15. Bad Behavior: Improving Reproducibility in Behavior Testing.

    Science.gov (United States)

    Andrews, Anne M; Cheng, Xinyi; Altieri, Stefanie C; Yang, Hongyan

    2018-01-24

    Systems neuroscience research is increasingly possible through the use of integrated molecular and circuit-level analyses. These studies depend on the use of animal models and, in many cases, molecular and circuit-level analyses. Associated with genetic, pharmacologic, epigenetic, and other types of environmental manipulations. We illustrate typical pitfalls resulting from poor validation of behavior tests. We describe experimental designs and enumerate controls needed to improve reproducibility in investigating and reporting of behavioral phenotypes.

  16. Reproducing Epidemiologic Research and Ensuring Transparency.

    Science.gov (United States)

    Coughlin, Steven S

    2017-08-15

    Measures for ensuring that epidemiologic studies are reproducible include making data sets and software available to other researchers so they can verify published findings, conduct alternative analyses of the data, and check for statistical errors or programming errors. Recent developments related to the reproducibility and transparency of epidemiologic studies include the creation of a global platform for sharing data from clinical trials and the anticipated future extension of the global platform to non-clinical trial data. Government agencies and departments such as the US Department of Veterans Affairs Cooperative Studies Program have also enhanced their data repositories and data sharing resources. The Institute of Medicine and the International Committee of Medical Journal Editors released guidance on sharing clinical trial data. The US National Institutes of Health has updated their data-sharing policies. In this issue of the Journal, Shepherd et al. (Am J Epidemiol. 2017;186:387-392) outline a pragmatic approach for reproducible research with sensitive data for studies for which data cannot be shared because of legal or ethical restrictions. Their proposed quasi-reproducible approach facilitates the dissemination of statistical methods and codes to independent researchers. Both reproducibility and quasi-reproducibility can increase transparency for critical evaluation, further dissemination of study methods, and expedite the exchange of ideas among researchers. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Reproducing {sup 137}Cs vertical migration in Spanish soils - Reproducing {sup 137}Cs and {sup 90}Sr vertical migration in Spanish mainland

    Energy Technology Data Exchange (ETDEWEB)

    Olondo, C.; Legarda, F.; Herranz, M.; Idoeta, R. [The University of the Basque Country - UPV/EHU, Nuclear Engineering and Fluid Mechanics Dept. Faculty of Engineering, Alda. Urquijo 48013, Bilbao (Spain)

    2014-07-01

    As a result of caesium's and strontium's activity migration study developed in Spanish mainland soils, there has been obtained convective - diffusive migration equation that will reproduce adequately the movement that an activity deposit would follow in this land. Taking into account the dependence on rain that apparent convection velocity shows, it has been defined a new migration parameter that depends only on soil's properties. By means of a least square method and fitting the migration equation to experimental activity profiles, the values showed by the migration parameters in the studied soils, characteristics of that area, have been obtained. After that, there have been obtained the mean values of these parameters for each defined group that, depending on soil's texture, have been observed in the study performed about the movement of both radionuclides in soils and to whom these soils belong. Using these mean values and obtained equation, it has been properly reproduce those vertical activity profiles that were experimentally determined. In order to validate these values, a new sampling programme is carrying out in the north of Spain and, with obtained new sampling points' information, is going to verify if, indeed, obtained mean values also reproduce these new sampling points' activity vertical profile. (authors)

  18. Evaluation of 11 terrestrial carbon–nitrogen cycle models against observations from two temperate Free-Air CO2 Enrichment studies

    Science.gov (United States)

    Zaehle, Sönke; Medlyn, Belinda E; De Kauwe, Martin G; Walker, Anthony P; Dietze, Michael C; Hickler, Thomas; Luo, Yiqi; Wang, Ying-Ping; El-Masri, Bassil; Thornton, Peter; Jain, Atul; Wang, Shusen; Warlind, David; Weng, Ensheng; Parton, William; Iversen, Colleen M; Gallet-Budynek, Anne; McCarthy, Heather; Finzi, Adrien; Hanson, Paul J; Prentice, I Colin; Oren, Ram; Norby, Richard J

    2014-01-01

    We analysed the responses of 11 ecosystem models to elevated atmospheric [CO2] (eCO2) at two temperate forest ecosystems (Duke and Oak Ridge National Laboratory (ORNL) Free-Air CO2 Enrichment (FACE) experiments) to test alternative representations of carbon (C)–nitrogen (N) cycle processes. We decomposed the model responses into component processes affecting the response to eCO2 and confronted these with observations from the FACE experiments. Most of the models reproduced the observed initial enhancement of net primary production (NPP) at both sites, but none was able to simulate both the sustained 10-yr enhancement at Duke and the declining response at ORNL: models generally showed signs of progressive N limitation as a result of lower than observed plant N uptake. Nonetheless, many models showed qualitative agreement with observed component processes. The results suggest that improved representation of above-ground–below-ground interactions and better constraints on plant stoichiometry are important for a predictive understanding of eCO2 effects. Improved accuracy of soil organic matter inventories is pivotal to reduce uncertainty in the observed C–N budgets. The two FACE experiments are insufficient to fully constrain terrestrial responses to eCO2, given the complexity of factors leading to the observed diverging trends, and the consequential inability of the models to explain these trends. Nevertheless, the ecosystem models were able to capture important features of the experiments, lending some support to their projections. PMID:24467623

  19. Enacting the International/Reproducing Eurocentrism

    Directory of Open Access Journals (Sweden)

    Zeynep Gülşah Çapan

    Full Text Available Abstract This article focuses on the way in which Eurocentric conceptualisations of the ‘international’ are reproduced in different geopolitical contexts. Even though the Eurocentrism of International Relations has received growing attention, it has predominantly been concerned with unearthing the Eurocentrism of the ‘centre’, overlooking its varied manifestations in other geopolitical contexts. The article seeks to contribute to discussions about Eurocentrism by examining how different conceptualisations of the international are at work at a particular moment, and how these conceptualisations continue to reproduce Eurocentrism. It will focus on the way in which Eurocentric designations of spatial and temporal hierarchies were reproduced in the context of Turkey through a reading of how the ‘Gezi Park protests’ of 2013 and ‘Turkey’ itself were written into the story of the international.

  20. Aircraft-based Observations and Modeling of Wintertime Submicron Aerosol Composition over the Northeastern U.S.

    Science.gov (United States)

    Shah, V.; Jaegle, L.; Schroder, J. C.; Campuzano-Jost, P.; Jimenez, J. L.; Guo, H.; Sullivan, A.; Weber, R. J.; Green, J. R.; Fiddler, M.; Bililign, S.; Lopez-Hilfiker, F.; Lee, B. H.; Thornton, J. A.

    2017-12-01

    Submicron aerosol particles (PM1) remain a major air pollution concern in the urban areas of northeastern U.S. While SO2 and NOx emission controls have been effective at reducing summertime PM1 concentrations, this has not been the case for wintertime sulfate and nitrate concentrations, suggesting a nonlinear response during winter. During winter, organic aerosol (OA) is also an important contributor to PM1 mass despite low biogenic emissions, suggesting the presence of important urban sources. We use aircraft-based observations collected during the Wintertime INvestigation of Transport, Emissions and Reactivity (WINTER) campaign (Feb-March 2015), together with the GEOS-Chem chemical transport model, to investigate the sources and chemical processes governing wintertime PM1 over the northeastern U.S. The mean observed concentration of PM1 between the surface and 1 km was 4 μg m-3, about 30% of which was composed of sulfate, 20% nitrate, 10% ammonium, and 40% OA. The model reproduces the observed sulfate, nitrate and ammonium concentrations after updates to HNO3 production and loss, SO2 oxidation, and NH3 emissions. We find that 65% of the sulfate formation occurs in the aqueous phase, and 55% of nitrate formation through N2O5 hydrolysis, highlighting the importance of multiphase and heterogeneous processes during winter. Aqueous-phase sulfate production and the gas-particle partitioning of nitrate and ammonium are affected by atmospheric acidity, which in turn depends on the concentration of these species. We examine these couplings with GEOS-Chem, and assess the response of wintertime PM1 concentrations to further emission reductions based on the U.S. EPA projections for the year 2023. For OA, we find that the standard GEOS-Chem simulation underestimates the observed concentrations, but a simple parameterization developed from previous summer field campaigns is able to reproduce the observations and the contribution of primary and secondary OA. We find that

  1. Reproducibility in Research: Systems, Infrastructure, Culture

    Directory of Open Access Journals (Sweden)

    Tom Crick

    2017-11-01

    Full Text Available The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around the ability to implement (and exploit novel algorithms and models. Taking a new approach from the literature and applying it to a new codebase frequently requires local knowledge missing from the published manuscripts and transient project websites. Alongside this issue, benchmarking, and the lack of open, transparent and fair benchmark sets present another barrier to the verification and validation of claimed results. In this paper, we outline several recommendations to address these issues, driven by specific examples from a range of scientific domains. Based on these recommendations, we propose a high-level prototype open automated platform for scientific software development which effectively abstracts specific dependencies from the individual researcher and their workstation, allowing easy sharing and reproduction of results. This new e-infrastructure for reproducible computational science offers the potential to incentivise a culture change and drive the adoption of new techniques to improve the quality and efficiency – and thus reproducibility – of scientific exploration.

  2. 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…

  3. Serous tubal intraepithelial carcinoma: diagnostic reproducibility and its implications.

    Science.gov (United States)

    Carlson, Joseph W; Jarboe, Elke A; Kindelberger, David; Nucci, Marisa R; Hirsch, Michelle S; Crum, Christopher P

    2010-07-01

    Serous tubal intraepithelial carcinoma (STIC) is detected in between 5% and 7% of women undergoing risk-reduction salpingooophorectomy for mutations in the BRCA1 or 2 genes (BRCA+), and seems to play a role in the pathogenesis of many ovarian and "primary peritoneal" serous carcinomas. The recognition of STIC is germane to the management of BRCA+ women; however, the diagnostic reproducibility of STIC is unknown. Twenty-one cases were selected and classified as STIC or benign, using both hematoxylin and eosin and immunohistochemical stains for p53 and MIB-1. Digital images of 30 hematoxylin and eosin-stained STICs (n=14) or benign tubal epithelium (n=16) were photographed and randomized for blind digital review in a Powerpoint format by 6 experienced gynecologic pathologists and 6 pathology trainees. A generalized kappa statistic for multiple raters was calculated for all groups. For all reviewers, the kappa was 0.333, indicating poor reproducibility; kappa was 0.453 for the experienced gynecologic pathologists (fair-to-good reproducibility), and kappa=0.253 for the pathology residents (poor reproducibility). In the experienced group, 3 of 14 STICs were diagnosed by all 6 reviewers, and 9 of 14 by a majority of the reviewers. These results show that interobserver concordance in the recognition of STIC in high-quality digital images is at best fair-to-good for even experienced gynecologic pathologists, and a proportion cannot be consistently identified even among experienced observers. In view of these findings, a diagnosis of STIC should be corroborated by a second pathologist, if feasible.

  4. Modeling of oxygen transport and cellular energetics explains observations on in vivo cardiac energy metabolism.

    Directory of Open Access Journals (Sweden)

    Daniel A Beard

    2006-09-01

    Full Text Available Observations on the relationship between cardiac work rate and the levels of energy metabolites adenosine triphosphate (ATP, adenosine diphosphate (ADP, and phosphocreatine (CrP have not been satisfactorily explained by theoretical models of cardiac energy metabolism. Specifically, the in vivo stability of ATP, ADP, and CrP levels in response to changes in work and respiratory rate has eluded explanation. Here a previously developed model of mitochondrial oxidative phosphorylation, which was developed based on data obtained from isolated cardiac mitochondria, is integrated with a spatially distributed model of oxygen transport in the myocardium to analyze data obtained from several laboratories over the past two decades. The model includes the components of the respiratory chain, the F0F1-ATPase, adenine nucleotide translocase, and the mitochondrial phosphate transporter at the mitochondrial level; adenylate kinase, creatine kinase, and ATP consumption in the cytoplasm; and oxygen transport between capillaries, interstitial fluid, and cardiomyocytes. The integrated model is able to reproduce experimental observations on ATP, ADP, CrP, and inorganic phosphate levels in canine hearts over a range of workload and during coronary hypoperfusion and predicts that cytoplasmic inorganic phosphate level is a key regulator of the rate of mitochondrial respiration at workloads for which the rate of cardiac oxygen consumption is less than or equal to approximately 12 mumol per minute per gram of tissue. At work rates corresponding to oxygen consumption higher than 12 mumol min(-1 g(-1, model predictions deviate from the experimental data, indicating that at high work rates, additional regulatory mechanisms that are not currently incorporated into the model may be important. Nevertheless, the integrated model explains metabolite levels observed at low to moderate workloads and the changes in metabolite levels and tissue oxygenation observed during graded

  5. Enriched reproducing kernel particle method for fractional advection-diffusion equation

    Science.gov (United States)

    Ying, Yuping; Lian, Yanping; Tang, Shaoqiang; Liu, Wing Kam

    2018-06-01

    The reproducing kernel particle method (RKPM) has been efficiently applied to problems with large deformations, high gradients and high modal density. In this paper, it is extended to solve a nonlocal problem modeled by a fractional advection-diffusion equation (FADE), which exhibits a boundary layer with low regularity. We formulate this method on a moving least-square approach. Via the enrichment of fractional-order power functions to the traditional integer-order basis for RKPM, leading terms of the solution to the FADE can be exactly reproduced, which guarantees a good approximation to the boundary layer. Numerical tests are performed to verify the proposed approach.

  6. Reproducibility of surface roughness in reaming

    DEFF Research Database (Denmark)

    Müller, Pavel; De Chiffre, Leonardo

    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 evaluat...

  7. Entangled states that cannot reproduce original classical games in their quantum version

    International Nuclear Information System (INIS)

    Shimamura, Junichi; Oezdemir, S.K.; Morikoshi, Fumiaki; Imoto, Nobuyuki

    2004-01-01

    A model of a quantum version of classical games should reproduce the original classical games in order to be able to make a comparative analysis of quantum and classical effects. We analyze a class of symmetric multipartite entangled states and their effect on the reproducibility of the classical games. We present the necessary and sufficient condition for the reproducibility of the original classical games. Satisfying this condition means that complete orthogonal bases can be constructed from a given multipartite entangled state provided that each party is restricted to two local unitary operators. We prove that most of the states belonging to the class of symmetric states with respect to permutations, including the N-qubit W state, do not satisfy this condition

  8. [Reproducibility of Fuhrman nuclear grade: advantages of a two-grade system].

    Science.gov (United States)

    Letourneux, Hervé; Lindner, Véronique; Lang, Hervé; Massfelder, Thierry; Meyer, Nicolas; Saussine, Christian; Jacqmin, Didier

    2006-06-01

    The Fuhrman nuclear grade is the reference histoprognostic grading system routinely used all over the world for renal cell carcinoma. Studies measuring the inter-observer and intra-observer concordance of Fuhrman grade show poor results in terms of reproducibility and repeatability. These variations are due to a certain degree of subjectivity of the pathologist in application of the definition of tumour grade, particularly nuclear grade. Elements able to account for this subjectivity in renal cell carcinoma are identified from a review of the literature. To improve the reliability of nuclear grade, the territory occupied by the highest grade must be specified and the grades should probably be combined. At the present time, regrouping of grade 1 and 2 tumours as low grade and grade 3 and 4 tumours as high grade would achieve better reproducibility, while preserving the prognostic: value for overall survival. The development of new treatment modalities and their use in adjuvant situations will imply the use of reliable histoprognostic factors to specify, indications.

  9. Reproducibility of tomographic evaluation of posterolateral lumbar arthrodesis consolidation

    Directory of Open Access Journals (Sweden)

    Marcelo Italo Risso Neto

    2015-06-01

    Full Text Available OBJECTIVE: To evaluate interobserver agreement of Glassman classification for posterolateral lumbar spine arthrodesis.METHODS: One hundred and thirty-four CT scans from patients who underwent posterolateral arthrodesis of the lumbar and lumbosacral spine were evaluated by four observers, namely two orthopedic surgeons experienced in spine surgery and two in training in this area. Using the reconstructed tomographic images at oblique coronal plane, 299 operated levels were systematically analyzed looking for arthrodesis signals. The appearance of bone healing in each operated level was classified in five categories as proposed by Glassman to the posterolateral arthrodesis: 1 bilateral solid arthrodesis; 2 unilateral solid arthrodesis; 3 bilateral partial arthrodesis; 4 unilateral partial arthrodesis; 5 absence of arthrodesis. In a second step, the evaluation of each operated level was divided into two categories: fusion (including type 1, 2, 3, and 4 and non fusion (type 5. Statistical analysis was performed by calculating the Kappa coefficient considering the paired analysis between the two experienced observers and between the two observers in training.RESULTS: The interobserver reproducibility by the kappa coefficient for arthrodesis consolidation analysis for the classification proposed, divided into 5 types, was 0.729 for both experienced surgeons and training surgeons. Considering only two categories kappa coefficient was 0.745 between experienced surgeons and 0.795 between training surgeons. In all analyzes, we obtained high concordance power.CONCLUSION: Interobserver reproducibility was observed with high concordance in the classification proposed by Glassman for posterolateral arthrodesis of the lumbar and lumbosacral spine.

  10. Efficient and reproducible myogenic differentiation from human iPS cells: prospects for modeling Miyoshi Myopathy in vitro.

    Directory of Open Access Journals (Sweden)

    Akihito Tanaka

    Full Text Available 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.

  11. 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

  12. Fluorine in the solar neighborhood: Chemical evolution models

    Science.gov (United States)

    Spitoni, E.; Matteucci, F.; Jönsson, H.; Ryde, N.; Romano, D.

    2018-04-01

    Context. In light of new observational data related to fluorine abundances in solar neighborhood stars, we present chemical evolution models testing various fluorine nucleosynthesis prescriptions with the aim to best fit those new data. Aim. We consider chemical evolution models in the solar neighborhood testing various nucleosynthesis prescriptions for fluorine production with the aim of reproducing the observed abundance ratios [F/O] versus [O/H] and [F/Fe] versus [Fe/H]. We study in detail the effects of various stellar yields on fluorine production. Methods: We adopted two chemical evolution models: the classical two-infall model, which follows the chemical evolution of halo-thick disk and thin disk phases; and the one-infall model, which is designed only for thin disk evolution. We tested the effects on the predicted fluorine abundance ratios of various nucleosynthesis yield sources, that is, asymptotic giant branch (AGB) stars, Wolf-Rayet (W-R) stars, Type II and Type Ia supernovae, and novae. Results: The fluorine production is dominated by AGB stars but the W-R stars are required to reproduce the trend of the observed data in the solar neighborhood with our chemical evolution models. In particular, the best model both for the two-infall and one-infall cases requires an increase by a factor of 2 of the W-R yields. We also show that the novae, even if their yields are still uncertain, could help to better reproduce the secondary behavior of F in the [F/O] versus [O/H] relation. Conclusions: The inclusion of the fluorine production by W-R stars seems to be essential to reproduce the new observed ratio [F/O] versus [O/H] in the solar neighborhood. Moreover, the inclusion of novae helps to reproduce the observed fluorine secondary behavior substantially.

  13. Energetic protons at Mars: interpretation of SLED/Phobos-2 observations by a kinetic model

    Directory of Open Access Journals (Sweden)

    E. Kallio

    2012-11-01

    Full Text Available Mars has neither a significant global intrinsic magnetic field nor a dense atmosphere. Therefore, solar energetic particles (SEPs from the Sun can penetrate close to the planet (under some circumstances reaching the surface. On 13 March 1989 the SLED instrument aboard the Phobos-2 spacecraft recorded the presence of SEPs near Mars while traversing a circular orbit (at 2.8 RM. In the present study the response of the Martian plasma environment to SEP impingement on 13 March was simulated using a kinetic model. The electric and magnetic fields were derived using a 3-D self-consistent hybrid model (HYB-Mars where ions are modelled as particles while electrons form a massless charge neutralizing fluid. The case study shows that the model successfully reproduced several of the observed features of the in situ observations: (1 a flux enhancement near the inbound bow shock, (2 the formation of a magnetic shadow where the energetic particle flux was decreased relative to its solar wind values, (3 the energy dependency of the flux enhancement near the bow shock and (4 how the size of the magnetic shadow depends on the incident particle energy. Overall, it is demonstrated that the Martian magnetic field environment resulting from the Mars–solar wind interaction significantly modulated the Martian energetic particle environment.

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

    KAUST Repository

    Correa, Andrea; Bahri-Laleh, Naeimeh; Cavallo, Luigi

    2013-01-01

    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

  15. Determinants, reproducibility, and seasonal variation of ergosterol levels in house dust.

    Science.gov (United States)

    Leppänen, H K; Nevalainen, A; Vepsäläinen, A; Roponen, M; Täubel, M; Laine, O; Rantakokko, P; von Mutius, E; Pekkanen, J; Hyvärinen, A

    2014-06-01

    This study aimed to clarify the determinants that affect the concentrations of ergosterol and viable fungi in house dust and to examine the seasonal variation and reproducibility of ergosterol concentrations indoors. In studying the determinants, dust samples from living room floors and vacuum cleaner dust bags were collected from 107 farming and 105 non-farming homes. Ergosterol levels were determined with gas chromatography-mass spectrometry,and the dust bag dust was cultivated for enumeration of fungal genera. Lifestyle and environmental factors, for example using of the fireplace, and visible mold observations in homes, explained 20–26% of the variation of fungal concentrations. For the reproducibility study, samples were collected from five urban homes in four different seasons. The reproducibility of ergosterol determinations within a sample was excellent (ICC = 89.8) for floor dust and moderate (ICC = 63.8) for dust bag dust, but poor when sampling the same home throughout a year (ICC = 31.3 and 12.6, respectively) due to large temporal variation in ergosterol concentrations. In conclusion, environmental characteristics only partially predicted the variation of fungal concentrations. Based on these studies, we recommend repeated sampling of dust over time if one seeks to adequately describe overall fungal levels and exposure in a home. This study shows that levels of ergosterol and viable fungi in house dust are related to visible mold observations. Only 20% of the variation in fungal levels can be explained with questionnaires, and therefore, environmental samples need to be taken in addition. Reproducibility of ergosterol determination was excellent for floor dust, and thus, ergosterol measurements from floor dust samples could be suitable for assessing the fungal load in building investigations. The temporal variation needs to be taken into account when describing the ergosterol concentration of urban homes.

  16. Tropically driven and externally forced patterns of Antarctic sea ice change: reconciling observed and modeled trends

    Science.gov (United States)

    Schneider, David P.; Deser, Clara

    2017-09-01

    Recent work suggests that natural variability has played a significant role in the increase of Antarctic sea ice extent during 1979-2013. The ice extent has responded strongly to atmospheric circulation changes, including a deepened Amundsen Sea Low (ASL), which in part has been driven by tropical variability. Nonetheless, this increase has occurred in the context of externally forced climate change, and it has been difficult to reconcile observed and modeled Antarctic sea ice trends. To understand observed-model disparities, this work defines the internally driven and radiatively forced patterns of Antarctic sea ice change and exposes potential model biases using results from two sets of historical experiments of a coupled climate model compared with observations. One ensemble is constrained only by external factors such as greenhouse gases and stratospheric ozone, while the other explicitly accounts for the influence of tropical variability by specifying observed SST anomalies in the eastern tropical Pacific. The latter experiment reproduces the deepening of the ASL, which drives an increase in regional ice extent due to enhanced ice motion and sea surface cooling. However, the overall sea ice trend in every ensemble member of both experiments is characterized by ice loss and is dominated by the forced pattern, as given by the ensemble-mean of the first experiment. This pervasive ice loss is associated with a strong warming of the ocean mixed layer, suggesting that the ocean model does not locally store or export anomalous heat efficiently enough to maintain a surface environment conducive to sea ice expansion. The pervasive upper-ocean warming, not seen in observations, likely reflects ocean mean-state biases.

  17. Tropically driven and externally forced patterns of Antarctic sea ice change: reconciling observed and modeled trends

    Science.gov (United States)

    Schneider, David P.; Deser, Clara

    2018-06-01

    Recent work suggests that natural variability has played a significant role in the increase of Antarctic sea ice extent during 1979-2013. The ice extent has responded strongly to atmospheric circulation changes, including a deepened Amundsen Sea Low (ASL), which in part has been driven by tropical variability. Nonetheless, this increase has occurred in the context of externally forced climate change, and it has been difficult to reconcile observed and modeled Antarctic sea ice trends. To understand observed-model disparities, this work defines the internally driven and radiatively forced patterns of Antarctic sea ice change and exposes potential model biases using results from two sets of historical experiments of a coupled climate model compared with observations. One ensemble is constrained only by external factors such as greenhouse gases and stratospheric ozone, while the other explicitly accounts for the influence of tropical variability by specifying observed SST anomalies in the eastern tropical Pacific. The latter experiment reproduces the deepening of the ASL, which drives an increase in regional ice extent due to enhanced ice motion and sea surface cooling. However, the overall sea ice trend in every ensemble member of both experiments is characterized by ice loss and is dominated by the forced pattern, as given by the ensemble-mean of the first experiment. This pervasive ice loss is associated with a strong warming of the ocean mixed layer, suggesting that the ocean model does not locally store or export anomalous heat efficiently enough to maintain a surface environment conducive to sea ice expansion. The pervasive upper-ocean warming, not seen in observations, likely reflects ocean mean-state biases.

  18. Reproducibility of central lumbar vertebral BMD

    International Nuclear Information System (INIS)

    Chan, F.; Pocock, N.; Griffiths, M.; Majerovic, Y.; Freund, J.

    1997-01-01

    Full text: Lumbar vertebral bone mineral density (BMD) using dual X-ray absorptiometry (DXA) has generally been calculated from a region of interest which includes the entire vertebral body. Although this region excludes part of the transverse processes, it does include the outer cortical shell of the vertebra. Recent software has been devised to calculate BMD in a central vertebral region of interest which excludes the outer cortical envelope. Theoretically this area may be more sensitive to detecting osteoporosis which affects trabecular bone to a greater extent than cortical bone. Apart from the sensitivity of BMD estimation, the reproducibility of any measurement is important owing to the slow rate of change of bone mass. We have evaluated the reproducibility of this new vertebral region of interest in 23 women who had duplicate lumbar spine DXA scans performed on the same day. The patients were repositioned between each measurement. Central vertebral analysis was performed for L2-L4 and the reproducibility of area, bone mineral content (BMC) and BMD calculated as the coefficient of variation; these values were compared with those from conventional analysis. Thus we have shown that the reproducibility of the central BMD is comparable to the conventional analysis which is essential if this technique is to provide any additional clinical data. The reasons for the decrease in reproducibility of the area and hence BMC requires further investigation

  19. Occurrence of blowing snow events at an alpine site over a 10-year period: Observations and modelling

    Science.gov (United States)

    Vionnet, V.; Guyomarc'h, G.; Naaim Bouvet, F.; Martin, E.; Durand, Y.; Bellot, H.; Bel, C.; Puglièse, P.

    2013-05-01

    Blowing snow events control the evolution of the snow pack in mountainous areas and cause inhomogeneous snow distribution. The goal of this study is to identify the main features of blowing snow events at an alpine site and assess the ability of the detailed snowpack model Crocus to reproduce the occurrence of these events in a 1D configuration. We created a database of blowing snow events observed over 10 years at our experimental site. Occurrences of blowing snow events were divided into cases with and without concurrent falling snow. Overall, snow transport is observed during 10.5% of the time in winter and occurs with concurrent falling snow 37.3% of the time. Wind speed and snow age control the frequency of occurrence. Model results illustrate the necessity of taking the wind-dependence of falling snow grain characteristics into account to simulate periods of snow transport and mass fluxes satisfactorily during those periods. The high rate of false alarms produced by the model is investigated in detail for winter 2010/2011 using measurements from snow particle counters.

  20. Evaluation of 11 terrestrial carbon-nitrogen cycle models against observations from two temperate Free-Air CO2 Enrichment studies.

    Science.gov (United States)

    Zaehle, Sönke; Medlyn, Belinda E; De Kauwe, Martin G; Walker, Anthony P; Dietze, Michael C; Hickler, Thomas; Luo, Yiqi; Wang, Ying-Ping; El-Masri, Bassil; Thornton, Peter; Jain, Atul; Wang, Shusen; Warlind, David; Weng, Ensheng; Parton, William; Iversen, Colleen M; Gallet-Budynek, Anne; McCarthy, Heather; Finzi, Adrien; Hanson, Paul J; Prentice, I Colin; Oren, Ram; Norby, Richard J

    2014-05-01

    We analysed the responses of 11 ecosystem models to elevated atmospheric [CO2 ] (eCO2 ) at two temperate forest ecosystems (Duke and Oak Ridge National Laboratory (ORNL) Free-Air CO2 Enrichment (FACE) experiments) to test alternative representations of carbon (C)-nitrogen (N) cycle processes. We decomposed the model responses into component processes affecting the response to eCO2 and confronted these with observations from the FACE experiments. Most of the models reproduced the observed initial enhancement of net primary production (NPP) at both sites, but none was able to simulate both the sustained 10-yr enhancement at Duke and the declining response at ORNL: models generally showed signs of progressive N limitation as a result of lower than observed plant N uptake. Nonetheless, many models showed qualitative agreement with observed component processes. The results suggest that improved representation of above-ground-below-ground interactions and better constraints on plant stoichiometry are important for a predictive understanding of eCO2 effects. Improved accuracy of soil organic matter inventories is pivotal to reduce uncertainty in the observed C-N budgets. The two FACE experiments are insufficient to fully constrain terrestrial responses to eCO2 , given the complexity of factors leading to the observed diverging trends, and the consequential inability of the models to explain these trends. Nevertheless, the ecosystem models were able to capture important features of the experiments, lending some support to their projections. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  1. In vivo evaluation of inter-operator reproducibility of digital dental and conventional impression techniques.

    Directory of Open Access Journals (Sweden)

    Emi Kamimura

    Full Text Available The aim of this study was to evaluate and compare the inter-operator reproducibility of three-dimensional (3D images of teeth captured by a digital impression technique to a conventional impression technique in vivo.Twelve participants with complete natural dentition were included in this study. A digital impression of the mandibular molars of these participants was made by two operators with different levels of clinical experience, 3 or 16 years, using an intra-oral scanner (Lava COS, 3M ESPE. A silicone impression also was made by the same operators using the double mix impression technique (Imprint3, 3M ESPE. Stereolithography (STL data were directly exported from the Lava COS system, while STL data of a plaster model made from silicone impression were captured by a three-dimensional (3D laboratory scanner (D810, 3shape. The STL datasets recorded by two different operators were compared using 3D evaluation software and superimposed using the best-fit-algorithm method (least-squares method, PolyWorks, InnovMetric Software for each impression technique. Inter-operator reproducibility as evaluated by average discrepancies of corresponding 3D data was compared between the two techniques (Wilcoxon signed-rank test.The visual inspection of superimposed datasets revealed that discrepancies between repeated digital impression were smaller than observed with silicone impression. Confirmation was forthcoming from statistical analysis revealing significantly smaller average inter-operator reproducibility using a digital impression technique (0.014± 0.02 mm than when using a conventional impression technique (0.023 ± 0.01 mm.The results of this in vivo study suggest that inter-operator reproducibility with a digital impression technique may be better than that of a conventional impression technique and is independent of the clinical experience of the operator.

  2. In vivo evaluation of inter-operator reproducibility of digital dental and conventional impression techniques

    Science.gov (United States)

    Kamimura, Emi; Tanaka, Shinpei; Takaba, Masayuki; Tachi, Keita; Baba, Kazuyoshi

    2017-01-01

    Purpose The aim of this study was to evaluate and compare the inter-operator reproducibility of three-dimensional (3D) images of teeth captured by a digital impression technique to a conventional impression technique in vivo. Materials and methods Twelve participants with complete natural dentition were included in this study. A digital impression of the mandibular molars of these participants was made by two operators with different levels of clinical experience, 3 or 16 years, using an intra-oral scanner (Lava COS, 3M ESPE). A silicone impression also was made by the same operators using the double mix impression technique (Imprint3, 3M ESPE). Stereolithography (STL) data were directly exported from the Lava COS system, while STL data of a plaster model made from silicone impression were captured by a three-dimensional (3D) laboratory scanner (D810, 3shape). The STL datasets recorded by two different operators were compared using 3D evaluation software and superimposed using the best-fit-algorithm method (least-squares method, PolyWorks, InnovMetric Software) for each impression technique. Inter-operator reproducibility as evaluated by average discrepancies of corresponding 3D data was compared between the two techniques (Wilcoxon signed-rank test). Results The visual inspection of superimposed datasets revealed that discrepancies between repeated digital impression were smaller than observed with silicone impression. Confirmation was forthcoming from statistical analysis revealing significantly smaller average inter-operator reproducibility using a digital impression technique (0.014± 0.02 mm) than when using a conventional impression technique (0.023 ± 0.01 mm). Conclusion The results of this in vivo study suggest that inter-operator reproducibility with a digital impression technique may be better than that of a conventional impression technique and is independent of the clinical experience of the operator. PMID:28636642

  3. The vertical structure of the Saharan boundary layer: Observations and modelling

    Science.gov (United States)

    Garcia-Carreras, L.; Parker, D. J.; Marsham, J. H.; Rosenberg, P.; Marenco, F.; Mcquaid, J.

    2012-04-01

    The vertical structure of the Saharan atmospheric boundary layer (SABL) is investigated with the use of aircraft data from the Fennec observational campaign, and high-resolution large-eddy model (LEM) simulations. The SABL is one of the deepest on Earth, and crucial in controlling the vertical redistribution and long-range transport of dust in the Sahara. The SABL is typically made up of an actively growing convective region driven by high sensible heating at the surface, with a deep, near-neutrally stratified Saharan residual layer (SRL) above it, which is mostly well mixed in humidity and temperature and reaches a height of ~500hPa. These two layers are usually separated by a weak (≤1K) temperature inversion, making the vertical structure very sensitive to the surface fluxes. Large-eddy model (LEM) simulations initialized with radiosonde data from Bordj Bardji Mokhtar (BBM), southern Algeria, are used to improve our understanding of the turbulence structure of the stratification of the SABL, and any mixing or exchanges between the different layers. The model can reproduce the typical SABL structure from observations, and a tracer is used to illustrate the growth of the convective boundary layer into the residual layer above. The heat fluxes show a deep entrainment zone between the convective region and the SRL, potentially enhanced by the combination of a weak lid and a neutral layer above. The horizontal variability in the depth of the convective layer was also significant even with homogeneous surface fluxes. Aircraft observations from a number of flights are used to validate the model results, and to highlight the variability present in a more realistic setting, where conditions are rarely homogeneous in space. Stacked legs were performed to get an estimate of the mean flux profile of the boundary layer, as well as the variations in the vertical structure of the SABL with heterogeneous atmospheric and surface conditions. Regular radiosondes from BBM put

  4. Timbral aspects of reproduced sound in small rooms. I

    DEFF Research Database (Denmark)

    Bech, Søren

    1995-01-01

    , has been simulated using an electroacoustic setup. The model included the direct sound, 17 individual reflections, and the reverberant field. The threshold of detection and just-noticeable differences for an increase in level were measured for individual reflections using eight subjects for noise......This paper reports some of the influences of individual reflections on the timbre of reproduced sound. A single loudspeaker with frequency-independent directivity characteristics, positioned in a listening room of normal size with frequency-independent absorption coefficients of the room surfaces...... and speech. The results have shown that the first-order floor and ceiling reflections are likely to individually contribute to the timbre of reproduced speech. For a noise signal, additional reflections from the left sidewall will contribute individually. The level of the reverberant field has been found...

  5. Scientific Reproducibility in Biomedical Research: Provenance Metadata Ontology for Semantic Annotation of Study Description.

    Science.gov (United States)

    Sahoo, Satya S; Valdez, Joshua; Rueschman, Michael

    2016-01-01

    Scientific reproducibility is key to scientific progress as it allows the research community to build on validated results, protect patients from potentially harmful trial drugs derived from incorrect results, and reduce wastage of valuable resources. The National Institutes of Health (NIH) recently published a systematic guideline titled "Rigor and Reproducibility " for supporting reproducible research studies, which has also been accepted by several scientific journals. These journals will require published articles to conform to these new guidelines. Provenance metadata describes the history or origin of data and it has been long used in computer science to capture metadata information for ensuring data quality and supporting scientific reproducibility. In this paper, we describe the development of Provenance for Clinical and healthcare Research (ProvCaRe) framework together with a provenance ontology to support scientific reproducibility by formally modeling a core set of data elements representing details of research study. We extend the PROV Ontology (PROV-O), which has been recommended as the provenance representation model by World Wide Web Consortium (W3C), to represent both: (a) data provenance, and (b) process provenance. We use 124 study variables from 6 clinical research studies from the National Sleep Research Resource (NSRR) to evaluate the coverage of the provenance ontology. NSRR is the largest repository of NIH-funded sleep datasets with 50,000 studies from 36,000 participants. The provenance ontology reuses ontology concepts from existing biomedical ontologies, for example the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), to model the provenance information of research studies. The ProvCaRe framework is being developed as part of the Big Data to Knowledge (BD2K) data provenance project.

  6. Cystic fibrosis in adults. Short-term and long-term reproducibility of the Brody score for lung morphology in low-dose MDCT scans

    Energy Technology Data Exchange (ETDEWEB)

    Weber, K.; Paolini, M.; Schmitz, M.; Coppenrath, E.; Reiser, M.; Mueller-Lisse, U.G. [Ludwig-Maximilians-Univ. Muenchen (Germany). Inst. fuer Klinische Radiologie; Fischer, R.; Huber, R. [Ludwig-Maximilians-Univ. Muenchen (Germany). Medical Hospital V

    2014-01-15

    Purpose: The semi-quantitative Brody score measures the severity of cystic fibrosis (CF)-related lung disease. We investigated the short-term (28 - 60 days) and long-term (2 - 7 years) intra- and inter-observer reproducibility of the Brody score in low-dose multidetector row computed tomography examinations performed in inspiration (LDCTs) of adult CF patients. Materials and Methods: Composite Brody scores and respective underlying bronchiectasis, mucus plugging, peribronchial thickening, parenchymal opacity, and hyperinflation subscores were evaluated twice (time interval, 1 - 84 months) by each of 3 independent radiologists (1 - 20 years of professional diagnostic radiology experience) in LDCTs (4 - 64 rows, 120 KVp, 10 - 15 mAs/slice, CTDIw approx. 1.0 mGy, effective dose approx. 0.5 mSv) of 15 adult patients with CF-related lung disease (8 female, 7 male, age, 18 - 50 years, mean, 33 years). Results: The average reproducibility of the Brody score was within +/-7 % (range, 2 - 30 %) between radiologists, and +/-6 % (3 - 12 %) within radiologists (short-term, 28 - 60 days, 4 %, 0 - 12 %, long-term, 2 - 7 years, 12 %, 1 - 36 %). For the different subscores, the reproducibility was within +/-25 % (15 - 41 %) between radiologists and +/-23 % (12 - 46 %) within radiologists. Conclusion: The Brody score shows high average inter-observer reproducibility in LDCTs of adult CF patients. The Brody score also demonstrates high average intra-observer reproducibility if subsequent assessments are made within 28 - 61 days. With time intervals of 2 - 7 years between subsequent evaluations, however, intra-observer reproducibility decreases. Respective subscores each demonstrate lower intra- and inter-observer reproducibility than does the composite Brody score. (orig.)

  7. Simulation of temperature extremes in the Tibetan Plateau from CMIP5 models and comparison with gridded observations

    Science.gov (United States)

    You, Qinglong; Jiang, Zhihong; Wang, Dai; Pepin, Nick; Kang, Shichang

    2017-09-01

    Understanding changes in temperature extremes in a warmer climate is of great importance for society and for ecosystem functioning due to potentially severe impacts of such extreme events. In this study, temperature extremes defined by the Expert Team on Climate Change Detection and Indices (ETCCDI) from CMIP5 models are evaluated by comparison with homogenized gridded observations at 0.5° resolution across the Tibetan Plateau (TP) for 1961-2005. Using statistical metrics, the models have been ranked in terms of their ability to reproduce similar patterns in extreme events to the observations. Four CMIP5 models have good performance (BNU-ESM, HadGEM2-ES, CCSM4, CanESM2) and are used to create an optimal model ensemble (OME). Most temperature extreme indices in the OME are closer to the observations than in an ensemble using all models. Best performance is given for threshold temperature indices and extreme/absolute value indices are slightly less well modelled. Thus the choice of model in the OME seems to have more influences on temperature extreme indices based on thresholds. There is no significant correlation between elevation and modelled bias of the extreme indices for both the optimal/all model ensembles. Furthermore, the minimum temperature (Tmin) is significanlty positive correlations with the longwave radiation and cloud variables, respectively, but the Tmax fails to find the correlation with the shortwave radiation and cloud variables. This suggests that the cloud-radiation differences influence the Tmin in each CMIP5 model to some extent, and result in the temperature extremes based on Tmin.

  8. 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.

  9. Local Scale Radiobrightness Modeling During the Intensive Observing Period-4 of the Cold Land Processes Experiment-1

    Science.gov (United States)

    Kim, E.; Tedesco, M.; de Roo, R.; England, A. W.; Gu, H.; Pham, H.; Boprie, D.; Graf, T.; Koike, T.; Armstrong, R.; Brodzik, M.; Hardy, J.; Cline, D.

    2004-12-01

    The NASA Cold Land Processes Field Experiment (CLPX-1) was designed to provide microwave remote sensing observations and ground truth for studies of snow and frozen ground remote sensing, particularly issues related to scaling. CLPX-1 was conducted in 2002 and 2003 in Colorado, USA. One of the goals of the experiment was to test the capabilities of microwave emission models at different scales. Initial forward model validation work has concentrated on the Local-Scale Observation Site (LSOS), a 0.8~ha study site consisting of open meadows separated by trees where the most detailed measurements were made of snow depth and temperature, density, and grain size profiles. Results obtained in the case of the 3rd Intensive Observing Period (IOP3) period (February, 2003, dry snow) suggest that a model based on Dense Medium Radiative Transfer (DMRT) theory is able to model the recorded brightness temperatures using snow parameters derived from field measurements. This paper focuses on the ability of forward DMRT modelling, combined with snowpack measurements, to reproduce the radiobrightness signatures observed by the University of Michigan's Truck-Mounted Radiometer System (TMRS) at 19 and 37~GHz during the 4th IOP (IOP4) in March, 2003. Unlike in IOP3, conditions during IOP4 include both wet and dry periods, providing a valuable test of DMRT model performance. In addition, a comparison will be made for the one day of coincident observations by the University of Tokyo's Ground-Based Microwave Radiometer-7 (GBMR-7) and the TMRS. The plot-scale study in this paper establishes a baseline of DMRT performance for later studies at successively larger scales. And these scaling studies will help guide the choice of future snow retrieval algorithms and the design of future Cold Lands observing systems.

  10. CONSTRAINING THE NFW POTENTIAL WITH OBSERVATIONS AND MODELING OF LOW SURFACE BRIGHTNESS GALAXY VELOCITY FIELDS

    International Nuclear Information System (INIS)

    Kuzio de Naray, Rachel; McGaugh, Stacy S.; Mihos, J. Christopher

    2009-01-01

    We model the Navarro-Frenk-White (NFW) potential to determine if, and under what conditions, the NFW halo appears consistent with the observed velocity fields of low surface brightness (LSB) galaxies. We present mock DensePak Integral Field Unit (IFU) velocity fields and rotation curves of axisymmetric and nonaxisymmetric potentials that are well matched to the spatial resolution and velocity range of our sample galaxies. We find that the DensePak IFU can accurately reconstruct the velocity field produced by an axisymmetric NFW potential and that a tilted-ring fitting program can successfully recover the corresponding NFW rotation curve. We also find that nonaxisymmetric potentials with fixed axis ratios change only the normalization of the mock velocity fields and rotation curves and not their shape. The shape of the modeled NFW rotation curves does not reproduce the data: these potentials are unable to simultaneously bring the mock data at both small and large radii into agreement with observations. Indeed, to match the slow rise of LSB galaxy rotation curves, a specific viewing angle of the nonaxisymmetric potential is required. For each of the simulated LSB galaxies, the observer's line of sight must be along the minor axis of the potential, an arrangement that is inconsistent with a random distribution of halo orientations on the sky.

  11. Fine resolution atmospheric sulfate model driven by operational meteorological data: Comparison with observations

    International Nuclear Information System (INIS)

    Benkovitz, C.M.; Schwartz, S.E.; Berkowitz, C.M.; Easter, R.C.

    1993-09-01

    The hypothesis that anthropogenic sulfur aerosol influences clear-sky and cloud albedo and can thus influence climate has been advanced by several investigators; current global-average climate forcing is estimated to be of comparable magnitude, but opposite sign, to longwave forcing by anthropogenic greenhouse gases. The high space and time variability of sulfate concentrations and column aerosol burdens have been established by observational data; however, geographic and time coverage provided by data from surface monitoring networks is very limited. Consistent regional and global estimates of sulfate aerosol loading, and the contributions to this loading from different sources can be obtained only by modeling studies. Here we describe a sub-hemispheric to global-scale Eulerian transport and transformation model for atmospheric sulfate and its precursors, driven by operational meteorological data, and report results of calculations for October, 1986 for the North Atlantic and adjacent continental regions. The model, which is based on the Global Chemistry Model uses meteorological data from the 6-hour forecast model of the European Center for Medium-Range Weather Forecast to calculate transport and transformation of sulfur emissions. Time- and location-dependent dry deposition velocities were estimated using the methodology of Wesely and colleagues. Chemical reactions includes gaseous oxidation of SO 2 and DMS by OH, and aqueous oxidation of SO 2 by H 2 O 2 and O 3 . Anthropogenic emissions were from the NAPAP and EMEP 1985 inventories and biogenic emissions based on Bates et al. Calculated sulfate concentrations and column burdens exhibit high variability on spatial scale of hundreds of km and temporal scale of days. Calculated daily average sulfate concentrations closely reproduce observed concentrations at locations widespread over the model domain

  12. Cooling Active Region Loops Observed With SXT and TRACE

    OpenAIRE

    Winebarger, Amy R.; Warren, Harry P.

    2005-01-01

    An Impulsive Heating Multiple Strand (IHMS) Model is able to reproduce the observational characteristics of EUV (~ 1 MK) active region loops. This model implies that some of the loops must reach temperatures where X-ray filters are sensitive (> 2.5 MK) before they cool to EUV temperatures. Hence, some bright EUV loops must be preceded by bright X-ray loops. Previous analysis of X-ray and EUV active region observations, however, have concluded that EUV loops are not preceded by X-ray loops. In...

  13. June 13, 2013 U.S. East Coast Meteotsunami: Comparing a Numerical Model With Observations

    Science.gov (United States)

    Wang, D.; Becker, N. C.; Weinstein, S.; Whitmore, P.; Knight, W.; Kim, Y.; Bouchard, R. H.; Grissom, K.

    2013-12-01

    On June 13, 2013, a tsunami struck the U.S. East Coast and caused several reported injuries. This tsunami occurred after a derecho moved offshore from North America into the Atlantic Ocean. The presence of this storm, the lack of a seismic source, and the fact that tsunami arrival times at tide stations and deep ocean-bottom pressure sensors cannot be attributed to a 'point-source' suggest this tsunami was caused by atmospheric forces, i.e., a meteotsunami. In this study we attempt to reproduce the observed phenomenon using a numerical model with idealized atmospheric pressure forcing resembling the propagation of the observed barometric anomaly. The numerical model was able to capture some observed features of the tsunami at some tide stations, including the time-lag between the time of pressure jump and the time of tsunami arrival. The model also captures the response at a deep ocean-bottom pressure gauge (DART 44402), including the primary wave and the reflected wave. There are two components of the oceanic response to the propagating pressure anomaly, inverted barometer response and dynamic response. We find that the dynamic response over the deep ocean to be much smaller than the inverted barometer response. The time lag between the pressure jump and tsunami arrival at tide stations is due to the dynamic response: waves generated and/or reflected at the shelf-break propagate shoreward and amplify due to the shoaling effect. The evolution of the derecho over the deep ocean (propagation direction and intensity) is not well defined, however, because of the lack of data so the forcing used for this study is somewhat speculative. Better definition of the pressure anomaly through increased observation or high resolution atmospheric models would improve meteotsunami forecast capabilities.

  14. Observability and synchronization of neuron models

    Science.gov (United States)

    Aguirre, Luis A.; Portes, Leonardo L.; Letellier, Christophe

    2017-10-01

    Observability is the property that enables recovering the state of a dynamical system from a reduced number of measured variables. In high-dimensional systems, it is therefore important to make sure that the variable recorded to perform the analysis conveys good observability of the system dynamics. The observability of a network of neuron models depends nontrivially on the observability of the node dynamics and on the topology of the network. The aim of this paper is twofold. First, to perform a study of observability using four well-known neuron models by computing three different observability coefficients. This not only clarifies observability properties of the models but also shows the limitations of applicability of each type of coefficients in the context of such models. Second, to study the emergence of phase synchronization in networks composed of neuron models. This is done performing multivariate singular spectrum analysis which, to the best of the authors' knowledge, has not been used in the context of networks of neuron models. It is shown that it is possible to detect phase synchronization: (i) without having to measure all the state variables, but only one (that provides greatest observability) from each node and (ii) without having to estimate the phase.

  15. Reproducibility of (n,γ) gamma ray spectrum in Pb under different ENDF/B releases

    Energy Technology Data Exchange (ETDEWEB)

    Kebwaro, J.M., E-mail: jeremiahkebwaro@gmail.com [Department of Physical Sciences, Karatina University, P.O. Box 1957-10101, Karatina (Kenya); He, C.H.; Zhao, Y.L. [School of Nuclear Science and Technology, Xian Jiaotong University, Xian, Shaanxi 710049 (China)

    2016-04-15

    Radiative capture reactions are of interest in shielding design and other fundamental research. In this study the reproducibility of (n,γ) reactions in Pb when cross-section data from different ENDF/B releases are used in the Monte-Carlo code, MCNP, was investigated. Pb was selected for this study because it is widely used in shielding applications where capture reactions are likely to occur. Four different neutron spectra were declared as source in the MCNP model which consisted of a simple spherical geometry. The gamma ray spectra due to the capture reactions were recorded at 10 cm from the center of the sphere. The results reveal that the gamma ray spectrum produced by ENDF/B-V is in reasonable agreement with that produced when ENDF/B-VI.6 is used. However the spectrum produced by ENDF/B-VII does not reveal any primary gamma rays in the higher energy region (E > 3 MeV). It is further observed that the intensities of the capture gamma rays produced when various releases are used differ by a some margin showing that the results are not reproducible. The generated spectra also vary with the spectrum of the source neutrons. The discrepancies observed among various ENDF/B releases could raise concerns to end users and need to be addressed properly during benchmarking calculations before the next release. The evaluation from ENDF to ACE format that is supplied with MCNP should also be examined because errors might have arisen during the evaluation.

  16. Holocene sediment stratigraphy and the generation of observed data

    International Nuclear Information System (INIS)

    Healy, M.G.

    1991-01-01

    The major difficulty with the climatic and global warming modelling approach is the essential lack of observed and reproducible data on which model assumptions can be based and model outputs verified. The development of additional techniques for data collection can contribute to a fuller understanding of how environmental change is manifested at a local and regional scale. The use of thermoluminescence as a possible dating mechanism receives special mention for stratigraphic analysis

  17. Evaluation of recent quantitative magnetospheric magnetic field models

    International Nuclear Information System (INIS)

    Walker, R.J.

    1976-01-01

    Recent quantitative magnetospheric field models contain many features not found in earlier models. Magnetopause models which include the effects of the dipole tilt were presented. More realistic models of the tail field include tail currents which close on the magnetopause, cross-tail currents of finite thickness, and cross-tail current models which model the position of the neutral sheet as a function of tilt. Finally, models have attempted to calculate the field of currents distributed in the inner magnetosphere. As the purpose of a magnetospheric model is to provide a mathematical description of the field that reasonably reproduces the observed magnetospheric field, several recent models were compared with the observed ΔB(B/sub observed/--B/sub main field/) contours. Models containing only contributions from magnetopause and tail current systems are able to reproduce the observed quiet time field only in an extremely qualitative way. The best quantitative agreement between models and observations occurs when currents distributed in the inner magnetosphere are added to the magnetopause and tail current systems. However, the distributed current models are valid only for zero tilt. Even the models which reproduce the average observed field reasonably well may not give physically reasonable field gradients. Three of the models evaluated contain regions in the near tail in which the field gradient reverses direction. One region in which all the models fall short is that around the polar cusp, though most can be used to calculate the position of the last closed field line reasonably well

  18. On the solutions of electrohydrodynamic flow with fractional differential equations by reproducing kernel method

    Directory of Open Access Journals (Sweden)

    Akgül Ali

    2016-01-01

    Full Text Available In this manuscript we investigate electrodynamic flow. For several values of the intimate parameters we proved that the approximate solution depends on a reproducing kernel model. Obtained results prove that the reproducing kernel method (RKM is very effective. We obtain good results without any transformation or discretization. Numerical experiments on test examples show that our proposed schemes are of high accuracy and strongly support the theoretical results.

  19. Evolution of Precipitation Structure During the November DYNAMO MJO Event: Cloud-Resolving Model Intercomparison and Cross Validation Using Radar Observations

    Science.gov (United States)

    Li, Xiaowen; Janiga, Matthew A.; Wang, Shuguang; Tao, Wei-Kuo; Rowe, Angela; Xu, Weixin; Liu, Chuntao; Matsui, Toshihisa; Zhang, Chidong

    2018-04-01

    Evolution of precipitation structures are simulated and compared with radar observations for the November Madden-Julian Oscillation (MJO) event during the DYNAmics of the MJO (DYNAMO) field campaign. Three ground-based, ship-borne, and spaceborne precipitation radars and three cloud-resolving models (CRMs) driven by observed large-scale forcing are used to study precipitation structures at different locations over the central equatorial Indian Ocean. Convective strength is represented by 0-dBZ echo-top heights, and convective organization by contiguous 17-dBZ areas. The multi-radar and multi-model framework allows for more stringent model validations. The emphasis is on testing models' ability to simulate subtle differences observed at different radar sites when the MJO event passed through. The results show that CRMs forced by site-specific large-scale forcing can reproduce not only common features in cloud populations but also subtle variations observed by different radars. The comparisons also revealed common deficiencies in CRM simulations where they underestimate radar echo-top heights for the strongest convection within large, organized precipitation features. Cross validations with multiple radars and models also enable quantitative comparisons in CRM sensitivity studies using different large-scale forcing, microphysical schemes and parameters, resolutions, and domain sizes. In terms of radar echo-top height temporal variations, many model sensitivity tests have better correlations than radar/model comparisons, indicating robustness in model performance on this aspect. It is further shown that well-validated model simulations could be used to constrain uncertainties in observed echo-top heights when the low-resolution surveillance scanning strategy is used.

  20. Reproducibility of lateral cephalometric landmarks on conventional radiographs and spatial frequency-processed digital images

    International Nuclear Information System (INIS)

    Shin, Jeong Won; Heo, Min Suk; Lee, Sam Sun; Choi, Hyun Bae; Choi, Soon Chul; Choi, Hang Moon

    2002-01-01

    Computed radiography (CR) has been used in cephalometric radiography and many studies have been carried out to improve image quality using various digital enhancement and filtering techniques. During CR image acquisition, the frequency rank and type affect to the image quality. The aim of this study was to compare the diagnostic quality of conventional cephalometric radiographs to those of computed radiography. The diagnostic quality of conventional cephalometric radiographs (M0) and their digital image counterparts were compared, and at the same time, six modalities (M1-M6) of spatial frequency-processed digital images were compared by evaluating the reproducibility of 23 cephalometric landmark locations. Reproducibility was defined as an observer's deviation (in mm) from the mean between all observers. In comparison with the conventional cephalometric radiograph (M0), M1 showed statistically significant differences in 8 locations, M2 in 9, M3 12, M4 in 7, M5 in 12, and M6 showed significant differences in 14 of 23 landmark locations (p<0.05). The number of reproducible landmarks that each modality possesses were 7 in M6, 6 in M5, 5 in M3, 4 in M4, 3 in M2, 2 in M1, and 1 location in M0. The image modality that observers selected as having the best image quality was M5.

  1. Mapping urban air quality in near real-time using observations from low-cost sensors and model information.

    Science.gov (United States)

    Schneider, Philipp; Castell, Nuria; Vogt, Matthias; Dauge, Franck R; Lahoz, William A; Bartonova, Alena

    2017-09-01

    The recent emergence of low-cost microsensors measuring various air pollutants has significant potential for carrying out high-resolution mapping of air quality in the urban environment. However, the data obtained by such sensors are generally less reliable than that from standard equipment and they are subject to significant data gaps in both space and time. In order to overcome this issue, we present here a data fusion method based on geostatistics that allows for merging observations of air quality from a network of low-cost sensors with spatial information from an urban-scale air quality model. The performance of the methodology is evaluated for nitrogen dioxide in Oslo, Norway, using both simulated datasets and real-world measurements from a low-cost sensor network for January 2016. The results indicate that the method is capable of producing realistic hourly concentration fields of urban nitrogen dioxide that inherit the spatial patterns from the model and adjust the prior values using the information from the sensor network. The accuracy of the data fusion method is dependent on various factors including the total number of observations, their spatial distribution, their uncertainty (both in terms of systematic biases and random errors), as well as the ability of the model to provide realistic spatial patterns of urban air pollution. A validation against official data from air quality monitoring stations equipped with reference instrumentation indicates that the data fusion method is capable of reproducing city-wide averaged official values with an R 2 of 0.89 and a root mean squared error of 14.3 μg m -3 . It is further capable of reproducing the typical daily cycles of nitrogen dioxide. Overall, the results indicate that the method provides a robust way of extracting useful information from uncertain sensor data using only a time-invariant model dataset and the knowledge contained within an entire sensor network. Copyright © 2017 The Authors. Published

  2. Ratio-scaling of listener preference of multichannel reproduced sound

    DEFF Research Database (Denmark)

    Choisel, Sylvain; Wickelmaier, Florian

    2005-01-01

    -trivial assumption in the case of complex spatial sounds. In the present study the Bradley-Terry-Luce (BTL) model was employed to investigate the unidimensionality of preference judgments made by 40 listeners on multichannel reproduced sound. Short musical excerpts played back in eight reproduction modes (mono...... music). As a main result, the BTL model was found to predict the choice frequencies well. This implies that listeners were able to integrate the complex nature of the sounds into a unidimensional preference judgment. It further implies the existence of a preference scale on which the reproduction modes...

  3. Automated analysis of phantom images for the evaluation of long-term reproducibility in digital mammography

    International Nuclear Information System (INIS)

    Gennaro, G; Ferro, F; Contento, G; Fornasin, F; Di Maggio, C

    2007-01-01

    The performance of an automatic software package was evaluated with phantom images acquired by a full-field digital mammography unit. After the validation, the software was used, together with a Leeds TORMAS test object, to model the image acquisition process. Process modelling results were used to evaluate the sensitivity of the method in detecting changes of exposure parameters from routine image quality measurements in digital mammography, which is the ultimate purpose of long-term reproducibility tests. Image quality indices measured by the software included the mean pixel value and standard deviation of circular details and surrounding background, contrast-to-noise ratio and relative contrast; detail counts were also collected. The validation procedure demonstrated that the software localizes the phantom details correctly and the difference between automatic and manual measurements was within few grey levels. Quantitative analysis showed sufficient sensitivity to relate fluctuations in exposure parameters (kV p or mAs) to variations in image quality indices. In comparison, detail counts were found less sensitive in detecting image quality changes, even when limitations due to observer subjectivity were overcome by automatic analysis. In conclusion, long-term reproducibility tests provided by the Leeds TORMAS phantom with quantitative analysis of multiple IQ indices have been demonstrated to be effective in predicting causes of deviation from standard operating conditions and can be used to monitor stability in full-field digital mammography

  4. Genotypic variability enhances the reproducibility of an ecological study.

    Science.gov (United States)

    Milcu, Alexandru; Puga-Freitas, Ruben; Ellison, Aaron M; Blouin, Manuel; Scheu, Stefan; Freschet, Grégoire T; Rose, Laura; Barot, Sebastien; Cesarz, Simone; Eisenhauer, Nico; Girin, Thomas; Assandri, Davide; Bonkowski, Michael; Buchmann, Nina; Butenschoen, Olaf; Devidal, Sebastien; Gleixner, Gerd; Gessler, Arthur; Gigon, Agnès; Greiner, Anna; Grignani, Carlo; Hansart, Amandine; Kayler, Zachary; Lange, Markus; Lata, Jean-Christophe; Le Galliard, Jean-François; Lukac, Martin; Mannerheim, Neringa; Müller, Marina E H; Pando, Anne; Rotter, Paula; Scherer-Lorenzen, Michael; Seyhun, Rahme; Urban-Mead, Katherine; Weigelt, Alexandra; Zavattaro, Laura; Roy, Jacques

    2018-02-01

    Many scientific disciplines are currently experiencing a 'reproducibility crisis' because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduce reproducibility by amplifying the impacts of laboratory-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the 'reproducibility crisis', deliberately including genetic variability may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.

  5. Hippocampal Astrocyte Cultures from Adult and Aged Rats Reproduce Changes in Glial Functionality Observed in the Aging Brain.

    Science.gov (United States)

    Bellaver, Bruna; Souza, Débora Guerini; Souza, Diogo Onofre; Quincozes-Santos, André

    2017-05-01

    Astrocytes are dynamic cells that maintain brain homeostasis, regulate neurotransmitter systems, and process synaptic information, energy metabolism, antioxidant defenses, and inflammatory response. Aging is a biological process that is closely associated with hippocampal astrocyte dysfunction. In this sense, we demonstrated that hippocampal astrocytes from adult and aged Wistar rats reproduce the glial functionality alterations observed in aging by evaluating several senescence, glutamatergic, oxidative and inflammatory parameters commonly associated with the aging process. Here, we show that the p21 senescence-associated gene and classical astrocyte markers, such as glial fibrillary acidic protein (GFAP), vimentin, and actin, changed their expressions in adult and aged astrocytes. Age-dependent changes were also observed in glutamate transporters (glutamate aspartate transporter (GLAST) and glutamate transporter-1 (GLT-1)) and glutamine synthetase immunolabeling and activity. Additionally, according to in vivo aging, astrocytes from adult and aged rats showed an increase in oxidative/nitrosative stress with mitochondrial dysfunction, an increase in RNA oxidation, NADPH oxidase (NOX) activity, superoxide levels, and inducible nitric oxide synthase (iNOS) expression levels. Changes in antioxidant defenses were also observed. Hippocampal astrocytes also displayed age-dependent inflammatory response with augmentation of proinflammatory cytokine levels, such as TNF-α, IL-1β, IL-6, IL-18, and messenger RNA (mRNA) levels of cyclo-oxygenase 2 (COX-2). Furthermore, these cells secrete neurotrophic factors, including glia-derived neurotrophic factor (GDNF), brain-derived neurotrophic factor (BDNF), S100 calcium-binding protein B (S100B) protein, and transforming growth factor-β (TGF-β), which changed in an age-dependent manner. Classical signaling pathways associated with aging, such as nuclear factor erythroid-derived 2-like 2 (Nrf2), nuclear factor kappa B (NFκ

  6. Prognostic Value and Reproducibility of Pretreatment CT Texture Features in Stage III Non-Small Cell Lung Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Fried, David V. [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, Texas (United States); Tucker, Susan L. [Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Zhou, Shouhao [Division of Quantitative Sciences, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Liao, Zhongxing [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mawlawi, Osama [Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, Texas (United States); Ibbott, Geoffrey [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, Texas (United States); Court, Laurence E., E-mail: LECourt@mdanderson.org [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, Texas (United States)

    2014-11-15

    Purpose: To determine whether pretreatment CT texture features can improve patient risk stratification beyond conventional prognostic factors (CPFs) in stage III non-small cell lung cancer (NSCLC). Methods and Materials: We retrospectively reviewed 91 cases with stage III NSCLC treated with definitive chemoradiation therapy. All patients underwent pretreatment diagnostic contrast enhanced computed tomography (CE-CT) followed by 4-dimensional CT (4D-CT) for treatment simulation. We used the average-CT and expiratory (T50-CT) images from the 4D-CT along with the CE-CT for texture extraction. Histogram, gradient, co-occurrence, gray tone difference, and filtration-based techniques were used for texture feature extraction. Penalized Cox regression implementing cross-validation was used for covariate selection and modeling. Models incorporating texture features from the 33 image types and CPFs were compared to those with models incorporating CPFs alone for overall survival (OS), local-regional control (LRC), and freedom from distant metastases (FFDM). Predictive Kaplan-Meier curves were generated using leave-one-out cross-validation. Patients were stratified based on whether their predicted outcome was above or below the median. Reproducibility of texture features was evaluated using test-retest scans from independent patients and quantified using concordance correlation coefficients (CCC). We compared models incorporating the reproducibility seen on test-retest scans to our original models and determined the classification reproducibility. Results: Models incorporating both texture features and CPFs demonstrated a significant improvement in risk stratification compared to models using CPFs alone for OS (P=.046), LRC (P=.01), and FFDM (P=.005). The average CCCs were 0.89, 0.91, and 0.67 for texture features extracted from the average-CT, T50-CT, and CE-CT, respectively. Incorporating reproducibility within our models yielded 80.4% (±3.7% SD), 78.3% (±4.0% SD), and 78

  7. Prognostic Value and Reproducibility of Pretreatment CT Texture Features in Stage III Non-Small Cell Lung Cancer

    International Nuclear Information System (INIS)

    Fried, David V.; Tucker, Susan L.; Zhou, Shouhao; Liao, Zhongxing; Mawlawi, Osama; Ibbott, Geoffrey; Court, Laurence E.

    2014-01-01

    Purpose: To determine whether pretreatment CT texture features can improve patient risk stratification beyond conventional prognostic factors (CPFs) in stage III non-small cell lung cancer (NSCLC). Methods and Materials: We retrospectively reviewed 91 cases with stage III NSCLC treated with definitive chemoradiation therapy. All patients underwent pretreatment diagnostic contrast enhanced computed tomography (CE-CT) followed by 4-dimensional CT (4D-CT) for treatment simulation. We used the average-CT and expiratory (T50-CT) images from the 4D-CT along with the CE-CT for texture extraction. Histogram, gradient, co-occurrence, gray tone difference, and filtration-based techniques were used for texture feature extraction. Penalized Cox regression implementing cross-validation was used for covariate selection and modeling. Models incorporating texture features from the 33 image types and CPFs were compared to those with models incorporating CPFs alone for overall survival (OS), local-regional control (LRC), and freedom from distant metastases (FFDM). Predictive Kaplan-Meier curves were generated using leave-one-out cross-validation. Patients were stratified based on whether their predicted outcome was above or below the median. Reproducibility of texture features was evaluated using test-retest scans from independent patients and quantified using concordance correlation coefficients (CCC). We compared models incorporating the reproducibility seen on test-retest scans to our original models and determined the classification reproducibility. Results: Models incorporating both texture features and CPFs demonstrated a significant improvement in risk stratification compared to models using CPFs alone for OS (P=.046), LRC (P=.01), and FFDM (P=.005). The average CCCs were 0.89, 0.91, and 0.67 for texture features extracted from the average-CT, T50-CT, and CE-CT, respectively. Incorporating reproducibility within our models yielded 80.4% (±3.7% SD), 78.3% (±4.0% SD), and 78

  8. Reproducibility and validity of the Shanghai Women's Health Study physical activity questionnaire.

    Science.gov (United States)

    Matthews, Charles E; Shu, Xiao-Ou; Yang, Gong; Jin, Fan; Ainsworth, Barbara E; Liu, Dake; Gao, Yu-Tang; Zheng, Wei

    2003-12-01

    In this investigation, the authors evaluated the reproducibility and validity of the Shanghai Women's Health Study (SWHS) physical activity questionnaire (PAQ), which was administered in a cohort study of approximately 75,000 Chinese women aged 40-70 years. Reproducibility (2-year test-retest) was evaluated using kappa statistics and intraclass correlation coefficients (ICCs). Validity was evaluated by comparing Spearman correlations (r) for the SWHS PAQ with two criterion measures administered over a period of 12 months: four 7-day physical activity logs and up to 28 7-day PAQs. Women were recruited from the SWHS cohort (n = 200). Results indicated that the reproducibility of adolescent and adult exercise participation (kappa = 0.85 and kappa = 0.64, respectively) and years of adolescent exercise and adult exercise energy expenditure (ICC = 0.83 and ICC = 0.70, respectively) was reasonable. Reproducibility values for adult lifestyle activities were lower (ICC = 0.14-0.54). Significant correlations between the PAQ and criterion measures of adult exercise were observed for the first PAQ administration (physical activity log, r = 0.50; 7-day PAQ, r = 0.62) and the second PAQ administration (physical activity log, r = 0.74; 7-day PAQ, r = 0.80). Significant correlations between PAQ lifestyle activities and the 7-day PAQ were also noted (r = 0.33-0.88). These data indicate that the SWHS PAQ is a reproducible and valid measure of exercise behaviors and that it demonstrates utility in stratifying women by levels of important lifestyle activities (e.g., housework, walking, cycling).

  9. 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.

  10. Does systematic variation improve the reproducibility of animal experiments?

    NARCIS (Netherlands)

    Jonker, R.M.; Guenther, A.; Engqvist, L.; Schmoll, T.

    2013-01-01

    Reproducibility of results is a fundamental tenet of science. In this journal, Richter et al.1 tested whether systematic variation in experimental conditions (heterogenization) affects the reproducibility of results. Comparing this approach with the current standard of ensuring reproducibility

  11. Observation models in radiocarbon calibration

    International Nuclear Information System (INIS)

    Jones, M.D.; Nicholls, G.K.

    2001-01-01

    The observation model underlying any calibration process dictates the precise mathematical details of the calibration calculations. Accordingly it is important that an appropriate observation model is used. Here this is illustrated with reference to the use of reservoir offsets where the standard calibration approach is based on a different model to that which the practitioners clearly believe is being applied. This sort of error can give rise to significantly erroneous calibration results. (author). 12 refs., 1 fig

  12. Inter-observer reproducibility before and after web-based education in the Gleason grading of the prostate adenocarcinoma among the Iranian pathologists.

    Directory of Open Access Journals (Sweden)

    Alireza Abdollahi

    2014-05-01

    Full Text Available This study was aimed at determining intra and inter-observer concordance rates in the Gleason scoring of prostatic adenocarcinoma, before and after a web-based educational course. In this self-controlled study, 150 tissue samples of prostatic adenocarcinoma are re-examined to be scored according to the Gleason scoring system. Then all pathologists attend a free web-based course. Afterwards, the same 150 samples [with different codes compared to the previous ones] are distributed differently among the pathologists to be assigned Gleason scores. After gathering the data, the concordance rate in the first and second reports of pathologists is determined. In the pre web-education, the mean kappa value of Interobserver agreement was 0.25 [fair agreement]. Post web-education significantly improved with the mean kappa value of 0.52 [moderate agreement]. Using weighted kappa values, significant improvement was observed in inter-observer agreement in higher scores of Gleason grade; Score 10 was achieved for the mean kappa value in post web-education was 0.68 [substantial agreement] compared to 0.25 (fair agreement in pre web-education. Web-based training courses are attractive to pathologists as they do not need to spend much time and money. Therefore, such training courses are strongly recommended for significant pathological issues including the grading of the prostate adenocarcinoma. Through web-based education, pathologists can exchange views and contribute to the rise in the level of reproducibility. Such programs need to be included in post-graduation programs.

  13. TU-AB-BRC-05: Creation of a Monte Carlo TrueBeam Model by Reproducing Varian Phase Space Data

    International Nuclear Information System (INIS)

    O’Grady, K; Davis, S; Seuntjens, J

    2016-01-01

    Purpose: To create a Varian TrueBeam 6 MV FFF Monte Carlo model using BEAMnrc/EGSnrc that accurately reproduces the Varian representative dataset, followed by tuning the model’s source parameters to accurately reproduce in-house measurements. Methods: A BEAMnrc TrueBeam model for 6 MV FFF has been created by modifying a validated 6 MV Varian CL21EX model. Geometric dimensions and materials were adjusted in a trial and error approach to match the fluence and spectra of TrueBeam phase spaces output by the Varian VirtuaLinac. Once the model’s phase space matched Varian’s counterpart using the default source parameters, it was validated to match 10 × 10 cm"2 Varian representative data obtained with the IBA CC13. The source parameters were then tuned to match in-house 5 × 5 cm"2 PTW microDiamond measurements. All dose to water simulations included detector models to include the effects of volume averaging and the non-water equivalence of the chamber materials, allowing for more accurate source parameter selection. Results: The Varian phase space spectra and fluence were matched with excellent agreement. The in-house model’s PDD agreement with CC13 TrueBeam representative data was within 0.9% local percent difference beyond the first 3 mm. Profile agreement at 10 cm depth was within 0.9% local percent difference and 1.3 mm distance-to-agreement in the central axis and penumbra regions, respectively. Once the source parameters were tuned, PDD agreement with microDiamond measurements was within 0.9% local percent difference beyond 2 mm. The microDiamond profile agreement at 10 cm depth was within 0.6% local percent difference and 0.4 mm distance-to-agreement in the central axis and penumbra regions, respectively. Conclusion: An accurate in-house Monte Carlo model of the Varian TrueBeam was achieved independently of the Varian phase space solution and was tuned to in-house measurements. KO acknowledges partial support by the CREATE Medical Physics Research

  14. Modeling hurricane evacuation traffic : testing the gravity and intervening opportunity models as models of destination choice in hurricane evacuation.

    Science.gov (United States)

    2006-09-01

    The test was conducted by estimating the models on a portion of evacuation data from South Carolina following Hurricane Floyd, and then observing how well the models reproduced destination choice at the county level on the remaining data. The tests s...

  15. A Reliable and Reproducible Model for Assessing the Effect of Different Concentrations of α-Solanine on Rat Bone Marrow Mesenchymal Stem Cells

    Directory of Open Access Journals (Sweden)

    Adriana Ordóñez-Vásquez

    2017-01-01

    Full Text Available Αlpha-solanine (α-solanine is a glycoalkaloid present in potato (Solanum tuberosum. It has been of particular interest because of its toxicity and potential teratogenic effects that include abnormalities of the central nervous system, such as exencephaly, encephalocele, and anophthalmia. Various types of cell culture have been used as experimental models to determine the effect of α-solanine on cell physiology. The morphological changes in the mesenchymal stem cell upon exposure to α-solanine have not been established. This study aimed to describe a reliable and reproducible model for assessing the structural changes induced by exposure of mouse bone marrow mesenchymal stem cells (MSCs to different concentrations of α-solanine for 24 h. The results demonstrate that nonlethal concentrations of α-solanine (2–6 μM changed the morphology of the cells, including an increase in the number of nucleoli, suggesting elevated protein synthesis, and the formation of spicules. In addition, treatment with α-solanine reduced the number of adherent cells and the formation of colonies in culture. Immunophenotypic characterization and staining of MSCs are proposed as a reproducible method that allows description of cells exposed to the glycoalkaloid, α-solanine.

  16. Reproducibility of image quality for moving objects using respiratory-gated computed tomography. A study using a phantom model

    International Nuclear Information System (INIS)

    Fukumitsu, Nobuyoshi; Ishida, Masaya; Terunuma, Toshiyuki

    2012-01-01

    To investigate the reproducibility of computed tomography (CT) imaging quality in respiratory-gated radiation treatment planning is essential in radiotherapy of movable tumors. Seven series of regular and six series of irregular respiratory motions were performed using a thorax dynamic phantom. For the regular respiratory motions, the respiratory cycle was changed from 2.5 to 4 s and the amplitude was changed from 4 to 10 mm. For the irregular respiratory motions, a cycle of 2.5 to 4 or an amplitude of 4 to 10 mm was added to the base data (id est (i.e.) 3.5-s cycle, 6-mm amplitude) every three cycles. Images of the object were acquired six times using respiratory-gated data acquisition. The volume of the object was calculated and the reproducibility of the volume was decided based on the variety. The registered image of the object was added and the reproducibility of the shape was decided based on the degree of overlap of objects. The variety in the volumes and shapes differed significantly as the respiratory cycle changed according to regular respiratory motions. In irregular respiratory motion, shape reproducibility was further inferior, and the percentage of overlap among the six images was 35.26% in the 2.5- and 3.5-s cycle mixed group. Amplitude changes did not produce significant differences in the variety of the volumes and shapes. Respiratory cycle changes reduced the reproducibility of the image quality in respiratory-gated CT. (author)

  17. Reproducibility of current perception threshold with the Neurometer(®) vs the Stimpod NMS450 peripheral nerve stimulator in healthy volunteers: an observational study.

    Science.gov (United States)

    Tsui, Ban C H; Shakespeare, Timothy J; Leung, Danika H; Tsui, Jeremy H; Corry, Gareth N

    2013-08-01

    Current methods of assessing nerve blocks, such as loss of perception to cold sensation, are subjective at best. Transcutaneous nerve stimulation is an alternative method that has previously been used to measure the current perception threshold (CPT) in individuals with neuropathic conditions, and various devices to measure CPT are commercially available. Nevertheless, the device must provide reproducible results to be used as an objective tool for assessing nerve blocks. We recruited ten healthy volunteers to examine CPT reproducibility using the Neurometer(®) and the Stimpod NMS450 peripheral nerve stimulator. Each subject's CPT was determined for the median (second digit) and ulnar (fifth digit) nerve sensory distributions on both hands - with the Neurometer at 5 Hz, 250 Hz, and 2000 Hz and with the Stimpod at pulse widths of 0.1 msec, 0.3 msec, 0.5 msec, and 1.0 msec, both at 5 Hz and 2 Hz. Intraclass correlation coefficients (ICC) were also calculated to assess reproducibility; acceptable ICCs were defined as ≥ 0.4. The ICC values for the Stimpod ranged from 0.425-0.79, depending on pulse width, digit, and stimulation; ICCs for the Neurometer were 0.615 and 0.735 at 250 and 2,000 Hz, respectively. These values were considered acceptable; however, the Neurometer performed less efficiently at 5 Hz (ICCs for the second and fifth digits were 0.292 and 0.318, respectively). Overall, the Stimpod device displayed good to excellent reproducibility in measuring CPT in healthy volunteers. The Neurometer displayed poor reproducibility at low frequency (5 Hz). These results suggest that peripheral nerve stimulators may be potential devices for measuring CPT to assess nerve blocks.

  18. 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.

  19. 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.

  20. Modeled and observed ozone sensitivity to mobile-source emissions in Mexico City

    Directory of Open Access Journals (Sweden)

    M. Zavala

    2009-01-01

    Full Text Available The emission characteristics of mobile sources in the Mexico City Metropolitan Area (MCMA have changed significantly over the past few decades in response to emission control policies, advancements in vehicle technologies and improvements in fuel quality, among others. Along with these changes, concurrent non-linear changes in photochemical levels and criteria pollutants have been observed, providing a unique opportunity to understand the effects of perturbations of mobile emission levels on the photochemistry in the region using observational and modeling approaches. The observed historical trends of ozone (O3, carbon monoxide (CO and nitrogen oxides (NOx suggest that ozone production in the MCMA has changed from a low to a high VOC-sensitive regime over a period of 20 years. Comparison of the historical emission trends of CO, NOx and hydrocarbons derived from mobile-source emission studies in the MCMA from 1991 to 2006 with the trends of the concentrations of CO, NOx, and the CO/NOx ratio during peak traffic hours also indicates that fuel-based fleet average emission factors have significantly decreased for CO and VOCs during this period whereas NOx emission factors do not show any strong trend, effectively reducing the ambient VOC/NOx ratio.

    This study presents the results of model analyses on the sensitivity of the observed ozone levels to the estimated historical changes in its precursors. The model sensitivity analyses used a well-validated base case simulation of a high pollution episode in the MCMA with the mathematical Decoupled Direct Method (DDM and the standard Brute Force Method (BFM in the 3-D CAMx chemical transport model. The model reproduces adequately the observed historical trends and current photochemical levels. Comparison of the BFM and the DDM sensitivity techniques indicates that the model yields ozone values that increase linearly with

  1. 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

  2. Eccentric Contraction-Induced Muscle Injury: Reproducible, Quantitative, Physiological Models to Impair Skeletal Muscle's Capacity to Generate Force.

    Science.gov (United States)

    Call, Jarrod A; Lowe, Dawn A

    2016-01-01

    In order to investigate the molecular and cellular mechanisms of muscle regeneration an experimental injury model is required. Advantages of eccentric contraction-induced injury are that it is a controllable, reproducible, and physiologically relevant model to cause muscle injury, with injury being defined as a loss of force generating capacity. While eccentric contractions can be incorporated into conscious animal study designs such as downhill treadmill running, electrophysiological approaches to elicit eccentric contractions and examine muscle contractility, for example before and after the injurious eccentric contractions, allows researchers to circumvent common issues in determining muscle function in a conscious animal (e.g., unwillingness to participate). Herein, we describe in vitro and in vivo methods that are reliable, repeatable, and truly maximal because the muscle contractions are evoked in a controlled, quantifiable manner independent of subject motivation. Both methods can be used to initiate eccentric contraction-induced injury and are suitable for monitoring functional muscle regeneration hours to days to weeks post-injury.

  3. Identification and reproducibility of dietary patterns in a Danish cohort: the Inter99 study.

    Science.gov (United States)

    Lau, Cathrine; Glümer, Charlotte; Toft, Ulla; Tetens, Inge; Carstensen, Bendix; Jørgensen, Torben; Borch-Johnsen, Knut

    2008-05-01

    We aimed to identify dietary patterns in a Danish adult population and assess the reproducibility of the dietary patterns identified. Baseline data of 3,372 women and 3,191 men (30-60 years old) from the population-based survey Inter99 was used. Food intake, assessed by a FFQ, was aggregated into thirty-four separate food groups. Dietary patterns were identified by principal component analysis. Confirmatory factor analysis and Bland Altman plots were used to assess the reproducibility of the dietary patterns identified. The Bland Altman plots were used as an alternative and new method. Two factors were retained for both women and men, which accounted for 15.1-17.4 % of the total variation. The 'Traditional' pattern was characterised by high loadings ( > or = 0.40) on paté or high-fat meat for sandwiches, mayonnaise salads, red meat, potatoes, butter and lard, low-fat fish, low-fat meat for sandwiches, and sauces. The 'Modern' pattern was characterised by high loadings on vegetables, fruit, mixed vegetable dishes, vegetable oil and vinegar dressing, poultry, and pasta, rice and wheat kernels. Small differences were observed between patterns identified for women and men. The root mean square error approximation from the confirmatory factor analysis was 0.08. The variation observed from the Bland Altman plots of factors from explorative v. confirmative analyses and explorative analyses from two sub-samples was between 18.8 and 47.7 %. Pearson's correlation was >0.89 (P < 0.0001). The reproducibility was better for women than for men. We conclude that the 'Traditional' and 'Modern' dietary patterns identified were reproducible.

  4. Wind Turbine Model and Observer in Takagi-Sugeno Model Structure

    International Nuclear Information System (INIS)

    Georg, Sören; Müller, Matthias; Schulte, Horst

    2014-01-01

    Based on a reduced-order, dynamic nonlinear wind turbine model in Takagi- Sugeno (TS) model structure, a TS state observer is designed as a disturbance observer to estimate the unknown effective wind speed. The TS observer model is an exact representation of the underlying nonlinear model, obtained by means of the sector-nonlinearity approach. The observer gain matrices are obtained by means of a linear matrix inequality (LMI) design approach for optimal fuzzy control, where weighting matrices for the individual system states and outputs are included. The observer is tested in simulations with the aero-elastic code FAST for the NREL 5 MW reference turbine, where it shows a stable behaviour in turbulent wind simulations

  5. Reproducibility of ultrasonic testing

    International Nuclear Information System (INIS)

    Lecomte, J.-C.; Thomas, Andre; Launay, J.-P.; Martin, Pierre

    The reproducibility of amplitude quotations for both artificial and natural reflectors was studied for several combinations of instrument/search unit, all being of the same type. This study shows that in industrial inspection if a range of standardized equipment is used, a margin of error of about 6 decibels has to be taken into account (confidence interval of 95%). This margin is about 4 to 5 dB for natural or artificial defects located in the central area and about 6 to 7 dB for artificial defects located on the back surface. This lack of reproducibility seems to be attributable first to the search unit and then to the instrument and operator. These results were confirmed by analysis of calibration data obtained from 250 tests performed by 25 operators under shop conditions. The margin of error was higher than the 6 dB obtained in the study [fr

  6. Reproducibility of P-31 spectroscopic imaging of normal human myocardium

    International Nuclear Information System (INIS)

    Tavares, N.J.; Chew, W.; Auffermann, W.; Higgins, C.B.

    1988-01-01

    To assess reproducibility of P-31 MR spectroscopy of human myocardium, ten normal male volunteers were studied on two separate occasions. Spectra were acquired on a clinical 1.5-T MR imaging unit (Signa, General Electric) using a one-dimensional gated spectroscopic imaging sequence (matrix size, 32 X 256) over 20 minutes. Peaks in the adenosine triphosphate (ATP) region, phosphocreatine (PCR), phosphodiesters (PD), and peaks attributable to 2,3 diphosphoglycerate from blood were observed. Interindividual and intraindividual variability expressed as standard errors of the mean (mean +- SEM) were 1.54 +- 0.04 (variability among subjects) and 0.04 (variability between first and second studies) for PCR/β ATP; 0.97 +- 0.18 and 0.06 for PD/β ATP; and 0.62 +- 0.10 and 0.05 for PD/PCR, respectively. In conclusion, P-31 MR spectroscopy yields consistent and reproducible myocardial spectra that might be useful in the future for the evaluation and monitoring of cardiac disease

  7. Collective Activity of Many Bistable Assemblies Reproduces Characteristic Dynamics of Multistable Perception.

    Science.gov (United States)

    Cao, Robin; Pastukhov, Alexander; Mattia, Maurizio; Braun, Jochen

    2016-06-29

    The timing of perceptual decisions depends on both deterministic and stochastic factors, as the gradual accumulation of sensory evidence (deterministic) is contaminated by sensory and/or internal noise (stochastic). When human observers view multistable visual displays, successive episodes of stochastic accumulation culminate in repeated reversals of visual appearance. Treating reversal timing as a "first-passage time" problem, we ask how the observed timing densities constrain the underlying stochastic accumulation. Importantly, mean reversal times (i.e., deterministic factors) differ enormously between displays/observers/stimulation levels, whereas the variance and skewness of reversal times (i.e., stochastic factors) keep characteristic proportions of the mean. What sort of stochastic process could reproduce this highly consistent "scaling property?" Here we show that the collective activity of a finite population of bistable units (i.e., a generalized Ehrenfest process) quantitatively reproduces all aspects of the scaling property of multistable phenomena, in contrast to other processes under consideration (Poisson, Wiener, or Ornstein-Uhlenbeck process). The postulated units express the spontaneous dynamics of attractor assemblies transitioning between distinct activity states. Plausible candidates are cortical columns, or clusters of columns, as they are preferentially connected and spontaneously explore a restricted repertoire of activity states. Our findings suggests that perceptual representations are granular, probabilistic, and operate far from equilibrium, thereby offering a suitable substrate for statistical inference. Spontaneous reversals of high-level perception, so-called multistable perception, conform to highly consistent and characteristic statistics, constraining plausible neural representations. We show that the observed perceptual dynamics would be reproduced quantitatively by a finite population of distinct neural assemblies, each with

  8. Preserve specimens for reproducibility

    Czech Academy of Sciences Publication Activity Database

    Krell, F.-T.; Klimeš, Petr; Rocha, L. A.; Fikáček, M.; Miller, S. E.

    2016-01-01

    Roč. 539, č. 7628 (2016), s. 168 ISSN 0028-0836 Institutional support: RVO:60077344 Keywords : reproducibility * specimen * biodiversity Subject RIV: EH - Ecology, Behaviour Impact factor: 40.137, year: 2016 http://www.nature.com/nature/journal/v539/n7628/full/539168b.html

  9. Extreme temperature events on Greenland in observations and the MAR regional climate model

    Science.gov (United States)

    Leeson, Amber A.; Eastoe, Emma; Fettweis, Xavier

    2018-03-01

    Meltwater from the Greenland Ice Sheet contributed 1.7-6.12 mm to global sea level between 1993 and 2010 and is expected to contribute 20-110 mm to future sea level rise by 2100. These estimates were produced by regional climate models (RCMs) which are known to be robust at the ice sheet scale but occasionally miss regional- and local-scale climate variability (e.g. Leeson et al., 2017; Medley et al., 2013). To date, the fidelity of these models in the context of short-period variability in time (i.e. intra-seasonal) has not been fully assessed, for example their ability to simulate extreme temperature events. We use an event identification algorithm commonly used in extreme value analysis, together with observations from the Greenland Climate Network (GC-Net), to assess the ability of the MAR (Modèle Atmosphérique Régional) RCM to reproduce observed extreme positive-temperature events at 14 sites around Greenland. We find that MAR is able to accurately simulate the frequency and duration of these events but underestimates their magnitude by more than half a degree Celsius/kelvin, although this bias is much smaller than that exhibited by coarse-scale Era-Interim reanalysis data. As a result, melt energy in MAR output is underestimated by between 16 and 41 % depending on global forcing applied. Further work is needed to precisely determine the drivers of extreme temperature events, and why the model underperforms in this area, but our findings suggest that biases are passed into MAR from boundary forcing data. This is important because these forcings are common between RCMs and their range of predictions of past and future ice sheet melting. We propose that examining extreme events should become a routine part of global and regional climate model evaluation and that addressing shortcomings in this area should be a priority for model development.

  10. Observation- and model-based estimates of particulate dry nitrogen deposition to the oceans

    Directory of Open Access Journals (Sweden)

    A. R. Baker

    2017-07-01

    expected to be more robust than TM4, while TM4 gives access to speciated parameters (NO3− and NH4+ that are more relevant to the observed parameters and which are not available in ACCMIP. Dry deposition fluxes (CalDep were calculated from the observed concentrations using estimates of dry deposition velocities. Model–observation ratios (RA, n, weighted by grid-cell area and number of observations, were used to assess the performance of the models. Comparison in the three study regions suggests that TM4 overestimates NO3− concentrations (RA, n =  1.4–2.9 and underestimates NH4+ concentrations (RA, n =  0.5–0.7, with spatial distributions in the tropical Atlantic and northern Indian Ocean not being reproduced by the model. In the case of NH4+ in the Indian Ocean, this discrepancy was probably due to seasonal biases in the sampling. Similar patterns were observed in the various comparisons of CalDep to ModDep (RA, n =  0.6–2.6 for NO3−, 0.6–3.1 for NH4+. Values of RA, n for NHx CalDep–ModDep comparisons were approximately double the corresponding values for NH4+ CalDep–ModDep comparisons due to the significant fraction of gas-phase NH3 deposition incorporated in the TM4 and ACCMIP NHx model products. All of the comparisons suffered due to the scarcity of observational data and the large uncertainty in dry deposition velocities used to derive deposition fluxes from concentrations. These uncertainties have been a major limitation on estimates of the flux of material to the oceans for several decades. Recommendations are made for improvements in N deposition estimation through changes in observations, modelling and model–observation comparison procedures. Validation of modelled dry deposition requires effective comparisons to observable aerosol-phase species' concentrations, and this cannot be achieved if model products only report dry deposition flux over the ocean.

  11. Reproducibility of 201Tl myocardial imaging

    International Nuclear Information System (INIS)

    McLaughlin, P.R.; Martin, R.P.; Doherty, P.; Daspit, S.; Goris, M.; Haskell, W.; Lewis, S.; Kriss, J.P.; Harrison, D.C.

    1977-01-01

    Seventy-six thallium-201 myocardial perfusion studies were performed on twenty-five patients to assess their reproducibility and the effect of varying the level of exercise on the results of imaging. Each patient had a thallium-201 study at rest. Fourteen patients had studies on two occasions at maximum exercise, and twelve patients had studies both at light and at maximum exercise. Of 70 segments in the 14 patients assessed on each of two maximum exercise tests, 64 (91 percent) were reproducible. Only 53 percent (16/30) of the ischemic defects present at maximum exercise were seen in the light exercise study in the 12 patients assessed at two levels of exercise. Correlation of perfusion defects with arteriographically proven significant coronary stenosis was good for the left anterior descending and right coronary arteries, but not as good for circumflex artery disease. Thallium-201 myocardial imaging at maximum exercise is reproducible within acceptable limits, but careful attention to exercise technique is essential for valid comparative studies

  12. Undefined cellulase formulations hinder scientific reproducibility.

    Science.gov (United States)

    Himmel, Michael E; Abbas, Charles A; Baker, John O; Bayer, Edward A; Bomble, Yannick J; Brunecky, Roman; Chen, Xiaowen; Felby, Claus; Jeoh, Tina; Kumar, Rajeev; McCleary, Barry V; Pletschke, Brett I; Tucker, Melvin P; Wyman, Charles E; Decker, Stephen R

    2017-01-01

    In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparations may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations.

  13. A Comparison between Physics-based and Polytropic MHD Models for Stellar Coronae and Stellar Winds of Solar Analogs

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, O. [Lowell Center for Space Science and Technology, University of Massachusetts, Lowell, MA 01854 (United States)

    2017-02-01

    The development of the Zeeman–Doppler Imaging (ZDI) technique has provided synoptic observations of surface magnetic fields of low-mass stars. This led the stellar astrophysics community to adopt modeling techniques that have been used in solar physics using solar magnetograms. However, many of these techniques have been neglected by the solar community due to their failure to reproduce solar observations. Nevertheless, some of these techniques are still used to simulate the coronae and winds of solar analogs. Here we present a comparative study between two MHD models for the solar corona and solar wind. The first type of model is a polytropic wind model, and the second is the physics-based AWSOM model. We show that while the AWSOM model consistently reproduces many solar observations, the polytropic model fails to reproduce many of them, and in the cases where it does, its solutions are unphysical. Our recommendation is that polytropic models, which are used to estimate mass-loss rates and other parameters of solar analogs, must first be calibrated with solar observations. Alternatively, these models can be calibrated with models that capture more detailed physics of the solar corona (such as the AWSOM model) and that can reproduce solar observations in a consistent manner. Without such a calibration, the results of the polytropic models cannot be validated, but they can be wrongly used by others.

  14. Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease.

    Science.gov (United States)

    Azuaje, Francisco; Zheng, Huiru; Camargo, Anyela; Wang, Haiying

    2011-08-01

    The discovery of novel disease biomarkers is a crucial challenge for translational bioinformatics. Demonstration of both their classification power and reproducibility across independent datasets are essential requirements to assess their potential clinical relevance. Small datasets and multiplicity of putative biomarker sets may explain lack of predictive reproducibility. Studies based on pathway-driven discovery approaches have suggested that, despite such discrepancies, the resulting putative biomarkers tend to be implicated in common biological processes. Investigations of this problem have been mainly focused on datasets derived from cancer research. We investigated the predictive and functional concordance of five methods for discovering putative biomarkers in four independently-generated datasets from the cardiovascular disease domain. A diversity of biosignatures was identified by the different methods. However, we found strong biological process concordance between them, especially in the case of methods based on gene set analysis. With a few exceptions, we observed lack of classification reproducibility using independent datasets. Partial overlaps between our putative sets of biomarkers and the primary studies exist. Despite the observed limitations, pathway-driven or gene set analysis can predict potentially novel biomarkers and can jointly point to biomedically-relevant underlying molecular mechanisms. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Gamma-Ray Emission in Dissipative Pulsar Magnetospheres: from Theory to Fermi Observations

    Science.gov (United States)

    Kalapotharakos, Konstantinos; Harding, Alice K.; Kazanas, Demosthenes

    2014-01-01

    We compute the patterns of gamma-ray emission due to curvature radiation in dissipative pulsar magnetospheres. Our ultimate goal is to construct macrophysical models that are able to reproduce the observed gamma-ray light curve phenomenology recently published in the Second Fermi Pulsar Catalog. We apply specific forms of Ohm's law on the open field lines using a broad range for the macroscopic conductivity values that result in solutions ranging, from near-vacuum to near-force-free. Using these solutions, we generate model gamma-ray light curves by calculating realistic trajectories and Lorentz factors of radiating particles under the influence of both the accelerating electric fields and curvature radiation reaction. We further constrain our models using the observed dependence of the phase lags between the radio and gamma-ray emission on the gamma-ray peak separation. We perform a statistical comparison of our model radio-lag versus peak-separation diagram and the one obtained for the Fermi standard pulsars. We find that for models of uniform conductivity over the entire open magnetic field line region, agreement with observations favors higher values of this parameter. We find, however, significant improvement in fitting the data with models that employ a hybrid form of conductivity, specifically, infinite conductivity interior to the light cylinder and high but finite conductivity on the outside. In these models the gamma-ray emission is produced in regions near the equatorial current sheet but modulated by the local physical properties. These models have radio lags near the observed values and statistically best reproduce the observed light curve phenomenology. Additionally, they also produce GeV photon cut-off energies.

  16. 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

  17. Impacts of bromine and iodine chemistry on tropospheric OH and HO2: comparing observations with box and global model perspectives

    Science.gov (United States)

    Stone, Daniel; Sherwen, Tomás; Evans, Mathew J.; Vaughan, Stewart; Ingham, Trevor; Whalley, Lisa K.; Edwards, Peter M.; Read, Katie A.; Lee, James D.; Moller, Sarah J.; Carpenter, Lucy J.; Lewis, Alastair C.; Heard, Dwayne E.

    2018-03-01

    The chemistry of the halogen species bromine and iodine has a range of impacts on tropospheric composition, and can affect oxidising capacity in a number of ways. However, recent studies disagree on the overall sign of the impacts of halogens on the oxidising capacity of the troposphere. We present simulations of OH and HO2 radicals for comparison with observations made in the remote tropical ocean boundary layer during the Seasonal Oxidant Study at the Cape Verde Atmospheric Observatory in 2009. We use both a constrained box model, using detailed chemistry derived from the Master Chemical Mechanism (v3.2), and the three-dimensional global chemistry transport model GEOS-Chem. Both model approaches reproduce the diurnal trends in OH and HO2. Absolute observed concentrations are well reproduced by the box model but are overpredicted by the global model, potentially owing to incomplete consideration of oceanic sourced radical sinks. The two models, however, differ in the impacts of halogen chemistry. In the box model, halogen chemistry acts to increase OH concentrations (by 9.8 % at midday at the Cape Verde Atmospheric Observatory), while the global model exhibits a small increase in OH at the Cape Verde Atmospheric Observatory (by 0.6 % at midday) but overall shows a decrease in the global annual mass-weighted mean OH of 4.5 %. These differences reflect the variety of timescales through which the halogens impact the chemical system. On short timescales, photolysis of HOBr and HOI, produced by reactions of HO2 with BrO and IO, respectively, increases the OH concentration. On longer timescales, halogen-catalysed ozone destruction cycles lead to lower primary production of OH radicals through ozone photolysis, and thus to lower OH concentrations. The global model includes more of the longer timescale responses than the constrained box model, and overall the global impact of the longer timescale response (reduced primary production due to lower O3 concentrations

  18. Introduction to interacting boson model

    International Nuclear Information System (INIS)

    Goutte, D.

    1986-01-01

    A very simple presentation of the interacting boson model is first given. The two computerized models which are presented allow, with few parameters, to reproduce an impressive quantity of data characterizing the deformed nuclei. Their excitation spectra, the reduced transition probabilities, the quadrupolar moments, the two nucleon transfer experiment results, ... Then a specific application of the model is given: radial extension reproduction of nuclear functions. It is shown first how the electron inelastic scattering allows to measure observables related to these radial functions, the transition charge densities, then, on some examples, how the model allows to reproduce them [fr

  19. Ionospheric detection of tsunami earthquakes: observation, modeling and ideas for future early warning

    Science.gov (United States)

    Occhipinti, G.; Manta, F.; Rolland, L.; Watada, S.; Makela, J. J.; Hill, E.; Astafieva, E.; Lognonne, P. H.

    2017-12-01

    Detection of ionospheric anomalies following the Sumatra and Tohoku earthquakes (e.g., Occhipinti 2015) demonstrated that ionosphere is sensitive to earthquake and tsunami propagation: ground and oceanic vertical displacement induces acoustic-gravity waves propagating within the neutral atmosphere and detectable in the ionosphere. Observations supported by modelling proved that ionospheric anomalies related to tsunamis are deterministic and reproducible by numerical modeling via the ocean/neutral-atmosphere/ionosphere coupling mechanism (Occhipinti et al., 2008). To prove that the tsunami signature in the ionosphere is routinely detected we show here perturbations of total electron content (TEC) measured by GPS and following tsunamigenic earthquakes from 2004 to 2011 (Rolland et al. 2010, Occhipinti et al., 2013), nominally, Sumatra (26 December, 2004 and 12 September, 2007), Chile (14 November, 2007), Samoa (29 September, 2009) and the recent Tohoku-Oki (11 Mars, 2011). Based on the observations close to the epicenter, mainly performed by GPS networks located in Sumatra, Chile and Japan, we highlight the TEC perturbation observed within the first 8 min after the seismic rupture. This perturbation contains information about the ground displacement, as well as the consequent sea surface displacement resulting in the tsunami. In addition to GNSS-TEC observations close to the epicenter, new exciting measurements in the far-field were performed by airglow measurement in Hawaii show the propagation of the internal gravity waves induced by the Tohoku tsunami (Occhipinti et al., 2011). This revolutionary imaging technique is today supported by two new observations of moderate tsunamis: Queen Charlotte (M: 7.7, 27 October, 2013) and Chile (M: 8.2, 16 September 2015). We finally detail here our recent work (Manta et al., 2017) on the case of tsunami alert failure following the Mw7.8 Mentawai event (25 October, 2010), and its twin tsunami alert response following the Mw7

  20. 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

  1. 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 ......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....

  2. Reproducible segmentation of white matter hyperintensities using a new statistical definition.

    Science.gov (United States)

    Damangir, Soheil; Westman, Eric; Simmons, Andrew; Vrenken, Hugo; Wahlund, Lars-Olof; Spulber, Gabriela

    2017-06-01

    We present a method based on a proposed statistical definition of white matter hyperintensities (WMH), which can work with any combination of conventional magnetic resonance (MR) sequences without depending on manually delineated samples. T1-weighted, T2-weighted, FLAIR, and PD sequences acquired at 1.5 Tesla from 119 subjects from the Kings Health Partners-Dementia Case Register (healthy controls, mild cognitive impairment, Alzheimer's disease) were used. The segmentation was performed using a proposed definition for WMH based on the one-tailed Kolmogorov-Smirnov test. The presented method was verified, given all possible combinations of input sequences, against manual segmentations and a high similarity (Dice 0.85-0.91) was observed. Comparing segmentations with different input sequences to one another also yielded a high similarity (Dice 0.83-0.94) that exceeded intra-rater similarity (Dice 0.75-0.91). We compared the results with those of other available methods and showed that the segmentation based on the proposed definition has better accuracy and reproducibility in the test dataset used. Overall, the presented definition is shown to produce accurate results with higher reproducibility than manual delineation. This approach can be an alternative to other manual or automatic methods not only because of its accuracy, but also due to its good reproducibility.

  3. Participant Nonnaiveté and the reproducibility of cognitive psychology.

    Science.gov (United States)

    Zwaan, Rolf A; Pecher, Diane; Paolacci, Gabriele; Bouwmeester, Samantha; Verkoeijen, Peter; Dijkstra, Katinka; Zeelenberg, René

    2017-07-25

    Many argue that there is a reproducibility crisis in psychology. We investigated nine well-known effects from the cognitive psychology literature-three each from the domains of perception/action, memory, and language, respectively-and found that they are highly reproducible. Not only can they be reproduced in online environments, but they also can be reproduced with nonnaïve participants with no reduction of effect size. Apparently, some cognitive tasks are so constraining that they encapsulate behavior from external influences, such as testing situation and prior recent experience with the experiment to yield highly robust effects.

  4. Impact of deep convection in the tropical tropopause layer in West Africa: in-situ observations and mesoscale modelling

    Directory of Open Access Journals (Sweden)

    F. Fierli

    2011-01-01

    Full Text Available We present the analysis of the impact of convection on the composition of the tropical tropopause layer region (TTL in West-Africa during the AMMA-SCOUT campaign. Geophysica M55 aircraft observations of water vapor, ozone, aerosol and CO2 during August 2006 show perturbed values at altitudes ranging from 14 km to 17 km (above the main convective outflow and satellite data indicates that air detrainment is likely to have originated from convective cloud east of the flights. Simulations of the BOLAM mesoscale model, nudged with infrared radiance temperatures, are used to estimate the convective impact in the upper troposphere and to assess the fraction of air processed by convection. The analysis shows that BOLAM correctly reproduces the location and the vertical structure of convective outflow. Model-aided analysis indicates that convection can influence the composition of the upper troposphere above the level of main outflow for an event of deep convection close to the observation site. Model analysis also shows that deep convection occurring in the entire Sahelian transect (up to 2000 km E of the measurement area has a non negligible role in determining TTL composition.

  5. Ultrasound characteristics of gouty tophi in the olecranon bursa and evaluation of their reproducibility

    International Nuclear Information System (INIS)

    Fernandes, Eloy A.; Lopes, Matheus G.; Mitraud, Sônia A.V.; Ferrari, Antonio J.L.; Fernandes, Artur R.C.

    2012-01-01

    Objectives: To describe the ultrasound characteristics of gouty tophi in the olecranon bursa and to evaluate their reproducibility. Methods: A prospective study of the ultrasound features of 35 sites of tophi nodulations in the elbows of 31 men (mean 54.6 years). The findings were evaluated dynamically following pre-established standards. The static images were evaluated by another radiologist and were reviewed by the first examiner. Results: The most frequent characteristics of tophi are: hyperechogenicity (91.7%), poorly defined contours (88.6%), multiple grouped nodules (85.6%) and heterogeneity (68.6%). Intra-observer agreement is almost perfect for echogenicity (K = 1.0), moderate for the involvement of the olecranon bursa (K = 0.47) and fair for other characteristics. Inter-observer agreement is substantial for the echogenicity (K = 0.65), fair for the echotexture (K = 0.27) and the presence of a perilesional hypoechoic halo (K = 0.34) and slight for other characteristics. Conclusions: The most frequent characteristic of tophi is hyperechogenicity. The intra-observer and inter-observer concordance for echogenicity are almost perfect and substantial, respectively. Knowledge of characteristics of the tophi in the elbow and their intra and inter-observer reproducibility may assist in establishing parameters for monitoring treatment and setting up criteria for differential diagnosis of processes involving the olecraneon bursa.

  6. Systematic heterogenization for better reproducibility in animal experimentation.

    Science.gov (United States)

    Richter, S Helene

    2017-08-31

    The scientific literature is full of articles discussing poor reproducibility of findings from animal experiments as well as failures to translate results from preclinical animal studies to clinical trials in humans. Critics even go so far as to talk about a "reproducibility crisis" in the life sciences, a novel headword that increasingly finds its way into numerous high-impact journals. Viewed from a cynical perspective, Fett's law of the lab "Never replicate a successful experiment" has thus taken on a completely new meaning. So far, poor reproducibility and translational failures in animal experimentation have mostly been attributed to biased animal data, methodological pitfalls, current publication ethics and animal welfare constraints. More recently, the concept of standardization has also been identified as a potential source of these problems. By reducing within-experiment variation, rigorous standardization regimes limit the inference to the specific experimental conditions. In this way, however, individual phenotypic plasticity is largely neglected, resulting in statistically significant but possibly irrelevant findings that are not reproducible under slightly different conditions. By contrast, systematic heterogenization has been proposed as a concept to improve representativeness of study populations, contributing to improved external validity and hence improved reproducibility. While some first heterogenization studies are indeed very promising, it is still not clear how this approach can be transferred into practice in a logistically feasible and effective way. Thus, further research is needed to explore different heterogenization strategies as well as alternative routes toward better reproducibility in animal experimentation.

  7. Runoff-generated debris flows: observations and modeling of surge initiation, magnitude, and frequency

    Science.gov (United States)

    Kean, Jason W.; McCoy, Scott W.; Tucker, Gregory E.; Staley, Dennis M.; Coe, Jeffrey A.

    2013-01-01

    Runoff during intense rainstorms plays a major role in generating debris flows in many alpine areas and burned steeplands. Yet compared to debris flow initiation from shallow landslides, the mechanics by which runoff generates a debris flow are less understood. To better understand debris flow initiation by surface water runoff, we monitored flow stage and rainfall associated with debris flows in the headwaters of two small catchments: a bedrock-dominated alpine basin in central Colorado (0.06 km2) and a recently burned area in southern California (0.01 km2). We also obtained video footage of debris flow initiation and flow dynamics from three cameras at the Colorado site. Stage observations at both sites display distinct patterns in debris flow surge characteristics relative to rainfall intensity (I). We observe small, quasiperiodic surges at low I; large, quasiperiodic surges at intermediate I; and a single large surge followed by small-amplitude fluctuations about a more steady high flow at high I. Video observations of surge formation lead us to the hypothesis that these flow patterns are controlled by upstream variations in channel slope, in which low-gradient sections act as “sediment capacitors,” temporarily storing incoming bed load transported by water flow and periodically releasing the accumulated sediment as a debris flow surge. To explore this hypothesis, we develop a simple one-dimensional morphodynamic model of a sediment capacitor that consists of a system of coupled equations for water flow, bed load transport, slope stability, and mass flow. This model reproduces the essential patterns in surge magnitude and frequency with rainfall intensity observed at the two field sites and provides a new framework for predicting the runoff threshold for debris flow initiation in a burned or alpine setting.

  8. The use of real-time cell analyzer technology in drug discovery: defining optimal cell culture conditions and assay reproducibility with different adherent cellular models.

    Science.gov (United States)

    Atienzar, Franck A; Tilmant, Karen; Gerets, Helga H; Toussaint, Gaelle; Speeckaert, Sebastien; Hanon, Etienne; Depelchin, Olympe; Dhalluin, Stephane

    2011-07-01

    The use of impedance-based label-free technology applied to drug discovery is nowadays receiving more and more attention. Indeed, such a simple and noninvasive assay that interferes minimally with cell morphology and function allows one to perform kinetic measurements and to obtain information on proliferation, migration, cytotoxicity, and receptor-mediated signaling. The objective of the study was to further assess the usefulness of a real-time cell analyzer (RTCA) platform based on impedance in the context of quality control and data reproducibility. The data indicate that this technology is useful to determine the best coating and cellular density conditions for different adherent cellular models including hepatocytes, cardiomyocytes, fibroblasts, and hybrid neuroblastoma/neuronal cells. Based on 31 independent experiments, the reproducibility of cell index data generated from HepG2 cells exposed to DMSO and to Triton X-100 was satisfactory, with a coefficient of variation close to 10%. Cell index data were also well reproduced when cardiomyocytes and fibroblasts were exposed to 21 compounds three times (correlation >0.91, p technology appears to be a powerful and reliable tool in drug discovery because of the reasonable throughput, rapid and efficient performance, technical optimization, and cell quality control.

  9. Intestinal microdialysis--applicability, reproducibility and local tissue response in a pig model

    DEFF Research Database (Denmark)

    Emmertsen, K J; Wara, P; Sørensen, Flemming Brandt

    2005-01-01

    BACKGROUND AND AIMS: Microdialysis has been applied to the intestinal wall for the purpose of monitoring local ischemia. The aim of this study was to investigate the applicability, reproducibility and local response to microdialysis in the intestinal wall. MATERIALS AND METHODS: In 12 pigs two...... the probes were processed for histological examination. RESULTS: Large intra- and inter-group differences in the relative recovery were found between all locations. Absolute values of metabolites showed no significant changes during the study period. The lactate in blood was 25-30% of the intra-tissue values...

  10. 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.

  11. The radio recombination line spectrum of Orion A: Observations and analysis

    International Nuclear Information System (INIS)

    Lockman, F.J.; Brown, R.L.

    1975-01-01

    The entire body of radio observations of Orion A has been considered, and the means by which the temperature and density can be derived from the ratio T/subL//T/subC/ and the line width Δv of the hydrogen radio recombination lines is examined. Since it is critical to determine the extent to which low-frequency line measurements are contaminated by ''baseline-subtraction'' problems, new observations are presented which, together with general considerations of the line shape and data reduction processes, support the following conclusions: T/subL//T/subC/ and Δv can be accurately determined in the low-frequency observations even when erroneous baselines are removed; in accord with other studies, a density gradient must exist in the nebula; isothermal models cannot reproduce the observed line strenghts; the most dense parts of the nebula must be somewhat cooler than the surrounding gas. A model of Orion A has been constructed that is derived directly from the radio continuum observations. These observations demand that the simplest possible model of the nebula be comprised of three regions whose gross properties: the electrons density and the size: are defined by the continuum measurements. This model has been used for an analysis of the radio recombination line data, and virtually all known radio data on the Orion Nebula including Δv and T/subL//T/subC/ of the H nα lines from 610 MHz to 85 GHz Δv and T/subL//T/subC/ of all the observed H nβ lines; the shape and magnitude of the radio continuum spectrum can be reproduced. The application of this model to the problem of the abundance and distribution of ionized helium with the nebula is also considered

  12. 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......). Process reproducibility was assessed as the ability of different operators to ensure a consistent rating of individual lubricants. Absolute average values as well as experimental standard deviations of the evaluation parameters were calculated, and uncertainty budgeting was performed. Results document...... 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....

  13. 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......). Process reproducibility was assessed as the ability of different operators to ensure a consistent rating of individual lubricants. Absolute average values as well as experimental standard deviations of the evaluation parameters were calculated, and uncertainty budgeting was performed. Results document...... 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....

  14. Novel burn device for rapid, reproducible burn wound generation.

    Science.gov (United States)

    Kim, J Y; Dunham, D M; Supp, D M; Sen, C K; Powell, H M

    2016-03-01

    Scarring following full thickness burns leads to significant reductions in range of motion and quality of life for burn patients. To effectively study scar development and the efficacy of anti-scarring treatments in a large animal model (female red Duroc pigs), reproducible, uniform, full-thickness, burn wounds are needed to reduce variability in observed results that occur with burn depth. Prior studies have proposed that initial temperature of the burner, contact time with skin, thermal capacity of burner material, and the amount of pressure applied to the skin need to be strictly controlled to ensure reproducibility. The purpose of this study was to develop a new burner that enables temperature and pressure to be digitally controlled and monitored in real-time throughout burn wound creation and compare it to a standard burn device. A custom burn device was manufactured with an electrically heated burn stylus and a temperature control feedback loop via an electronic microstat. Pressure monitoring was controlled by incorporation of a digital scale into the device, which measured downward force. The standard device was comprised of a heat resistant handle with a long rod connected to the burn stylus, which was heated using a hot plate. To quantify skin surface temperature and internal stylus temperature as a function of contact time, the burners were heated to the target temperature (200±5°C) and pressed into the skin for 40s to create the thermal injuries. Time to reach target temperature and elapsed time between burns were recorded. In addition, each unit was evaluated for reproducibility within and across three independent users by generating burn wounds at contact times spanning from 5 to 40s at a constant pressure and at pressures of 1 or 3lbs with a constant contact time of 40s. Biopsies were collected for histological analysis and burn depth quantification using digital image analysis (ImageJ). The custom burn device maintained both its internal

  15. Model for behavior observation training programs

    International Nuclear Information System (INIS)

    Berghausen, P.E. Jr.

    1987-01-01

    Continued behavior observation is mandated by ANSI/ANS 3.3. This paper presents a model for behavior observation training that is in accordance with this standard and the recommendations contained in US NRC publications. The model includes seventeen major topics or activities. Ten of these are discussed: Pretesting of supervisor's knowledge of behavior observation requirements, explanation of the goals of behavior observation programs, why behavior observation training programs are needed (legal and psychological issues), early indicators of emotional instability, use of videotaped interviews to demonstrate significant psychopathology, practice recording behaviors, what to do when unusual behaviors are observed, supervisor rationalizations for noncompliance, when to be especially vigilant, and prevention of emotional instability

  16. Two-Finger Tightness: What Is It? Measuring Torque and Reproducibility in a Simulated Model.

    Science.gov (United States)

    Acker, William B; Tai, Bruce L; Belmont, Barry; Shih, Albert J; Irwin, Todd A; Holmes, James R

    2016-05-01

    Residents in training are often directed to insert screws using "two-finger tightness" to impart adequate torque but minimize the chance of a screw stripping in bone. This study seeks to quantify and describe two-finger tightness and to assess the variability of its application by residents in training. Cortical bone was simulated using a polyurethane foam block (30-pcf density) that was prepared with predrilled holes for tightening 3.5 × 14-mm long cortical screws and mounted to a custom-built apparatus on a load cell to capture torque data. Thirty-three residents in training, ranging from the first through fifth years of residency, along with 8 staff members, were directed to tighten 6 screws to two-finger tightness in the test block, and peak torque values were recorded. The participants were blinded to their torque values. Stripping torque (2.73 ± 0.56 N·m) was determined from 36 trials and served as a threshold for failed screw placement. The average torques varied substantially with regard to absolute torque values, thus poorly defining two-finger tightness. Junior residents less consistently reproduced torque compared with other groups (0.29 and 0.32, respectively). These data quantify absolute values of two-finger tightness but demonstrate considerable variability in absolute torque values, percentage of stripping torque, and ability to consistently reproduce given torque levels. Increased years in training are weakly correlated with reproducibility, but experience does not seem to affect absolute torque levels. These results question the usefulness of two-finger tightness as a teaching tool and highlight the need for improvement in resident motor skill training and development within a teaching curriculum. Torque measuring devices may be a useful simulation tools for this purpose.

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

    Science.gov (United States)

    Nada, Rania M; Maal, Thomas J J; Breuning, K Hero; Bergé, Stefaan J; Mostafa, Yehya A; Kuijpers-Jagtman, Anne Marie

    2011-02-09

    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.

  18. Discrepancy between simulated and observed ethane and propane levels explained by underestimated fossil emissions

    Science.gov (United States)

    Dalsøren, Stig B.; Myhre, Gunnar; Hodnebrog, Øivind; Myhre, Cathrine Lund; Stohl, Andreas; Pisso, Ignacio; Schwietzke, Stefan; Höglund-Isaksson, Lena; Helmig, Detlev; Reimann, Stefan; Sauvage, Stéphane; Schmidbauer, Norbert; Read, Katie A.; Carpenter, Lucy J.; Lewis, Alastair C.; Punjabi, Shalini; Wallasch, Markus

    2018-03-01

    Ethane and propane are the most abundant non-methane hydrocarbons in the atmosphere. However, their emissions, atmospheric distribution, and trends in their atmospheric concentrations are insufficiently understood. Atmospheric model simulations using standard community emission inventories do not reproduce available measurements in the Northern Hemisphere. Here, we show that observations of pre-industrial and present-day ethane and propane can be reproduced in simulations with a detailed atmospheric chemistry transport model, provided that natural geologic emissions are taken into account and anthropogenic fossil fuel emissions are assumed to be two to three times higher than is indicated in current inventories. Accounting for these enhanced ethane and propane emissions results in simulated surface ozone concentrations that are 5-13% higher than previously assumed in some polluted regions in Asia. The improved correspondence with observed ethane and propane in model simulations with greater emissions suggests that the level of fossil (geologic + fossil fuel) methane emissions in current inventories may need re-evaluation.

  19. Reproducibility of graph metrics in fMRI networks

    Directory of Open Access Journals (Sweden)

    Qawi K Telesford

    2010-12-01

    Full Text Available The reliability of graph metrics calculated in network analysis is essential to the interpretation of complex network organization. These graph metrics are used to deduce the small-world properties in networks. In this study, we investigated the test-retest reliability of graph metrics from functional magnetic resonance imaging (fMRI data collected for two runs in 45 healthy older adults. Graph metrics were calculated on data for both runs and compared using intraclass correlation coefficient (ICC statistics and Bland-Altman (BA plots. ICC scores describe the level of absolute agreement between two measurements and provide a measure of reproducibility. For mean graph metrics, ICC scores were high for clustering coefficient (ICC=0.86, global efficiency (ICC=0.83, path length (ICC=0.79, and local efficiency (ICC=0.75; the ICC score for degree was found to be low (ICC=0.29. ICC scores were also used to generate reproducibility maps in brain space to test voxel-wise reproducibility for unsmoothed and smoothed data. Reproducibility was uniform across the brain for global efficiency and path length, but was only high in network hubs for clustering coefficient, local efficiency and degree. BA plots were used to test the measurement repeatability of all graph metrics. All graph metrics fell within the limits for repeatability. Together, these results suggest that with exception of degree, mean graph metrics are reproducible and suitable for clinical studies. Further exploration is warranted to better understand reproducibility across the brain on a voxel-wise basis.

  20. Language-Agnostic Reproducible Data Analysis Using Literate Programming.

    Science.gov (United States)

    Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

    2016-01-01

    A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.

  1. On the use of MOZAIC-IAGOS data to assess the ability of the MACC reanalysis to reproduce the distribution of ozone and CO in the UTLS over Europe

    Directory of Open Access Journals (Sweden)

    Audrey Gaudel

    2015-12-01

    Full Text Available MOZAIC-IAGOS data are used to assess the ability of the MACC reanalysis (REAN to reproduce distributions of ozone (O3 and carbon monoxide (CO, along with vertical and inter-annual variability in the upper troposphere/lower stratosphere region (UTLS over Europe for the period 2003–2010. A control run (CNTRL, without assimilation is compared with the MACC reanalysis (REAN, with assimilation to assess the impact of assimilation. On average over the period, REAN underestimates ozone by 60 ppbv in the lower stratosphere (LS, whilst CO is overestimated by 20 ppbv. In the upper troposphere (UT, ozone is overestimated by 50 ppbv, while CO is partly over or underestimated by up to 20 ppbv. As expected, assimilation generally improves model results but there are some exceptions. Assimilation leads to increased CO mixing ratios in the UT which reduce the biases of the model in this region but the difference in CO mixing ratios between LS and UT has not changed and remains underestimated after assimilation. Therefore, this leads to a significant positive bias of CO in the LS after assimilation. Assimilation improves estimates of the amplitude of the seasonal cycle for both species. Additionally, the observations clearly show a general negative trend of CO in the UT which is rather well reproduced by REAN. However, REAN misses the observed inter-annual variability in summer. The O3–CO correlation in the Ex-UTLS is rather well reproduced by the CNTRL and REAN, although REAN tends to miss the lowest CO mixing ratios for the four seasons and tends to oversample the extra-tropical transition layer (ExTL region in spring. This evaluation stresses the importance of the model gradients for a good description of the mixing in the Ex-UTLS region, which is inherently difficult to observe from satellite instruments.

  2. Validity and Reproducibility of a Food Frequency Questionnaire for Dietary Factors Related to Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Daniel Nigusse Tollosa

    2017-11-01

    Full Text Available Dietary factors play a major role in the development of colorectal cancer. This study evaluated the reproducibility and validity of a 109-food item Food Frequency Questionnaire (FFQ to measure the consumption of foods and nutrients related to the development of colorectal cancer in a population aged ≥50 years in Flanders, Belgium. A semi-quantitative FFQ was administered two times in a period of two weeks to evaluate reproducibility (FFQ1 and FFQ2. The validity of the FFQ was assessed by comparing FFQ1 against the 3-day diary method (3 DD. A total of 162 respondents (mean age 57.5 years provided data for the FFQ, of whom 156 also participated in the validity assessment. Mean differences in the intake of foods and nutrients between FFQ1 and FFQ2 were, overall, small and statistically insignificant. However, a higher estimation was observed by FFQ1 as compared to the 3-DD method for the majority of food groups and nutrient intake in the validity assessment. A systematic mean difference (g/day was observed for eight food groups in the Bland–Altman agreement test; the largest was for fruit intake. Regarding the nutrients, a systematic mean difference was observed in calcium, fat, and vitamin D intake. Overall, the reproducibility of the FFQ was good, and its validity could be satisfactory for estimating absolute food and nutrient intakes and ranking individuals according to high and low intake categories.

  3. Validity and Reproducibility of a Food Frequency Questionnaire for Dietary Factors Related to Colorectal Cancer.

    Science.gov (United States)

    Tollosa, Daniel Nigusse; Van Camp, John; Huybrechts, Inge; Huybregts, Lieven; Van Loco, Joris; De Smet, Stefaan; Sterck, Ellen; Rabâi, Céline; Van Hecke, Thomas; Vanhaecke, Lynn; Vossen, Els; Peeters, Marc; Lachat, Carl

    2017-11-17

    Dietary factors play a major role in the development of colorectal cancer. This study evaluated the reproducibility and validity of a 109-food item Food Frequency Questionnaire (FFQ) to measure the consumption of foods and nutrients related to the development of colorectal cancer in a population aged ≥50 years in Flanders, Belgium. A semi-quantitative FFQ was administered two times in a period of two weeks to evaluate reproducibility (FFQ1 and FFQ2). The validity of the FFQ was assessed by comparing FFQ1 against the 3-day diary method (3 DD). A total of 162 respondents (mean age 57.5 years) provided data for the FFQ, of whom 156 also participated in the validity assessment. Mean differences in the intake of foods and nutrients between FFQ1 and FFQ2 were, overall, small and statistically insignificant. However, a higher estimation was observed by FFQ1 as compared to the 3-DD method for the majority of food groups and nutrient intake in the validity assessment. A systematic mean difference (g/day) was observed for eight food groups in the Bland-Altman agreement test; the largest was for fruit intake. Regarding the nutrients, a systematic mean difference was observed in calcium, fat, and vitamin D intake. Overall, the reproducibility of the FFQ was good, and its validity could be satisfactory for estimating absolute food and nutrient intakes and ranking individuals according to high and low intake categories.

  4. Seasonal changes in the tropospheric carbon monoxide profile over the remote Southern Hemisphere evaluated using multi-model simulations and aircraft observations

    Directory of Open Access Journals (Sweden)

    J. A. Fisher

    2015-03-01

    Pole-to-Pole Observations (HIPPO, together with model output from the SH Model Intercomparison Project, to elucidate the drivers of CO vertical structure in the remote SH. Observed CO vertical profiles from Cape Grim are remarkably consistent with those observed over the southern mid-latitudes Pacific 10–20 years later, despite major differences in time periods, flight locations, and sampling strategies between the two data sets. These similarities suggest the processes driving observed vertical gradients are coherent across much of the remote SH and have not changed significantly over the past 2 decades. Model ability to simulate CO profiles reflects the interplay between biogenic emission sources, the chemical mechanisms that drive CO production from these sources, and the transport that redistributes this CO throughout the SH. The four chemistry-climate and chemical transport models included in the intercomparison show large variability in their abilities to reproduce the observed CO profiles. In particular, two of the four models significantly underestimate vertical gradients in austral summer and autumn, which we find are driven by long-range transport of CO produced from oxidation of biogenic compounds. Comparisons between the models show that more complex chemical mechanisms do not necessarily provide more accurate simulation of CO vertical gradients due to the convolved impacts of emissions, chemistry, and transport. Our results imply a large sensitivity of the remote SH troposphere to biogenic emissions and chemistry, both of which remain key uncertainties in global modeling. We suggest that the CO vertical gradient can be used as a metric for future model evaluation as it provides a sensitive test of the processes that define the chemical state of the background atmosphere.

  5. Dark blood versus bright blood T2* acquisition in cardiovascular magnetic resonance (CMR) for thalassaemia major (TM) patients: Evaluation of feasibility, reproducibility and image quality

    Energy Technology Data Exchange (ETDEWEB)

    Liguori, Carlo, E-mail: c.liguori@unicampus.it [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Di Giampietro, Ilenia; Pitocco, Francesca; De Vivo, Aldo Eros [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Schena, Emiliano [Unit of Measurements and Biomedical Instrumentation, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Mortato, Luca [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Pirro, Federica [Department of Biomaging and Radiological Sciences, Catholic University of Sacred Herart, Largo A. Gemelli 1, 00135 Rome (Italy); Cianciulli, Paolo [Thalassemia Unit, Ospedale Sant Eugenio, Piazzale dell’Umanesimo 10, 00143 Rome (Italy); Zobel, Bruno Beomonte [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy)

    2014-01-15

    Objectives: To compare the effectiveness of dark blood (DB) versus bright blood (BB) sequences. To assess the intra and inter-observer variability and inter-study reproducibility between BB versus DB. To evaluate image quality level in the two sequences. Methods: In a setting of 138 patients we performed CMR using cardiac gated Gradient-multiecho single breath-hold BB and DB sequences in the middle ventricular septum. Each acquisition was repeated during the same exam. Truncation method was used to account for background noise. Image quality (IQ) was assessed using a 5 point grading scale and image analysis was conducted by 2 experienced observers. Results: Compared with the conventional BB acquisition, the coefficient of correlation and significance of the DB technique was superior for intra-observer reproducibility (p < 0.001), inter-observer reproducibility (p < 0.001) and inter-study reproducibility (p < 0.001). The variability is also lower for DB sequences for T2* values <14 ms. Assessment of artifacts showed a superior score for DB versus BB scans (4 versus 3, p < 0.001). Conclusions: Improvement in terms of inter observer and inter study variability using DB sequences was obtained. The greatest disparity between them was seen in inter-study reproducibility and higher IQ in DB was seen. Study demonstrates better performance of DB imaging compared to BB in presence of comparable effectiveness.

  6. Climatology of the HOPE-G global ocean general circulation model - Sea ice general circulation model

    Energy Technology Data Exchange (ETDEWEB)

    Legutke, S. [Deutsches Klimarechenzentrum (DKRZ), Hamburg (Germany); Maier-Reimer, E. [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany)

    1999-12-01

    The HOPE-G global ocean general circulation model (OGCM) climatology, obtained in a long-term forced integration is described. HOPE-G is a primitive-equation z-level ocean model which contains a dynamic-thermodynamic sea-ice model. It is formulated on a 2.8 grid with increased resolution in low latitudes in order to better resolve equatorial dynamics. The vertical resolution is 20 layers. The purpose of the integration was both to investigate the models ability to reproduce the observed general circulation of the world ocean and to obtain an initial state for coupled atmosphere - ocean - sea-ice climate simulations. The model was driven with daily mean data of a 15-year integration of the atmosphere general circulation model ECHAM4, the atmospheric component in later coupled runs. Thereby, a maximum of the flux variability that is expected to appear in coupled simulations is included already in the ocean spin-up experiment described here. The model was run for more than 2000 years until a quasi-steady state was achieved. It reproduces the major current systems and the main features of the so-called conveyor belt circulation. The observed distribution of water masses is reproduced reasonably well, although with a saline bias in the intermediate water masses and a warm bias in the deep and bottom water of the Atlantic and Indian Oceans. The model underestimates the meridional transport of heat in the Atlantic Ocean. The simulated heat transport in the other basins, though, is in good agreement with observations. (orig.)

  7. 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

  8. A phenomenological model of the electrically stimulated auditory nerve fiber: temporal and biphasic response properties

    Directory of Open Access Journals (Sweden)

    Colin eHorne

    2016-02-01

    Full Text Available We present a phenomenological model of electrically stimulated auditory nerve fibers (ANFs. The model reproduces the probabilistic and temporal properties of the ANF response to both monophasic and biphasic stimuli, in isolation. The main contribution of the model lies in its ability to reproduce statistics of the ANF response (mean latency, jitter, and firing probability under both monophasic and cathodic-anodic biphasic stimulation, without changing the model’s parameters. The response statistics of the model depend on stimulus level and duration of the stimulating pulse, reproducing trends observed in the ANF. In the case of biphasic stimulation, the model reproduces the effects of pseudomonophasic pulse shapes and also the dependence on the interphase gap (IPG of the stimulus pulse, an effect that is quantitatively reproduced. The model is fitted to ANF data using a procedure that uniquely determines each model parameter. It is thus possible to rapidly parameterize a large population of neurons to reproduce a given set of response statistic distributions.Our work extends the stochastic leaky integrate and fire (SLIF neuron, a well-studied phenomenological model of the electrically stimulated neuron. We extend the SLIF neuron so as to produce a realistic latency distribution by delaying the moment of spiking. During this delay, spiking may be abolished by anodic current. By this means, the probability of the model neuron responding to a stimulus is reduced when a trailing phase of opposite polarity is introduced. By introducing a minimum wait period that must elapse before a spike may be emitted, the model is able to reproduce the differences in the threshold level observed in the ANF for monophasic and biphasic stimuli. Thus, the ANF response to a large variety of pulse shapes are reproduced correctly by this model.

  9. Beyond Bundles - Reproducible Software Environments with GNU Guix

    CERN Multimedia

    CERN. Geneva; Wurmus, Ricardo

    2018-01-01

    Building reproducible data analysis pipelines and numerical experiments is a key challenge for reproducible science, in which tools to reproduce software environments play a critical role. The advent of “container-based” deployment tools such as Docker and Singularity has made it easier to replicate software environments. These tools are very much about bundling the bits of software binaries in a convenient way, not so much about describing how software is composed. Science is not just about replicating, though—it demands the ability to inspect and to experiment. In this talk we will present GNU Guix, a software management toolkit. Guix departs from container-based solutions in that it enables declarative composition of software environments. It is comparable to “package managers” like apt or yum, but with a significant difference: Guix provides accurate provenance tracking of build artifacts, and bit-reproducible software. We will illustrate the many ways in which Guix can improve how software en...

  10. [Natural head position's reproducibility on photographs].

    Science.gov (United States)

    Eddo, Marie-Line; El Hayeck, Émilie; Hoyeck, Maha; Khoury, Élie; Ghoubril, Joseph

    2017-12-01

    The purpose of this study is to evaluate the reproducibility of natural head position with time on profile photographs. Our sample is composed of 96 students (20-30 years old) at the department of dentistry of Saint Joseph University in Beirut. Two profile photographs were taken in natural head position about a week apart. No significant differences were found between T0 and T1 (E = 1.065°). Many studies confirmed this reproducibility with time. Natural head position can be adopted as an orientation for profile photographs in orthodontics. © EDP Sciences, SFODF, 2017.

  11. Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction.

    Science.gov (United States)

    Watanabe, Eiji; Kitaoka, Akiyoshi; Sakamoto, Kiwako; Yasugi, Masaki; Tanaka, Kenta

    2018-01-01

    The cerebral cortex predicts visual motion to adapt human behavior to surrounding objects moving in real time. Although the underlying mechanisms are still unknown, predictive coding is one of the leading theories. Predictive coding assumes that the brain's internal models (which are acquired through learning) predict the visual world at all times and that errors between the prediction and the actual sensory input further refine the internal models. In the past year, deep neural networks based on predictive coding were reported for a video prediction machine called PredNet. If the theory substantially reproduces the visual information processing of the cerebral cortex, then PredNet can be expected to represent the human visual perception of motion. In this study, PredNet was trained with natural scene videos of the self-motion of the viewer, and the motion prediction ability of the obtained computer model was verified using unlearned videos. We found that the computer model accurately predicted the magnitude and direction of motion of a rotating propeller in unlearned videos. Surprisingly, it also represented the rotational motion for illusion images that were not moving physically, much like human visual perception. While the trained network accurately reproduced the direction of illusory rotation, it did not detect motion components in negative control pictures wherein people do not perceive illusory motion. This research supports the exciting idea that the mechanism assumed by the predictive coding theory is one of basis of motion illusion generation. Using sensory illusions as indicators of human perception, deep neural networks are expected to contribute significantly to the development of brain research.

  12. Short- and long-term reproducibility of radioisotopic examination of gastric emptying

    Energy Technology Data Exchange (ETDEWEB)

    Jonderko, K. (Silesian School of Medicine, Katowice (Poland). Dept. of Gastroenterology)

    1990-01-01

    Reproducibility of gastric emptying (GE) of a radiolabelled solid meal was assessed. The short-term reproducibility was evaluated on the basis of 12 paired GE examinations performed 1-3 days apart. Twelve paired GE examinations taken 3-8 months apart enabled long-term reproducibility assessment. Reproducibility of GE parameters was expressed in terms of the coefficient of variation, CV. No significant between-day variation of solid GE was found either regarding the short-term or the long-term reproducibility. Although slightly higher CV values characterized the long-term reproducibility of the GE parameters considered, the variations of the differences between repeated GE examinations did not differ significantly between short- and long-term GE reproducibility. The results obtained justify the use of radioisotopic GE measurement for the assessment of early and late results of pharmacologic or surgical management. (author).

  13. 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.

  14. On the dependence of the OH* Meinel emission altitude on vibrational level: SCIAMACHY observations and model simulations

    Directory of Open Access Journals (Sweden)

    J. P. Burrows

    2012-09-01

    Full Text Available Measurements of the OH Meinel emissions in the terrestrial nightglow are one of the standard ground-based techniques to retrieve upper mesospheric temperatures. It is often assumed that the emission peak altitudes are not strongly dependent on the vibrational level, although this assumption is not based on convincing experimental evidence. In this study we use Envisat/SCIAMACHY (Scanning Imaging Absorption spectroMeter for Atmospheric CHartographY observations in the near-IR spectral range to retrieve vertical volume emission rate profiles of the OH(3-1, OH(6-2 and OH(8-3 Meinel bands in order to investigate whether systematic differences in emission peak altitudes can be observed between the different OH Meinel bands. The results indicate that the emission peak altitudes are different for the different vibrational levels, with bands originating from higher vibrational levels having higher emission peak altitudes. It is shown that this finding is consistent with the majority of the previously published results. The SCIAMACHY observations yield differences in emission peak altitudes of up to about 4 km between the OH(3-1 and the OH(8-3 band. The observations are complemented by model simulations of the fractional population of the different vibrational levels and of the vibrational level dependence of the emission peak altitude. The model simulations reproduce the observed vibrational level dependence of the emission peak altitude well – both qualitatively and quantitatively – if quenching by atomic oxygen as well as multi-quantum collisional relaxation by O2 is considered. If a linear relationship between emission peak altitude and vibrational level is assumed, then a peak altitude difference of roughly 0.5 km per vibrational level is inferred from both the SCIAMACHY observations and the model simulations.

  15. Size Control of Sessile Microbubbles for Reproducibly Driven Acoustic Streaming

    Science.gov (United States)

    Volk, Andreas; Kähler, Christian J.

    2018-05-01

    Acoustically actuated bubbles are receiving growing interest in microfluidic applications, as they induce a streaming field that can be used for particle sorting and fluid mixing. An essential but often unspoken challenge in such applications is to maintain a constant bubble size to achieve reproducible conditions. We present an automatized system for the size control of a cylindrical bubble that is formed at a blind side pit of a polydimethylsiloxane microchannel. Using a pressure control system, we adapt the protrusion depth of the bubble into the microchannel to a precision of approximately 0.5 μ m on a timescale of seconds. By comparing the streaming field generated by bubbles of width 80 μ m with a protrusion depth between -12 and 60 μ m , we find that the mean velocity of the induced streaming fields varies by more than a factor of 4. We also find a qualitative change of the topology of the streaming field. Both observations confirm the importance of the bubble size control system in order to achieve reproducible and reliable bubble-driven streaming experiments.

  16. Peripheral nerve MRI: precision and reproducibility of T2*-derived measurements at 3.0-T. A feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    Tagliafico, Alberto [University of Genoa, Institute of Anatomy, Department of Experimental Medicine, Genoa (Italy); Bignotti, Bianca; Martinoli, Carlo [University of Genoa, Radiology Department, Genoa, Genova (Italy); Tagliafico, Giulio [CNR-IMATI, Consiglio Nazionale delle Ricerche, Istituto di Matematica Applicata e Tecnologie Informatiche, Genova (Italy)

    2015-05-01

    To prospectively evaluate the precision and reproducibility of T2*-derived measurements of the peripheral nerves. The study was approved by the local ethics committee and written informed consent was obtained. Bilateral upper and lower limb MRI examination was performed in 40 healthy subjects on a 3.0-T scanner. MRI protocol included T1-turbo spin-echo, T2-turbo spin-echo with fat suppression, and multiecho gradient recalled echo. Measurements of T2* times on T2* maps at different anatomical levels were performed. Three authors measured independently and in different sessions at baseline and after 4 weeks. Non-parametric tests and Bland-Altman statistics were used. Minimum and maximum percentage variability were 10 % and 19 % for T2* (84-91 % of reproducibility). Maximum values of minimum detectable differences between limbs was 16 % (with 95 % CI: 2-37). Intra- and inter-observer agreement of the three radiologists for T2* was considered good. Evaluating the combined influence of the observer and of the repeated measurements the reproducibility was 87-98 %. T2* measurement of the peripheral nerves is precise and reproducible. The healthy contralateral side can be used as an internal control. Variations in T2* values up to 16 % have to be considered. (orig.)

  17. Visual-stratigraphic dating of the GISP2 ice core: Basis, reproducibility, and application

    Science.gov (United States)

    Alley, R. B.; Shuman, C. A.; Meese, D. A.; Gow, A. J.; Taylor, K. C.; Cuffey, K. M.; Fitzpatrick, J. J.; Grootes, P. M.; Zielinski, G. A.; Ram, M.; Spinelli, G.; Elder, B.

    1997-11-01

    Annual layers are visible in the Greenland Ice Sheet Project 2 ice core from central Greenland, allowing rapid dating of the core. Changes in bubble and grain structure caused by near-surface, primarily summertime formation of hoar complexes provide the main visible annual marker in the Holocene, and changes in "cloudiness" of the ice correlated with dustiness mark Wisconsinan annual cycles; both markers are evident and have been intercalibrated in early Holocene ice. Layer counts are reproducible between different workers and for one worker at different times, with 1% error over century-length times in the Holocene. Reproducibility is typically 5% in Wisconsinan ice-age ice and decreases with increasing age and depth. Cumulative ages from visible stratigraphy are not significantly different from independent ages of prominent events for ice older than the historical record and younger than approximately 50,000 years. Visible observations are not greatly degraded by "brittle ice" or many other core-quality problems, allowing construction of long, consistently sampled time series. High accuracy requires careful study of the core by dedicated observers.

  18. Automated Generation of Technical Documentation and Provenance for Reproducible Research

    Science.gov (United States)

    Jolly, B.; Medyckyj-Scott, D.; Spiekermann, R.; Ausseil, A. G.

    2017-12-01

    Data provenance and detailed technical documentation are essential components of high-quality reproducible research, however are often only partially addressed during a research project. Recording and maintaining this information during the course of a project can be a difficult task to get right as it is a time consuming and often boring process for the researchers involved. As a result, provenance records and technical documentation provided alongside research results can be incomplete or may not be completely consistent with the actual processes followed. While providing access to the data and code used by the original researchers goes some way toward enabling reproducibility, this does not count as, or replace, data provenance. Additionally, this can be a poor substitute for good technical documentation and is often more difficult for a third-party to understand - particularly if they do not understand the programming language(s) used. We present and discuss a tool built from the ground up for the production of well-documented and reproducible spatial datasets that are created by applying a series of classification rules to a number of input layers. The internal model of the classification rules required by the tool to process the input data is exploited to also produce technical documentation and provenance records with minimal additional user input. Available provenance records that accompany input datasets are incorporated into those that describe the current process. As a result, each time a new iteration of the analysis is performed the documentation and provenance records are re-generated to provide an accurate description of the exact process followed. The generic nature of this tool, and the lessons learned during its creation, have wider application to other fields where the production of derivative datasets must be done in an open, defensible, and reproducible way.

  19. Shell model studies in the N = 54 isotones 99Rh, 100Pd

    International Nuclear Information System (INIS)

    Ghugre, S.S.; Sarkar, S.; Chintalapudi, S.N.

    1996-01-01

    The shell model in reproducing the observed level is used to investigate the observed level sequences in 99 Rh and 100 Pd within the spherical shell model framework. Shell model calculations have been performed using the code OXBASH

  20. Reproducibility of computer-aided detection system in digital mammograms

    International Nuclear Information System (INIS)

    Kim, Seung Ja; Cho, Nariya; Cha, Joo Hee; Chung, Hye Kyung; Lee, Sin Ho; Cho, Kyung Soo; Kim, Sun Mi; Moon, Woo Kyung

    2005-01-01

    To evaluate the reproducibility of the computer-aided detection (CAD) system for digital mammograms. We applied the CAD system (ImageChecker M1000-DM, version 3.1; R2 Technology) to full field digital mammograms. These mammograms were taken twice at an interval of 10-45 days (mean:25 days) for 34 preoperative patients (breast cancer n=27, benign disease n=7, age range:20-66 years, mean age:47.9 years). On the mammograms, lesions were visible in 19 patients and these were depicted as 15 masses and 12 calcification clusters. We analyzed the sensitivity, the false positive rate (FPR) and the reproducibility of the CAD marks. The broader sensitivities of the CAD system were 80% (12 of 15), 67%(10 of 15) for masses and those for calcification clusters were 100% (12 of 12). The strict sensitivities were 50% (15 of 30) and 50% (15 of 30) for masses and 92% (22 of 24) and 79% (19 of 24) for the clusters. The FPR for the masses was 0.21-0.22/image, the FPR for the clusters was 0.03-0.04/image and the total FPR was 0.24-0.26/image. Among 132 mammography images, the identical images regardless of the existence of CAD marks were 59% (78 of 132), and the identical images with CAD marks were 22% (15 of 69). The reproducibility of the CAD marks for the true positive mass was 67% (12 of 18) and 71% (17 of 24) for the true positive cluster. The reproducibility of CAD marks for the false positive mass was 8% (4 of 53), and the reproducibility of CAD marks for the false positive clusters was 14% (1 of 7). The reproducibility of the total mass marks was 23% (16 of 71), and the reproducibility of the total cluster marks was 58% (18 of 31). CAD system showed higher sensitivity and reproducibility of CAD marks for the calcification clusters which are related to breast cancer. Yet the overall reproducibility of CAD marks was low; therefore, the CAD system must be applied considering this limitation

  1. Towards reproducible experimental studies for non-convex polyhedral shaped particles

    Directory of Open Access Journals (Sweden)

    Wilke Daniel N.

    2017-01-01

    Full Text Available The packing density and flat bottomed hopper discharge of non-convex polyhedral particles are investigated in a systematic experimental study. The motivation for this study is two-fold. Firstly, to establish an approach to deliver quality experimental particle packing data for non-convex polyhedral particles that can be used for characterization and validation purposes of discrete element codes. Secondly, to make the reproducibility of experimental setups as convenient and readily available as possible using affordable and accessible technology. The primary technology for this study is fused deposition modeling used to 3D print polylactic acid (PLA particles using readily available 3D printer technology. A total of 8000 biodegradable particles were printed, 1000 white particles and 1000 black particles for each of the four particle types considered in this study. Reproducibility is one benefit of using fused deposition modeling to print particles, but an extremely important additional benefit is that specific particle properties can be explicitly controlled. As an example in this study the volume fraction of each particle can be controlled i.e. the effective particle density can be adjusted. In this study the particle volumes reduces drastically as the non-convexity is increased, however all printed white particles in this study have the same mass within 2% of each other.

  2. Towards reproducible experimental studies for non-convex polyhedral shaped particles

    Science.gov (United States)

    Wilke, Daniel N.; Pizette, Patrick; Govender, Nicolin; Abriak, Nor-Edine

    2017-06-01

    The packing density and flat bottomed hopper discharge of non-convex polyhedral particles are investigated in a systematic experimental study. The motivation for this study is two-fold. Firstly, to establish an approach to deliver quality experimental particle packing data for non-convex polyhedral particles that can be used for characterization and validation purposes of discrete element codes. Secondly, to make the reproducibility of experimental setups as convenient and readily available as possible using affordable and accessible technology. The primary technology for this study is fused deposition modeling used to 3D print polylactic acid (PLA) particles using readily available 3D printer technology. A total of 8000 biodegradable particles were printed, 1000 white particles and 1000 black particles for each of the four particle types considered in this study. Reproducibility is one benefit of using fused deposition modeling to print particles, but an extremely important additional benefit is that specific particle properties can be explicitly controlled. As an example in this study the volume fraction of each particle can be controlled i.e. the effective particle density can be adjusted. In this study the particle volumes reduces drastically as the non-convexity is increased, however all printed white particles in this study have the same mass within 2% of each other.

  3. Reproducibility of intrarenal kinetics of Gd-DOTA with rabbits with dynamic MRI

    International Nuclear Information System (INIS)

    Grenier, N.; Broussin, J.; Barat, J.L.; Ducassou, D.

    1989-01-01

    Ten normal rabbits and seven rabbits with experimental acute renal failure by tubular necrosis were studied with dynamic MR to evaluate the reproducibility of intrarenal kinetics of Gd-DOTA. Sequential spin-echo sequences with short TR (200 msec)/TE (26 msec) were used yielding a 29 sec acquisition time. A usual semi-quantitative analysis of intrarenal contrast demonstrated the reproducilibity of some phases of the dynamic sequence in particular a drop in the signal within inner medulla between the third and the fourth minute after infusion. This effect, related to a high concentration of Gd-DOTA within the tubules was observed in 9 over 10 normal rabbits and in none of the rabbits with acute renal failure. The quantitative analysis calculation was based on relative signal intensity and contrast-to-noise ratio from the absolute signal intensity measure on regions-of-interest (ROI) on the cortex, outer medulla and inner medulla. No reproducibility of the variations with time of these parameters could be assessed. A gread number of factors of variations or error, mainly during the measurements of signal intensity with ROI, could explain this lack of reproducibility. At the present, dynamic MR is therefore not able to quantitatively evaluate the renal function. Only a semi-quantitative estimation of tubular concentration can be deduced [fr

  4. Magnetic resonance elastography of the pancreas: Measurement reproducibility and relationship with age.

    Science.gov (United States)

    Kolipaka, Arunark; Schroeder, Samuel; Mo, Xiaokui; Shah, Zarine; Hart, Phil A; Conwell, Darwin L

    2017-10-01

    To determine magnetic resonance elastography (MRE)-derived stiffness of pancreas in healthy volunteers with emphasis on: 1) short term and midterm repeatability; and 2) variance as a function of age. Pancreatic MRE was performed on 22 healthy volunteers (age range:20-64years) in a 3T-scanner. For evaluation of reproducibility of stiffness estimates, the scans were repeated per volunteer on the same day (short term) and one month apart (midterm). MRE wave images were analyzed using 3D inversion to estimate the stiffness of overall pancreas and different anatomic regions (i.e., head, neck, body, and tail). Concordance and Spearman correlation tests were performed to determine reproducibility of stiffness measurements and relationship to age. A strong concordance correlation (ρ c =0.99; p-value0.81; p45yrs) had significantly higher stiffness compared to the younger group (≤45yrs) (p0.05) in stiffness measurements was observed between different anatomical regions of pancreas, except neck stiffness was slightly lower (ppancreas at month 1. MRE-derived pancreatic stiffness measurements are highly reproducible in the short and midterm and increase linearly with age in healthy volunteers. Further studies are needed to examine these effects in patients with various pancreatic diseases to understand potential clinical applications. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. 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.

  6. Banff initiative for quality assurance in transplantation (BIFQUIT): reproducibility of C4d immunohistochemistry in kidney allografts.

    Science.gov (United States)

    Mengel, M; Chan, S; Climenhaga, J; Kushner, Y B; Regele, H; Colvin, R B; Randhawa, P

    2013-05-01

    Detection of C4d is crucial for diagnosing antibody-mediated-rejection. We conducted a multicenter trial to assess the reproducibility for C4d immunohistochemistry on paraffin tissue. Unstained slides from a tissue microarray (TMA) comprising 44 kidney allograft specimens representing a full analytical spectrum for C4d were distributed to 73 institutions. Participants stained TMA slides using local protocols and evaluated their slides following the Banff C4d schema. Local staining details and evaluation scores were collected online. Stained slides were returned for centralized panel re-evaluation. Kappa statistics were used to determine reproducibility. Poor interinstitutional reproducibility was observed (kappa 0.17), which was equally due to limitations in interobserver (kappa 0.44) and interlaboratory reproducibility (kappa 0.46). Depending on the cut-off, reproducibility could be improved by omitting C4d grading and only considering ± calls. Heat-induced epitope recovery (pH 6-7, 20-30 min, citrate buffer) with polyclonal antibody incubation (40 min) appeared as best practice. The BIFQUIT trial results indicated that C4d staining on paraffin sections varies considerably between laboratories. Refinement of the current Banff C4d scoring schema and harmonization of tissue processing and staining protocols is necessary to achieve acceptable reproducibility. © Copyright 2013 The American Society of Transplantation and the American Society of Transplant Surgeons.

  7. Navicular bone position determined by positional MRI: a reproducibility study

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Philip; Nybing, Janus D. [Copenhagen University Hospital Frederiksberg and Bispebjerg, Department of Radiology, Frederiksberg (Denmark); Johannsen, Finn E.; Stallknecht, Sandra E. [Copenhagen University Hospital Bispebjerg, Institute of Sports Medicine Copenhagen, Copenhagen, NV (Denmark); Hangaard, Stine; Hansen, Bjarke B. [Copenhagen University Hospital Frederiksberg, Parker Institute, Department of Rheumatology, Frederiksberg (Denmark); Boesen, Mikael [Copenhagen University Hospital Frederiksberg and Bispebjerg, Department of Radiology, Frederiksberg (Denmark); Copenhagen University Hospital Frederiksberg, Parker Institute, Department of Rheumatology, Frederiksberg (Denmark)

    2016-02-15

    To examine intraobserver, interobserver and between-day reproducibility of positional MRI for evaluation of navicular bone height (NVH) and medial navicular position (MNP). Positional MRI (pMRI) of the foot was performed on ten healthy participants (0.25 T G-scanner). Scanning was performed in supine and standing position, respectively. Two radiologists evaluated the images in a blinded manner. Reliability and agreement were assessed by calculation of intraclass correlation coefficient (ICC) and 95 % limits of agreement as a percentage of the mean (LOA%). Intraobserver and interobserver reliability was ''substantial'' in both supine and standing position (ICC 0.86-0.98) and showed good agreement (LOA% 4.9-14.7 %). Between-day reliability of navicular height and medial navicular position in standing position remained substantial (ICC 0.85-0.92) with adequate agreement (LOA% 8.3-19.8 %). In supine position between-day reliability was ''moderate'' for NVH (ICC 0.72) and ''slight'' for MNP (ICC 0.39). Agreement remained adequate between-days for MNP in supine position (LOA% 17.7 %), but it was less than adequate for NVH in supine position (LOA% 24.2 %). Navicular height and medial navicular position can be measured by pMRI in a very reproducible manner within and between observers. Increased measurement variation is observed between-days in supine position, which may be due to small positional differences or other unknown biomechanical factors. (orig.)

  8. Navicular bone position determined by positional MRI: a reproducibility study

    International Nuclear Information System (INIS)

    Hansen, Philip; Nybing, Janus D.; Johannsen, Finn E.; Stallknecht, Sandra E.; Hangaard, Stine; Hansen, Bjarke B.; Boesen, Mikael

    2016-01-01

    To examine intraobserver, interobserver and between-day reproducibility of positional MRI for evaluation of navicular bone height (NVH) and medial navicular position (MNP). Positional MRI (pMRI) of the foot was performed on ten healthy participants (0.25 T G-scanner). Scanning was performed in supine and standing position, respectively. Two radiologists evaluated the images in a blinded manner. Reliability and agreement were assessed by calculation of intraclass correlation coefficient (ICC) and 95 % limits of agreement as a percentage of the mean (LOA%). Intraobserver and interobserver reliability was ''substantial'' in both supine and standing position (ICC 0.86-0.98) and showed good agreement (LOA% 4.9-14.7 %). Between-day reliability of navicular height and medial navicular position in standing position remained substantial (ICC 0.85-0.92) with adequate agreement (LOA% 8.3-19.8 %). In supine position between-day reliability was ''moderate'' for NVH (ICC 0.72) and ''slight'' for MNP (ICC 0.39). Agreement remained adequate between-days for MNP in supine position (LOA% 17.7 %), but it was less than adequate for NVH in supine position (LOA% 24.2 %). Navicular height and medial navicular position can be measured by pMRI in a very reproducible manner within and between observers. Increased measurement variation is observed between-days in supine position, which may be due to small positional differences or other unknown biomechanical factors. (orig.)

  9. On the reproducibility of expert-operated and robotic ultrasound acquisitions.

    Science.gov (United States)

    Kojcev, Risto; Khakzar, Ashkan; Fuerst, Bernhard; Zettinig, Oliver; Fahkry, Carole; DeJong, Robert; Richmon, Jeremy; Taylor, Russell; Sinibaldi, Edoardo; Navab, Nassir

    2017-06-01

    We present the evaluation of the reproducibility of measurements performed using robotic ultrasound imaging in comparison with expert-operated sonography. Robotic imaging for interventional procedures may be a valuable contribution, but requires reproducibility for its acceptance in clinical routine. We study this by comparing repeated measurements based on robotic and expert-operated ultrasound imaging. Robotic ultrasound acquisition is performed in three steps under user guidance: First, the patient is observed using a 3D camera on the robot end effector, and the user selects the region of interest. This allows for automatic planning of the robot trajectory. Next, the robot executes a sweeping motion following the planned trajectory, during which the ultrasound images and tracking data are recorded. As the robot is compliant, deviations from the path are possible, for instance due to patient motion. Finally, the ultrasound slices are compounded to create a volume. Repeated acquisitions can be performed automatically by comparing the previous and current patient surface. After repeated image acquisitions, the measurements based on acquisitions performed by the robotic system and expert are compared. Within our case series, the expert measured the anterior-posterior, longitudinal, transversal lengths of both of the left and right thyroid lobes on each of the 4 healthy volunteers 3 times, providing 72 measurements. Subsequently, the same procedure was performed using the robotic system resulting in a cumulative total of 144 clinically relevant measurements. Our results clearly indicated that robotic ultrasound enables more repeatable measurements. A robotic ultrasound platform leads to more reproducible data, which is of crucial importance for planning and executing interventions.

  10. Comet assay in reconstructed 3D human epidermal skin models—investigation of intra- and inter-laboratory reproducibility with coded chemicals

    Science.gov (United States)

    Pfuhler, Stefan

    2013-01-01

    Reconstructed 3D human epidermal skin models are being used increasingly for safety testing of chemicals. Based on EpiDerm™ tissues, an assay was developed in which the tissues were topically exposed to test chemicals for 3h followed by cell isolation and assessment of DNA damage using the comet assay. Inter-laboratory reproducibility of the 3D skin comet assay was initially demonstrated using two model genotoxic carcinogens, methyl methane sulfonate (MMS) and 4-nitroquinoline-n-oxide, and the results showed good concordance among three different laboratories and with in vivo data. In Phase 2 of the project, intra- and inter-laboratory reproducibility was investigated with five coded compounds with different genotoxicity liability tested at three different laboratories. For the genotoxic carcinogens MMS and N-ethyl-N-nitrosourea, all laboratories reported a dose-related and statistically significant increase (P 30% cell loss), and the overall response was comparable in all laboratories despite some differences in doses tested. The results of the collaborative study for the coded compounds were generally reproducible among the laboratories involved and intra-laboratory reproducibility was also good. These data indicate that the comet assay in EpiDerm™ skin models is a promising model for the safety assessment of compounds with a dermal route of exposure. PMID:24150594

  11. Characterization and reproducibility of HepG2 hanging drop spheroids toxicology in vitro.

    Science.gov (United States)

    Hurrell, Tracey; Ellero, Andrea Antonio; Masso, Zelie Flavienne; Cromarty, Allan Duncan

    2018-02-21

    Hepatotoxicity remains a major challenge in drug development despite preclinical toxicity screening using hepatocytes of human origin. To overcome some limitations of reproducing the hepatic phenotype, more structurally and functionally authentic cultures in vitro can be introduced by growing cells in 3D spheroid cultures. Characterisation and reproducibility of HepG2 spheroid cultures using a high-throughput hanging drop technique was performed and features contributing to potential phenotypic variation highlighted. Cultured HepG2 cells were seeded into Perfecta 3D® 96-well hanging drop plates and assessed over time for morphology, viability, cell cycle distribution, protein content and protein-mass profiles. Divergent aspects which were assessed included cell stocks, seeding density, volume of culture medium and use of extracellular matrix additives. Hanging drops are advantageous due to no complex culture matrix being present, enabling background free extractions for downstream experimentation. Varying characteristics were observed across cell stocks and batches, seeding density, culture medium volume and extracellular matrix when using immortalized HepG2 cells. These factors contribute to wide-ranging cellular responses and highlights concerns with respect to generating a reproducible phenotype in HepG2 hanging drop spheroids. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Highly reproducible polyol synthesis for silver nanocubes

    Science.gov (United States)

    Han, Hye Ji; Yu, Taekyung; Kim, Woo-Sik; Im, Sang Hyuk

    2017-07-01

    We could synthesize the Ag nanocubes highly reproducibly by conducting the polyol synthesis using HCl etchant in dark condition because the photodecomposition/photoreduction of AgCl nanoparticles formed at initial reaction stage were greatly depressed and consequently the selective self-nucleation of Ag single crystals and their selective growth reaction could be promoted. Whereas the reproducibility of the formation of Ag nanocubes were very poor when we synthesize the Ag nanocubes in light condition due to the photoreduction of AgCl to Ag.

  13. The Chemistry of Atmosphere-Forest Exchange (CAFE Model – Part 2: Application to BEARPEX-2007 observations

    Directory of Open Access Journals (Sweden)

    G. M. Wolfe

    2011-02-01

    Full Text Available In a companion paper, we introduced the Chemistry of Atmosphere-Forest Exchange (CAFE model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. Here, we apply CAFE to noontime observations from the 2007 Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX-2007. In this work we evaluate the CAFE modeling approach, demonstrate the significance of in-canopy chemistry for forest-atmosphere exchange and identify key shortcomings in the current understanding of intra-canopy processes.

    CAFE generally reproduces BEARPEX-2007 observations but requires an enhanced radical recycling mechanism to overcome a factor of 6 underestimate of hydroxyl (OH concentrations observed during a warm (~29 °C period. Modeled fluxes of acyl peroxy nitrates (APN are quite sensitive to gradients in chemical production and loss, demonstrating that chemistry may perturb forest-atmosphere exchange even when the chemical timescale is long relative to the canopy mixing timescale. The model underestimates peroxy acetyl nitrate (PAN fluxes by 50% and the exchange velocity by nearly a factor of three under warmer conditions, suggesting that near-surface APN sinks are underestimated relative to the sources. Nitric acid typically dominates gross dry N deposition at this site, though other reactive nitrogen (NOy species can comprise up to 28% of the N deposition budget under cooler conditions. Upward NO2 fluxes cause the net above-canopy NOy flux to be ~30% lower than the gross depositional flux. CAFE under-predicts ozone fluxes and exchange velocities by ~20%. Large uncertainty in the parameterization of cuticular and ground deposition precludes conclusive attribution of non-stomatal fluxes to chemistry or surface uptake. Model-measurement comparisons of vertical concentration gradients for several emitted species suggests that the lower canopy airspace may be

  14. T2-mapping of the sacroiliac joints at 1.5 Tesla: a feasibility and reproducibility study.

    Science.gov (United States)

    Albano, Domenico; Chianca, Vito; Cuocolo, Renato; Bignone, Rodolfo; Ciccia, Francesco; Sconfienza, Luca Maria; Midiri, Massimo; Brunetti, Arturo; Lagalla, Roberto; Galia, Massimo

    2018-04-20

    To evaluate the reproducibility of T2 relaxation time measurements of the sacroiliac joints at 1.5 T. Healthy volunteers underwent an oblique axial multislice multiecho spin-echo sequence of the sacroiliac joints at 1.5 T. Regions of interest were manually drawn using a dedicated software by two musculoskeletal radiologists to include the cartilaginous part of the sacroiliac joints. A senior radiologist performed the measurement twice, while a resident measured once. Intra- and inter-observer reproducibility was tested using the Bland-Altman method. Association between sex and T2 relaxation times was tested using the Mann-Whitney U test. Correlation between T2 relaxation times and body mass index (BMI) was tested using the Spearman's rho. Eighty sacroiliac joints of 40 subjects (mean age: 28 ± 4.8 years, range: 20-43; mean BMI: 23.3 ± 3.1, range: 18.9-30) were imaged. The mean T2 values obtained by the senior radiologist in the first series of measurements were 42 ± 4.4 ms, whereas in the second series were 40.7 ± 4.5 ms. The mean T2 values obtained by the radiology resident were 41.1 ± 4.2 ms. Intra-observer reproducibility was 88% (coefficient of repeatability = 3.8; bias = 1.28; p sacroiliac joints seems to be highly reproducible at 1.5 T. Further studies could investigate the potential clinical application of this tool in the sacroiliac joints.

  15. 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...

  16. Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction

    Directory of Open Access Journals (Sweden)

    Eiji Watanabe

    2018-03-01

    Full Text Available The cerebral cortex predicts visual motion to adapt human behavior to surrounding objects moving in real time. Although the underlying mechanisms are still unknown, predictive coding is one of the leading theories. Predictive coding assumes that the brain's internal models (which are acquired through learning predict the visual world at all times and that errors between the prediction and the actual sensory input further refine the internal models. In the past year, deep neural networks based on predictive coding were reported for a video prediction machine called PredNet. If the theory substantially reproduces the visual information processing of the cerebral cortex, then PredNet can be expected to represent the human visual perception of motion. In this study, PredNet was trained with natural scene videos of the self-motion of the viewer, and the motion prediction ability of the obtained computer model was verified using unlearned videos. We found that the computer model accurately predicted the magnitude and direction of motion of a rotating propeller in unlearned videos. Surprisingly, it also represented the rotational motion for illusion images that were not moving physically, much like human visual perception. While the trained network accurately reproduced the direction of illusory rotation, it did not detect motion components in negative control pictures wherein people do not perceive illusory motion. This research supports the exciting idea that the mechanism assumed by the predictive coding theory is one of basis of motion illusion generation. Using sensory illusions as indicators of human perception, deep neural networks are expected to contribute significantly to the development of brain research.

  17. PROPERTIES AND MODELING OF UNRESOLVED FINE STRUCTURE LOOPS OBSERVED IN THE SOLAR TRANSITION REGION BY IRIS

    Energy Technology Data Exchange (ETDEWEB)

    Brooks, David H. [College of Science, George Mason University, 4400 University Drive, Fairfax, VA 22030 (United States); Reep, Jeffrey W.; Warren, Harry P. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States)

    2016-08-01

    Recent observations from the Interface Region Imaging Spectrograph ( IRIS ) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads. We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.

  18. Reproducing Kernels and Coherent States on Julia Sets

    Energy Technology Data Exchange (ETDEWEB)

    Thirulogasanthar, K., E-mail: santhar@cs.concordia.ca; Krzyzak, A. [Concordia University, Department of Computer Science and Software Engineering (Canada)], E-mail: krzyzak@cs.concordia.ca; Honnouvo, G. [Concordia University, Department of Mathematics and Statistics (Canada)], E-mail: g_honnouvo@yahoo.fr

    2007-11-15

    We construct classes of coherent states on domains arising from dynamical systems. An orthonormal family of vectors associated to the generating transformation of a Julia set is found as a family of square integrable vectors, and, thereby, reproducing kernels and reproducing kernel Hilbert spaces are associated to Julia sets. We also present analogous results on domains arising from iterated function systems.

  19. Reproducing Kernels and Coherent States on Julia Sets

    International Nuclear Information System (INIS)

    Thirulogasanthar, K.; Krzyzak, A.; Honnouvo, G.

    2007-01-01

    We construct classes of coherent states on domains arising from dynamical systems. An orthonormal family of vectors associated to the generating transformation of a Julia set is found as a family of square integrable vectors, and, thereby, reproducing kernels and reproducing kernel Hilbert spaces are associated to Julia sets. We also present analogous results on domains arising from iterated function systems

  20. In vivo reproducibility of robotic probe placement for an integrated US-CT image-guided radiation therapy system

    Science.gov (United States)

    Lediju Bell, Muyinatu A.; Sen, H. Tutkun; Iordachita, Iulian; Kazanzides, Peter; Wong, John

    2014-03-01

    Radiation therapy is used to treat cancer by delivering high-dose radiation to a pre-defined target volume. Ultrasound (US) has the potential to provide real-time, image-guidance of radiation therapy to identify when a target moves outside of the treatment volume (e.g. due to breathing), but the associated probe-induced tissue deformation causes local anatomical deviations from the treatment plan. If the US probe is placed to achieve similar tissue deformations in the CT images required for treatment planning, its presence causes streak artifacts that will interfere with treatment planning calculations. To overcome these challenges, we propose robot-assisted placement of a real ultrasound probe, followed by probe removal and replacement with a geometrically-identical, CT-compatible model probe. This work is the first to investigate in vivo deformation reproducibility with the proposed approach. A dog's prostate, liver, and pancreas were each implanted with three 2.38-mm spherical metallic markers, and the US probe was placed to visualize the implanted markers in each organ. The real and model probes were automatically removed and returned to the same position (i.e. position control), and CT images were acquired with each probe placement. The model probe was also removed and returned with the same normal force measured with the real US probe (i.e. force control). Marker positions in CT images were analyzed to determine reproducibility, and a corollary reproducibility study was performed on ex vivo tissue. In vivo results indicate that tissue deformations with the real probe were repeatable under position control for the prostate, liver, and pancreas, with median 3D reproducibility of 0.3 mm, 0.3 mm, and 1.6 mm, respectively, compared to 0.6 mm for the ex vivo tissue. For the prostate, the mean 3D tissue displacement errors between the real and model probes were 0.2 mm under position control and 0.6 mm under force control, which are both within acceptable

  1. The use of long-term observations in combination with modeling and their effect on the estimation of the North Sea storm surge climate

    Energy Technology Data Exchange (ETDEWEB)

    Aspelien, T.

    2006-07-01

    The aim of this PhD thesis is to design, implement and assess a method to combine long-term observations with multi-decadal model simulations. In this work a computationally cost-efficient nudging method, well suited for multi-decadal simulations, is chosen. First, the nudging method was tested for its sensitivity to different parameters. Then the long-term observations of sea level height from the UK tide gauge Aberdeen were combined with a multi-decadal hindcast for the North Sea. Compared to a control simulation, in which no observed values of sea level height were combined with the model, the nudging method generally improves the modeled water levels with respect to the observed values, especially for surge. The estimation of long-term fluctuations and biases of extreme values of high waters in the nudged simulation are generally considerably improved after nudging and closer to the observed. The effect is largest in the German Bight and at the West coast of Denmark. It is concluded that the cost-efficient nudging method, in which external processes, such as external surges, are additionally taken into account, provides a considerable improvement in reproducing long-term variations and trends, especially for surge. Without additional data from e.g. observed values from tide gauges taken into account, the meteorological induced long-term variations in a hindcast are not fully captured. (orig.)

  2. Reproducibility of preclinical animal research improves with heterogeneity of study samples

    Science.gov (United States)

    Vogt, Lucile; Sena, Emily S.; Würbel, Hanno

    2018-01-01

    Single-laboratory studies conducted under highly standardized conditions are the gold standard in preclinical animal research. Using simulations based on 440 preclinical studies across 13 different interventions in animal models of stroke, myocardial infarction, and breast cancer, we compared the accuracy of effect size estimates between single-laboratory and multi-laboratory study designs. Single-laboratory studies generally failed to predict effect size accurately, and larger sample sizes rendered effect size estimates even less accurate. By contrast, multi-laboratory designs including as few as 2 to 4 laboratories increased coverage probability by up to 42 percentage points without a need for larger sample sizes. These findings demonstrate that within-study standardization is a major cause of poor reproducibility. More representative study samples are required to improve the external validity and reproducibility of preclinical animal research and to prevent wasting animals and resources for inconclusive research. PMID:29470495

  3. Reproducibility of the World Health Organization 2008 criteria for myelodysplastic syndromes.

    Science.gov (United States)

    Senent, Leonor; Arenillas, Leonor; Luño, Elisa; Ruiz, Juan C; Sanz, Guillermo; Florensa, Lourdes

    2013-04-01

    The reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is uncertain and its assessment was the major aim of this study. The different peripheral blood and bone marrow variables required for an adequate morphological classification were blindly evaluated by four cytomorphologists in samples from 50 patients with myelodysplastic syndromes. The degree of agreement among observers was calculated using intraclass correlation coefficient and the generalized kappa statistic for multiple raters. The degree of agreement for the percentages of blasts in bone marrow and peripheral blood, ring sideroblasts in bone marrow, and erythroid, granulocytic and megakaryocytic dysplastic cells was strong (P<0.001 in all instances). After stratifying the percentages according to the categories required for the assignment of World Health Organization subtypes, the degree of agreement was not statistically significant for cases with 5-9% blasts in bone marrow (P=0.07), 0.1-1% blasts in peripheral blood (P=0.47), or percentage of erythroid dysplastic cells (P=0.49). Finally, the interobserver concordance for World Health Organization-defined subtypes showed a moderate overall agreement (P<0.001), the reproducibility being lower for cases with refractory anemia with excess of blasts type 1 (P=0.05) and refractory anemia with ring sideroblasts (P=0.09). In conclusion, the reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is acceptable but the defining criteria for blast cells and features of erythroid dysplasia need to be refined.

  4. Reproducibility of blood pressure variation in older ambulatory and bedridden subjects.

    Science.gov (United States)

    Tsuchihashi, Takuya; Kawakami, Yasunobu; Imamura, Tsuyoshi; Abe, Isao

    2002-06-01

    We investigated the influence of ambulation on the reproducibility of circadian blood pressure variation in older nursing home residents. Ambulatory blood pressure monitoring was performed twice in 37 older nursing home residents. Nursing home in Japan. Subjects included 18 ambulatory nursing home residents who had no limitation on physical activity and 19 bedridden residents who did not participate in physical activity. Twenty-four-hour, daytime, and nighttime blood pressure levels and their variability. The 24-hour and daytime variability of systolic blood pressure (SBP) was significantly greater in ambulatory than in bedridden subjects, whereas nighttime variability was similar. Significant correlations in SBP averaged for the whole day, daytime, and nighttime were observed between the two examinations in ambulatory (r =.80-.83) and bedridden (r =.83-.91) subjects, but the variabilities of SBP for the whole day and during the daytime of the first measurement were correlated with those of the second measurement in bedridden (r =.67 and r =.47, respectively) but not in ambulatory (r =.39 and r =.28, respectively) subjects. Significant correlations were found between the nocturnal SBP changes at two occasions in both ambulatory (r =.50) and bedridden (r =.51) subjects, but the dipper versus nondipper profiles, defined as reduction in SBP of greater than 10% versus not, showed low reproducibility in ambulatory subjects; five ambulatory (28%) and one bedridden (5%) subjects showed divergent profiles between the two examinations. The reproducibility of blood pressure variation in nursing home residents is influenced by ambulation.

  5. Musical training generalises across modalities and reveals efficient and adaptive mechanisms for reproducing temporal intervals.

    Science.gov (United States)

    Aagten-Murphy, David; Cappagli, Giulia; Burr, David

    2014-03-01

    Expert musicians are able to time their actions accurately and consistently during a musical performance. We investigated how musical expertise influences the ability to reproduce auditory intervals and how this generalises across different techniques and sensory modalities. We first compared various reproduction strategies and interval length, to examine the effects in general and to optimise experimental conditions for testing the effect of music, and found that the effects were robust and consistent across different paradigms. Focussing on a 'ready-set-go' paradigm subjects reproduced time intervals drawn from distributions varying in total length (176, 352 or 704 ms) or in the number of discrete intervals within the total length (3, 5, 11 or 21 discrete intervals). Overall, Musicians performed more veridical than Non-Musicians, and all subjects reproduced auditory-defined intervals more accurately than visually-defined intervals. However, Non-Musicians, particularly with visual stimuli, consistently exhibited a substantial and systematic regression towards the mean interval. When subjects judged intervals from distributions of longer total length they tended to regress more towards the mean, while the ability to discriminate between discrete intervals within the distribution had little influence on subject error. These results are consistent with a Bayesian model that minimizes reproduction errors by incorporating a central tendency prior weighted by the subject's own temporal precision relative to the current distribution of intervals. Finally a strong correlation was observed between all durations of formal musical training and total reproduction errors in both modalities (accounting for 30% of the variance). Taken together these results demonstrate that formal musical training improves temporal reproduction, and that this improvement transfers from audition to vision. They further demonstrate the flexibility of sensorimotor mechanisms in adapting to

  6. Reproducibility of the interpretation of coronal 3D ultrasound view of the uterus to evaluate the position of Essure® 3 months after hysteroscopic procedure.

    Science.gov (United States)

    Capmas, P; Letendre, I; Levaillant, J-M; Fuchs, F; Panel, P; Chambon, G; Villefranque, V; Levy-Zauberman, Y; Fernandez, H

    2017-09-01

    Three-dimensional sonography is a good alternative method to assess the position of microinserts. Adequate position after three months allows for the interruption of other contraception. Objective is to evaluate inter-observer reproducibility of the interpretation of coronal transvaginal 3D ultrasound view of the uterus to evaluate the position of Essure ® . Inter-observer reproducibility study. Fifty women underwent successful bilateral placement of microinserts (Essure ® ) by hysteroscopy in the Department of Gynaecology of a teaching hospital and were included in the study. At three month, 3D ultrasound coronal views of the fifty uterus (accounting for one hundred microinserts) were assessed by five different observers and microinsert position was classified according to the classification described by Legendre et al. Inter-observer reproducibility in reading the 3D coronal view of the uterus was evaluated. The k-value was disparate, from 0.26 to 0.82. Inter-observer reproducibility then ranged from fair to almost perfect, depending on a prior knowledge of the position classification. Transvaginal 3D coronal view of the uterus is sufficient to assess the positioning of the microinserts when the practionner or the surgeon is familiar with the classification method. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  7. When Quality Beats Quantity: Decision Theory, Drug Discovery, and the Reproducibility Crisis.

    Directory of Open Access Journals (Sweden)

    Jack W Scannell

    Full Text Available A striking contrast runs through the last 60 years of biopharmaceutical discovery, research, and development. Huge scientific and technological gains should have increased the quality of academic science and raised industrial R&D efficiency. However, academia faces a "reproducibility crisis"; inflation-adjusted industrial R&D costs per novel drug increased nearly 100 fold between 1950 and 2010; and drugs are more likely to fail in clinical development today than in the 1970s. The contrast is explicable only if powerful headwinds reversed the gains and/or if many "gains" have proved illusory. However, discussions of reproducibility and R&D productivity rarely address this point explicitly. The main objectives of the primary research in this paper are: (a to provide quantitatively and historically plausible explanations of the contrast; and (b identify factors to which R&D efficiency is sensitive. We present a quantitative decision-theoretic model of the R&D process. The model represents therapeutic candidates (e.g., putative drug targets, molecules in a screening library, etc. within a "measurement space", with candidates' positions determined by their performance on a variety of assays (e.g., binding affinity, toxicity, in vivo efficacy, etc. whose results correlate to a greater or lesser degree. We apply decision rules to segment the space, and assess the probability of correct R&D decisions. We find that when searching for rare positives (e.g., candidates that will successfully complete clinical development, changes in the predictive validity of screening and disease models that many people working in drug discovery would regard as small and/or unknowable (i.e., an 0.1 absolute change in correlation coefficient between model output and clinical outcomes in man can offset large (e.g., 10 fold, even 100 fold changes in models' brute-force efficiency. We also show how validity and reproducibility correlate across a population of simulated

  8. Skill of ship-following large-eddy simulations in reproducing MAGIC observations across the northeast Pacific stratocumulus to cumulus transition region

    Science.gov (United States)

    McGibbon, J.; Bretherton, C. S.

    2017-06-01

    During the Marine ARM GPCI Investigation of Clouds (MAGIC) in October 2011 to September 2012, a container ship making periodic cruises between Los Angeles, CA, and Honolulu, HI, was instrumented with surface meteorological, aerosol and radiation instruments, a cloud radar and ceilometer, and radiosondes. Here large-eddy simulation (LES) is performed in a ship-following frame of reference for 13 four day transects from the MAGIC field campaign. The goal is to assess if LES can skillfully simulate the broad range of observed cloud characteristics and boundary layer structure across the subtropical stratocumulus to cumulus transition region sampled during different seasons and meteorological conditions. Results from Leg 15A, which sampled a particularly well-defined stratocumulus to cumulus transition, demonstrate the approach. The LES reproduces the observed timing of decoupling and transition from stratocumulus to cumulus and matches the observed evolution of boundary layer structure, cloud fraction, liquid water path, and precipitation statistics remarkably well. Considering the simulations of all 13 cruises, the LES skillfully simulates the mean diurnal variation of key measured quantities, including liquid water path (LWP), cloud fraction, measures of decoupling, and cloud radar-derived precipitation. The daily mean quantities are well represented, and daily mean LWP and cloud fraction show the expected correlation with estimated inversion strength. There is a -0.6 K low bias in LES near-surface air temperature that results in a high bias of 5.6 W m-2 in sensible heat flux (SHF). Overall, these results build confidence in the ability of LES to represent the northeast Pacific stratocumulus to trade cumulus transition region.Plain Language SummaryDuring the Marine ARM GPCI Investigation of Clouds (MAGIC) field campaign in October 2011 to September 2012, a cargo container ship making regular cruises between Los Angeles, CA, and Honolulu, HI, was fitted with tools to

  9. Correlation between human observer performance and model observer performance in differential phase contrast CT

    International Nuclear Information System (INIS)

    Li, Ke; Garrett, John; Chen, Guang-Hong

    2013-01-01

    Purpose: With the recently expanding interest and developments in x-ray differential phase contrast CT (DPC-CT), the evaluation of its task-specific detection performance and comparison with the corresponding absorption CT under a given radiation dose constraint become increasingly important. Mathematical model observers are often used to quantify the performance of imaging systems, but their correlations with actual human observers need to be confirmed for each new imaging method. This work is an investigation of the effects of stochastic DPC-CT noise on the correlation of detection performance between model and human observers with signal-known-exactly (SKE) detection tasks.Methods: The detectabilities of different objects (five disks with different diameters and two breast lesion masses) embedded in an experimental DPC-CT noise background were assessed using both model and human observers. The detectability of the disk and lesion signals was then measured using five types of model observers including the prewhitening ideal observer, the nonprewhitening (NPW) observer, the nonprewhitening observer with eye filter and internal noise (NPWEi), the prewhitening observer with eye filter and internal noise (PWEi), and the channelized Hotelling observer (CHO). The same objects were also evaluated by four human observers using the two-alternative forced choice method. The results from the model observer experiment were quantitatively compared to the human observer results to assess the correlation between the two techniques.Results: The contrast-to-detail (CD) curve generated by the human observers for the disk-detection experiments shows that the required contrast to detect a disk is inversely proportional to the square root of the disk size. Based on the CD curves, the ideal and NPW observers tend to systematically overestimate the performance of the human observers. The NPWEi and PWEi observers did not predict human performance well either, as the slopes of their CD

  10. A model based approach in observing the activity of neuronal populations for the prediction of epileptic seizures

    International Nuclear Information System (INIS)

    Chong, M.S.; Nesic, D.; Kuhlmann, L.; Postoyan, R.; Varsavsky, A.; Cook, M.

    2010-01-01

    Full text: Epilepsy is a common neurological disease that affects 0.5-1 % of the world's population. In cases where known treatments cannot achieve complete recovery, seizure prediction is essential so that preventive measures can be undertaken to prevent resultant injury. The elcctroencephalogram (EEG) is a widely used diagnostic tool for epilepsy. However, the EEG does not provide a detailed view of the underlying seizure causing neuronal mechanisms. Knowing the dynamics of the neuronal population is useful because tracking the evolution of the neuronal mechanisms will allow us to track the brain's progression from interictal to ictal state. Wendling and colleagues proposed a parameterised mathematical model that represents the activity of interconnected neuronal populations. By modifying the parameters, this model is able to reproduce signals that are very similar to the real EEG depicting commonly observed patterns during interictal and ictal periods. The transition from non-seizure to seizure activity, as seen in the EEG. is hypothesised to be due to the impairment of inhibition. Using Wendling's model, we designed a deterministic nonlinear estimator to recover the average membrane potential of the neuronal populations from a single channel EEG signal. for any fixed and known parameter values. Our nonlinear estimator is analytically proven to asymptotically converge to the true state of the model and illustrated in simulations. We were able to computationally observe the dynamics of the three neuronal populations described in the model: excitatory, fast and slow inhibitory populations. This forms a first step towards the prediction of epileptic seiwres. (author)

  11. Reproducible diagnosis of Chronic Lymphocytic Leukemia by flow cytometry

    DEFF Research Database (Denmark)

    Rawstron, Andy C; Kreuzer, Karl-Anton; Soosapilla, Asha

    2018-01-01

    The diagnostic criteria for CLL rely on morphology and immunophenotype. Current approaches have limitations affecting reproducibility and there is no consensus on the role of new markers. The aim of this project was to identify reproducible criteria and consensus on markers recommended for the di...

  12. Participant Nonnaiveté and the reproducibility of cognitive psychology

    NARCIS (Netherlands)

    R.A. Zwaan (Rolf); D. Pecher (Diane); G. Paolacci (Gabriele); S. Bouwmeester (Samantha); P.P.J.L. Verkoeijen (Peter); K. Dijkstra (Katinka); R. Zeelenberg (René)

    2017-01-01

    textabstractMany argue that there is a reproducibility crisis in psychology. We investigated nine well-known effects from the cognitive psychology literature—three each from the domains of perception/action, memory, and language, respectively—and found that they are highly reproducible. Not only can

  13. Ceramic molar crown reproducibility by digital workflow manufacturing: An in vitro study.

    Science.gov (United States)

    Jeong, Ii-Do; Kim, Woong-Chul; Park, Jinyoung; Kim, Chong-Myeong; Kim, Ji-Hwan

    2017-08-01

    This in vitro study aimed to analyze and compare the reproducibility of zirconia and lithium disilicate crowns manufactured by digital workflow. A typodont model with a prepped upper first molar was set in a phantom head, and a digital impression was obtained with a video intraoral scanner (CEREC Omnicam; Sirona GmbH), from which a single crown was designed and manufactured with CAD/CAM into a zirconia crown and lithium disilicate crown (n=12). Reproducibility of each crown was quantitatively retrieved by superimposing the digitized data of the crown in 3D inspection software, and differences were graphically mapped in color. Areas with large differences were analyzed with digital microscopy. Mean quadratic deviations (RMS) quantitatively obtained from each ceramic group were statistically analyzed with Student's t-test (α=.05). The RMS value of lithium disilicate crown was 29.2 (4.1) µm and 17.6 (5.5) µm on the outer and inner surfaces, respectively, whereas these values were 18.6 (2.0) µm and 20.6 (5.1) µm for the zirconia crown. Reproducibility of zirconia and lithium disilicate crowns had a statistically significant difference only on the outer surface ( P <.001). The outer surface of lithium disilicate crown showed over-contouring on the buccal surface and under-contouring on the inner occlusal surface. The outer surface of zirconia crown showed both over- and under-contouring on the buccal surface, and the inner surface showed under-contouring in the marginal areas. Restoration manufacturing by digital workflow will enhance the reproducibility of zirconia single crowns more than that of lithium disilicate single crowns.

  14. Reproducing 2D breast mammography images with 3D printed phantoms

    Science.gov (United States)

    Clark, Matthew; Ghammraoui, Bahaa; Badal, Andreu

    2016-03-01

    Mammography is currently the standard imaging modality used to screen women for breast abnormalities and, as a result, it is a tool of great importance for the early detection of breast cancer. Physical phantoms are commonly used as surrogates of breast tissue to evaluate some aspects of the performance of mammography systems. However, most phantoms do not reproduce the anatomic heterogeneity of real breasts. New fabrication technologies, such as 3D printing, have created the opportunity to build more complex, anatomically realistic breast phantoms that could potentially assist in the evaluation of mammography systems. The primary objective of this work is to present a simple, easily reproducible methodology to design and print 3D objects that replicate the attenuation profile observed in real 2D mammograms. The secondary objective is to evaluate the capabilities and limitations of the competing 3D printing technologies, and characterize the x-ray properties of the different materials they use. Printable phantoms can be created using the open-source code introduced in this work, which processes a raw mammography image to estimate the amount of x-ray attenuation at each pixel, and outputs a triangle mesh object that encodes the observed attenuation map. The conversion from the observed pixel gray value to a column of printed material with equivalent attenuation requires certain assumptions and knowledge of multiple imaging system parameters, such as x-ray energy spectrum, source-to-object distance, compressed breast thickness, and average breast material attenuation. A detailed description of the new software, a characterization of the printed materials using x-ray spectroscopy, and an evaluation of the realism of the sample printed phantoms are presented.

  15. A Framework for Reproducible Latent Fingerprint Enhancements.

    Science.gov (United States)

    Carasso, Alfred S

    2014-01-01

    Photoshop processing of latent fingerprints is the preferred methodology among law enforcement forensic experts, but that appproach is not fully reproducible and may lead to questionable enhancements. Alternative, independent, fully reproducible enhancements, using IDL Histogram Equalization and IDL Adaptive Histogram Equalization, can produce better-defined ridge structures, along with considerable background information. Applying a systematic slow motion smoothing procedure to such IDL enhancements, based on the rapid FFT solution of a Lévy stable fractional diffusion equation, can attenuate background detail while preserving ridge information. The resulting smoothed latent print enhancements are comparable to, but distinct from, forensic Photoshop images suitable for input into automated fingerprint identification systems, (AFIS). In addition, this progressive smoothing procedure can be reexamined by displaying the suite of progressively smoother IDL images. That suite can be stored, providing an audit trail that allows monitoring for possible loss of useful information, in transit to the user-selected optimal image. Such independent and fully reproducible enhancements provide a valuable frame of reference that may be helpful in informing, complementing, and possibly validating the forensic Photoshop methodology.

  16. Observations and NLTE modeling of Ellerman bombs

    Science.gov (United States)

    Berlicki, A.; Heinzel, P.

    2014-07-01

    Context. Ellerman bombs (EBs) are short-lived, compact, and spatially well localized emission structures that are observed well in the wings of the hydrogen Hα line. EBs are also observed in the chromospheric CaII lines and in UV continua as bright points located within active regions. Hα line profiles of EBs show a deep absorption at the line center and enhanced emission in the line wings with maxima around ±1 Å from the line center. Similar shapes of the line profiles are observed for the CaII IR line at 8542 Å. In CaII H and K lines the emission peaks are much stronger, and EBs emission is also enhanced in the line center. Aims: It is generally accepted that EBs may be considered as compact microflares located in lower solar atmosphere that contribute to the heating of these low-lying regions, close to the temperature minimum of the atmosphere. However, it is still not clear where exactly the emission of EBs is formed in the solar atmosphere. High-resolution spectrophotometric observations of EBs were used for determining of their physical parameters and construction of semi-empirical models. Obtained models allow us to determine the position of EBs in the solar atmosphere, as well as the vertical structure of the activated EB atmosphere Methods: In our analysis we used observations of EBs obtained in the Hα and CaII H lines with the Dutch Open Telescope (DOT). These one-hour long simultaneous sequences obtained with high temporal and spatial resolution were used to determine the line emissions. To analyze them, we used NLTE numerical codes for the construction of grids of 243 semi-empirical models simulating EBs structures. In this way, the observed emission could be compared with the synthetic line spectra calculated for all such models. Results: For a specific model we found reasonable agreement between the observed and theoretical emission and thus we consider such model as a good approximation to EBs atmospheres. This model is characterized by an

  17. An aging elasto-viscoplastic model for ceramics

    International Nuclear Information System (INIS)

    Soulacroix, Julian; Michel, Bruno; Gatt, Jean-Marie; Kubler, Regis; Barrallier, Laurent

    2014-01-01

    A model reproducing strain softening behavior in ceramic materials is proposed. This model is base on a critical treatment of previous mechanical experimental results, mainly on uranium dioxide. The main hypothesis is that the strain softening phenomenon is related to an aging process, where some point defects move towards the dislocations and modify their velocity. This is different from most of models used up to now, as they were based on the hypothesis that only the initial lack of dislocations was responsible of the strain softening behavior. A model is first developed in a simple 1D framework. Evolution of the mechanical behavior with strain rate and temperature is well reproduced by this model. Then, the 1D model is extended to a 3D mechanical model, and mechanical compressive tests on UO 2 pellets are simulated. The 3D model well reproduces the observed asymmetrical shape of the compressed pellet if one considers that the material is not initially perfectly homogeneous, which highlights the importance of accounting for spatial heterogeneity of materials in models. (authors)

  18. An improved cost-effective, reproducible method for evaluation of bone loss in a rodent model.

    Science.gov (United States)

    Fine, Daniel H; Schreiner, Helen; Nasri-Heir, Cibele; Greenberg, Barbara; Jiang, Shuying; Markowitz, Kenneth; Furgang, David

    2009-02-01

    This study was designed to investigate the utility of two "new" definitions for assessment of bone loss in a rodent model of periodontitis. Eighteen rats were divided into three groups. Group 1 was infected by Aggregatibacter actinomycetemcomitans (Aa), group 2 was infected with an Aa leukotoxin knock-out, and group 3 received no Aa (controls). Microbial sampling and antibody titres were determined. Initially, two examiners measured the distance from the cemento-enamel-junction to alveolar bone crest using the three following methods; (1) total area of bone loss by radiograph, (2) linear bone loss by radiograph, (3) a direct visual measurement (DVM) of horizontal bone loss. Two "new" definitions were adopted; (1) any site in infected animals showing bone loss >2 standard deviations above the mean seen at that site in control animals was recorded as bone loss, (2) any animal with two or more sites in any quadrant affected by bone loss was considered as diseased. Using the "new" definitions both evaluators independently found that infected animals had significantly more disease than controls (DVM system; p<0.05). The DVM method provides a simple, cost effective, and reproducible method for studying periodontal disease in rodents.

  19. An analysis of reproducibility and non-determinism in HEP software and ROOT data

    Science.gov (United States)

    Ivie, Peter; Zheng, Charles; Lannon, Kevin; Thain, Douglas

    2017-10-01

    Reproducibility is an essential component of the scientific method. In order to validate the correctness or facilitate the extension of a computational result, it should be possible to re-run a published result and verify that the same results are produced. However, reproducing a computational result is surprisingly difficult: non-determinism and other factors may make it impossible to get the same result, even when running the same code on the same machine on the same day. We explore this problem in the context of HEP codes and data, showing three high level methods for dealing with non-determinism in general: 1) Domain specific methods; 2) Domain specific comparisons; and 3) Virtualization adjustments. Using a CMS workflow with output data stored in ROOT files, we use these methods to prevent, detect, and eliminate some sources of non-determinism. We observe improved determinism using pre-determined random seeds, a predictable progression of system timestamps, and fixed process identifiers. Unfortunately, sources of non-determinism continue to exist despite the combination of all three methods. Hierarchical data comparisons also allow us to appropriately ignore some non-determinism when it is unavoidable. We conclude that there is still room for improvement, and identify directions that can be taken in each method to make an experiment more reproducible.

  20. Cosmological observables in the quasi-spherical Szekeres model

    Science.gov (United States)

    Buckley, Robert G.

    2014-10-01

    The standard model of cosmology presents a homogeneous universe, and we interpret cosmological data through this framework. However, structure growth creates nonlinear inhomogeneities that may affect observations, and even larger structures may be hidden by our limited vantage point and small number of independent observations. As we determine the universe's parameters with increasing precision, the accuracy is contingent on our understanding of the effects of such structures. For instance, giant void models can explain some observations without dark energy. Because perturbation theory cannot adequately describe nonlinear inhomogeneities, exact solutions to the equations of general relativity are important for these questions. The most general known solution capable of describing inhomogeneous matter distributions is the Szekeres class of models. In this work, we study the quasi-spherical subclass of these models, using numerical simulations to calculate the inhomogeneities' effects on observations. We calculate the large-angle CMB in giant void models and compare with simpler, symmetric void models that have previously been found inadequate to matchobservations. We extend this by considering models with early-time inhomogeneities as well. Then, we study distance observations, including selection effects, in models which are homogeneous on scales around 100 Mpc---consistent with standard cosmology---but inhomogeneous on smaller scales. Finally, we consider photon polarizations, and show that they are not directly affected by inhomogeneities. Overall, we find that while Szekeres models have some advantages over simpler models, they are still seriously limited in their ability to alter our parameter estimation while remaining within the bounds of current observations.

  1. Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography—Tandem Mass Spectrometry

    Science.gov (United States)

    Tabb, David L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Variyath, Asokan Mulayath; Ham, Amy-Joan L.; Bunk, David M.; Kilpatrick, Lisa E.; Billheimer, Dean D.; Blackman, Ronald K.; Cardasis, Helene L.; Carr, Steven A.; Clauser, Karl R.; Jaffe, Jacob D.; Kowalski, Kevin A.; Neubert, Thomas A.; Regnier, Fred E.; Schilling, Birgit; Tegeler, Tony J.; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fisher, Susan J.; Gibson, Bradford W.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Stein, Steven E.; Tempst, Paul; Paulovich, Amanda G.; Liebler, Daniel C.; Spiegelman, Cliff

    2009-01-01

    The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs of technical replicates overlapped by 35–60%, giving a range for peptide-level repeatability in these experiments. Sample complexity did not appear to affect peptide identification repeatability, even as numbers of identified spectra changed by an order of magnitude. Statistical analysis of protein spectral counts revealed greater stability across technical replicates for Orbitraps, making them superior to LTQ instruments for biomarker candidate discovery. The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides. Reproducibility among different instruments of the same type lagged behind

  2. Observable cosmology and cosmological models

    International Nuclear Information System (INIS)

    Kardashev, N.S.; Lukash, V.N.; Novikov, I.D.

    1987-01-01

    Modern state of observation cosmology is briefly discussed. Among other things, a problem, related to Hibble constant and slowdown constant determining is considered. Within ''pancake'' theory hot (neutrino) cosmological model explains well the large-scale structure of the Universe, but does not explain the galaxy formation. A cold cosmological model explains well light object formation, but contradicts data on large-scale structure

  3. Inter- and intra-rater reproducibility of semiautomatic determination of volume parameters in cardiac magnetic resonance imaging

    International Nuclear Information System (INIS)

    Trieb, Thomas; Glodny, Bernhard; Scheiblhofer, Martin; Wolf, Christian; Metzler, Bernhard; Pachinger, Otmar; Jaschke, Werner R.; Schocke, Michael F.H.

    2008-01-01

    Purpose: The purpose of this study was to evaluate inter- and intra-rater reproducibility in volume assessment using cardiac magnetic resonance imaging (CMRI). Methods: Twenty-five healthy volunteers and 106 patients were included into this retrospective study and received CMRI. The patients were divided in three groups (group I, 80 patients with arrhythmia; group II, 20 patients with cardiomyopathy; group III, 6 patients after correction of septum defects). Therefore, the images were semiautomatically segmented by an experienced and an unexperienced radiologists. The analysis of end-diastolic volume (EDV), end-systolic volume (ESV) and stroke volume (SV) as well as ejection fraction (EF) and myocardial mass (MM) were performed twice by an experienced and an unexperienced radiologists. The intra-class correlation coefficients (ICC) were determined for the evaluation of inter- and intra-rater variance. Results: The intra-rater reproducibility for determination of EF, ESV, EDV and MM was excellent with ICCs ranging from 0.88 to 0.99 (all p < 0.001). The inter-observer reproducibility for these parameters was also excellent with ICCs ranging from 0.91 to 0.98 (all p < 0.001). The assessment of the SV showed an excellent intra-rater agreement with ICCs of 0.96 and 0.92 (both p < 0.001), but only a moderate ICC for the inter-rater reproducibility (0.54, p < 0.001). Conclusions: Our study shows that assessment of cardiac volumes can be performed on CMRIs with an excellent reproducibility by both experienced and unexperienced investigators

  4. Validation and reproducibility of an Australian caffeine food frequency questionnaire.

    Science.gov (United States)

    Watson, E J; Kohler, M; Banks, S; Coates, A M

    2017-08-01

    The aim of this study was to measure validity and reproducibility of a caffeine food frequency questionnaire (C-FFQ) developed for the Australian population. The C-FFQ was designed to assess average daily caffeine consumption using four categories of food and beverages including; energy drinks; soft drinks/soda; coffee and tea and chocolate (food and drink). Participants completed a seven-day food diary immediately followed by the C-FFQ on two consecutive days. The questionnaire was first piloted in 20 adults, and then, a validity/reproducibility study was conducted (n = 90 adults). The C-FFQ showed moderate correlations (r = .60), fair agreement (mean difference 63 mg) and reasonable quintile rankings indicating fair to moderate agreement with the seven-day food diary. To test reproducibility, the C-FFQ was compared to itself and showed strong correlations (r = .90), good quintile rankings and strong kappa values (κ = 0.65), indicating strong reproducibility. The C-FFQ shows adequate validity and reproducibility and will aid researchers in Australia to quantify caffeine consumption.

  5. Evaluation of normality and reproducibility parameters of scintigraphy with (99m)Tc-MAA in the diagnosis of intrapulmonary vascular dilatations.

    Science.gov (United States)

    de Queirós, Andréa Simone Siqueira; Brandão, Simone Cristina Soares; Macedo, Liana Gonçalves; Ourem, Maira Souto; Mota, Vitor Gomes; Leite, Luiz Arthur Calheiros; Lopes, Edmundo Pessoa Almeida; Domingues, Ana Lúcia Coutinho

    2015-01-01

    The formation of intrapulmonary vascular dilations (IPVD) is the key event for the onset of hepatopulmonary syndrome, vascular changes secondary to portal hypertension that leads to hypoxemia. The diagnosis of IPVD can be made by contrasted transthoracic echocardiography or scintigraphy with technetium-macroaggregated albumin-((99m)Tc-MAA)-that is a sensitive and specific diagnostic method and quantifies the IPVD magnitude. However, its procedure and diagnostic indices are not yet standardized and well defined in health services. The aims of this study were to define normality values and evaluate the inter- and intra-observer reproducibility degree of diagnostic indexes of IPVD through (99m)Tc-MAA scintigraphy. Cross-sectional study was conducted at the Clinical Hospital, Federal University of Pernambuco (HC-UFPE) between July and December 2012. Fifteen patients with hepatosplenic schistosomiasis and nine patients without liver or heart disease (control group) were assessed. After clinical assessment, ultrasound and echocardiography, patients underwent (99m)Tc-MAA scintigraphy, and a relative brain uptake value exceeding 6 % or systemic uptake value exceeding 11 % was considered diagnostic of IPVD. Each assessment was performed by two independent observers. To analyze the results of the normal group, the nonparametric Bootsptrap method simulation model combined with the Monte Carlo method was used and to analyze inter- and intra-observer reproducibility indexes, the kappa and intra-class correlation coefficient were used. In normal subjects, the average brain uptake of (99m)Tc-MAA was 7.9 ± 0.01 % and systemic uptake was 12.4 ± 0.03 %, with low dispersal rates for both measures. The intra-observer agreement was 100 %, with kappa index of 1.0 (p brain uptake; however, systemic uptake showed kappa = 0.25 (p = 0.07), which features tolerable concordance. The intra-class correlation was excellent for both uptake indexes. The normality values were

  6. Supply based on demand dynamical model

    Science.gov (United States)

    Levi, Asaf; Sabuco, Juan; Sanjuán, Miguel A. F.

    2018-04-01

    We propose and numerically analyze a simple dynamical model that describes the firm behaviors under uncertainty of demand. Iterating this simple model and varying some parameter values, we observe a wide variety of market dynamics such as equilibria, periodic, and chaotic behaviors. Interestingly, the model is also able to reproduce market collapses.

  7. Observations involving broadband impedance modelling

    Energy Technology Data Exchange (ETDEWEB)

    Berg, J S [Stanford Linear Accelerator Center, Menlo Park, CA (United States)

    1996-08-01

    Results for single- and multi-bunch instabilities can be significantly affected by the precise model that is used for the broadband impedance. This paper discusses three aspects of broadband impedance modelling. The first is an observation of the effect that a seemingly minor change in an impedance model has on the single-bunch mode coupling threshold. The second is a successful attempt to construct a model for the high-frequency tails of an r.f. cavity. The last is a discussion of requirements for the mathematical form of an impedance which follow from the general properties of impedances. (author)

  8. Observations involving broadband impedance modelling

    International Nuclear Information System (INIS)

    Berg, J.S.

    1995-08-01

    Results for single- and multi-bunch instabilities can be significantly affected by the precise model that is used for the broadband impendance. This paper discusses three aspects of broadband impendance modeling. The first is an observation of the effect that a seemingly minor change in an impedance model has on the single-bunch mode coupling threshold. The second is a successful attempt to construct a model for the high-frequency tails of an r.f cavity. The last is a discussion of requirements for the mathematical form of an impendance which follow from the general properties of impendances

  9. An Exospheric Temperature Model Based On CHAMP Observations and TIEGCM Simulations

    Science.gov (United States)

    Ruan, Haibing; Lei, Jiuhou; Dou, Xiankang; Liu, Siqing; Aa, Ercha

    2018-02-01

    In this work, thermospheric densities from the accelerometer measurement on board the CHAMP satellite during 2002-2009 and the simulations from the National Center for Atmospheric Research Thermosphere Ionosphere Electrodynamics General Circulation Model (NCAR-TIEGCM) are employed to develop an empirical exospheric temperature model (ETM). The two-dimensional basis functions of the ETM are first provided from the principal component analysis of the TIEGCM simulations. Based on the exospheric temperatures derived from CHAMP thermospheric densities, a global distribution of the exospheric temperatures is reconstructed. A parameterization is conducted for each basis function amplitude as a function of solar-geophysical and seasonal conditions. Thus, the ETM can be utilized to model the thermospheric temperature and mass density under a specified condition. Our results showed that the averaged standard deviation of the ETM is generally less than 10% than approximately 30% in the MSIS model. Besides, the ETM reproduces the global thermospheric evolutions including the equatorial thermosphere anomaly.

  10. Seasonal & Daily Amazon Column CO2 & CO Observations from Ground & Space Used to Evaluate Tropical Ecosystem Models

    Science.gov (United States)

    Dubey, M. K.; Parker, H. A.; Wennberg, P. O.; Wunch, D.; Jacobson, A. R.; Kawa, S. R.; Keppel-Aleks, G.; Basu, S.; O'Dell, C.; Frankenberg, C.; Michalak, A. M.; Baker, D. F.; Christofferson, B.; Restrepo-Coupe, N.; Saleska, S. R.; De Araujo, A. C.; Miller, J. B.

    2016-12-01

    The Amazon basin stores 150-200 PgC, exchanges 18 PgC with the atmosphere every year and has taken up 0.42-0.65 PgC/y over the past two decades. Despite its global significance, the response of the tropical carbon cycle to climate variability and change is ill constrained as evidenced by the large negative and positive feedbacks in future climate simulations. The complex interplay of radiation, water and ecosystem phenology remains unresolved in current tropical ecosystem models. We use high frequency regional scale TCCON observations of column CO2, CO and CH4 near Manaus, Brazil that began in October 2014 to understand the aforementioned interplay of processes in regulating biosphere-atmosphere exchange. We observe a robust daily column CO2 uptake of about 2 ppm (4 ppm to 0.5 ppm) over 8 hours and evaluate how it changes as we transition to the dry season. Back-trajectory calculations show that the daily CO2 uptake footprint is terrestrial and influenced by the heterogeneity of the Amazon rain forests. The column CO falls from above 120 ppb to below 80 ppb as we transition from the biomass burning to wet seasons. The daily mean column CO2 rises by 3 ppm from October through June. Removal of biomass burning, secular CO2 increase and variations from transport (by Carbon tracker simulations) implies an increase of 2.3 ppm results from tropical biospheric processes (respiration and photosynthesis). This is consistent with ground-based remote sensing and eddy flux observations that indicate that leaf development and demography drives the tropical carbon cycle in regions that are not water limited and is not considered in current models. We compare our observations with output from 7 CO2 inversion transport models with assimilated meteorology and find that while 5 models reproduce the CO2 seasonal cycle all of them under predict the daily drawdown of CO2 by a factor of 3. This indicates that the CO2 flux partitioning between photosynthesis and respiration is incorrect

  11. Hydrological Modeling in Northern Tunisia with Regional Climate Model Outputs: Performance Evaluation and Bias-Correction in Present Climate Conditions

    Directory of Open Access Journals (Sweden)

    Asma Foughali

    2015-07-01

    Full Text Available This work aims to evaluate the performance of a hydrological balance model in a watershed located in northern Tunisia (wadi Sejnane, 378 km2 in present climate conditions using input variables provided by four regional climate models. A modified version (MBBH of the lumped and single layer surface model BBH (Bucket with Bottom Hole model, in which pedo-transfer parameters estimated using watershed physiographic characteristics are introduced is adopted to simulate the water balance components. Only two parameters representing respectively the water retention capacity of the soil and the vegetation resistance to evapotranspiration are calibrated using rainfall-runoff data. The evaluation criterions for the MBBH model calibration are: relative bias, mean square error and the ratio of mean actual evapotranspiration to mean potential evapotranspiration. Daily air temperature, rainfall and runoff observations are available from 1960 to 1984. The period 1960–1971 is selected for calibration while the period 1972–1984 is chosen for validation. Air temperature and precipitation series are provided by four regional climate models (DMI, ARP, SMH and ICT from the European program ENSEMBLES, forced by two global climate models (GCM: ECHAM and ARPEGE. The regional climate model outputs (precipitation and air temperature are compared to the observations in terms of statistical distribution. The analysis was performed at the seasonal scale for precipitation. We found out that RCM precipitation must be corrected before being introduced as MBBH inputs. Thus, a non-parametric quantile-quantile bias correction method together with a dry day correction is employed. Finally, simulated runoff generated using corrected precipitation from the regional climate model SMH is found the most acceptable by comparison with runoff simulated using observed precipitation data, to reproduce the temporal variability of mean monthly runoff. The SMH model is the most accurate to

  12. Ecosystem function in complex mountain terrain: Combining models and long-term observations to advance process-based understanding

    Science.gov (United States)

    Wieder, William R.; Knowles, John F.; Blanken, Peter D.; Swenson, Sean C.; Suding, Katharine N.

    2017-04-01

    Abiotic factors structure plant community composition and ecosystem function across many different spatial scales. Often, such variation is considered at regional or global scales, but here we ask whether ecosystem-scale simulations can be used to better understand landscape-level variation that might be particularly important in complex terrain, such as high-elevation mountains. We performed ecosystem-scale simulations by using the Community Land Model (CLM) version 4.5 to better understand how the increased length of growing seasons may impact carbon, water, and energy fluxes in an alpine tundra landscape. The model was forced with meteorological data and validated with observations from the Niwot Ridge Long Term Ecological Research Program site. Our results demonstrate that CLM is capable of reproducing the observed carbon, water, and energy fluxes for discrete vegetation patches across this heterogeneous ecosystem. We subsequently accelerated snowmelt and increased spring and summer air temperatures in order to simulate potential effects of climate change in this region. We found that vegetation communities that were characterized by different snow accumulation dynamics showed divergent biogeochemical responses to a longer growing season. Contrary to expectations, wet meadow ecosystems showed the strongest decreases in plant productivity under extended summer scenarios because of disruptions in hydrologic connectivity. These findings illustrate how Earth system models such as CLM can be used to generate testable hypotheses about the shifting nature of energy, water, and nutrient limitations across space and through time in heterogeneous landscapes; these hypotheses may ultimately guide further experimental work and model development.

  13. 3D-modeling of the spine using EOS imaging system: Inter-reader reproducibility and reliability.

    Directory of Open Access Journals (Sweden)

    Johannes Rehm

    Full Text Available To retrospectively assess the interreader reproducibility and reliability of EOS 3D full spine reconstructions in patients with adolescent idiopathic scoliosis (AIS.73 patients with mean age of 17 years and a moderate AIS (median Cobb Angle 18.2° obtained low-dose standing biplanar radiographs with EOS. Two independent readers performed "full spine" 3D reconstructions of the spine with the "full-spine" method adjusting the bone contour of every thoracic and lumbar vertebra (Th1-L5. Interreader reproducibility was assessed regarding rotation of every single vertebra in the coronal (i.e. frontal, sagittal (i.e. lateral, and axial plane, T1/T12 kyphosis, T4/T12 kyphosis, L1/L5 lordosis, L1/S1 lordosis and pelvic parameters. Radiation exposure, scan-time and 3D reconstruction time were recorded.Interclass correlation (ICC ranged between 0.83 and 0.98 for frontal vertebral rotation, between 0.94 and 0.99 for lateral vertebral rotation and between 0.51 and 0.88 for axial vertebral rotation. ICC was 0.92 for T1/T12 kyphosis, 0.95 for T4/T12 kyphosis, 0.90 for L1/L5 lordosis, 0.85 for L1/S1 lordosis, 0.97 for pelvic incidence, 0.96 for sacral slope, 0.98 for sagittal pelvic tilt and 0.94 for lateral pelvic tilt. The mean time for reconstruction was 14.9 minutes (reader 1: 14.6 minutes, reader 2: 15.2 minutes, p<0.0001. The mean total absorbed dose was 593.4μGy ±212.3 per patient.EOS "full spine" 3D angle measurement of vertebral rotation proved to be reliable and was performed in an acceptable reconstruction time. Interreader reproducibility of axial rotation was limited to some degree in the upper and middle thoracic spine due the obtuse angulation of the pedicles and the processi spinosi in the frontal view somewhat complicating their delineation.

  14. Reproducible and controllable induction voltage adder for scaled beam experiments

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, Yasuo; Nakajima, Mitsuo; Horioka, Kazuhiko [Department of Energy Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502 (Japan)

    2016-08-15

    A reproducible and controllable induction adder was developed using solid-state switching devices and Finemet cores for scaled beam compression experiments. A gate controlled MOSFET circuit was developed for the controllable voltage driver. The MOSFET circuit drove the induction adder at low magnetization levels of the cores which enabled us to form reproducible modulation voltages with jitter less than 0.3 ns. Preliminary beam compression experiments indicated that the induction adder can improve the reproducibility of modulation voltages and advance the beam physics experiments.

  15. Understanding the persistence of measles: reconciling theory, simulation and observation.

    Science.gov (United States)

    Keeling, Matt J; Grenfell, Bryan T

    2002-01-01

    Ever since the pattern of localized extinction associated with measles was discovered by Bartlett in 1957, many models have been developed in an attempt to reproduce this phenomenon. Recently, the use of constant infectious and incubation periods, rather than the more convenient exponential forms, has been presented as a simple means of obtaining realistic persistence levels. However, this result appears at odds with rigorous mathematical theory; here we reconcile these differences. Using a deterministic approach, we parameterize a variety of models to fit the observed biennial attractor, thus determining the level of seasonality by the choice of model. We can then compare fairly the persistence of the stochastic versions of these models, using the 'best-fit' parameters. Finally, we consider the differences between the observed fade-out pattern and the more theoretically appealing 'first passage time'. PMID:11886620

  16. Dwarf novae in outburst: modelling the observations

    International Nuclear Information System (INIS)

    Pringle, J.E.; Verbunt, F.

    1986-01-01

    Time-dependent accretion-disc models are constructed and used to calculate theoretical spectra in order to try to fit the ultraviolet and optical observations of outbursts of the two dwarf novae VW Hydri and CN Orionis. It is found that the behaviour on the rise to outburst is the strongest discriminator between theoretical models. The mass-transfer burst model is able to fit the spectral behaviour for both objects. The disc-instability model is unable to fit the rise to outburst in VW Hydri, and gives a poor fit to the observations of CN Orionis. (author)

  17. Numerical modeling of an estuary: A comprehensive skill assessment

    Science.gov (United States)

    Warner, J.C.; Geyer, W.R.; Lerczak, J.A.

    2005-01-01

    Numerical simulations of the Hudson River estuary using a terrain-following, three-dimensional model (Regional Ocean Modeling System (ROMS)) are compared with an extensive set of time series and spatially resolved measurements over a 43 day period with large variations in tidal forcing and river discharge. The model is particularly effective at reproducing the observed temporal variations in both the salinity and current structure, including tidal, spring neap, and river discharge-induced variability. Large observed variations in stratification between neap and spring tides are captured qualitatively and quantitatively by the model. The observed structure and variations of the longitudinal salinity gradient are also well reproduced. The most notable discrepancy between the model and the data is in the vertical salinity structure. While the surface-to-bottom salinity difference is well reproduced, the stratification in the model tends to extend all the way to the water surface, whereas the observations indicate a distinct pycnocline and a surface mixed layer. Because the southern boundary coindition is located near the mouth the estuary, the salinity within the domain is particularly sensitive to the specification of salinity at the boundary. A boundary condition for the horizontal salinity gradient, based on the local value of salinity, is developed to incorporate physical processes beyond the open boundary not resolved by the model. Model results are sensitive to the specification of the bottom roughness length and vertical stability functions, insofar as they influence the intensity of vertical mixing. The results only varied slightly between different turbulence closure methods of k-??, k-??, and k-kl. Copyright 2005 by the American Geophysical Union.

  18. Reproducibility of small animal cine and scar cardiac magnetic resonance imaging using a clinical 3.0 tesla system

    International Nuclear Information System (INIS)

    Manka, Robert; Jahnke, Cosima; Hucko, Thomas; Dietrich, Thore; Gebker, Rolf; Schnackenburg, Bernhard; Graf, Kristof; Paetsch, Ingo

    2013-01-01

    To evaluate the inter-study, inter-reader and intra-reader reproducibility of cardiac cine and scar imaging in rats using a clinical 3.0 Tesla magnetic resonance (MR) system. Thirty-three adult rats (Sprague–Dawley) were imaged 24 hours after surgical occlusion of the left anterior descending coronary artery using a 3.0 Tesla clinical MR scanner (Philips Healthcare, Best, The Netherlands) equipped with a dedicated 70 mm solenoid receive-only coil. Left-ventricular (LV) volumes, mass, ejection fraction and amount of myocardial scar tissue were measured. Intra-and inter-observer reproducibility was assessed in all animals. In addition, repeat MR exams were performed in 6 randomly chosen rats within 24 hours to assess inter-study reproducibility. The MR imaging protocol was successfully completed in 32 (97%) animals. Bland-Altman analysis demonstrated high intra-reader reproducibility (mean bias%: LV end-diastolic volume (LVEDV), -1.7%; LV end-systolic volume (LVESV), -2.2%; LV ejection fraction (LVEF), 1.0%; LV mass, -2.7%; and scar mass, -1.2%) and high inter-reader reproducibility (mean bias%: LVEDV, 3.3%; LVESV, 6.2%; LVEF, -4.8%; LV mass, -1.9%; and scar mass, -1.8%). In addition, a high inter-study reproducibility was found (mean bias%: LVEDV, 0.1%; LVESV, -1.8%; LVEF, 1.0%; LV mass, -4.6%; and scar mass, -6.2%). Cardiac MR imaging of rats yielded highly reproducible measurements of cardiac volumes/function and myocardial infarct size on a clinical 3.0 Tesla MR scanner system. Consequently, more widely available high field clinical MR scanners can be employed for small animal imaging of the heart e.g. when aiming at serial assessments during therapeutic intervention studies

  19. Interannual sedimentary effluxes of alkalinity in the southern North Sea: model results compared with summer observations

    Directory of Open Access Journals (Sweden)

    J. Pätsch

    2018-06-01

    Full Text Available For the sediments of the central and southern North Sea different sources of alkalinity generation are quantified by a regional modelling system for the period 2000–2014. For this purpose a formerly global ocean sediment model coupled with a pelagic ecosystem model is adapted to shelf sea dynamics, where much larger turnover rates than in the open and deep ocean occur. To track alkalinity changes due to different nitrogen-related processes, the open ocean sediment model was extended by the state variables particulate organic nitrogen (PON and ammonium. Directly measured alkalinity fluxes and those derived from Ra isotope flux observation from the sediment into the pelagic are reproduced by the model system, but calcite building and calcite dissolution are underestimated. Both fluxes cancel out in terms of alkalinity generation and consumption. Other simulated processes altering alkalinity in the sediment, like net sulfate reduction, denitrification, nitrification, and aerobic degradation, are quantified and compare well with corresponding fluxes derived from observations. Most of these fluxes exhibit a strong positive gradient from the open North Sea to the coast, where large rivers drain nutrients and organic matter. Atmospheric nitrogen deposition also shows a positive gradient from the open sea towards land and supports alkalinity generation in the sediments. An additional source of spatial variability is introduced by the use of a 3-D heterogenous porosity field. Due to realistic porosity variations (0.3–0.5 the alkalinity fluxes vary by about 4 %. The strongest impact on interannual variations of alkalinity fluxes is exhibited by the temporal varying nitrogen inputs from large rivers directly governing the nitrate concentrations in the coastal bottom water, thus providing nitrate necessary for benthic denitrification. Over the time investigated the alkalinity effluxes decrease due to the decrease in the nitrogen supply by the rivers.

  20. Reproducibility of the chamber scarification test

    DEFF Research Database (Denmark)

    Andersen, Klaus Ejner

    1996-01-01

    The chamber scarification test is a predictive human skin irritation test developed to rank the irritation potential of products and ingredients meant for repeated use on normal and diseased skin. 12 products or ingredients can be tested simultaneously on the forearm skin of each volunteer....... The test combines with the procedure scratching of the skin at each test site and subsequent closed patch tests with the products, repeated daily for 3 days. The test is performed on groups of human volunteers: a skin irritant substance or products is included in each test as a positive control...... high reproducibility of the test. Further, intra-individual variation in skin reaction to the 2 control products in 26 volunteers, who participated 2x, is shown, which supports the conclusion that the chamber scarification test is a useful short-term human skin irritation test with high reproducibility....

  1. Reproducibility of tumor uptake heterogeneity characterization through textural feature analysis in 18F-FDG PET.

    Science.gov (United States)

    Tixier, Florent; Hatt, Mathieu; Le Rest, Catherine Cheze; Le Pogam, Adrien; Corcos, Laurent; Visvikis, Dimitris

    2012-05-01

    (18)F-FDG PET measurement of standardized uptake value (SUV) is increasingly used for monitoring therapy response and predicting outcome. Alternative parameters computed through textural analysis were recently proposed to quantify the heterogeneity of tracer uptake by tumors as a significant predictor of response. The primary objective of this study was to evaluate the reproducibility of these heterogeneity measurements. Double baseline (18)F-FDG PET scans were acquired within 4 d of each other for 16 patients before any treatment was considered. A Bland-Altman analysis was performed on 8 parameters based on histogram measurements and 17 parameters based on textural heterogeneity features after discretization with values between 8 and 128. The reproducibility of maximum and mean SUV was similar to that in previously reported studies, with a mean percentage difference of 4.7% ± 19.5% and 5.5% ± 21.2%, respectively. By comparison, better reproducibility was measured for some textural features describing local heterogeneity of tracer uptake, such as entropy and homogeneity, with a mean percentage difference of -2% ± 5.4% and 1.8% ± 11.5%, respectively. Several regional heterogeneity parameters such as variability in the intensity and size of regions of homogeneous activity distribution had reproducibility similar to that of SUV measurements, with 95% confidence intervals of -22.5% to 3.1% and -1.1% to 23.5%, respectively. These parameters were largely insensitive to the discretization range. Several parameters derived from textural analysis describing heterogeneity of tracer uptake by tumors on local and regional scales had reproducibility similar to or better than that of simple SUV measurements. These reproducibility results suggest that these (18)F-FDG PET-derived parameters, which have already been shown to have predictive and prognostic value in certain cancer models, may be used to monitor therapy response and predict patient outcome.

  2. Evaluation of internal noise methods for Hotelling observer models

    International Nuclear Information System (INIS)

    Zhang Yani; Pham, Binh T.; Eckstein, Miguel P.

    2007-01-01

    The inclusion of internal noise in model observers is a common method to allow for quantitative comparisons between human and model observer performance in visual detection tasks. In this article, we studied two different strategies for inserting internal noise into Hotelling model observers. In the first strategy, internal noise was added to the output of individual channels: (a) Independent nonuniform channel noise, (b) independent uniform channel noise. In the second strategy, internal noise was added to the decision variable arising from the combination of channel responses. The standard deviation of the zero mean internal noise was either constant or proportional to: (a) the decision variable's standard deviation due to the external noise, (b) the decision variable's variance caused by the external noise, (c) the decision variable magnitude on a trial to trial basis. We tested three model observers: square window Hotelling observer (HO), channelized Hotelling observer (CHO), and Laguerre-Gauss Hotelling observer (LGHO) using a four alternative forced choice (4AFC) signal known exactly but variable task with a simulated signal embedded in real x-ray coronary angiogram backgrounds. The results showed that the internal noise method that led to the best prediction of human performance differed across the studied model observers. The CHO model best predicted human observer performance with the channel internal noise. The HO and LGHO best predicted human observer performance with the decision variable internal noise. The present results might guide researchers with the choice of methods to include internal noise into Hotelling model observers when evaluating and optimizing medical image quality

  3. Comprehensive models of diffuse interstellar clouds : physical conditions and molecular abundances

    NARCIS (Netherlands)

    Dishoeck, van E.F.; Black, J.H.

    1986-01-01

    The limitations of steady state models of interstellar clouds are explored by means of comparison with observational data corresponding to clouds in front of Zeta Per, Zeta Oph, Chi Oph, and Omicron Per. The improved cloud models were constructed to reproduce the observed H and H2(J) column

  4. A national drug related problems database: evaluation of use in practice, reliability and reproducibility

    DEFF Research Database (Denmark)

    Kjeldsen, Lene Juel; Birkholm, Trine; Fischer, Hanne Lis

    2014-01-01

    Background A drug related problems database (DRP-database) was developed on request by clinical pharmacists. The information from the DRP-database has only been used locally e.g. to identify focus areas and to communicate identified DRPs to the hospital wards. Hence the quality of the data...... by clinical pharmacists with categorization performed by the project group. Reproducibility was explored by re-categorization of a sample of existing records in the DRP-database by two project group members individually. Main outcome measures Observed proportion of agreement and Fleiss' kappa as measures...... reliability study of 34 clinical pharmacists showed high inter-rater reliability with the project group (Fleiss' kappa = 0.79 with 95 % CI (0.70; 0.88)), and the reproducibility study also documented high inter-rater reliability of a sample of 379 records from the DRP-database re-categorized by two project...

  5. Efficient and reproducible identification of mismatch repair deficient colon cancer

    DEFF Research Database (Denmark)

    Joost, Patrick; Bendahl, Pär-Ola; Halvarsson, Britta

    2013-01-01

    BACKGROUND: The identification of mismatch-repair (MMR) defective colon cancer is clinically relevant for diagnostic, prognostic and potentially also for treatment predictive purposes. Preselection of tumors for MMR analysis can be obtained with predictive models, which need to demonstrate ease...... of application and favorable reproducibility. METHODS: We validated the MMR index for the identification of prognostically favorable MMR deficient colon cancers and compared performance to 5 other prediction models. In total, 474 colon cancers diagnosed ≥ age 50 were evaluated with correlation between...... clinicopathologic variables and immunohistochemical MMR protein expression. RESULTS: Female sex, age ≥60 years, proximal tumor location, expanding growth pattern, lack of dirty necrosis, mucinous differentiation and presence of tumor-infiltrating lymphocytes significantly correlated with MMR deficiency. Presence...

  6. A Community Data Model for Hydrologic Observations

    Science.gov (United States)

    Tarboton, D. G.; Horsburgh, J. S.; Zaslavsky, I.; Maidment, D. R.; Valentine, D.; Jennings, B.

    2006-12-01

    The CUAHSI Hydrologic Information System project is developing information technology infrastructure to support hydrologic science. Hydrologic information science involves the description of hydrologic environments in a consistent way, using data models for information integration. This includes a hydrologic observations data model for the storage and retrieval of hydrologic observations in a relational database designed to facilitate data retrieval for integrated analysis of information collected by multiple investigators. It is intended to provide a standard format to facilitate the effective sharing of information between investigators and to facilitate analysis of information within a single study area or hydrologic observatory, or across hydrologic observatories and regions. The observations data model is designed to store hydrologic observations and sufficient ancillary information (metadata) about the observations to allow them to be unambiguously interpreted and used and provide traceable heritage from raw measurements to usable information. The design is based on the premise that a relational database at the single observation level is most effective for providing querying capability and cross dimension data retrieval and analysis. This premise is being tested through the implementation of a prototype hydrologic observations database, and the development of web services for the retrieval of data from and ingestion of data into the database. These web services hosted by the San Diego Supercomputer center make data in the database accessible both through a Hydrologic Data Access System portal and directly from applications software such as Excel, Matlab and ArcGIS that have Standard Object Access Protocol (SOAP) capability. This paper will (1) describe the data model; (2) demonstrate the capability for representing diverse data in the same database; (3) demonstrate the use of the database from applications software for the performance of hydrologic analysis

  7. 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.

  8. Simulating flaring events in complex active regions driven by observed magnetograms

    Science.gov (United States)

    Dimitropoulou, M.; Isliker, H.; Vlahos, L.; Georgoulis, M. K.

    2011-05-01

    Context. We interpret solar flares as events originating in active regions that have reached the self organized critical state, by using a refined cellular automaton model with initial conditions derived from observations. Aims: We investigate whether the system, with its imposed physical elements, reaches a self organized critical state and whether well-known statistical properties of flares, such as scaling laws observed in the distribution functions of characteristic parameters, are reproduced after this state has been reached. Methods: To investigate whether the distribution functions of total energy, peak energy and event duration follow the expected scaling laws, we first applied a nonlinear force-free extrapolation that reconstructs the three-dimensional magnetic fields from two-dimensional vector magnetograms. We then locate magnetic discontinuities exceeding a threshold in the Laplacian of the magnetic field. These discontinuities are relaxed in local diffusion events, implemented in the form of cellular automaton evolution rules. Subsequent loading and relaxation steps lead the system to self organized criticality, after which the statistical properties of the simulated events are examined. Physical requirements, such as the divergence-free condition for the magnetic field vector, are approximately imposed on all elements of the model. Results: Our results show that self organized criticality is indeed reached when applying specific loading and relaxation rules. Power-law indices obtained from the distribution functions of the modeled flaring events are in good agreement with observations. Single power laws (peak and total flare energy) are obtained, as are power laws with exponential cutoff and double power laws (flare duration). The results are also compared with observational X-ray data from the GOES satellite for our active-region sample. Conclusions: We conclude that well-known statistical properties of flares are reproduced after the system has

  9. A Unimodal Model for Double Observer Distance Sampling Surveys.

    Directory of Open Access Journals (Sweden)

    Earl F Becker

    Full Text Available Distance sampling is a widely used method to estimate animal population size. Most distance sampling models utilize a monotonically decreasing detection function such as a half-normal. Recent advances in distance sampling modeling allow for the incorporation of covariates into the distance model, and the elimination of the assumption of perfect detection at some fixed distance (usually the transect line with the use of double-observer models. The assumption of full observer independence in the double-observer model is problematic, but can be addressed by using the point independence assumption which assumes there is one distance, the apex of the detection function, where the 2 observers are assumed independent. Aerially collected distance sampling data can have a unimodal shape and have been successfully modeled with a gamma detection function. Covariates in gamma detection models cause the apex of detection to shift depending upon covariate levels, making this model incompatible with the point independence assumption when using double-observer data. This paper reports a unimodal detection model based on a two-piece normal distribution that allows covariates, has only one apex, and is consistent with the point independence assumption when double-observer data are utilized. An aerial line-transect survey of black bears in Alaska illustrate how this method can be applied.

  10. Reproducibility of qualitative assessments of temporal lobe atrophy in MRI studies.

    Science.gov (United States)

    Sarria-Estrada, S; Acevedo, C; Mitjana, R; Frascheri, L; Siurana, S; Auger, C; Rovira, A

    2015-01-01

    To determine the reproducibility of the Scheltens visual rating scale in establishing atrophy of the medial temporal lobe. We used coronal T1-weighted inversion recovery sequences on a 1.5 Tesla MRI scanner to study 25 patients with clinically diagnosed Alzheimer's disease or mild cognitive decline and 25 subjects without cognitive decline. Five neuroradiologists trained to apply the Scheltens visual rating scale analyzed the images. We used the interclass correlation coefficient to evaluate interrater and intrarater agreement. Raters scored 20 (80%) of the 25 patients with mild cognitive decline or Alzheimer's disease between 2 and 4; by contrast, they scored 21 (84%) of the 25 subjects without cognitive decline between 0 and 1. The interrater agreement was consistently greater than 0.82, with a 95% confidence interval of (0.7-0.9). The intrarater agreement ranged from 0.82 to 0.87, with a 95% confidence interval of (0.56-0.93). The Scheltens visual rating scale is reproducible among observers, and this finding supports its use in clinical practice. Copyright © 2013 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

  11. Reproducibility problems of in-service ultrasonic testing results

    International Nuclear Information System (INIS)

    Honcu, E.

    1974-01-01

    The reproducibility of the results of ultrasonic testing is the basic precondition for its successful application in in-service inspection of changes in the quality of components of nuclear power installations. The results of periodic ultrasonic inspections are not satisfactory from the point of view of reproducibility. Regardless, the ultrasonic pulse-type method is suitable for evaluating the quality of most components of nuclear installations and often the sole method which may be recommended for inspection with regard to its technical and economic aspects. (J.B.)

  12. Comment on "Most computational hydrology is not reproducible, so is it really science?" by Christopher Hutton et al.

    Science.gov (United States)

    Añel, Juan A.

    2017-03-01

    Nowadays, the majority of the scientific community is not aware of the risks and problems associated with an inadequate use of computer systems for research, mostly for reproducibility of scientific results. Such reproducibility can be compromised by the lack of clear standards and insufficient methodological description of the computational details involved in an experiment. In addition, the inappropriate application or ignorance of copyright laws can have undesirable effects on access to aspects of great importance of the design of experiments and therefore to the interpretation of results.Plain Language SummaryThis article highlights several important issues to ensure the scientific reproducibility of results within the current scientific framework, going beyond simple documentation. Several specific examples are discussed in the field of hydrological modeling.

  13. The MIMIC Code Repository: enabling reproducibility in critical care research.

    Science.gov (United States)

    Johnson, Alistair Ew; Stone, David J; Celi, Leo A; Pollard, Tom J

    2018-01-01

    Lack of reproducibility in medical studies is a barrier to the generation of a robust knowledge base to support clinical decision-making. In this paper we outline the Medical Information Mart for Intensive Care (MIMIC) Code Repository, a centralized code base for generating reproducible studies on an openly available critical care dataset. Code is provided to load the data into a relational structure, create extractions of the data, and reproduce entire analysis plans including research studies. Concepts extracted include severity of illness scores, comorbid status, administrative definitions of sepsis, physiologic criteria for sepsis, organ failure scores, treatment administration, and more. Executable documents are used for tutorials and reproduce published studies end-to-end, providing a template for future researchers to replicate. The repository's issue tracker enables community discussion about the data and concepts, allowing users to collaboratively improve the resource. The centralized repository provides a platform for users of the data to interact directly with the data generators, facilitating greater understanding of the data. It also provides a location for the community to collaborate on necessary concepts for research progress and share them with a larger audience. Consistent application of the same code for underlying concepts is a key step in ensuring that research studies on the MIMIC database are comparable and reproducible. By providing open source code alongside the freely accessible MIMIC-III database, we enable end-to-end reproducible analysis of electronic health records. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.

  14. The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

    Energy Technology Data Exchange (ETDEWEB)

    Alcaraz, Olga; Trullàs, Joaquim, E-mail: quim.trullas@upc.edu [Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord UPC B4-B5, 08034 Barcelona (Spain); Tahara, Shuta [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, Okinawa 903-0213 (Japan); Kawakita, Yukinobu [J-PARC Center, Japan Atomic Energy Agency (JAEA), Ibaraki 319-1195 (Japan); Takeda, Shin’ichi [Department of Physics, Faculty of Sciences, Kyushu University, Fukuoka 819-0395 (Japan)

    2016-09-07

    The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å{sup −1} related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.

  15. The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

    International Nuclear Information System (INIS)

    Alcaraz, Olga; Trullàs, Joaquim; Tahara, Shuta; Kawakita, Yukinobu; Takeda, Shin’ichi

    2016-01-01

    The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å −1 related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.

  16. Mate-finding as an overlooked critical determinant of dispersal variation in sexually-reproducing animals.

    Science.gov (United States)

    Gilroy, James J; Lockwood, Julie L

    2012-01-01

    Dispersal is a critically important process in ecology, but robust predictive models of animal dispersal remain elusive. We identify a potentially ubiquitous component of variation in animal dispersal that has been largely overlooked until now: the influence of mate encounters on settlement probability. We use an individual-based model to simulate dispersal in sexually-reproducing organisms that follow a simple set of movement rules based on conspecific encounters, within an environment lacking spatial habitat heterogeneity. We show that dispersal distances vary dramatically with fluctuations in population density in such a model, even in the absence of variation in dispersive traits between individuals. In a simple random-walk model with promiscuous mating, dispersal distributions become increasingly 'fat-tailed' at low population densities due to the increasing scarcity of mates. Similar variation arises in models incorporating territoriality. In a model with polygynous mating, we show that patterns of sex-biased dispersal can even be reversed across a gradient of population density, despite underlying dispersal mechanisms remaining unchanged. We show that some widespread dispersal patterns found in nature (e.g. fat tailed distributions) can arise as a result of demographic variability in the absence of heterogeneity in dispersive traits across the population. This implies that models in which individual dispersal distances are considered to be fixed traits might be unrealistic, as dispersal distances vary widely under a single dispersal mechanism when settlement is influenced by mate encounters. Mechanistic models offer a promising means of advancing our understanding of dispersal in sexually-reproducing organisms.

  17. Evaluation of Multiclass Model Observers in PET LROC Studies

    Science.gov (United States)

    Gifford, H. C.; Kinahan, P. E.; Lartizien, C.; King, M. A.

    2007-02-01

    A localization ROC (LROC) study was conducted to evaluate nonprewhitening matched-filter (NPW) and channelized NPW (CNPW) versions of a multiclass model observer as predictors of human tumor-detection performance with PET images. Target localization is explicitly performed by these model observers. Tumors were placed in the liver, lungs, and background soft tissue of a mathematical phantom, and the data simulation modeled a full-3D acquisition mode. Reconstructions were performed with the FORE+AWOSEM algorithm. The LROC study measured observer performance with 2D images consisting of either coronal, sagittal, or transverse views of the same set of cases. Versions of the CNPW observer based on two previously published difference-of-Gaussian channel models demonstrated good quantitative agreement with human observers. One interpretation of these results treats the CNPW observer as a channelized Hotelling observer with implicit internal noise

  18. Type I supernova models vs observations

    International Nuclear Information System (INIS)

    Weaver, T.A.; Axelrod, T.S.; Woosley, S.E.

    1980-01-01

    This paper explores tHe observational consequences of models for Type I supernovae based on the detonation (or deflagration) of the degenerate cores of white dwarfs or intermediate mass (approx. = 9 M/sub sun/) stars. Such nuclear burning can be initiated either at the center of the core or near its edge. The model examined in most detail is that of a 0.5M/sub sun/ C/O white dwarf which undergoes an edge-lit He/C/O detonation after accreting 0.62 M/sub sun/ of he at 10 -8 M/sub sun//yr. The light curve resulting from this model is found to be in excellent agreement with those observed for Type I supernovae, particularly those in the fast subclass. The physical processes involved in the detailed numerical calculations which lead to this conclusion are quantitatively elucidated by simple analytic models, and effects of uncertainties in the input physics are explored

  19. Which processes drive observed variations of HCHO columns over India?

    Science.gov (United States)

    Surl, Luke; Palmer, Paul I.; González Abad, Gonzalo

    2018-04-01

    We interpret HCHO column variations observed by the Ozone Monitoring Instrument (OMI), aboard the NASA Aura satellite, over India during 2014 using the GEOS-Chem atmospheric chemistry and transport model. We use a nested version of the model with a horizontal resolution of approximately 25 km. HCHO columns are related to local emissions of volatile organic compounds (VOCs) with a spatial smearing that increases with the VOC lifetime. Over India, HCHO has biogenic, pyrogenic, and anthropogenic VOC sources. Using a 0-D photochemistry model, we find that isoprene has the largest molar yield of HCHO which is typically realized within a few hours. We also find that forested regions that neighbour major urban conurbations are exposed to high levels of nitrogen oxides. This results in depleted hydroxyl radical concentrations and a delay in the production of HCHO from isoprene oxidation. We find that propene is the only anthropogenic VOC emitted in major Indian cities that produces HCHO at a comparable (but slower) rate to isoprene. The GEOS-Chem model reproduces the broad-scale annual mean HCHO column distribution observed by OMI (r = 0.6), which is dominated by a distinctive meridional gradient in the northern half of the country, and by localized regions of high columns that coincide with forests. Major discrepancies are noted over the Indo-Gangetic Plain (IGP) and Delhi. We find that the model has more skill at reproducing observations during winter (JF) and pre-monsoon (MAM) months with Pearson correlations r > 0.5 but with a positive model bias of x≃1×1015 molec cm-2. During the monsoon season (JJAS) we reproduce only a diffuse version of the observed meridional gradient (r = 0.4). We find that on a continental scale most of the HCHO column seasonal cycle is explained by monthly variations in surface temperature (r = 0.9), suggesting a role for biogenic VOCs, in agreement with the 0-D and GEOS-Chem model calculations. We also find that the seasonal cycle during

  20. Reproducibility of scoring emphysema by HRCT

    International Nuclear Information System (INIS)

    Malinen, A.; Partanen, K.; Rytkoenen, H.; Vanninen, R.; Erkinjuntti-Pekkanen, R.

    2002-01-01

    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

  1. Using prediction markets to estimate the reproducibility of scientific research

    Science.gov (United States)

    Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A.; Johannesson, Magnus

    2015-01-01

    Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants’ individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a “statistically significant” finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications. PMID:26553988

  2. Using prediction markets to estimate the reproducibility of scientific research.

    Science.gov (United States)

    Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A; Johannesson, Magnus

    2015-12-15

    Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants' individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a "statistically significant" finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications.

  3. Reproducibility of biomarkers in induced sputum and in serum from chronic smokers.

    Science.gov (United States)

    Zuiker, Rob G J A; Kamerling, Ingrid M C; Morelli, Nicoletta; Calderon, Cesar; Boot, J Diderik; de Kam, Marieke; Diamant, Zuzana; Burggraaf, Jacobus; Cohen, Adam F

    2015-08-01

    Soluble inflammatory markers obtained from non-invasive airway sampling such as induced sputum may be useful biomarkers for targeted pharmaceutical interventions. However, before these soluble markers can be used as potential targets, their variability and reproducibility need to be established in distinct study populations. This study aimed to assess the reproducibility of biomarkers obtained from induced sputum and serum in chronic smokers and non-smokers. Sputum and serum samples were obtained from 16 healthy non-smokers and 16 asymptomatic chronic smokers (for both groups: 8M/8F, 30-52 years, FEV1 ≥80% pred.; ≥10 pack years for the smokers) on 2 separate visits 4-10 days apart. Soluble markers in serum and sputum were analysed by ELISA. The differences between smokers vs non-smokers were analysed with a t-test and variability was assessed on log-transformed data by a mixed model ANOVA. Analysable sputum samples could be obtained from all 32 subjects. In both study populations neutrophils and macrophages were the predominant cell types. Serum Pulmonary Surfactant Associated Protein D had favourable reproducibility criteria for reliability ratio (0.99), intra-subject coefficient of variation (11.2%) and the Bland Altman limits of agreement. Furthermore, chronic smokers, compared to non-smokers, had significantly higher sputum concentrations of IL-8 (1094.6 pg/mL vs 460.8 pg/mL, p = 0.006)), and higher serum concentrations of Pulmonary Surfactant Associated Protein D (110.9 pg/mL vs 64.7 pg/mL, p = 0.019), and lower concentrations of Serum Amyloid A (1352.4 pg/mL vs 2297.5 pg/mL, p = 0.022). Serum Pulmonary Surfactant Associated Protein D proved to be a biomarker that fulfilled the criteria for reproducibility in both study groups. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Determining the optimal number of independent components for reproducible transcriptomic data analysis.

    Science.gov (United States)

    Kairov, Ulykbek; Cantini, Laura; Greco, Alessandro; Molkenov, Askhat; Czerwinska, Urszula; Barillot, Emmanuel; Zinovyev, Andrei

    2017-09-11

    Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data. Here we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets. We suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.

  5. Observability of global rivers with future SWOT observations

    Science.gov (United States)

    Fisher, Colby; Pan, Ming; Wood, Eric

    2017-04-01

    The Surface Water and Ocean Topography (SWOT) mission is designed to provide global observations of water surface elevation and slope from which river discharge can be estimated using a data assimilation system. This mission will provide increased spatial and temporal coverage compared to current altimeters, with an expected accuracy for water level elevations of 10 cm on rivers greater than 100 m wide. Within the 21-day repeat cycle, a river reach will be observed 2-4 times on average. Due to the relationship between the basin orientation and the orbit, these observations are not evenly distributed in time, which will impact the derived discharge values. There is, then, a need for a better understanding of how the mission will observe global river basins. In this study, we investigate how SWOT will observe global river basins and how the temporal and spatial sampling impacts the discharge estimated from assimilation. SWOT observations can be assimilated using the Inverse Streamflow Routing (ISR) model of Pan and Wood [2013] with a fixed interval Kalman smoother. Previous work has shown that the ISR assimilation method can be used to reproduce the spatial and temporal dynamics of discharge within many global basins: however, this performance was strongly impacted by the spatial and temporal availability of discharge observations. In this study, we apply the ISR method to 32 global basins with different geometries and crossing patterns for the future orbit, assimilating theoretical SWOT-retrieved "gauges". Results show that the model performance varies significantly across basins and is driven by the orientation, flow distance, and travel time in each. Based on these properties, we quantify the "observability" of each basin and relate this to the performance of the assimilation. Applying this metric globally to a large variety of basins we can gain a better understanding of the impact that SWOT observations may have across basin scales. By determining the

  6. A comparison of RANZCR and Singapore-designed radiation oncology practice audit instruments: how does reproducibility affect future approaches to revalidation

    International Nuclear Information System (INIS)

    Lu, Jiade J.; Wynne, Christopher J.; Kumar, Mahesh B.; Shakespeare, Thomas P.; Mukherjee, Rahul; Back, Michael F.

    2004-01-01

    Physician competency assessment requires the use of validated methods and instruments. The Royal Australian and New Zealand College of Radiologists (RANZCR) developed a draft audit form to be evaluated as a competency assessment instrument for radiation oncologists (ROs) in Australasia. We evaluated the reliability of the RANZCR instrument as well as a separate The Cancer Institute (TCI) Singapore-designed instrument by having two ROs perform an independent chart review of 80 randomly selected patients seen at The Cancer Institute (TCI), Singapore. Both RANZCR and TCI Singapore instruments were used to score each chart. Inter- and intra-observer reliability for both audit instruments were compared using misclassification rates as the primary end-point. Overall, for inter-observer reproducibility, 2.3% of TCI Singapore items were misclassified compared to 22.3% of RANZCR items (P < 0.0001, 100.00% confidence that TCI instrument has less inter-observer misclassification). For intra-observer reproducibility, 2.4% of TCI Singapore items were misclassified compared to 13.6% of RANZCR items (P < 0.0001, 100.00% confidence that TCI instrument has less intra-observer misclassification). The proposed RANZCR RO revalidation audit instrument requires further refinement to improve validity. Several items require modification or removal because of lack of reliability, whereas inclusion of other important and reproducible items can be incorporated as demonstrated by the TCI Singapore instrument. The TCI Singapore instrument also has the advantage of incorporating a simple scoring system and criticality index to allow discrimination between ROs and comparisons against future College standards Copyright (2004) Blackwell Publishing Asia Pty Ltd

  7. Investigation of the Intra- and Interlaboratory Reproducibility of a Small Scale Standardized Supersaturation and Precipitation Method

    DEFF Research Database (Denmark)

    Plum, Jakob; Madsen, Cecilie M; Teleki, Alexandra

    2017-01-01

    order for the three model compounds using the SSPM (aprepitant > felodipine ≈ fenofibrate). The α-value is dependent on the experimental setup and can be used as a parameter to evaluate the uniformity of the data set. This study indicated that the SSPM was able to obtain the same rank order of the β...... compound available for absorption. However, due to the stochastic nature of nucleation, supersaturating drug delivery systems may lead to inter- and intrapersonal variability. The ability to define a feasible range with respect to the supersaturation level is a crucial factor for a successful formulation...... reproducibility study of felodipine was conducted, after which seven partners contributed with data for three model compounds; aprepitant, felodipine, and fenofibrate, to determine the interlaboratory reproducibility of the SSPM. The first part of the SSPM determines the apparent degrees of supersaturation (a...

  8. Repeatability, Reproducibility and Standardisation of a Laser Doppler Imaging Technique for the Evaluation of Normal Mouse Hindlimb Perfusion

    Directory of Open Access Journals (Sweden)

    Arturo Brunetti

    2012-12-01

    Full Text Available Background. Preclinical perfusion studies are useful for the improvement of diagnosis and therapy in dermatologic, cardiovascular and rheumatic human diseases. The Laser Doppler Perfusion Imaging (LDPI technique has been used to evaluate superficial alterations of the skin microcirculation in surgically induced murine hindlimb ischemia. We assessed the reproducibility and the accuracy of LDPI acquisitions and identified several critical factors that could affect LDPI measurements in mice. Methods. Twenty mice were analysed. Statistical standardisation and a repeatability and reproducibility analysis were performed on mouse perfusion signals with respect to differences in body temperature, the presence or absence of hair, the type of anaesthesia used for LDPI measurements and the position of the mouse body. Results. We found excellent correlations among measurements made by the same operator (i.e., repeatability under the same experimental conditions and by two different operators (i.e., reproducibility. A Bland-Altman analysis showed the absence of bias in repeatability (p = 0.29 or reproducibility (p = 0.89. The limits of agreement for repeatability were –0.357 and –0.033, and for reproducibility, they were –0.270 and 0.238. Significant differences in perfusion values were observed in different experimental groups. Conclusions. Different experimental conditions must be considered as a starting point for the evaluation of new drugs and strategic therapies.

  9. Analysis of a general circulation model product. I - Frontal systems in the Brazil/Malvinas and Kuroshio/Oyashio regions

    Science.gov (United States)

    Garzoli, Silvia L.; Garraffo, Zulema; Podesta, Guillermo; Brown, Otis

    1992-01-01

    The general circulation model (GCM) of Semtner and Chervin (1992) is tested by comparing the fields produced by this model with available observations in two western boundary current regions, the Brazil/Malvinas and the Kuroshio/Oyashio confluences. The two sets of data used are the sea surface temperature from satellite observations and the temperature field product from the GCM at levels 1 (12.5 m), 2 (37.5 m), and 6 (160 m). It is shown that the model reproduces intense thermal fronts at the sea surface and in the upper layers (where they are induced by the internal dynamics of the model). The location of the fronts are reproduced in the model within 4 to 5 deg, compared with observations. However, the variability of these fronts was found to be less pronounced in the model than in the observations.

  10. Giant planet population synthesis: comparing theory with observations

    International Nuclear Information System (INIS)

    Benz, W; Mordasini, C; Alibert, Y; Naef, D

    2008-01-01

    The characteristics of the now over 250 known extra-solar giant planets begin to provide a database with which current planet formation theories can be put to the test. To do this, we synthesize the expected planet population based on the core-accretion scenario by sampling initial conditions in a Monte Carlo fashion. We then apply appropriate observational detection biases and compare the resulting population with the one actually detected. Quantitative statistical tests allow us to determine how well the models are reproducing the observed samples. The model can be applied to compute the expected planet population detectable with different techniques (radial velocity measurements, transits, gravitational lensing, etc) or orbiting stars of different masses. In the latter case, we show that forming Jupiter-mass planets orbiting M dwarfs within the lifetime of proto-planetary disks is indeed possible. However, the models predict that with decreasing stellar mass, the ratio of Jupiter- to Neptune-mass planets will sharply decrease

  11. Giant planet population synthesis: comparing theory with observations

    Science.gov (United States)

    Benz, W.; Mordasini, C.; Alibert, Y.; Naef, D.

    2008-08-01

    The characteristics of the now over 250 known extra-solar giant planets begin to provide a database with which current planet formation theories can be put to the test. To do this, we synthesize the expected planet population based on the core-accretion scenario by sampling initial conditions in a Monte Carlo fashion. We then apply appropriate observational detection biases and compare the resulting population with the one actually detected. Quantitative statistical tests allow us to determine how well the models are reproducing the observed samples. The model can be applied to compute the expected planet population detectable with different techniques (radial velocity measurements, transits, gravitational lensing, etc) or orbiting stars of different masses. In the latter case, we show that forming Jupiter-mass planets orbiting M dwarfs within the lifetime of proto-planetary disks is indeed possible. However, the models predict that with decreasing stellar mass, the ratio of Jupiter- to Neptune-mass planets will sharply decrease.

  12. Scan-rescan reproducibility of segmental aortic wall shear stress as assessed by phase-specific segmentation with 4D flow MRI in healthy volunteers.

    Science.gov (United States)

    van der Palen, Roel L F; Roest, Arno A W; van den Boogaard, Pieter J; de Roos, Albert; Blom, Nico A; Westenberg, Jos J M

    2018-05-26

    The aim was to investigate scan-rescan reproducibility and observer variability of segmental aortic 3D systolic wall shear stress (WSS) by phase-specific segmentation with 4D flow MRI in healthy volunteers. Ten healthy volunteers (age 26.5 ± 2.6 years) underwent aortic 4D flow MRI twice. Maximum 3D systolic WSS (WSSmax) and mean 3D systolic WSS (WSSmean) for five thoracic aortic segments over five systolic cardiac phases by phase-specific segmentations were calculated. Scan-rescan analysis and observer reproducibility analysis were performed. Scan-rescan data showed overall good reproducibility for WSSmean (coefficient of variation, COV 10-15%) with moderate-to-strong intraclass correlation coefficient (ICC 0.63-0.89). The variability in WSSmax was high (COV 16-31%) with moderate-to-good ICC (0.55-0.79) for different aortic segments. Intra- and interobserver reproducibility was good-to-excellent for regional aortic WSSmax (ICC ≥ 0.78; COV ≤ 17%) and strong-to-excellent for WSSmean (ICC ≥ 0.86; COV ≤ 11%). In general, ascending aortic segments showed more WSSmax/WSSmean variability compared to aortic arch or descending aortic segments for scan-rescan, intraobserver and interobserver comparison. Scan-rescan reproducibility was good for WSSmean and moderate for WSSmax for all thoracic aortic segments over multiple systolic phases in healthy volunteers. Intra/interobserver reproducibility for segmental WSS assessment was good-to-excellent. Variability of WSSmax is higher and should be taken into account in case of individual follow-up or in comparative rest-stress studies to avoid misinterpretation.

  13. Reproducibility of esophageal scintigraphy using semi-solid yoghurt

    Energy Technology Data Exchange (ETDEWEB)

    Imai, Yukinori; Kinoshita, Manabu; Asakura, Yasushi; Kakinuma, Tohru; Shimoji, Katsunori; Fujiwara, Kenji; Suzuki, Kenji; Miyamae, Tatsuya [Saitama Medical School, Moroyama (Japan)

    1999-10-01

    Esophageal scintigraphy is a non-invasive method which evaluate esophageal function quantitatively. We applied new technique using semi-solid yoghurt, which can evaluate esophageal function in a sitting position. To evaluate the reproducibility of this method, scintigraphy were performed in 16 healthy volunteers. From the result of four swallows except the first one, the mean coefficients of variation in esophageal transit time and esophageal emptying time were 12.8% and 13.4% respectively (interday variation). As regards the interday variation, this method had also good reproducibility from the result on the 2 separate days. (author)

  14. 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.

  15. 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; Hartgerink, Chris; Krijnen, Job; Nuijten, Michele B.; van 't Veer, Anna E.; Van Aert, Robbie; van Assen, M.A.L.M.; Wissink, Joeri; Zeelenberg, Marcel

    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

  16. 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.

  17. POLARIMETRIC OBSERVATIONS OF {sigma} ORIONIS E

    Energy Technology Data Exchange (ETDEWEB)

    Carciofi, A. C.; Faes, D. M. [Instituto de Astronomia, Geofisica e Ciencias Atmosfericas, Universidade de Sao Paulo, Rua do Matao 1226, Cidade Universitaria, 05508-900 Sao Paulo, SP (Brazil); Townsend, R. H. D. [Department of Astronomy, University of Wisconsin-Madison, Sterling Hall, 475 N. Charter Street, Madison, WI 53706 (United States); Bjorkman, J. E., E-mail: carciofi@usp.br [Ritter Observatory, Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606 (United States)

    2013-03-20

    Some massive stars possess strong magnetic fields that confine plasma in the circumstellar environment. These magnetospheres have been studied spectroscopically, photometrically, and, more recently, interferometrically. Here we report on the first firm detection of a magnetosphere in continuum linear polarization, as a result of monitoring {sigma} Ori E at the Pico dos Dias Observatory. The non-zero intrinsic polarization indicates an asymmetric structure whose minor elongation axis is oriented 150. Degree-Sign 0 east of the celestial north. A modulation of the polarization was observed with a period of half of the rotation period, which supports the theoretical prediction of the presence of two diametrally opposed, corotating blobs of gas. A phase lag of -0.085 was detected between the polarization minimum and the primary minimum of the light curve, suggestive of a complex shape of the plasma clouds. We present a preliminary analysis of the data with the Rigidly Rotating Magnetosphere model, which could not reproduce simultaneously the photometric and polarimetric data. A toy model comprising two spherical corotating blobs joined by a thin disk proved more successful in reproducing the polarization modulation. With this model we were able to determine that the total scattering mass of the thin disk is similar to the mass of the blobs (2M{sub b}/M{sub d} = 1.2) and that the blobs are rotating counterclockwise on the plane of the sky. This result shows that polarimetry can provide a diagnostic of the geometry of clouds, which will serve as an important constraint for improving the Rigidly Rotating Magnetosphere model.

  18. Observing farming systems

    DEFF Research Database (Denmark)

    Noe, Egon; Alrøe, Hugo Fjelsted

    2012-01-01

    of analysis from individual farmers to communication and social relations. This is where Luhmann’s social systems theory can offer new insights. Firstly, it can help observe and understand the operational closure and system logic of a farming system and how this closure is produced and reproduced. Secondly...

  19. Evaluation of modeled changes in extreme precipitation in Europe and the Rhine basin

    NARCIS (Netherlands)

    Haren, van R.; Oldenborgh, van G.J.; Lenderink, G.; Hazeleger, W.

    2013-01-01

    In this study, we investigate the change in multi-day precipitation extremes in late winter in Europe using observations and climate models. The objectives of the analysis are to determine whether climate models can accurately reproduce observed trends and, if not, to find the causes of the

  20. Observational modeling of topological spaces

    International Nuclear Information System (INIS)

    Molaei, M.R.

    2009-01-01

    In this paper a model for a multi-dimensional observer by using of the fuzzy theory is presented. Relative form of Tychonoff theorem is proved. The notion of topological entropy is extended. The persistence of relative topological entropy under relative conjugate relation is proved.

  1. Modeling and observational constraints on the sulfur cycle in the marine troposphere: a focus on reactive halogens and multiphase chemistry

    Science.gov (United States)

    Chen, Q.; Breider, T.; Schmidt, J.; Sherwen, T.; Evans, M. J.; Xie, Z.; Quinn, P.; Bates, T. S.; Alexander, B.

    2017-12-01

    The radiative forcing from marine boundary layer clouds is still highly uncertain, which partly stems from our poor understanding of cloud condensation nuclei (CCN) formation. The oxidation of dimethyl sulfide (DMS) and subsequent chemical evolution of its products (e.g. DMSO) are key processes in CCN formation, but are generally very simplified in large-scale models. Recent research has pointed out the importance of reactive halogens (e.g. BrO and Cl) and multiphase chemistry in the tropospheric sulfur cycle. In this study, we implement a series of sulfur oxidation mechanisms into the GEOS-Chem global chemical transport model, involving both gas-phase and multiphase oxidation of DMS, DMSO, MSIA and MSA, to improve our understanding of the sulfur cycle in the marine troposphere. DMS observations from six locations around the globe and MSA/nssSO42- ratio observations from two ship cruises covering a wide range of latitudes and longitudes are used to assess the model. Preliminary results reveal the important role of BrO for DMS oxidation at high latitudes (up to 50% over Southern Ocean). Oxidation of DMS by Cl radicals is small in the model (within 10% in the marine troposphere), probably due to an underrepresentation of Cl sources. Multiphase chemistry (e.g. oxidation by OH and O3 in cloud droplets) is not important for DMS oxidation but is critical for DMSO oxidation and MSA production and removal. In our model, about half of the DMSO is oxidized in clouds, leading to the formation of MSIA, which is further oxidized to form MSA. Overall, with the addition of reactive halogens and multiphase chemistry, the model is able to better reproduce observations of seasonal variations of DMS and MSA/nssSO42- ratios.

  2. 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.

  3. A computational model for lower hybrid current drive

    International Nuclear Information System (INIS)

    Englade, R.C.; Bonoli, P.T.; Porkolab, M.

    1983-01-01

    A detailed simulation model for lower hybrid (LH) current drive in toroidal devices is discussed. This model accounts reasonably well for the magnitude of radio frequency (RF) current observed in the PLT and Alcator C devices. It also reproduces the experimental dependencies of RF current generation on toroidal magnetic field and has provided insights about mechanisms which may underlie the observed density limit of current drive. (author)

  4. A construction of observables for AKSZ sigma models

    OpenAIRE

    Mnev, Pavel

    2012-01-01

    A construction of gauge-invariant observables is suggested for a class of topological field theories, the AKSZ sigma-models. The observables are associated to extensions of the target Q-manifold of the sigma model to a Q-bundle over it with additional Hamiltonian structure in fibers.

  5. Observation and simulation of the ionosphere disturbance waves triggered by rocket exhausts

    Science.gov (United States)

    Lin, Charles C. H.; Chen, Chia-Hung; Matsumura, Mitsuru; Lin, Jia-Ting; Kakinami, Yoshihiro

    2017-08-01

    Observations and theoretical modeling of the ionospheric disturbance waves generated by rocket launches are investigated. During the rocket passage, time rate change of total electron content (rTEC) enhancement with the V-shape shock wave signature is commonly observed, followed by acoustic wave disturbances and region of negative rTEC centered along the trajectory. Ten to fifteen min after the rocket passage, delayed disturbance waves appeared and propagated along direction normal to the V-shape wavefronts. These observation features appeared most prominently in the 2016 North Korea rocket launch showing a very distinct V-shape rTEC enhancement over enormous areas along the southeast flight trajectory despite that it was also appeared in the 2009 North Korea rocket launch with the eastward flight trajectory. Numerical simulations using the physical-based nonlinear and nonhydrostatic coupled model of neutral atmosphere and ionosphere reproduce promised results in qualitative agreement with the characteristics of ionospheric disturbance waves observed in the 2009 event by considering the released energy of the rocket exhaust as the disturbance source. Simulations reproduce the shock wave signature of electron density enhancement, acoustic wave disturbances, the electron density depletion due to the rocket-induced pressure bulge, and the delayed disturbance waves. The pressure bulge results in outward neutral wind flows carrying neutrals and plasma away from it and leading to electron density depletions. Simulations further show, for the first time, that the delayed disturbance waves are produced by the surface reflection of the earlier arrival acoustic wave disturbances.

  6. 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

  7. In-vitro accuracy and reproducibility evaluation of probing depth measurements of selected periodontal probes

    Directory of Open Access Journals (Sweden)

    K.N. Al Shayeb

    2014-01-01

    Conclusion: Depth measurements with the Chapple UB-CF-15 probe were more accurate and reproducible compared to measurements with the Vivacare TPS and Williams 14 W probes. This in vitro model may be useful for intra-examiner calibration or clinician training prior to the clinical evaluation of patients or in longitudinal studies involving periodontal evaluation.

  8. Influence of primary fragment excitation energy and spin distributions on fission observables

    Science.gov (United States)

    Litaize, Olivier; Thulliez, Loïc; Serot, Olivier; Chebboubi, Abdelaziz; Tamagno, Pierre

    2018-03-01

    Fission observables in the case of 252Cf(sf) are investigated by exploring several models involved in the excitation energy sharing and spin-parity assignment between primary fission fragments. In a first step the parameters used in the FIFRELIN Monte Carlo code "reference route" are presented: two parameters for the mass dependent temperature ratio law and two constant spin cut-off parameters for light and heavy fragment groups respectively. These parameters determine the initial fragment entry zone in excitation energy and spin-parity (E*, Jπ). They are chosen to reproduce the light and heavy average prompt neutron multiplicities. When these target observables are achieved all other fission observables can be predicted. We show here the influence of input parameters on the saw-tooth curve and we discuss the influence of a mass and energy-dependent spin cut-off model on gamma-rays related fission observables. The part of the model involving level densities, neutron transmission coefficients or photon strength functions remains unchanged.

  9. CONFRONTING THREE-DIMENSIONAL TIME-DEPENDENT JET SIMULATIONS WITH HUBBLE SPACE TELESCOPE OBSERVATIONS

    International Nuclear Information System (INIS)

    Staff, Jan E.; Niebergal, Brian P.; Ouyed, Rachid; Pudritz, Ralph E.; Cai, Kai

    2010-01-01

    We perform state-of-the-art, three-dimensional, time-dependent simulations of magnetized disk winds, carried out to simulation scales of 60 AU, in order to confront optical Hubble Space Telescope observations of protostellar jets. We 'observe' the optical forbidden line emission produced by shocks within our simulated jets and compare these with actual observations. Our simulations reproduce the rich structure of time-varying jets, including jet rotation far from the source, an inner (up to 400 km s -1 ) and outer (less than 100 km s -1 ) component of the jet, and jet widths of up to 20 AU in agreement with observed jets. These simulations when compared with the data are able to constrain disk wind models. In particular, models featuring a disk magnetic field with a modest radial spatial variation across the disk are favored.

  10. An evaluation of WRF's ability to reproduce the surface wind over complex terrain based on typical circulation patterns.

    NARCIS (Netherlands)

    Jiménez, P.A.; Dudhia, J.; González-Rouco, J.F.; Montávez, J.P.; Garcia-Bustamante, E.; Navarro, J.; Vilà-Guerau de Arellano, J.; Munoz-Roldán, A.

    2013-01-01

    [1] The performance of the Weather Research and Forecasting (WRF) model to reproduce the surface wind circulations over complex terrain is examined. The atmospheric evolution is simulated using two versions of the WRF model during an over 13¿year period (1992 to 2005) over a complex terrain region

  11. Low-Z impurity transport in DIII-D - observations and implications

    International Nuclear Information System (INIS)

    Wade, M.R.; Houlberg, W.A.; Baylor, L.R.; West, W.P.; Baker, D.R.

    2001-01-01

    Impurity transport studies on DIII-D have revealed transport phenomena that are qualitatively consistent with that expected from turbulence transport theory in some cases and neoclassical transport theory in other cases. The transport model proposed here, which assumes that the total impurity transport is a linear sum of turbulence-driven transport and neoclassical transport, is shown to reproduce many of these observed features. This transport model is then applied to burn condition calculations, revealing that profile effects associated with neoclassical transport have a large effect on the maximum allowable impurity fraction in machines based on achieving neoclassical transport levels

  12. In vivo quantification of intracerebral GABA by single-voxel 1H-MRS-How reproducible are the results?

    International Nuclear Information System (INIS)

    Bogner, W.; Gruber, S.; Doelken, M.; Stadlbauer, A.; Ganslandt, O.; Boettcher, U.; Trattnig, S.; Doerfler, A.; Stefan, H.; Hammen, T.

    2010-01-01

    Gamma aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the human brain. It plays a decisive role in a variety of nervous system disorders, such as anxiety disorders, epilepsy, schizophrenia, insomnia, and many others. The reproducibility of GABA quantification results obtained with a single-voxel spectroscopy J-difference editing sequence with Point Resolved Spectroscopy localization (MEGA-PRESS) was determined on a 3.0 Tesla MR scanner in healthy adults. Eleven volunteers were measured in long- and short-term intervals. Intra- and inter-subject reproducibility were evaluated. Internal referencing of GABA+ to total creatine (tCr) and water (H 2 O), as well as two different post-processing methods for the evaluation (signal integration and time-domain fitting) were compared. In all subjects lower coefficient of variation and therefore higher reproducibility can be observed for fitting compared to integration. The GABA+/tCr ratio performs better than the GABA+/H 2 O ratio or GABA+ without internal referencing for both fitting and integration (GABA+/tCr: 13.3% and 17.0%; GABA+/H 2 O: 15.0% and 17.8%; GABA+: 19.2% and 21.7%). Four-day measurements on three subjects showed higher intra- than inter-subject reproducibility (GABA+/tCr ∼10-12%). With a coefficient of variation of about 13% for inter-subject and 10-12% for intra-subject variability of GABA+/tCr, this technique seems to be a precise tool that can detect GABA confidently. The results of this study show the reproducibility limitations of GABA quantification in vivo, which are necessary for further clinical studies.

  13. Using surface imaging and visual coaching to improve the reproducibility and stability of deep-inspiration breath hold for left-breast-cancer radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Cervino, Laura I; Gupta, Sonia; Rose, Mary A; Yashar, Catheryn; Jiang, Steve B [Department of Radiation Oncology, University of California San Diego, 3855 Health Sciences Dr, La Jolla, CA 92037-0843 (United States)], E-mail: sbjiang@ucsd.edu

    2009-11-21

    Late cardiac complications may arise after left-breast radiation therapy. Deep-inspiration breath hold (DIBH) allows reduction of the irradiated heart volume at the same time as it reduces tumor bed motion and increases lung sparing. In the present study, we have evaluated the improvement in reproducibility and stability of the DIBH for left-breast-cancer treatment when visual coaching is provided with the aid of 3D video surface imaging and video goggles. Five left-breast-cancer patients and fifteen healthy volunteers were asked to perform a series of DIBHs without and with visual coaching. Reproducibility and stability of DIBH were measured for each individual with and without visual coaching. The average reproducibility and stability changed from 2.1 mm and 1.5 mm, respectively, without visual feedback to 0.5 mm and 0.7 mm with visual feedback, showing a significant statistical difference (p < 0.001 for reproducibility, p < 0.01 for stability). Significant changes (>2 mm) in reproducibility and stability were observed in 35% and 15% of the subjects, respectively. The average chest wall excursion of the DIBH with respect to the free breathing preceding the DIBH was found to be 11.3 mm. The reproducibility and stability of the DIBH improve significantly from the visual coaching provided to the patient, especially in those patients with poor reproducibility and stability.

  14. Energy exchange in thermal energy atom-surface scattering: impulsive models

    International Nuclear Information System (INIS)

    Barker, J.A.; Auerbach, D.J.

    1979-01-01

    Energy exchange in thermal energy atom surface collisions is studied using impulsive ('hard cube' and 'hard sphere') models. Both models reproduce the observed nearly linear relation between outgoing and incoming energies. In addition, the hard-sphere model accounts for the widths of the outcoming energy distributions. (Auth.)

  15. The reproducibility of organ position using active breathing control (ABC) during liver radiotherapy

    International Nuclear Information System (INIS)

    Dawson, Laura A.; Brock, Kristy K.; Kazanjian, Sahira; Fitch, Dwight; McGinn, Cornelius J.; Lawrence, Theodore S.; Haken, Randall K. ten; Balter, James

    2001-01-01

    Purpose: To evaluate the intrafraction and interfraction reproducibility of liver immobilization using active breathing control (ABC). Methods and Materials: Patients with unresectable intrahepatic tumors who could comfortably hold their breath for at least 20 s were treated with focal liver radiation using ABC for liver immobilization. Fluoroscopy was used to measure any potential motion during ABC breath holds. Preceding each radiotherapy fraction, with the patient setup in the nominal treatment position using ABC, orthogonal radiographs were taken using room-mounted diagnostic X-ray tubes and a digital imager. The radiographs were compared to reference images using a 2D alignment tool. The treatment table was moved to produce acceptable setup, and repeat orthogonal verification images were obtained. The positions of the diaphragm and the liver (assessed by localization of implanted radiopaque intra-arterial microcoils) relative to the skeleton were subsequently analyzed. The intrafraction reproducibility (from repeat radiographs obtained within the time period of one fraction before treatment) and interfraction reproducibility (from comparisons of the first radiograph for each treatment with a reference radiograph) of the diaphragm and the hepatic microcoil positions relative to the skeleton with repeat breath holds using ABC were then measured. Caudal-cranial (CC), anterior-posterior (AP), and medial-lateral (ML) reproducibility of the hepatic microcoils relative to the skeleton were also determined from three-dimensional alignment of repeat CT scans obtained in the treatment position. Results: A total of 262 fractions of radiation were delivered using ABC breath holds in 8 patients. No motion of the diaphragm or hepatic microcoils was observed on fluoroscopy during ABC breath holds. From analyses of 158 sets of positioning radiographs, the average intrafraction CC reproducibility (σ) of the diaphragm and hepatic microcoil position relative to the skeleton

  16. 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

    2016-01-01

    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.

  17. Modeling and interpretation of line observations*

    Directory of Open Access Journals (Sweden)

    Kamp Inga

    2015-01-01

    Full Text Available Models for the interpretation of line observations from protoplanetary disks are summarized. The spectrum ranges from 1D LTE slab models to 2D thermo-chemical radiative transfer models and their use depends largely on the type/nature of observational data that is analyzed. I discuss the various types of observational data and their interpretation in the context of disk physical and chemical properties. The most simple spatially and spectral unresolved data are line fluxes, which can be interpreted using so-called Boltzmann diagrams. The interpretation is often tricky due to optical depth and non-LTE effects and requires care. Line profiles contain kinematic information and thus indirectly the spatial origin of the emission. Using series of line profiles, we can for example deduce radial temperature gradients in disks (CO pure rotational ladder. Spectro-astrometry of e.g. CO ro-vibrational line profiles probes the disk structure in the 1–30 AU region, where planet formation through core accretion should be most efficient. Spatially and spectrally resolved line images from (submm interferometers are the richest datasets we have to date and they enable us to unravel exciting details of the radial and vertical disk structure such as winds and asymmetries.

  18. Reproducibility of quantitative planar thallium-201 scintigraphy: quantitative criteria for reversibility of myocardial perfusion defects

    International Nuclear Information System (INIS)

    Sigal, S.L.; Soufer, R.; Fetterman, R.C.; Mattera, J.A.; Wackers, F.J.

    1991-01-01

    Fifty-two paired stress/delayed planar 201 TI studies (27 exercise studies, 25 dipyridamole studies) were processed twice by seven technologists to assess inter- and intraobserver variability. The reproducibility was inversely related to the size of 201 Tl perfusion abnormalities. Intraobserver variability was not different between exercise and dipyridamole studies for lesions of similar size. Based upon intraobserver variability, objective quantitative criteria for reversibility of perfusion abnormalities were defined. These objective criteria were tested prospectively in a separate group of 35 201 Tl studies and compared with the subjective interpretation of quantitative circumferential profiles. Overall, exact agreement existed in 78% of images (kappa statistic k = 0.66). We conclude that quantification of planar 201 Tl scans is highly reproducible, with acceptable inter- and intraobserver variability. Objective criteria for lesion reversibility correlated well with analysis by experienced observers

  19. Microwave assisted in situ synthesis of Ag–NaCMC films and their reproducible surface-enhanced Raman scattering signals

    International Nuclear Information System (INIS)

    Jiang, Tao; Li, Junpeng; Zhang, Li; Wang, Binbing; Zhou, Jun

    2014-01-01

    Graphical abstract: Two kinds of Ag–NaCMC films for surface-enhanced Raman scattering (SERS) were prepared by conventional heating and microwave assisted in situ reduction methods without any additional capping or reducing agents. A relatively narrow and symmetric surface plasmon resonance band was observed in the absorption spectra of the films fabricated by the microwave assisted in situ reduction method. More uniform silver nanoparticles (NPs) implied by the symmetric absorption spectrum were further confirmed by the scanning electron microscopy images. After the simulation of the E-field intensity distribution around the silver NPs in NaCMC film, the Raman scattering enhancement factors (EFs) of these films were then investigated with 4-mercaptobenzoic acid molecule as a SERS reporter. Improved reproducibility of SERS signal was obtained in the microwave assisted synthesized Ag–NaCMC film, although it maintained an EF as only 1.11 × 10 8 . The reproducible SERS signal of the Ag–NaCMC film is particularly attractive and this microwave assisted in situ reduction method is suitable for the production of excellent substrate for biosensor application. - Highlights: • The synthesis of Ag–NaCMC films was successfully fulfilled by a low-cost microwave method. • More uniform silver nanoparticles were observed in Ag–NaCMC film synthesized by microwave. • Improved reproducibility of SERS signal was obtained in microwave synthesized Ag–NaCMC film. - Abstract: Two kinds of Ag–NaCMC films for surface-enhanced Raman scattering (SERS) were prepared by conventional heating and microwave assisted in situ reduction methods without any additional capping or reducing agents. A relatively narrow and symmetric surface plasmon resonance band was observed in the absorption spectra of the films fabricated by the microwave assisted in situ reduction method. More uniform silver nanoparticles (NPs) implied by the symmetric absorption spectrum were further confirmed by

  20. Reproducibility in cyclostratigraphy: initiating an intercomparison project

    Science.gov (United States)

    Sinnesael, Matthias; De Vleeschouwer, David; Zeeden, Christian; Claeys, Philippe

    2017-04-01

    The study of astronomical climate forcing and the application of cyclostratigraphy have experienced a spectacular growth over the last decades. In the field of cyclostratigraphy a broad range in methodological approaches exist. However, comparative study between the different approaches is lacking. Different cases demand different approaches, but with the growing importance of the field, questions arise about reproducibility, uncertainties and standardization of results. The radioisotopic dating community, in particular, has done far-reaching efforts to improve reproducibility and intercomparison of radioisotopic dates and their errors. To satisfy this need in cyclostratigraphy, we initiate a comparable framework for the community. The aims are to investigate and quantify reproducibility of, and uncertainties related to cyclostratigraphic studies and to provide a platform to discuss the merits and pitfalls of different methodologies, and their applicabilities. With this poster, we ask the feedback from the community on how to design this comparative framework in a useful, meaningful and productive manner. In parallel, we would like to discuss how reproducibility should be tested and what uncertainties should stand for in cyclostratigraphy. On the other hand, we intend to trigger interest for a cyclostratigraphic intercomparison project. This intercomparison project would imply the analysis of artificial and genuine geological records by individual researchers. All participants would be free to determine their method of choice. However, a handful of criterions will be required for an outcome to be comparable. The different results would be compared (e.g. during a workshop or a special session), and the lessons learned from the comparison could potentially be reported in a review paper. The aim of an intercomparison project is not to rank the different methods according to their merits, but to get insight into which specific methods are most suitable for which

  1. Reproducibility of the interpretation of pelvic x-ray 3 months after hysteroscopic sterilization with Essure.

    Science.gov (United States)

    Veersema, Sebastiaan; Mol, Ben W J; Brölmann, Hans A M

    2010-09-01

    To estimate the diagnostic accuracy and the interobserver reproducibility of pelvic x-rays in the diagnosis of successful bilateral sterilization with Essure after a 3-month follow-up period. Interobserver study. Outpatient department of obstetrics and gynecology in a Dutch teaching hospital. Patients with successful bilateral Essure placement. Hysteroscopic sterilization with Essure and pelvic x-ray and hysterosalpingography after a 3-month follow-up period. Six observers evaluations of 47 pelvic x-rays from 47 patients 3 months after a technical successful bilateral placement of microinserts to estimate the reliability of the sterilization. Diagnostic accuracy of pelvic x-ray per observer in detecting incorrectly positioned microinserts was expressed in terms of sensitivity and specificity, with hysterosalpingography as the reference strategy. Reproducibility of the interpretation of the pelvic x-ray was expressed as kappa-values. The sensitivity and specificity for x-rays read by gynecologists was 0.67 (95% confidence interval [CI], 0.29-0.96) and 0.79 (95% CI, 0.58-1.00) and for radiologists 1.0 and 0.5 (95% CI, 0.36-0.64). The interobserver agreement in reliability of pelvic x-ray of hysteroscopic sterilization assessment with Essure ranged from slight (kappa-value=0.09) for gynecologists to moderate (kappa-value=0.52) for radiologists. Test characteristics of pelvic x-ray as the imaging technique to assess the position of the Essure microinserts and tubal patency were poor, as was the reproducibility, particularly if gynecologists performed the evaluation. We do not recommend the use of pelvic x-ray for the assessment of the positioning of microinserts after hysteroscopic sterilization. Copyright (c) 2010 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  2. Reproducibility and consistency of proteomic experiments on natural populations of a non-model aquatic insect.

    Science.gov (United States)

    Hidalgo-Galiana, Amparo; Monge, Marta; Biron, David G; Canals, Francesc; Ribera, Ignacio; Cieslak, Alexandra

    2014-01-01

    Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (Agabus ramblae) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2-3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments.

  3. The quest for improved reproducibility in MALDI mass spectrometry.

    Science.gov (United States)

    O'Rourke, Matthew B; Djordjevic, Steven P; Padula, Matthew P

    2018-03-01

    Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018. © 2016 Wiley Periodicals, Inc.

  4. Intra- and interobserver reproducibility of vertebral endplate signal (modic) changes in the lumbar spine

    DEFF Research Database (Denmark)

    Jensen, Tue Secher; Sorensen, Joan Solgaard; Kjær, Per

    2007-01-01

    . PURPOSE: To assess the intra- and interobserver reliability of the "Nordic Modic classification" protocol. MATERIAL AND METHODS: MRI scans of 50 individuals representative of the general Danish population aged 40 were evaluated by two observers. Criteria for grading the changes were developed...... by the Nordic Modic Consensus Group. After consensus was established, all 50 MRI examinations were evaluated independently by each observer. Intraobserver reliability was assessed by re-evaluation of the 50 examinations by one of the observers. Kappa statistics were used to calculate agreement. RESULTS: Intra....... CONCLUSION: In this study, we found convincing reproducibility of a detailed evaluation protocol of vertebral endplate signal changes, the "Nordic Modic Classification." The authors recommend that the evaluation protocol should be used in future studies investigating vertebral endplate signal changes....

  5. Reproducibility of the cutoff probe for the measurement of electron density

    Energy Technology Data Exchange (ETDEWEB)

    Kim, D. W.; Oh, W. Y. [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701 (Korea, Republic of); You, S. J., E-mail: sjyou@cnu.ac.kr [Department of Physics, Chungnam National University, Daejeon 305-701 (Korea, Republic of); Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H., E-mail: jhkim86@kriss.re.kr [Center for Vacuum Technology, Korea Research Institute of Standards and Science, Daejeon 305-306 (Korea, Republic of); Yoon, J.-S. [Plasma Technology Research Center, National Fusion Research Institute, Gunsan 573-540 (Korea, Republic of)

    2016-06-15

    Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

  6. Reproducibility of the cutoff probe for the measurement of electron density

    International Nuclear Information System (INIS)

    Kim, D. W.; Oh, W. Y.; You, S. J.; Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H.; Yoon, J.-S.

    2016-01-01

    Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

  7. Multi-model study of mercury dispersion in the atmosphere: vertical and interhemispheric distribution of mercury species

    Directory of Open Access Journals (Sweden)

    J. Bieser

    2017-06-01

    Full Text Available Atmospheric chemistry and transport of mercury play a key role in the global mercury cycle. However, there are still considerable knowledge gaps concerning the fate of mercury in the atmosphere. This is the second part of a model intercomparison study investigating the impact of atmospheric chemistry and emissions on mercury in the atmosphere. While the first study focused on ground-based observations of mercury concentration and deposition, here we investigate the vertical and interhemispheric distribution and speciation of mercury from the planetary boundary layer to the lower stratosphere. So far, there have been few model studies investigating the vertical distribution of mercury, mostly focusing on single aircraft campaigns. Here, we present a first comprehensive analysis based on various aircraft observations in Europe, North America, and on intercontinental flights. The investigated models proved to be able to reproduce the distribution of total and elemental mercury concentrations in the troposphere including interhemispheric trends. One key aspect of the study is the investigation of mercury oxidation in the troposphere. We found that different chemistry schemes were better at reproducing observed oxidized mercury patterns depending on altitude. High concentrations of oxidized mercury in the upper troposphere could be reproduced with oxidation by bromine while elevated concentrations in the lower troposphere were better reproduced by OH and ozone chemistry. However, the results were not always conclusive as the physical and chemical parameterizations in the chemistry transport models also proved to have a substantial impact on model results.

  8. Reproducibility between conventional and digital periapical radiography for bone height measurement

    Directory of Open Access Journals (Sweden)

    Miguel Simancas Pallares

    2015-10-01

    Conclusions. Reproducibility between methods was considered poor, including subgroup analysis, therefore, reproducibility between methods is minimal. Usage of these methods in periodontics should be made implementing the whole knowledge of the technical features and the advantages of these systems.

  9. Predicting the future completing models of observed complex systems

    CERN Document Server

    Abarbanel, Henry

    2013-01-01

    Predicting the Future: Completing Models of Observed Complex Systems provides a general framework for the discussion of model building and validation across a broad spectrum of disciplines. This is accomplished through the development of an exact path integral for use in transferring information from observations to a model of the observed system. Through many illustrative examples drawn from models in neuroscience, fluid dynamics, geosciences, and nonlinear electrical circuits, the concepts are exemplified in detail. Practical numerical methods for approximate evaluations of the path integral are explored, and their use in designing experiments and determining a model's consistency with observations is investigated. Using highly instructive examples, the problems of data assimilation and the means to treat them are clearly illustrated. This book will be useful for students and practitioners of physics, neuroscience, regulatory networks, meteorology and climate science, network dynamics, fluid dynamics, and o...

  10. Reproducibility Between Brain Uptake Ratio Using Anatomic Standardization and Patlak-Plot Methods.

    Science.gov (United States)

    Shibutani, Takayuki; Onoguchi, Masahisa; Noguchi, Atsushi; Yamada, Tomoki; Tsuchihashi, Hiroko; Nakajima, Tadashi; Kinuya, Seigo

    2015-12-01

    The Patlak-plot and conventional methods of determining brain uptake ratio (BUR) have some problems with reproducibility. We formulated a method of determining BUR using anatomic standardization (BUR-AS) in a statistical parametric mapping algorithm to improve reproducibility. The objective of this study was to demonstrate the inter- and intraoperator reproducibility of mean cerebral blood flow as determined using BUR-AS in comparison to the conventional-BUR (BUR-C) and Patlak-plot methods. The images of 30 patients who underwent brain perfusion SPECT were retrospectively used in this study. The images were reconstructed using ordered-subset expectation maximization and processed using an automatic quantitative analysis for cerebral blood flow of ECD tool. The mean SPECT count was calculated from axial basal ganglia slices of the normal side (slices 31-40) drawn using a 3-dimensional stereotactic region-of-interest template after anatomic standardization. The mean cerebral blood flow was calculated from the mean SPECT count. Reproducibility was evaluated using coefficient of variation and Bland-Altman plotting. For both inter- and intraoperator reproducibility, the BUR-AS method had the lowest coefficient of variation and smallest error range about the Bland-Altman plot. Mean CBF obtained using the BUR-AS method had the highest reproducibility. Compared with the Patlak-plot and BUR-C methods, the BUR-AS method provides greater inter- and intraoperator reproducibility of cerebral blood flow measurement. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  11. Delectability of low contrast in CT. Comparison between human observes and observer model

    International Nuclear Information System (INIS)

    Hernandez-Giron, I.; Geleijins, J.; Calzado, A.; Joemai, R. M. S.; Veldkamp, W. J. H.

    2013-01-01

    The objective of this work is to study the real images of TC and other simulated LCD with white noise through a model of observer. The results are compared with those obtained in a similar experiment by human observers. (Author)

  12. A Combined Observational and Modeling Approach to Study Modern Dust Transport from the Patagonia Desert to East Antarctica

    Science.gov (United States)

    Gasso, S.; Stein, A.; Marino, F.; Castellano, E.; Udisti, R.; Ceratto, J.

    2010-01-01

    The understanding of present atmospheric transport processes from Southern Hemisphere (SH) landmasses to Antarctica can improve the interpretation of stratigraphic data in Antarctic ice cores. In addition, long range transport can deliver key nutrients normally not available to marine ecosystems in the Southern Ocean and may trigger or enhance primary productivity. However, there is a dearth of observational based studies of dust transport in the SH. This work aims to improve current understanding of dust transport in the SH by showing a characterization of two dust events originating in the Patagonia desert (south end of South America). The approach is based on a combined and complementary use of satellite retrievals (detectors MISR, MODIS, GLAS ,POLDER, OMI,), transport model simulation (HYSPLIT) and surface observations near the sources and aerosol measurements in Antarctica (Neumayer and Concordia sites). Satellite imagery and visibility observations confirm dust emission in a stretch of dry lakes along the coast of the Tierra del Fuego (TdF) island (approx.54deg S) and from the shores of the Colihue Huapi lake in Central Patagonia (approx.46deg S) in February 2005. Model simulations initialized by these observations reproduce the timing of an observed increase in dust concentration at the Concordia Station and some of the observed increases in atmospheric aerosol absorption (here used as a dust proxy) in the Neumayer station. The TdF sources were the largest contributors of dust at both sites. The transit times from TdF to the Neumayer and Concordia sites are 6-7 and 9-10 days respectively. Lidar observations and model outputs coincide in placing most of the dust cloud in the boundary layer and suggest significant de- position over the ocean immediately downwind. Boundary layer dust was detected as far as 1800 km from the source and approx.800 km north of the South Georgia Island over the central sub-Antarctic Atlantic Ocean. Although the analysis suggests the

  13. 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

  14. Using surface imaging and visual coaching to improve the reproducibility and stability of deep-inspiration breath hold for left-breast-cancer radiotherapy

    International Nuclear Information System (INIS)

    Cervino, Laura I; Gupta, Sonia; Rose, Mary A; Yashar, Catheryn; Jiang, Steve B

    2009-01-01

    Late cardiac complications may arise after left-breast radiation therapy. Deep-inspiration breath hold (DIBH) allows reduction of the irradiated heart volume at the same time as it reduces tumor bed motion and increases lung sparing. In the present study, we have evaluated the improvement in reproducibility and stability of the DIBH for left-breast-cancer treatment when visual coaching is provided with the aid of 3D video surface imaging and video goggles. Five left-breast-cancer patients and fifteen healthy volunteers were asked to perform a series of DIBHs without and with visual coaching. Reproducibility and stability of DIBH were measured for each individual with and without visual coaching. The average reproducibility and stability changed from 2.1 mm and 1.5 mm, respectively, without visual feedback to 0.5 mm and 0.7 mm with visual feedback, showing a significant statistical difference (p 2 mm) in reproducibility and stability were observed in 35% and 15% of the subjects, respectively. The average chest wall excursion of the DIBH with respect to the free breathing preceding the DIBH was found to be 11.3 mm. The reproducibility and stability of the DIBH improve significantly from the visual coaching provided to the patient, especially in those patients with poor reproducibility and stability.

  15. Reproducibility of 3.0 Tesla Magnetic Resonance Spectroscopy for Measuring Hepatic Fat Content

    NARCIS (Netherlands)

    van Werven, Jochem R.; Hoogduin, Johannes M.; Nederveen, Aart J.; van Vliet, Andre A.; Wajs, Ewa; Vandenberk, Petra; Stroes, Erik S. G.; Stoker, Jaap

    Purpose: To investigate reproducibility of proton magnetic resonance spectroscopy (H-1-MRS) to measure hepatic triglyceride content (HTGC). Materials and Methods: In 24 subjects, HTGC was evaluated using H-1-MRS at 3.0 Tesla. We studied "between-weeks" reproducibility and reproducibility of H-1-MRS

  16. Reproducibility and Practical Adoption of GEOBIA with Open-Source Software in Docker Containers

    Directory of Open Access Journals (Sweden)

    Christian Knoth

    2017-03-01

    Full Text Available Geographic Object-Based Image Analysis (GEOBIA mostly uses proprietary software,but the interest in Free and Open-Source Software (FOSS for GEOBIA is growing. This interest stems not only from cost savings, but also from benefits concerning reproducibility and collaboration. Technical challenges hamper practical reproducibility, especially when multiple software packages are required to conduct an analysis. In this study, we use containerization to package a GEOBIA workflow in a well-defined FOSS environment. We explore the approach using two software stacks to perform an exemplary analysis detecting destruction of buildings in bi-temporal images of a conflict area. The analysis combines feature extraction techniques with segmentation and object-based analysis to detect changes using automatically-defined local reference values and to distinguish disappeared buildings from non-target structures. The resulting workflow is published as FOSS comprising both the model and data in a ready to use Docker image and a user interface for interaction with the containerized workflow. The presented solution advances GEOBIA in the following aspects: higher transparency of methodology; easier reuse and adaption of workflows; better transferability between operating systems; complete description of the software environment; and easy application of workflows by image analysis experts and non-experts. As a result, it promotes not only the reproducibility of GEOBIA, but also its practical adoption.

  17. A comprehensive study on rotation reversal in KSTAR: experimental observations and modelling

    Science.gov (United States)

    Na, D. H.; Na, Yong-Su; Angioni, C.; Yang, S. M.; Kwon, J. M.; Jhang, Hogun; Camenen, Y.; Lee, S. G.; Shi, Y. J.; Ko, W. H.; Lee, J. A.; Hahm, T. S.; KSTAR Team

    2017-12-01

    Dedicated experiments have been performed in KSTAR Ohmic plasmas to investigate the detailed physics of the rotation reversal phenomena. Here we adapt the more general definition of rotation reversal, a large change of the intrinsic toroidal rotation gradient produced by minor changes in the control parameters (Camenen et al 2017 Plasma Phys. Control. Fusion 59 034001), which is commonly observed in KSTAR regardless of the operating conditions. The two main phenomenological features of the rotation reversal are the normalized toroidal rotation gradient ({{u}\\prime} ) change in the gradient region and the existence of an anchor point. For the KSTAR Ohmic plasma database including the experiment results up to the 2016 experimental campaign, both features were investigated. First, the observations show that the locations of the gradient and the anchor point region are dependent on {{q}95} . Second, a strong dependence of {{u}\\prime} on {νeff} is clearly observed in the gradient region, whereas the dependence on R/{{L}{{Ti}}} , R/{{L}{{Te}}} , and R/{{L}{{ne}}} is unclear considering the usual variation of the normalized gradient length in KSTAR. The experimental observations were compared against several theoretical models. The rotation reversal might not occur due to the transition of the dominant turbulence from the trapped electron mode to the ion temperature gradient mode or the neoclassical equilibrium effect in KSTAR. Instead, it seems that the profile shearing effects associated with a finite ballooning tilting well reproduce the experimental observations of both the gradient region and the anchor point; the difference seems to be related to the magnetic shear and the q value. Further analysis implies that the increase of {{u}\\prime} in the gradient region with the increase of the collisionality would occur when the reduction of the momentum diffusivity is comparatively larger than the reduction of the residual stress. It is supported by the perturbative

  18. Recent changes in county-level corn yield variability in the United States from observations and crop models

    Energy Technology Data Exchange (ETDEWEB)

    Leng, Guoyong

    2017-12-01

    The United States is responsible for 35% and 60% of global corn supply and exports. Enhanced supply stability through a reduction in the year-to-year variability of US corn yield would greatly benefit global food security. Important in this regard is to understand how corn yield variability has evolved geographically in the history and how it relates to climatic and non-climatic factors. Results showed that year-to-year variation of US corn yield has decreased significantly during 1980-2010, mainly in Midwest Corn Belt, Nebraska and western arid regions. Despite the country-scale decreasing variability, corn yield variability exhibited an increasing trend in South Dakota, Texas and Southeast growing regions, indicating the importance of considering spatial scales in estimating yield variability. The observed pattern is partly reproduced by process-based crop models, simulating larger areas experiencing increasing variability and underestimating the magnitude of decreasing variability. And 3 out of 11 models even produced a differing sign of change from observations. Hence, statistical model which produces closer agreement with observations is used to explore the contribution of climatic and non-climatic factors to the changes in yield variability. It is found that climate variability dominate the change trends of corn yield variability in the Midwest Corn Belt, while the ability of climate variability in controlling yield variability is low in southeastern and western arid regions. Irrigation has largely reduced the corn yield variability in regions (e.g. Nebraska) where separate estimates of irrigated and rain-fed corn yield exist, demonstrating the importance of non-climatic factors in governing the changes in corn yield variability. The results highlight the distinct spatial patterns of corn yield variability change as well as its influencing factors at the county scale. I also caution the use of process-based crop models, which have substantially underestimated

  19. [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.

  20. Atmospheric methane variability at the Peterhof station (Russia): ground-based observations and modeling

    Science.gov (United States)

    Makarova, Maria; Kirner, Oliver; Poberovskii, Anatoliy; Imhasin, Humud; Timofeyev, Yuriy; Virolainen, Yana; Makarov, Boris

    2014-05-01

    The Peterhof station (59.88 N, 29.83 E, 20 m asl) for atmospheric monitoring was founded by Saint - Petersburg State University, Russia. FTIR (Fourier transform IR) observations of methane total column are being carried out by Bruker IFS125 HR since 2009. The study presents a joint analysis of experimental data and EMAC (ECHAM/MESSy Atmospheric Chemistry model) model simulations for Peterhof over the period of 2009-2012. It was shown that CH4 total columns (TC) and column-averaged dry-air mole fractions (MF) obtained from observations are higher than model results with the difference of 1.3% and 0.3 % respectively. The correlation coefficients between FTIR and EMAC data are statistically significant (with 95% confidence) and equal to 0.82 ± 0.08 and 0.4 ± 0.1 for TC and MF of CH4 respectively. The high correlation for TCs shows that EMAC adequately reproduces CH4 variability due to meteorological processes in the atmosphere. On the other hand, the relatively low correlation coefficient for CH4 MF probably indicates an insufficiently precise knowledge of sources and sinks of the atmospheric methane. Amplitudes of the mean annual cycle of CH4 TC for experimental and model datasets (2009-2012) are of 2.1 % and 1.5 % respectively. The same amplitudes calculated for MF are less than for TC: 1.1% for FTIR and 0.6% for EMAC. Difference between FTIR and EMAC annual variations has pronounced seasonality with a maximum in September - November. It could be attributed to the underestimation of methane natural sources in the emission inventory used for EMAC simulations or by relatively coarse horizontal grid of the model (2.8°x2.8°). The analysis of modeling results allowed us to estimate the influence of the limited number of sunny days with FTIR measurement (i.e. specific meteorological conditions which usually take place during FTIR observations) on obtained FTIR estimates of the mean levels of TC and MF over 2009-2012. The systematic shifts of FTIR mean levels of TC and

  1. PDB-NMA of a protein homodimer reproduces distinct experimental motility asymmetry

    Science.gov (United States)

    Tirion, Monique M.; ben-Avraham, Daniel

    2018-03-01

    We have extended our analytically derived PDB-NMA formulation, Atomic Torsional Modal Analysis or ATMAN (Tirion and ben-Avraham 2015 Phys. Rev. E 91 032712), to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3 {\\mathringA} resolution model of a small homodimer, ActVA-ORF6, consisting of two 112-residue subunits identically folded in a compact 50 {\\mathringA} sphere, reproduces the distinct experimental Debye-Waller motility asymmetry for the two chains, demonstrating that structure sensitively selects vibrational signatures. The vibrational analysis of this PDB entry, together with biochemical and crystallographic data, demonstrates the cooperative nature of the dimeric interaction of the two subunits and suggests a mechanical model for subunit interconversion during the catalytic cycle.

  2. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

    Science.gov (United States)

    Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

    2011-12-15

    The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research

  3. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    Science.gov (United States)

    2011-01-01

    Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from

  4. Modelling planktic foraminifer growth and distribution using an ecophysiological multi-species approach

    DEFF Research Database (Denmark)

    Lombard, Fabien; Labeyrie, L.; Michel, E.

    2011-01-01

    We present an eco-physiological model reproducing the growth of eight foraminifer species (Neogloboquadrina pachyderma, Neogloboquadrina incompta, Neogloboquadrina dutertrei, Globigerina bulloides, Globigerinoides ruber, Globigerinoides sacculifer, Globigerinella siphonifera and Orbulina universa...... in the marine carbon cycle....... ocean (PISCES) instead of satellite images as forcing variables gives also good results, but with lower efficiency (58.9%). Compared to core tops observations, the model also correctly reproduces the relative worldwide abundance and the diversity of the eight species when using either satellite data...

  5. Evaluating climate model performance with various parameter sets using observations over the recent past

    Directory of Open Access Journals (Sweden)

    M. F. Loutre

    2011-05-01

    Full Text Available Many sources of uncertainty limit the accuracy of climate projections. Among them, we focus here on the parameter uncertainty, i.e. the imperfect knowledge of the values of many physical parameters in a climate model. Therefore, we use LOVECLIM, a global three-dimensional Earth system model of intermediate complexity and vary several parameters within a range based on the expert judgement of model developers. Nine climatic parameter sets and three carbon cycle parameter sets are selected because they yield present-day climate simulations coherent with observations and they cover a wide range of climate responses to doubled atmospheric CO2 concentration and freshwater flux perturbation in the North Atlantic. Moreover, they also lead to a large range of atmospheric CO2 concentrations in response to prescribed emissions. Consequently, we have at our disposal 27 alternative versions of LOVECLIM (each corresponding to one parameter set that provide very different responses to some climate forcings. The 27 model versions are then used to illustrate the range of responses provided over the recent past, to compare the time evolution of climate variables over the time interval for which they are available (the last few decades up to more than one century and to identify the outliers and the "best" versions over that particular time span. For example, between 1979 and 2005, the simulated global annual mean surface temperature increase ranges from 0.24 °C to 0.64 °C, while the simulated increase in atmospheric CO2 concentration varies between 40 and 50 ppmv. Measurements over the same period indicate an increase in global annual mean surface temperature of 0.45 °C (Brohan et al., 2006 and an increase in atmospheric CO2 concentration of 44 ppmv (Enting et al., 1994; GLOBALVIEW-CO2, 2006. Only a few parameter sets yield simulations that reproduce the observed key variables of the climate system over the last

  6. Completely reproducible description of digital sound data with cellular automata

    International Nuclear Information System (INIS)

    Wada, Masato; Kuroiwa, Jousuke; Nara, Shigetoshi

    2002-01-01

    A novel method of compressive and completely reproducible description of digital sound data by means of rule dynamics of CA (cellular automata) is proposed. The digital data of spoken words and music recorded with the standard format of a compact disk are reproduced completely by this method with use of only two rules in a one-dimensional CA without loss of information

  7. Reproducibility of gene expression across generations of Affymetrix microarrays

    Directory of Open Access Journals (Sweden)

    Haslett Judith N

    2003-06-01

    Full Text Available Abstract Background The development of large-scale gene expression profiling technologies is rapidly changing the norms of biological investigation. But the rapid pace of change itself presents challenges. Commercial microarrays are regularly modified to incorporate new genes and improved target sequences. Although the ability to compare datasets across generations is crucial for any long-term research project, to date no means to allow such comparisons have been developed. In this study the reproducibility of gene expression levels across two generations of Affymetrix GeneChips® (HuGeneFL and HG-U95A was measured. Results Correlation coefficients were computed for gene expression values across chip generations based on different measures of similarity. Comparing the absolute calls assigned to the individual probe sets across the generations found them to be largely unchanged. Conclusion We show that experimental replicates are highly reproducible, but that reproducibility across generations depends on the degree of similarity of the probe sets and the expression level of the corresponding transcript.

  8. Inferring internal properties of Earth's core dynamics and their evolution from surface observations and a numerical geodynamo model

    Directory of Open Access Journals (Sweden)

    J. Aubert

    2011-10-01

    Full Text Available Over the past decades, direct three-dimensional numerical modelling has been successfully used to reproduce the main features of the geodynamo. Here we report on efforts to solve the associated inverse problem, aiming at inferring the underlying properties of the system from the sole knowledge of surface observations and the first principle dynamical equations describing the convective dynamo. To this end we rely on twin experiments. A reference model time sequence is first produced and used to generate synthetic data, restricted here to the large-scale component of the magnetic field and its rate of change at the outer boundary. Starting from a different initial condition, a second sequence is next run and attempts are made to recover the internal magnetic, velocity and buoyancy anomaly fields from the sparse surficial data. In order to reduce the vast underdetermination of this problem, we use stochastic inversion, a linear estimation method determining the most likely internal state compatible with the observations and some prior knowledge, and we also implement a sequential evolution algorithm in order to invert time-dependent surface observations. The prior is the multivariate statistics of the numerical model, which are directly computed from a large number of snapshots stored during a preliminary direct run. The statistics display strong correlation between different harmonic degrees of the surface observations and internal fields, provided they share the same harmonic order, a natural consequence of the linear coupling of the governing dynamical equations and of the leading influence of the Coriolis force. Synthetic experiments performed with a weakly nonlinear model yield an excellent quantitative retrieval of the internal structure. In contrast, the use of a strongly nonlinear (and more realistic model results in less accurate static estimations, which in turn fail to constrain the unobserved small scales in the time integration of the

  9. A new strategy to deliver synthetic protein drugs: self-reproducible biologics using minicircles.

    Science.gov (United States)

    Yi, Hyoju; Kim, Youngkyun; Kim, Juryun; Jung, Hyerin; Rim, Yeri Alice; Jung, Seung Min; Park, Sung-Hwan; Ju, Ji Hyeon

    2014-08-05

    Biologics are the most successful drugs used in anticytokine therapy. However, they remain partially unsuccessful because of the elevated cost of their synthesis and purification. Development of novel biologics has also been hampered by the high cost. Biologics are made of protein components; thus, theoretically, they can be produced in vivo. Here we tried to invent a novel strategy to allow the production of synthetic drugs in vivo by the host itself. The recombinant minicircles encoding etanercept or tocilizumab, which are synthesized currently by pharmaceutical companies, were injected intravenously into animal models. Self-reproduced etanercept and tocilizumab were detected in the serum of mice. Moreover, arthritis subsided in mice that were injected with minicircle vectors carrying biologics. Self-reproducible biologics need neither factory facilities for drug production nor clinical processes, such as frequent drug injection. Although this novel strategy is in its very early conceptual stage, it seems to represent a potential alternative method for the delivery of biologics.

  10. Reproducibility of abdominal fat assessment by ultrasound and computed tomography.

    Science.gov (United States)

    Mauad, Fernando Marum; Chagas-Neto, Francisco Abaeté; Benedeti, Augusto César Garcia Saab; Nogueira-Barbosa, Marcello Henrique; Muglia, Valdair Francisco; Carneiro, Antonio Adilton Oliveira; Muller, Enrico Mattana; Elias Junior, Jorge

    2017-01-01

    To test the accuracy and reproducibility of ultrasound and computed tomography (CT) for the quantification of abdominal fat in correlation with the anthropometric, clinical, and biochemical assessments. Using ultrasound and CT, we determined the thickness of subcutaneous and intra-abdominal fat in 101 subjects-of whom 39 (38.6%) were men and 62 (61.4%) were women-with a mean age of 66.3 years (60-80 years). The ultrasound data were correlated with the anthropometric, clinical, and biochemical parameters, as well as with the areas measured by abdominal CT. Intra-abdominal thickness was the variable for which the correlation with the areas of abdominal fat was strongest (i.e., the correlation coefficient was highest). We also tested the reproducibility of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater reproducibility, having higher intraobserver and interobserver reliability than had the ultrasound measurements. There was a significant correlation between ultrasound and CT, with a correlation coefficient of 0.71. In the assessment of abdominal fat, the intraobserver and interobserver reliability were greater for CT than for ultrasound, although both methods showed high accuracy and good reproducibility.

  11. An empirical analysis of journal policy effectiveness for computational reproducibility.

    Science.gov (United States)

    Stodden, Victoria; Seiler, Jennifer; Ma, Zhaokun

    2018-03-13

    A key component of scientific communication is sufficient information for other researchers in the field to reproduce published findings. For computational and data-enabled research, this has often been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters. Many journals are revising author guidelines to include data and code availability. This work evaluates the effectiveness of journal policy that requires the data and code necessary for reproducibility be made available postpublication by the authors upon request. We assess the effectiveness of such a policy by ( i ) requesting data and code from authors and ( ii ) attempting replication of the published findings. We chose a random sample of 204 scientific papers published in the journal Science after the implementation of their policy in February 2011. We found that we were able to obtain artifacts from 44% of our sample and were able to reproduce the findings for 26%. We find this policy-author remission of data and code postpublication upon request-an improvement over no policy, but currently insufficient for reproducibility.

  12. Climate model biases in seasonality of continental water storage revealed by satellite gravimetry

    Science.gov (United States)

    Swenson, Sean; Milly, P.C.D.

    2006-01-01

    Satellite gravimetric observations of monthly changes in continental water storage are compared with outputs from five climate models. All models qualitatively reproduce the global pattern of annual storage amplitude, and the seasonal cycle of global average storage is reproduced well, consistent with earlier studies. However, global average agreements mask systematic model biases in low latitudes. Seasonal extrema of low‐latitude, hemispheric storage generally occur too early in the models, and model‐specific errors in amplitude of the low‐latitude annual variations are substantial. These errors are potentially explicable in terms of neglected or suboptimally parameterized water stores in the land models and precipitation biases in the climate models.

  13. Premaximum observations of the type Ia SN 1990N

    International Nuclear Information System (INIS)

    Leibundgut, B.; Kirshner, R.P.; Filippenko, A.V.; Shields, J.C.; Foltz, C.B.; Phillips, M.M.; Sonneborn, G.

    1991-01-01

    Spectroscopic and photometric observations of SN 1990N were obtained at ultraviolet and optical wavelengths, beginning 14 days before maximum light. The early observations reveal important differences from spectra of SN Ia's around maximum light. Photometry and spectroscopy obtained after maximum show that SN 1990N is a typical SN Ia and that most of the observed differences are due to the early epoch of the observations. The most significant characteristics are (1) the high velocities of Ca and Si up to 22,000 km/s; (2) the presence of Co and Fe 2 weeks before maximum; and (3) the more rapid increase in the UV flux compared to the optical. The most popular models for white dwarf deflagration that have provided the standard interpretation for SN Ia's at maximum light do not reproduce the high velocities of Ca II and Si II lines observed in SN 1990N. 37 refs

  14. Is the island universe model consistent with observations?

    OpenAIRE

    Piao, Yun-Song

    2005-01-01

    We study the island universe model, in which initially the universe is in a cosmological constant sea, then the local quantum fluctuations violating the null energy condition create the islands of matter, some of which might corresponds to our observable universe. We examine the possibility that the island universe model is regarded as an alternative scenario of the origin of observable universe.

  15. Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements.

    Science.gov (United States)

    Taumer, Christoph; Griesbaum, Lena; Kovacevic, Alen; Soufi, Boumediene; Nalpas, Nicolas C; Macek, Boris

    2018-03-29

    Increasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy more than two thirds of the proteome, the abundance of protein phosphorylation is much lower in bacteria. Even the state-of-the-art phosphopeptide enrichment protocols fail to remove the high background of abundant unmodified peptides, leading to low signal intensity and undersampling of phosphopeptide precursor ions in consecutive data-dependent MS runs. Consequently, large-scale bacterial phosphoproteomic datasets often suffer from poor reproducibility and a high number of missing values. Here we explore the application of parallel reaction monitoring (PRM) on a Q Exactive mass spectrometer in bacterial phosphoproteome analysis, focusing especially on run-to-run sampling reproducibility. In multiple measurements of identical phosphopeptide-enriched samples, we show that PRM outperforms data-dependent acquisition (DDA) in terms of detection frequency, reaching almost complete sampling efficiency, compared to 20% in DDA. We observe a similar trend over multiple heterogeneous phosphopeptide-enriched samples and conclude that PRM shows a great promise in bacterial phosphoproteomics analyses where reproducible detection and quantification of a relatively small set of phosphopeptides is desired. Bacterial phosphorylated peptides occur in low abundance compared to their unmodified counterparts, and are therefore rarely reproducibly detected in shotgun (DDA) proteomics measurements. Here we show that parallel reaction monitoring complements DDA analyses and makes detection of known, targeted phosphopeptides more reproducible. This will be of significance in replicated MS measurements that have a goal to reproducibly detect and quantify phosphopeptides of interest. Copyright

  16. Correlation between model observer and human observer performance in CT imaging when lesion location is uncertain

    Energy Technology Data Exchange (ETDEWEB)

    Leng, Shuai; Yu, Lifeng; Zhang, Yi; McCollough, Cynthia H. [Department of Radiology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905 (United States); Carter, Rickey [Department of Biostatistics, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905 (United States); Toledano, Alicia Y. [Biostatistics Consulting, LLC, 10606 Wheatley Street, Kensington, Maryland 20895 (United States)

    2013-08-15

    Purpose: The purpose of this study was to investigate the correlation between model observer and human observer performance in CT imaging for the task of lesion detection and localization when the lesion location is uncertain.Methods: Two cylindrical rods (3-mm and 5-mm diameters) were placed in a 35 × 26 cm torso-shaped water phantom to simulate lesions with −15 HU contrast at 120 kV. The phantom was scanned 100 times on a 128-slice CT scanner at each of four dose levels (CTDIvol = 5.7, 11.4, 17.1, and 22.8 mGy). Regions of interest (ROIs) around each lesion were extracted to generate images with signal-present, with each ROI containing 128 × 128 pixels. Corresponding ROIs of signal-absent images were generated from images without lesion mimicking rods. The location of the lesion (rod) in each ROI was randomly distributed by moving the ROIs around each lesion. Human observer studies were performed by having three trained observers identify the presence or absence of lesions, indicating the lesion location in each image and scoring confidence for the detection task on a 6-point scale. The same image data were analyzed using a channelized Hotelling model observer (CHO) with Gabor channels. Internal noise was added to the decision variables for the model observer study. Area under the curve (AUC) of ROC and localization ROC (LROC) curves were calculated using a nonparametric approach. The Spearman's rank order correlation between the average performance of the human observers and the model observer performance was calculated for the AUC of both ROC and LROC curves for both the 3- and 5-mm diameter lesions.Results: In both ROC and LROC analyses, AUC values for the model observer agreed well with the average values across the three human observers. The Spearman's rank order correlation values for both ROC and LROC analyses for both the 3- and 5-mm diameter lesions were all 1.0, indicating perfect rank ordering agreement of the figures of merit (AUC

  17. Reproducing Kernel Method for Solving Nonlinear Differential-Difference Equations

    Directory of Open Access Journals (Sweden)

    Reza Mokhtari

    2012-01-01

    Full Text Available On the basis of reproducing kernel Hilbert spaces theory, an iterative algorithm for solving some nonlinear differential-difference equations (NDDEs is presented. The analytical solution is shown in a series form in a reproducing kernel space, and the approximate solution , is constructed by truncating the series to terms. The convergence of , to the analytical solution is also proved. Results obtained by the proposed method imply that it can be considered as a simple and accurate method for solving such differential-difference problems.

  18. 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...

  19. Conceptual models of microseismicity induced by fluid injection

    Science.gov (United States)

    Baro Urbea, J.; Lord-May, C.; Eaton, D. W. S.; Joern, D.

    2017-12-01

    Variations in the pore pressure due to fluid invasion are accountable for microseismic activity recorded in geothermal systems and during hydraulic fracturing operations. To capture this phenomenon on a conceptual level, invasion percolation models have been suggested to represent the flow network of fluids within a porous media and seismic activity is typically considered to be directly related to the expansion of the percolated area. Although such models reproduce scale-free frequency-magnitude distributions, the associated b-values of the Gutenberg-Richter relation do not align with observed data. Here, we propose an alternative conceptual invasion percolation model that decouples the fluid propagation from the microseismic events. Instead of a uniform pressure, the pressure is modeled to decay along the distance from the injection site. Wet fracture events are simulated with a stochastic spring block model exhibiting stick-slip dynamics as a result of the variations of the pore pressure. We show that the statistics of the stick-slip events are scale-free, but now the b-values depend on the level of heterogeneity in the local static friction coefficients. Thus, this model is able to reproduce the wide spectrum of b-values observed in field catalogs associated with fluid induced microseismicity. Moreover, the spatial distribution of microseismic events is also consistent with observations.

  20. Nutrient cycle benchmarks for earth system land model

    Science.gov (United States)

    Zhu, Q.; Riley, W. J.; Tang, J.; Zhao, L.

    2017-12-01

    Projecting future biosphere-climate feedbacks using Earth system models (ESMs) relies heavily on robust modeling of land surface carbon dynamics. More importantly, soil nutrient (particularly, nitrogen (N) and phosphorus (P)) dynamics strongly modulate carbon dynamics, such as plant sequestration of atmospheric CO2. Prevailing ESM land models all consider nitrogen as a potentially limiting nutrient, and several consider phosphorus. However, including nutrient cycle processes in ESM land models potentially introduces large uncertainties that could be identified and addressed by improved observational constraints. We describe the development of two nutrient cycle benchmarks for ESM land models: (1) nutrient partitioning between plants and soil microbes inferred from 15N and 33P tracers studies and (2) nutrient limitation effects on carbon cycle informed by long-term fertilization experiments. We used these benchmarks to evaluate critical hypotheses regarding nutrient cycling and their representation in ESMs. We found that a mechanistic representation of plant-microbe nutrient competition based on relevant functional traits best reproduced observed plant-microbe nutrient partitioning. We also found that for multiple-nutrient models (i.e., N and P), application of Liebig's law of the minimum is often inaccurate. Rather, the Multiple Nutrient Limitation (MNL) concept better reproduces observed carbon-nutrient interactions.

  1. On the Realistic Stochastic Model of GPS Observables: Implementation and Performance

    Science.gov (United States)

    Zangeneh-Nejad, F.; Amiri-Simkooei, A. R.; Sharifi, M. A.; Asgari, J.

    2015-12-01

    High-precision GPS positioning requires a realistic stochastic model of observables. A realistic GPS stochastic model of observables should take into account different variances for different observation types, correlations among different observables, the satellite elevation dependence of observables precision, and the temporal correlation of observables. Least-squares variance component estimation (LS-VCE) is applied to GPS observables using the geometry-based observation model (GBOM). To model the satellite elevation dependent of GPS observables precision, an exponential model depending on the elevation angles of the satellites are also employed. Temporal correlation of the GPS observables is modelled by using a first-order autoregressive noise model. An important step in the high-precision GPS positioning is double difference integer ambiguity resolution (IAR). The fraction or percentage of success among a number of integer ambiguity fixing is called the success rate. A realistic estimation of the GNSS observables covariance matrix plays an important role in the IAR. We consider the ambiguity resolution success rate for two cases, namely a nominal and a realistic stochastic model of the GPS observables using two GPS data sets collected by the Trimble R8 receiver. The results confirm that applying a more realistic stochastic model can significantly improve the IAR success rate on individual frequencies, either on L1 or on L2. An improvement of 20% was achieved to the empirical success rate results. The results also indicate that introducing the realistic stochastic model leads to a larger standard deviation for the baseline components by a factor of about 2.6 on the data sets considered.

  2. A semiclassical model for quark jet fragmentation

    International Nuclear Information System (INIS)

    Andersson, B.; Gustafson, G.; Peterson, C.

    1979-01-01

    A semiclassical model is presented for the way the energy of a fast quark is transformed into observable hadrons. It reproduces the features of 1+1 dimensional QED (the Schwinger model) concerning a flat rapidity distribution in the central region. It also reproduces results from phenomenological considerations, which, based upon scaling, predict that meson formation in the fragmentation region can be described by an iterative scheme, implying a set of coupled integral equations. In particular the model predicts that the probability to find a meson containing the leading quark is independent of the Feynman scaling variable z. The iterative structure corresponds to a Brownian motion with relevance both to the cofinement problems and to the distribution of mass in the quark jet. (orig.) [de

  3. Reproducibility of cervical range of motion in patients with neck pain

    NARCIS (Netherlands)

    Pool, JJM; van Mameren, H; Deville, WJLM; Assendelft, WJJ; de Vet, HCW; de Winter, AF; Koes, BW; Bouter, LM; Hoving, J.L.

    2005-01-01

    Background: Reproducibility measurements of the range of motion are an important prerequisite for the interpretation of study results. The aim of the study is to assess the intra-rater and interrater reproducibility of the measurement of active Range of Motion ( ROM) in patients with neck pain using

  4. Observed and simulated temperature extremes during the recent warming hiatus

    International Nuclear Information System (INIS)

    Sillmann, Jana; Donat, Markus G; Fyfe, John C; Zwiers, Francis W

    2014-01-01

    The discrepancy between recent observed and simulated trends in global mean surface temperature has provoked a debate about possible causes and implications for future climate change projections. However, little has been said in this discussion about observed and simulated trends in global temperature extremes. Here we assess trend patterns in temperature extremes and evaluate the consistency between observed and simulated temperature extremes over the past four decades (1971–2010) in comparison to the recent 15 years (1996–2010). We consider the coldest night and warmest day in a year in the observational dataset HadEX2 and in the current generation of global climate models (CMIP5). In general, the observed trends fall within the simulated range of trends, with better consistency for the longer period. Spatial trend patterns differ for the warm and cold extremes, with the warm extremes showing continuous positive trends across the globe and the cold extremes exhibiting a coherent cooling pattern across the Northern Hemisphere mid-latitudes that has emerged in the recent 15 years and is not reproduced by the models. This regional inconsistency between models and observations might be a key to understanding the recent hiatus in global mean temperature warming. (letters)

  5. Detailed modeling of mountain wave PSCs

    Directory of Open Access Journals (Sweden)

    S. Fueglistaler

    2003-01-01

    Full Text Available Polar stratospheric clouds (PSCs play a key role in polar ozone depletion. In the Arctic, PSCs can occur on the mesoscale due to orographically induced gravity waves. Here we present a detailed study of a mountain wave PSC event on 25-27 January 2000 over Scandinavia. The mountain wave PSCs were intensively observed by in-situ and remote-sensing techniques during the second phase of the SOLVE/THESEO-2000 Arctic campaign. We use these excellent data of PSC observations on 3 successive days to analyze the PSCs and to perform a detailed comparison with modeled clouds. We simulated the 3-dimensional PSC structure on all 3 days with a mesoscale numerical weather prediction (NWP model and a microphysical box model (using best available nucleation rates for ice and nitric acid trihydrate particles. We show that the combined mesoscale/microphysical model is capable of reproducing the PSC measurements within the uncertainty of data interpretation with respect to spatial dimensions, temporal development and microphysical properties, without manipulating temperatures or using other tuning parameters. In contrast, microphysical modeling based upon coarser scale global NWP data, e.g. current ECMWF analysis data, cannot reproduce observations, in particular the occurrence of ice and nitric acid trihydrate clouds. Combined mesoscale/microphysical modeling may be used for detailed a posteriori PSC analysis and for future Arctic campaign flight and mission planning. The fact that remote sensing alone cannot further constrain model results due to uncertainities in the interpretation of measurements, underlines the need for synchronous in-situ PSC observations in campaigns.

  6. Reproducibility of clinical research in critical care: a scoping review.

    Science.gov (United States)

    Niven, Daniel J; McCormick, T Jared; Straus, Sharon E; Hemmelgarn, Brenda R; Jeffs, Lianne; Barnes, Tavish R M; Stelfox, Henry T

    2018-02-21

    The ability to reproduce experiments is a defining principle of science. Reproducibility of clinical research has received relatively little scientific attention. However, it is important as it may inform clinical practice, research agendas, and the design of future studies. We used scoping review methods to examine reproducibility within a cohort of randomized trials examining clinical critical care research and published in the top general medical and critical care journals. To identify relevant clinical practices, we searched the New England Journal of Medicine, The Lancet, and JAMA for randomized trials published up to April 2016. To identify a comprehensive set of studies for these practices, included articles informed secondary searches within other high-impact medical and specialty journals. We included late-phase randomized controlled trials examining therapeutic clinical practices in adults admitted to general medical-surgical or specialty intensive care units (ICUs). Included articles were classified using a reproducibility framework. An original study was the first to evaluate a clinical practice. A reproduction attempt re-evaluated that practice in a new set of participants. Overall, 158 practices were examined in 275 included articles. A reproduction attempt was identified for 66 practices (42%, 95% CI 33-50%). Original studies reported larger effects than reproduction attempts (primary endpoint, risk difference 16.0%, 95% CI 11.6-20.5% vs. 8.4%, 95% CI 6.0-10.8%, P = 0.003). More than half of clinical practices with a reproduction attempt demonstrated effects that were inconsistent with the original study (56%, 95% CI 42-68%), among which a large number were reported to be efficacious in the original study and to lack efficacy in the reproduction attempt (34%, 95% CI 19-52%). Two practices reported to be efficacious in the original study were found to be harmful in the reproduction attempt. A minority of critical care practices with research published

  7. Reproducibility of Psychological Experiments as a Problem of Post-Nonclassical Science

    Directory of Open Access Journals (Sweden)

    Vachkov I.V.,

    2016-04-01

    Full Text Available A fundamental project on reproducibility carried out in the USA by Brian Nosek in 2015 (the Reproducibility Project revealed a serious methodological problem in psychology: the issue of replication of psycho- logical experiments. Reproducibility has been traditionally perceived as one of the basic principles of the scientific method. However, methodological analysis of the modern post-nonclassical stage in the development of science suggests that this might be a bit too uncompromising as applied to psychology. It seems that the very criteria of scientific research need to be reconsidered with regard to the specifics of post-nonclassical science, and, as the authors put it, as a result, reproducibility might lose its key status or even be excluded at all. The reviewed problem and the proposed ways of coping with it are of high importance to research and practice in psychology as they define the strategies for organizing, conducting and evaluating experimental research.

  8. Link between laboratory/field observations and models

    International Nuclear Information System (INIS)

    Cole, C.R.; Foley, M.G.

    1985-10-01

    The various linkages in system performance assessments that integrate disposal program elements must be understood. The linkage between model development and field/laboratory observations is described as the iterative program of site and system characterization for development of an observational-confirmatory data base to develop, improve, and support conceptual models for site and system behavior. The program consists of data gathering and experiments to demonstrate understanding at various spatial and time scales and degrees of complexity. Understanding and accounting for the decreasing characterization certainty that arises with increasing space and time scales is an important aspect of the link between models and observations. The performance allocation process for setting performance goals and confidence levels coupled with a performance assessment approach that provides these performance and confidence estimates will resolve when sufficient characterization has been achieved. At each iteration performance allocation goals are reviewed and revised as necessary. The updated data base and appropriate performance assessment tools and approaches are utilized to identify and design additional tests and data needs necessary to meet current performance allocation goals. 9 refs

  9. RECONCILING THE OBSERVED STAR-FORMING SEQUENCE WITH THE OBSERVED STELLAR MASS FUNCTION

    International Nuclear Information System (INIS)

    Leja, Joel; Van Dokkum, Pieter G.; Franx, Marijn; Whitaker, Katherine E.

    2015-01-01

    We examine the connection between the observed star-forming sequence (SFR ∝ M α ) and the observed evolution of the stellar mass function in the range 0.2 < z < 2.5. We find that the star-forming sequence cannot have a slope α ≲ 0.9 at all masses and redshifts because this would result in a much higher number density at 10 < log (M/M ☉ ) < 11 by z = 1 than is observed. We show that a transition in the slope of the star-forming sequence, such that α = 1 at log (M/M ☉ ) < 10.5 and α = 0.7-0.13z (Whitaker et al.) at log (M/M ☉ ) > 10.5, greatly improves agreement with the evolution of the stellar mass function. We then derive a star-forming sequence that reproduces the evolution of the mass function by design. This star-forming sequence is also well described by a broken power law, with a shallow slope at high masses and a steep slope at low masses. At z = 2, it is offset by ∼0.3 dex from the observed star-forming sequence, consistent with the mild disagreement between the cosmic star formation rate (SFR) and recent observations of the growth of the stellar mass density. It is unclear whether this problem stems from errors in stellar mass estimates, errors in SFRs, or other effects. We show that a mass-dependent slope is also seen in other self-consistent models of galaxy evolution, including semianalytical, hydrodynamical, and abundance-matching models. As part of the analysis, we demonstrate that neither mergers nor hidden low-mass quiescent galaxies are likely to reconcile the evolution of the mass function and the star-forming sequence. These results are supported by observations from Whitaker et al

  10. Fast neutrons and the optical model: some observations

    International Nuclear Information System (INIS)

    Smith, A.B.; Lawson, R.D.; Guenther, P.T.

    1985-01-01

    The optical model of fast-neutron-induced phenomena is considered from the observational viewpoint. Experimental characteristics governing the reliability of the modeling are outlined with attention to implications on model parameters and their uncertainties. The physical characteristics of experimentally-deduced ''regional'' and ''specific'' model parameters are examined including: parameter trends with mass and energy, implications of collective effects, and fundamental relations between real and imaginary potentials. These physical properties are illustrated by studies in the A=60 and 90 regions. General trends are identified and outstanding issues cited. Throughout, the approach is that of observational interpretation for basic and applied purposes. 20 refs., 11 figs., 2 tabs

  11. Importance of hydrological parameters in contaminant transport modeling in a terrestrial environment

    International Nuclear Information System (INIS)

    Tsuduki, Katsunori; Matsunaga, Takeshi

    2007-01-01

    A grid type multi-layered distributed parameter model for calculating discharge in a watershed was described. Model verification with our field observation resulted in different sets of hydrological parameter values, all of which reproduced the observed discharge. The effect of those varied hydrological parameters on contaminant transport calculation was examined and discussed by simulation of event water transfer. (author)

  12. Coupled RipCAS-DFLOW (CoRD) Software and Data Management System for Reproducible Floodplain Vegetation Succession Modeling

    Science.gov (United States)

    Turner, M. A.; Miller, S.; Gregory, A.; Cadol, D. D.; Stone, M. C.; Sheneman, L.

    2016-12-01

    We present the Coupled RipCAS-DFLOW (CoRD) modeling system created to encapsulate the workflow to analyze the effects of stream flooding on vegetation succession. CoRD provides an intuitive command-line and web interface to run DFLOW and RipCAS in succession over many years automatically, which is a challenge because, for our application, DFLOW must be run on a supercomputing cluster via the PBS job scheduler. RipCAS is a vegetation succession model, and DFLOW is a 2D open channel flow model. Data adaptors have been developed to seamlessly connect DFLOW output data to be RipCAS inputs, and vice-versa. CoRD provides automated statistical analysis and visualization, plus automatic syncing of input and output files and model run metadata to the hydrological data management system HydroShare using its excellent Python REST client. This combination of technologies and data management techniques allows the results to be shared with collaborators and eventually published. Perhaps most importantly, it allows results to be easily reproduced via either the command-line or web user interface. This system is a result of collaboration between software developers and hydrologists participating in the Western Consortium for Watershed Analysis, Visualization, and Exploration (WC-WAVE). Because of the computing-intensive nature of this particular workflow, including automating job submission/monitoring and data adaptors, software engineering expertise is required. However, the hydrologists provide the software developers with a purpose and ensure a useful, intuitive tool is developed. Our hydrologists contribute software, too: RipCAS was developed from scratch by hydrologists on the team as a specialized, open-source version of the Computer Aided Simulation Model for Instream Flow and Riparia (CASiMiR) vegetation model; our hydrologists running DFLOW provided numerous examples and help with the supercomputing system. This project is written in Python, a popular language in the

  13. Multiple Model Adaptive Control Using Dual Youla-Kucera Factorisation

    DEFF Research Database (Denmark)

    Bendtsen, Jan Dimon; Trangbæk, Klaus

    2012-01-01

    We propose a multi-model adaptive control scheme for uncertain linear plants based on the concept of model unfalsification. The approach relies on examining the ability of a pre-computed set of plant-controller candidates and choosing the one that is best able to reproduce observed in- and output...

  14. Scapular dyskinesis in trapezius myalgia and intraexaminer reproducibility of clinical tests

    DEFF Research Database (Denmark)

    Juul-Kristensen, Birgit; Hilt, Kenneth; Enoch, Flemming

    2011-01-01

    dyskinesis, general health, and work ability, and 19 cases and 14 controls participated in the reproducibility study. Intraexaminer reproducibility was good to excellent for 6 of 10 clinical variables (Intraclass Correlation Coefficient [ICC] 0.76-0.91; kappa 0.84-1.00), and fair to good for four variables...

  15. Reproducibility of cervical range of motion in patients with neck pain

    NARCIS (Netherlands)

    Hoving, Jan Lucas; Pool, Jan J. M.; van Mameren, Henk; Devillé, Walter J. L. M.; Assendelft, Willem J. J.; de Vet, Henrica C. W.; de Winter, Andrea F.; Koes, Bart W.; Bouter, Lex M.

    2005-01-01

    BACKGROUND: Reproducibility measurements of the range of motion are an important prerequisite for the interpretation of study results. The aim of the study is to assess the intra-rater and inter-rater reproducibility of the measurement of active Range of Motion (ROM) in patients with neck pain using

  16. Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

    Science.gov (United States)

    Wen, Chongqing; Wu, Liyou; Qin, Yujia; Van Nostrand, Joy D; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

    2017-01-01

    Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, pdeep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates

  17. Predicting detection performance with model observers: Fourier domain or spatial domain?

    Science.gov (United States)

    Chen, Baiyu; Yu, Lifeng; Leng, Shuai; Kofler, James; Favazza, Christopher; Vrieze, Thomas; McCollough, Cynthia

    2016-02-27

    The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images.

  18. Hydrological model performance and parameter estimation in the wavelet-domain

    Directory of Open Access Journals (Sweden)

    B. Schaefli

    2009-10-01

    Full Text Available This paper proposes a method for rainfall-runoff model calibration and performance analysis in the wavelet-domain by fitting the estimated wavelet-power spectrum (a representation of the time-varying frequency content of a time series of a simulated discharge series to the one of the corresponding observed time series. As discussed in this paper, calibrating hydrological models so as to reproduce the time-varying frequency content of the observed signal can lead to different results than parameter estimation in the time-domain. Therefore, wavelet-domain parameter estimation has the potential to give new insights into model performance and to reveal model structural deficiencies. We apply the proposed method to synthetic case studies and a real-world discharge modeling case study and discuss how model diagnosis can benefit from an analysis in the wavelet-domain. The results show that for the real-world case study of precipitation – runoff modeling for a high alpine catchment, the calibrated discharge simulation captures the dynamics of the observed time series better than the results obtained through calibration in the time-domain. In addition, the wavelet-domain performance assessment of this case study highlights the frequencies that are not well reproduced by the model, which gives specific indications about how to improve the model structure.

  19. The Impact of Modeling Assumptions in Galactic Chemical Evolution Models

    Science.gov (United States)

    Côté, Benoit; O'Shea, Brian W.; Ritter, Christian; Herwig, Falk; Venn, Kim A.

    2017-02-01

    We use the OMEGA galactic chemical evolution code to investigate how the assumptions used for the treatment of galactic inflows and outflows impact numerical predictions. The goal is to determine how our capacity to reproduce the chemical evolution trends of a galaxy is affected by the choice of implementation used to include those physical processes. In pursuit of this goal, we experiment with three different prescriptions for galactic inflows and outflows and use OMEGA within a Markov Chain Monte Carlo code to recover the set of input parameters that best reproduces the chemical evolution of nine elements in the dwarf spheroidal galaxy Sculptor. This provides a consistent framework for comparing the best-fit solutions generated by our different models. Despite their different degrees of intended physical realism, we found that all three prescriptions can reproduce in an almost identical way the stellar abundance trends observed in Sculptor. This result supports the similar conclusions originally claimed by Romano & Starkenburg for Sculptor. While the three models have the same capacity to fit the data, the best values recovered for the parameters controlling the number of SNe Ia and the strength of galactic outflows, are substantially different and in fact mutually exclusive from one model to another. For the purpose of understanding how a galaxy evolves, we conclude that only reproducing the evolution of a limited number of elements is insufficient and can lead to misleading conclusions. More elements or additional constraints such as the Galaxy’s star-formation efficiency and the gas fraction are needed in order to break the degeneracy between the different modeling assumptions. Our results show that the successes and failures of chemical evolution models are predominantly driven by the input stellar yields, rather than by the complexity of the Galaxy model itself. Simple models such as OMEGA are therefore sufficient to test and validate stellar yields. OMEGA

  20. Quantized correlation coefficient for measuring reproducibility of ChIP-chip data

    Directory of Open Access Journals (Sweden)

    Kuroda Mitzi I

    2010-07-01

    Full Text Available Abstract Background Chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip is used to study protein-DNA interactions and histone modifications on a genome-scale. To ensure data quality, these experiments are usually performed in replicates, and a correlation coefficient between replicates is used often to assess reproducibility. However, the correlation coefficient can be misleading because it is affected not only by the reproducibility of the signal but also by the amount of binding signal present in the data. Results We develop the Quantized correlation coefficient (QCC that is much less dependent on the amount of signal. This involves discretization of data into set of quantiles (quantization, a merging procedure to group the background probes, and recalculation of the Pearson correlation coefficient. This procedure reduces the influence of the background noise on the statistic, which then properly focuses more on the reproducibility of the signal. The performance of this procedure is tested in both simulated and real ChIP-chip data. For replicates with different levels of enrichment over background and coverage, we find that QCC reflects reproducibility more accurately and is more robust than the standard Pearson or Spearman correlation coefficients. The quantization and the merging procedure can also suggest a proper quantile threshold for separating signal from background for further analysis. Conclusions To measure reproducibility of ChIP-chip data correctly, a correlation coefficient that is robust to the amount of signal present should be used. QCC is one such measure. The QCC statistic can also be applied in a variety of other contexts for measuring reproducibility, including analysis of array CGH data for DNA copy number and gene expression data.