DMFC performance and methanol cross-over: Experimental analysis and model validation

Energy Technology Data Exchange (ETDEWEB)

Casalegno, A.; Marchesi, R. [Dipartimento di Energia, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

2008-10-15

A combined experimental and modelling approach is proposed to analyze methanol cross-over and its effect on DMFC performance. The experimental analysis is performed in order to allow an accurate investigation of methanol cross-over influence on DMFC performance, hence measurements were characterized in terms of uncertainty and reproducibility. The findings suggest that methanol cross-over is mainly determined by diffusion transport and affects cell performance partly via methanol electro-oxidation at the cathode. The modelling analysis is carried out to further investigate methanol cross-over phenomenon. A simple model evaluates the effectiveness of two proposed interpretations regarding methanol cross-over and its effects. The model is validated using the experimental data gathered. Both the experimental analysis and the proposed and validated model allow a substantial step forward in the understanding of the main phenomena associated with methanol cross-over. The findings confirm the possibility to reduce methanol cross-over by optimizing anode feeding. (author)

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

New experimental model for training in videosurgery Novo modelo experimental para treinamento em videocirurgia

Directory of Open Access Journals (Sweden)

Danilo Malta Batista

2012-10-01

Full Text Available PURPOSE: To develop a new experimental model of lower cost for training in videosurgery. METHODS: This project was performed at the Nucleus of Experimental Surgery of the Bahiana School of Medicine and Public Health, based on previous models described in the literature and under the supervision of the full professor of Operative Technique and Experimental Surgery II. It was made a model cube-shaped, made of wood, with holes distributed in various locations, rubber stoppers for the holes and lined externally with carpet, and internally with laminate. RESULTS: The new experimental model is of low cost and reproduces quite faithfully several videosurgical procedures. CONCLUSION: Medical schools interested in the subject may adopt the new model for training in videosurgery without the need of high costs for making and using these models.OBJETIVO: Desenvolver um novo modelo experimental de baixo custo para treinamento em videocirurgia MÉTODOS: Este projeto foi conduzido no Núcleo de Cirurgia Experimental da Escola Bahiana de Medicina e Saúde Pública, baseado em modelos prévios descritos na literatura e sob a supervisão do professor titular de Técnica Operatória e Cirurgia Experimental II. Foi feito um modelo em formato de cubo, de madeira, com furos distribuídos em vários locais, tampas de borracha para os orifícios e forrado externamente com carpete e internamente com laminado. RESULTADOS: O novo modelo experimental desenvolvido é de baixo custo e reproduz de forma bastante fiel diversos procedimentos videocirúrgicos. CONCLUSÃO: Faculdades médicas interessadas no tema poderão adotar o novo modelo para o treinamento em videocirurgia sem que sejam necessários gastos elevados para a confecção e o uso desses modelos.

DMFC anode polarization: Experimental analysis and model validation

Energy Technology Data Exchange (ETDEWEB)

Casalegno, A.; Marchesi, R. [Dipartimento di Energetica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

2008-01-03

Anode two-phase flow has an important influence on DMFC performance and methanol crossover. In order to elucidate two-phase flow influence on anode performance, in this work, anode polarization is investigated combining experimental and modelling approach. A systematic experimental analysis of operating conditions influence on anode polarization is presented. Hysteresis due to operating condition is observed; experimental results suggest that it arises from methanol accumulation and has to be considered in evaluating DMFC performances and measurements reproducibility. A model of DMFC anode polarization is presented and utilised as tool to investigate anode two-phase flow. The proposed analysis permits one to produce a confident interpretation of the main involved phenomena. In particular, it confirms that methanol electro-oxidation kinetics is weakly dependent on methanol concentration and that methanol transport in gas phase produces an important contribution in anode feeding. Moreover, it emphasises the possibility to optimise anode flow rate in order to improve DMFC performance and reduce methanol crossover. (author)

Experimental consequences of SU(3) symmetry in an sdg boson model

International Nuclear Information System (INIS)

Akiyama, Y.; Brentano, P. von; Gelberg, A.

1987-01-01

Energies of collective levels in 178 Hf and 234 U are compared wth predictions of the SU(3) limiz of the sdg interacting boson model. All known positive parity states of 178 Hf below 1.8 MeV (with the expection of a 0 + band) have been satisfactorily reproduced. Most of the bands in 234 U are also described by the model. However, a few predicted states have no experimental counterpart. The introduction of the g-basons strongly reduces the previously observed discrepancies between experimental B(E2)'s in 238 U and the sd-IBM calculation. (orig.)

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.

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

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.

Experimental consequences of SU(3) symmetry in an sdg boson model

Energy Technology Data Exchange (ETDEWEB)

Akiyama, Y.; Brentano, P. von; Gelberg, A.

1987-05-01

Energies of collective levels in /sup 178/Hf and /sup 234/U are compared wth predictions of the SU(3) limiz of the sdg interacting boson model. All known positive parity states of /sup 178/Hf below 1.8 MeV (with the expection of a 0/sup +/ band) have been satisfactorily reproduced. Most of the bands in /sup 234/U are also described by the model. However, a few predicted states have no experimental counterpart. The introduction of the g-basons strongly reduces the previously observed discrepancies between experimental B(E2)'s in /sup 238/U and the sd-IBM calculation.

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.

Macroscopic Dynamic Modeling of Sequential Batch Cultures of Hybridoma Cells: An Experimental Validation

Directory of Open Access Journals (Sweden)

Laurent Dewasme

2017-02-01

Full Text Available Hybridoma cells are commonly grown for the production of monoclonal antibodies (MAb. For monitoring and control purposes of the bioreactors, dynamic models of the cultures are required. However these models are difficult to infer from the usually limited amount of available experimental data and do not focus on target protein production optimization. This paper explores an experimental case study where hybridoma cells are grown in a sequential batch reactor. The simplest macroscopic reaction scheme translating the data is first derived using a maximum likelihood principal component analysis. Subsequently, nonlinear least-squares estimation is used to determine the kinetic laws. The resulting dynamic model reproduces quite satisfactorily the experimental data, as evidenced in direct and cross-validation tests. Furthermore, model predictions can also be used to predict optimal medium renewal time and composition.

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.

A Harmony Search Algorithm for the Reproduction of Experimental Data in the Social Force Model

Directory of Open Access Journals (Sweden)

Osama Moh'd Alia

2014-01-01

Full Text Available Crowd dynamics is a discipline dealing with the management and flow of crowds in congested places and circumstances. Pedestrian congestion is a pressing issue where crowd dynamics models can be applied. The reproduction of experimental data (velocity-density relation and specific flow rate is a major component for the validation and calibration of such models. In the social force model, researchers have proposed various techniques to adjust essential parameters governing the repulsive social force, which is an effort at reproducing such experimental data. Despite that and various other efforts, the optimal reproduction of the real life data is unachievable. In this paper, a harmony search-based technique called HS-SFM is proposed to overcome the difficulties of the calibration process for SFM, where the fundamental diagram of velocity-density relation and the specific flow rate are reproduced in conformance with the related empirical data. The improvisation process of HS is modified by incorporating the global best particle concept from particle swarm optimization (PSO to increase the convergence rate and overcome the high computational demands of HS-SFM. Simulation results have shown HS-FSM’s ability to produce near optimal SFM parameter values, which makes it possible for SFM to almost reproduce the related empirical data.

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

Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model.

Science.gov (United States)

Casey, F P; Baird, D; Feng, Q; Gutenkunst, R N; Waterfall, J J; Myers, C R; Brown, K S; Cerione, R A; Sethna, J P

2007-05-01

We apply the methods of optimal experimental design to a differential equation model for epidermal growth factor receptor signalling, trafficking and down-regulation. The model incorporates the role of a recently discovered protein complex made up of the E3 ubiquitin ligase, Cbl, the guanine exchange factor (GEF), Cool-1 (beta -Pix) and the Rho family G protein Cdc42. The complex has been suggested to be important in disrupting receptor down-regulation. We demonstrate that the model interactions can accurately reproduce the experimental observations, that they can be used to make predictions with accompanying uncertainties, and that we can apply ideas of optimal experimental design to suggest new experiments that reduce the uncertainty on unmeasurable components of the system.

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.

The effects of profound hypothermia on pancreas ischemic injury: a new experimental model.

Science.gov (United States)

Rocha-Santos, Vinicius; Ferro, Oscar Cavalcante; Pantanali, Carlos Andrés; Seixas, Marcel Povlovistsch; Pecora, Rafael Antonio Arruda; Pinheiro, Rafael Soares; Claro, Laura Carolina López; Abdo, Emílio Elias; Chaib, Eleazar; D'Albuquerque, Luiz Augusto Carneiro

2014-08-01

Pancreatic ischemia-reperfusion (IR) has a key role in pancreas surgery and transplantation. Most experimental models evaluate the normothermic phase of the IR. We proposed a hypothermic model of pancreas IR to evaluate the benefic effects of the cold ischemic phase. We performed a reproducible model of hypothermic pancreatic IR. The ischemia was induced in the pancreatic tail portion (1-hour ischemia, 4-hour reperfusion) in 36 Wistar rats. They are divided in 3 groups as follows: group 1 (control), sham; group 2, normothermic IR; and group 3, hypothermic IR. In group 3, the temperature was maintained as close to 4.5°C. After reperfusion, serum amylase and lipase levels, inflammatory mediators (tumor necrosis factor α, interleukin 6), and pancreas histology were evaluated. In pancreatic IR groups, amylase, cytokines, and histological damage were significantly increased when compared with group 1. In the group 3, we observed a significant decrease in tumor necrosis factor α (P = 0.004) and interleukin 6 (P = 0.001) when compared with group 2. We did not observe significant difference in amylase (P = 0.867), lipase (P = 0.993), and histology (P = 0.201). In our experimental model, we reproduced the cold phase of pancreas IR, and the pancreas hypothermia reduced the inflammatory mediators after reperfusion.

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.

Tracer transfer in consolidated porous medium and fractured porous medium: experimentations and modelling; Transferts d'un traceur en milieu poreux consolide et en milieu poreux fissure: experimentations et modelisations

Energy Technology Data Exchange (ETDEWEB)

Dalla Costa, C

2007-07-15

We try to identify and model physical and chemical mechanisms governing the water flow and the solute transport in fractured consolidated porous medium. An original experimental device was built. The 'cube' consists of an idealized fractured medium reproduced by piling up consolidated porous cubes of 5 cm edge. Meanwhile, columns of the homogeneous consolidated porous medium are studied. The same anionic tracing technique is used in both cases. Using a system analysis approach, we inject concentration pulses in the device to obtain breakthrough curves. After identifying the mass balance and the residence time, we fit the CD and the MIM models to the experimental data. The MIM model is able to reproduce experimental curves of the homogeneous consolidated porous medium better than the CD model. The mobile water fraction is in accordance with the porous medium geometry. The study of the flow rate influence highlights an interference dispersion regime. It was not possible to highlight the observation length influence in this case. On the contrary, we highlight the effect of the observation scale on the fractured and porous medium, comparing the results obtained on a small 'cube' and a big 'cube'. The CD model is not satisfactory in this case. Even if the MIM model can fit the experimental breakthrough curves, it was not possible to obtain unique parameters for the set of experiments. (author)

Experimental model of cutaneous radiation injury in rabbits

Energy Technology Data Exchange (ETDEWEB)

Meirelles, Rafael Panisi de Campos [Universidade Federal de Sao Paulo (EPM/UNIFESP), SP (Brazil). Escola Paulista de Medicina; Hochman, Bernardo [Universidade Federal de Sao Paulo (EPM/UNIFESP), SP (Brazil). Escola Paulista de Medicina. Dept. de Cirurgia; Helene Junior, Americo; Fraga, Murillo Francisco Pires [Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo (FCMSCSP), SP (Brazil). Dept. de Cirurgia. Divisao de Cirurgia Plastica; Lellis, Rute [Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo (FCMSCSP), SP (Brazil). Divisao de Patologia; Ferreira, Lydia Masako, E-mail: rpcmeirelles@yahoo.com.br, E-mail: lydia.dcir@epm.br [Universidade Federal de Sao Paulo (EPM/UNIFESP), SP (Brazil). Escola Paulista de Mediciana. Divisao de Cirugia Plastica

2013-07-01

Purpose: to describe an experimental model of cutaneous radiation injury in rabbits. Methods: on this study eight six-month-old New Zealand male rabbits, with an average weight of 2.5kg were used. They were distributed in four groups (n=2 per group). The control group did not receive radiotherapy and the others received one radiotherapy session of 2000, 3000 and 4500 cGy, respectively. Photographic analysis and histopathological evaluation of the irradiated areas were carried out. Results: after 30 days, the animals from the control group had all their hair grown. In spite of that, the animals from group 2000 cGy had a 60-day alopecia and from group 3000 cGy, a 90-day alopecia. After the 30th day, the 3000cGy group demonstrated 90-day cutaneous radiation injuries, graded 3 and 4. One of the animals from group 4500 cGy died on the 7th day with visceral necrosis. The other from the same group had total skin necrosis. A progressive reduction of glands and blood vessels count and an increase on collagen deposition was observed. Conclusion: The proposed experimental model is reproducible. This study suggests that the dosage 4500cGy is excessive and the 3000 cGy is the most effective for this experimental model of cutaneous radiation injury in rabbits. (author)

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.

Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies.

Directory of Open Access Journals (Sweden)

Tanmay A Gokhale

2017-01-01

Full Text Available To understand how excitable tissues give rise to arrhythmias, it is crucially necessary to understand the electrical dynamics of cells in the context of their environment. Multicellular monolayer cultures have proven useful for investigating arrhythmias and other conduction anomalies, and because of their relatively simple structure, these constructs lend themselves to paired computational studies that often help elucidate mechanisms of the observed behavior. However, tissue cultures of cardiomyocyte monolayers currently require the use of neonatal cells with ionic properties that change rapidly during development and have thus been poorly characterized and modeled to date. Recently, Kirkton and Bursac demonstrated the ability to create biosynthetic excitable tissues from genetically engineered and immortalized HEK293 cells with well-characterized electrical properties and the ability to propagate action potentials. In this study, we developed and validated a computational model of these excitable HEK293 cells (called "Ex293" cells using existing electrophysiological data and a genetic search algorithm. In order to reproduce not only the mean but also the variability of experimental observations, we examined what sources of variation were required in the computational model. Random cell-to-cell and inter-monolayer variation in both ionic conductances and tissue conductivity was necessary to explain the experimentally observed variability in action potential shape and macroscopic conduction, and the spatial organization of cell-to-cell conductance variation was found to not impact macroscopic behavior; the resulting model accurately reproduces both normal and drug-modified conduction behavior. The development of a computational Ex293 cell and tissue model provides a novel framework to perform paired computational-experimental studies to study normal and abnormal conduction in multidimensional excitable tissue, and the methodology of modeling

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.

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.

Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

Science.gov (United States)

Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

2015-12-28

Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

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....

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....

Implementation of an experimental pilot reproducing the fouling of the exhaust gas recirculation system in diesel engines

Directory of Open Access Journals (Sweden)

Crepeau Gérald

2012-04-01

Full Text Available The European emission standards EURO 5 and EURO 6 define more stringent acceptable limits for exhaust emissions of new vehicles. The Exhaust Gas Recirculation (EGR system is a partial but essential solution for lowering the emission of nitrogen oxides and soot particulates. Yet, due to a more intensive use than in the past, the fouling of the EGR system is increased. Ensuring the reliability of the EGR system becomes a main challenge. In partnership with PSA Peugeot Citroën, we designed an experimental setup that mimics an operating EGR system. Its distinctive features are (1 its ability to reproduce precisely the operating conditions and (2 its ability to measure the temperature field on the heat exchanger surface with an Infra Red camera for detecting in real time the evolution of the fooling deposit based on its thermal resistance. Numerical codes are used in conjunction with this experimental setup to determine the evolution of the fouling thickness from its thermal resistance.

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

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.

Experimental study and modelling of selenite sorption onto illite and smectite clays.

Science.gov (United States)

Missana, T; Alonso, U; García-Gutiérrez, M

2009-06-15

This study provides a large set of experimental selenite sorption data for pure smectite and illite. Similar sorption behavior existed in both clays: linear within a large range of the Se concentrations investigated (from 1x10(-10) to 1x10(-3) M); and independent of ionic strength. Selenite sorption was also analysed in the illite/smectite system with the clays mixed in two different proportions, as follows: (a) 30% illite-70% smectite and (b) 43% illite-57% smectite. The objective of the study was to provide the simplest model possible to fit the experimental data, a model also capable of describing selenite sorption in binary illite/smectite clay systems. Selenite sorption data, separately obtained in the single mineral systems, were modeled using both a one- and a two-site non-electrostatic model that took into account the formation of two complexes at the edge sites of the clay. Although the use of a two-site model slightly improved the fit of data at a pH below 4, the simpler one-site model reproduced satisfactorily all the sorption data from pH 3 to 8. The complexation constants obtained by fitting sorption data of the individual minerals were incorporated into a model to predict the adsorption of selenium in the illite/smectite mixtures; the model's predictions were consistent with the experimental adsorption data.

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 (P−E.

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

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.

Numerical Validation of a Vortex Model against ExperimentalData on a Straight-Bladed Vertical Axis Wind Turbine

Directory of Open Access Journals (Sweden)

Eduard Dyachuk

2015-10-01

Full Text Available Cyclic blade motion during operation of vertical axis wind turbines (VAWTs imposes challenges on the simulations models of the aerodynamics of VAWTs. A two-dimensional vortex model is validated against the new experimental data on a 12-kW straight-bladed VAWT, which is operated at an open site. The results on the normal force on one blade are analyzed. The model is assessed against the measured data in the wide range of tip speed ratios: from 1.8 to 4.6. The predicted results within one revolution have a similar shape and magnitude as the measured data, though the model does not reproduce every detail of the experimental data. The present model can be used when dimensioning the turbine for maximum loads.

Proposal and experimental validation of analytical models for seismic and vibration isolation devices in nuclear and non-nuclear facilities

International Nuclear Information System (INIS)

Serino, G.; Bonacina, G.; Bettinali, F.

1993-01-01

Two analytical-experimental models of HDLRBs having different levels of approximations are presented. Comparison with available experimental data shows that a non-linear hysteretic model, defined by three rubber parameters only, allows a very good complete simulation of the dynamic behavior of the isolation devices. A simpler equivalent linear viscous model reproduces less exactly the experimental behavior, but permits a good prediction of peak response values in the earthquake analysis of an isolated structure, if bearing stiffness and damping parameters are properly selected. The models have been used in preliminary design and subsequent check of the isolation system of two different types of Gas-Insulated Electric Substations (GIS), in view of possible future installation of isolated GISes in areas of high seismic risk. (author)

Experimental oligopolies modeling: A dynamic approach based on heterogeneous behaviors

Science.gov (United States)

Cerboni Baiardi, Lorenzo; Naimzada, Ahmad K.

2018-05-01

In the rank of behavioral rules, imitation-based heuristics has received special attention in economics (see [14] and [12]). In particular, imitative behavior is considered in order to understand the evidences arising in experimental oligopolies which reveal that the Cournot-Nash equilibrium does not emerge as unique outcome and show that an important component of the production at the competitive level is observed (see e.g.[1,3,9] or [7,10]). By considering the pioneering groundbreaking approach of [2], we build a dynamical model of linear oligopolies where heterogeneous decision mechanisms of players are made explicit. In particular, we consider two different types of quantity setting players characterized by different decision mechanisms that coexist and operate simultaneously: agents that adaptively adjust their choices towards the direction that increases their profit are embedded with imitator agents. The latter ones use a particular form of proportional imitation rule that considers the awareness about the presence of strategic interactions. It is noteworthy that the Cournot-Nash outcome is a stationary state of our models. Our thesis is that the chaotic dynamics arousing from a dynamical model, where heterogeneous players are considered, are capable to qualitatively reproduce the outcomes of experimental oligopolies.

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.

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.

Experimental Object-Oriented Modelling

DEFF Research Database (Denmark)

Hansen, Klaus Marius

through, e.g., technical prototyping and active user involvement. We introduce and examine “experimental object-oriented modelling” as the intersection of these practices. The contributions of this thesis are expected to be within three perspectives on models and modelling in experimental system...... development: Grounding We develop an empirically based conceptualization of modelling and use of models in system development projects characterized by a high degree of uncertainty in requirements and point to implications for tools and techniques for modelling in such a setting. Techniques We introduce......This thesis examines object-oriented modelling in experimental system development. Object-oriented modelling aims at representing concepts and phenomena of a problem domain in terms of classes and objects. Experimental system development seeks active experimentation in a system development project...

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,

Intravenous nitroglycerin as an experimental model of vascular headache. Basic characteristics

DEFF Research Database (Denmark)

Iversen, Helle Klingenberg; Olesen, J; Tfelt-Hansen, P

1989-01-01

To develop a reliable experimental model of vascular headache, we studied the dose-response relationship between headache and i.v. nitroglycerin (NTG) in 10 healthy subjects. NTG was infused intravenously over periods of 10 min separated by wash-out periods. Doses of 0.25, 0.50, 1.00 and 2......) at various doses and declined rapidly after NTG discontinuation. Wash-out periods of 10-20 min were sufficient. The reproducibility of headache intensity and character was satisfactory in the retest experiment. There were no unpleasant side effects and no visible flushing. Thus blindness was maintained. I...

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.

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

In experimental musculoskeletal oncology, there remains a need for animal models that can be used to assess the efficacy of new and innovative treatment methodologies for bone tumors. Rat plays a very important role in the bone field especially in the evaluation of metabolic bone diseases. The objective of this study was to develop a rat osteosarcoma model for evaluation of new surgical and molecular methods of treatment for extremity sarcoma. One hundred male SD rats weighing 125.45+/-8.19 g were divided into 5 groups and anesthetized intraperitoneally with 10% chloral hydrate. Orthotopic implantation models of rat osteosarcoma were performed by injecting directly into the SD rat femur with a needle for inoculation with SD tumor cells. In the first step of the experiment, 2x10(5) to 1x10(6) UMR106 cells in 50 microl were injected intraosseously into median or distal part of the femoral shaft and the tumor take rate was determined. The second stage consisted of determining tumor volume, correlating findings from ultrasound with findings from necropsia and determining time of survival. In the third stage, the orthotopically implanted tumors and lung nodules were resected entirely, sectioned, and then counter stained with hematoxylin and eosin for histopathologic evaluation. The tumor take rate was 100% for implants with 8x10(5) tumor cells or more, which was much less than the amount required for subcutaneous implantation, with a high lung metastasis rate of 93.0%. Ultrasound and necropsia findings matched closely (r=0.942; p<0.01), which demonstrated that Doppler ultrasonography is a convenient and reliable technique for measuring cancer at any stage. Tumor growth curve showed that orthotopically implanted tumors expanded vigorously with time-lapse, especially in the first 3 weeks. The median time of survival was 38 days and surgical mortality was 0%. The UMR106 cell line has strong carcinogenic capability and high lung metastasis frequency. The present rat

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

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.

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

Experimental investigation and numerical modelling of positive corona discharge: ozone generation

Energy Technology Data Exchange (ETDEWEB)

Yanallah, K; Castellanos, A [Departamento de Electronica y Electromagnetismo, Universidad de Sevilla (Spain); Pontiga, F; Fernandez-Rueda, A [Departamento de FIsica Aplicada II, Universidad de Sevilla (Spain)

2009-03-21

The spatial distribution of the species generated in a wire-cylinder positive corona discharge in pure oxygen has been computed using a plasma chemistry model that includes the most significant reactions between electrons, ions, atoms and molecules. The plasma chemistry model is included in the continuity equations of each species, which are coupled with Poisson's equation for the electric field and the energy conservation equation for the gas temperature. The current-voltage characteristic measured in the experiments has been used as an input data to the numerical simulation. The numerical model is able to reproduce the basic structure of the positive corona discharge and highlights the importance of Joule heating on ozone generation. The average ozone density has been computed as a function of current intensity and compared with the experimental measurements of ozone concentration determined by UV absorption spectroscopy.

Experimental investigation and numerical modelling of positive corona discharge: ozone generation

International Nuclear Information System (INIS)

Yanallah, K; Castellanos, A; Pontiga, F; Fernandez-Rueda, A

2009-01-01

The spatial distribution of the species generated in a wire-cylinder positive corona discharge in pure oxygen has been computed using a plasma chemistry model that includes the most significant reactions between electrons, ions, atoms and molecules. The plasma chemistry model is included in the continuity equations of each species, which are coupled with Poisson's equation for the electric field and the energy conservation equation for the gas temperature. The current-voltage characteristic measured in the experiments has been used as an input data to the numerical simulation. The numerical model is able to reproduce the basic structure of the positive corona discharge and highlights the importance of Joule heating on ozone generation. The average ozone density has been computed as a function of current intensity and compared with the experimental measurements of ozone concentration determined by UV absorption spectroscopy.

Experimental investigation and numerical modelling of positive corona discharge: ozone generation

Science.gov (United States)

Yanallah, K; Pontiga, F; Fernández-Rueda, A; Castellanos, A

2009-03-01

The spatial distribution of the species generated in a wire-cylinder positive corona discharge in pure oxygen has been computed using a plasma chemistry model that includes the most significant reactions between electrons, ions, atoms and molecules. The plasma chemistry model is included in the continuity equations of each species, which are coupled with Poisson's equation for the electric field and the energy conservation equation for the gas temperature. The current-voltage characteristic measured in the experiments has been used as an input data to the numerical simulation. The numerical model is able to reproduce the basic structure of the positive corona discharge and highlights the importance of Joule heating on ozone generation. The average ozone density has been computed as a function of current intensity and compared with the experimental measurements of ozone concentration determined by UV absorption spectroscopy.

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

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

Modelling of PEM Fuel Cell Performance: Steady-State and Dynamic Experimental Validation

Directory of Open Access Journals (Sweden)

Idoia San Martín

2014-02-01

Full Text Available This paper reports on the modelling of a commercial 1.2 kW proton exchange membrane fuel cell (PEMFC, based on interrelated electrical and thermal models. The electrical model proposed is based on the integration of the thermodynamic and electrochemical phenomena taking place in the FC whilst the thermal model is established from the FC thermal energy balance. The combination of both models makes it possible to predict the FC voltage, based on the current demanded and the ambient temperature. Furthermore, an experimental characterization is conducted and the parameters for the models associated with the FC electrical and thermal performance are obtained. The models are implemented in Matlab Simulink and validated in a number of operating environments, for steady-state and dynamic modes alike. In turn, the FC models are validated in an actual microgrid operating environment, through the series connection of 4 PEMFC. The simulations of the models precisely and accurately reproduce the FC electrical and thermal performance.

Configuration and validation of an analytical model predicting secondary neutron radiation in proton therapy using Monte Carlo simulations and experimental measurements.

Science.gov (United States)

Farah, J; Bonfrate, A; De Marzi, L; De Oliveira, A; Delacroix, S; Martinetti, F; Trompier, F; Clairand, I

2015-05-01

This study focuses on the configuration and validation of an analytical model predicting leakage neutron doses in proton therapy. Using Monte Carlo (MC) calculations, a facility-specific analytical model was built to reproduce out-of-field neutron doses while separately accounting for the contribution of intra-nuclear cascade, evaporation, epithermal and thermal neutrons. This model was first trained to reproduce in-water neutron absorbed doses and in-air neutron ambient dose equivalents, H*(10), calculated using MCNPX. Its capacity in predicting out-of-field doses at any position not involved in the training phase was also checked. The model was next expanded to enable a full 3D mapping of H*(10) inside the treatment room, tested in a clinically relevant configuration and finally consolidated with experimental measurements. Following the literature approach, the work first proved that it is possible to build a facility-specific analytical model that efficiently reproduces in-water neutron doses and in-air H*(10) values with a maximum difference less than 25%. In addition, the analytical model succeeded in predicting out-of-field neutron doses in the lateral and vertical direction. Testing the analytical model in clinical configurations proved the need to separate the contribution of internal and external neutrons. The impact of modulation width on stray neutrons was found to be easily adjustable while beam collimation remains a challenging issue. Finally, the model performance agreed with experimental measurements with satisfactory results considering measurement and simulation uncertainties. Analytical models represent a promising solution that substitutes for time-consuming MC calculations when assessing doses to healthy organs. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

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.

Integration of THM-experimental work and modelling

International Nuclear Information System (INIS)

Pintado, Xavier; Autio, Jorma; Koskinen, Kari

2010-01-01

strains. Some constitutive laws approximate all these phenomena. These laws relate gradients with fluxes in transport phenomena and stresses with strains in mechanical phenomena. The parameters necessary to establish these relations are necessary to reproduce correctly the clay barrier behaviour. This work uses CODE-BRIGHT (Coupled Deformation Brine, Gas and Heat Transport). This code was developed initially for studying multiphase flow in saline materials but some constitutive laws for rocks and clays have been implemented, so it is possible to simulate the clay barrier behaviour. The key aspects of the tests presented below are modelled and later compared to results. The experimental program to provide data and reference to observed behaviour has consisted of following tests: - Small scale laboratory tests: Provide the different parameters. Due the complexity of the processes which take place inside the samples, the numerical methods could be necessary for analyze the test results. Although there is the theoretical possibility to have more than one parameter from one test, it is better to consider one test for calculate one parameter and use the results to check rest of parameters. Sometimes, one test is used for one parameter but the measures allow to check other parameters. - Large scale laboratory tests: these tests are used to reproduce in small scale the phenomena which take place in the barrier. Modelling these tests is useful to understand better the processes inside the barrier under the qualitatively point of view and it is possible to quantify other phenomena like piping or crack formation although modelling these phenomena is quite difficult. - Large scale tests: With the parameters from the small scale laboratory tests and the validation of these parameters with the large scale laboratory tests, plus a better understanding of the phenomena, it is possible to design and simulate the large scale tests, where the conditions of the repository are reproduced. In

Experimental models of chronic subdural hematoma.

Science.gov (United States)

D'Abbondanza, Josephine A; Loch Macdonald, R

2014-02-01

Chronic subdural hematoma (CSDH) is a common neurosurgical problem. Most studies of pathogenesis and treatment involve humans. Advances in understanding of human diseases may be made using animal models. We reviewed all animal models of CSDH and report here their results, conclusions and limitations in order to set a baseline upon which further advanced experimental work related to this disease can be made. PubMed, Medline, Embase and ISI Web of Knowledge were searched with no time limits using the keyword 'chronic subdural hematoma' and MeSH term 'hematoma, subdural, chronic'. The authors reviewed all papers written related to this disease and selected all publications involving animals. There were no other restrictions. The findings and conclusions of the papers are summarized here. No formal analysis was done because of the variation in species used, methods for induction of CSDH, times of assessment and reporting of results. Attempts to create CSDH have been made in mice, rats, cats, dogs and monkeys. Methods include injection or surgical implantation of clotted blood or various other blood products and mixtures into the potential subdural space or the subcutaneous space. No intracranial model produced a progressively expanding CSDH. Transient hematoma expansion with liquification could be produced by subcutaneous injections in some models. Spontaneous subdural blood collections were found after creation of hydrocephalus in mice by systemic injection of the neurotoxin, 6-aminonicotinamide. The histology of the hematoma membranes in several models resembles the appearance in humans. None of the models has been replicated since its first description. We did not find a report of a reproducible, well-described animal model of human CSDH.

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.

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

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.

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)

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...

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.

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.)

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

Elastase-induced pulmonary emphysema: insights from experimental models

Directory of Open Access Journals (Sweden)

Mariana A. Antunes

2011-12-01

Full Text Available Several distinct stimuli can be used to reproduce histological and functional features of human emphysema, a leading cause of disability and death. Since cigarette smoke is the main cause of emphysema in humans, experimental researches have attempted to reproduce this situation. However, this is an expensive and cumbersome method of emphysema induction, and simpler, more efficacious alternatives have been sought. Among these approaches, elastolytic enzymes have been widely used to reproduce some characteristics of human cigarette smoke-induced disease, such as: augmentation of airspaces, inflammatory cell influx into the lungs, and systemic inflammation. Nevertheless, the use of elastase-induced emphysema models is still controversial, since the disease pathways involved in elastase induction may differ from those occurring in smoke-induced emphysema. This indicates that the choice of an emphysema model may impact the results of new therapies or drugs being tested. The aim of this review is to compare the mechanisms of disease induction in smoke and elastase emphysema models, to describe the differences among various elastase models, and to establish the advantages and disadvantages of elastase-induced emphysema models. More studies are required to shed light on the mechanisms of elastase-induced emphysema.Diversos estímulos podem ser utilizados para reproduzir características histológicas e funcionais do enfisema humano, uma das principais causas de incapacidade e morte. Uma vez que a fumaça de cigarro é a principal causa de enfisema em humanos, estudos experimentais têm tentado reproduzir esta situação. No entanto, esse é um método dispendioso e complicado para a indução do enfisema e, alternativas mais simples e eficazes, têm sido pesquisadas. Entre essas abordagens, enzimas elastolíticas vêm sendo amplamente utilizadas para reproduzir algumas das características do enfisema humano, tais como: aumento dos espaços a

A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns.

Science.gov (United States)

Azzam, Sausan; Broadwater, Laurie; Li, Shuo; Freeman, Ernest J; McDonough, Jennifer; Gregory, Roger B

2013-05-01

Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears to play a role in the development of neuropathology in MS and may also play a role in disease pathology in EAE. Here, surface enhanced laser desorption ionization mass spectrometry (SELDI-MS) has been employed to obtain protein expression profiles from mitochondrially enriched fractions derived from EAE and control mouse brain. To gain insight into experimental variation, the reproducibility of sub-cellular fractionation, anion exchange fractionation as well as spot-to-spot and chip-to-chip variation using pooled samples from brain tissue was examined. Variability of SELDI mass spectral peak intensities indicates a coefficient of variation (CV) of 15.6% and 17.6% between spots on a given chip and between different chips, respectively. Thinly slicing tissue prior to homogenization with a rotor homogenizer showed better reproducibility (CV = 17.0%) than homogenization of blocks of brain tissue with a Teflon® pestle (CV = 27.0%). Fractionation of proteins with anion exchange beads prior to SELDI-MS analysis gave overall CV values from 16.1% to 18.6%. SELDI mass spectra of mitochondrial fractions obtained from brain tissue from EAE mice and controls displayed 39 differentially expressed proteins (p≤ 0.05) out of a total of 241 protein peaks observed in anion exchange fractions. Hierarchical clustering analysis showed that protein fractions from EAE animals with severe disability clearly segregated from controls. Several components of electron transport chain complexes (cytochrome c oxidase subunit 6b1, subunit 6C, and subunit 4; NADH dehydrogenase flavoprotein 3, alpha subcomplex subunit 2, Fe-S protein 4, and Fe-S protein 6; and ATP synthase subunit e) were identified as possible differentially expressed proteins. Myelin Basic Protein isoform 8 (MBP8) (14.2 k

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.

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.

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.

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.

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.

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

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.

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.

New tools for Content Innovation and data sharing: Enhancing reproducibility and rigor in biomechanics research.

Science.gov (United States)

Guilak, Farshid

2017-03-21

We are currently in one of the most exciting times for science and engineering as we witness unprecedented growth in our computational and experimental capabilities to generate new data and models. To facilitate data and model sharing, and to enhance reproducibility and rigor in biomechanics research, the Journal of Biomechanics has introduced a number of tools for Content Innovation to allow presentation, sharing, and archiving of methods, models, and data in our articles. The tools include an Interactive Plot Viewer, 3D Geometric Shape and Model Viewer, Virtual Microscope, Interactive MATLAB Figure Viewer, and Audioslides. Authors are highly encouraged to make use of these in upcoming journal submissions. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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

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.

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.

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.

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?

Nonlinear instabilities induced by the F coil power amplifier at FTU: Modeling and control

International Nuclear Information System (INIS)

Zaccarian, L.; Boncagni, L.; Cascone, D.; Centioli, C.; Cerino, S.; Gravanti, F.; Iannone, F.; Mecocci, F.; Pangione, L.; Podda, S.; Vitale, V.; Vitelli, R.

2009-01-01

In this paper we focus on the instabilities caused by the nonlinear behavior of the F coil current amplifier at FTU. This behavior induces closed-loop instability of the horizontal position stabilizing loop whenever the requested current is below the circulating current level. In the paper we first illustrate a modeling phase where nonlinear dynamics are derived and identified to reproduce the open-loop responses measured by the F coil current amplifier. The derived model is shown to successfully reproduce the experimental behavior by direct comparison with experimental data. Based on this dynamic model, we then reproduce the closed-loop scenario of the experiment and show that the proposed nonlinear model successfully reproduces the nonlinear instabilities experienced in the experimental sessions. Given the simulation setup, we next propose a nonlinear control solution to this instability problem. The proposed solution is shown to recover stability in closed-loop simulations. Experimental tests are scheduled for the next experimental campaign after the FTU restart.

Experimental study and modelling of the high temperature mechanical behavior of oxide dispersion strengthened ferritic steels

International Nuclear Information System (INIS)

Steckmeyer, A.

2012-01-01

The strength of metals, and therefore their maximum operating temperature, can be improved by oxide dispersion strengthening (ODS). Numerous research studies are carried out at the French Atomic Energy Commission (CEA) in order to develop a cladding tube material for Gen IV nuclear power reactors. Oxide dispersion strengthened steels appear to be the most promising candidates for such application, which demands a minimum operating temperature of 650 C. The present dissertation intends to improve the understanding of the mechanical properties of ODS steels, in terms of creep lifetime and mechanical anisotropy. The methodology of this work includes mechanical tests between room temperature and 900 C as well as macroscopic and polycrystalline modelling. These tests are carried out on a Fe-14Cr1W0,26Ti + 0,3 Y 2 O 3 ODS ferritic steel processed at CEA by mechanical alloying and hot extrusion. The as-received material is a bar with a circular section. The mechanical tests reveal the high mechanical strength of this steel at high temperature. A strong influence of the strain rate on the ductility and the mechanical strength is also observed. A macroscopic mechanical model has been developed on the basis of some experimental statements such as the high kinematic contribution to the flow stress. This model has a strong ability to reproduce the mechanical behaviour of the studied material. Two different polycrystalline models have also been developed in order to reproduce the mechanical anisotropy of the material. They are based on its specific grain morphology and crystallographic texture. The discrepancy between the predictions of both models and experimental results reveal the necessity to formulate alternate assumptions on the deformation mechanisms of ODS ferritic steels. (author) [fr

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.

Experimental Testing and Model Validation of a Decoupled-Phase On-Load Tap Changer Transformer in an Active Network

DEFF Research Database (Denmark)

Zecchino, Antonio; Hu, Junjie; Coppo, Massimiliano

2016-01-01

Due to the increasing penetration of single-phase small generation units and electric vehicles connected to distribution grids, system operators are facing challenges related to local unbalanced voltage rise or drop issues, which may lead to a violation of the allowed voltage band. To address...... this problem, distribution transformers with on-load tapping capability are under development. This paper presents model and experimental validation of a 35 kVA three-phase power distribution transformer with independent on-load tap changer control capability on each phase. With the purpose of investigating...... to reproduce the main feature of an unbalanced grid. The experimental activities are recreated in by carrying out dynamics simulation studies, aiming at validating the implemented models of both the transformer as well as the other grid components. Phase-neutral voltages’ deviations are limited, proving...

Inflammatory pain in experimental burns in man

DEFF Research Database (Denmark)

Pedersen, J L

2000-01-01

stimuli may be more reproducible. A methodological study also demonstrated that habituation to experimental pain developed as the study proceeded. Habituation is common in experimental pain models, and dividing analgesics and placebo evenly between the study days is one way of eliminating the effects......Human experimental pain models are important tools in pain research. The primary aims of pain research in normal man is 1) to provide insight in pain mechanisms, 2) to provide a rational basis for clinical trials of pain relieving interventions, and 3) to confirm the anti-nociceptive effects...... demonstrated in animal models. Most often clinical pain is due to tissue damage leading to acute inflammation and hyperalgesia, but only few human pain models have examined pain responses in injured tissues. Therefore, models with controlled and reversible tissue trauma are needed. The human burn model...

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.

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...

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.

Modernized Approach for Generating Reproducible Heterogeneity Using Transmitted-Light for Flow Visualization Experiments

Science.gov (United States)

Jones, A. A.; Holt, R. M.

2017-12-01

Image capturing in flow experiments has been used for fluid mechanics research since the early 1970s. Interactions of fluid flow between the vadose zone and permanent water table are of great interest because this zone is responsible for all recharge waters, pollutant transport and irrigation efficiency for agriculture. Griffith, et al. (2011) developed an approach where constructed reproducible "geologically realistic" sand configurations are deposited in sandfilled experimental chambers for light-transmitted flow visualization experiments. This method creates reproducible, reverse graded, layered (stratified) thin-slab sand chambers for point source experiments visualizing multiphase flow through porous media. Reverse-graded stratification of sand chambers mimic many naturally occurring sedimentary deposits. Sandfilled chambers use light as nonintrusive tools for measuring water saturation in two-dimensions (2-D). Homogeneous and heterogeneous sand configurations can be produced to visualize the complex physics of the unsaturated zone. The experimental procedure developed by Griffith, et al. (2011) was designed using now outdated and obsolete equipment. We have modernized this approach with new Parker Deadel linear actuator and programed projects/code for multiple configurations. We have also updated the Roper CCD software and image processing software with the latest in industry standards. Modernization of transmitted-light source, robotic equipment, redesigned experimental chambers, and newly developed analytical procedures have greatly reduced time and cost per experiment. We have verified the ability of the new equipment to generate reproducible heterogeneous sand-filled chambers and demonstrated the functionality of the new equipment and procedures by reproducing several gravity-driven fingering experiments conducted by Griffith (2008).

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

Experimental models of sepsis and septic shock: an overview

Directory of Open Access Journals (Sweden)

Garrido Alejandra G.

2004-01-01

Full Text Available Sepsis remains a major cause of morbidity and mortality in surgical patients and trauma victims, mainly due to sepsis-induced multiple organ dysfunction. In contrast to preclinical studies, most clinical trials of promising new treatment strategies for sepsis have fails to demonstrate efficacy. Although many reasons could account for this discrepancy, the misinterpretation of preclinical data obtained from experimental studies, and especially the use of animal models that do not adequately mimic human sepsis may have been contributing factors. In this review, the benefits and limitations of various animal models of sepsis are discussed to clarify the extend to which findings are relevant to human sepsis, particularly with respect to the subsequent design and execution of clinical trials. Such models include intravascular infusion of endotoxin or live bacteria, bacterial peritonitis, cecal ligation and perforation, soft tissue infection, pneumonia or meningitis models, using different animal species including rats, mice, rabbits, dogs, pigs, sheep and nonhuman primates. Despite several limitations, animal models remain essential in the development of all new therapies for sepsis and septic shock, because they provide fundamental information about the pharmacokinetics, toxicity, and mechanism of drug action that cannot be duplicated by other methods. New therapeutic agents should be studies in infection models, even after the initiation of the septic process. Furthermore, debility conditions need to be reproduced to avoid the exclusive use of healthy animals, which often do not represent the human septic patient.

Considering RNAi experimental design in parasitic helminths.

Science.gov (United States)

Dalzell, Johnathan J; Warnock, Neil D; McVeigh, Paul; Marks, Nikki J; Mousley, Angela; Atkinson, Louise; Maule, Aaron G

2012-04-01

Almost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.

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.

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

Meniscectomia parcial como modelo experimental de osteoartrite em coelhos e efeito protetor do difosfato de cloroquina Partial meniscectomy as an experimental model of osteoarthritis in rabbits and protector effect of chloroquine diphosphate

Directory of Open Access Journals (Sweden)

Ana Paula P. Velosa

2007-12-01

Full Text Available OBJETIVO: Estabelecer as alterações morfológicas e o remodelamento do tecido cartilaginoso na progressão da osteoartrite (OA experimental para estudar o efeito do difosfato de cloroquina na cartilagem osteoartrítica. MÉTODOS: A osteoartrite experimental foi induzida em coelhos por meio de meniscectomia parcial. Para analisar a evolução da doença experimental foram estudados três grupos de dez animais, sacrificados a 3, 14 e 22 semanas de indução da doença. Para avaliar o efeito do difosfato de cloroquina um grupo de animais (n = 6 foi tratado preventivamente com 3 mg/kg ao dia, iniciados um mês antes da indução da osteoartrite, e mantidos até o sacrifício (22 semanas. Realizou-se análise histológica das articulações (H&E, tricrômico de Masson e imunofluorescência para colágeno dos tipos I, II e XI. A intensidade da agressão articular foi quantificada pelo escore de Mankin. RESULTADOS: O modelo experimental reproduziu todas as alterações morfológicas observadas na osteoartrite humana. Animais que receberam difosfato de cloroquina não desenvolveram lesões histológicas observadas na OA. Neste grupo houve significante preservação da estrutura da cartilagem articular (p OBJECTIVE: The aim of this study was to develop an experimental model of osteoarthritis (OA that could reproduce morphologic alterations viewed in this disease and to study the effect of chloroquine diphosphate on cartilage remodeling. METHODS: osteoarthritis was induced in rabbits by performing partial meniscectomy. To establish the experimental disease evolution, three groups of ten animals were sacrificed at 3, 14, 22 weeks after disease induction. To evaluate the effect of chloroquine diphosfate in OA progression, a group of six animals was treated preventively with 3 mg/kg/day, started one month prior to osteoarthritis induction and kept until the day of sacrifice (22 weeks. Histopathological (Masson trychrome, H&E, biochemical and

Experimental models of demyelination and remyelination.

Science.gov (United States)

Torre-Fuentes, L; Moreno-Jiménez, L; Pytel, V; Matías-Guiu, J A; Gómez-Pinedo, U; Matías-Guiu, J

2017-08-29

Experimental animal models constitute a useful tool to deepen our knowledge of central nervous system disorders. In the case of multiple sclerosis, however, there is no such specific model able to provide an overview of the disease; multiple models covering the different pathophysiological features of the disease are therefore necessary. We reviewed the different in vitro and in vivo experimental models used in multiple sclerosis research. Concerning in vitro models, we analysed cell cultures and slice models. As for in vivo models, we examined such models of autoimmunity and inflammation as experimental allergic encephalitis in different animals and virus-induced demyelinating diseases. Furthermore, we analysed models of demyelination and remyelination, including chemical lesions caused by cuprizone, lysolecithin, and ethidium bromide; zebrafish; and transgenic models. Experimental models provide a deeper understanding of the different pathogenic mechanisms involved in multiple sclerosis. Choosing one model or another depends on the specific aims of the study. Copyright © 2017 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

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....

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.

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...

Comparing DINA code simulations with TCV experimental plasma equilibrium responses

International Nuclear Information System (INIS)

Khayrutdinov, R.R.; Lister, J.B.; Lukash, V.E.; Wainwright, J.P.

2000-08-01

The DINA non-linear time dependent simulation code has been validated against an extensive set of plasma equilibrium response experiments carried out on the TCV tokamak. Limited and diverted plasmas are found to be well modelled during the plasma current flat top. In some simulations the application of the PF coil voltage stimulation pulse sufficiently changed the plasma equilibrium that the vertical position feedback control loop became unstable. This behaviour was also found in the experimental work, and cannot be reproduced using linear time-independent models. A single null diverted plasma discharge was also simulated from start-up to shut-down and the results were found to accurately reproduce their experimental equivalents. The most significant difference noted was the penetration time of the poloidal flux, leading to a delayed onset of sawtoothing in the DINA simulation. The complete set of frequency stimulation experiments used to measure the open loop tokamak plasma equilibrium response was also simulated using DINA and the results were analysed in an identical fashion to the experimental data. The frequency response of the DINA simulations agrees with the experimental results. Comparisons with linear models are also discussed to identify areas of good and only occasionally less good agreement. (author)

Experimental Study and Modelling of Poly (Methyl Methacrylate) and Polycarbonate Compressive Behavior from Low to High Strain Rates

Science.gov (United States)

El-Qoubaa, Z.; Colard, L.; Matadi Boumbimba, R.; Rusinek, A.

2018-03-01

This paper concerns an experimental investigation of Polycarbonate and Poly (methyl methacrylate) compressive behavior from low to high strain rates. Experiments were conducted from 0.001/s to ≈ 5000/s for PC and from 0.001/s to ≈ 2000/s for PMMA. The true strain-stress behavior is established and analyzed at various stain rates. Both PC and PMMA mechanical behavior appears as known, to be strain rate and temperature dependent. The DSGZ model is selected for modelling the strain-stress curves while the yield stress is reproduced using the cooperative model and a modified Eyring equation based on Eyring first process theory. All the three models predictions are in agreement with experiments performed on PC and PMMA.

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.

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.

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

Experimental and modelling studies of the shape memory properties of amorphous polymer network composites

International Nuclear Information System (INIS)

Arrieta, J S; Diani, J; Gilormini, P

2014-01-01

Shape memory polymer composites (SMPCs) have become an important way to leverage improvements in the development of applications featuring shape memory polymers (SMPs). In this study, an amorphous SMP matrix has been filled with different types of reinforcements. An experimental set of results is presented and then compared to three-dimensional (3D) finite-element simulations. Thermomechanical shape memory cycles were performed in uniaxial tension. The fillers effect was studied in stress-free and constrained-strain recoveries. Experimental observations indicate complete shape recovery and put in evidence the increased sensitivity of constrained length stress recoveries to the heating ramp on the tested composites. The simulations reproduced a simplified periodic reinforced composite and used a model for the matrix material that has been previously tested on regular SMPs. The latter combines viscoelasticity at finite strain and time-temperature superposition. The simulations easily allow representation of the recovery properties of a reinforced SMP. (paper)

Morphological and functional determinants of fluoxetine (Prozac)-induced pulmonary disease in an experimental model.

Science.gov (United States)

Capelozzi, Marco A; Leick-Maldonado, Edna A; Parra, Edwin R; Martins, Mílton A; Tibério, Iolanda F L C; Capelozzi, Vera L

2007-05-14

Fluoxetine treatment effects were determined by evaluating respiratory mechanics (elastance/resistance) and exhaled nitric oxide, as well as mononuclear and polymorphonuclear cell recruitment into the lungs, in an experimental guinea pig model. Guinea pigs were divided into four groups: Fl (fluoxetine only, n=7); Fl+Sw (fluoxetine and forced swimming, n=7); Ns+Sw (normal saline and forced swimming, n=8); and Ns (normal saline only, n=8). Treated animals received oral fluoxetine (10 mg/(kg day)) for 30 consecutive days. On day 31, all animals were anesthetized and mechanically ventilated so that respiratory system elastance and resistance, as well exhaled nitric oxide, could be determined. The lungs were then excised en bloc for histological and immunohistochemical evaluation. Forced swimming induced bronchodilation in untreated animals and bronchoconstriction in fluoxetine-treated animals. Fluoxetine treatment was also associated with mononuclear infiltration (predominantly into alveolar walls) and neutrophil recruitment. In addition, levels of exhaled nitric oxide, an inflammatory marker, were higher in fluoxetine-treated animals. Swimming-induced stress also amplified mononuclear cell recruitment to the lungs. These results show that, in this experimental model, fluoxetine treatment reproduces the pathology of chronic interstitial pneumonia in humans.

Plausible carrier transport model in organic-inorganic hybrid perovskite resistive memory devices

Science.gov (United States)

Park, Nayoung; Kwon, Yongwoo; Choi, Jaeho; Jang, Ho Won; Cha, Pil-Ryung

2018-04-01

We demonstrate thermally assisted hopping (TAH) as an appropriate carrier transport model for CH3NH3PbI3 resistive memories. Organic semiconductors, including organic-inorganic hybrid perovskites, have been previously speculated to follow the space-charge-limited conduction (SCLC) model. However, the SCLC model cannot reproduce the temperature dependence of experimental current-voltage curves. Instead, the TAH model with temperature-dependent trap densities and a constant trap level are demonstrated to well reproduce the experimental results.

[Experimental model of tooth decay as an educational tool for school-age children].

Science.gov (United States)

de Araújo Silva, Thiago Fernando; Feitosa, José Leonilson; Medeiros Dantas, Rodrigo Maristony; Dantas de Medeiros, Fabianna da Conceição; Cavalcanti Lima, Isabela Pinheiro; Guerra Seabra, Eduardo José

2016-04-01

Objective This work consisted of the construction of an educational in vitro model of dental caries that started with an adaptation of Miller's classic experiment. Methods In a sterilized and sealed glass jar, a sample paste of human saliva was collected and a substrate of manufactured sugar (sucrose) was added. In addition, a human tooth with healthy dental crown extracted in dental treatment but otherwise healthy was added. Research phase I had the negative control sample test (tooth + saliva without added) and the others were opened after 1, 2, 3 and 4 months of incubation. This phase was essential for the next experimental time development. In phase II, two saliva donors with poor levels of oral health habits were recruited. The incubation time (defined by phase I) was 2 and 3 months for each donor. Results This research data gives the possibility of building educational materials about the etiology of tooth decay and its clinical evolution. It also makes possible the production of an explanatory sheet about how to reproduce this experimental model to be used by school children in secondary education. Conclusions Doing this kind of work together at school can help reduce inequities in oral health, especially since there is an approximation toward the discourses, facilitating the process of information dissemination.

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.

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)

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.

Plausible carrier transport model in organic-inorganic hybrid perovskite resistive memory devices

Directory of Open Access Journals (Sweden)

Nayoung Park

2018-04-01

Full Text Available We demonstrate thermally assisted hopping (TAH as an appropriate carrier transport model for CH3NH3PbI3 resistive memories. Organic semiconductors, including organic-inorganic hybrid perovskites, have been previously speculated to follow the space-charge-limited conduction (SCLC model. However, the SCLC model cannot reproduce the temperature dependence of experimental current-voltage curves. Instead, the TAH model with temperature-dependent trap densities and a constant trap level are demonstrated to well reproduce the experimental results.

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...

Tackling the Reproducibility Problem in Systems Research with Declarative Experiment Specifications

Energy Technology Data Exchange (ETDEWEB)

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

2015-05-04

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

ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

Directory of Open Access Journals (Sweden)

Dazard Jean-Eudes

2012-06-01

Full Text Available Abstract Background Affinity-Purification Mass-Spectrometry (AP-MS provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. Methods To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. Results We illustrate the performance of our method by applying

Reproducible methods for experimental infection with Flavobacterium psychrophilum in rainbow trout Oncorhynchus mykiss

DEFF Research Database (Denmark)

Madsen, Lone; Dalsgaard, Inger

1999-01-01

, and this method was tested using isolates with different elastin- degrading profiles and representing different serotypes. Injecting trout, average weight 1 g, with 10(4) CFU (colony- forming units) per fish caused cumulative mortalities around 60 to 70%. The virulent strains belonged to certain serotypes...... and degraded elastin. The intraperitoneal injection challenge method could be used on larger fish, but the infection dose was 10(7) CFU per fish before mortalities occurred. Bath infection and bath infection in combination with formalin treatment (stress) seemed to be reproducible methods that could be used...

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

P2X7 receptor-mediated calcium dynamics in HEK293 cells: experimental characterization and modelling approach

International Nuclear Information System (INIS)

Di Garbo, A; Alloisio, S; Nobile, M

2012-01-01

The P2X7 receptor (P2X7R) induces ionotropic Ca 2+  signalling in different cell types. It plays an important role in the immune response and in the nervous system. Here, the mechanisms underlying intracellular Ca 2+  variations evoked by 3′-O-(4-benzoyl)benzoyl-ATP (BzATP), a potent agonist of the P2X7R, in transfected HEK293 cells, are investigated both experimentally and theoretically. We propose a minimal model of P2X7R that is capable of reproducing, qualitatively and quantitatively, the experimental data. This approach was also adopted for the P2X7R variant, which lacks the entire C-terminus tail (trP2X7R). Then we introduce a biophysical model describing the Ca 2+  dynamics in HEK293. Our model gives an account of the ionotropic Ca 2+  influx evoked by BzATP on the basis of the kinetics model of P2X7R. To explain the complex Ca 2+  responses evoked by BzATP, the model predicted that an impairment in Ca 2+  extrusion flux through the plasma membrane is a key factor for Ca 2+ homeostasis in HEK293 cells. (paper)

P2X7 receptor-mediated calcium dynamics in HEK293 cells: experimental characterization and modelling approach

Science.gov (United States)

Di Garbo, A.; Alloisio, S.; Nobile, M.

2012-04-01

The P2X7 receptor (P2X7R) induces ionotropic Ca2 + signalling in different cell types. It plays an important role in the immune response and in the nervous system. Here, the mechanisms underlying intracellular Ca2 + variations evoked by 3‧-O-(4-benzoyl)benzoyl-ATP (BzATP), a potent agonist of the P2X7R, in transfected HEK293 cells, are investigated both experimentally and theoretically. We propose a minimal model of P2X7R that is capable of reproducing, qualitatively and quantitatively, the experimental data. This approach was also adopted for the P2X7R variant, which lacks the entire C-terminus tail (trP2X7R). Then we introduce a biophysical model describing the Ca2 + dynamics in HEK293. Our model gives an account of the ionotropic Ca2 + influx evoked by BzATP on the basis of the kinetics model of P2X7R. To explain the complex Ca2 + responses evoked by BzATP, the model predicted that an impairment in Ca2 + extrusion flux through the plasma membrane is a key factor for Ca2 + homeostasis in HEK293 cells.

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.

Preparation of a reproducible long-acting formulation of risperidone-loaded PLGA microspheres using microfluidic method.

Science.gov (United States)

Jafarifar, Elham; Hajialyani, Marziyeh; Akbari, Mona; Rahimi, Masoud; Shokoohinia, Yalda; Fattahi, Ali

2017-09-01

The aim of the present study is to prepare risperidone-loaded poly lactic-co-glycolic acid (PLGA) microspheres within microfluidic system and to achieve a formulation with uniform size and monotonic and reproducible release profile. In comparison to batch method, T-junction and serpentine chips were utilized and optimizing study was carried out at different processing parameters (e.g. PLGA and surfactant concentration and flow rates ratio of outer to inner phase). The computational fluid dynamic (CFD) modeling was performed, and loading and release study were carried out. CFD simulation indicates that increasing the flow rate of aqueous phase cause to decrease the droplet size, while the change in size of microspheres did not follow a specific pattern in the experimental results. The most uniform microspheres and narrowest standard deviation (66.79 μm ± 3.32) were achieved using T-junction chip, 1% polyvinylalcohol, 1% PLGA and flow rates ratio of 20. The microfluidic-assisted microspheres were more uniform with narrower size distribution. The release of risperidone from microspheres produced by the microfluidic method was more reproducible and closer to zero-order kinetic model. The release profile of formulation with 2:1 drug-to-polymer ratio was the most favorable release, in which 41.85% release could be achieved during 24 days.

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

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.

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

Injury Based on Its Study in Experimental Models

Directory of Open Access Journals (Sweden)

M. Mendes-Braz

2012-01-01

Full Text Available The present review focuses on the numerous experimental models used to study the complexity of hepatic ischemia/reperfusion (I/R injury. Although experimental models of hepatic I/R injury represent a compromise between the clinical reality and experimental simplification, the clinical transfer of experimental results is problematic because of anatomical and physiological differences and the inevitable simplification of experimental work. In this review, the strengths and limitations of the various models of hepatic I/R are discussed. Several strategies to protect the liver from I/R injury have been developed in animal models and, some of these, might find their way into clinical practice. We also attempt to highlight the fact that the mechanisms responsible for hepatic I/R injury depend on the experimental model used, and therefore the therapeutic strategies also differ according to the model used. Thus, the choice of model must therefore be adapted to the clinical question being answered.

The reproducibility of 31-phosphorus MRS measures of muscle energetics at 3 Tesla in trained men.

Directory of Open Access Journals (Sweden)

Lindsay M Edwards

Full Text Available OBJECTIVE: Magnetic resonance spectroscopy (MRS provides an exceptional opportunity for the study of in vivo metabolism. MRS is widely used to measure phosphorus metabolites in trained muscle, although there are no published data regarding its reproducibility in this specialized cohort. Thus, the aim of this study was to assess the reproducibility of (31P-MRS in trained skeletal muscle. METHODS: We recruited fifteen trained men (VO(2peak = 4.7±0.8 L min(-1/58±8 mL kg(-1 min(-1 and performed duplicate MR experiments during plantar flexion exercise, three weeks apart. RESULTS: Measures of resting phosphorus metabolites were reproducible, with 1.7 mM the smallest detectable difference in phosphocreatine (PCr. Measures of metabolites during exercise were less reliable: exercising PCr had a coefficient of variation (CV of 27% during exercise, compared with 8% at rest. Estimates of mitochondrial function were variable, but experimentally useful. The CV of PCr(1/2t was 40%, yet much of this variance was inter-subject such that differences of <20% were detectable with n = 15, given a significance threshold of p<0.05. CONCLUSIONS: 31-phosphorus MRS provides reproducible and experimentally useful measures of phosphorus metabolites and mitochondrial function in trained human skeletal muscle.

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...

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

Modeling of Experimental Adsorption Isotherm Data

Directory of Open Access Journals (Sweden)

Xunjun Chen

2015-01-01

Full Text Available Adsorption is considered to be one of the most effective technologies widely used in global environmental protection areas. Modeling of experimental adsorption isotherm data is an essential way for predicting the mechanisms of adsorption, which will lead to an improvement in the area of adsorption science. In this paper, we employed three isotherm models, namely: Langmuir, Freundlich, and Dubinin-Radushkevich to correlate four sets of experimental adsorption isotherm data, which were obtained by batch tests in lab. The linearized and non-linearized isotherm models were compared and discussed. In order to determine the best fit isotherm model, the correlation coefficient (r2 and standard errors (S.E. for each parameter were used to evaluate the data. The modeling results showed that non-linear Langmuir model could fit the data better than others, with relatively higher r2 values and smaller S.E. The linear Langmuir model had the highest value of r2, however, the maximum adsorption capacities estimated from linear Langmuir model were deviated from the experimental data.

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...

Experimental/analytical approaches to modeling, calibrating and optimizing shaking table dynamics for structural dynamic applications

Science.gov (United States)

Trombetti, Tomaso

This thesis presents an Experimental/Analytical approach to modeling and calibrating shaking tables for structural dynamic applications. This approach was successfully applied to the shaking table recently built in the structural laboratory of the Civil Engineering Department at Rice University. This shaking table is capable of reproducing model earthquake ground motions with a peak acceleration of 6 g's, a peak velocity of 40 inches per second, and a peak displacement of 3 inches, for a maximum payload of 1500 pounds. It has a frequency bandwidth of approximately 70 Hz and is designed to test structural specimens up to 1/5 scale. The rail/table system is mounted on a reaction mass of about 70,000 pounds consisting of three 12 ft x 12 ft x 1 ft reinforced concrete slabs, post-tensioned together and connected to the strong laboratory floor. The slip table is driven by a hydraulic actuator governed by a 407 MTS controller which employs a proportional-integral-derivative-feedforward-differential pressure algorithm to control the actuator displacement. Feedback signals are provided by two LVDT's (monitoring the slip table relative displacement and the servovalve main stage spool position) and by one differential pressure transducer (monitoring the actuator force). The dynamic actuator-foundation-specimen system is modeled and analyzed by combining linear control theory and linear structural dynamics. The analytical model developed accounts for the effects of actuator oil compressibility, oil leakage in the actuator, time delay in the response of the servovalve spool to a given electrical signal, foundation flexibility, and dynamic characteristics of multi-degree-of-freedom specimens. In order to study the actual dynamic behavior of the shaking table, the transfer function between target and actual table accelerations were identified using experimental results and spectral estimation techniques. The power spectral density of the system input and the cross power spectral

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

Understanding reproducibility of human IVF traits to predict next IVF cycle outcome.

Science.gov (United States)

Wu, Bin; Shi, Juanzi; Zhao, Wanqiu; Lu, Suzhen; Silva, Marta; Gelety, Timothy J

2014-10-01

Evaluating the failed IVF cycle often provides useful prognostic information. Before undergoing another attempt, patients experiencing an unsuccessful IVF cycle frequently request information about the probability of future success. Here, we introduced the concept of reproducibility and formulae to predict the next IVF cycle outcome. The experimental design was based on the retrospective review of IVF cycle data from 2006 to 2013 in two different IVF centers and statistical analysis. The reproducibility coefficients (r) of IVF traits including number of oocytes retrieved, oocyte maturity, fertilization, embryo quality and pregnancy were estimated using the interclass correlation coefficient between the repeated IVF cycle measurements for the same patient by variance component analysis. The formulae were designed to predict next IVF cycle outcome. The number of oocytes retrieved from patients and their fertilization rate had the highest reproducibility coefficients (r = 0.81 ~ 0.84), which indicated a very close correlation between the first retrieval cycle and subsequent IVF cycles. Oocyte maturity and number of top quality embryos had middle level reproducibility (r = 0.38 ~ 0.76) and pregnancy rate had a relative lower reproducibility (r = 0.23 ~ 0.27). Based on these parameters, the next outcome for these IVF traits might be accurately predicted by the designed formulae. The introduction of the concept of reproducibility to our human IVF program allows us to predict future IVF cycle outcomes. The traits of oocyte numbers retrieved, oocyte maturity, fertilization, and top quality embryos had higher or middle reproducibility, which provides a basis for accurate prediction of future IVF outcomes. Based on this prediction, physicians may counsel their patients or change patient's stimulation plans, and laboratory embryologists may improve their IVF techniques accordingly.

Experimental test of a four-level kinetic model for excited-state intramolecular proton transfer dye lasers

Energy Technology Data Exchange (ETDEWEB)

Costela, A; Munnoz, J M; Douhal, A; Figuera, J M; Acuna, A U [Inst. de Quimica Fisica ' ' Rocasolano' ' , C.S.I.C., Madrid (Spain)

1989-11-01

The nanosecond pulses of a dye laser oscillator based on the excited-state intramolecular proton-transfer reaction (IPT) of salicylamide and 2'-hydroxylphenyl benzimidazole dyes have been studied as a function of several experimental parameters. To explain the operation of this laser a numerical four-level kinetic model was developed until the lasing properties of these dyes, in the presence of a variable oxygen concentration and pumped with a double pulse technique, could be reproduced. This was possible only by assuming that the efficiency of the laser is controlled by the absorption cross-section of a transient state with a lifetime in the nanosecond-picosecond range, which was tentatively identified as a ground state tautomeric species. (orig.).

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....

Region-specific protein misfolding cyclic amplification reproduces brain tropism of prion strains.

Science.gov (United States)

Privat, Nicolas; Levavasseur, Etienne; Yildirim, Serfildan; Hannaoui, Samia; Brandel, Jean-Philippe; Laplanche, Jean-Louis; Béringue, Vincent; Seilhean, Danielle; Haïk, Stéphane

2017-10-06

Human prion diseases such as Creutzfeldt-Jakob disease are transmissible brain proteinopathies, characterized by the accumulation of a misfolded isoform of the host cellular prion protein (PrP) in the brain. According to the prion model, prions are defined as proteinaceous infectious particles composed solely of this abnormal isoform of PrP (PrP Sc ). Even in the absence of genetic material, various prion strains can be propagated in experimental models. They can be distinguished by the pattern of disease they produce and especially by the localization of PrP Sc deposits within the brain and the spongiform lesions they induce. The mechanisms involved in this strain-specific targeting of distinct brain regions still are a fundamental, unresolved question in prion research. To address this question, we exploited a prion conversion in vitro assay, protein misfolding cyclic amplification (PMCA), by using experimental scrapie and human prion strains as seeds and specific brain regions from mice and humans as substrates. We show here that region-specific PMCA in part reproduces the specific brain targeting observed in experimental, acquired, and sporadic Creutzfeldt-Jakob diseases. Furthermore, we provide evidence that, in addition to cellular prion protein, other region- and species-specific molecular factors influence the strain-dependent prion conversion process. This important step toward understanding prion strain propagation in the human brain may impact research on the molecular factors involved in protein misfolding and the development of ultrasensitive methods for diagnosing prion disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

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

Developing Phenomena Models from Experimental Data

DEFF Research Database (Denmark)

Kristensen, Niels Rode; Madsen, Henrik; Jørgensen, Sten Bay

2003-01-01

A systematic approach for developing phenomena models from experimental data is presented. The approach is based on integrated application of stochastic differential equation (SDE) modelling and multivariate nonparametric regression, and it is shown how these techniques can be used to uncover...... unknown functionality behind various phenomena in first engineering principles models using experimental data. The proposed modelling approach has significant application potential, e.g. for determining unknown reaction kinetics in both chemical and biological processes. To illustrate the performance...... of the approach, a case study is presented, which shows how an appropriate phenomena model for the growth rate of biomass in a fed-batch bioreactor can be inferred from data....

Developing Phenomena Models from Experimental Data

DEFF Research Database (Denmark)

A systematic approach for developing phenomena models from experimental data is presented. The approach is based on integrated application of stochastic differential equation (SDE) modelling and multivariate nonparametric regression, and it is shown how these techniques can be used to uncover...... unknown functionality behind various phenomena in first engineering principles models using experimental data. The proposed modelling approach has significant application potential, e.g. for determining unknown reaction kinetics in both chemical and biological processes. To illustrate the performance...... of the approach, a case study is presented, which shows how an appropriate phenomena model for the growth rate of biomass in a fed-batch bioreactor can be inferred from data....

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.

Enhancing Scientific Foundations to Ensure Reproducibility: A New Paradigm.

Science.gov (United States)

Hsieh, Terry; Vaickus, Max H; Remick, Daniel G

2018-01-01

Progress in science is dependent on a strong foundation of reliable results. The publish or perish paradigm in research, coupled with an increase in retracted articles from the peer-reviewed literature, is beginning to erode the trust of both the scientific community and the public. The NIH is combating errors by requiring investigators to follow new guidelines addressing scientific premise, experimental design, biological variables, and authentication of reagents. Herein, we discuss how implementation of NIH guidelines will help investigators proactively address pitfalls of experimental design and methods. Careful consideration of the variables contributing to reproducibility helps ensure robust results. The NIH, investigators, and journals must collaborate to ensure that quality science is funded, explored, and published. Copyright © 2018 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

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...

Modeling Stop-and-Go Waves in Pedestrian Dynamics

OpenAIRE

Portz, Andrea; Seyfried, Armin

2010-01-01

Several spatially continuous pedestrian dynamics models have been validated against empirical data. We try to reproduce the experimental fundamental diagram (velocity versus density) with simulations. In addition to this quantitative criterion, we tried to reproduce stop-and-go waves as a qualitative criterion. Stop-and-go waves are a characteristic phenomenon for the single file movement. Only one of three investigated models satisfies both criteria.

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.

Modelling the dynamics of an experimental host-pathogen microcosm within a hierarchical Bayesian framework.

Directory of Open Access Journals (Sweden)

David Lunn

Full Text Available The advantages of Bayesian statistical approaches, such as flexibility and the ability to acknowledge uncertainty in all parameters, have made them the prevailing method for analysing the spread of infectious diseases in human or animal populations. We introduce a Bayesian approach to experimental host-pathogen systems that shares these attractive features. Since uncertainty in all parameters is acknowledged, existing information can be accounted for through prior distributions, rather than through fixing some parameter values. The non-linear dynamics, multi-factorial design, multiple measurements of responses over time and sampling error that are typical features of experimental host-pathogen systems can also be naturally incorporated. We analyse the dynamics of the free-living protozoan Paramecium caudatum and its specialist bacterial parasite Holospora undulata. Our analysis provides strong evidence for a saturable infection function, and we were able to reproduce the two waves of infection apparent in the data by separating the initial inoculum from the parasites released after the first cycle of infection. In addition, the parameter estimates from the hierarchical model can be combined to infer variations in the parasite's basic reproductive ratio across experimental groups, enabling us to make predictions about the effect of resources and host genotype on the ability of the parasite to spread. Even though the high level of variability between replicates limited the resolution of the results, this Bayesian framework has strong potential to be used more widely in experimental ecology.

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...

Regulating Ultrasound Cavitation in order to Induce Reproducible Sonoporation

Science.gov (United States)

Mestas, J.-L.; Alberti, L.; El Maalouf, J.; Béra, J.-C.; Gilles, B.

2010-03-01

Sonoporation would be linked to cavitation, which generally appears to be a non reproducible and unstationary phenomenon. In order to obtain an acceptable trade-off between cell mortality and transfection, a regulated cavitation generator based on an acoustical cavitation measurement was developed and tested. The medium to be sonicated is placed in a sample tray. This tray is immersed in in degassed water and positioned above the face of a flat ultrasonic transducer (frequency: 445 kHz; intensity range: 0.08-1.09 W/cm2). This technical configuration was admitted to be conducive to standing-wave generation through reflection at the air/medium interface in the well thus enhancing the cavitation phenomenon. Laterally to the transducer, a homemade hydrophone was oriented to receive the acoustical signal from the bubbles. From this spectral signal recorded at intervals of 5 ms, a cavitation index was calculated as the mean of the cavitation spectrum integration in a logarithmic scale, and the excitation power is automatically corrected. The device generates stable and reproducible cavitation level for a wide range of cavitation setpoint from stable cavitation condition up to full-developed inertial cavitation. For the ultrasound intensity range used, the time delay of the response is lower than 200 ms. The cavitation regulation device was evaluated in terms of chemical bubble collapse effect. Hydroxyl radical production was measured on terephthalic acid solutions. In open loop, the results present a great variability whatever the excitation power. On the contrary the closed loop allows a great reproducibility. This device was implemented for study of sonodynamic effect. The regulation provides more reproducible results independent of cell medium and experimental conditions (temperature, pressure). Other applications of this regulated cavitation device concern internalization of different particles (Quantum Dot) molecules (SiRNA) or plasmids (GFP, DsRed) into different

PEMFC modeling and experimental validation

Energy Technology Data Exchange (ETDEWEB)

Vargas, J.V.C. [Federal University of Parana (UFPR), Curitiba, PR (Brazil). Dept. of Mechanical Engineering], E-mail: jvargas@demec.ufpr.br; Ordonez, J.C.; Martins, L.S. [Florida State University, Tallahassee, FL (United States). Center for Advanced Power Systems], Emails: ordonez@caps.fsu.edu, martins@caps.fsu.edu

2009-07-01

In this paper, a simplified and comprehensive PEMFC mathematical model introduced in previous studies is experimentally validated. Numerical results are obtained for an existing set of commercial unit PEM fuel cells. The model accounts for pressure drops in the gas channels, and for temperature gradients with respect to space in the flow direction, that are investigated by direct infrared imaging, showing that even at low current operation such gradients are present in fuel cell operation, and therefore should be considered by a PEMFC model, since large coolant flow rates are limited due to induced high pressure drops in the cooling channels. The computed polarization and power curves are directly compared to the experimentally measured ones with good qualitative and quantitative agreement. The combination of accuracy and low computational time allow for the future utilization of the model as a reliable tool for PEMFC simulation, control, design and optimization purposes. (author)

An experimental and modeling study of propene oxidation. Part 2: Ignition delay time and flame speed measurements

KAUST Repository

Burke, Siné ad M.; Burke, Ultan; Mc Donagh, Reuben; Mathieu, Olivier; Osorio, Irmis; Keesee, Charles L.; Morones, Aní bal; Petersen, Eric L.; Wang, Weijing; DeVerter, Trent A.; Oehlschlaeger, Matthew A.; Rhodes, Brandie; Hanson, Ronald K.; Davidson, David F.; Weber, Bryan W.; Sung, Chihjen; Santner, Jeffrey S.; Ju, Yiguang; Haas, Francis M.; Dryer, Frederick L.; Volkov, Evgeniy N.; Nilsson, Elna J K; Konnov, Alexander A.; Alrefae, Majed; Khaled, Fathi; Farooq, Aamir; Dirrenberger, Patricia; Glaude, Pierre Alexandre; Battin-Leclerc, F.; Curran, Henry J.

2015-01-01

Experimental data obtained in this study (Part II) complement the speciation data presented in Part I, but also offer a basis for extensive facility cross-comparisons for both experimental ignition delay time (IDT) and laminar flame speed (LFS) observables. To improve our understanding of the ignition characteristics of propene, a series of IDT experiments were performed in six different shock tubes and two rapid compression machines (RCMs) under conditions not previously studied. This work is the first of its kind to directly compare ignition in several different shock tubes over a wide range of conditions. For common nominal reaction conditions among these facilities, cross-comparison of shock tube IDTs suggests 20-30% reproducibility (2σ) for the IDT observable. The combination of shock tube and RCM data greatly expands the data available for validation of propene oxidation models to higher pressures (2-40. atm) and lower temperatures (750-1750. K).Propene flames were studied at pressures from 1 to 20. atm and unburned gas temperatures of 295-398. K for a range of equivalence ratios and dilutions in different facilities. The present propene-air LFS results at 1. atm were also compared to LFS measurements from the literature. With respect to initial reaction conditions, the present experimental LFS cross-comparison is not as comprehensive as the IDT comparison; however, it still suggests reproducibility limits for the LFS observable. For the LFS results, there was agreement between certain data sets and for certain equivalence ratios (mostly in the lean region), but the remaining discrepancies highlight the need to reduce uncertainties in laminar flame speed experiments amongst different groups and different methods. Moreover, this is the first study to investigate the burning rate characteristics of propene at elevated pressures (>5. atm).IDT and LFS measurements are compared to predictions of the chemical kinetic mechanism presented in Part I and good

An experimental and modeling study of propene oxidation. Part 2: Ignition delay time and flame speed measurements

KAUST Repository

Burke, Sinéad M.

2015-02-01

Experimental data obtained in this study (Part II) complement the speciation data presented in Part I, but also offer a basis for extensive facility cross-comparisons for both experimental ignition delay time (IDT) and laminar flame speed (LFS) observables. To improve our understanding of the ignition characteristics of propene, a series of IDT experiments were performed in six different shock tubes and two rapid compression machines (RCMs) under conditions not previously studied. This work is the first of its kind to directly compare ignition in several different shock tubes over a wide range of conditions. For common nominal reaction conditions among these facilities, cross-comparison of shock tube IDTs suggests 20-30% reproducibility (2σ) for the IDT observable. The combination of shock tube and RCM data greatly expands the data available for validation of propene oxidation models to higher pressures (2-40. atm) and lower temperatures (750-1750. K).Propene flames were studied at pressures from 1 to 20. atm and unburned gas temperatures of 295-398. K for a range of equivalence ratios and dilutions in different facilities. The present propene-air LFS results at 1. atm were also compared to LFS measurements from the literature. With respect to initial reaction conditions, the present experimental LFS cross-comparison is not as comprehensive as the IDT comparison; however, it still suggests reproducibility limits for the LFS observable. For the LFS results, there was agreement between certain data sets and for certain equivalence ratios (mostly in the lean region), but the remaining discrepancies highlight the need to reduce uncertainties in laminar flame speed experiments amongst different groups and different methods. Moreover, this is the first study to investigate the burning rate characteristics of propene at elevated pressures (>5. atm).IDT and LFS measurements are compared to predictions of the chemical kinetic mechanism presented in Part I and good

A model of cardiac ryanodine receptor gating predicts experimental Ca2+-dynamics and Ca2+-triggered arrhythmia in the long QT syndrome

Science.gov (United States)

Wilson, Dan; Ermentrout, Bard; Němec, Jan; Salama, Guy

2017-09-01

Abnormal Ca2+ handling is well-established as the trigger of cardiac arrhythmia in catecholaminergic polymorphic ventricular tachycardia and digoxin toxicity, but its role remains controversial in Torsade de Pointes (TdP), the arrhythmia associated with the long QT syndrome (LQTS). Recent experimental results show that early afterdepolarizations (EADs) that initiate TdP are caused by spontaneous (non-voltage-triggered) Ca2+ release from Ca2+-overloaded sarcoplasmic reticulum (SR) rather than the activation of the L-type Ca2+-channel window current. In bradycardia and long QT type 2 (LQT2), a second, non-voltage triggered cytosolic Ca2+ elevation increases gradually in amplitude, occurs before overt voltage instability, and then precedes the rise of EADs. Here, we used a modified Shannon-Puglisi-Bers model of rabbit ventricular myocytes to reproduce experimental Ca2+ dynamics in bradycardia and LQT2. Abnormal systolic Ca2+-oscillations and EADs caused by SR Ca2+-release are reproduced in a modified 0-dimensional model, where 3 gates in series control the ryanodine receptor (RyR2) conductance. Two gates control RyR2 activation and inactivation and sense cytosolic Ca2+ while a third gate senses luminal junctional SR Ca2+. The model predicts EADs in bradycardia and low extracellular [K+] and cessation of SR Ca2+-release terminate salvos of EADs. Ca2+-waves, systolic cell-synchronous Ca2+-release, and multifocal diastolic Ca2+ release seen in subcellular Ca2+-mapping experiments are observed in the 2-dimensional version of the model. These results support the role of SR Ca2+-overload, abnormal SR Ca2+-release, and the subsequent activation of the electrogenic Na+/Ca2+-exchanger as the mechanism of TdP. The model offers new insights into the genesis of cardiac arrhythmia and new therapeutic strategies.

Modeling of confined and unconfined laminar premixed flames on slit and tube burners

NARCIS (Netherlands)

Mallens, R.M.M.; Lange, de H.C.; Ven, van de C.J.H.; Goey, de L.P.H.

1995-01-01

A model is presented for laminar premixed Bunsen flames on slit and cylindrical burners burning in a surrounding atmosphere. A comparison between modeling and experimental results shows that the model can reproduce the experimental results within 10% accuracy. The influence of a surrounding

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.

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.

Appraisal on the wound healing activity of different extracts obtained from Aegle marmelos and Mucuna pruriens by in vivo experimental models.

Science.gov (United States)

Toppo, F A; Pawar, R S

2016-01-01

The use of a simple and reproducible model is inevitable for an objective statement of the effects of external factors on wound healing. Hence, the present study was conducted to evaluate wound healing activities of sequential different extracts of Aegle marmelos leaves (AM) and Mucuna pruriens seeds (MP) by in vivo experimental models. Wistar albino rats were subjected to excision, incision and dead space wounds measuring approximately 250 mm2, 3 cm and implanting sterilized polyvinyl chloride tube on the back of each rat near either side of the vertebral column respectively. The experimental animals were randomized into eight groups (n = 6), control, standard and treatment groups. Hydrogel of different extracts were applied topically once daily. The parameters observed were percentage of wound contraction, epithelization period, tensile strength, hydroxyproline content of the granulation tissue, and histological changes during wound healing. The statistical study revealed that in excision, incision, and dead space wound models all formulations have significant (P < 0.01) wound healing potential. However, methanolic extract formulation was found to be superior to all other treatments as evidenced by rapid wound contraction, lesser number of days required for complete epithelization, increased tensile strength and significant increase in hydroxyproline content. As compared to the reference standard treated group the wound healing process of the experimental groups was decelerated. All extracts obtained from AM and MP facilitated the wound healing process in all experimental models.

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.

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

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.

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

Using semantics for representing experimental protocols.

Science.gov (United States)

Giraldo, Olga; García, Alexander; López, Federico; Corcho, Oscar

2017-11-13

An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols. In this paper we present "SMART Protocols ontology", an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample. Improving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/ .

Molecular dynamics simulations with electronic stopping can reproduce experimental sputtering yields of metals impacted by large cluster ions

Science.gov (United States)

Tian, Jiting; Zhou, Wei; Feng, Qijie; Zheng, Jian

2018-03-01

An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons-atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10-20 keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.

Modeling microtubule oscillations

DEFF Research Database (Denmark)

Jobs, E.; Wolf, D.E.; Flyvbjerg, H.

1997-01-01

Synchronization of molecular reactions in a macroscopic volume may cause the volume's physical properties to change dynamically and thus reveal much about the reactions. As an example, experimental time series for so-called microtubule oscillations are analyzed in terms of a minimal model...... for this complex polymerization-depolymerization cycle. The model reproduces well the qualitatively different time series that result from different experimental conditions, and illuminates the role and importance of individual processes in the cycle. Simple experiments are suggested that can further test...... and define the model and the polymer's reaction cycle....

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

ANALYSIS OF INDIVIDUAL BIOLOGICAL CHARACTERISTICS OF AMUR CARP (CYPRINUS CARPIO HAEMATOPTERUS REPRODUCED USING CRYOPRESERVED SPERM

Directory of Open Access Journals (Sweden)

N. Kolisnyk

2014-12-01

Full Text Available Purpose. To reproduce Amur carp population using cryopreserved sperm and analyze some biological and fish culture peculiarities of the reproduced fish stock. Methodology. Generally accepted methods for fish culture [1]. Experimental reproduction was carried out in pond conditions of «Carpathian vodogray» LTD (Lisnevychi village, Pustomytivsky district, Lviv region. Hydrochemical analysis was carried out classically by O. Alуokin (1970 [2], hydrobiological studies in the fatting ponds according to V. Zhadin (1956, 1960 [3, 4]. Haemoglobin concentration was determined by hemocyanin method of G. Dervis, A. Vorobiov [5]. Blood for this method was collected from fish heart with the use of Pasteur pipettes in Eppendorf tubes with heparin. Following exterior morphometric parameters were analysed: body weight (m, g, standard fish body length (l, cm, largest body height (H, cm and body circumference (O cm. Following exterior indices were calculated based on these parameters: body depth index (l/H, body circumference index (l/O and Fulton’s condition factor (Kv. The study was carried out using two groups of carp: control and experimental. The first group was reproduced from the native sperm, the second from the cryopreserved sperm. Findings. Carp reproduction and growing was carried out using native and cryopreserved sperm. This work contains the results of growing 1+ Amur carp of experimental and control groups. Hydrochemical and hydrobiological parameters of the fattening ponds were studied. Peculiarities of the exterior and some hematological parameters of the carp of different origin were characterized. Originality. For the first time we performed a comparison of some biological parameters of Amur carp reproduced using native and cryopreserved sperm. Practical Value. Considering the economic importance of Amur carp due to its use in hybridization, reproduction of its population plays an important role in the development of the stocks of the pure

Simple computational modeling for human extracorporeal irradiation using the BNCT facility of the RA-3 Reactor

International Nuclear Information System (INIS)

Farias, Ruben; Gonzalez, S.J.; Bellino, A.; Sztenjberg, M.; Pinto, J.; Thorp, Silvia I.; Gadan, M.; Pozzi, Emiliano; Schwint, Amanda E.; Heber, Elisa M.; Trivillin, V.A.; Zarza, Leandro G.; Estryk, Guillermo; Miller, M.; Bortolussi, S.; Soto, M.S.; Nigg, D.W.

2009-01-01

We present a simple computational model of the reactor RA-3 developed using Monte Carlo transport code MCNP. The model parameters are adjusted in order to reproduce experimental measured points in air and the source validation is performed in an acrylic phantom. Performance analysis is carried out using computational models of animal extracorporeal irradiation in liver and lung. Analysis is also performed inside a neutron shielded receptacle use for the irradiation of rats with a model of hepatic metastases.The computational model reproduces the experimental behavior in all the analyzed cases with a maximum difference of 10 percent. (author)

An Agent-Based Model of a Hepatic Inflammatory Response to Salmonella: A Computational Study under a Large Set of Experimental Data.

Science.gov (United States)

Shi, Zhenzhen; Chapes, Stephen K; Ben-Arieh, David; Wu, Chih-Hang

2016-01-01

We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as "sepsis". Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-α ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies.

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.

The Web system of visualization and analysis equipped with reproducibility

International Nuclear Information System (INIS)

Ueshima, Yutaka; Saito, Kanji; Takeda, Yasuhiro; Nakai, Youichi; Hayashi, Sachiko

2005-01-01

In the advanced photon experimental research, real-time visualization and steering system is thought as desirable method of data analysis. This approach is valid only in the fixed analysis at one time or in the easily reproducible experiment. But, in the research for an unknown problem like the advanced photon experimental research, it is necessary that the observation data can be analyzed many times because profitable analysis is difficult at the first time. Consequently, output data should be filed to refer and analyze at any time. To support the research, we need the followed automatic functions, transporting data files from data generator to data storage, analyzing data, tracking history of data handling, and so on. The supporting system will be integrated database system with several functional servers distributed on the network. (author)

INFORMATIVE ENERGY METRIC FOR SIMILARITY MEASURE IN REPRODUCING KERNEL HILBERT SPACES

Directory of Open Access Journals (Sweden)

Songhua Liu

2012-02-01

Full Text Available In this paper, information energy metric (IEM is obtained by similarity computing for high-dimensional samples in a reproducing kernel Hilbert space (RKHS. Firstly, similar/dissimilar subsets and their corresponding informative energy functions are defined. Secondly, IEM is proposed for similarity measure of those subsets, which converts the non-metric distances into metric ones. Finally, applications of this metric is introduced, such as classification problems. Experimental results validate the effectiveness of the proposed method.

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.

Experimental and Monte Carlo simulated spectra of a liquid-metal-jet x-ray source

International Nuclear Information System (INIS)

Marziani, M.; Gambaccini, M.; Di Domenico, G.; Taibi, A.; Cardarelli, P.

2014-01-01

A prototype x-ray system based on a liquid-metal-jet anode was evaluated within the framework of the LABSYNC project. The generated spectrum was measured using a CZT-based spectrometer and was compared with spectra simulated by three Monte Carlo codes: MCNPX, PENELOPE and EGS5. Notable differences in the simulated spectra were found. These are mainly attributable to differences in the models adopted for the electron-impact ionization cross section. The simulation that more closely reproduces the experimentally measured spectrum was provided by PENELOPE. - Highlights: • The x-ray spectrum of a liquid-jet x-ray anode was measured with a CZT spectrometer. • Results were compared with Monte Carlo simulations using MCNPX, PENELOPE, EGS5. • Notable differences were found among the Monte Carlo simulated spectra. • The key role was played by the electron-impact ionization cross-section model used. • The experimentally measured spectrum was closely reproduced by the PENELOPE code

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.

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

Science.gov (United States)

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

2017-01-01

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

Modelling concentration-analgesia relationships for morphine to evaluate experimental pain models

DEFF Research Database (Denmark)

Sverrisdóttir, Eva; Foster, David John Richard; Upton, Richard Neil

2015-01-01

The aim of this study was to develop population pharmacokinetic-pharmacodynamic models for morphine in experimental pain induced by skin heat and muscle pressure, and to evaluate the experimental pain models with regard to assessment of morphine pharmacodynamics. In a randomized, double......-blind, placebo-controlled, crossover study, 39 healthy volunteers received an oral dose of 30 mg morphine hydrochloride or placebo. Non-linear mixed effects modelling was used to describe the plasma concentrations of morphine and metabolites, and the analgesic effect of morphine on experimental pain in skin...... and muscle. Baseline pain metrics varied between individuals and occasions, and were described with interindividual and interoccasion variability. Placebo-response did not change with time. For both pain metrics, morphine effect was proportional to baseline pain and was described with a linear model...

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.

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.

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.

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…

Reproducible research: a minority opinion

Science.gov (United States)

Drummond, Chris

2018-01-01

Reproducible research, a growing movement within many scientific fields, including machine learning, would require the code, used to generate the experimental results, be published along with any paper. Probably the most compelling argument for this is that it is simply following good scientific practice, established over the years by the greats of science. The implication is that failure to follow such a practice is unscientific, not a label any machine learning researchers would like to carry. It is further claimed that misconduct is causing a growing crisis of confidence in science. That, without this practice being enforced, science would inevitably fall into disrepute. This viewpoint is becoming ubiquitous but here I offer a differing opinion. I argue that far from being central to science, what is being promulgated is a narrow interpretation of how science works. I contend that the consequences are somewhat overstated. I would also contend that the effort necessary to meet the movement's aims, and the general attitude it engenders would not serve well any of the research disciplines, including our own.

Experimental and theoretical investigation of the magnetization dynamics of an artificial square spin ice cluster

Energy Technology Data Exchange (ETDEWEB)

Pohlit, Merlin, E-mail: pohlit@physik.uni-frankfurt.de; Porrati, Fabrizio; Huth, Michael; Müller, Jens [Institute of Physics, Goethe-University Frankfurt, Frankfurt/Main (Germany); Stockem, Irina; Schröder, Christian [Bielefeld Institute for Applied Materials Research, FH Bielefeld-University of Applied Sciences, Bielefeld (Germany)

2016-10-14

We study the magnetization dynamics of a spin ice cluster which is a building block of an artificial square spin ice fabricated by focused electron-beam-induced deposition both experimentally and theoretically. The spin ice cluster is composed of twelve interacting Co nanoislands grown directly on top of a high-resolution micro-Hall sensor. By employing micromagnetic simulations and a macrospin model, we calculate the magnetization and the experimentally investigated stray field emanating from a single nanoisland. The parameters determined from a comparison with the experimental hysteresis loop are used to derive an effective single-dipole macrospin model that allows us to investigate the dynamics of the spin ice cluster. Our model reproduces the experimentally observed non-deterministic sequences in the magnetization curves as well as the distinct temperature dependence of the hysteresis loop.

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.

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...

Hemorrhoids: an experimental model in monkeys

Directory of Open Access Journals (Sweden)

Plapler Hélio

2006-01-01

Full Text Available PURPOSE: Hemorrhoids are a matter of concern due to a painful outcome. We describe a simple, easy and reliable experimental model to produce hemorrhoids in monkeys. METHODS: 14 monkeys (Cebus apella were used. After general anesthesia, hemorrhoids were induced by ligation of the inferior hemorrhoidal vein, which is very alike to humans. The vein was located through a perianal incision, dissected and ligated with a 3-0 vicryl. The skin was sutured with a 4-0 catgut thread. Animals were kept in appropriate cages and evaluated daily. RESULTS: Nine days later there were hemorrhoidal piles in the anus in fifty percent (50% of the animals. Outcome was unremarkable. There was no bleeding and all animals showed no signs of pain or suffering. CONCLUSION: This is an affordable and reliable experimental model to induce hemorrhoids for experimental studies.

Experimentally induced cam impingement in the sheep hip.

Science.gov (United States)

Siebenrock, Klaus A; Fiechter, Ruth; Tannast, Moritz; Mamisch, Tallal C; von Rechenberg, Brigitte

2013-04-01

Sheep hips have a natural non-spherical femoral head similar to a cam-type deformity in human beings. By performing an intertrochanteric varus osteotomy, cam-type femoro-acetabular impingement (FAI) during flexion can be created. We tested the hypotheses that macroscopic lesions of the articular cartilage and an increased Mankin score (MS) can be reproduced by an experimentally induced cam-type FAI in this ovine in vivo model. Furthermore, we hypothesized that the MS increases with longer ambulatory periods. Sixteen sheep underwent unilateral intertrochanteric varus osteotomy of the hip with the non-operated hip as a control. Four sheep were sacrificed after 14, 22, 30, and 38-weeks postoperatively. We evaluated macroscopic chondrolabral alterations, and recorded the MS, based on histochemical staining, for each ambulatory period. A significantly higher prevalence of macroscopic chondrolabral lesions was found in the impingement zone of the operated hips. The MS was significantly higher in the acetabular/femoral cartilage of the operated hips. Furthermore, these scores increased as the length of the ambulatory period increased. Cam-type FAI can be induced in an ovine in vivo model. Localized chondrolabral degeneration of the hip, similar to that seen in humans (Tannast et al., Clin Orthop Relat Res 2008; 466: 273-280; Beck et al., J Bone Joint Surg Br 2005; 87: 1012-1018), can be reproduced. This experimental sheep model can be used to study cam-type FAI. Copyright © 2012 Orthopaedic Research Society.

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

Improving the physiological realism of experimental models.

Science.gov (United States)

Vinnakota, Kalyan C; Cha, Chae Y; Rorsman, Patrik; Balaban, Robert S; La Gerche, Andre; Wade-Martins, Richard; Beard, Daniel A; Jeneson, Jeroen A L

2016-04-06

The Virtual Physiological Human (VPH) project aims to develop integrative, explanatory and predictive computational models (C-Models) as numerical investigational tools to study disease, identify and design effective therapies and provide an in silico platform for drug screening. Ultimately, these models rely on the analysis and integration of experimental data. As such, the success of VPH depends on the availability of physiologically realistic experimental models (E-Models) of human organ function that can be parametrized to test the numerical models. Here, the current state of suitable E-models, ranging from in vitro non-human cell organelles to in vivo human organ systems, is discussed. Specifically, challenges and recent progress in improving the physiological realism of E-models that may benefit the VPH project are highlighted and discussed using examples from the field of research on cardiovascular disease, musculoskeletal disorders, diabetes and Parkinson's disease.

Experimental processing of a model data set using Geobit seismic software

Energy Technology Data Exchange (ETDEWEB)

Suh, Sang Yong [Korea Inst. of Geology Mining and Materials, Taejon (Korea, Republic of)

1995-12-01

A seismic data processing software, Geobit, has been developed and is continuously updated to implement newer processing techniques and to support more hardware platforms. Geobit is intended to support all Unix platforms ranging from PC to CRAY. The current version supports two platform, i.e., PC/Linux and Sun Sparc based Sun OS 4.1.x. PC/Linux attracted geophysicists in some universities trying to install Geobit in their laboratories to be used as their research tool. However, one of the problem is the difficulty in getting the seismic data. The primary reason is its huge volume. The field data is too bulky to fit their relatively small storage media, such as PC disk. To solve the problem, KIGAM released a model seismic data set via ftp.kigam.re.kr. This study aims two purposes. The first one is testing Geobit software for its suitability in seismic data processing. The test includes reproducing the model through the seismic data processing. If it fails to reproduce the original model, the software is considered buggy and incomplete. However, if it can successfully reproduce the input model, I would be proud of what I have accomplished for the last few years in writing Geobit. The second purpose is to give a guide on Geobit usage by providing an example set of job files needed to process a given data. This example will help scientists lacking Geobit experience to concentrate on their study more easily. Once they know the Geobit processing technique, and later on Geobit programming, they can implement their own processing idea, contributing newer technologies to Geobit. The complete Geobit job files needed to process the model data is written, in the following job sequence: (1) data loading, (2) CDP sort, (3) decon analysis, (4) velocity analysis, (5) decon verification, (6) stack, (7) filter analysis, (8) filtered stack, (9) time migration, (10) depth migration. The control variables in the job files are discussed. (author). 10 figs., 1 tab.

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.

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

Guidelines for pre-clinical assessment of the acetylcholine receptor-specific passive transfer myasthenia gravis model - recommendations for methods and experimental designs

Science.gov (United States)

Kusner, Linda L.; Losen, Mario; Vincent, Angela; Lindstrom, Jon; Tzartos, Socrates; Lazaridis, Konstantinos; Martinez-Martinez, Pilar

2015-01-01

Antibodies against the muscle acetylcholine receptor (AChR) are the most common cause of myasthenia gravis (MG). Passive transfer of AChR antibodies from MG patients into animals reproduces key features of human disease, including antigenic modulation of the AChR, complement-mediated damage of the neuromuscular junction, and muscle weakness. Similarly, AChR antibodies generated by active immunization in experimental autoimmune MG models can subsequently be passively transferred to other animals and induce weakness. The passive transfer model is useful to test therapeutic strategies aimed at the effector mechanism of the autoantibodies. Here we summarize published and unpublished experience using the AChR passive transfer MG model in mice, rats and rhesus monkeys, and give recommendations for the design of preclinical studies in order to facilitate translation of positive and negative results to improve MG therapies. PMID:25743217

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

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

Ideal Experimental Rat Models for Liver Diseases.

Science.gov (United States)

Lee, Sang Woo; Kim, Sung Hoon; Min, Seon Ok; Kim, Kyung Sik

2011-05-01

There are many limitations for conducting liver disease research in human beings due to the high cost and potential ethical issues. For this reason, conducting a study that is difficult to perform in humans using appropriate animal models, can be beneficial in ascertaining the pathological physiology, and in developing new treatment modalities. However, it is difficult to determine the appropriate animal model which is suitable for research purposes, since every patient has different and diverse clinical symptoms, adverse reactions, and complications due to the pathological physiology. Also, it is not easy to reproduce identically various clinical situations in animal models. Recently, the Guide for the Care and Use of Laboratory Animals has tightened up the regulations, and therefore it is advisable to select the appropriate animals and decide upon the appropriate quantities through scientific and systemic considerations before conducting animal testing. Therefore, in this review article the authors examined various white rat animal testing models and determined the appropriate usable rat model, and the pros and cons of its application in liver disease research. The authors believe that this review will be beneficial in selecting proper laboratory animals for research purposes.

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.

Analysis of ITER NbTi and Nb3Sn CICCs experimental minimum quench energy with JackPot, MCM and THEA models

Science.gov (United States)

Bagni, T.; Duchateau, J. L.; Breschi, M.; Devred, A.; Nijhuis, A.

2017-09-01

Cable-in-conduit conductors (CICCs) for ITER magnets are subjected to fast changing magnetic fields during the plasma-operating scenario. In order to anticipate the limitations of conductors under the foreseen operating conditions, it is essential to have a better understanding of the stability margin of magnets. In the last decade ITER has launched a campaign for characterization of several types of NbTi and Nb3Sn CICCs comprising quench tests with a singular sine wave fast magnetic field pulse and relatively small amplitude. The stability tests, performed in the SULTAN facility, were reproduced and analyzed using two codes: JackPot-AC/DC, an electromagnetic-thermal numerical model for CICCs, developed at the University of Twente (van Lanen and Nijhuis 2010 Cryogenics 50 139-148) and multi-constant-model (MCM) (Turck and Zani 2010 Cryogenics 50 443-9), an analytical model for CICCs coupling losses. The outputs of both codes were combined with thermal, hydraulic and electric analysis of superconducting cables to predict the minimum quench energy (MQE) (Bottura et al 2000 Cryogenics 40 617-26). The experimental AC loss results were used to calibrate the JackPot and MCM models and to reproduce the energy deposited in the cable during an MQE test. The agreement between experiments and models confirm a good comprehension of the various CICCs thermal and electromagnetic phenomena. The differences between the analytical MCM and numerical JackPot approaches are discussed. The results provide a good basis for further investigation of CICC stability under plasma scenario conditions using magnetic field pulses with lower ramp rate and higher amplitude.

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

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

P-HS-SFM: a parallel harmony search algorithm for the reproduction of experimental data in the continuous microscopic crowd dynamic models

Science.gov (United States)

Jaber, Khalid Mohammad; Alia, Osama Moh'd.; Shuaib, Mohammed Mahmod

2018-03-01

Finding the optimal parameters that can reproduce experimental data (such as the velocity-density relation and the specific flow rate) is a very important component of the validation and calibration of microscopic crowd dynamic models. Heavy computational demand during parameter search is a known limitation that exists in a previously developed model known as the Harmony Search-Based Social Force Model (HS-SFM). In this paper, a parallel-based mechanism is proposed to reduce the computational time and memory resource utilisation required to find these parameters. More specifically, two MATLAB-based multicore techniques (parfor and create independent jobs) using shared memory are developed by taking advantage of the multithreading capabilities of parallel computing, resulting in a new framework called the Parallel Harmony Search-Based Social Force Model (P-HS-SFM). The experimental results show that the parfor-based P-HS-SFM achieved a better computational time of about 26 h, an efficiency improvement of ? 54% and a speedup factor of 2.196 times in comparison with the HS-SFM sequential processor. The performance of the P-HS-SFM using the create independent jobs approach is also comparable to parfor with a computational time of 26.8 h, an efficiency improvement of about 30% and a speedup of 2.137 times.

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...

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.

Experimental study on thermal dispersion in and near the surf zone

International Nuclear Information System (INIS)

Komori, Shuzo; Tanaka, Hiroyoshi; Wada, Akira

1978-01-01

The site of Fukushima No. 1 Nuclear Power Station of Tokyo Electric Power Company was selected, and first, irregular waves with the typical wave spectra (in usual time and in storm time) in the sea region of the site were reproduced in the hydraulic model, then the characteristics of thermal dispersion and the velocityfield of warmed water (its discharge is 25.3 m 3 /sec.) in and near the surf zone under the action of those irregular waves were discussed. Finally, the similarity was investigated between the dispersion phenomenon in the hydraulic model and that in the prototype by comparing the experimental results of the dispersion range of warmed water with the results of field measurements. It may be concluded that the enveloped range of thermal dispersion in prototype can be predicted fairly correctly under almost the same discharge condition as this experiment if the prototype conditions of waves and currents are considered carefully and reproduced in a hydraulic model. (Kobatake, H.)

Ozone production in the reaction of T2 and O2 gas: A comparison of experimental results and model predictions

International Nuclear Information System (INIS)

Failor, R.A.; Souers, P.C.; Magnotta, F.

1992-01-01

Ozone, predicted to be an important intermediate species in T 2 oxidation, was monitored in situ by UV absorption spectroscopy for 0.01-1.0 mol % T 2 in O 2 (1 atm, 298 K). These are the first measurements of a tritium oxidation reaction intermediate. The experimental results were compared with the predictions of the author's comprehensive model of tritium oxidation. The experimentally determined temporal variation in ozone concentration is qualitatively reproduced by the model. As predicted, the measured initial rate of ozone production varied linearly with the initial T 2 concentration ([T 2 ] o ), but with a value one-third of that predicted. The steady-state ozone concentration ([O 3 ] ss ) a factor of 4 larger than predicted for a 1.0% T 2 -O 2 mixture. Addition of H 2 to the T 2 O 2 mixture, to differentiate between the radiolytic and chemical behavior of the tritium, produced a decrease in [O 3 ] ss which was larger than predicted. Changing the reaction cell surface-to-volume ratio showed indications of minor surface removal of ozone. No reasonable variation in model input parameters brought both the predicted initial ozone production rates and steady-state concentrations of ozone into agreement with the experimental results. Though qualitative agreement was achieved, further studies, with emphasis on surface effects, are necessary to explain quantitative differences and gain a greater understanding of the oxidation mechanism. 27 refs., 11 figs., 4 tabs

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.

Establishment of a head injury by club model in rabbits and experimental conditions

International Nuclear Information System (INIS)

Cao Yunxing; Xi Huanjiu; Zhang Jing; Li Hongwei; Yin Zhiyong; Zhao Hui

2013-01-01

Objective: To establish an animal model to replicate the injury by club in forensic medicine. Methods: Twenty-four New Zealand white rabbits were divided into control group (n=4), minor injury group (n=10), and severe injury group (n=10). Based on the BIM-Ⅱ Horizontal Bio-impact Machine, a self-designed iron bar was used to produce head injury by club. Six hours after injury, all the rabbits were subjected to a CT examination and dissected to observe the injury morphology and undergo routine pathological examination. Four control, six minor and severe rabbits were given moisture content examination. Results: Varying degrees of positive signs of the nervous system were observed in all the injured rabbits within 6 hours. The mortality rate was 1/10 in the minor injury group and 6/10 in the severe injury group. The morphological changes consisted of different levels of scalp hematoma, skull fracture, epidural hematoma, subdural hematoma, subarachnoid hemorrhage and brain injury. The difference in moisture content between the three groups was of statistical significance. Conclusion: Under the rigidly-controlled experimental condition, this animal model produces good reproducibility and stable results. Meanwhile, it can simulate the morphology of injury by club and be used to study the mechanism of injury by club in forensic medicine. (authors)

Experimental Investigation of Unsteady Aerodynamic Forces on Airfoil in Harmonic Translatory Motion

DEFF Research Database (Denmark)

Gaunaa, Mac; Sørensen, Jens Nørkær

2003-01-01

The present paper describes the main results from an experimental investigation of the unsteady aerodynamic forces on a NACA 0015 airfoil subject to 1-degree-of-freedom (DOF) harmonic translatory motion. The focus of the experimental investigations was to determine the factors that influence...... maximum lift for both stationary and moving airfoil configurations. The mean as well as the dynamic characteristics of the different stall levels were found to differ from each other. An investigation of the negative aerodynamically damped cases showed that the damping decrease as the reduced frequency...... is decreased. Comparison between the experimental data, 2D Navier-Stokes computations and two commonly used dynamic stall models reveal that all models failed to reproduce the dynamic characteristics of the flow for incidences above maximum lift, however the Navier-Stokes computations generally captured...

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.

A novel numerical model for estimating the collapse pressure of flexible pipes

Energy Technology Data Exchange (ETDEWEB)

Nogueira, Victor P.P.; Antoun Netto, Theodoro [Universidade Federal do Rio de Janeiro (COPPE/UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao em Engenharia], e-mail: victor@lts.coppe.ufrj.br

2009-07-01

As the worldwide oil and gas industry operational environments move to ultra-deep waters, failure mechanisms in flexible pipes such as instability of the armor layers under compression and hydrostatic collapse are more likely to occur. Therefore, it is important to develop reliable numerical tools to reproduce the failure mechanisms that may occur in flexible pipes. This work presents a representative finite element model of flexible pipe capable to reproduce its pre and post-collapse behavior under hydrostatic pressure. The model, developed in the scope of this work, uses beam elements and includes nonlinear kinematics and material behavior influences. The dependability of the numerical results is assessed in light of experimental tests on flexible pipes with 4 inches and 8 inches nominal diameter available in the literature (Souza, 2002). The applied methodology provided coherent values regarding the estimation of the collapse pressures and results have shown that the proposed model is capable to reproduce experimental results. (author)

Cephalopod Experimental Projected Habitat (CEPH: Virtual Reality for Underwater Organisms

Directory of Open Access Journals (Sweden)

Noam Josef

2018-03-01

Full Text Available Cephalopods' visually driven, dynamic, and diverse skin display makes them a key animal model in sensory ethology and camouflage research. Development of novel methods is critically important in order to monitor and objectively quantify cephalopod behavior. In this work, the development of Cephalopod Experimental Projected Habitat (CEPH is described. This newly developed experimental design bridges computational and ethological sciences, providing a visually controlled arena which requires limited physical space and minimal previous technical background. Created from relatively inexpensive and readily available materials, the experimental apparatus utilizes reflected light which closely resembles natural settings. Preliminary results suggest the experimental design reproducibly challenges marine organisms with visually dynamic surroundings, including videos of prey and predator. This new approach should offer new avenues for marine organism sensory research and may serve researchers from various fields.

Experimental Modeling of Dynamic Systems

DEFF Research Database (Denmark)

Knudsen, Morten Haack

2006-01-01

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

Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment

Directory of Open Access Journals (Sweden)

Andrew J. Percy

2015-09-01

Full Text Available The reproducibility of plasma protein quantitation between laboratories and between instrument types was examined in a large-scale international study involving 16 laboratories and 19 LC–MS/MS platforms, using two kits designed to evaluate instrument performance and one kit designed to evaluate the entire bottom-up workflow. There was little effect of instrument type on the quality of the results, demonstrating the robustness of LC/MRM-MS with isotopically labeled standards. Technician skill was a factor, as errors in sample preparation and sub-optimal LC–MS performance were evident. This highlights the importance of proper training and routine quality control before quantitation is done on patient samples.

Interactive Sonification Exploring Emergent Behavior Applying Models for Biological Information and Listening

Science.gov (United States)

Choi, Insook

2018-01-01

Sonification is an open-ended design task to construct sound informing a listener of data. Understanding application context is critical for shaping design requirements for data translation into sound. Sonification requires methodology to maintain reproducibility when data sources exhibit non-linear properties of self-organization and emergent behavior. This research formalizes interactive sonification in an extensible model to support reproducibility when data exhibits emergent behavior. In the absence of sonification theory, extensibility demonstrates relevant methods across case studies. The interactive sonification framework foregrounds three factors: reproducible system implementation for generating sonification; interactive mechanisms enhancing a listener's multisensory observations; and reproducible data from models that characterize emergent behavior. Supramodal attention research suggests interactive exploration with auditory feedback can generate context for recognizing irregular patterns and transient dynamics. The sonification framework provides circular causality as a signal pathway for modeling a listener interacting with emergent behavior. The extensible sonification model adopts a data acquisition pathway to formalize functional symmetry across three subsystems: Experimental Data Source, Sound Generation, and Guided Exploration. To differentiate time criticality and dimensionality of emerging dynamics, tuning functions are applied between subsystems to maintain scale and symmetry of concurrent processes and temporal dynamics. Tuning functions accommodate sonification design strategies that yield order parameter values to render emerging patterns discoverable as well as rehearsable, to reproduce desired instances for clinical listeners. Case studies are implemented with two computational models, Chua's circuit and Swarm Chemistry social agent simulation, generating data in real-time that exhibits emergent behavior. Heuristic Listening is introduced

Interactive Sonification Exploring Emergent Behavior Applying Models for Biological Information and Listening

Directory of Open Access Journals (Sweden)

Insook Choi

2018-04-01

Full Text Available Sonification is an open-ended design task to construct sound informing a listener of data. Understanding application context is critical for shaping design requirements for data translation into sound. Sonification requires methodology to maintain reproducibility when data sources exhibit non-linear properties of self-organization and emergent behavior. This research formalizes interactive sonification in an extensible model to support reproducibility when data exhibits emergent behavior. In the absence of sonification theory, extensibility demonstrates relevant methods across case studies. The interactive sonification framework foregrounds three factors: reproducible system implementation for generating sonification; interactive mechanisms enhancing a listener's multisensory observations; and reproducible data from models that characterize emergent behavior. Supramodal attention research suggests interactive exploration with auditory feedback can generate context for recognizing irregular patterns and transient dynamics. The sonification framework provides circular causality as a signal pathway for modeling a listener interacting with emergent behavior. The extensible sonification model adopts a data acquisition pathway to formalize functional symmetry across three subsystems: Experimental Data Source, Sound Generation, and Guided Exploration. To differentiate time criticality and dimensionality of emerging dynamics, tuning functions are applied between subsystems to maintain scale and symmetry of concurrent processes and temporal dynamics. Tuning functions accommodate sonification design strategies that yield order parameter values to render emerging patterns discoverable as well as rehearsable, to reproduce desired instances for clinical listeners. Case studies are implemented with two computational models, Chua's circuit and Swarm Chemistry social agent simulation, generating data in real-time that exhibits emergent behavior. Heuristic

Experimental modeling of swirl flows in power plants

Science.gov (United States)

Shtork, S. I.; Litvinov, I. V.; Gesheva, E. S.; Tsoy, M. A.; Skripkin, S. G.

2018-03-01

The article presents an overview of the methods and approaches to experimental modeling of various thermal and hydropower units - furnaces of pulverized coal boilers and flow-through elements of hydro turbines. The presented modeling approaches based on a combination of experimentation and rapid prototyping of working parts may be useful in optimizing energy equipment to improve safety and efficiency of industrial energy systems.

Reproducibility of swollen sinuses in broilers by experimental infection with avian metapneumovirus subtypes A and B of turkey origin and their comparative pathogenesis.

Science.gov (United States)

Aung, Ye Htut; Liman, Martin; Neumann, Ulrich; Rautenschlein, Silke

2008-02-01

Swollen head syndrome (SHS) associated with avian metapneumovirus (aMPV) subtype A or subtype B in broilers and broiler breeders has been reported worldwide. Data about pathogenesis of aMPV subtypes A and B in broilers are scarce. It has been difficult to reproduce swollen sinuses in chickens with aMPV under experimental conditions. In the field, SHS in broilers is suspected to be induced by combined infections with different respiratory pathogens. The objectives of the present study were to compare the pathogenesis of subtypes A and B aMPV in commercial broilers and to investigate the reproducibility of clinical disease. In two repeat experiments, commercial broilers free of aMPV maternal antibodies were inoculated with aMPV subtypes A and B of turkey origin. The clinical signs such as depression, coughing, nasal exudates, and frothy eyes appeared at 4 days post inoculation, followed by swelling of periorbital sinuses at 5 days post inoculation. Higher numbers of broilers showed clinical signs in subtype-B-inoculated compared with subtype-A-inoculated groups. Seroconversion to aMPV was detectable from 10 to 11 days post inoculation. The appearance of serum aMPV enzyme-linked immunosorbent assay antibodies and the clearance of the aMPV genome coincided. Subtype B aMPV showed a broader tissue distribution and longer persistence than subtype A. Histopathological changes were observed in the respiratory tract tissues of aMPV-inoculated broilers, and also in paraocular glands, such as the Harderian and lachrymal glands. Overall, our study shows that representative strains of both aMPV turkey isolates induced lesions in the respiratory tract, accompanied by swelling of infraorbital sinuses, indicating the role of aMPV as a primary pathogen for broilers.

An experimental set-up for carbon isotopic analysis of atmospheric ...

Indian Academy of Sciences (India)

We present here, an experimental set-up developed for the first time in India for the ... The internal reproducibility (precision) for the δ13C ... interaction of CO2 and water, and reproduce iso- ..... enhanced emission of anthropogenic CO2, varia-.

Endometriose: modelo experimental em ratas Endometriosis: experimental model in rats

Directory of Open Access Journals (Sweden)

Eduardo Schor

1999-06-01

that the free portion of the endometrium was directed towards the lumen of the abdominal cavity. After 21 days the animals were again operated to observe the size of the implants and to remove the ectopic endometrium for microscopic analysis. Results: we macroscopically observed a significant growth of the endometrial implants. Microscopic examination showed presence of glandular epithelium and stroma similar to topic epithelium. Conclusion: this model reproduces endometriosis in the female rat allowing a better study of this pathology, mainly the action of drugs on these implants.

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.

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)

A comparative study of two statistical approaches for the analysis of real seismicity sequences and synthetic seismicity generated by a stick-slip experimental model

Science.gov (United States)

Flores-Marquez, Leticia Elsa; Ramirez Rojaz, Alejandro; Telesca, Luciano

2015-04-01

The study of two statistical approaches is analyzed for two different types of data sets, one is the seismicity generated by the subduction processes occurred at south Pacific coast of Mexico between 2005 and 2012, and the other corresponds to the synthetic seismic data generated by a stick-slip experimental model. The statistical methods used for the present study are the visibility graph in order to investigate the time dynamics of the series and the scaled probability density function in the natural time domain to investigate the critical order of the system. This comparison has the purpose to show the similarities between the dynamical behaviors of both types of data sets, from the point of view of critical systems. The observed behaviors allow us to conclude that the experimental set up globally reproduces the behavior observed in the statistical approaches used to analyses the seismicity of the subduction zone. The present study was supported by the Bilateral Project Italy-Mexico Experimental Stick-slip models of tectonic faults: innovative statistical approaches applied to synthetic seismic sequences, jointly funded by MAECI (Italy) and AMEXCID (Mexico) in the framework of the Bilateral Agreement for Scientific and Technological Cooperation PE 2014-2016.

Experimental identification of a comb-shaped chaotic region in multiple parameter spaces simulated by the Hindmarsh—Rose neuron model

Science.gov (United States)

Jia, Bing

2014-03-01

A comb-shaped chaotic region has been simulated in multiple two-dimensional parameter spaces using the Hindmarsh—Rose (HR) neuron model in many recent studies, which can interpret almost all of the previously simulated bifurcation processes with chaos in neural firing patterns. In the present paper, a comb-shaped chaotic region in a two-dimensional parameter space was reproduced, which presented different processes of period-adding bifurcations with chaos with changing one parameter and fixed the other parameter at different levels. In the biological experiments, different period-adding bifurcation scenarios with chaos by decreasing the extra-cellular calcium concentration were observed from some neural pacemakers at different levels of extra-cellular 4-aminopyridine concentration and from other pacemakers at different levels of extra-cellular caesium concentration. By using the nonlinear time series analysis method, the deterministic dynamics of the experimental chaotic firings were investigated. The period-adding bifurcations with chaos observed in the experiments resembled those simulated in the comb-shaped chaotic region using the HR model. The experimental results show that period-adding bifurcations with chaos are preserved in different two-dimensional parameter spaces, which provides evidence of the existence of the comb-shaped chaotic region and a demonstration of the simulation results in different two-dimensional parameter spaces in the HR neuron model. The results also present relationships between different firing patterns in two-dimensional parameter spaces.

Experimental identification of a comb-shaped chaotic region in multiple parameter spaces simulated by the Hindmarsh—Rose neuron model

International Nuclear Information System (INIS)

Jia Bing

2014-01-01

A comb-shaped chaotic region has been simulated in multiple two-dimensional parameter spaces using the Hindmarsh—Rose (HR) neuron model in many recent studies, which can interpret almost all of the previously simulated bifurcation processes with chaos in neural firing patterns. In the present paper, a comb-shaped chaotic region in a two-dimensional parameter space was reproduced, which presented different processes of period-adding bifurcations with chaos with changing one parameter and fixed the other parameter at different levels. In the biological experiments, different period-adding bifurcation scenarios with chaos by decreasing the extra-cellular calcium concentration were observed from some neural pacemakers at different levels of extra-cellular 4-aminopyridine concentration and from other pacemakers at different levels of extra-cellular caesium concentration. By using the nonlinear time series analysis method, the deterministic dynamics of the experimental chaotic firings were investigated. The period-adding bifurcations with chaos observed in the experiments resembled those simulated in the comb-shaped chaotic region using the HR model. The experimental results show that period-adding bifurcations with chaos are preserved in different two-dimensional parameter spaces, which provides evidence of the existence of the comb-shaped chaotic region and a demonstration of the simulation results in different two-dimensional parameter spaces in the HR neuron model. The results also present relationships between different firing patterns in two-dimensional parameter spaces

Experimental modeling of injectivity loss; Modelagem experimental da perda de injetividade

Energy Technology Data Exchange (ETDEWEB)

Bonato, Adriano Jose do Amaral Mello; Silva, Pedro Glauto de Farias e; Gomes, Vanessa Limeira Azevedo; Santos, Adriano dos [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil)

2012-07-01

Produced water reinjection, suspended particles are retained in the porous media causing formation damage and injectivity decline. In general the retention of the particles occurs near the side of injection, this fact occurs in most cases, due to the size exclusion. The modeling of filtration and the consequent formation damage is essential to the project management of water injection in oil reservoirs. Thus, mathematical models are studied to better predict the distribution of particles throughout the porous media and determine the parameters of adjustment to injectivity decline. Among these models, there is the classic model which consists in determining these parameters (coefficient of filtration and formation damage). The methodology used in modeling is given from the equations the mass conservation, kinetic particle retention, the modified Darcy equation and the function formation damage. This study aimed to improve experimental modeling, including development of software for acquisition and processing of experimental data, considering the variable number of pressure measurements along the sample. The software was developed using the Labview 2011 platform and allows the determination of relevant parameters to predict injectivity loss in water injection wells. Furthermore, based on the traditional model of filtration in porous media (including depth filtration and formation of the external plaster), the software was applied to predict injectivity loss in addition to the properties of the grout. Finally, the classical models for transporting suspensions and damage to the formation were observed. (author)

Endogenous opioid antagonism in physiological experimental pain models

DEFF Research Database (Denmark)

Werner, Mads U; Pereira, Manuel P; Andersen, Lars Peter H

2015-01-01

hyperalgesia models (6 studies), 'pain' models (25 studies), summation models (2 studies), nociceptive reflex models (3 studies) and miscellaneous models (2 studies). A consistent reversal of analgesia by a MOR-antagonist was demonstrated in 10 of the 25 ITP-studies, including stress-induced analgesia and r...... ratings, threshold assessments and somatosensory evoked potentials (SSEP), did not appear consistent in 28 out of 32 'pain' model studies. In conclusion, only in 2 experimental human pain models, i.e., stress-induced analgesia and rTMS, administration of MOR-antagonist demonstrated a consistent effect......Opioid antagonists are pharmacological tools applied as an indirect measure to detect activation of the endogenous opioid system (EOS) in experimental pain models. The objective of this systematic review was to examine the effect of mu-opioid-receptor (MOR) antagonists in placebo-controlled, double...

CFD modeling of secondary flows in fuel rod bundles

International Nuclear Information System (INIS)

Baglietto, Emilio; Ninokata, Hisashi

2004-01-01

An optimized non-linear eddy viscosity model is introduced, for calculations of detailed coolant velocity distribution in a tight lattice fuel bundle. The low Reynolds formulation has been optimized based on DNS data for channel flow. The non-linear stress-strain relationship has been modified in the coefficients to model the flow anisotropy, which causes the formation of turbulence driven secondary flows inside the bundle subchannels. Predictions of the model are first compared to experimental measurements of secondary flows in a triangularly arrayed rod bundle with p/d=1.3. Subsequently wall shear stress and velocity predictions are compared with different experimental data for a rod bundle with p/d=1.17. The model shows to be able to correctly reproduce the scale of the secondary motion, and to accurately reproduce both wall shear stress and velocity distributions inside the rod bundle subchannels. (author)

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...

EXPERIMENTAL MODEL OF THE PRIMARY MALE HYPOGONADISM

Directory of Open Access Journals (Sweden)

P. A. Kulikova

2014-01-01

Full Text Available Background: Development of the new methods of treatment of primary male hypogonadism is an urgent medical problem. Its solution requires a suitable experimental model of the disease. Aim: The creation of new experimental model of primary male hypogonadism. Materials and methods: The study was conducted on the male Wistar rats, hypogonadism was modeled by temporary ligation of the distal part of the spermatic cord. Results: It was shown that three-day ligation of the spermatic cord led to persistent disturbance of the testosterone-producing and reproductive functions. These manifestations were reversible at shorter duration of the exposure. Conclusion: The created model of primary male hypogonadism is characterized by the persistent testosterone-producing and reproductive functions disturbance, technical availability, non-toxicity to the other organs and systems. Availability of the model provides new opportunities for the development of approaches to treating diseases of the reproductive organs in men.

Understanding Leadership: An Experimental-Experiential Model

Science.gov (United States)

Hole, George T.

2014-01-01

Books about leadership are dangerous to readers who fantasize about being leaders or apply leadership ideas as if they were proven formulas. As an antidote, I offer an experimental framework in which any leadership-management model can be tested to gain experiential understanding of the model. As a result one can gain reality-based insights about…

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

Numerical modelling and experimental validation of hydrodynamics of an emulsion in an extraction column

International Nuclear Information System (INIS)

Paisant, Jean-Francois

2014-01-01

Industrial reprocessing of spent fuel is based on chemical separation processes by liquid-liquid extraction into pulsed column. The current context of sustainable development and acceptance of nuclear energy drive the industry to improve the efficiency of this process. Pulsed column efficiency is bound to the amount of available exchange surface, which depends on the geometrical parameters of the column and the operating conditions. A better design would improve the efficiency. In this context, the work presented in this manuscript revolves around physical and numerical modelling of the hydrodynamics of the emulsion coupled with the evolution of the interfacial area, as well as an experimental characterization of the quantities which describe the emulsion. The emulsion is modelled based on the work of D. LHUILLIER. It is an Eulerian approach which describes each phase as a continuous medium as well as the interface which is thought as a third phase moving continuously in the flow field. This thesis contributes to describe of the hydrodynamics of dispersed and continuous phases, in order to determine the slip velocity needed for the design. The written transport equation for interfacial area is based on the thesis of T. RANDRIAMANANTENA. The simulation of this physical model was performed using the method of finite elements (FEM) and implementation was carried out under the software CAST3M. The numerical simulation have shown their abilities to correctly reproduce the expected physical behaviour, in particular, they allow to obtain the slip velocity which is essential to the scale up. In a first experimental approach, the single phase flow has been studied in a pulsed column using particle image velocimetry (PIV), for different amplitude and frequency parameters. A method of synchronization between the recording and the pulsation cycle was used in order to achieve this study. The average behavior, for different regimes of pulsation, has been studied by this way. In

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.

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.

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

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

Experimental and theoretical evidence for the chaotic dynamics of complex structures

International Nuclear Information System (INIS)

Agop, M; Dimitriu, D G; Poll, E; Niculescu, O; Radu, V

2013-01-01

This paper presents the experimental results on the formation, dynamics and evolution towards chaos of complex space charge structures that emerge in front of a positively biased electrode immersed in a quiescent plasma. In certain experimental conditions, we managed to obtain the so-called multiple double layers (MDLs) with non-concentric configuration. Our experiments show that the interactions between each MDL's constituent entities are held responsible for the complex dynamics and eventually for its transition to chaos through cascades of spatio-temporal sub-harmonic bifurcations. Further, we build a theoretical model based on the fractal approximation (scale relativity theory) in order to reproduce the experimental results (plasma self-structuring and scenario of evolution to chaos). Comparing the experimental results with the theoretical ones, we observe a good correlation between them. (paper)

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.

Models of experimental saccular aneurysms of carotid arteries in canine

International Nuclear Information System (INIS)

Zhang Haixia; Cheng Yingsheng; Li Minghua

2006-01-01

Objective: To study the availability by making experimental saccular aneurysm models of carotid arteries in canine similar to human intracranial aneurysms. Methods: Twenty healthy canines with experimental saccular side-wall aneurysms of carotid arteries were created successfully by surgery. Results: Forty experimental saccular side-wall aneurysms of carotid arteries were created successfully with 36 aneurysms and parent arteries maintaining patency with each other and four spontaneously occluded confirmed by angiography. Model successful rate reached 90%. Conclusions: Experimental saccular side-wall aneurysms of carotid arteries in canines were one of best models created for simulating human intracranial aneurysms. (authors)

Experimental and simulated beam-foil decay curves for some transitions in Zn II

International Nuclear Information System (INIS)

Hultberg, S.; Liljeby, L.; Mannervik, S.; Veje, E.; Lindgaard, A.

1980-01-01

Experimental beam-foil decay curves for the 4s-4p, 4p-4d, 4d-4f, and the 4p-5s transitions in Zn II are compared to decay curves synthesized from transition probabilities calculated in the numerical Coulomb approximation and either measured initial level populations or population models. Good agreement exists between experimental curves and those based on the measured initial level populations for the 5s, 4d, and 4f levels while certain deviations are noted for the 4p term. None of the applied population models reproduce all experimental curves satisfyingly well. In addition, lifetimes are determined experimentally for 7 terms in Zn II, and good agreement with the numerical Coulomb approximation lifetimes is generally found except for some p terms. Beam-foil excitation-mechanism results for zinc are presented and compared to previous results from light projectiles. (Auth.)

A sEMG model with experimentally based simulation parameters.

Science.gov (United States)

Wheeler, Katherine A; Shimada, Hiroshima; Kumar, Dinesh K; Arjunan, Sridhar P

2010-01-01

A differential, time-invariant, surface electromyogram (sEMG) model has been implemented. While it is based on existing EMG models, the novelty of this implementation is that it assigns more accurate distributions of variables to create realistic motor unit (MU) characteristics. Variables such as muscle fibre conduction velocity, jitter (the change in the interpulse interval between subsequent action potential firings) and motor unit size have been considered to follow normal distributions about an experimentally obtained mean. In addition, motor unit firing frequencies have been considered to have non-linear and type based distributions that are in accordance with experimental results. Motor unit recruitment thresholds have been considered to be related to the MU type. The model has been used to simulate single channel differential sEMG signals from voluntary, isometric contractions of the biceps brachii muscle. The model has been experimentally verified by conducting experiments on three subjects. Comparison between simulated signals and experimental recordings shows that the Root Mean Square (RMS) increases linearly with force in both cases. The simulated signals also show similar values and rates of change of RMS to the experimental signals.

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

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

NARCIS (Netherlands)

Bachmann, H.; Starrenburg, M.J.C.; Molenaar, D.; Kleerebezem, M.; Hylckama Vlieg, van J.E.T.

2012-01-01

Experimental evolution is a powerful approach to unravel how selective forces shape microbial genotypes and phenotypes. To this date, the available examples focus on the adaptation to conditions specific to the laboratory. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution.

NARCIS (Netherlands)

Bachmann, H.; Starrenburg, M.J.; Molenaar, D.; Kleerebezem, M.; van Hylckama Vlieg, J.E.T.

2012-01-01

Experimental evolution is a powerful approach to unravel how selective forces shape microbial genotypes and phenotypes. To this date, the available examples focus on the adaptation to conditions specific to the laboratory. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and

A rolling constraint reproduces ground reaction forces and moments in dynamic simulations of walking, running, and crouch gait.

Science.gov (United States)

Hamner, Samuel R; Seth, Ajay; Steele, Katherine M; Delp, Scott L

2013-06-21

Recent advances in computational technology have dramatically increased the use of muscle-driven simulation to study accelerations produced by muscles during gait. Accelerations computed from muscle-driven simulations are sensitive to the model used to represent contact between the foot and ground. A foot-ground contact model must be able to calculate ground reaction forces and moments that are consistent with experimentally measured ground reaction forces and moments. We show here that a rolling constraint can model foot-ground contact and reproduce measured ground reaction forces and moments in an induced acceleration analysis of muscle-driven simulations of walking, running, and crouch gait. We also illustrate that a point constraint and a weld constraint used to model foot-ground contact in previous studies produce inaccurate reaction moments and lead to contradictory interpretations of muscle function. To enable others to use and test these different constraint types (i.e., rolling, point, and weld constraints) we have included them as part of an induced acceleration analysis in OpenSim, a freely-available biomechanics simulation package. Copyright © 2013 Elsevier Ltd. All rights reserved.

PSYCHOLOGY. Estimating the reproducibility of psychological science.

Science.gov (United States)

2015-08-28

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. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams. Copyright © 2015, American Association for the Advancement of Science.

Adjustment model of thermoluminescence experimental data

International Nuclear Information System (INIS)

Moreno y Moreno, A.; Moreno B, A.

2002-01-01

This model adjusts the experimental results for thermoluminescence according to the equation: I (T) = I (a i * exp (-1/b i * (T-C i )) where: a i , b i , c i are the i-Th peak adjusted to a gaussian curve. The adjustments of the curve can be operated manual or analytically using the macro function and the solver.xla complement installed previously in the computational system. In this work it is shown: 1. The information of experimental data from a LiF curve obtained from the Physics Institute of UNAM which the data adjustment model is operated in the macro type. 2. A LiF curve of four peaks obtained from Harshaw information simulated in Microsoft Excel, discussed in previous works, as a reference not in macro. (Author)

Development and characterization of an experimental model of diet-induced metabolic syndrome in rabbit.

Directory of Open Access Journals (Sweden)

Oscar Julián Arias-Mutis

Full Text Available Metabolic syndrome (MetS has become one of the main concerns for public health because of its link to cardiovascular disease. Murine models have been used to study the effect of MetS on the cardiovascular system, but they have limitations for studying cardiac electrophysiology. In contrast, the rabbit cardiac electrophysiology is similar to human, but a detailed characterization of the different components of MetS in this animal is still needed. Our objective was to develop and characterize a diet-induced experimental model of MetS that allows the study of cardiovascular remodeling and arrhythmogenesis. Male NZW rabbits were assigned to control (n = 15 or MetS group (n = 16, fed during 28 weeks with high-fat, high-sucrose diet. We measured weight, morphological characteristics, blood pressure, glycaemia, standard plasma biochemistry and the metabolomic profile at weeks 14 and 28. Liver histological changes were evaluated using hematoxylin-eosin staining. A mixed model ANOVA or unpaired t-test were used for statistical analysis (P<0.05. Weight, abdominal contour, body mass index, systolic, diastolic and mean arterial pressure increased in the MetS group at weeks 14 and 28. Glucose, triglycerides, LDL, GOT-AST, GOT/GPT, bilirubin and bile acid increased, whereas HDL decreased in the MetS group at weeks 14 and 28. We found a 40% increase in hepatocyte area and lipid vacuoles infiltration in the liver from MetS rabbits. Metabolomic analysis revealed differences in metabolites related to fatty acids, energetic metabolism and microbiota, compounds linked with cardiovascular disease. Administration of high-fat and high-sucrose diet during 28 weeks induced obesity, glucose intolerance, hypertension, non-alcoholic hepatic steatosis and metabolic alterations, thus reproducing the main clinical manifestations of the metabolic syndrome in humans. This experimental model should provide a valuable tool for studies into the mechanisms of cardiovascular

Evaluated experimental database on critical heat flux in WWER FA models

International Nuclear Information System (INIS)

Artamonov, S.; Sergeev, V.; Volkov, S.

2015-01-01

The paper presents the description of the evaluated experimental database on critical heat flux in WWER FA models of new designs. This database was developed on the basis of the experimental data obtained in the years of 2009-2012. In the course of its development, the database was reviewed in terms of completeness of the information about the experiments and its compliance with the requirements of Rostekhnadzor regulatory documents. The description of the experimental FA model characteristics and experimental conditions was specified. Besides, the experimental data were statistically processed with the aim to reject incorrect ones and the sets of experimental data on critical heat fluxes (CHF) were compared for different FA models. As a result, for the fi rst time, the evaluated database on CHF in FA models of new designs was developed, that was complemented with analysis functions, and its main purpose is to be used in the process of development, verification and upgrading of calculation techniques. The developed database incorporates the data of 4183 experimental conditions obtained in 53 WWER FA models of various designs. Keywords: WWER reactor, fuel assembly, CHF, evaluated experimental data, database, statistical analysis. (author)

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)

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.

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.

Hopping models for ion conduction in noncrystals

DEFF Research Database (Denmark)

Dyre, Jeppe; Schrøder, Thomas

2007-01-01

semiconductors). These universalities are subject of much current interest, for instance interpreted in the context of simple hopping models. In the present paper we first discuss the temperature dependence of the dc conductivity in hopping models and the importance of the percolation phenomenon. Next......, the experimental (quasi)universality of the ac conductivity is discussed. It is shown that hopping models are able to reproduce the experimental finding that the response obeys time-temperature superposition, while at the same time a broad range of activation energies is involved in the conduction process. Again...

Modeling the self-assembly of clathrin coats

NARCIS (Netherlands)

Giani, Matteo

2017-01-01

The assembly of clathrin coats in the presence of adaptor proteins was studied through computer simulations using coarse-grained models and through statistical mechanics. Adopting a reductionist approach based on recent experimental results, we aimed at reproducing and studying the minimal

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

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.

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

Serpentinization reaction pathways: implications for modeling approach

Energy Technology Data Exchange (ETDEWEB)

Janecky, D.R.

1986-01-01

Experimental seawater-peridotite reaction pathways to form serpentinites at 300/sup 0/C, 500 bars, can be accurately modeled using the EQ3/6 codes in conjunction with thermodynamic and kinetic data from the literature and unpublished compilations. These models provide both confirmation of experimental interpretations and more detailed insight into hydrothermal reaction processes within the oceanic crust. The accuracy of these models depends on careful evaluation of the aqueous speciation model, use of mineral compositions that closely reproduce compositions in the experiments, and definition of realistic reactive components in terms of composition, thermodynamic data, and reaction rates.

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

The experimental and shell model approach to 100Sn

International Nuclear Information System (INIS)

Grawe, H.; Maier, K.H.; Fitzgerald, J.B.; Heese, J.; Spohr, K.; Schubart, R.; Gorska, M.; Rejmund, M.

1995-01-01

The present status of experimental approach to 100 Sn and its shell model structure is given. New developments in experimental techniques, such as low background isomer spectroscopy and charged particle detection in 4π are surveyed. Based on recent experimental data shell model calculations are used to predict the structure of the single- and two-nucleon neighbours of 100 Sn. The results are compared to the systematic of Coulomb energies and spin-orbit splitting and discussed with respect to future experiments. (author). 51 refs, 11 figs, 1 tab

Mutant mice: experimental organisms as materialised models in biomedicine.

Science.gov (United States)

Huber, Lara; Keuck, Lara K

2013-09-01

Animal models have received particular attention as key examples of material models. In this paper, we argue that the specificities of establishing animal models-acknowledging their status as living beings and as epistemological tools-necessitate a more complex account of animal models as materialised models. This becomes particularly evident in animal-based models of diseases that only occur in humans: in these cases, the representational relation between animal model and human patient needs to be generated and validated. The first part of this paper presents an account of how disease-specific animal models are established by drawing on the example of transgenic mice models for Alzheimer's disease. We will introduce an account of validation that involves a three-fold process including (1) from human being to experimental organism; (2) from experimental organism to animal model; and (3) from animal model to human patient. This process draws upon clinical relevance as much as scientific practices and results in disease-specific, yet incomplete, animal models. The second part of this paper argues that the incompleteness of models can be described in terms of multi-level abstractions. We qualify this notion by pointing to different experimental techniques and targets of modelling, which give rise to a plurality of models for a specific disease. Copyright © 2013 Elsevier Ltd. All rights reserved.

Improving the seismic small-scale modelling by comparison with numerical methods

Science.gov (United States)

Pageot, Damien; Leparoux, Donatienne; Le Feuvre, Mathieu; Durand, Olivier; Côte, Philippe; Capdeville, Yann

2017-10-01

The potential of experimental seismic modelling at reduced scale provides an intermediate step between numerical tests and geophysical campaigns on field sites. Recent technologies such as laser interferometers offer the opportunity to get data without any coupling effects. This kind of device is used in the Mesures Ultrasonores Sans Contact (MUSC) measurement bench for which an automated support system makes possible to generate multisource and multireceivers seismic data at laboratory scale. Experimental seismic modelling would become a great tool providing a value-added stage in the imaging process validation if (1) the experimental measurement chain is perfectly mastered, and thus if the experimental data are perfectly reproducible with a numerical tool, as well as if (2) the effective source is reproducible along the measurement setup. These aspects for a quantitative validation concerning devices with piezoelectrical sources and a laser interferometer have not been yet quantitatively studied in published studies. Thus, as a new stage for the experimental modelling approach, these two key issues are tackled in the proposed paper in order to precisely define the quality of the experimental small-scale data provided by the bench MUSC, which are available in the scientific community. These two steps of quantitative validation are dealt apart any imaging techniques in order to offer the opportunity to geophysicists who want to use such data (delivered as free data) of precisely knowing their quality before testing any imaging technique. First, in order to overcome the 2-D-3-D correction usually done in seismic processing when comparing 2-D numerical data with 3-D experimental measurement, we quantitatively refined the comparison between numerical and experimental data by generating accurate experimental line sources, avoiding the necessity of geometrical spreading correction for 3-D point-source data. The comparison with 2-D and 3-D numerical modelling is based on

Experimental models of hepatotoxicity related to acute liver failure

Energy Technology Data Exchange (ETDEWEB)

Maes, Michaël [Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels (Belgium); Vinken, Mathieu, E-mail: mvinken@vub.ac.be [Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Brussels (Belgium); Jaeschke, Hartmut [Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City (United States)

2016-01-01

Acute liver failure can be the consequence of various etiologies, with most cases arising from drug-induced hepatotoxicity in Western countries. Despite advances in this field, the management of acute liver failure continues to be one of the most challenging problems in clinical medicine. The availability of adequate experimental models is of crucial importance to provide a better understanding of this condition and to allow identification of novel drug targets, testing the efficacy of new therapeutic interventions and acting as models for assessing mechanisms of toxicity. Experimental models of hepatotoxicity related to acute liver failure rely on surgical procedures, chemical exposure or viral infection. Each of these models has a number of strengths and weaknesses. This paper specifically reviews commonly used chemical in vivo and in vitro models of hepatotoxicity associated with acute liver failure. - Highlights: • The murine APAP model is very close to what is observed in patients. • The Gal/ET model is useful to study TNFα-mediated apoptotic signaling mechanisms. • Fas receptor activation is an effective model of apoptosis and secondary necrosis. • The ConA model is a relevant model of auto-immune hepatitis and viral hepatitis. • Multiple time point evaluation needed in experimental models of acute liver injury.

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

Development of experimental alloxan model of diabetes mellitus

Directory of Open Access Journals (Sweden)

V.V. Semenko

2017-05-01

Full Text Available Background. One of the main causes that lead to the disability of diabetic patients is diabetic retinopathy (DR. The relevance of the problem of DR necessitates the development of optimal experimental models on experimental animals to find effective ways of correcting this pathology. The purpose of our work was to develop an experimental alloxan model of type 1 diabetes mellitus (DM for the study of DR, which would not result in the lethal outcome of experimental animals under the action of alloxan; histological examination of changes in the tissues of the eyeball in the reproduction of the DM model for the selection of new effective methods for the metabolic treatment of DR in the early stages. Materials and methods. The experiment was carried out on white outbred Wistar rats weighing 180–200 g. The first group consisted of 20 animals that were not subjected to any influence, served as a control; second group — 30 animals, in which DM was modeled by administration of alloxan and fructose. Results. When modeling DR, vessel changes in the form of wall fibrosis, edema of the endothelium and vasospasm were found. There was also a decrease in the amount of pigment granules, dystrophic changes in the cells of the ganglionic layer and a layer of retinal rods and cones, which coincides with the descriptions of damage to the coats of the eyeball in patients with DM. Conclusions. In our studies, we have calculated the optimal dose of alloxan administration, which does not lead to the death of rats (the lethality of rats was absent and is an effective model not only of DM in general, but also of DR.

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

Experimental Evidence for LENR in a Polarized Pd/D Lattice

Science.gov (United States)

Szpak, S.

2005-03-01

Experimental evidence in support of claims that excess enthalpy production in a polarized Pd/D lattice is of a nuclear origin is questioned on various grounds, eg marginal intensity and difficulty in reproducing. Here, evidence is presented that is 100% reproducible and of sufficient intensity to be well outside of experimental errors. In addition to the thermal behavior, the nuclear manifestations include: X-ray emission; tritium production; and, when an operating cell is placed in an external electric field, fusion to create heavier metals such as Ca, Al, Mg, and Zn.

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

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....

Structure of Li, Be And B isotopes studied with quantum molecular dynamic model

International Nuclear Information System (INIS)

Abdel-Hafiez, A.; Saleh, Z.A.

2000-01-01

Quantum molecular dynamics (QMD) is applied to study the ground state properties of Li, Be and B isotopes. The model Hamiltonian includes both two-and three-body density dependent interactions, a Coulomb term, and a momentum dependent Pauli potential. With parameters which guarantee the infinite nuclear matter properties, the QMD model can only reproduce the binding energies for Be and B isotopes. The experimental root mean square radii of the Li, Be and B isotopes are not sufficiently reproduced by these parameters. It is shown, however, that the binding energies and root mean square radii of these isotopes can simultaneously be reproduced in the lower density limit of the potential parameters

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.

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

Experimental data and dose-response models

International Nuclear Information System (INIS)

Ullrich, R.L.

1985-01-01

Dose-response relationships for radiation carcinogenesis have been of interest to biologists, modelers, and statisticians for many years. Despite his interest there are few instances in which there are sufficient experimental data to allow the fitting of various dose-response models. In those experimental systems for which data are available the dose-response curves for tumor induction for the various systems cannot be described by a single model. Dose-response models which have been observed following acute exposures to gamma rays include threshold, quadratic, and linear models. Data on sex, age, and environmental influences of dose suggest a strong role of host factors on the dose response. With decreasing dose rate the effectiveness of gamma ray irradiation tends to decrease in essentially every instance. In those cases in which the high dose rate dose response could be described by a quadratic model, the effect of dose rate is consistent with predictions based on radiation effects on the induction of initial events. Whether the underlying reasons for the observed dose-rate effect is a result of effects on the induction of initial events or is due to effects on the subsequent steps in the carcinogenic process is unknown. Information on the dose response for tumor induction for high LET (linear energy transfer) radiations such as neutrons is even more limited. The observed dose and dose rate data for tumor induction following neutron exposure are complex and do not appear to be consistent with predictions based on models for the induction of initial events

Experimental approach and micro-mechanical modeling of the mechanical behavior of irradiated zirconium alloys

International Nuclear Information System (INIS)

Onimus, F.

2003-12-01

Zirconium alloys cladding tubes containing nuclear fuel of the Pressurized Water Reactors constitute the first safety barrier against the dissemination of radioactive elements. Thus, it is essential to predict the mechanical behavior of the material in-reactor conditions. This study aims, on the one hand, to identify and characterize the mechanisms of the plastic deformation of irradiated zirconium alloys and, on the other hand, to propose a micro-mechanical modeling based on these mechanisms. The experimental analysis shows that, for the irradiated material, the plastic deformation occurs by dislocation channeling. For transverse tensile test and internal pressure test this channeling occurs in the basal planes. However, for axial tensile test, the study revealed that the plastic deformation also occurs by channeling but in the prismatic and pyramidal planes. In addition, the study of the macroscopic mechanical behavior, compared to the deformation mechanisms observed by TEM, suggested that the internal stress is higher in the case of irradiated material than in the case of non-irradiated material, because of the very heterogeneous character of the plastic deformation. This analysis led to a coherent interpretation of the mechanical behavior of irradiated materials, in terms of deformation mechanisms. The mechanical behavior of irradiated materials was finally modeled by applying homogenization methods for heterogeneous materials. This model is able to reproduce adequately the mechanical behavior of the irradiated material, in agreement with the TEM observations. (author)

Robust Bayesian Experimental Design for Conceptual Model Discrimination

Science.gov (United States)

Pham, H. V.; Tsai, F. T. C.

2015-12-01

A robust Bayesian optimal experimental design under uncertainty is presented to provide firm information for model discrimination, given the least number of pumping wells and observation wells. Firm information is the maximum information of a system can be guaranteed from an experimental design. The design is based on the Box-Hill expected entropy decrease (EED) before and after the experiment design and the Bayesian model averaging (BMA) framework. A max-min programming is introduced to choose the robust design that maximizes the minimal Box-Hill EED subject to that the highest expected posterior model probability satisfies a desired probability threshold. The EED is calculated by the Gauss-Hermite quadrature. The BMA method is used to predict future observations and to quantify future observation uncertainty arising from conceptual and parametric uncertainties in calculating EED. Monte Carlo approach is adopted to quantify the uncertainty in the posterior model probabilities. The optimal experimental design is tested by a synthetic 5-layer anisotropic confined aquifer. Nine conceptual groundwater models are constructed due to uncertain geological architecture and boundary condition. High-performance computing is used to enumerate all possible design solutions in order to identify the most plausible groundwater model. Results highlight the impacts of scedasticity in future observation data as well as uncertainty sources on potential pumping and observation locations.

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.

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.

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...

Preclinical models of shock and sepsis: what can they tell us?

NARCIS (Netherlands)

Marshall, John C.; Deitch, Edwin; Moldawer, Lyle L.; Opal, Steven; Redl, Heinz; van der Poll, Tom

2005-01-01

The goal of translational research is to transform biologic knowledge into new treatments for human disease. Although preclinical models replicate some of the features of the disease process modeled, they invariably fail to reproduce the complexity of human illness, and by their very experimental

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

International Nuclear Information System (INIS)

Gierlotka, Wojciech; Jendrzejczyk-Handzlik, Dominika; Fitzner, Krzysztof; Handzlik, Piotr

2015-01-01

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

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.

IVIM: modeling, experimental validation and application to animal models

International Nuclear Information System (INIS)

Fournet, Gabrielle

2016-01-01

This PhD thesis is centered on the study of the IVIM ('Intravoxel Incoherent Motion') MRI sequence. This sequence allows for the study of the blood microvasculature such as the capillaries, arterioles and venules. To be sensitive only to moving groups of spins, diffusion gradients are added before and after the 180 degrees pulse of a spin echo (SE) sequence. The signal component corresponding to spins diffusing in the tissue can be separated from the one related to spins travelling in the blood vessels which is called the IVIM signal. These two components are weighted by f IVIM which represents the volume fraction of blood inside the tissue. The IVIM signal is usually modelled by a mono-exponential (ME) function and characterized by a pseudo-diffusion coefficient, D*. We propose instead a bi-exponential IVIM model consisting of a slow pool, characterized by F slow and D* slow corresponding to the capillaries as in the ME model, and a fast pool, characterized by F fast and D* fast, related to larger vessels such as medium-size arterioles and venules. This model was validated experimentally and more information was retrieved by comparing the experimental signals to a dictionary of simulated IVIM signals. The influence of the pulse sequence, the repetition time and the diffusion encoding time was also studied. Finally, the IVIM sequence was applied to the study of an animal model of Alzheimer's disease. (author) [fr

Multiphysics modelling and experimental validation of high concentration photovoltaic modules

International Nuclear Information System (INIS)

Theristis, Marios; Fernández, Eduardo F.; Sumner, Mike; O'Donovan, Tadhg S.

2017-01-01

Highlights: • A multiphysics modelling approach for concentrating photovoltaics was developed. • An experimental campaign was conducted to validate the models. • The experimental results were in good agreement with the models. • The multiphysics modelling allows the concentrator’s optimisation. - Abstract: High concentration photovoltaics, equipped with high efficiency multijunction solar cells, have great potential in achieving cost-effective and clean electricity generation at utility scale. Such systems are more complex compared to conventional photovoltaics because of the multiphysics effect that is present. Modelling the power output of such systems is therefore crucial for their further market penetration. Following this line, a multiphysics modelling procedure for high concentration photovoltaics is presented in this work. It combines an open source spectral model, a single diode electrical model and a three-dimensional finite element thermal model. In order to validate the models and the multiphysics modelling procedure against actual data, an outdoor experimental campaign was conducted in Albuquerque, New Mexico using a high concentration photovoltaic monomodule that is thoroughly described in terms of its geometry and materials. The experimental results were in good agreement (within 2.7%) with the predicted maximum power point. This multiphysics approach is relatively more complex when compared to empirical models, but besides the overall performance prediction it can also provide better understanding of the physics involved in the conversion of solar irradiance into electricity. It can therefore be used for the design and optimisation of high concentration photovoltaic modules.

Repeatability and reproducibility of ribotyping and its computer interpretation.

Science.gov (United States)

Lefresne, Gwénola; Latrille, Eric; Irlinger, Françoise; Grimont, Patrick A D

2004-04-01

Many molecular typing methods are difficult to interpret because their repeatability (within-laboratory variance) and reproducibility (between-laboratory variance) have not been thoroughly studied. In the present work, ribotyping of coryneform bacteria was the basis of a study involving within-gel and between-gel repeatability and between-laboratory reproducibility (two laboratories involved). The effect of different technical protocols, different algorithms, and different software for fragment size determination was studied. Analysis of variance (ANOVA) showed, within a laboratory, that there was no significant added variance between gels. However, between-laboratory variance was significantly higher than within-laboratory variance. This may be due to the use of different protocols. An experimental function was calculated to transform the data and make them compatible (i.e., erase the between-laboratory variance). The use of different interpolation algorithms (spline, Schaffer and Sederoff) was a significant source of variation in one laboratory only. The use of either Taxotron (Institut Pasteur) or GelCompar (Applied Maths) was not a significant source of added variation when the same algorithm (spline) was used. However, the use of Bio-Gene (Vilber Lourmat) dramatically increased the error (within laboratory, within gel) in one laboratory, while decreasing the error in the other laboratory; this might be due to automatic normalization attempts. These results were taken into account for building a database and performing automatic pattern identification using Taxotron. Conversion of the data considerably improved the identification of patterns irrespective of the laboratory in which the data were obtained.

Integrated experimental and modeling assessment of potential effects of gas leakages on groundwater composition

Science.gov (United States)

Berta, Marton; Dethlefsen, Frank; Ebert, Markus; Schäfer, Dirk

2017-04-01

pyrite content, oxygen dissolution kinetics, groundwater composition including the carbonate buffer, and diffusive and advective transport parameters. The results of site-scale multiphase reactive transport modeling revealed the expected spatial distribution of redox-sensitive species such as oxygen, pyrite, and sulfate in an aquifer following a leakage. The changes in concentration of sulfate, dissolved oxygen, and H+ observed in the lab-scale experiments were qualitatively reproduced by the models applying the same boundary conditions on a site-scale. This integrated study acknowledged that the combination of experiments and models is a powerful tool to prognose the geochemical consequences of gas leakage on site scale. However, it is yet unknown how the passivation would be effected if the carbonate buffer depleted on the long term and under what circumstances a transition from the passivating pyrite oxidation process to the non-passivating process observed for instance in acid mine drainage setups occurs. These restrictions mark the limits of validity of our experimental and modeling concept. This conclusion suggests the feasibility of the presented integrated approach also when evaluating comparable scenarios on methane and hydrogen storage based on experimental results gathered similarly[2]. [1]Berta et al. Environ Earth Sci (2016) 75:1175, DOI 10.1007/s12665-016-5985-7. [2]Berta et al. First Break (2015) 33,93-95, ISSN 1365-2397. This work is part of the ANGUS+ project funded by the BMBF-FK03EK3022.

Evaluation of a musculoskeletal model with prosthetic knee through six experimental gait trials.

Science.gov (United States)

Kia, Mohammad; Stylianou, Antonis P; Guess, Trent M

2014-03-01

Knowledge of the forces acting on musculoskeletal joint tissues during movement benefits tissue engineering, artificial joint replacement, and our understanding of ligament and cartilage injury. Computational models can be used to predict these internal forces, but musculoskeletal models that simultaneously calculate muscle force and the resulting loading on joint structures are rare. This study used publicly available gait, skeletal geometry, and instrumented prosthetic knee loading data [1] to evaluate muscle driven forward dynamics simulations of walking. Inputs to the simulation were measured kinematics and outputs included muscle, ground reaction, ligament, and joint contact forces. A full body musculoskeletal model with subject specific lower extremity geometries was developed in the multibody framework. A compliant contact was defined between the prosthetic femoral component and tibia insert geometries. Ligament structures were modeled with a nonlinear force-strain relationship. The model included 45 muscles on the right lower leg. During forward dynamics simulations a feedback control scheme calculated muscle forces using the error signal between the current muscle lengths and the lengths recorded during inverse kinematics simulations. Predicted tibio-femoral contact force, ground reaction forces, and muscle forces were compared to experimental measurements for six different gait trials using three different gait types (normal, trunk sway, and medial thrust). The mean average deviation (MAD) and root mean square deviation (RMSD) over one gait cycle are reported. The muscle driven forward dynamics simulations were computationally efficient and consistently reproduced the inverse kinematics motion. The forward simulations also predicted total knee contact forces (166Nphysiological motor control patterns during gait. Consequently, the simulations did not accurately predict medial/lateral tibio-femoral force distribution and muscle activation timing. Copyright

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.

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

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.

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.

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.

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.

[RESEARCH PROGRESS OF EXPERIMENTAL ANIMAL MODELS OF AVASCULAR NECROSIS OF FEMORAL HEAD].

Science.gov (United States)

Yu, Kaifu; Tan, Hongbo; Xu, Yongqing

2015-12-01

To summarize the current researches and progress on experimental animal models of avascular necrosis of the femoral head. Domestic and internation literature concerning experimental animal models of avascular necrosis of the femoral head was reviewed and analyzed. The methods to prepare the experimental animal models of avascular necrosis of the femoral head can be mainly concluded as traumatic methods (including surgical, physical, and chemical insult), and non-traumatic methods (including steroid, lipopolysaccharide, steroid combined with lipopolysaccharide, steroid combined with horse serum, etc). Each method has both merits and demerits, yet no ideal methods have been developed. There are many methods to prepare the experimental animal models of avascular necrosis of the femoral head, but proper model should be selected based on the aim of research. The establishment of ideal experimental animal models needs further research in future.

Experimental In Vivo Models of Candidiasis

Directory of Open Access Journals (Sweden)

Esther Segal

2018-02-01

Full Text Available Candidiasis is a multifaceted fungal disease including mucosal-cutaneous, visceral, and disseminated infections caused by yeast species of the genus Candida. Candida infections are among the most common human mycoses. Candida species are the third to fourth most common isolates from bloodstream infections in neutropenic or immunocompromised hospitalized patients. The mucosal-cutaneous forms—particularly vaginal infections—have a high prevalence. Vaginitis caused by Candida species is the second most common vaginal infection. Hence, candidiasis is a major subject for research, including experimental in vivo models to study pathogenesis, prevention, or therapy of the disease. The following review article will focus on various experimental in vivo models in different laboratory animals, such as mammals (mice, rats, rabbits, the fruit fly–Drosophila melanogaster, the larvae of the moth Galleria mellonella, or the free-living nematode Caenorhabditis elegans. The review will describe the induction of the different clinical forms of candidiasis in the various models and the validity of such models in mimicking the human clinical situations. The use of such models for the assessment of antifungal drugs, evaluation of potential vaccines to protect before candidiasis, exploration of Candida virulence factors, and comparison of pathogenicity of different Candida species will be included in the review. All of the above will be reported as based on published studies of numerous investigators as well as on the research of the author and his group.

Experimental and analytical study on cesium iodide behavior in piping in wave experiment

Energy Technology Data Exchange (ETDEWEB)

Hidaka, A; Igarashi, M; Hashimoto, K; Sugimoto, J [Japan Atomic Energy Research Inst., Dep. of Reactor Safety Research, Tokai-mura (Japan); Yoshino, T [Toshiba Advanced System Corp., Isago Kawasaki-ku (Japan)

1996-12-01

The WAVE (Wide range Aerosol model VErification) experiments have been performed at JAERI to investigate cesium iodide (CsI) deposition onto an inner surface of piping wall under typical severe accident conditions. The test facility consists of a dish containing CsI powder, electrical heaters and a straight pipe of 1.5 m in length with diameter of 0.042m. Nitrogen gas and superheated steam were injected into the pipe to carry the vaporized CsI and to simulate the thermohydraulic condition for the PWR hot-leg inlet. Analyses of the experiments have been conducted with a three-dimensional thermohydraulic code, SPRAC and the radionuclide behavior analysis codes, ART and VICTORIA. A clear difference was found in the deposition behavior between nitrogen and steam conditions as carrier gases. For nitrogen gas, the analyses well reproduced the experimental results by closely coupling the CsI behavior and the detailed thermohydraulic analyses. For steam carrier gas, on the contrary, the experimental results could not be well reproduced without the use of larger aerosol size. Since the observed enhancement of aerosol size in superheated steam cannot be explained by existing models, it is necessary to further investigate this mechanisms by experiment and analysis. (author) 34 figs., 23 refs.

Experimental comparison of models for ultrafast impact ionization is silicon

DEFF Research Database (Denmark)

Tarekegne, Abebe Tilahun; Iwaszczuk, Krzysztof; Jepsen, Peter Uhd

2016-01-01

We compare experimentally the exponential and quadratic (Keldysh formula) impact ionization models using THz induced impact ionization in silicon. We demonstrate that the exponential model offers the best description of impact ionization process for ultrashort electric filed pulses.......We compare experimentally the exponential and quadratic (Keldysh formula) impact ionization models using THz induced impact ionization in silicon. We demonstrate that the exponential model offers the best description of impact ionization process for ultrashort electric filed pulses....

Modelling and experimental studies on the transfer of radionuclides to fruit

International Nuclear Information System (INIS)

Carini, F.; Atkinson, C.J.; Collins, C.; Coughtrey, P.J.; Eged, K.; Fulker, M.; Green, N.; Kinnersley, R.; Linkov, I.; Mitchell, N.G.; Mourlon, C.; Ould-Dada, Z.; Quinault, J.M.; Robles, B.; Stewart, A.; Sweeck, L.; Venter, A.

2005-01-01

Although fruit is an important component of the diet, the extent to which it contributes to radiological exposure remains unclear, partially as a consequence of uncertainties in models and data used to assess transfer of radionuclides in the food chain. A Fruits Working Group operated as part of the IAEA BIOMASS (BIOsphere Modelling and ASSessment) programme from 1997 to 2000, with the aim of improving the robustness of the models that are used for radiological assessment. The Group completed a number of modelling and experimental activities including: (i) a review of experimental, field and modelling information on the transfer of radionuclides to fruit; (ii) discussion of recently completed or ongoing experimental studies; (iii) development of a database on the transfer of radionuclides to fruit; (iv) development of a conceptual model for fruit and (v) two model intercomparison studies and a model validation study. The Group achieved significant advances in understanding the processes involved in transfer of radionuclides to fruit. The work demonstrated that further experimental and modelling studies are required to ensure that the current generation of models can be applied to a wide range of scenarios

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...

Models for Experimental High Density Housing

Science.gov (United States)

Bradecki, Tomasz; Swoboda, Julia; Nowak, Katarzyna; Dziechciarz, Klaudia

2017-10-01

The article presents the effects of research on models of high density housing. The authors present urban projects for experimental high density housing estates. The design was based on research performed on 38 examples of similar housing in Poland that have been built after 2003. Some of the case studies show extreme density and that inspired the researchers to test individual virtual solutions that would answer the question: How far can we push the limits? The experimental housing projects show strengths and weaknesses of design driven only by such indexes as FAR (floor attenuation ratio - housing density) and DPH (dwellings per hectare). Although such projects are implemented, the authors believe that there are reasons for limits since high index values may be in contradiction to the optimum character of housing environment. Virtual models on virtual plots presented by the authors were oriented toward maximising the DPH index and DAI (dwellings area index) which is very often the main driver for developers. The authors also raise the question of sustainability of such solutions. The research was carried out in the URBAN model research group (Gliwice, Poland) that consists of academic researchers and architecture students. The models reflect architectural and urban regulations that are valid in Poland. Conclusions might be helpful for urban planners, urban designers, developers, architects and architecture students.

[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.

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

On the use of the Prandtl mixing length model in the cutting torch modeling

Energy Technology Data Exchange (ETDEWEB)

Mancinelli, B [Grupo de Descargas Electricas, Departamento Ing. Electromecanica, Universidad Tecnologica Nacional, Regional Venado Tuerto, Laprida 651, Venado Tuerto (2600), Santa Fe (Argentina); Minotti, F O; Kelly, H, E-mail: bmancinelli@arnet.com.ar [Instituto de Fisica del Plasma (CONICET), Departamento de Fisica, Facultad de Ciencias Exactas y Naturales (UBA) Ciudad Universitaria Pab. I, 1428 Buenos Aires (Argentina)

2011-05-01

The Prandtl mixing length model has been used to take into account the turbulent effects in a 30 A high-energy density cutting torch model. In particular, the model requires the introduction of only one adjustable coefficient c corresponding to the length of action of the turbulence. It is shown that the c value has little effect on the plasma temperature profiles outside the nozzle (the differences being less than 10 %), but severely affects the plasma velocity distribution, with differences reaching about 100% at the middle of the nozzle-anode gap. Within the experimental uncertainties it was also found that the value c = 0.08 allows to reproduce both, the experimental data of velocity and temperature

On the use of the Prandtl mixing length model in the cutting torch modeling

International Nuclear Information System (INIS)

Mancinelli, B; Minotti, F O; Kelly, H

2011-01-01

The Prandtl mixing length model has been used to take into account the turbulent effects in a 30 A high-energy density cutting torch model. In particular, the model requires the introduction of only one adjustable coefficient c corresponding to the length of action of the turbulence. It is shown that the c value has little effect on the plasma temperature profiles outside the nozzle (the differences being less than 10 %), but severely affects the plasma velocity distribution, with differences reaching about 100% at the middle of the nozzle-anode gap. Within the experimental uncertainties it was also found that the value c = 0.08 allows to reproduce both, the experimental data of velocity and temperature

Experimental Validation of a Dynamic Model for Lightweight Robots

Directory of Open Access Journals (Sweden)

Alessandro Gasparetto

2013-03-01

Full Text Available Nowadays, one of the main topics in robotics research is dynamic performance improvement by means of a lightening of the overall system structure. The effective motion and control of these lightweight robotic systems occurs with the use of suitable motion planning and control process. In order to do so, model-based approaches can be adopted by exploiting accurate dynamic models that take into account the inertial and elastic terms that are usually neglected in a heavy rigid link configuration. In this paper, an effective method for modelling spatial lightweight industrial robots based on an Equivalent Rigid Link System approach is considered from an experimental validation perspective. A dynamic simulator implementing the formulation is used and an experimental test-bench is set-up. Experimental tests are carried out with a benchmark L-shape mechanism.

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.

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.

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).

Development of a fault test experimental facility model using Matlab

Energy Technology Data Exchange (ETDEWEB)

Pereira, Iraci Martinez; Moraes, Davi Almeida, E-mail: martinez@ipen.br, E-mail: dmoraes@dk8.com.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2015-07-01

The Fault Test Experimental Facility was developed to simulate a PWR nuclear power plant and is instrumented with temperature, level and pressure sensors. The Fault Test Experimental Facility can be operated to generate normal and fault data, and these failures can be added initially small, and their magnitude being increasing gradually. This work presents the Fault Test Experimental Facility model developed using the Matlab GUIDE (Graphical User Interface Development Environment) toolbox that consists of a set of functions designed to create interfaces in an easy and fast way. The system model is based on the mass and energy inventory balance equations. Physical as well as operational aspects are taken into consideration. The interface layout looks like a process flowchart and the user can set the input variables. Besides the normal operation conditions, there is the possibility to choose a faulty variable from a list. The program also allows the user to set the noise level for the input variables. Using the model, data were generated for different operational conditions, both under normal and fault conditions with different noise levels added to the input variables. Data generated by the model will be compared with Fault Test Experimental Facility data. The Fault Test Experimental Facility theoretical model results will be used for the development of a Monitoring and Fault Detection System. (author)

Development of a fault test experimental facility model using Matlab

International Nuclear Information System (INIS)

Pereira, Iraci Martinez; Moraes, Davi Almeida

2015-01-01

The Fault Test Experimental Facility was developed to simulate a PWR nuclear power plant and is instrumented with temperature, level and pressure sensors. The Fault Test Experimental Facility can be operated to generate normal and fault data, and these failures can be added initially small, and their magnitude being increasing gradually. This work presents the Fault Test Experimental Facility model developed using the Matlab GUIDE (Graphical User Interface Development Environment) toolbox that consists of a set of functions designed to create interfaces in an easy and fast way. The system model is based on the mass and energy inventory balance equations. Physical as well as operational aspects are taken into consideration. The interface layout looks like a process flowchart and the user can set the input variables. Besides the normal operation conditions, there is the possibility to choose a faulty variable from a list. The program also allows the user to set the noise level for the input variables. Using the model, data were generated for different operational conditions, both under normal and fault conditions with different noise levels added to the input variables. Data generated by the model will be compared with Fault Test Experimental Facility data. The Fault Test Experimental Facility theoretical model results will be used for the development of a Monitoring and Fault Detection System. (author)

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

A model of breakdown in parallel-plate detectors

International Nuclear Information System (INIS)

Fonte, P.

1996-01-01

Parallel-plate avalanche chambers (PPAC's) have many desirable properties, such as a fast, large area particle detector. However, the maximum gain is limited by a form of violent breakdown that limits the usefulness of this detector, despite its other evident qualities. The exact nature of this phenomenon is not yet sufficiently clear to sustain possible improvements. A previous experimental study is complemented in the present work by a quantitative model of the breakdown phenomenon in PPAC's, based on the streamer theory. The model reproduces well the peculiar behavior of the external current observed in PPAC's and resistive-plate chambers. Other breakdown properties measured in PPAC's are also well reproduced

Application of Iterative Robust Model-based Optimal Experimental Design for the Calibration of Biocatalytic Models

DEFF Research Database (Denmark)

Van Daele, Timothy; Gernaey, Krist V.; Ringborg, Rolf Hoffmeyer

2017-01-01

The aim of model calibration is to estimate unique parameter values from available experimental data, here applied to a biocatalytic process. The traditional approach of first gathering data followed by performing a model calibration is inefficient, since the information gathered during...... experimentation is not actively used to optimise the experimental design. By applying an iterative robust model-based optimal experimental design, the limited amount of data collected is used to design additional informative experiments. The algorithm is used here to calibrate the initial reaction rate of an ω......-transaminase catalysed reaction in a more accurate way. The parameter confidence region estimated from the Fisher Information Matrix is compared with the likelihood confidence region, which is a more accurate, but also a computationally more expensive method. As a result, an important deviation between both approaches...

Experimental study of Au+Au collisions at E/A=150 and 400 MeV: comparison with the GQMD-matrix model

International Nuclear Information System (INIS)

Ramillien, V.

1995-07-01

We present new experimental data obtained with the FOPI detector at the SIS Heavy ions accelerator (Darmstadt, Germany), for the Au + Au heavy ion collisions at 150 and 400 A.MeV incident energy. The sideward flow, determined form the method of Danielewicz without reaction plane reconstruction, and the nuclear stopping are studied as a function of the centrality of the collisions and as a function of the fragment charge. In order to study the nuclear in-medium effects, which act on the N-N cross-sections and potential and hence on experimental observables like the nuclear matter flow and stopping, these results are compared with the predictions of two different QMD versions. The first one (GQMD) offers a fully microscopic calculation of the cross-sections and potential in the G-matrix formalism and naturally includes the in-medium effects. This version is for the first time confronted to experiment. The second one (IQMD) uses a standard Skyrme potential plus a momentum dependent term in order to mimic the in-medium effects. We find that the experimental stopping is overestimated for 30-40% in the models IQMD and GQMD. Concerning the flow, we find that the momentum dependence of the potential in GQMD is somewhat stronger as can be seen for the more peripheral events and fits better the data in this case. On the other hand, the model GQMD clearly lacks of density dependence to reproduce the more central events. (author). 52 refs., 57 figs., 11 tabs

Correction factor for the experimental prompt neutron decay constant

International Nuclear Information System (INIS)

Talamo, Alberto; Gohar, Y.; Sadovich, S.; Kiyavitskaya, H.; Bournos, V.; Fokov, Y.; Routkovskaya, C.

2013-01-01

Highlights: • Definition of a spatial correction factor for the experimental prompt neutron decay constant. • Introduction of a MCNP6 calculation methodology to simulate Rossi-alpha distribution for pulsed neutron sources. • Comparison of MCNP6 results with experimental data for count rate, Rossi-alpha, and Feynman-alpha distributions. • Improvement of the comparison between numerical and experimental results by taking into account the dead-time effect. - Abstract: This study introduces a new correction factor to obtain the experimental effective multiplication factor of subcritical assemblies by the point kinetics formulation. The correction factor is defined as the ratio between the MCNP6 prompt neutron decay constant obtained in criticality mode and the one obtained in source mode. The correction factor mainly takes into account the longer neutron lifetime in the reflector region and the effects of the external neutron source. For the YALINA Thermal facility, the comparison between the experimental and computational effective multiplication factors noticeably improves after the application of the correction factor. The accuracy of the MCNP6 computational model of the YALINA Thermal subcritical assembly has been verified by reproducing the neutron count rate, Rossi-α, and Feynman-α distributions obtained from the experimental data

Experimental models of developmental hypothyroidism.

Science.gov (United States)

Argumedo, G S; Sanz, C R; Olguín, H J

2012-02-01

Hypothyroidism is a systemic disease resulting from either thyroid gland's anatomical and functional absence or lack of hypophyseal stimulation, both of which can lead to deficiency in thyroid hormone (TH) production. TH is essential for human and animal development, growth, and function of multiple organs. Children with deficient TH can develop alterations in central nervous system (CNS), striated muscle, bone tissue, liver, bone marrow, and cardiorespiratory system. Among the clinical outlook are signs like breathing difficulty, cardiac insufficiency, dysphagia, and repeated bronchial aspiration, constipation, muscle weakness, cognitive alterations, cochlear dysfunction, reduced height, defects in temperature regulation, anaemia, jaundice, susceptibility to infection, and others. Experimental and clinical studies have shown that TH is very essential for normal brain development. Other research work based on mice pointed out that a reduced level of TH in pregnant mother leads to congenital hypothyroidism in animal models and it is associated with mental retardation, deep neurologic deficiency that impacts on cognitive, learning, and memory functions. The principal experimental model studies that have focused on hypothyroidism are reviewed in this study. This is important on considering the fact that almost all animal species require thyroid hormones for their metabolism. © Georg Thieme Verlag KG Stuttgart · New York.

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.

Optimal Experimental Design for Model Discrimination

Science.gov (United States)

Myung, Jay I.; Pitt, Mark A.

2009-01-01

Models of a psychological process can be difficult to discriminate experimentally because it is not easy to determine the values of the critical design variables (e.g., presentation schedule, stimulus structure) that will be most informative in differentiating them. Recent developments in sampling-based search methods in statistics make it…

Statistical and non statistical models for delayed neutron emission: applications to nuclei near A = 90

International Nuclear Information System (INIS)

De Oliveira, Z.M.

1980-01-01

A detailed analysis of the simple statistical model description for delayed neutron emission of 87 Br, 137 I, 85 As and 135 Sb has been performed. In agreement with experimental findings, structure in the #betta#-strength function is required to reproduce the envelope of the neutron spectrum from 87 Br. For 85 As and 135 Sb the model is found incapable of simultaneously reproducing envelopes of delayed neutron spectra and neutron branching ratios to excited states in the final nuclei for any choice of #betta#-strength function. The results indicate that partial widths for neutron emission are not compatible with optical-model transmission coefficients. The simple shell model with pairing is shown to qualitatively describe the main features of the #betta#-strength functions for decay of 87 Br and 91 93 95 97 Rb. It is found that the location of apparent resonances in the experimental data are in rough agreement with the location of centroids of strength calculated with this model. An extension of the shell model picture which includes the Gamow-Teller residual interaction is used to investigate decay properties of 84 86 As, 86 92 Br and 88 102 Rb. For a realistic choice of interaction strength, the half lives of these isotopes are fairly well reproduced and semiquantitative agreement with experimental #betta#-strength functions is found. Delayed neutron emission probabilities are reproduced for precursors nearer stability with systematic deviations being observed for the heavier nuclei. Contrary to the assumption of a structureless Gamow-Teller giant resonance as embodied gross theory of #betta#-decay, we find that structures in the tail of the Gamow-Teller giant resonances are expected which strongly influence the decay properties of nuclides in this region

Atmospheric Dust Modeling from Meso to Global Scales with the Online NMMB/BSC-Dust Model Part 2: Experimental Campaigns in Northern Africa

Science.gov (United States)

Haustein, K.; Perez, C.; Baldasano, J. M.; Jorba, O.; Basart, S.; Miller, R. L.; Janjic, Z.; Black, T.; Nickovic, S.; Todd, M. C.;

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

On the accuracy of DFT methods in reproducing ligand substitution energies for transition metal complexes in solution: The role of dispersive interactions

KAUST Repository

Jacobsen, Heiko; Cavallo, Luigi

2011-01-01

phosphanes, while functionals not including dispersion interaction reproduce the experimental trends with reasonable accuracy. In case of the DFT-D functionals, inclusion of a cut-off distance on the dispersive term resolves this issue, and results in a

Hydrodynamic characteristics of the two-phase flow field at gas-evolving electrodes: numerical and experimental studies

Science.gov (United States)

Liu, Cheng-Lin; Sun, Ze; Lu, Gui-Min; Yu, Jian-Guo

2018-05-01

Gas-evolving vertical electrode system is a typical electrochemical industrial reactor. Gas bubbles are released from the surfaces of the anode and affect the electrolyte flow pattern and even the cell performance. In the current work, the hydrodynamics induced by the air bubbles in a cold model was experimentally and numerically investigated. Particle image velocimetry and volumetric three-component velocimetry techniques were applied to experimentally visualize the hydrodynamics characteristics and flow fields in a two-dimensional (2D) plane and a three-dimensional (3D) space, respectively. Measurements were performed at different gas rates. Furthermore, the corresponding mathematical model was developed under identical conditions for the qualitative and quantitative analyses. The experimental measurements were compared with the numerical results based on the mathematical model. The study of the time-averaged flow field, three velocity components, instantaneous velocity and turbulent intensity indicate that the numerical model qualitatively reproduces liquid motion. The 3D model predictions capture the flow behaviour more accurately than the 2D model in this study.

XX. Animal models of pneumocystosis

DEFF Research Database (Denmark)

Dei-Cas, E.; Brun-Pascaud, M.; Bille-Hansen, Vivi

1998-01-01

As in vitro culture systems allowing to isolate Pneumocystis samples from patients or other mammal hosts are still not available, animal models have critical importance in Pneumocystis research. The parasite was reported in numerous mammals but P. carinii pneumonia (PCP) experimental models were...... a source of parasites taxonomically related to P. carinii sp. f hominis. Moreover, primates might be used as experimental hosts to human Pneumocystis. A marked variability of parasite levels among corticosteroid-treated animals and the fact that the origin of the parasite strain remains unknown......, are important drawbacks of the corticosteroid-treated models. For these reasons, inoculated animal models of PCP were developed. The intratracheal inoculation of lung homogenates containing viable parasites in corticosteroid-treated non-latently infected rats resulted in extensive, reproducible Pneumocystis...

Oxidative Stress and Pulmonary Changes in Experimental Liver Cirrhosis

Directory of Open Access Journals (Sweden)

Renata Salatti Ferrari

2012-01-01

Full Text Available The use of carbon tetrachloride (CCl4 in rats is an experimental model of hepatic tissue damage; which leads to fibrosis, and at the long term, cirrhosis. Cirrhosis is the consequence of progressive continued liver damage, it may be reversible when the damaging noxae have been withdrawn. The aim of this study is to evaluate the changes caused by cirrhosis in lung and liver, through the experimental model of intraperitoneal CCI4 administration. We used 18 male Wistar rats divided into three groups: control (CO and two groups divided by the time of cirrhosis induction by CCI4: G1 (11 weeks, G2 (16 weeks. We found significant increase of transaminase levels and lipid peroxidation (TBARS in liver and lung tissue and also increased antioxidant enzymes SOD and CAT, as well as the expression of TNF-α and IL-1β in the lung of cirrhotic animals. We observed changes in gas exchange in both cirrhotic groups. We can conclude that our model reproduces a model of liver cirrhosis, which causes alterations in the pulmonary system that leads to changes in gas exchange and size of pulmonary vessels.

Numerical Modelling of Soot Formation in Laminar Axisymmetric Ethylene-Air Coflow Flames at Atmospheric and Elevated Pressures

KAUST Repository

Abdelgadir, Ahmed; Rakha, Ihsan Allah; Steinmetz, Scott A.; Attili, Antonio; Bisetti, Fabrizio; Roberts, William L.

2015-01-01

, coupled with detailed transport and kinetic models, to reproduce experimental measurements of a series of ethylene-air coflow flames. Detailed finite rate chemistry describing the formation of Polycyclic Aromatic Hydro-carbons is used. Soot is modeled

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.

Electronic stability and reproducible accuracy of HARSHAW 2000(A,B) TLD-analyzer

International Nuclear Information System (INIS)

Yossef, S.K.; Henaish, B.A.

1985-01-01

Nowadays, the thermoluminescence techniques utilizing natural materials and assorted chemical compound of various geometrical configurations are widely and popularly used on the international scale as a dose evaluation system. The main problems which are usually encounting the accuracy of the evaluated dose by means of such various dosimeter forms are the long and short term stability of the measuring system. Also this manuscript is a very essential details stated out the principle mechanisms which cause that produced TL-readers instability. As it is stated out through the different sections of this issue, it is mainly due to the interior mechanisms of the TLD measuring systems. Further more, the various detailed discussions availed through the different sections of such issue are mainly accompanied by long term experiences gained by the authors. A novel heating cycle mechanism applied to HARSHOW 2000(A and b) TLD analyzer is tested experimentally. Also long and short term stability beside the reproducibility of the TLD reader system were experimentally tested under various seasonable environmental thermal conditions. The results of experimental measurements were noted for a total duration of six months during continuous operation of the TLD reader for one year. 1 fig., 3 tab

Morphofunctional analysis of experimental model of esophageal achalasia in rats.

Science.gov (United States)

Sabirov, A G; Raginov, I S; Burmistrov, M V; Chelyshev, Y A; Khasanov, R Sh; Moroshek, A A; Grigoriev, P N; Zefirov, A L; Mukhamedyarov, M A

2010-10-01

We carried out a detailed analysis of rat model of esophageal achalasia previously developed by us. Manifest morphological and functional disorders were observed in experimental achalasia: hyperplasia of the squamous epithelium, reduced number of nerve fibers, excessive growth of fibrous connective tissue in the esophageal wall, high contractile activity of the lower esophageal sphincter, and reduced motility of the longitudinal muscle layer. Changes in rat esophagus observed in experimental achalasia largely correlate with those in esophageal achalasia in humans. Hence, our experimental model can be used for the development of new methods of disease treatment.

Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

Science.gov (United States)

Salsbury, Freddie R.; Poole, Leslie B.; Fetrow, Jacquelyn S.

2013-01-01

One of the most popular and simple models for the calculation of pKas from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pKas. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pKas; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pKas. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pKa values (where the calculation should reproduce the pKa within experimental error). Both the general behavior of cysteines in proteins and the perturbed pKa in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pKa should be shifted, and validation of force field parameters for cysteine residues. PMID:22777874

Stochastic approach to pitting-corrosion-extreme modelling in low-carbon steel

Energy Technology Data Exchange (ETDEWEB)

Valor, A. [Facultad de Fisica, Universidad de La Habana, San Lazaro y L, Vedado 10400, La Habana (Cuba); Caleyo, F. [Departamento de Ingenieria Metalurgica, IPN-ESIQIE, UPALM Edif. 7, Zacatenco, Mexico DF 07738 (Mexico)], E-mail: fcaleyo@gmail.com; Rivas, D.; Hallen, J.M. [Departamento de Ingenieria Metalurgica, IPN-ESIQIE, UPALM Edif. 7, Zacatenco, Mexico DF 07738 (Mexico)

2010-03-15

A stochastic model previously developed by the authors using Markov chains has been improved in the light of new experimental evidence. The new model has been successfully applied to reproduce the time evolution of extreme pitting corrosion depths in low-carbon steel. The model is shown to provide a better physical understanding of the pitting process.

Stochastic approach to pitting-corrosion-extreme modelling in low-carbon steel

International Nuclear Information System (INIS)

Valor, A.; Caleyo, F.; Rivas, D.; Hallen, J.M.

2010-01-01

A stochastic model previously developed by the authors using Markov chains has been improved in the light of new experimental evidence. The new model has been successfully applied to reproduce the time evolution of extreme pitting corrosion depths in low-carbon steel. The model is shown to provide a better physical understanding of the pitting process.

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.

Effects of Erdosteine on Experimental Acute Pancreatitis Model.

Science.gov (United States)

Karapolat, Banu; Karapolat, Sami; Gurleyik, Emin; Yasar, Mehmet

2017-10-01

To create acute pancreatitis condition experimentally in rats using cerulein, and to reveal histopathological effects in pancreatic tissue with erdosteine. An experimental study. Department of General Surgery, Duzce University, Turkey, from June to October 2014. Thirty male Wistar albino rats were divided into three groups. No procedures were applied to Group 1. The rats in Group 2 and Group 3 were injected cerulein, to establish an experimental pancreatitis model and the blood amylase and lipase values were examined. The rats in Group 3 were given 10 mg/kg erdosteine. This treatment was continued for another 2 days and the rats were sacrificed. The pancreatic tissues were examined histopathologically for edema, inflammation, acinar necrosis, fat necrosis, and vacuolization. The lipase and amylase values and the histopathological examination of pancreatic tissues evidenced that the experimental acute pancreatitis model was established and edema, inflammation, acinar necrosis, fat necrosis, and vacuolization were observed in the pancreatic tissues. The statistical results suggest that erdosteine can decrease the edema, inflammation, acinar necrosis, fat necrosis and vacuolization scores in the tissues. The severity of acute pancreatitis, induced by cerulein in rats, is reduced with the use of erdosteine.

Study of the behaviour of trace elements in estuaries: experimental approaches and modeling

International Nuclear Information System (INIS)

Dange, Catherine

2002-01-01

the biogeochemistry of Cd, Co and Cs in the estuarine environment and the knowledge obtained on the field. Experiments performed both in laboratory and in situ were necessary to check the validity of the assumptions of the model and to evaluate model parameters, which cannot be measured directly like to the sorption properties of natural particles. Radiotracers ("1"0"9Cd, "5"7Co,"1"3"4Cs) were used to determine physico-chemical key processes and environmental variables that control the speciation and the fate of Cd, Co and Cs. This approach, based on the use of spike with various radionuclides, allowed us to evaluate the affinity constants of particles to the four estuaries for the studied metals (global intrinsic complexation and exchange constants) and also the exchangeable particulate fraction estimated from the comparison of measured natural metals coefficients of distribution and coefficient of distribution of their radioactive equivalents. Other parameters, which are necessary to build the model (specific surface area, concentration of active surface sites, mean intrinsic acid-base constants,...), were independently estimated by various experimental approaches, applied in laboratory to particle samples taken throughout estuaries (electrochemical measurements, nitrogen adsorption using the BET method,...). The results of the validation indicate that in spite of its simplifications, the model reproduces in a satisfactory way the dissolved/particulate distributions measured for Cd, Co and Cs. With a predictive aim, this type of model must be coupled with a hydro-sedimentary transport model. (author)

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

Experimental validation of a 2D overland flow model using high resolution water depth and velocity data

Science.gov (United States)

Cea, L.; Legout, C.; Darboux, F.; Esteves, M.; Nord, G.

2014-05-01

This paper presents a validation of a two-dimensional overland flow model using empirical laboratory data. Unlike previous publications in which model performance is evaluated as the ability to predict an outlet hydrograph, we use high resolution 2D water depth and velocity data to analyze to what degree the model is able to reproduce the spatial distribution of these variables. Several overland flow conditions over two impervious surfaces of the order of one square meter with different micro and macro-roughness characteristics are studied. The first surface is a simplified representation of a sinusoidal terrain with three crests and furrows, while the second one is a mould of a real agricultural seedbed terrain. We analyze four different bed friction parameterizations and we show that the performance of formulations which consider the transition between laminar, smooth turbulent and rough turbulent flow do not improve the results obtained with Manning or Keulegan formulas for rough turbulent flow. The simulations performed show that using Keulegan formula with a physically-based definition of the bed roughness coefficient, a two-dimensional shallow water model is able to reproduce satisfactorily the flow hydrodynamics. It is shown that, even if the resolution of the topography data and numerical mesh are high enough to include all the small scale features of the bed surface, the roughness coefficient must account for the macro-roughness characteristics of the terrain in order to correctly reproduce the flow hydrodynamics.

Experimental tests of proton spin models

International Nuclear Information System (INIS)

Ramsey, G.P.; Argonne National Lab., IL

1989-01-01

We have developed models for the spin-weighted quark and gluon distribution in a longitudinally polarized proton. The model parameters are determined from current algebra sum rules and polarized deep-inelastic scattering data. A number of different scenarios are presented for the fraction of spin carried the constituent parton distributions. A possible long-range experimental program is suggested for measuring various hard scattering processes using polarized lepton and proton beams. With the knowledge gained from these experiments, we can begin to understand the parton contributions to the proton spin. 28 refs., 5 figs

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.

Experimental designs for autoregressive models applied to industrial maintenance

International Nuclear Information System (INIS)

Amo-Salas, M.; López-Fidalgo, J.; Pedregal, D.J.

2015-01-01

Some time series applications require data which are either expensive or technically difficult to obtain. In such cases scheduling the points in time at which the information should be collected is of paramount importance in order to optimize the resources available. In this paper time series models are studied from a new perspective, consisting in the use of Optimal Experimental Design setup to obtain the best times to take measurements, with the principal aim of saving costs or discarding useless information. The model and the covariance function are expressed in an explicit form to apply the usual techniques of Optimal Experimental Design. Optimal designs for various approaches are computed and their efficiencies are compared. The methods working in an application of industrial maintenance of a critical piece of equipment at a petrochemical plant are shown. This simple model allows explicit calculations in order to show openly the procedure to find the correlation structure, needed for computing the optimal experimental design. In this sense the techniques used in this paper to compute optimal designs may be transferred to other situations following the ideas of the paper, but taking into account the increasing difficulty of the procedure for more complex models. - Highlights: • Optimal experimental design theory is applied to AR models to reduce costs. • The first observation has an important impact on any optimal design. • Either the lack of precision or small starting observations claim for large times. • Reasonable optimal times were obtained relaxing slightly the efficiency. • Optimal designs were computed in a predictive maintenance context

Theoretical-experimental modelling of the momentum equation for PWR reactor steam generators

International Nuclear Information System (INIS)

Rodrigues, L.A.H.

1994-01-01

A mathematical model in steady-state conditions of the momentum equation at the secondary side of a vertical U-tube steam generator with recirculation is presented. The U-tube test section was the 150 bar - Circuito Termoidraulico Experimental - CTE-150. This facility is a Experimental Thermal-hydraulic Circuit and operates at the same conditions (pressure and temperature) of a typical PWR reactor. A comparison between the Homogeneous and Separate Flow models was done. those models were verified and compared with experimental data for several operational conditions. The results show that the model fits very well the experimental data and seems to be appropriate to study water recirculation of a steam generator secondary side. (author)

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...

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.

Experimental animal data and modeling of late somatic effects

International Nuclear Information System (INIS)

Fry, R.J.M.

1988-01-01

This section is restricted to radiation-induced life shortening and cancer and mainly to studies with external radiation. The emphasis will be on the experimental data that are available and the experimental systems that could provide the type of data with which to either formulate or test models. Genetic effects which are of concern are not discussed in this section. Experimental animal radiation studies fall into those that establish general principles and those that demonstrate mechanisms. General principles include the influence of dose, radiation quality, dose rate, fractionation, protraction and such biological factors as age and gender. The influence of these factors are considered as general principles because they are independent, at least qualitatively, of the species studied. For example, if an increase in the LET of the radiation causes an increased effectiveness in cancer induction in a mouse a comparable increase in effectiveness can be expected in humans. Thus, models, whether empirical or mechanistic, formulated from experimental animal data should be generally applicable

Electrochemical desalination of bricks - Experimental and modeling

DEFF Research Database (Denmark)

Skibsted, Gry; Ottosen, Lisbeth M.; Jensen, Pernille Erland

2015-01-01

Chlorides, nitrates and sulfates play an important role in the salt-decay of porous materials in buildings and monuments. Electrochemical desalination is a technology able to remove salts from such porous materials in order to stop or prevent the decay. In this paper, experimental and numerical......-contaminated bricks with respect to the monovalent ions is discussed. Comparison between the experimental and the simulation results showed that the proposed numerical model is able to predict electrochemical desalination treatments with remarkable accuracy, and it can be used as a predictive tool...

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.

[Reproducibility and accuracy in the morphometric and mechanical quantification of trabecular bone from 3 Tesla magnetic resonance images].

Science.gov (United States)

Alberich-Bayarri, A; Martí-Bonmatí, L; Sanz-Requena, R; Sánchez-González, J; Hervás Briz, V; García-Martí, G; Pérez, M Á

2014-01-01

We used an animal model to analyze the reproducibility and accuracy of certain biomarkers of bone image quality in comparison to a gold standard of computed microtomography (μCT). We used magnetic resonance (MR) imaging and μCT to study the metaphyses of 5 sheep tibiae. The MR images (3 Teslas) were acquired with a T1-weighted gradient echo sequence and an isotropic spatial resolution of 180μm. The μCT images were acquired using a scanner with a spatial resolution of 7.5μm isotropic voxels. In the preparation of the images, we applied equalization, interpolation, and thresholding algorithms. In the quantitative analysis, we calculated the percentage of bone volume (BV/TV), the trabecular thickness (Tb.Th), the trabecular separation (Tb.Sp), the trabecular index (Tb.N), the 2D fractal dimension (D(2D)), the 3D fractal dimension (D(3D)), and the elastic module in the three spatial directions (Ex, Ey and Ez). The morphometric and mechanical quantification of trabecular bone by MR was very reproducible, with percentages of variation below 9% for all the parameters. Its accuracy compared to the gold standard (μCT) was high, with errors less than 15% for BV/TV, D(2D), D(3D), and E(app)x, E(app)y and E(app)z. Our experimental results in animals confirm that the parameters of BV/TV, D(2D), D(3D), and E(app)x, E(app)y and E(app)z obtained by MR have excellent reproducibility and accuracy and can be used as imaging biomarkers for the quality of trabecular bone. Copyright © 2013 SERAM. Published by Elsevier Espana. All rights reserved.

Contact Modelling in Resistance Welding, Part II: Experimental Validation

DEFF Research Database (Denmark)

Song, Quanfeng; Zhang, Wenqi; Bay, Niels

2006-01-01

Contact algorithms in resistance welding presented in the previous paper are experimentally validated in the present paper. In order to verify the mechanical contact algorithm, two types of experiments, i.e. sandwich upsetting of circular, cylindrical specimens and compression tests of discs...... with a solid ring projection towards a flat ring, are carried out at room temperature. The complete algorithm, involving not only the mechanical model but also the thermal and electrical models, is validated by projection welding experiments. The experimental results are in satisfactory agreement...

Hybrid Electric Vehicle Experimental Model with CAN Network Real Time Control

Directory of Open Access Journals (Sweden)

RATOI, M.

2010-05-01

Full Text Available In this paper an experimental model with a distributed control system of a hybrid electrical vehicle is presented. A communication CAN network of high speed (1 Mbps assures a distributed control of the all components. The modeling and the control of different operating regimes are realized on an experimental test-bench of a hybrid electrical vehicle. The experimental results concerning the variations of the mains variables (currents, torques, speeds are presented.

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.

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

Atmospheric dust modeling from meso to global scales with the online NMMB/BSC-Dust model – Part 2: Experimental campaigns in Northern Africa

Directory of Open Access Journals (Sweden)

K. Haustein

2012-03-01

Full Text Available The new NMMB/BSC-Dust model is intended to provide short to medium-range weather and dust forecasts from regional to global scales. It is an online model in which the dust aerosol dynamics and physics are solved at each model time step. The companion paper (Pérez et al., 2011 develops the dust model parameterizations and provides daily to annual evaluations of the model for its global and regional configurations. Modeled aerosol optical depth (AOD was evaluated against AERONET Sun photometers over Northern Africa, Middle East and Europe with correlations around 0.6–0.7 on average without dust data assimilation. In this paper we analyze in detail the behavior of the model using data from the Saharan Mineral dUst experiment (SAMUM-1 in 2006 and the Bodélé Dust Experiment (BoDEx in 2005. AOD from satellites and Sun photometers, vertically resolved extinction coefficients from lidars and particle size distributions at the ground and in the troposphere are used, complemented by wind profile data and surface meteorological measurements. All simulations were performed at the regional scale for the Northern African domain at the expected operational horizontal resolution of 25 km. Model results for SAMUM-1 generally show good agreement with satellite data over the most active Saharan dust sources. The model reproduces the AOD from Sun photometers close to sources and after long-range transport, and the dust size spectra at different height levels. At this resolution, the model is not able to reproduce a large haboob that occurred during the campaign. Some deficiencies are found concerning the vertical dust distribution related to the representation of the mixing height in the atmospheric part of the model. For the BoDEx episode, we found the diurnal temperature cycle to be strongly dependant on the soil moisture, which is underestimated in the NCEP analysis used for model initialization. The low level jet (LLJ and the dust AOD over the Bodélé are

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

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

Endothelial Dysfunction in Experimental Models of Arterial Hypertension: Cause or Consequence?

Directory of Open Access Journals (Sweden)

Iveta Bernatova

2014-01-01

Full Text Available Hypertension is a risk factor for other cardiovascular diseases and endothelial dysfunction was found in humans as well as in various commonly employed animal experimental models of arterial hypertension. Data from the literature indicate that, in general, endothelial dysfunction would not be the cause of experimental hypertension and may rather be secondary, that is, resulting from high blood pressure (BP. The initial mechanism of endothelial dysfunction itself may be associated with a lack of endothelium-derived relaxing factors (mainly nitric oxide and/or accentuation of various endothelium-derived constricting factors. The involvement and role of endothelium-derived factors in the development of endothelial dysfunction in individual experimental models of hypertension may vary, depending on the triggering stimulus, strain, age, and vascular bed investigated. This brief review was focused on the participation of endothelial dysfunction, individual endothelium-derived factors, and their mechanisms of action in the development of high BP in the most frequently used rodent experimental models of arterial hypertension, including nitric oxide deficient models, spontaneous (prehypertension, stress-induced hypertension, and selected pharmacological and diet-induced models.

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

Soil pH controls the environmental availability of phosphorus: Experimental and mechanistic modelling approaches

International Nuclear Information System (INIS)

Devau, Nicolas; Cadre, Edith Le; Hinsinger, Philippe; Jaillard, Benoit; Gerard, Frederic

2009-01-01

Inorganic P is the least mobile major nutrient in most soils and is frequently the prime limiting factor for plant growth in terrestrial ecosystems. In this study, the extraction of soil inorganic P with CaCl 2 (P-CaCl 2 ) and geochemical modelling were combined in order to unravel the processes controlling the environmentally available P (EAP) of a soil over a range of pH values (pH ∼ 4-10). Mechanistic descriptions of the adsorption of cations and anions by the soil constituents were used (1-pK Triple Plane, ion-exchange and NICA-Donnan models). These models are implemented into the geochemical code Visual MINTEQ. An additive approach was used for their application to the surface horizon of a Cambisol. The geochemical code accurately reproduced the concentration of extracted P at the different soil pH values (R 2 = 0.9, RMSE = 0.03 mg kg -1 ). Model parameters were either directly found in the literature or estimated by fitting published experimental results in single mineral systems. The strong agreement between measurements and modelling results demonstrated that adsorption processes exerted a major control on the EAP of the soil over a large range of pH values. An influence of the precipitation of P-containing mineral is discounted based on thermodynamic calculations. Modelling results indicated that the variations in P-CaCl 2 with soil pH were controlled by the deprotonation/protonation of the surface hydroxyl groups, the distribution of P surface complexes, and the adsorption of Ca and Cl from the electrolyte background. Iron-oxides and gibbsite were found to be the major P-adsorbing soil constituents at acidic and alkaline pHs, whereas P was mainly adsorbed by clay minerals at intermediate pH values. This study demonstrates the efficacy of geochemical modelling to understand soil processes, and the applicability of mechanistic adsorption models to a 'real' soil, with its mineralogical complexity and the additional contribution of soil organic matter.

Soil pH controls the environmental availability of phosphorus: Experimental and mechanistic modelling approaches

Energy Technology Data Exchange (ETDEWEB)

Devau, Nicolas [INRA, UMR 1222 Eco and Sols - Ecologie Fonctionnelle et Biogeochimie des Sols (INRA-IRD-SupAgro), Place Viala, F-34060 Montpellier (France); Cadre, Edith Le [Supagro, UMR 1222 Eco and Sols - Ecologie Fonctionnelle et Biogeochimie des Sols (INRA-IRD-SupAgro), Place Viala, F-34060 Montpellier (France); Hinsinger, Philippe; Jaillard, Benoit [INRA, UMR 1222 Eco and Sols - Ecologie Fonctionnelle et Biogeochimie des Sols (INRA-IRD-SupAgro), Place Viala, F-34060 Montpellier (France); Gerard, Frederic, E-mail: gerard@supagro.inra.fr [INRA, UMR 1222 Eco and Sols - Ecologie Fonctionnelle et Biogeochimie des Sols (INRA-IRD-SupAgro), Place Viala, F-34060 Montpellier (France)

2009-11-15

Inorganic P is the least mobile major nutrient in most soils and is frequently the prime limiting factor for plant growth in terrestrial ecosystems. In this study, the extraction of soil inorganic P with CaCl{sub 2} (P-CaCl{sub 2}) and geochemical modelling were combined in order to unravel the processes controlling the environmentally available P (EAP) of a soil over a range of pH values (pH {approx} 4-10). Mechanistic descriptions of the adsorption of cations and anions by the soil constituents were used (1-pK Triple Plane, ion-exchange and NICA-Donnan models). These models are implemented into the geochemical code Visual MINTEQ. An additive approach was used for their application to the surface horizon of a Cambisol. The geochemical code accurately reproduced the concentration of extracted P at the different soil pH values (R{sup 2} = 0.9, RMSE = 0.03 mg kg{sup -1}). Model parameters were either directly found in the literature or estimated by fitting published experimental results in single mineral systems. The strong agreement between measurements and modelling results demonstrated that adsorption processes exerted a major control on the EAP of the soil over a large range of pH values. An influence of the precipitation of P-containing mineral is discounted based on thermodynamic calculations. Modelling results indicated that the variations in P-CaCl{sub 2} with soil pH were controlled by the deprotonation/protonation of the surface hydroxyl groups, the distribution of P surface complexes, and the adsorption of Ca and Cl from the electrolyte background. Iron-oxides and gibbsite were found to be the major P-adsorbing soil constituents at acidic and alkaline pHs, whereas P was mainly adsorbed by clay minerals at intermediate pH values. This study demonstrates the efficacy of geochemical modelling to understand soil processes, and the applicability of mechanistic adsorption models to a 'real' soil, with its mineralogical complexity and the additional

A method to reproduce alpha-particle spectra measured with semiconductor detectors.

Science.gov (United States)

Timón, A Fernández; Vargas, M Jurado; Sánchez, A Martín

2010-01-01

A method is proposed to reproduce alpha-particle spectra measured with silicon detectors, combining analytical and computer simulation techniques. The procedure includes the use of the Monte Carlo method to simulate the tracks of alpha-particles within the source and in the detector entrance window. The alpha-particle spectrum is finally obtained by the convolution of this simulated distribution and the theoretical distributions representing the contributions of the alpha-particle spectrometer to the spectrum. Experimental spectra from (233)U and (241)Am sources were compared with the predictions given by the proposed procedure, showing good agreement. The proposed method can be an important aid for the analysis and deconvolution of complex alpha-particle spectra. Copyright 2009 Elsevier Ltd. All rights reserved.

Experimental animal modelling for TB vaccine development

Directory of Open Access Journals (Sweden)

Pere-Joan Cardona

2017-03-01

Full Text Available Research for a novel vaccine to prevent tuberculosis is an urgent medical need. The current vaccine, BCG, has demonstrated a non-homogenous efficacy in humans, but still is the gold standard to be improved upon. In general, the main indicator for testing the potency of new candidates in animal models is the reduction of the bacillary load in the lungs at the acute phase of the infection. Usually, this reduction is similar to that induced by BCG, although in some cases a weak but significant improvement can be detected, but none of candidates are able to prevent establishment of infection. The main characteristics of several laboratory animals are reviewed, reflecting that none are able to simulate the whole characteristics of human tuberculosis. As, so far, no surrogate of protection has been found, it is important to test new candidates in several models in order to generate convincing evidence of efficacy that might be better than that of BCG in humans. It is also important to investigate the use of “in silico” and “ex vivo” models to better understand experimental data and also to try to replace, or at least reduce and refine experimental models in animals.

Experimental Validation of a Permeability Model for Enrichment Membranes

International Nuclear Information System (INIS)

Orellano, Pablo; Brasnarof, Daniel; Florido Pablo

2003-01-01

An experimental loop with a real scale diffuser, in a single enrichment-stage configuration, was operated with air at different process conditions, in order to characterize the membrane permeability.Using these experimental data, an analytical geometric-and-morphologic-based model was validated.It is conclude that a new set of independent measurements, i.e. enrichment, is necessary in order to fully characterize diffusers, because of its internal parameters are not univocally determinated with permeability experimental data only

Investigation of wax precipitation in crude oil: Experimental and modeling

Directory of Open Access Journals (Sweden)

Taraneh Jafari Behbahani

2015-09-01

Full Text Available In this work, a series of experiments were carried to investigation of rheological behavior of crude oil using waxy crude oil sample in the absence/presence of flow improver such as ethylene-vinyl acetate copolymer. The rheological data covered the temperature range of 5–30 °C. The results indicated that the performance of flow improver was dependent on its molecular weight. Addition of small quantities of flow improver, can improve viscosity and pour point of crude oil. Also, an Artificial Neural Network (ANN model using Multi-Layer Perceptron (MLP topology has been developed to account wax appearance temperature and the amount of precipitated wax and the model was verified using experimental data given in this work and reported in the literature. In order to compare the performance of the proposed model based on Artificial Neural Network, the wax precipitation experimental data at different temperatures were predicted using solid solution model and multi-solid phase model. The results showed that the developed model based on Artificial Neural Network can predict more accurately the wax precipitation experimental data in comparison to the previous models such as solid solution and multi-solid phase model with AADs less than 0.5%. Furthermore, the number of parameters required for the Artificial Neural Network (ANN model is less than the studied thermodynamic models.

4D Visualization of Experimental Procedures in Rock Physics

Science.gov (United States)

Vanorio, T.; di Bonito, C.

2010-12-01

Engaging students in laboratory classes in geophysics is becoming more and more difficult. This is primarily because of an ever-widening gap between the less appealing aspects that characterize these courses (e.g., lengthiness of the experimental operations, high student/instrument ratio, limited time associated with lack of previous hands-on experiences, and logistical and safety concerns) and the life style of the 21st century generations (i.e., extensive practice to high-tech tools, high-speed communications and computing, 3D graphics and HD videos). To bridge the gap and enhance the teaching strategy of laboratory courses in geophysics, we have created simulator-training tools for use in preparation for the actual experimental phase. We are using a modeling, animation, and rendering package to create (a) 3D models that accurately reproduce actual scenarios and instruments used for the measurement of rock physics properties and (b) 4D interactive animations that simulate hands-on demonstrations of the experimental procedures. We present here a prototype describing step-by-step the experimental protocol and the principles behind the measurement of rock porosity. The tool reproduces an actual helium porosimeter and makes use of interactive animations, guided text, and a narrative voice guiding the audience through the different phases of the experimental process. Our strategy is to make the most of new technologies while preserving the accuracy of classical laboratory methods and practices. These simulations are not intended to replace traditional lab work; rather they provide students with the opportunity for review and repetition. The primary goal is thus to help students familiarize themselves during their earlier curricula with lab methodologies, thus minimizing apparent hesitation and frustration in later classes. This may also increase the level of interest and involvement of undergraduate students and, in turn, enhance their keenness to pursue their

Search procedure for models based on the evolution of experimental curves

International Nuclear Information System (INIS)

Delforge, J.

1975-01-01

The possibilities offered by numerical analysis regarding the identification of parameters for the model are outlined. The use of a large number of experimental measurements is made possible by the flexibility of the proposed method. It is shown that the errors of numerical identification over all parameters are proportional to experimental errors, and to a proportionality factor called conditioning of the identification problem which is easily computed. Moreover, it is possible to define and calculate, for each parameter, a factor of sensitivity to experimental errors. The numerical values of conditioning and sensitivity factor depend on all experimental conditions, that is, on the one hand, the specific definition of the experiments, and on the other hand, the number and quality of the undertaken measurements. The identification procedure proposed includes several phases. The preliminary phase consists in a first definition of experimental conditions, in agreement with the experimenter. From the data thus obtained, it is generally possible to evaluate the minimum number of equivalence classes required for an interpretation compatible with the morphology of experimental curves. Possibly, from this point, some additional measurements may prove useful or required. The numerical phase comes afterwards to determine a first approximate model by means of the methods previously described. Next phases again require a close collaboration between experimenters and theoreticians. They consist mainly in refining the first model [fr

An experimental and mathematical analysis of lymphopoiesis dynamics under continuous irradiation

International Nuclear Information System (INIS)

Zukhbaya, T.M.; Smirnova, O.A.

1991-01-01

A mathematical model describing the dynamics of lymphopoiesis in mammals continuously exposed to ionizing radiation has been developed. It is based on the theory of chalone regulation of hematopoiesis. The model comprises a system of nine differential equations. Results from the model were compared with our experimental data for bone marrow and blood lymphocytes of rats continuously exposed to gamma radiation in a wide range of dose rates. The model reproduces the lymphopoiesis dynamics that we observed in our experiment, in particular, the radiation hormesis at low dose rates, the reduction of lymphopoiesis at intermediate dose rates, and extinction of lymphopoiesis at high dose rates of continuous radiation. The possible explanation of the hormesis is suggested by the framework of the model. The model can be used for predicting the lymphopoiesis dynamics in mammals under continuous irradiation

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.

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.

Surface tension modelling of liquid Cd-Sn-Zn alloys

Science.gov (United States)

Fima, Przemyslaw; Novakovic, Rada

2018-06-01

The thermodynamic model in conjunction with Butler equation and the geometric models were used for the surface tension calculation of Cd-Sn-Zn liquid alloys. Good agreement was found between the experimental data for limiting binaries and model calculations performed with Butler model. In the case of ternary alloys, the surface tension variation with Cd content is better reproduced in the case of alloys lying on vertical sections defined by high Sn to Zn molar fraction ratio. The calculated surface tension is in relatively good agreement with the available experimental data. In addition, the surface segregation of liquid ternary Cd-Sn-Zn and constituent binaries has also been calculated.

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...

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

Experimental Simulations of Lunar Magma Ocean Crystallization: The Plot (But Not the Crust) Thickens

Science.gov (United States)

Draper, D. S.; Rapp, J. F.; Elardo, S. M.; Shearer, C. K., Jr.; Neal, C. R.

2016-01-01

Numerical models of differentiation of a global-scale lunar magma ocean (LMO) have raised as many questions as they have answered. Recent orbital missions and sample studies have provided new context for a large range of lithologies, from the comparatively magnesian "purest anorthosite" reported by to Si-rich domes and spinel-rich clasts with widespread areal distributions. In addition, the GRAIL mission provided strong constraints on lunar crustal density and average thickness. Can this increasingly complex geology be accounted for via the formation and evolution of the LMO? We have in recent years been conducting extensive sets of petrologic experiments designed to fully simulate LMO crystallization, which had not been attempted previously. Here we review the key results from these experiments, which show that LMO differentiation is more complex than initial models suggested. Several important features expected from LMO crystallization models have yet to be reproduced experimentally; combined modelling and experimental work by our group is ongoing.

Animal models for clinical and gestational diabetes: maternal and fetal outcomes.

Science.gov (United States)

Kiss, Ana Ci; Lima, Paula Ho; Sinzato, Yuri K; Takaku, Mariana; Takeno, Marisa A; Rudge, Marilza Vc; Damasceno, Débora C

2009-10-19

Diabetes in pregnant women is associated with an increased risk of maternal and neonatal morbidity and remains a significant medical challenge. Diabetes during pregnancy may be divided into clinical diabetes and gestational diabetes. Experimental models are developed with the purpose of enhancing understanding of the pathophysiological mechanisms of diseases that affect humans. With regard to diabetes in pregnancy, experimental findings from models will lead to the development of treatment strategies to maintain a normal metabolic intrauterine milieu, improving perinatal development by preventing fetal growth restriction or macrosomia. Based on animal models of diabetes during pregnancy previously reported in the medical literature, the present study aimed to compare the impact of streptozotocin-induced severe (glycemia >300 mg/dl) and mild diabetes (glycemia between 120 and 300 mg/dl) on glycemia and maternal reproductive and fetal outcomes of Wistar rats to evaluate whether the animal model reproduces the maternal and perinatal results of clinical and gestational diabetes in humans. On day 5 of life, 96 female Wistar rats were assigned to three experimental groups: control (n = 16), severe (n = 50) and mild diabetes (n = 30). At day 90 of life, rats were mated. On day 21 of pregnancy, rats were killed and their uterine horns were exposed to count implantation and fetus numbers to determine pre- and post-implantation loss rates. The fetuses were classified according to their birth weight. Severe and mild diabetic dams showed different glycemic responses during pregnancy, impairing fetal glycemia and weight, confirming that maternal glycemia is directly associated with fetal development. Newborns from severe diabetic mothers presented growth restriction, but mild diabetic mothers were not associated with an increased rate of macrosomic fetuses. Experimental models of severe diabetes during pregnancy reproduced maternal and fetal outcomes of pregnant women

Animal models for clinical and gestational diabetes: maternal and fetal outcomes

Directory of Open Access Journals (Sweden)

Kiss Ana CI

2009-10-01

Full Text Available Abstract Background Diabetes in pregnant women is associated with an increased risk of maternal and neonatal morbidity and remains a significant medical challenge. Diabetes during pregnancy may be divided into clinical diabetes and gestational diabetes. Experimental models are developed with the purpose of enhancing understanding of the pathophysiological mechanisms of diseases that affect humans. With regard to diabetes in pregnancy, experimental findings from models will lead to the development of treatment strategies to maintain a normal metabolic intrauterine milieu, improving perinatal development by preventing fetal growth restriction or macrosomia. Based on animal models of diabetes during pregnancy previously reported in the medical literature, the present study aimed to compare the impact of streptozotocin-induced severe (glycemia >300 mg/dl and mild diabetes (glycemia between 120 and 300 mg/dl on glycemia and maternal reproductive and fetal outcomes of Wistar rats to evaluate whether the animal model reproduces the maternal and perinatal results of clinical and gestational diabetes in humans. Methods On day 5 of life, 96 female Wistar rats were assigned to three experimental groups: control (n = 16, severe (n = 50 and mild diabetes (n = 30. At day 90 of life, rats were mated. On day 21 of pregnancy, rats were killed and their uterine horns were exposed to count implantation and fetus numbers to determine pre- and post-implantation loss rates. The fetuses were classified according to their birth weight. Results Severe and mild diabetic dams showed different glycemic responses during pregnancy, impairing fetal glycemia and weight, confirming that maternal glycemia is directly associated with fetal development. Newborns from severe diabetic mothers presented growth restriction, but mild diabetic mothers were not associated with an increased rate of macrosomic fetuses. Conclusion Experimental models of severe diabetes during pregnancy

Modelo experimental de trauma medular agudo produzido por aparelho estereotáxico modificado Experimental model of acute spinal cord injury produced by modified steriotaxic equipment

Directory of Open Access Journals (Sweden)

B.B.J. Torres

2010-02-01

Full Text Available Foram utilizados 55 ratos machos da espécie Rattus novergicus, variedade Wistar, com o objetivo de propor um modelo experimental de trauma medular produzido por aparelho estereotáxico modificado, capaz de reproduzir clinicamente lesões medulares padronizadas. Após realização de laminectomia dorsal de T13, utilizou-se peso compressivo de 50,5g (25 animais - grupo I ou 70,5g (30 animais - grupo II, durante cinco minutos, comprimindo a medula espinhal. Os animais foram assistidos durante oito dias, por meio de testes comportamentais para avaliar a sensibilidade dolorosa, a capacidade motora, o posicionamento tátil e proprioceptivo e a capacidade de manter-se em plano inclinado. No grupo I, observaram-se déficits neurológicos moderados e transitórios, que variaram entre os animais. No grupo II, foi possível obter um trauma padronizado, caracterizado por paraplegia bilateral e simétrica dos membros posteriores, perda de propriocepção e da sensibilidade dolorosa de todos os animais. A utilização do aparelho estereotáxico desenvolvido permite reproduzir clinicamente trauma medular padronizado em ratos, de maneira simples, econômica e satisfatória, o que poderá proporcionar avanços nas investigações terapêuticas, abrangendo doenças neurodegenerativas, como é o caso do trauma medular agudo.Fifty-five male rats (Rattus novergicus, Wistar variety, were used with the purpose of suggesting an experimental model of spinal cord trauma performed by using a modified stereotaxic equipment capable to reproduce clinically (standardized pattern spinal cord injury. After dorsal laminectomy of T13, a compression was performed with 50.5g (25 animals - group I or 70.5g (30 animals - group II during five minutes on spinal cord. The animals were assisted during eight days by behavioral tests to evaluate painful sensibility, motor capacity, proprioceptive and tactil placing, and stability on inclined plan. In the group I, moderate and transitory

Experimental and numerical study on free surface behavior of windowless target

International Nuclear Information System (INIS)

Su Guanyu; Gu Hanyang; Cheng Xu

2012-01-01

The formation and control method of coolant free surface is one of the key technologies for the design of windowless target in accelerator driven sub-critical system (ADS). Experimental and CFD investigations on free surface behavior were performed in a scaled windowless target model by using water as test fluid. Laser induced fluorescence was applied for flow field visualization. The free surface and flow field visualization were obtained at Re=30000-50000. Under high Re conditions, an unsteady vortex pair was obtained. By decreasing Re, the structure of the vortex becomes more turbulent. CFD simulation was performed using LES and kω-SST turbulence models, separately. The numerical results show that LES model can qualitatively reproduce the characteristics of flow field and free surface. (authors)

Experimental, statistical, and biological models of radon carcinogenesis

International Nuclear Information System (INIS)

Cross, F.T.

1991-09-01

Risk models developed for underground miners have not been consistently validated in studies of populations exposed to indoor radon. Imprecision in risk estimates results principally from differences between exposures in mines as compared to domestic environments and from uncertainties about the interaction between cigarette-smoking and exposure to radon decay products. Uncertainties in extrapolating miner data to domestic exposures can be reduced by means of a broad-based health effects research program that addresses the interrelated issues of exposure, respiratory tract dose, carcinogenesis (molecular/cellular and animal studies, plus developing biological and statistical models), and the relationship of radon to smoking and other copollutant exposures. This article reviews experimental animal data on radon carcinogenesis observed primarily in rats at Pacific Northwest Laboratory. Recent experimental and mechanistic carcinogenesis models of exposures to radon, uranium ore dust, and cigarette smoke are presented with statistical analyses of animal data. 20 refs., 1 fig

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.

Simulation and experimental validation of the performance of a absorption refrigerator

International Nuclear Information System (INIS)

Olbricht, Michael; Luke, Andrea

2015-01-01

The two biggest obstacles to a stronger market penetration of absorption refrigerators are their high cost and the size of the apparatus, which are due to the inaccurate methods for plant design. In order to contribute to an improved design a thermodynamic model is presented to describe the performance of a absorption refrigerator with the working fluid water/lithium. In this model, the processes are displayed in the single apparatus and coupled to each other in the systemic context. Thereby the interactions between the apparatus can specifically investigated and thus the process limiting component can be identified under the respective conditions. A validation of the simulation model and the boundary conditions used is done based on experimental data operating a self-developed absorption refrigerator. In the simulation, the heat transfer surfaces in accordance with the real system can be specified. The heat transport is taken into account based on typical values for the heat transfer in the individual apparatuses. Simulation results show good agreement with the experimental data. The physical relationships and influences externally defined operating parameters are correctly reproduced. Due to the chosen low heat transfer coefficient, the calculated cooling capacities by the model are below the experimentally measured. Finally, the possibilities and limitations are discussed by using the model and further improvement possibilities are suggested. [de

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)

Particle Shape Effect on Macroscopic Behaviour of Underground Structures: Numerical and Experimental Study

Directory of Open Access Journals (Sweden)

Szarf Krzysztof

2015-02-01

Full Text Available The mechanical performance of underground flexible structures such as buried pipes or culverts made of plastics depend not only on the properties of the structure, but also on the material surrounding it. Flexible drains can deflect by 30% with the joints staying tight, or even invert. Large deformations of the structure are difficult to model in the framework of Finite Element Method, but straightforward in Discrete Element Methods. Moreover, Discrete Element approach is able to provide information about the grain-grain and grain-structure interactions at the microscale. This paper presents numerical and experimental investigations of flexible buried pipe behaviour with focus placed on load transfer above the buried structure. Numerical modeling was able to reproduce the experimental results. Load repartition was observed, being affected by a number of factors such as particle shape, pipe friction and pipe stiffness.

Nonlocal Regularized Algebraic Reconstruction Techniques for MRI: An Experimental Study

Directory of Open Access Journals (Sweden)

Xin Li

2013-01-01

Full Text Available We attempt to revitalize researchers' interest in algebraic reconstruction techniques (ART by expanding their capabilities and demonstrating their potential in speeding up the process of MRI acquisition. Using a continuous-to-discrete model, we experimentally study the application of ART into MRI reconstruction which unifies previous nonuniform-fast-Fourier-transform- (NUFFT- based and gridding-based approaches. Under the framework of ART, we advocate the use of nonlocal regularization techniques which are leveraged from our previous research on modeling photographic images. It is experimentally shown that nonlocal regularization ART (NR-ART can often outperform their local counterparts in terms of both subjective and objective qualities of reconstructed images. On one real-world k-space data set, we find that nonlocal regularization can achieve satisfactory reconstruction from as few as one-third of samples. We also address an issue related to image reconstruction from real-world k-space data but overlooked in the open literature: the consistency of reconstructed images across different resolutions. A resolution-consistent extension of NR-ART is developed and shown to effectively suppress the artifacts arising from frequency extrapolation. Both source codes and experimental results of this work are made fully reproducible.

Validation of a buffet meal design in an experimental restaurant.

Science.gov (United States)

Allirot, Xavier; Saulais, Laure; Disse, Emmanuel; Roth, Hubert; Cazal, Camille; Laville, Martine

2012-06-01

We assessed the reproducibility of intakes and meal mechanics parameters (cumulative energy intake (CEI), number of bites, bite rate, mean energy content per bite) during a buffet meal designed in a natural setting, and their sensitivity to food deprivation. Fourteen men were invited to three lunch sessions in an experimental restaurant. Subjects ate their regular breakfast before sessions A and B. They skipped breakfast before session FAST. The same ad libitum buffet was offered each time. Energy intakes and meal mechanics were assessed by foods weighing and video recording. Intrasubject reproducibility was evaluated by determining intraclass correlation coefficients (ICC). Mixed-models were used to assess the effects of the sessions on CEI. We found a good reproducibility between A and B for total energy (ICC=0.82), carbohydrate (ICC=0.83), lipid (ICC=0.81) and protein intake (ICC=0.79) and for meal mechanics parameters. Total energy, lipid and carbohydrate intake were higher in FAST than in A and B. CEI were found sensitive to differences in hunger level while the other meal mechanics parameters were stable between sessions. In conclusion, a buffet meal in a normal eating environment is a valid tool for assessing the effects of interventions on intakes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Predictive modelling of the impact of argon injection on H-mode plasmas in JET with the RITM code

International Nuclear Information System (INIS)

Unterberg, B; Kalupin, D; Tokar', M Z; Corrigan, G; Dumortier, P; Huber, A; Jachmich, S; Kempenaars, M; Kreter, A; Messiaen, A M; Monier-Garbet, P; Ongena, J; Puiatti, M E; Valisa, M; Hellermann, M von

2004-01-01

Self-consistent modelling of energy and particle transport of the plasma background and impurities has been performed with the code RITM for argon seeded high density H-mode plasmas in JET. The code can reproduce both the profiles in the plasma core and the structure of the edge pedestal. The impact of argon on core transport is found to be small; in particular, no significant change in confinement is observed in both experimental and modelling results. The same transport model, which has been used to reproduce density peaking in the radiative improved mode in TEXTOR, reveals a flat density profile in Ar seeded JET H-mode plasmas in agreement with the experimental observations. This behaviour is attributed to the rather flat profile of the safety factor in the bulk of H-mode discharges

Quantitative comparisons between experimentally measured 2-D carbon radiation and Monte Carlo impurity (MCI) code simulations

International Nuclear Information System (INIS)

Evans, T.E.; Leonard, A.W.; West, W.P.; Finkenthal, D.F.; Fenstermacher, M.E.; Porter, G.D.

1998-08-01

Experimentally measured carbon line emissions and total radiated power distributions from the DIII-D divertor and Scrape-Off Layer (SOL) are compared to those calculated with the Monte Carlo Impurity (MCI) model. A UEDGE background plasma is used in MCI with the Roth and Garcia-Rosales (RG-R) chemical sputtering model and/or one of six physical sputtering models. While results from these simulations do not reproduce all of the features seen in the experimentally measured radiation patterns, the total radiated power calculated in MCI is in relatively good agreement with that measured by the DIII-D bolometric system when the Smith78 physical sputtering model is coupled to RG-R chemical sputtering in an unaltered UEDGE plasma. Alternatively, MCI simulations done with UEDGE background ion temperatures along the divertor target plates adjusted to better match those measured in the experiment resulted in three physical sputtering models which when coupled to the RG-R model gave a total radiated power that was within 10% of measured value

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

Ultraviolet radiation-induced carcinogenesis: mechanisms and experimental models

International Nuclear Information System (INIS)

Ramasamy, Karthikeyan; Shanmugam, Mohana; Balupillai, Agilan; Govindhasamy, Kanimozhi; Gunaseelan, Srithar; Muthusamy, Ganesan; Robert, Beualah Mary; Nagarajan, Rajendra Prasad

2017-01-01

Ultraviolet radiation (UVR) is a very prominent environmental toxic agent. UVR has been implicated in the initiation and progression of photocarcinogenesis. UVR exposure elicits numerous cellular and molecular events which include the generation of inflammatory mediators, DNA damage, epigenetic modifications, and oxidative damages mediated activation of signaling pathways. UVR-initiated signal transduction pathways are believed to be responsible for tumor promotion effects. UVR-induced carcinogenic mechanism has been well studied using various animal and cellular models. Human skin-derived dermal fibroblasts, epidermal keratinocytes, and melanocytes served as excellent cellular model systems for the understanding of UVR-mediated carcinogenic events. Apart from this, scientists developed reconstituted three-dimensional normal human skin equivalent models for the study of UVR signaling pathways. Moreover, hairless mice such as SKH-1, devoid of Hr gene, served as a valuable model for experimental carcinogenesis. Scientists have also used transgenic mice and dorsal portion shaved Swiss albino mice for UVR carcinogenesis studies. In this review, we have discussed the current progress in the study on ultraviolet B (UVB)-mediated carcinogenesis and outlined appropriate experimental models for both ultraviolet A- and UVB-mediated carcinogenesis. (author)

Comparison between a Computational Seated Human Model and Experimental Verification Data

Directory of Open Access Journals (Sweden)

Christian G. Olesen

2014-01-01

Full Text Available Sitting-acquired deep tissue injuries (SADTI are the most serious type of pressure ulcers. In order to investigate the aetiology of SADTI a new approach is under development: a musculo-skeletal model which can predict forces between the chair and the human body at different seated postures. This study focuses on comparing results from a model developed in the AnyBody Modeling System, with data collected from an experimental setup. A chair with force-measuring equipment was developed, an experiment was conducted with three subjects, and the experimental results were compared with the predictions of the computational model. The results show that the model predicted the reaction forces for different chair postures well. The correlation coefficients of how well the experiment and model correlate for the seat angle, backrest angle and footrest height was 0.93, 0.96, and 0.95. The study show a good agreement between experimental data and model prediction of forces between a human body and a chair. The model can in the future be used in designing wheelchairs or automotive seats.

Modelling and experimental studies on a mixed-mode natural convection solar crop-dryer

Energy Technology Data Exchange (ETDEWEB)

Forson, F.K. [Department of Mechanical Engineering, Kwame Nkrumah University of Science and Technology, Kumasi (Ghana); Nazha, M.A.A.; Rajakaruna, H. [School of Engineering and Technology, De Montfort University, Queens Building, Leicester LE1 9BH (United Kingdom)

2007-03-15

A mathematical model for drying agricultural products in a mixed-mode natural convection solar crop dryer (MNCSCD) using a single-pass double-duct solar air-heater (SPDDSAH) is presented. The model was developed in parallel with experimental work. The model comprises the air-heating process model, the drying model and the technical performance criteria model. The governing equations of the drying air temperature and humidity ratio; the material temperature and its moisture content; and performance criteria indicators are derived. The model requires the solution of a number of interrelated non-linear equations and a set of simultaneous differential equations. Results from experimental studies used for generating the required experimental data for validating the model are presented. Results of simulation runs using the model are presented and compared with the experimental data. It is shown that the model can predict the performance of the MNCSCD fairly accurately and therefore can be used as a design tool for prototype development. (author)

An improved empirical model for diversity gain on Earth-space propagation paths

Science.gov (United States)

Hodge, D. B.

1981-01-01

An empirical model was generated to estimate diversity gain on Earth-space propagation paths as a function of Earth terminal separation distance, link frequency, elevation angle, and angle between the baseline and the path azimuth. The resulting model reproduces the entire experimental data set with an RMS error of 0.73 dB.

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.

Modelization of ratcheting in biaxial experiments

International Nuclear Information System (INIS)

Guionnet, C.

1989-08-01

A new unified viscoplastic constitutive equation has been developed in order to interpret ratcheting experiments on mechanical structures of fast reactors. The model is based essentially on a generalized Armstrong Frederick equation for the kinematic variable; the coefficients of the dynamic recovery term in this equation is a function of both instantaneous and accumulated inelastic strain which is allowed to vary in an appropriate manner in order to reproduce the experimental ratcheting rate. The validity of the model is verified by comparing predictions with experimental results for austenitic stainless steel (17-12 SPH) tubular specimens subjected to cyclic torsional loading under constant tensile stress at 600 0 C [fr

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.

Using an experimental model for the study of therapeutic touch.

Science.gov (United States)

dos Santos, Daniella Soares; Marta, Ilda Estéfani Ribeiro; Cárnio, Evelin Capellari; de Quadros, Andreza Urba; Cunha, Thiago Mattar; de Carvalho, Emilia Campos

2013-02-01

to verify whether the Paw Edema Model can be used in investigations about the effects of Therapeutic Touch on inflammation by measuring the variables pain, edema and neutrophil migration. this is a pilot and experimental study, involving ten male mice of the same genetic strain and divided into experimental and control group, submitted to the chemical induction of local inflammation in the right back paw. The experimental group received a daily administration of Therapeutic Touch for 15 minutes during three days. the data showed statistically significant differences in the nociceptive threshold and in the paw circumference of the animals from the experimental group on the second day of the experiment. the experiment model involving animals can contribute to study the effects of Therapeutic Touch on inflammation, and adjustments are suggested in the treatment duration, number of sessions and experiment duration.

Experimental study and mathematical model on remediation of Cd spiked kaolinite by electrokinetics

International Nuclear Information System (INIS)

Mascia, Michele; Palmas, Simonetta; Polcaro, Anna Maria; Vacca, Annalisa; Muntoni, Aldo

2007-01-01

An experimental study on electrokinetic removal of cadmium from kaolinitic clays is presented in this work, which is aimed to investigate the effect of surface reactions on the electrokinetic process. Enhanced electrokinetic tests were performed in which the pH of the compartments was controlled. Cadmium spiked kaolin was adopted in the experimental runs. On the basis of the experimental results, a numerical model was formulated to simulate the cadmium (Cd) transport under an electric field by combining a one-dimensional diffusion-advection model with a geochemical model: the combined model describes the contaminant transport driven by chemical and electrical gradients, as well as the effect of the surface reactions. The geochemical model utilized parameters derived from the literature, and it was validated by experimental data obtained by sorption and titration experiments. Electrokinetic tests were utilized to validate the results of the proposed model. A good prediction of the behaviour of the soil/cadmium ions system under electrical field was obtained: the differences between experimental and model predicted profiles for the species considered were less than 5% in all the examined conditions

Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

Science.gov (United States)

Salsbury, Freddie R; Poole, Leslie B; Fetrow, Jacquelyn S

2012-11-01

One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pK(a) values (where the calculation should reproduce the pK(a) within experimental error). Both the general behavior of cysteines in proteins and the perturbed pK(a) in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pK(a) should be shifted, and validation of force field parameters for cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

Electrowetting on dielectric: experimental and model study of oil conductivity on rupture voltage

Science.gov (United States)

Zhao, Qing; Tang, Biao; Dong, Baoqin; Li, Hui; Zhou, Rui; Guo, Yuanyuan; Dou, Yingying; Deng, Yong; Groenewold, Jan; Henzen, Alexander Victor; Zhou, Guofu

2018-05-01

Electrowetting on dielectric devices uses a conducting (water) and insulating (oil) liquid phase in conjunction on a dielectric layer. In these devices, the wetting properties of the liquid phases can be manipulated by applying an electric field. The electric field can rupture the initially flat oil film and promotes further dewetting of the oil. Here, we investigate a problem in the operation of electrowetting on dielectric caused by a finite conductivity of the oil. In particular, we find that the voltage at which the oil film ruptures is sensitive to the application of relatively low DC voltages prior to switching. Here, we systematically investigate this dependence using controlled driving schemes. The mechanism behind these history effects point to charge transport processes in the dielectric and the oil, which can be modeled and characterized by a decay time. To quantify the effects the typical response timescales have been measured with a high-speed video camera. The results have been reproduced in simulations. In addition, a simplified yet accurate equivalent circuit model is developed to analyze larger data sets more conveniently. The experimental data support the hypothesis that each pixel can be characterized by a single decay time. We studied an ensemble of pixels and found that they showed a rather broad distribution of decay times with an average value of about 440 ms. This decay time can be interpreted as a discharge timescale of the oil, not to be confused with discharge of the entire system which is generally much faster (<1 ms). Through the equivalent circuit model, we also found that variations in the fluoropolymer (FP) conductivity cannot explain the distribution of decay times, while variations in oil conductivity can.

Falsification of Leggett's model using neutron matter waves

International Nuclear Information System (INIS)

Hasegawa, Yuji; Sponar, Stephan; Durstberger-Rennhofer, Katharina; Badurek, Gerald; Schmitzer, Claus; Bartosik, Hannes; Klepp, Jürgen

2012-01-01

According to Bell's theorem, no theory based on the joint assumption of realism and locality can reproduce certain predictions of quantum mechanics. Another class of realistic models, proposed by Leggett, that demands realism but abandons reliance on locality, is predicted to be in conflict with quantum mechanics. In this paper, we report on an experimental test of a contextual realistic model analogous to the model of Leggett performed with matter waves, more precisely with neutrons. Correlation measurements of the spin-energy entangled single-particle system show violation of a Leggett-type inequality by more than 7.6 standard deviations. Our experimental data falsify the contextual realistic model and are fully in favor of quantum mechanics. (paper)

Experimental Evaluation for the Microvibration Performance of a Segmented PC Method Based High Technology Industrial Facility Using 1/2 Scale Test Models

Directory of Open Access Journals (Sweden)

Sijun Kim

2017-01-01

Full Text Available The precast concrete (PC method used in the construction process of high technology industrial facilities is limited when applied to those with greater span lengths, due to the transport length restriction (maximum length of 15~16 m in Korea set by traffic laws. In order to resolve this, this study introduces a structural system with a segmented PC system, and a 1/2 scale model with a width of 9000 mm (hereafter Segmented Model is manufactured to evaluate vibration performance. Since a real vibrational environment cannot be reproduced for vibration testing using a scale model, a comparative analysis of their relative performances is conducted in this study. For this purpose, a 1/2 scale model with a width of 7200 mm (hereafter Nonsegmented Model of a high technology industrial facility is additionally prepared using the conventional PC method. By applying the same experiment method for both scale models and comparing the results, the relative vibration performance of the Segmented Model is observed. Through impact testing, the natural frequencies of the two scale models are compared. Also, in order to analyze the estimated response induced by the equipment, the vibration responses due to the exciter are compared. The experimental results show that the Segmented Model exhibits similar or superior performances when compared to the Nonsegmented Model.

Waterlike glass polyamorphism in a monoatomic isotropic Jagla model.

Science.gov (United States)

Xu, Limei; Giovambattista, Nicolas; Buldyrev, Sergey V; Debenedetti, Pablo G; Stanley, H Eugene

2011-02-14

We perform discrete-event molecular dynamics simulations of a system of particles interacting with a spherically-symmetric (isotropic) two-scale Jagla pair potential characterized by a hard inner core, a linear repulsion at intermediate separations, and a weak attractive interaction at larger separations. This model system has been extensively studied due to its ability to reproduce many thermodynamic, dynamic, and structural anomalies of liquid water. The model is also interesting because: (i) it is very simple, being composed of isotropically interacting particles, (ii) it exhibits polyamorphism in the liquid phase, and (iii) its slow crystallization kinetics facilitate the study of glassy states. There is interest in the degree to which the known polyamorphism in glassy water may have parallels in liquid water. Motivated by parallels between the properties of the Jagla potential and those of water in the liquid state, we study the metastable phase diagram in the glass state. Specifically, we perform the computational analog of the protocols followed in the experimental studies of glassy water. We find that the Jagla potential calculations reproduce three key experimental features of glassy water: (i) the crystal-to-high-density amorphous solid (HDA) transformation upon isothermal compression, (ii) the low-density amorphous solid (LDA)-to-HDA transformation upon isothermal compression, and (iii) the HDA-to-very-high-density amorphous solid (VHDA) transformation upon isobaric annealing at high pressure. In addition, the HDA-to-LDA transformation upon isobaric heating, observed in water experiments, can only be reproduced in the Jagla model if a free surface is introduced in the simulation box. The HDA configurations obtained in cases (i) and (ii) are structurally indistinguishable, suggesting that both processes result in the same glass. With the present parametrization, the evolution of density with pressure or temperature is remarkably similar to the