Cyberinfrastructure to Support Collaborative and Reproducible Computational Hydrologic Modeling

Science.gov (United States)

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

2017-12-01

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

Reproducibility of quantitative susceptibility mapping in the brain at two field strengths from two vendors.

Science.gov (United States)

Deh, Kofi; Nguyen, Thanh D; Eskreis-Winkler, Sarah; Prince, Martin R; Spincemaille, Pascal; Gauthier, Susan; Kovanlikaya, Ilhami; Zhang, Yan; Wang, Yi

2015-12-01

To assess the reproducibility of brain quantitative susceptibility mapping (QSM) in healthy subjects and in patients with multiple sclerosis (MS) on 1.5 and 3T scanners from two vendors. Ten healthy volunteers and 10 patients were scanned twice on a 3T scanner from one vendor. The healthy volunteers were also scanned on a 1.5T scanner from the same vendor and on a 3T scanner from a second vendor. Similar imaging parameters were used for all scans. QSM images were reconstructed using a recently developed nonlinear morphology-enabled dipole inversion (MEDI) algorithm with L1 regularization. Region-of-interest (ROI) measurements were obtained for 20 major brain structures. Reproducibility was evaluated with voxel-wise and ROI-based Bland-Altman plots and linear correlation analysis. ROI-based QSM measurements showed excellent correlation between all repeated scans (correlation coefficient R ≥ 0.97), with a mean difference of less than 1.24 ppb (healthy subjects) and 4.15 ppb (patients), and 95% limits of agreements of within -25.5 to 25.0 ppb (healthy subjects) and -35.8 to 27.6 ppb (patients). Voxel-based QSM measurements had a good correlation (0.64 ≤ R ≤ 0.88) and limits of agreements of -60 to 60 ppb or less. Brain QSM measurements have good interscanner and same-scanner reproducibility for healthy and MS subjects, respectively, on the systems evaluated in this study. © 2015 Wiley Periodicals, Inc.

Hippocampal volume change measurement: quantitative assessment of the reproducibility of expert manual outlining and the automated methods FreeSurfer and FIRST.

Science.gov (United States)

Mulder, Emma R; de Jong, Remko A; Knol, Dirk L; van Schijndel, Ronald A; Cover, Keith S; Visser, Pieter J; Barkhof, Frederik; Vrenken, Hugo

2014-05-15

To measure hippocampal volume change in Alzheimer's disease (AD) or mild cognitive impairment (MCI), expert manual delineation is often used because of its supposed accuracy. It has been suggested that expert outlining yields poorer reproducibility as compared to automated methods, but this has not been investigated. To determine the reproducibilities of expert manual outlining and two common automated methods for measuring hippocampal atrophy rates in healthy aging, MCI and AD. From the Alzheimer's Disease Neuroimaging Initiative (ADNI), 80 subjects were selected: 20 patients with AD, 40 patients with mild cognitive impairment (MCI) and 20 healthy controls (HCs). Left and right hippocampal volume change between baseline and month-12 visit was assessed by using expert manual delineation, and by the automated software packages FreeSurfer (longitudinal processing stream) and FIRST. To assess reproducibility of the measured hippocampal volume change, both back-to-back (BTB) MPRAGE scans available for each visit were analyzed. Hippocampal volume change was expressed in μL, and as a percentage of baseline volume. Reproducibility of the 1-year hippocampal volume change was estimated from the BTB measurements by using linear mixed model to calculate the limits of agreement (LoA) of each method, reflecting its measurement uncertainty. Using the delta method, approximate p-values were calculated for the pairwise comparisons between methods. Statistical analyses were performed both with inclusion and exclusion of visibly incorrect segmentations. Visibly incorrect automated segmentation in either one or both scans of a longitudinal scan pair occurred in 7.5% of the hippocampi for FreeSurfer and in 6.9% of the hippocampi for FIRST. After excluding these failed cases, reproducibility analysis for 1-year percentage volume change yielded LoA of ±7.2% for FreeSurfer, ±9.7% for expert manual delineation, and ±10.0% for FIRST. Methods ranked the same for reproducibility of 1

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.

Computed Tomography of the Human Pineal Gland for Study of the Sleep-Wake Rhythm: Reproducibility of a Semi-Quantitative Approach

Energy Technology Data Exchange (ETDEWEB)

Schmitz, S.A.; Platzek, I.; Kunz, D.; Mahlberg, R.; Wolf, K.J.; Heidenreich, J.O. [Charite - Universitaetsmedizin Berlin, Campus Benjamin Franklin, Berlin (Germany). Dept. of Radiology and Nuclear Medicine

2006-10-15

Purpose: To propose a semi-quantitative computed tomography (CT) protocol for determining uncalcified pineal tissue (UCPT), and to evaluate its reproducibility in modification of studies showing that the degree of calcification is a potential marker of deficient melatonin production and may prove an instability marker of circadian rhythm. Material and Methods: Twenty-two pineal gland autopsy specimens were scanned in a skull phantom with different slice thickness twice and the uncalcified tissue visually assessed using a four-point scale. The maximum gland density was measured and its inverse graded on a non-linear four-point scale. The sum of both scores was multiplied by the gland volume to yield the UCPT. The within-subject variance of UCPT was determined and compared between scans of different slice thickness. Results: The UCPT of the first measurement, in arbitrary units, was 39{+-}52.5 for 1 mm slice thickness, 44{+-}51.1 for 2 mm, 45{+-}34.8 for 4 mm, and 84{+-}58.0 for 8 mm. Significant differences of within-subject variance of UCPT were found between 1 and 4 mm, 1 and 8 mm, and 2 and 8 mm slice thicknesses ( P <0.05). Conclusion: A superior reproducibility of the semi-quantitative CT determination of UCPT was found using 1 and 2 mm slice thicknesses. These data support the use of thin slices of 1 and 2 mm. The benefit in reproducibility from thin slices has to be carefully weighted against their considerably higher radiation exposure.

Relative validity and reproducibility of a parent-administered semi-quantitative FFQ for assessing food intake in Danish children aged 3-9 years

DEFF Research Database (Denmark)

Buch-Andersen, Tine; Perez-Cueto, Armando; Toft, Ulla Marie Nørgaard

2016-01-01

OBJECTIVE: To assess the relative validity and reproducibility of the semi-quantitative FFQ (SFFQ) applied in the evaluation of a community intervention study, SoL-Bornholm, for estimating food intakes. DESIGN: The reference measure was a 4 d estimated food record. The SFFQ was completed two time...

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

Science.gov (United States)

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

2015-01-01

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

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

Qualitative and quantitative histopathology in transitional cell carcinomas of the urinary bladder. An international investigation of intra- and interobserver reproducibility

DEFF Research Database (Denmark)

Sørensen, Flemming Brandt; Sasaki, M; Fukuzawa, S

1994-01-01

a random, systematic sampling scheme.RESULTS: The results were compared by bivariate correlation analyses and Kendall's tau. The international interobserver reproducibility of qualitative gradings was rather poor (kappa = 0.51), especially for grade 2 tumors (kappa = 0.28). Likewise, the interobserver.......54). This can probably be related to the manual design of the sampling scheme and may be solved by introducing a motorized object stage in the systematic selection of fields of vision for quantitative measurements. However, the nuclear mean size estimators are unaffected by such sampling variability...... of both qualitative and quantitative grading methods. Grading of malignancy was performed by one observer in Japan (using the World Health Organization scheme), and by two observers in Denmark (using the Bergkvist system). A "translation" between the systems, grade for grade, and kappa statistics were...

Efficient Generation and Selection of Virtual Populations in Quantitative Systems Pharmacology Models.

Science.gov (United States)

Allen, R J; Rieger, T R; Musante, C J

2016-03-01

Quantitative systems pharmacology models mechanistically describe a biological system and the effect of drug treatment on system behavior. Because these models rarely are identifiable from the available data, the uncertainty in physiological parameters may be sampled to create alternative parameterizations of the model, sometimes termed "virtual patients." In order to reproduce the statistics of a clinical population, virtual patients are often weighted to form a virtual population that reflects the baseline characteristics of the clinical cohort. Here we introduce a novel technique to efficiently generate virtual patients and, from this ensemble, demonstrate how to select a virtual population that matches the observed data without the need for weighting. This approach improves confidence in model predictions by mitigating the risk that spurious virtual patients become overrepresented in virtual populations.

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.

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

Directory of Open Access Journals (Sweden)

Monica J. Justice

2016-02-01

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

Reproducibility of the assessment of myocardial function using gated Tc-99m-MIBI SPECT and quantitative software

International Nuclear Information System (INIS)

Lee, Dong Soo; Cheon, Gi Jeong; Ahn, Ji Young; Jeong, Joon Ki; Lee, Myung Chul

1998-01-01

We investigated reproducibility of the quantification of left ventricular volume and ejection fraction, and grading of myocardial wall motion and systolic thickening when we used gated myocardial SPECT and Cedars quantification software. We performed gated myocardial SPECT in 33 consecutive patients twice in the same position after Tc-99m-MIBI SPECT. We used 16 frames per cycle for the gating of sequential Tc-99m-MIBI SPECT. After reconstruction, we used Cedars quantitative gated SPECT and calculated ventricular volume and ejection fraction (EF). Wall motion was graded using 5 point score. Wall thickening was graded using 4 point score. Coefficient of variation for re-examination of volume and fraction were calculated. Kappa values (k-value) for assessing reproducibility of wall motion or wall thickening were calculated. Enddiastolic volumes (EDV) ranged from 58 ml to 248 ml (122 ml +/-42 ml), endsystolic volumes (ESV) from 20 ml to 174 ml (65 ml+/-39 ml), and EF from 20% to 68% (51%+/-14%). Geometric mean of standard deviations of 33 patients was 5.0 ml for EDV, 3.9 ml for ESV and 1.9% for EF. Their average differences were not different from zero (p>0.05). k-value for wall motion using 2 consecutive images was 0.76 (confidence interval: 0.71-0.81). k-value was 0.87 (confidence interval: 0.83-0.90) for assessment of wall thickening. We concluded that quantification of functional indices, assessment of wall motion and wall thickening using gated Tc-99m MIBI SPECT was reproducible and we could use this method for the evaluation of short-acting drug effect

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.

The quest for improved reproducibility in MALDI mass spectrometry.

Science.gov (United States)

O'Rourke, Matthew B; Djordjevic, Steven P; Padula, Matthew P

2018-03-01

Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018. © 2016 Wiley Periodicals, Inc.

Archiving Reproducible Research with R and Dataverse

DEFF Research Database (Denmark)

Leeper, Thomas

2014-01-01

Reproducible research and data archiving are increasingly important issues in research involving statistical analyses of quantitative data. This article introduces the dvn package, which allows R users to publicly archive datasets, analysis files, codebooks, and associated metadata in Dataverse...

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.

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.

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

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

Science.gov (United States)

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

2016-01-01

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

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.

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.

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

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.

Reproducibility of esophageal scintigraphy using semi-solid yoghurt

Energy Technology Data Exchange (ETDEWEB)

Imai, Yukinori; Kinoshita, Manabu; Asakura, Yasushi; Kakinuma, Tohru; Shimoji, Katsunori; Fujiwara, Kenji; Suzuki, Kenji; Miyamae, Tatsuya [Saitama Medical School, Moroyama (Japan)

1999-10-01

Esophageal scintigraphy is a non-invasive method which evaluate esophageal function quantitatively. We applied new technique using semi-solid yoghurt, which can evaluate esophageal function in a sitting position. To evaluate the reproducibility of this method, scintigraphy were performed in 16 healthy volunteers. From the result of four swallows except the first one, the mean coefficients of variation in esophageal transit time and esophageal emptying time were 12.8% and 13.4% respectively (interday variation). As regards the interday variation, this method had also good reproducibility from the result on the 2 separate days. (author)

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

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

Examination of reproducibility in microbiological degredation experiments

DEFF Research Database (Denmark)

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

1998-01-01

Experimental data indicate that certain microbiological degradation experiments have a limited reproducibility. Nine identical batch experiments were carried out on 3 different days to examine reproducibility. A pure culture, isolated from soil, grew with toluene as the only carbon and energy...... source. Toluene was degraded under aerobic conditions at a constant temperature of 28 degreesC. The experiments were modelled by a Monod model - extended to meet the air/liquid system, and the parameter values were estimated using a statistical nonlinear estimation procedure. Model reduction analysis...... resulted in a simpler model without the biomass decay term. In order to test for model reduction and reproducibility of parameter estimates, a likelihood ratio test was employed. The limited reproducibility for these experiments implied that all 9 batch experiments could not be described by the same set...

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.

Quantitative reactive modeling and verification.

Science.gov (United States)

Henzinger, Thomas A

Formal verification aims to improve the quality of software by detecting errors before they do harm. At the basis of formal verification is the logical notion of correctness , which purports to capture whether or not a program behaves as desired. We suggest that the boolean partition of software into correct and incorrect programs falls short of the practical need to assess the behavior of software in a more nuanced fashion against multiple criteria. We therefore propose to introduce quantitative fitness measures for programs, specifically for measuring the function, performance, and robustness of reactive programs such as concurrent processes. This article describes the goals of the ERC Advanced Investigator Project QUAREM. The project aims to build and evaluate a theory of quantitative fitness measures for reactive models. Such a theory must strive to obtain quantitative generalizations of the paradigms that have been success stories in qualitative reactive modeling, such as compositionality, property-preserving abstraction and abstraction refinement, model checking, and synthesis. The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology. In particular, we will use the quantitative reactive models and fitness measures developed in this project for testing hypotheses about the mechanisms behind data from biological experiments.

A Cytomorphic Chip for Quantitative Modeling of Fundamental Bio-Molecular Circuits.

Science.gov (United States)

2015-08-01

We describe a 0.35 μm BiCMOS silicon chip that quantitatively models fundamental molecular circuits via efficient log-domain cytomorphic transistor equivalents. These circuits include those for biochemical binding with automatic representation of non-modular and loading behavior, e.g., in cascade and fan-out topologies; for representing variable Hill-coefficient operation and cooperative binding; for representing inducer, transcription-factor, and DNA binding; for probabilistic gene transcription with analogic representations of log-linear and saturating operation; for gain, degradation, and dynamics of mRNA and protein variables in transcription and translation; and, for faithfully representing biological noise via tunable stochastic transistor circuits. The use of on-chip DACs and ADCs enables multiple chips to interact via incoming and outgoing molecular digital data packets and thus create scalable biochemical reaction networks. The use of off-chip digital processors and on-chip digital memory enables programmable connectivity and parameter storage. We show that published static and dynamic MATLAB models of synthetic biological circuits including repressilators, feed-forward loops, and feedback oscillators are in excellent quantitative agreement with those from transistor circuits on the chip. Computationally intensive stochastic Gillespie simulations of molecular production are also rapidly reproduced by the chip and can be reliably tuned over the range of signal-to-noise ratios observed in biological cells.

Currency risk and prices of oil and petroleum products: a simulation with a quantitative model

International Nuclear Information System (INIS)

Aniasi, L.; Ottavi, D.; Rubino, E.; Saracino, A.

1992-01-01

This paper analyzes the relationship between the exchange rates of the US Dollar against the four major European currencies and the prices of oil and its main products in those countries. In fact, the sensitivity of the prices to the exchange rate movements is of fundamental importance for the refining and distribution industries of importing countries. The result of the analysis shows that in neither free market conditions, as those present in Great Britain, France and Germany, nor in regulated markets, i.e. the italian one, do the variations of petroleum product prices fully absorb the variation of the exchange rates. In order to assess the above relationship, we first tested the order of co-integration of the time series of exchange rates of EMS currencies with those of international prices of oil and its derivative products; then we used a transfer-function model to reproduce the quantitative relationships between those variables. Using these results, we then reproduced domestic price functions with partial adjustment mechanisms. Finally, we used the above model to run a simulation of the deviation from the steady-state pattern caused by exchange-rate exogenous shocks. 21 refs., 5 figs., 3 tabs

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.

Quantitative Modeling of Landscape Evolution, Treatise on Geomorphology

NARCIS (Netherlands)

Temme, A.J.A.M.; Schoorl, J.M.; Claessens, L.F.G.; Veldkamp, A.; Shroder, F.S.

2013-01-01

This chapter reviews quantitative modeling of landscape evolution – which means that not just model studies but also modeling concepts are discussed. Quantitative modeling is contrasted with conceptual or physical modeling, and four categories of model studies are presented. Procedural studies focus

Operations management research methodologies using quantitative modeling

NARCIS (Netherlands)

Bertrand, J.W.M.; Fransoo, J.C.

2002-01-01

Gives an overview of quantitative model-based research in operations management, focusing on research methodology. Distinguishes between empirical and axiomatic research, and furthermore between descriptive and normative research. Presents guidelines for doing quantitative model-based research in

The Harm Done to Reproducibility by the Culture of Null Hypothesis Significance Testing.

Science.gov (United States)

Lash, Timothy L

2017-09-15

In the last few years, stakeholders in the scientific community have raised alarms about a perceived lack of reproducibility of scientific results. In reaction, guidelines for journals have been promulgated and grant applicants have been asked to address the rigor and reproducibility of their proposed projects. Neither solution addresses a primary culprit, which is the culture of null hypothesis significance testing that dominates statistical analysis and inference. In an innovative research enterprise, selection of results for further evaluation based on null hypothesis significance testing is doomed to yield a low proportion of reproducible results and a high proportion of effects that are initially overestimated. In addition, the culture of null hypothesis significance testing discourages quantitative adjustments to account for systematic errors and quantitative incorporation of prior information. These strategies would otherwise improve reproducibility and have not been previously proposed in the widely cited literature on this topic. Without discarding the culture of null hypothesis significance testing and implementing these alternative methods for statistical analysis and inference, all other strategies for improving reproducibility will yield marginal gains at best. © 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.

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

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

Reproducibility in light microscopy: Maintenance, standards and SOPs.

Science.gov (United States)

Deagle, Rebecca C; Wee, Tse-Luen Erika; Brown, Claire M

2017-08-01

Light microscopy has grown to be a valuable asset in both the physical and life sciences. It is a highly quantitative method available in individual research laboratories and often centralized in core facilities. However, although quantitative microscopy is becoming a customary tool in research, it is rarely standardized. To achieve accurate quantitative microscopy data and reproducible results, three levels of standardization must be considered: (1) aspects of the microscope, (2) the sample, and (3) the detector. The accuracy of the data is only as reliable as the imaging system itself, thereby imposing the need for routine standard performance testing. Depending on the task some maintenance procedures should be performed once a month, some before each imaging session, while others conducted annually. This text should be implemented as a resource for researchers to integrate with their own standard operating procedures to ensure the highest quality quantitative microscopy data. Copyright © 2017. Published by Elsevier Ltd.

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

Science.gov (United States)

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

2016-01-01

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

Quantitative analysis of patient-specific dosimetric IMRT verification

International Nuclear Information System (INIS)

Budgell, G J; Perrin, B A; Mott, J H L; Fairfoul, J; Mackay, R I

2005-01-01

Patient-specific dosimetric verification methods for IMRT treatments are variable, time-consuming and frequently qualitative, preventing evidence-based reduction in the amount of verification performed. This paper addresses some of these issues by applying a quantitative analysis parameter to the dosimetric verification procedure. Film measurements in different planes were acquired for a series of ten IMRT prostate patients, analysed using the quantitative parameter, and compared to determine the most suitable verification plane. Film and ion chamber verification results for 61 patients were analysed to determine long-term accuracy, reproducibility and stability of the planning and delivery system. The reproducibility of the measurement and analysis system was also studied. The results show that verification results are strongly dependent on the plane chosen, with the coronal plane particularly insensitive to delivery error. Unexpectedly, no correlation could be found between the levels of error in different verification planes. Longer term verification results showed consistent patterns which suggest that the amount of patient-specific verification can be safely reduced, provided proper caution is exercised: an evidence-based model for such reduction is proposed. It is concluded that dose/distance to agreement (e.g., 3%/3 mm) should be used as a criterion of acceptability. Quantitative parameters calculated for a given criterion of acceptability should be adopted in conjunction with displays that show where discrepancies occur. Planning and delivery systems which cannot meet the required standards of accuracy, reproducibility and stability to reduce verification will not be accepted by the radiotherapy community

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

International Nuclear Information System (INIS)

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

2007-01-01

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

Reproducibility and relative validity of a brief quantitative food frequency questionnaire for assessing fruit and vegetable intakes in North-African women.

Science.gov (United States)

Landais, E; Gartner, A; Bour, A; McCullough, F; Delpeuch, F; Holdsworth, M

2014-04-01

In the context of a rapidly increasing prevalence of noncommunicable diseases, fruit and vegetables could play a key preventive role. To date, there is no rapid assessment tool available for measuring the fruit and vegetable intakes of North-African women. The present study aimed to investigate the reproducibility and relative validity of an eight-item quantitative food frequency questionnaire that measures the fruit and vegetable intakes (FV-FFQ) of Moroccan women. During a 1-week period, 100 women, living in the city of Rabat, Morocco (aged 20-49 years) completed the short FV-FFQ twice: once at baseline (FV-FFQ1) and once at the end of the study (FV-FFQ2). In the mean time, participants completed three 24-h dietary recalls. All questionnaires were administered by interviewers. Reproducibility was assessed by computing Spearman's correlation coefficients, intraclass correlation (ICC) coefficients and kappa statistics. Relative validity was assessed by computing Wilcoxon signed-rank tests and Spearman's correlation coefficients, as well as by performing Bland-Altman plots. In terms of reproducibility, Spearman's correlation coefficient was 0.56; ICC coefficient was 0.68; and weighted kappa was 0.35. In terms of relative validity, compared with the three 24-h recalls, the FV-FFQ slightly underestimated mean fruit and vegetable intakes (-10.9%; P = 0.006); Spearman's correlation coefficient was 0.69; at the individual level, intakes measured by the FV-FFQ were between 0.39 and 2.19 times those measured by the 24-h recalls. The brief eight-item FV-FFQ is a reliable and relatively valid tool for measuring mean fruit and vegetable intakes at the population level, although this is not the case at the individual level. © 2013 The Authors Journal of Human Nutrition and Dietetics © 2013 The British Dietetic Association Ltd.

International Interlaboratory Digital PCR Study Demonstrating High Reproducibility for the Measurement of a Rare Sequence Variant.

Science.gov (United States)

Whale, Alexandra S; Devonshire, Alison S; Karlin-Neumann, George; Regan, Jack; Javier, Leanne; Cowen, Simon; Fernandez-Gonzalez, Ana; Jones, Gerwyn M; Redshaw, Nicholas; Beck, Julia; Berger, Andreas W; Combaret, Valérie; Dahl Kjersgaard, Nina; Davis, Lisa; Fina, Frederic; Forshew, Tim; Fredslund Andersen, Rikke; Galbiati, Silvia; González Hernández, Álvaro; Haynes, Charles A; Janku, Filip; Lacave, Roger; Lee, Justin; Mistry, Vilas; Pender, Alexandra; Pradines, Anne; Proudhon, Charlotte; Saal, Lao H; Stieglitz, Elliot; Ulrich, Bryan; Foy, Carole A; Parkes, Helen; Tzonev, Svilen; Huggett, Jim F

2017-02-07

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate laboratories. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using quantitative PCR (qPCR) or next generation sequencing (NGS) due to the presence of competing wild type sequences and the need for calibration. Using dPCR, 18 laboratories were able to quantify the G12D marker within 12% of each other in all samples. Three laboratories appeared to measure consistently outlying results; however, proper application of a follow-up analysis recommendation rectified their data. Our findings show that dPCR has demonstrable reproducibility across a large number of laboratories without calibration. This could enable the reproducible application of molecular stratification to guide therapy and, potentially, for molecular diagnostics.

Improvement of the ID model for quantitative network data

DEFF Research Database (Denmark)

Sørensen, Peter Borgen; Damgaard, Christian Frølund; Dupont, Yoko Luise

2015-01-01

Many interactions are often poorly registered or even unobserved in empirical quantitative networks. Hence, the output of the statistical analyses may fail to differentiate between patterns that are statistical artefacts and those which are real characteristics of ecological networks. Such artefa......Many interactions are often poorly registered or even unobserved in empirical quantitative networks. Hence, the output of the statistical analyses may fail to differentiate between patterns that are statistical artefacts and those which are real characteristics of ecological networks......)1. This presentation will illustrate the application of the ID method based on a data set which consists of counts of visits by 152 pollinator species to 16 plant species. The method is based on two definitions of the underlying probabilities for each combination of pollinator and plant species: (1), pi...... reproduce the high number of zero valued cells in the data set and mimic the sampling distribution. 1 Sørensen et al, Journal of Pollination Ecology, 6(18), 2011, pp129-139...

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.

Compositional and Quantitative Model Checking

DEFF Research Database (Denmark)

Larsen, Kim Guldstrand

2010-01-01

This paper gives a survey of a composition model checking methodology and its succesfull instantiation to the model checking of networks of finite-state, timed, hybrid and probabilistic systems with respect; to suitable quantitative versions of the modal mu-calculus [Koz82]. The method is based...

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,

Modeling reproducibility of porescale multiphase flow experiments

Science.gov (United States)

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

2017-12-01

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

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.

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

Quantitative modeling of the ionospheric response to geomagnetic activity

Directory of Open Access Journals (Sweden)

T. J. Fuller-Rowell

Full Text Available A physical model of the coupled thermosphere and ionosphere has been used to determine the accuracy of model predictions of the ionospheric response to geomagnetic activity, and assess our understanding of the physical processes. The physical model is driven by empirical descriptions of the high-latitude electric field and auroral precipitation, as measures of the strength of the magnetospheric sources of energy and momentum to the upper atmosphere. Both sources are keyed to the time-dependent TIROS/NOAA auroral power index. The output of the model is the departure of the ionospheric F region from the normal climatological mean. A 50-day interval towards the end of 1997 has been simulated with the model for two cases. The first simulation uses only the electric fields and auroral forcing from the empirical models, and the second has an additional source of random electric field variability. In both cases, output from the physical model is compared with F-region data from ionosonde stations. Quantitative model/data comparisons have been performed to move beyond the conventional "visual" scientific assessment, in order to determine the value of the predictions for operational use. For this study, the ionosphere at two ionosonde stations has been studied in depth, one each from the northern and southern mid-latitudes. The model clearly captures the seasonal dependence in the ionospheric response to geomagnetic activity at mid-latitude, reproducing the tendency for decreased ion density in the summer hemisphere and increased densities in winter. In contrast to the "visual" success of the model, the detailed quantitative comparisons, which are necessary for space weather applications, are less impressive. The accuracy, or value, of the model has been quantified by evaluating the daily standard deviation, the root-mean-square error, and the correlation coefficient between the data and model predictions. The modeled quiet-time variability, or standard

Quantitative modeling of the ionospheric response to geomagnetic activity

Directory of Open Access Journals (Sweden)

T. J. Fuller-Rowell

2000-07-01

Full Text Available A physical model of the coupled thermosphere and ionosphere has been used to determine the accuracy of model predictions of the ionospheric response to geomagnetic activity, and assess our understanding of the physical processes. The physical model is driven by empirical descriptions of the high-latitude electric field and auroral precipitation, as measures of the strength of the magnetospheric sources of energy and momentum to the upper atmosphere. Both sources are keyed to the time-dependent TIROS/NOAA auroral power index. The output of the model is the departure of the ionospheric F region from the normal climatological mean. A 50-day interval towards the end of 1997 has been simulated with the model for two cases. The first simulation uses only the electric fields and auroral forcing from the empirical models, and the second has an additional source of random electric field variability. In both cases, output from the physical model is compared with F-region data from ionosonde stations. Quantitative model/data comparisons have been performed to move beyond the conventional "visual" scientific assessment, in order to determine the value of the predictions for operational use. For this study, the ionosphere at two ionosonde stations has been studied in depth, one each from the northern and southern mid-latitudes. The model clearly captures the seasonal dependence in the ionospheric response to geomagnetic activity at mid-latitude, reproducing the tendency for decreased ion density in the summer hemisphere and increased densities in winter. In contrast to the "visual" success of the model, the detailed quantitative comparisons, which are necessary for space weather applications, are less impressive. The accuracy, or value, of the model has been quantified by evaluating the daily standard deviation, the root-mean-square error, and the correlation coefficient between the data and model predictions. The modeled quiet-time variability, or standard

Development of a Rapid Real-Time PCR Assay for Quantitation of Pneumocystis carinii f. sp. Carinii

DEFF Research Database (Denmark)

Larsen, Hans Henrik; Kovacs, Joseph A; Stock, Frida

2002-01-01

A method for reliable quantification of Pneumocystis carinii in research models of P. carinii pneumonia (PCP) that is more convenient and reproducible than microscopic enumeration of organisms would greatly facilitate investigations of this organism. We developed a rapid quantitative touchdown (QTD......) PCR assay for detecting P. carinii f. sp. carinii, the subspecies of P. carinii commonly used in research models of PCP. The assay was based on the single-copy dihydrofolate reductase gene and was able to detect ... 6 log values for standards containing > or =5 copies/tube. Application of the assay to a series of 10-fold dilutions of P. carinii organisms isolated from rat lung demonstrated that it was reproducibly quantitative over 5 log values (r = 0.99). The assay was applied to a recently reported in vitro...

Generalized PSF modeling for optimized quantitation in PET imaging.

Science.gov (United States)

Ashrafinia, Saeed; Mohy-Ud-Din, Hassan; Karakatsanis, Nicolas A; Jha, Abhinav K; Casey, Michael E; Kadrmas, Dan J; Rahmim, Arman

2017-06-21

Point-spread function (PSF) modeling offers the ability to account for resolution degrading phenomena within the PET image generation framework. PSF modeling improves resolution and enhances contrast, but at the same time significantly alters image noise properties and induces edge overshoot effect. Thus, studying the effect of PSF modeling on quantitation task performance can be very important. Frameworks explored in the past involved a dichotomy of PSF versus no-PSF modeling. By contrast, the present work focuses on quantitative performance evaluation of standard uptake value (SUV) PET images, while incorporating a wide spectrum of PSF models, including those that under- and over-estimate the true PSF, for the potential of enhanced quantitation of SUVs. The developed framework first analytically models the true PSF, considering a range of resolution degradation phenomena (including photon non-collinearity, inter-crystal penetration and scattering) as present in data acquisitions with modern commercial PET systems. In the context of oncologic liver FDG PET imaging, we generated 200 noisy datasets per image-set (with clinically realistic noise levels) using an XCAT anthropomorphic phantom with liver tumours of varying sizes. These were subsequently reconstructed using the OS-EM algorithm with varying PSF modelled kernels. We focused on quantitation of both SUV mean and SUV max , including assessment of contrast recovery coefficients, as well as noise-bias characteristics (including both image roughness and coefficient of-variability), for different tumours/iterations/PSF kernels. It was observed that overestimated PSF yielded more accurate contrast recovery for a range of tumours, and typically improved quantitative performance. For a clinically reasonable number of iterations, edge enhancement due to PSF modeling (especially due to over-estimated PSF) was in fact seen to lower SUV mean bias in small tumours. Overall, the results indicate that exactly matched PSF

Inter-examiner reproducibility of tests for lumbar motor control

Directory of Open Access Journals (Sweden)

Elkjaer Arne

2011-05-01

Full Text Available Abstract Background Many studies show a relation between reduced lumbar motor control (LMC and low back pain (LBP. However, test circumstances vary and during test performance, subjects may change position. In other words, the reliability - i.e. reproducibility and validity - of tests for LMC should be based on quantitative data. This has not been considered before. The aim was to analyse the reproducibility of five different quantitative tests for LMC commonly used in daily clinical practice. Methods The five tests for LMC were: repositioning (RPS, sitting forward lean (SFL, sitting knee extension (SKE, and bent knee fall out (BKFO, all measured in cm, and leg lowering (LL, measured in mm Hg. A total of 40 subjects (14 males, 26 females 25 with and 15 without LBP, with a mean age of 46.5 years (SD 14.8, were examined independently and in random order by two examiners on the same day. LBP subjects were recruited from three physiotherapy clinics with a connection to the clinic's gym or back-school. Non-LBP subjects were recruited from the clinic's staff acquaintances, and from patients without LBP. Results The means and standard deviations for each of the tests were 0.36 (0.27 cm for RPS, 1.01 (0.62 cm for SFL, 0.40 (0.29 cm for SKE, 1.07 (0.52 cm for BKFO, and 32.9 (7.1 mm Hg for LL. All five tests for LMC had reproducibility with the following ICCs: 0.90 for RPS, 0.96 for SFL, 0.96 for SKE, 0.94 for BKFO, and 0.98 for LL. Bland and Altman plots showed that most of the differences between examiners A and B were less than 0.20 cm. Conclusion These five tests for LMC displayed excellent reproducibility. However, the diagnostic accuracy of these tests needs to be addressed in larger cohorts of subjects, establishing values for the normal population. Also cut-points between subjects with and without LBP must be determined, taking into account age, level of activity, degree of impairment and participation in sports. Whether reproducibility of these

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.

Reproducibility and variability of quantitative magnetic resonance imaging markers in cerebral small vessel disease

NARCIS (Netherlands)

De Guio, F. (François); Jouvent, E. (Eric); G.J. Biessels (Geert Jan); S.E. Black (Sandra); C. Brayne (Carol); C. Chen (Christopher); C. Cordonnier (Charlotte); H.F. de Leeuw (Frank); C. Kubisch (Christian); Doubal, F. (Fergus); Duering, M. (Marco); C. Dufouil (Carole); Duzel, E. (Emrah); F. Fazekas (Franz); V. Hachinski (Vladimir); M.K. Ikram (Kamran); J. Linn (Jennifer); P.M. Matthews (P.); B. Mazoyer (Bernard); Mok, V. (Vincent); B. Norrving (Bo); O'Brien, J.T. (John T.); Pantoni, L. (Leonardo); S. Ropele (Stefan); P.S. Sachdev (Perminder); R. Schmidt (Reinhold); S. Seshadri (Sudha); E.E. Smith (Eric); L.A. Sposato (Luciano A); B.C.M. Stephan; Swartz, R.H. (Richard H.); C. Tzourio (Christophe); M.A. van Buchem (Mark); A. van der Lugt (Aad); R.J. van Oostenbrugge (Robert); M.W. Vernooij (Meike); Viswanathan, A. (Anand); D.J. Werring (David); Wollenweber, F. (Frank); J.M. Wardlaw (J.); Chabriat, H. (Hugues)

2016-01-01

textabstractBrain imaging is essential for the diagnosis and characterization of cerebral small vessel disease. Several magnetic resonance imaging markers have therefore emerged, providing new information on the diagnosis, progression, and mechanisms of small vessel disease. Yet, the reproducibility

Reproducibility and variability of quantitative magnetic resonance imaging markers in cerebral small vessel disease

NARCIS (Netherlands)

Guio, F. De; Jouvent, E.; Biessels, G.J.; Black, S.E.; Brayne, C.; Chen, C.; Cordonnier, C.; Leeuw, F.E. de; Dichgans, M.; Doubal, F.; Duering, M.; Dufouil, C.; Duzel, E.; Fazekas, F.; Hachinski, V.; Ikram, M.A.; Linn, J.; Matthews, P.M.; Mazoyer, B.; Mok, V.; Norrving, B.; O'Brien, J.T.; Pantoni, L.; Ropele, S.; Sachdev, P.; Schmidt, R.; Seshadri, S.; Smith, E.E.; Sposato, L.A.; Stephan, B.; Swartz, R.H.; Tzourio, C.; Buchem, M. van; Lugt, A. van der; Oostenbrugge, R.; Vernooij, M.W.; Viswanathan, A.; Werring, D.; Wollenweber, F.; Wardlaw, J.M.; Chabriat, H.

2016-01-01

Brain imaging is essential for the diagnosis and characterization of cerebral small vessel disease. Several magnetic resonance imaging markers have therefore emerged, providing new information on the diagnosis, progression, and mechanisms of small vessel disease. Yet, the reproducibility of these

UK quantitative WB-DWI technical workgroup: consensus meeting recommendations on optimisation, quality control, processing and analysis of quantitative whole-body diffusion-weighted imaging for cancer.

Science.gov (United States)

Barnes, Anna; Alonzi, Roberto; Blackledge, Matthew; Charles-Edwards, Geoff; Collins, David J; Cook, Gary; Coutts, Glynn; Goh, Vicky; Graves, Martin; Kelly, Charles; Koh, Dow-Mu; McCallum, Hazel; Miquel, Marc E; O'Connor, James; Padhani, Anwar; Pearson, Rachel; Priest, Andrew; Rockall, Andrea; Stirling, James; Taylor, Stuart; Tunariu, Nina; van der Meulen, Jan; Walls, Darren; Winfield, Jessica; Punwani, Shonit

2018-01-01

Application of whole body diffusion-weighted MRI (WB-DWI) for oncology are rapidly increasing within both research and routine clinical domains. However, WB-DWI as a quantitative imaging biomarker (QIB) has significantly slower adoption. To date, challenges relating to accuracy and reproducibility, essential criteria for a good QIB, have limited widespread clinical translation. In recognition, a UK workgroup was established in 2016 to provide technical consensus guidelines (to maximise accuracy and reproducibility of WB-MRI QIBs) and accelerate the clinical translation of quantitative WB-DWI applications for oncology. A panel of experts convened from cancer centres around the UK with subspecialty expertise in quantitative imaging and/or the use of WB-MRI with DWI. A formal consensus method was used to obtain consensus agreement regarding best practice. Questions were asked about the appropriateness or otherwise on scanner hardware and software, sequence optimisation, acquisition protocols, reporting, and ongoing quality control programs to monitor precision and accuracy and agreement on quality control. The consensus panel was able to reach consensus on 73% (255/351) items and based on consensus areas made recommendations to maximise accuracy and reproducibly of quantitative WB-DWI studies performed at 1.5T. The panel were unable to reach consensus on the majority of items related to quantitative WB-DWI performed at 3T. This UK Quantitative WB-DWI Technical Workgroup consensus provides guidance on maximising accuracy and reproducibly of quantitative WB-DWI for oncology. The consensus guidance can be used by researchers and clinicians to harmonise WB-DWI protocols which will accelerate clinical translation of WB-DWI-derived QIBs.

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

Science.gov (United States)

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

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Christopher M Walker

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

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.

Quantitative Modeling of Earth Surface Processes

Science.gov (United States)

Pelletier, Jon D.

This textbook describes some of the most effective and straightforward quantitative techniques for modeling Earth surface processes. By emphasizing a core set of equations and solution techniques, the book presents state-of-the-art models currently employed in Earth surface process research, as well as a set of simple but practical research tools. Detailed case studies demonstrate application of the methods to a wide variety of processes including hillslope, fluvial, aeolian, glacial, tectonic, and climatic systems. Exercises at the end of each chapter begin with simple calculations and then progress to more sophisticated problems that require computer programming. All the necessary computer codes are available online at www.cambridge.org/9780521855976. Assuming some knowledge of calculus and basic programming experience, this quantitative textbook is designed for advanced geomorphology courses and as a reference book for professional researchers in Earth and planetary science looking for a quantitative approach to Earth surface processes. More details...

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model.

Science.gov (United States)

Manabe, Sho; Morimoto, Chie; Hamano, Yuya; Fujimoto, Shuntaro; Tamaki, Keiji

2017-01-01

In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software "Kongoh" for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1-4 persons' contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR) of a POI's contribution in true contributors and non-contributors by using 2-4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI's contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples.

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model.

Directory of Open Access Journals (Sweden)

Sho Manabe

Full Text Available In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI from these samples are challenging. In this study, we developed a new open-source software "Kongoh" for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1-4 persons' contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR of a POI's contribution in true contributors and non-contributors by using 2-4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI's contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples.

Towards reproducible MSMS data preprocessing, quality control and quantification

OpenAIRE

Gatto, Laurent; Lilley, Kathryn S.

2010-01-01

The development of MSnbase aims at providing researchers dealing with labelled quantitative proteomics data with a transparent, portable, extensible and open-source collaborative framework to easily manipulate and analyse MS2-level raw tandem mass spectrometry data. The implementation in R gives users and developers a great variety of powerful tools to be used in a controlled and reproducible way. Furthermore, MSnbase has been developed following an object-oriented programming paradigm: all i...

Preclinical Magnetic Resonance Fingerprinting (MRF) at 7 T: Effective Quantitative Imaging for Rodent Disease Models

Science.gov (United States)

Gao, Ying; Chen, Yong; Ma, Dan; Jiang, Yun; Herrmann, Kelsey A.; Vincent, Jason A.; Dell, Katherine M.; Drumm, Mitchell L.; Brady-Kalnay, Susann M.; Griswold, Mark A.; Flask, Chris A.; Lu, Lan

2015-01-01

High field, preclinical magnetic resonance imaging (MRI) scanners are now commonly used to quantitatively assess disease status and efficacy of novel therapies in a wide variety of rodent models. Unfortunately, conventional MRI methods are highly susceptible to respiratory and cardiac motion artifacts resulting in potentially inaccurate and misleading data. We have developed an initial preclinical, 7.0 T MRI implementation of the highly novel Magnetic Resonance Fingerprinting (MRF) methodology that has been previously described for clinical imaging applications. The MRF technology combines a priori variation in the MRI acquisition parameters with dictionary-based matching of acquired signal evolution profiles to simultaneously generate quantitative maps of T1 and T2 relaxation times and proton density. This preclinical MRF acquisition was constructed from a Fast Imaging with Steady-state Free Precession (FISP) MRI pulse sequence to acquire 600 MRF images with both evolving T1 and T2 weighting in approximately 30 minutes. This initial high field preclinical MRF investigation demonstrated reproducible and differentiated estimates of in vitro phantoms with different relaxation times. In vivo preclinical MRF results in mouse kidneys and brain tumor models demonstrated an inherent resistance to respiratory motion artifacts as well as sensitivity to known pathology. These results suggest that MRF methodology may offer the opportunity for quantification of numerous MRI parameters for a wide variety of preclinical imaging applications. PMID:25639694

Effective Form of Reproducing the Total Financial Potential of Ukraine

Directory of Open Access Journals (Sweden)

Portna Oksana V.

2015-03-01

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

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

Quantitative modelling of the biomechanics of the avian syrinx

DEFF Research Database (Denmark)

Elemans, Coen P. H.; Larsen, Ole Næsbye; Hoffmann, Marc R.

2003-01-01

We review current quantitative models of the biomechanics of bird sound production. A quantitative model of the vocal apparatus was proposed by Fletcher (1988). He represented the syrinx (i.e. the portions of the trachea and bronchi with labia and membranes) as a single membrane. This membrane acts...

Reproducibility Between Brain Uptake Ratio Using Anatomic Standardization and Patlak-Plot Methods.

Science.gov (United States)

Shibutani, Takayuki; Onoguchi, Masahisa; Noguchi, Atsushi; Yamada, Tomoki; Tsuchihashi, Hiroko; Nakajima, Tadashi; Kinuya, Seigo

2015-12-01

The Patlak-plot and conventional methods of determining brain uptake ratio (BUR) have some problems with reproducibility. We formulated a method of determining BUR using anatomic standardization (BUR-AS) in a statistical parametric mapping algorithm to improve reproducibility. The objective of this study was to demonstrate the inter- and intraoperator reproducibility of mean cerebral blood flow as determined using BUR-AS in comparison to the conventional-BUR (BUR-C) and Patlak-plot methods. The images of 30 patients who underwent brain perfusion SPECT were retrospectively used in this study. The images were reconstructed using ordered-subset expectation maximization and processed using an automatic quantitative analysis for cerebral blood flow of ECD tool. The mean SPECT count was calculated from axial basal ganglia slices of the normal side (slices 31-40) drawn using a 3-dimensional stereotactic region-of-interest template after anatomic standardization. The mean cerebral blood flow was calculated from the mean SPECT count. Reproducibility was evaluated using coefficient of variation and Bland-Altman plotting. For both inter- and intraoperator reproducibility, the BUR-AS method had the lowest coefficient of variation and smallest error range about the Bland-Altman plot. Mean CBF obtained using the BUR-AS method had the highest reproducibility. Compared with the Patlak-plot and BUR-C methods, the BUR-AS method provides greater inter- and intraoperator reproducibility of cerebral blood flow measurement. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

A reproducible accelerated in vitro release testing method for PLGA microspheres.

Science.gov (United States)

Shen, Jie; Lee, Kyulim; Choi, Stephanie; Qu, Wen; Wang, Yan; Burgess, Diane J

2016-02-10

The objective of the present study was to develop a discriminatory and reproducible accelerated in vitro release method for long-acting PLGA microspheres with inner structure/porosity differences. Risperidone was chosen as a model drug. Qualitatively and quantitatively equivalent PLGA microspheres with different inner structure/porosity were obtained using different manufacturing processes. Physicochemical properties as well as degradation profiles of the prepared microspheres were investigated. Furthermore, in vitro release testing of the prepared risperidone microspheres was performed using the most common in vitro release methods (i.e., sample-and-separate and flow through) for this type of product. The obtained compositionally equivalent risperidone microspheres had similar drug loading but different inner structure/porosity. When microsphere particle size appeared similar, porous risperidone microspheres showed faster microsphere degradation and drug release compared with less porous microspheres. Both in vitro release methods investigated were able to differentiate risperidone microsphere formulations with differences in porosity under real-time (37 °C) and accelerated (45 °C) testing conditions. Notably, only the accelerated USP apparatus 4 method showed good reproducibility for highly porous risperidone microspheres. These results indicated that the accelerated USP apparatus 4 method is an appropriate fast quality control tool for long-acting PLGA microspheres (even with porous structures). Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative digital radiography with two dimensional flat panels

International Nuclear Information System (INIS)

Dinten, J.M.; Robert-Coutant, C.; Darboux, M.

2003-01-01

Purpose: Attenuation law relates radiographic images to irradiated object thickness and chemical composition. Film radiography exploits qualitatively this property for diagnosis. Digital radiographic flat panels present large dynamic range, reproducibility and linearity properties which open the gate for quantification. We will present, through two applications (mammography and bone densitometry), an approach to extract quantitative information from digital 2D radiographs. Material and method: The main difficulty for quantification is X-rays scatter, which superimposes to acquisition data. Because of multiple scatterings and 3D geometry dependence, it cannot be directly exploited through an exact analytical model. Therefore we have developed an approach for its estimation and subtraction from medical radiographs, based on approximations and derivations of analytical models of scatter formation in human tissues. Results: In digital mammography, the objective is to build a map of the glandular tissue thickness. Its separation from fat tissue is based on two equations: height of compression and attenuation. This last equation needs X-Rays scatter correction. In bone densitometry, physicians look for quantitative bone mineral density. Today, clinical DEXA systems use collimated single or linear detectors to eliminate scatter. This scanning technology induces poor image quality. By applying our scatter correction approach, we have developed a bone densitometer using a digital flat panel (Lexxos, DMS). It provides with accurate and reproducible measurements while presenting radiological image quality. Conclusion: These applications show how information processing, and especially X-Rays scatter processing, enables to extract quantitative information from digital radiographs. This approach, associated to Computer Aided Diagnosis algorithms or reconstructions algorithms, gives access to useful information for diagnosis. (author)

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.

Angiographic core laboratory reproducibility analyses: implications for planning clinical trials using coronary angiography and left ventriculography end-points.

Science.gov (United States)

Steigen, Terje K; Claudio, Cheryl; Abbott, David; Schulzer, Michael; Burton, Jeff; Tymchak, Wayne; Buller, Christopher E; John Mancini, G B

2008-06-01

To assess reproducibility of core laboratory performance and impact on sample size calculations. Little information exists about overall reproducibility of core laboratories in contradistinction to performance of individual technicians. Also, qualitative parameters are being adjudicated increasingly as either primary or secondary end-points. The comparative impact of using diverse indexes on sample sizes has not been previously reported. We compared initial and repeat assessments of five quantitative parameters [e.g., minimum lumen diameter (MLD), ejection fraction (EF), etc.] and six qualitative parameters [e.g., TIMI myocardial perfusion grade (TMPG) or thrombus grade (TTG), etc.], as performed by differing technicians and separated by a year or more. Sample sizes were calculated from these results. TMPG and TTG were also adjudicated by a second core laboratory. MLD and EF were the most reproducible, yielding the smallest sample size calculations, whereas percent diameter stenosis and centerline wall motion require substantially larger trials. Of the qualitative parameters, all except TIMI flow grade gave reproducibility characteristics yielding sample sizes of many 100's of patients. Reproducibility of TMPG and TTG was only moderately good both within and between core laboratories, underscoring an intrinsic difficulty in assessing these. Core laboratories can be shown to provide reproducibility performance that is comparable to performance commonly ascribed to individual technicians. The differences in reproducibility yield huge differences in sample size when comparing quantitative and qualitative parameters. TMPG and TTG are intrinsically difficult to assess and conclusions based on these parameters should arise only from very large trials.

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.

Validity and reproducibility of a food frequency questionnaire for dietary factors related to colorectal cancer

OpenAIRE

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

2017-01-01

Abstract: Dietary factors play a major role in the development of colorectal cancer. This study evaluated the reproducibility and validity of a 109-food item Food Frequency Questionnaire (FFQ) to measure the consumption of foods and nutrients related to the development of colorectal cancer in a population aged 50 years in Flanders, Belgium. A semi-quantitative FFQ was administered two times in a period of two weeks to evaluate reproducibility (FFQ1 and FFQ2). The validity of the FFQ was asses...

Reproducibility of CSF quantitative culture methods for estimating rate of clearance in cryptococcal meningitis.

Science.gov (United States)

Dyal, Jonathan; Akampurira, Andrew; Rhein, Joshua; Morawski, Bozena M; Kiggundu, Reuben; Nabeta, Henry W; Musubire, Abdu K; Bahr, Nathan C; Williams, Darlisha A; Bicanic, Tihana; Larsen, Robert A; Meya, David B; Boulware, David R

2016-05-01

Quantitative cerebrospinal fluid (CSF) cultures provide a measure of disease severity in cryptococcal meningitis. The fungal clearance rate by quantitative cultures has become a primary endpoint for phase II clinical trials. This study determined the inter-assay accuracy of three different quantitative culture methodologies. Among 91 participants with meningitis symptoms in Kampala, Uganda, during August-November 2013, 305 CSF samples were prospectively collected from patients at multiple time points during treatment. Samples were simultaneously cultured by three methods: (1) St. George's 100 mcl input volume of CSF with five 1:10 serial dilutions, (2) AIDS Clinical Trials Group (ACTG) method using 1000, 100, 10 mcl input volumes, and two 1:100 dilutions with 100 and 10 mcl input volume per dilution on seven agar plates; and (3) 10 mcl calibrated loop of undiluted and 1:100 diluted CSF (loop). Quantitative culture values did not statistically differ between St. George-ACTG methods (P= .09) but did for St. George-10 mcl loop (Pmethods was high (r≥0.88). For detecting sterility, the ACTG-method had the highest negative predictive value of 97% (91% St. George, 60% loop), but the ACTG-method had occasional (∼10%) difficulties in quantification due to colony clumping. For CSF clearance rate, St. George-ACTG methods did not differ overall (mean -0.05 ± 0.07 log10CFU/ml/day;P= .14) on a group level; however, individual-level clearance varied. The St. George and ACTG quantitative CSF culture methods produced comparable but not identical results. Quantitative cultures can inform treatment management strategies. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Qualitative and Quantitative Integrated Modeling for Stochastic Simulation and Optimization

Directory of Open Access Journals (Sweden)

Xuefeng Yan

2013-01-01

Full Text Available The simulation and optimization of an actual physics system are usually constructed based on the stochastic models, which have both qualitative and quantitative characteristics inherently. Most modeling specifications and frameworks find it difficult to describe the qualitative model directly. In order to deal with the expert knowledge, uncertain reasoning, and other qualitative information, a qualitative and quantitative combined modeling specification was proposed based on a hierarchical model structure framework. The new modeling approach is based on a hierarchical model structure which includes the meta-meta model, the meta-model and the high-level model. A description logic system is defined for formal definition and verification of the new modeling specification. A stochastic defense simulation was developed to illustrate how to model the system and optimize the result. The result shows that the proposed method can describe the complex system more comprehensively, and the survival probability of the target is higher by introducing qualitative models into quantitative simulation.

Improvement of reproducibility and quality control of human growth hormone radioiodination

International Nuclear Information System (INIS)

Bartolini, P.; Ribela, M.T.C.P.; Camilo, M.A.

1988-01-01

The labelling reaction of human growth hormone (hGH) with 125 I and its chromatographic purification have been studied with emphasis on the reproducibility of the yields, quantitaTive recoveries and resulting activities. Through the accurate standardization of a monitoring technique, it is confirmed that there are no significant losses in radioactivity or protein during the labelling or purification process. By strict control of the reaction conditions a fairily good reproducibility is also obtained in the labelling of various hGH extracts with diferent 125 I shipments used after short or long storage. Finally, the specific activity (or absolute mass) of the radioiodinated protein is determined by this Analysis of the Reaction Mixture and compared to the widely used radioimmunological assay (Self-displacement). (M.A.C.) [pt

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.

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

Science.gov (United States)

Pedretti, Daniele; Bianchi, Marco

2018-03-01

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

Modeling with Young Students--Quantitative and Qualitative.

Science.gov (United States)

Bliss, Joan; Ogborn, Jon; Boohan, Richard; Brosnan, Tim; Mellar, Harvey; Sakonidis, Babis

1999-01-01

A project created tasks and tools to investigate quality and nature of 11- to 14-year-old pupils' reasoning with quantitative and qualitative computer-based modeling tools. Tasks and tools were used in two innovative modes of learning: expressive, where pupils created their own models, and exploratory, where pupils investigated an expert's model.…

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.

A website evaluation model by integration of previous evaluation models using a quantitative approach

Directory of Open Access Journals (Sweden)

Ali Moeini

2015-01-01

Full Text Available Regarding the ecommerce growth, websites play an essential role in business success. Therefore, many authors have offered website evaluation models since 1995. Although, the multiplicity and diversity of evaluation models make it difficult to integrate them into a single comprehensive model. In this paper a quantitative method has been used to integrate previous models into a comprehensive model that is compatible with them. In this approach the researcher judgment has no role in integration of models and the new model takes its validity from 93 previous models and systematic quantitative approach.

Development of quantitative atomic modeling for tungsten transport study using LHD plasma with tungsten pellet injection

Science.gov (United States)

Murakami, I.; Sakaue, H. A.; Suzuki, C.; Kato, D.; Goto, M.; Tamura, N.; Sudo, S.; Morita, S.

2015-09-01

Quantitative tungsten study with reliable atomic modeling is important for successful achievement of ITER and fusion reactors. We have developed tungsten atomic modeling for understanding the tungsten behavior in fusion plasmas. The modeling is applied to the analysis of tungsten spectra observed from plasmas of the large helical device (LHD) with tungsten pellet injection. We found that extreme ultraviolet (EUV) emission of W24+ to W33+ ions at 1.5-3.5 nm are sensitive to electron temperature and useful to examine the tungsten behavior in edge plasmas. We can reproduce measured EUV spectra at 1.5-3.5 nm by calculated spectra with the tungsten atomic model and obtain charge state distributions of tungsten ions in LHD plasmas at different temperatures around 1 keV. Our model is applied to calculate the unresolved transition array (UTA) seen at 4.5-7 nm tungsten spectra. We analyze the effect of configuration interaction on population kinetics related to the UTA structure in detail and find the importance of two-electron-one-photon transitions between 4p54dn+1- 4p64dn-14f. Radiation power rate of tungsten due to line emissions is also estimated with the model and is consistent with other models within factor 2.

Validity and reproducibility of a food frequency questionnaire for dietary factors related to colorectal cancer

OpenAIRE

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

2017-01-01

Dietary factors play a major role in the development of colorectal cancer. This study evaluated the reproducibility and validity of a 109-food item Food Frequency Questionnaire (FFQ) to measure the consumption of foods and nutrients related to the development of colorectal cancer in a population aged ≥50 years in Flanders, Belgium. A semi-quantitative FFQ was administered two times in a period of two weeks to evaluate reproducibility (FFQ1 and FFQ2). The validity of the FFQ was assessed by co...

Quantitative MRI of kidneys in renal disease.

Science.gov (United States)

Kline, Timothy L; Edwards, Marie E; Garg, Ishan; Irazabal, Maria V; Korfiatis, Panagiotis; Harris, Peter C; King, Bernard F; Torres, Vicente E; Venkatesh, Sudhakar K; Erickson, Bradley J

2018-03-01

To evaluate the reproducibility and utility of quantitative magnetic resonance imaging (MRI) sequences for the assessment of kidneys in young adults with normal renal function (eGFR ranged from 90 to 130 mL/min/1.73 m 2 ) and patients with early renal disease (autosomal dominant polycystic kidney disease). This prospective case-control study was performed on ten normal young adults (18-30 years old) and ten age- and sex-matched patients with early renal parenchymal disease (autosomal dominant polycystic kidney disease). All subjects underwent a comprehensive kidney MRI protocol, including qualitative imaging: T1w, T2w, FIESTA, and quantitative imaging: 2D cine phase contrast of the renal arteries, and parenchymal diffusion weighted imaging (DWI), magnetization transfer imaging (MTI), blood oxygen level dependent (BOLD) imaging, and magnetic resonance elastography (MRE). The normal controls were imaged on two separate occasions ≥24 h apart (range 24-210 h) to assess reproducibility of the measurements. Quantitative MR imaging sequences were found to be reproducible. The mean ± SD absolute percent difference between quantitative parameters measured ≥24 h apart were: MTI-derived ratio = 4.5 ± 3.6%, DWI-derived apparent diffusion coefficient (ADC) = 6.5 ± 3.4%, BOLD-derived R2* = 7.4 ± 5.9%, and MRE-derived tissue stiffness = 7.6 ± 3.3%. Compared with controls, the ADPKD patient's non-cystic renal parenchyma (NCRP) had statistically significant differences with regard to quantitative parenchymal measures: lower MTI percent ratios (16.3 ± 4.4 vs. 23.8 ± 1.2, p quantitative measurements was obtained in all cases. Significantly different quantitative MR parenchymal measurement parameters between ADPKD patients and normal controls were obtained by MT, DWI, BOLD, and MRE indicating the potential for detecting and following renal disease at an earlier stage than the conventional qualitative imaging techniques.

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.

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?

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...

Development of a Rapid Real-Time PCR Assay for Quantitation of Pneumocystis carinii f. sp. Carinii

DEFF Research Database (Denmark)

Larsen, Hans Henrik; Kovacs, Joseph A; Stock, Frida

2002-01-01

6 log values for standards containing > or =5 copies/tube. Application of the assay to a series of 10-fold dilutions of P. carinii organisms isolated from rat lung demonstrated that it was reproducibly quantitative over 5 log values (r = 0.99). The assay was applied to a recently reported in vitro...... axenic cultivation system for P. carinii and confirmed our microscopy findings that no organism multiplication had occurred during culture. For all cultures analyzed, QTD PCR assays showed a decrease in P. carinii DNA that exceeded the expected decrease due to dilution of the inoculum upon transfer......A method for reliable quantification of Pneumocystis carinii in research models of P. carinii pneumonia (PCP) that is more convenient and reproducible than microscopic enumeration of organisms would greatly facilitate investigations of this organism. We developed a rapid quantitative touchdown (QTD...

Development of a Rapid Real-Time PCR Assay for Quantitation of Pneumocystis carinii f. sp. Carinii

DEFF Research Database (Denmark)

Larsen, Hans Henrik; Kovacs, Joseph A; Stock, Frida

2002-01-01

) PCR assay for detecting P. carinii f. sp. carinii, the subspecies of P. carinii commonly used in research models of PCP. The assay was based on the single-copy dihydrofolate reductase gene and was able to detect r = 0.99) over...... 6 log values for standards containing > or =5 copies/tube. Application of the assay to a series of 10-fold dilutions of P. carinii organisms isolated from rat lung demonstrated that it was reproducibly quantitative over 5 log values (r = 0.99). The assay was applied to a recently reported in vitro....... In conclusion, a rapid, sensitive, and reproducible quantitative PCR assay for P. carinii f. sp. carinii has been developed and is applicable to in vivo as well as in vitro systems. The assay should prove useful for conducting studies in which quantification of organism burden or growth assessment is critical...

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.

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

Empirical evaluation of cross-site reproducibility in radiomic features for characterizing prostate MRI

Science.gov (United States)

Chirra, Prathyush; Leo, Patrick; Yim, Michael; Bloch, B. Nicolas; Rastinehad, Ardeshir R.; Purysko, Andrei; Rosen, Mark; Madabhushi, Anant; Viswanath, Satish

2018-02-01

The recent advent of radiomics has enabled the development of prognostic and predictive tools which use routine imaging, but a key question that still remains is how reproducible these features may be across multiple sites and scanners. This is especially relevant in the context of MRI data, where signal intensity values lack tissue specific, quantitative meaning, as well as being dependent on acquisition parameters (magnetic field strength, image resolution, type of receiver coil). In this paper we present the first empirical study of the reproducibility of 5 different radiomic feature families in a multi-site setting; specifically, for characterizing prostate MRI appearance. Our cohort comprised 147 patient T2w MRI datasets from 4 different sites, all of which were first pre-processed to correct acquisition-related for artifacts such as bias field, differing voxel resolutions, as well as intensity drift (non-standardness). 406 3D voxel wise radiomic features were extracted and evaluated in a cross-site setting to determine how reproducible they were within a relatively homogeneous non-tumor tissue region; using 2 different measures of reproducibility: Multivariate Coefficient of Variation and Instability Score. Our results demonstrated that Haralick features were most reproducible between all 4 sites. By comparison, Laws features were among the least reproducible between sites, as well as performing highly variably across their entire parameter space. Similarly, the Gabor feature family demonstrated good cross-site reproducibility, but for certain parameter combinations alone. These trends indicate that despite extensive pre-processing, only a subset of radiomic features and associated parameters may be reproducible enough for use within radiomics-based machine learning classifier schemes.

Quantitative image analysis of synovial tissue

NARCIS (Netherlands)

van der Hall, Pascal O.; Kraan, Maarten C.; Tak, Paul Peter

2007-01-01

Quantitative image analysis is a form of imaging that includes microscopic histological quantification, video microscopy, image analysis, and image processing. Hallmarks are the generation of reliable, reproducible, and efficient measurements via strict calibration and step-by-step control of the

Quantitative Phase-Field Approach for Simulating Grain Growth in Anisotropic Systems with Arbitrary Inclination and Misorientation Dependence

International Nuclear Information System (INIS)

Moelans, N.; Blanpain, B.; Wollants, P.

2008-01-01

A phase-field approach for quantitative simulations of grain growth in anisotropic systems is introduced, together with a new methodology to derive appropriate model parameters that reproduce given misorientation and inclination dependent grain boundary energy and mobility in the simulations. The proposed model formulation and parameter choice guarantee a constant diffuse interface width and consequently give high controllability of the accuracy in grain growth simulations

Current Challenges in the First Principle Quantitative Modelling of the Lower Hybrid Current Drive in Tokamaks

Science.gov (United States)

Peysson, Y.; Bonoli, P. T.; Chen, J.; Garofalo, A.; Hillairet, J.; Li, M.; Qian, J.; Shiraiwa, S.; Decker, J.; Ding, B. J.; Ekedahl, A.; Goniche, M.; Zhai, X.

2017-10-01

The Lower Hybrid (LH) wave is widely used in existing tokamaks for tailoring current density profile or extending pulse duration to steady-state regimes. Its high efficiency makes it particularly attractive for a fusion reactor, leading to consider it for this purpose in ITER tokamak. Nevertheless, if basics of the LH wave in tokamak plasma are well known, quantitative modeling of experimental observations based on first principles remains a highly challenging exercise, despite considerable numerical efforts achieved so far. In this context, a rigorous methodology must be carried out in the simulations to identify the minimum number of physical mechanisms that must be considered to reproduce experimental shot to shot observations and also scalings (density, power spectrum). Based on recent simulations carried out for EAST, Alcator C-Mod and Tore Supra tokamaks, the state of the art in LH modeling is reviewed. The capability of fast electron bremsstrahlung, internal inductance li and LH driven current at zero loop voltage to constrain all together LH simulations is discussed, as well as the needs of further improvements (diagnostics, codes, LH model), for robust interpretative and predictive simulations.

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

Testing process predictions of models of risky choice: a quantitative model comparison approach

Science.gov (United States)

Pachur, Thorsten; Hertwig, Ralph; Gigerenzer, Gerd; Brandstätter, Eduard

2013-01-01

This article presents a quantitative model comparison contrasting the process predictions of two prominent views on risky choice. One view assumes a trade-off between probabilities and outcomes (or non-linear functions thereof) and the separate evaluation of risky options (expectation models). Another view assumes that risky choice is based on comparative evaluation, limited search, aspiration levels, and the forgoing of trade-offs (heuristic models). We derived quantitative process predictions for a generic expectation model and for a specific heuristic model, namely the priority heuristic (Brandstätter et al., 2006), and tested them in two experiments. The focus was on two key features of the cognitive process: acquisition frequencies (i.e., how frequently individual reasons are looked up) and direction of search (i.e., gamble-wise vs. reason-wise). In Experiment 1, the priority heuristic predicted direction of search better than the expectation model (although neither model predicted the acquisition process perfectly); acquisition frequencies, however, were inconsistent with both models. Additional analyses revealed that these frequencies were primarily a function of what Rubinstein (1988) called “similarity.” In Experiment 2, the quantitative model comparison approach showed that people seemed to rely more on the priority heuristic in difficult problems, but to make more trade-offs in easy problems. This finding suggests that risky choice may be based on a mental toolbox of strategies. PMID:24151472

Testing Process Predictions of Models of Risky Choice: A Quantitative Model Comparison Approach

Directory of Open Access Journals (Sweden)

Thorsten ePachur

2013-09-01

Full Text Available This article presents a quantitative model comparison contrasting the process predictions of two prominent views on risky choice. One view assumes a trade-off between probabilities and outcomes (or nonlinear functions thereof and the separate evaluation of risky options (expectation models. Another view assumes that risky choice is based on comparative evaluation, limited search, aspiration levels, and the forgoing of trade-offs (heuristic models. We derived quantitative process predictions for a generic expectation model and for a specific heuristic model, namely the priority heuristic (Brandstätter, Gigerenzer, & Hertwig, 2006, and tested them in two experiments. The focus was on two key features of the cognitive process: acquisition frequencies (i.e., how frequently individual reasons are looked up and direction of search (i.e., gamble-wise vs. reason-wise. In Experiment 1, the priority heuristic predicted direction of search better than the expectation model (although neither model predicted the acquisition process perfectly; acquisition frequencies, however, were inconsistent with both models. Additional analyses revealed that these frequencies were primarily a function of what Rubinstein (1988 called similarity. In Experiment 2, the quantitative model comparison approach showed that people seemed to rely more on the priority heuristic in difficult problems, but to make more trade-offs in easy problems. This finding suggests that risky choice may be based on a mental toolbox of strategies.

Quantitative sociodynamics stochastic methods and models of social interaction processes

CERN Document Server

Helbing, Dirk

1995-01-01

Quantitative Sociodynamics presents a general strategy for interdisciplinary model building and its application to a quantitative description of behavioural changes based on social interaction processes. Originally, the crucial methods for the modeling of complex systems (stochastic methods and nonlinear dynamics) were developed in physics but they have very often proved their explanatory power in chemistry, biology, economics and the social sciences. Quantitative Sociodynamics provides a unified and comprehensive overview of the different stochastic methods, their interrelations and properties. In addition, it introduces the most important concepts from nonlinear dynamics (synergetics, chaos theory). The applicability of these fascinating concepts to social phenomena is carefully discussed. By incorporating decision-theoretical approaches a very fundamental dynamic model is obtained which seems to open new perspectives in the social sciences. It includes many established models as special cases, e.g. the log...

Quantitative Sociodynamics Stochastic Methods and Models of Social Interaction Processes

CERN Document Server

Helbing, Dirk

2010-01-01

This new edition of Quantitative Sociodynamics presents a general strategy for interdisciplinary model building and its application to a quantitative description of behavioral changes based on social interaction processes. Originally, the crucial methods for the modeling of complex systems (stochastic methods and nonlinear dynamics) were developed in physics and mathematics, but they have very often proven their explanatory power in chemistry, biology, economics and the social sciences as well. Quantitative Sociodynamics provides a unified and comprehensive overview of the different stochastic methods, their interrelations and properties. In addition, it introduces important concepts from nonlinear dynamics (e.g. synergetics, chaos theory). The applicability of these fascinating concepts to social phenomena is carefully discussed. By incorporating decision-theoretical approaches, a fundamental dynamic model is obtained, which opens new perspectives in the social sciences. It includes many established models a...

Quantitative analysis of elevation of serum creatinine via renal transporter inhibition by trimethoprim in healthy subjects using physiologically-based pharmacokinetic model.

Science.gov (United States)

Nakada, Tomohisa; Kudo, Toshiyuki; Kume, Toshiyuki; Kusuhara, Hiroyuki; Ito, Kiyomi

2018-02-01

Serum creatinine (SCr) levels rise during trimethoprim therapy for infectious diseases. This study aimed to investigate whether the elevation of SCr can be quantitatively explained using a physiologically-based pharmacokinetic (PBPK) model incorporating inhibition by trimethoprim on tubular secretion of creatinine via renal transporters such as organic cation transporter 2 (OCT2), OCT3, multidrug and toxin extrusion protein 1 (MATE1), and MATE2-K. Firstly, pharmacokinetic parameters in the PBPK model of trimethoprim were determined to reproduce the blood concentration profile after a single intravenous and oral administration of trimethoprim in healthy subjects. The model was verified with datasets of both cumulative urinary excretions after a single administration and the blood concentration profile after repeated oral administration. The pharmacokinetic model of creatinine consisted of the creatinine synthesis rate, distribution volume, and creatinine clearance (CL cre ), including tubular secretion via each transporter. When combining the models for trimethoprim and creatinine, the predicted increments in SCr from baseline were 29.0%, 39.5%, and 25.8% at trimethoprim dosages of 5 mg/kg (b.i.d.), 5 mg/kg (q.i.d.), and 200 mg (b.i.d.), respectively, which were comparable with the observed values. The present model analysis enabled us to quantitatively explain increments in SCr during trimethoprim treatment by its inhibition of renal transporters. Copyright © 2017 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

The Reproducibility of Nuclear Morphometric Measurements in Invasive Breast Carcinoma

Directory of Open Access Journals (Sweden)

Pauliina Kronqvist

1997-01-01

Full Text Available The intraobserver and interobserver reproducibility of computerized nuclear morphometry was determined in repeated measurements of 212 samples of invasive breast cancer. The influence of biological variation and the selection of the measurement area was also tested. Morphometrically determined mean nuclear profile area (Pearson’s r 0.89, grading efficiency (GE 0.95 and standard deviation (SD of nuclear profile area (Pearson’s r 0.84, GE 0.89 showed high reproducibility. In this respect, nuclear morphometry equals with other established methods of quantitative pathology and exceeds the results of subjective grading of nuclear atypia in invasive breast cancer. A training period of eight days was sufficient to produce clear improvement in consistency of nuclear morphometry results. By estimating the sources of variation it could be shown that the variation associated with the measurement procedure itself is small. Instead, sample associated variation is responsible for the majority of variation in the measurements (82.9% in mean nuclear profile area and 65.9% in SD of nuclear profile area. This study points out that when standardized methods are applied computerized morphometry is a reproducible and reliable method of assessing nuclear atypia in invasive breast cancer. For further improvement special emphasize should be put on sampling rules of selecting the microscope fields and measurement areas.

Reproducibility of automated simplified voxel-based analysis of PET amyloid ligand [11C]PIB uptake using 30-min scanning data

International Nuclear Information System (INIS)

Aalto, Sargo; Scheinin, Noora M.; Naagren, Kjell; Rinne, Juha O.; Kemppainen, Nina M.; Kailajaervi, Marita; Leinonen, Mika; Scheinin, Mika

2009-01-01

Positron emission tomography (PET) with 11 C-labelled Pittsburgh compound B ([ 11 C]PIB) enables the quantitation of β-amyloid accumulation in the brain of patients with Alzheimer's disease (AD). Voxel-based image analysis techniques conducted in a standard brain space provide an objective, rapid and fully automated method to analyze [ 11 C]PIB PET data. The purpose of this study was to evaluate both region- and voxel-level reproducibility of automated and simplified [ 11 C]PIB quantitation when using only 30 min of imaging data. Six AD patients and four healthy controls were scanned twice with an average interval of 6 weeks. To evaluate the feasibility of short scanning (convenient for AD patients), [ 11 C]PIB uptake was quantitated using 30 min of imaging data (60 to 90 min after tracer injection) for region-to-cerebellum ratio calculations. To evaluate the reproducibility, a test-retest design was used to derive absolute variability (VAR) estimates and intraclass correlation coefficients at both region-of-interest (ROI) and voxel level. The reproducibility both at the region level (VAR 0.9-5.5%) and at the voxel level (VAR 4.2-6.4%) was good to excellent. Based on the variability estimates obtained, power calculations indicated that 90% power to obtain statistically significant difference can be achieved using a sample size of five subjects per group when a 15% change from baseline (increase or decrease) in [ 11 C]PIB accumulation in the frontal cortex is anticipated in one group compared to no change in another group. Our results showed that an automated analysis method based on an efficient scanning protocol provides reproducible results for [ 11 C]PIB uptake and appears suitable for PET studies aiming at the quantitation of amyloid accumulation in the brain of AD patients for the evaluation of progression and treatment effects. (orig.)

Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry.

Science.gov (United States)

Fu, Qin; Kowalski, Michael P; Mastali, Mitra; Parker, Sarah J; Sobhani, Kimia; van den Broek, Irene; Hunter, Christie L; Van Eyk, Jennifer E

2018-01-05

Sample preparation for protein quantification by mass spectrometry requires multiple processing steps including denaturation, reduction, alkylation, protease digestion, and peptide cleanup. Scaling these procedures for the analysis of numerous complex biological samples can be tedious and time-consuming, as there are many liquid transfer steps and timed reactions where technical variations can be introduced and propagated. We established an automated sample preparation workflow with a total processing time for 96 samples of 5 h, including a 2 h incubation with trypsin. Peptide cleanup is accomplished by online diversion during the LC/MS/MS analysis. In a selected reaction monitoring (SRM) assay targeting 6 plasma biomarkers and spiked β-galactosidase, mean intraday and interday cyclic voltammograms (CVs) for 5 serum and 5 plasma samples over 5 days were samples repeated on 3 separate days had total CVs below 20%. Similar results were obtained when the workflow was transferred to a second site: 93% of peptides had CVs below 20%. An automated trypsin digestion workflow yields uniformly processed samples in less than 5 h. Reproducible quantification of peptides was observed across replicates, days, instruments, and laboratory sites, demonstrating the broad applicability of this approach.

Reproducibility of Ultrasound and Magnetic Resonance Imaging Measurements of Tendon Size

International Nuclear Information System (INIS)

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

2006-01-01

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

A Review of Quantitative Situation Assessment Models for Nuclear Power Plant Operators

International Nuclear Information System (INIS)

Lee, Hyun Chul; Seong, Poong Hyun

2009-01-01

Situation assessment is the process of developing situation awareness and situation awareness is defined as 'the perception of the elements in the environment within a volume of time and space, the comprehension of their meaning and the projection of their status in the near future.' Situation awareness is an important element influencing human actions because human decision making is based on the result of situation assessment or situation awareness. There are many models for situation awareness and those models can be categorized into qualitative or quantitative. As the effects of some input factors on situation awareness can be investigated through the quantitative models, the quantitative models are more useful for the design of operator interfaces, automation strategies, training program, and so on, than the qualitative models. This study presents the review of two quantitative models of situation assessment (SA) for nuclear power plant operators

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....

Quantitative diffusion MRI using reduced field-of-view and multi-shot acquisition techniques: Validation in phantoms and prostate imaging.

Science.gov (United States)

Zhang, Yuxin; Holmes, James; Rabanillo, Iñaki; Guidon, Arnaud; Wells, Shane; Hernando, Diego

2018-04-17

To evaluate the reproducibility of quantitative diffusion measurements obtained with reduced Field of View (rFOV) and Multi-shot EPI (msEPI) acquisitions, using single-shot EPI (ssEPI) as a reference. Diffusion phantom experiments, and prostate diffusion-weighted imaging in healthy volunteers and patients with known or suspected prostate cancer were performed across the three different sequences. Quantitative diffusion measurements of apparent diffusion coefficient, and diffusion kurtosis parameters (healthy volunteers), were obtained and compared across diffusion sequences (rFOV, msEPI, and ssEPI). Other possible confounding factors like b-value combinations and acquisition parameters were also investigated. Both msEPI and rFOV have shown reproducible quantitative diffusion measurements relative to ssEPI; no significant difference in ADC was observed across pulse sequences in the standard diffusion phantom (p = 0.156), healthy volunteers (p ≥ 0.12) or patients (p ≥ 0.26). The ADC values within the non-cancerous central gland and peripheral zone of patients were 1.29 ± 0.17 × 10 -3  mm 2 /s and 1.74 ± 0.23 × 10 -3  mm 2 /s respectively. However, differences in quantitative diffusion parameters were observed across different number of averages for rFOV, and across b-value groups and diffusion models for all the three sequences. Both rFOV and msEPI have the potential to provide high image quality with reproducible quantitative diffusion measurements in prostate diffusion MRI. Copyright © 2018 Elsevier Inc. All rights reserved.

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...

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.

Quantitative system validation in model driven design

DEFF Research Database (Denmark)

Hermanns, Hilger; Larsen, Kim Guldstrand; Raskin, Jean-Francois

2010-01-01

The European STREP project Quasimodo1 develops theory, techniques and tool components for handling quantitative constraints in model-driven development of real-time embedded systems, covering in particular real-time, hybrid and stochastic aspects. This tutorial highlights the advances made, focus...

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

Quantitative skeletal scintiscanning

International Nuclear Information System (INIS)

Haushofer, R.

1982-01-01

330 patients were examined by skeletal scintiscanning with sup(99m)Tc pyrophosphate and sup(99m)methylene diphosphonate in the years between 1977 and 1979. Course control examinations were carried out in 12 patients. The collective of patients presented with primary skeletal tumours, metastases, inflammatory and degenerative skeletal diseases. Bone scintiscanning combined with the ''region of interest'' technique was found to be an objective and reproducible technique for quantitative measurement of skeletal radioactivity concentrations. The validity of nuclear skeletal examinations can thus be enhanced as far as diagnosis, course control, and differential diagnosis are concerned. Quantitative skeletal scintiscanning by means of the ''region of interest'' technique has opened up a new era in skeletal diagnosis by nuclear methods. (orig./MG) [de

Accurate virus quantitation using a Scanning Transmission Electron Microscopy (STEM) detector in a scanning electron microscope.

Science.gov (United States)

Blancett, Candace D; Fetterer, David P; Koistinen, Keith A; Morazzani, Elaine M; Monninger, Mitchell K; Piper, Ashley E; Kuehl, Kathleen A; Kearney, Brian J; Norris, Sarah L; Rossi, Cynthia A; Glass, Pamela J; Sun, Mei G

2017-10-01

A method for accurate quantitation of virus particles has long been sought, but a perfect method still eludes the scientific community. Electron Microscopy (EM) quantitation is a valuable technique because it provides direct morphology information and counts of all viral particles, whether or not they are infectious. In the past, EM negative stain quantitation methods have been cited as inaccurate, non-reproducible, and with detection limits that were too high to be useful. To improve accuracy and reproducibility, we have developed a method termed Scanning Transmission Electron Microscopy - Virus Quantitation (STEM-VQ), which simplifies sample preparation and uses a high throughput STEM detector in a Scanning Electron Microscope (SEM) coupled with commercially available software. In this paper, we demonstrate STEM-VQ with an alphavirus stock preparation to present the method's accuracy and reproducibility, including a comparison of STEM-VQ to viral plaque assay and the ViroCyt Virus Counter. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Quantitative interface models for simulating microstructure evolution

International Nuclear Information System (INIS)

Zhu, J.Z.; Wang, T.; Zhou, S.H.; Liu, Z.K.; Chen, L.Q.

2004-01-01

To quantitatively simulate microstructural evolution in real systems, we investigated three different interface models: a sharp-interface model implemented by the software DICTRA and two diffuse-interface models which use either physical order parameters or artificial order parameters. A particular example is considered, the diffusion-controlled growth of a γ ' precipitate in a supersaturated γ matrix in Ni-Al binary alloys. All three models use the thermodynamic and kinetic parameters from the same databases. The temporal evolution profiles of composition from different models are shown to agree with each other. The focus is on examining the advantages and disadvantages of each model as applied to microstructure evolution in alloys

Hidden Markov Model for quantitative prediction of snowfall

Indian Academy of Sciences (India)

A Hidden Markov Model (HMM) has been developed for prediction of quantitative snowfall in Pir-Panjal and Great Himalayan mountain ranges of Indian Himalaya. The model predicts snowfall for two days in advance using daily recorded nine meteorological variables of past 20 winters from 1992–2012. There are six ...

Modeling conflict : research methods, quantitative modeling, and lessons learned.

Energy Technology Data Exchange (ETDEWEB)

Rexroth, Paul E.; Malczynski, Leonard A.; Hendrickson, Gerald A.; Kobos, Peter Holmes; McNamara, Laura A.

2004-09-01

This study investigates the factors that lead countries into conflict. Specifically, political, social and economic factors may offer insight as to how prone a country (or set of countries) may be for inter-country or intra-country conflict. Largely methodological in scope, this study examines the literature for quantitative models that address or attempt to model conflict both in the past, and for future insight. The analysis concentrates specifically on the system dynamics paradigm, not the political science mainstream approaches of econometrics and game theory. The application of this paradigm builds upon the most sophisticated attempt at modeling conflict as a result of system level interactions. This study presents the modeling efforts built on limited data and working literature paradigms, and recommendations for future attempts at modeling conflict.

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)

Quantitative Models and Analysis for Reactive Systems

DEFF Research Database (Denmark)

Thrane, Claus

phones and websites. Acknowledging that now more than ever, systems come in contact with the physical world, we need to revise the way we construct models and verification algorithms, to take into account the behavior of systems in the presence of approximate, or quantitative information, provided...

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.

Reproducibility of MR-based Attenuation Maps in PET/MRI and the Impact on PET Quantification in Lung Cancer

DEFF Research Database (Denmark)

Olin, Anders; Ladefoged, Claes N; Langer, Natasha H

2018-01-01

AIM: Quantitative positron emission tomography/magnetic resonance imaging (PET/MRI) is dependent upon reliable and reproducible MR-based attenuation correction (MR-AC). In this study we evaluated the quality of current vendor-provided thoracic MR-AC maps, and further investigated...... affecting the reproducibility of PET/MRI. This, in combination with other well-known sources of error associated with PET/MRI examinations, leads to inconsistent SUV measurements in serial studies and follow-up scenarios, which may affect the reliability of therapy response assessment. A thorough visual...

The reproducibility of quantitative measurements in lumbar magnetic resonance imaging of children from the general population

DEFF Research Database (Denmark)

Masharawi, Y; Kjær, Per; Bendix, T

2008-01-01

--zygoappophyseal tranverse superior facet angles, sagittal VB, and disc wedging, lumbar lordosis, and sacral inclination. Statistical analysis included the concordance correlation coefficient (CCC), and Bland and Altman's limits of agreement (LOA). RESULTS: A total of 6160 measurements were analyzed. Good to excellent...... intratester reproducibility (0.75 lordosis, and sacral inclination (LOA: 11.22 degrees ; 12.34 degrees). VB and disc...

Quantitative model analysis with diverse biological data: applications in developmental pattern formation.

Science.gov (United States)

Pargett, Michael; Umulis, David M

2013-07-15

Mathematical modeling of transcription factor and signaling networks is widely used to understand if and how a mechanism works, and to infer regulatory interactions that produce a model consistent with the observed data. Both of these approaches to modeling are informed by experimental data, however, much of the data available or even acquirable are not quantitative. Data that is not strictly quantitative cannot be used by classical, quantitative, model-based analyses that measure a difference between the measured observation and the model prediction for that observation. To bridge the model-to-data gap, a variety of techniques have been developed to measure model "fitness" and provide numerical values that can subsequently be used in model optimization or model inference studies. Here, we discuss a selection of traditional and novel techniques to transform data of varied quality and enable quantitative comparison with mathematical models. This review is intended to both inform the use of these model analysis methods, focused on parameter estimation, and to help guide the choice of method to use for a given study based on the type of data available. Applying techniques such as normalization or optimal scaling may significantly improve the utility of current biological data in model-based study and allow greater integration between disparate types of data. Copyright © 2013 Elsevier Inc. All rights reserved.

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...

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-06-15

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

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Interpretation of protein quantitation using the Bradford assay: comparison with two calculation models.

Science.gov (United States)

Ku, Hyung-Keun; Lim, Hyuk-Min; Oh, Kyong-Hwa; Yang, Hyo-Jin; Jeong, Ji-Seon; Kim, Sook-Kyung

2013-03-01

The Bradford assay is a simple method for protein quantitation, but variation in the results between proteins is a matter of concern. In this study, we compared and normalized quantitative values from two models for protein quantitation, where the residues in the protein that bind to anionic Coomassie Brilliant Blue G-250 comprise either Arg and Lys (Method 1, M1) or Arg, Lys, and His (Method 2, M2). Use of the M2 model yielded much more consistent quantitation values compared with use of the M1 model, which exhibited marked overestimations against protein standards. Copyright © 2012 Elsevier Inc. All rights reserved.

An Automated High Throughput Proteolysis and Desalting Platform for Quantitative Proteomic Analysis

Directory of Open Access Journals (Sweden)

Albert-Baskar Arul

2013-06-01

Full Text Available Proteomics for biomarker validation needs high throughput instrumentation to analyze huge set of clinical samples for quantitative and reproducible analysis at a minimum time without manual experimental errors. Sample preparation, a vital step in proteomics plays a major role in identification and quantification of proteins from biological samples. Tryptic digestion a major check point in sample preparation for mass spectrometry based proteomics needs to be more accurate with rapid processing time. The present study focuses on establishing a high throughput automated online system for proteolytic digestion and desalting of proteins from biological samples quantitatively and qualitatively in a reproducible manner. The present study compares online protein digestion and desalting of BSA with conventional off-line (in-solution method and validated for real time sample for reproducibility. Proteins were identified using SEQUEST data base search engine and the data were quantified using IDEALQ software. The present study shows that the online system capable of handling high throughput samples in 96 well formats carries out protein digestion and peptide desalting efficiently in a reproducible and quantitative manner. Label free quantification showed clear increase of peptide quantities with increase in concentration with much linearity compared to off line method. Hence we would like to suggest that inclusion of this online system in proteomic pipeline will be effective in quantification of proteins in comparative proteomics were the quantification is really very crucial.

Quantitative Analysis of Probabilistic Models of Software Product Lines with Statistical Model Checking

DEFF Research Database (Denmark)

ter Beek, Maurice H.; Legay, Axel; Lluch Lafuente, Alberto

2015-01-01

We investigate the suitability of statistical model checking techniques for analysing quantitative properties of software product line models with probabilistic aspects. For this purpose, we enrich the feature-oriented language FLAN with action rates, which specify the likelihood of exhibiting pa...

Quantitative computed tomography for measuring bone mineral content

International Nuclear Information System (INIS)

Felsenberg, D.; Kalender, W.A.; Banzer, D.; Schmilinsky, G.; Heyse, M.; Fischer, E.; Schneider, U.; Siemens A.G., Erlangen; Krankenhaus Zehlendorf, Berlin

1988-01-01

Quantitative computed tomography (QCT) for measuring bone mineral content of lumbar vertebrae is increasingly used internationally. The effect of using conventional CT (single energy CT, SE-CT) and dual energy CT (DE-CT) on reproducibility has been examined. We defined a standard measurement protocol, which automatically evaluates a calibration phantom. This should ensure an in vivo reproducibility of 1 to 2%. Reference data, which has been obtained with this protocol from 113 normal subjects, using SE-CT ad DE-CT, are presented. (orig.) [de

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

Science.gov (United States)

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

2017-12-01

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

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.

Effect of Genital Sampling Site on the Detection and Quantification of Ureaplasma Species with Quantitative Polymerase Chain Reaction during Pregnancy

OpenAIRE

Faron, Gilles; Vancutsem, Ellen; Naessens, Anne; Buyl, Ronald; Gucciardo, Leonardo; Foulon, Walter

2017-01-01

Objective. This study aimed to compare the qualitative and quantitative reproducibility of quantitative PCR (qPCR) for Ureaplasma species (Ureaplasma spp.) throughout pregnancy and according to the genital sampling site. Study Design. Between 5 and 14 weeks of gestation (T1), vaginal, fornix, and two cervical samples were taken. Sampling was repeated during the 2nd (T2) and 3rd (T3) trimester in randomly selected T1 positive and negative women. Qualitative and quantitative reproducibility wer...

Reproducibility of polar map generation and assessment of defect severity and extent assessment in myocardial perfusion imaging using positron emission tomography

International Nuclear Information System (INIS)

Nekolla, S.G.; Miethaner, C.; Nguyen, N.; Ziegler, S.I.; Schwaiger, M.

1998-01-01

The purpose of this study was to determine the reliability of new software developed for the analysis of cardiac tomographic data. The algorithm delineates the long axis and defines the basal plane and subsequently generates polar maps to quantitatively and reproducibly assess the size and severity of perfusion defects. The developed technique requires an initial manual estimate of the left ventricular long axis and calculates the volumetric maximum myocardial activity distribution. This surface is used to map three-dimensional tracer accumulation onto a two-dimensional representation (polar map), which is the basis for further processing. The spatial information is used to compute geometrical and mechanical properties of a solid model of the left ventricle including the left heart chamber. A new estimate of the axis is determined from this model, and the previously outlined procedure is repeated together with an automated definition of the valve plane until differences between the polar maps can be neglected. This quantitative analysis software was validated in phantom studies with defects of known masses and in ten data sets from normals and patients with coronary artery disease of various severity. We investigated the reproducibility of the maps with the introduction of a similarity criterion where the ratio of two corresponding polar map elements lies within a 10% interval. The maps were also used to measure intra-and interobserver variability in respect of defect size and severity. In the phantom studies, it was possible to reliably assess mass information over a wide range of defects from 5 to 60 g (slope: 1.02, offset -0.68, r = 0.972). Patient studies revealed a statistically significant increase in the reproducibility of the automatic technique compared with the manual approach: 54%±19% (manual) compared with 88%±9% (automatic) for observer 1 and 61%±20% vs 82%±5% for observer 2, respectively. The intervariability analysis showed a significant

Linking agent-based models and stochastic models of financial markets.

Science.gov (United States)

Feng, Ling; Li, Baowen; Podobnik, Boris; Preis, Tobias; Stanley, H Eugene

2012-05-29

It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that "fat" tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting.

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.

Model for Quantitative Evaluation of Enzyme Replacement Treatment

Directory of Open Access Journals (Sweden)

Radeva B.

2009-12-01

Full Text Available Gaucher disease is the most frequent lysosomal disorder. Its enzyme replacement treatment was the new progress of modern biotechnology, successfully used in the last years. The evaluation of optimal dose of each patient is important due to health and economical reasons. The enzyme replacement is the most expensive treatment. It must be held continuously and without interruption. Since 2001, the enzyme replacement therapy with Cerezyme*Genzyme was formally introduced in Bulgaria, but after some time it was interrupted for 1-2 months. The dose of the patients was not optimal. The aim of our work is to find a mathematical model for quantitative evaluation of ERT of Gaucher disease. The model applies a kind of software called "Statistika 6" via the input of the individual data of 5-year-old children having the Gaucher disease treated with Cerezyme. The output results of the model gave possibilities for quantitative evaluation of the individual trends in the development of the disease of each child and its correlation. On the basis of this results, we might recommend suitable changes in ERT.

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

A Review on Quantitative Models for Sustainable Food Logistics Management

Directory of Open Access Journals (Sweden)

M. Soysal

2012-12-01

Full Text Available The last two decades food logistics systems have seen the transition from a focus on traditional supply chain management to food supply chain management, and successively, to sustainable food supply chain management. The main aim of this study is to identify key logistical aims in these three phases and analyse currently available quantitative models to point out modelling challenges in sustainable food logistics management (SFLM. A literature review on quantitative studies is conducted and also qualitative studies are consulted to understand the key logistical aims more clearly and to identify relevant system scope issues. Results show that research on SFLM has been progressively developing according to the needs of the food industry. However, the intrinsic characteristics of food products and processes have not yet been handled properly in the identified studies. The majority of the works reviewed have not contemplated on sustainability problems, apart from a few recent studies. Therefore, the study concludes that new and advanced quantitative models are needed that take specific SFLM requirements from practice into consideration to support business decisions and capture food supply chain dynamics.

Quantitative patterns in drone wars

Science.gov (United States)

Garcia-Bernardo, Javier; Dodds, Peter Sheridan; Johnson, Neil F.

2016-02-01

Attacks by drones (i.e., unmanned combat air vehicles) continue to generate heated political and ethical debates. Here we examine the quantitative nature of drone attacks, focusing on how their intensity and frequency compare with that of other forms of human conflict. Instead of the power-law distribution found recently for insurgent and terrorist attacks, the severity of attacks is more akin to lognormal and exponential distributions, suggesting that the dynamics underlying drone attacks lie beyond these other forms of human conflict. We find that the pattern in the timing of attacks is consistent with one side having almost complete control, an important if expected result. We show that these novel features can be reproduced and understood using a generative mathematical model in which resource allocation to the dominant side is regulated through a feedback loop.

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...

In utero diffusion tensor imaging of the fetal brain: A reproducibility study.

Science.gov (United States)

Jakab, András; Tuura, Ruth; Kellenberger, Christian; Scheer, Ianina

2017-01-01

Our purpose was to evaluate the within-subject reproducibility of in utero diffusion tensor imaging (DTI) metrics and the visibility of major white matter structures. Images for 30 fetuses (20-33. postmenstrual weeks, normal neurodevelopment: 6 cases, cerebral pathology: 24 cases) were acquired on 1.5 T or 3.0 T MRI. DTI with 15 diffusion-weighting directions was repeated three times for each case, TR/TE: 2200/63 ms, voxel size: 1 ∗ 1 mm, slice thickness: 3-5 mm, b-factor: 700 s/mm 2 . Reproducibility was evaluated from structure detectability, variability of DTI measures using the coefficient of variation (CV), image correlation and structural similarity across repeated scans for six selected structures. The effect of age, scanner type, presence of pathology was determined using Wilcoxon rank sum test. White matter structures were detectable in the following percentage of fetuses in at least two of the three repeated scans: corpus callosum genu 76%, splenium 64%, internal capsule, posterior limb 60%, brainstem fibers 40% and temporooccipital association pathways 60%. The mean CV of DTI metrics ranged between 3% and 14.6% and we measured higher reproducibility in fetuses with normal brain development. Head motion was negatively correlated with reproducibility, this effect was partially ameliorated by motion-correction algorithm using image registration. Structures on 3.0 T had higher variability both with- and without motion correction. Fetal DTI is reproducible for projection and commissural bundles during mid-gestation, however, in 16-30% of the cases, data were corrupted by artifacts, resulting in impaired detection of white matter structures. To achieve robust results for the quantitative analysis of diffusivity and anisotropy values, fetal-specific image processing is recommended and repeated DTI is needed to ensure the detectability of fiber pathways.

A quantitative phase field model for hydride precipitation in zirconium alloys: Part I. Development of quantitative free energy functional

International Nuclear Information System (INIS)

Shi, San-Qiang; Xiao, Zhihua

2015-01-01

A temperature dependent, quantitative free energy functional was developed for the modeling of hydride precipitation in zirconium alloys within a phase field scheme. The model takes into account crystallographic variants of hydrides, interfacial energy between hydride and matrix, interfacial energy between hydrides, elastoplastic hydride precipitation and interaction with externally applied stress. The model is fully quantitative in real time and real length scale, and simulation results were compared with limited experimental data available in the literature with a reasonable agreement. The work calls for experimental and/or theoretical investigations of some of the key material properties that are not yet available in the literature

Quantitative Simulation of QARBM Challenge Events During Radiation Belt Enhancements

Science.gov (United States)

Li, W.; Ma, Q.; Thorne, R. M.; Bortnik, J.; Chu, X.

2017-12-01

Various physical processes are known to affect energetic electron dynamics in the Earth's radiation belts, but their quantitative effects at different times and locations in space need further investigation. This presentation focuses on discussing the quantitative roles of various physical processes that affect Earth's radiation belt electron dynamics during radiation belt enhancement challenge events (storm-time vs. non-storm-time) selected by the GEM Quantitative Assessment of Radiation Belt Modeling (QARBM) focus group. We construct realistic global distributions of whistler-mode chorus waves, adopt various versions of radial diffusion models (statistical and event-specific), and use the global evolution of other potentially important plasma waves including plasmaspheric hiss, magnetosonic waves, and electromagnetic ion cyclotron waves from all available multi-satellite measurements. These state-of-the-art wave properties and distributions on a global scale are used to calculate diffusion coefficients, that are then adopted as inputs to simulate the dynamical electron evolution using a 3D diffusion simulation during the storm-time and the non-storm-time acceleration events respectively. We explore the similarities and differences in the dominant physical processes that cause radiation belt electron dynamics during the storm-time and non-storm-time acceleration events. The quantitative role of each physical process is determined by comparing against the Van Allen Probes electron observations at different energies, pitch angles, and L-MLT regions. This quantitative comparison further indicates instances when quasilinear theory is sufficient to explain the observed electron dynamics or when nonlinear interaction is required to reproduce the energetic electron evolution observed by the Van Allen Probes.

Modeling Logistic Performance in Quantitative Microbial Risk Assessment

NARCIS (Netherlands)

Rijgersberg, H.; Tromp, S.O.; Jacxsens, L.; Uyttendaele, M.

2010-01-01

In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage

Quantitative models for sustainable supply chain management

DEFF Research Database (Denmark)

Brandenburg, M.; Govindan, Kannan; Sarkis, J.

2014-01-01

and directions of this research area, this paper provides a content analysis of 134 carefully identified papers on quantitative, formal models that address sustainability aspects in the forward SC. It was found that a preponderance of the publications and models appeared in a limited set of six journals......Sustainability, the consideration of environmental factors and social aspects, in supply chain management (SCM) has become a highly relevant topic for researchers and practitioners. The application of operations research methods and related models, i.e. formal modeling, for closed-loop SCM...... and reverse logistics has been effectively reviewed in previously published research. This situation is in contrast to the understanding and review of mathematical models that focus on environmental or social factors in forward supply chains (SC), which has seen less investigation. To evaluate developments...

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.

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....

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.

Performance Theories for Sentence Coding: Some Quantitative Models

Science.gov (United States)

Aaronson, Doris; And Others

1977-01-01

This study deals with the patterns of word-by-word reading times over a sentence when the subject must code the linguistic information sufficiently for immediate verbatim recall. A class of quantitative models is considered that would account for reading times at phrase breaks. (Author/RM)

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

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

Science.gov (United States)

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

2016-06-29

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

Minimum joint space width (mJSW) of patellofemoral joint on standing ''skyline'' radiographs: test-retest reproducibility and comparison with quantitative magnetic resonance imaging (qMRI)

International Nuclear Information System (INIS)

Simoni, Paolo; Jamali, Sanaa; Alvarez Miezentseva, Victoria; Albert, Adelin; Totterman, Saara; Schreyer, Edward; Tamez-Pena, Jose G.; Zobel, Bruno Beomonte; Gillet, Philippe

2013-01-01

To assess the intraobserver, interobserver, and test-retest reproducibility of minimum joint space width (mJSW) measurement of medial and lateral patellofemoral joints on standing ''skyline'' radiographs and to compare the mJSW of the patellofemoral joint to the mean cartilage thickness calculated by quantitative magnetic resonance imaging (qMRI). A couple of standing ''skyline'' radiographs of the patellofemoral joints and MRI of 55 knees of 28 volunteers (18 females, ten males, mean age, 48.5 ± 16.2 years) were obtained on the same day. The mJSW of the patellofemoral joint was manually measured and Kellgren and Lawrence grade (KLG) was independently assessed by two observers. The mJSW was compared to the mean cartilage thickness of patellofemoral joint calculated by qMRI. mJSW of the medial and lateral patellofemoral joint showed an excellent intraobserver agreement (interclass correlation (ICC) = 0.94 and 0.96), interobserver agreement (ICC = 0.90 and 0.95) and test-retest agreement (ICC = 0.92 and 0.96). The mJSW measured on radiographs was correlated to mean cartilage thickness calculated by qMRI (r = 0.71, p < 0.0001 for the medial PFJ and r = 0.81, p < 0.0001 for the lateral PFJ). However, there was a lack of concordance between radiographs and qMRI for extreme values of joint width and KLG. Radiographs yielded higher joint space measures than qMRI in knees with a normal joint space, while qMRI yielded higher joint space measures than radiographs in knees with joint space narrowing and higher KLG. Standing ''skyline'' radiographs are a reproducible tool for measuring the mJSW of the patellofemoral joint. The mJSW of the patellofemoral joint on radiographs are correlated with, but not concordant with, qMRI measurements. (orig.)

Methodologies for quantitative systems pharmacology (QSP) models : Design and Estimation

NARCIS (Netherlands)

Ribba, B.; Grimm, Hp; Agoram, B.; Davies, M.R.; Gadkar, K.; Niederer, S.; van Riel, N.; Timmis, J.; van der Graaf, Ph.

2017-01-01

With the increased interest in the application of quantitative systems pharmacology (QSP) models within medicine research and development, there is an increasing need to formalize model development and verification aspects. In February 2016, a workshop was held at Roche Pharma Research and Early

Methodologies for Quantitative Systems Pharmacology (QSP) Models: Design and Estimation

NARCIS (Netherlands)

Ribba, B.; Grimm, H. P.; Agoram, B.; Davies, M. R.; Gadkar, K.; Niederer, S.; van Riel, N.; Timmis, J.; van der Graaf, P. H.

2017-01-01

With the increased interest in the application of quantitative systems pharmacology (QSP) models within medicine research and development, there is an increasing need to formalize model development and verification aspects. In February 2016, a workshop was held at Roche Pharma Research and Early

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...

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-11-15

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

Reproducibility of mean nuclear volume and correlation with mean nuclear area in breast cancer

DEFF Research Database (Denmark)

Baak, J P; Ladekarl, M; Sørensen, Flemming Brandt

1994-01-01

reproducible and strongly correlated with nuclear vv assessed in the TOTAL. In invasive breast cancer assessments in the whole tumor section can be used if delineation of the measurement area cannot be done easily. In small areas with a limited number of nuclei (eg, microinvasive parts) MNA can be easier......Previous studies have shown that quantitative, histopathologic features obtained from a carefully selected area in the tumor section ("selective" approach) have a strong prognostic value in breast cancer. On the other hand, it was found that mean nuclear volume estimation in the whole area...... as to their intraobserver and interobserver reproducibility in 22 invasive breast cancer cases. The mean nuclear volume (nuclear vv) was assessed both in the most atypical area (AREA) (selected on morphologic criteria) and in the whole tumor section (TOTAL). Furthermore, the correlation with mean nuclear (profile) area...

Empirical questions for collective-behaviour modelling

Indian Academy of Sciences (India)

The collective behaviour of groups of social animals has been an active topic of study ... Models have been successful at reproducing qualitative features of ... quantitative and detailed empirical results for a range of animal systems. ... standard method [23], the redundant information recorded by the cameras can be used to.

Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

Directory of Open Access Journals (Sweden)

Shah Imran

2011-07-01

Full Text Available Abstract Background With increasing knowledge about the potential mechanisms underlying cellular functions, it is becoming feasible to predict the response of biological systems to genetic and environmental perturbations. Due to the lack of homogeneity in living tissues it is difficult to estimate the physiological effect of chemicals, including potential toxicity. Here we investigate a biologically motivated model for estimating tissue level responses by aggregating the behavior of a cell population. We assume that the molecular state of individual cells is independently governed by discrete non-deterministic signaling mechanisms. This results in noisy but highly reproducible aggregate level responses that are consistent with experimental data. Results We developed an asynchronous threshold Boolean network simulation algorithm to model signal transduction in a single cell, and then used an ensemble of these models to estimate the aggregate response across a cell population. Using published data, we derived a putative crosstalk network involving growth factors and cytokines - i.e., Epidermal Growth Factor, Insulin, Insulin like Growth Factor Type 1, and Tumor Necrosis Factor α - to describe early signaling events in cell proliferation signal transduction. Reproducibility of the modeling technique across ensembles of Boolean networks representing cell populations is investigated. Furthermore, we compare our simulation results to experimental observations of hepatocytes reported in the literature. Conclusion A systematic analysis of the results following differential stimulation of this model by growth factors and cytokines suggests that: (a using Boolean network ensembles with asynchronous updating provides biologically plausible noisy individual cellular responses with reproducible mean behavior for large cell populations, and (b with sufficient data our model can estimate the response to different concentrations of extracellular ligands. Our

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.

A technique for reproducible roentgenprograms of the intercondylar sulcus for the study of the femoropatellar

International Nuclear Information System (INIS)

Koelbel, R.; Bergmann, G.; Rohlmann, A.

1979-01-01

Roentgenographic documentation of certain features of FP-joint geometry and orientation may serve as guideline in deciding on the form of treatment for chondromalacia or recurrent patellar dislocation. Reproducible conditions for taking roentgen films are equally important for this purpose as well as for quantitative measurements and possible statistical work. A new positioning device for the patient's legs has been designed utilizing a parallellogram frame. The roentgenographic technique for skyline views at 30 0 , 60 0 and 90 0 inclination of the central beam relative to the femoral axis is described. The advantages over previous techniques are the ease of handling the positioning frame, the need for only vertical and horizontal adjustment of the roentgen tube, independence of the type of tube or table, reproducibility of cassette and patient positioning. (orig.) [de

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...

Enhancing the Quantitative Representation of Socioeconomic Conditions in the Shared Socio-economic Pathways (SSPs) using the International Futures Model

Science.gov (United States)

Rothman, D. S.; Siraj, A.; Hughes, B.

2013-12-01

The international research community is currently in the process of developing new scenarios for climate change research. One component of these scenarios are the Shared Socio-economic Pathways (SSPs), which describe a set of possible future socioeconomic conditions. These are presented in narrative storylines with associated quantitative drivers. The core quantitative drivers include total population, average GDP per capita, educational attainment, and urbanization at the global, regional, and national levels. At the same time there have been calls, particularly by the IAV community, for the SSPs to include additional quantitative information on other key social factors, such as income inequality, governance, health, and access to key infrastructures, which are discussed in the narratives. The International Futures system (IFs), based at the Pardee Center at the University of Denver, is able to provide forecasts of many of these indicators. IFs cannot use the SSP drivers as exogenous inputs, but we are able to create development pathways that closely reproduce the core quantitative drivers defined by the different SSPs, as well as incorporating assumptions on other key driving factors described in the qualitative narratives. In this paper, we present forecasts for additional quantitative indicators based upon the implementation of the SSP development pathways in IFs. These results will be of value to many researchers.

Quantitative metal magnetic memory reliability modeling for welded joints

Science.gov (United States)

Xing, Haiyan; Dang, Yongbin; Wang, Ben; Leng, Jiancheng

2016-03-01

Metal magnetic memory(MMM) testing has been widely used to detect welded joints. However, load levels, environmental magnetic field, and measurement noises make the MMM data dispersive and bring difficulty to quantitative evaluation. In order to promote the development of quantitative MMM reliability assessment, a new MMM model is presented for welded joints. Steel Q235 welded specimens are tested along the longitudinal and horizontal lines by TSC-2M-8 instrument in the tensile fatigue experiments. The X-ray testing is carried out synchronously to verify the MMM results. It is found that MMM testing can detect the hidden crack earlier than X-ray testing. Moreover, the MMM gradient vector sum K vs is sensitive to the damage degree, especially at early and hidden damage stages. Considering the dispersion of MMM data, the K vs statistical law is investigated, which shows that K vs obeys Gaussian distribution. So K vs is the suitable MMM parameter to establish reliability model of welded joints. At last, the original quantitative MMM reliability model is first presented based on the improved stress strength interference theory. It is shown that the reliability degree R gradually decreases with the decreasing of the residual life ratio T, and the maximal error between prediction reliability degree R 1 and verification reliability degree R 2 is 9.15%. This presented method provides a novel tool of reliability testing and evaluating in practical engineering for welded joints.

Quantitative chemogenomics: machine-learning models of protein-ligand interaction.

Science.gov (United States)

Andersson, Claes R; Gustafsson, Mats G; Strömbergsson, Helena

2011-01-01

Chemogenomics is an emerging interdisciplinary field that lies in the interface of biology, chemistry, and informatics. Most of the currently used drugs are small molecules that interact with proteins. Understanding protein-ligand interaction is therefore central to drug discovery and design. In the subfield of chemogenomics known as proteochemometrics, protein-ligand-interaction models are induced from data matrices that consist of both protein and ligand information along with some experimentally measured variable. The two general aims of this quantitative multi-structure-property-relationship modeling (QMSPR) approach are to exploit sparse/incomplete information sources and to obtain more general models covering larger parts of the protein-ligand space, than traditional approaches that focuses mainly on specific targets or ligands. The data matrices, usually obtained from multiple sparse/incomplete sources, typically contain series of proteins and ligands together with quantitative information about their interactions. A useful model should ideally be easy to interpret and generalize well to new unseen protein-ligand combinations. Resolving this requires sophisticated machine-learning methods for model induction, combined with adequate validation. This review is intended to provide a guide to methods and data sources suitable for this kind of protein-ligand-interaction modeling. An overview of the modeling process is presented including data collection, protein and ligand descriptor computation, data preprocessing, machine-learning-model induction and validation. Concerns and issues specific for each step in this kind of data-driven modeling will be discussed. © 2011 Bentham Science Publishers

Probe colorimeter for quantitating enzyme-linked immunosorbent assays and other colorimetric assays performed with microplates.

Science.gov (United States)

Ackerman, S B; Kelley, E A

1983-03-01

The performance of a fiberoptic probe colorimeter (model PC800; Brinkmann Instruments, Inc., Westbury, N.Y.) for quantitating enzymatic or colorimetric assays in 96-well microtiter plates was compared with the performances of a spectrophotometer (model 240; Gilford Instrument Laboratories, Inc., Oberlin, Ohio) and a commercially available enzyme immunoassay reader (model MR590; Dynatech Laboratories, Inc., Alexandria, Va.). Alkaline phosphatase-p-nitrophenyl phosphate in 3 M NaOH was used as the chromophore source. Six types of plates were evaluated for use with the probe colorimeter; they generated reproducibility values (100% coefficient of variation) ranging from 91 to 98% when one individual made 24 independent measurements on the same dilution of chromophore on each plate. Eleven individuals each performed 24 measurements with the colorimeter on either a visually light (absorbance of 0.10 at 420 nm) or a dark (absorbance of 0.80 at 420 nm) dilution of chromophore; reproducibilities averaged 87% for the light dilution and 97% for the dark dilution. When one individual measured the same chromophore sample at least 20 times in the colorimeter, in the spectrophotometer or in the enzyme immunoassay reader, reproducibility for each instrument was greater than 99%. Measurements of a dilution series of chromophore in a fixed volume indicated that the optical responses of each instrument were linear in a range of 0.05 to 1.10 absorbance units.

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.

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.

Quantitative Model for Economic Analyses of Information Security Investment in an Enterprise Information System

Directory of Open Access Journals (Sweden)

Bojanc Rok

2012-11-01

Full Text Available The paper presents a mathematical model for the optimal security-technology investment evaluation and decision-making processes based on the quantitative analysis of security risks and digital asset assessments in an enterprise. The model makes use of the quantitative analysis of different security measures that counteract individual risks by identifying the information system processes in an enterprise and the potential threats. The model comprises the target security levels for all identified business processes and the probability of a security accident together with the possible loss the enterprise may suffer. The selection of security technology is based on the efficiency of selected security measures. Economic metrics are applied for the efficiency assessment and comparative analysis of different protection technologies. Unlike the existing models for evaluation of the security investment, the proposed model allows direct comparison and quantitative assessment of different security measures. The model allows deep analyses and computations providing quantitative assessments of different options for investments, which translate into recommendations facilitating the selection of the best solution and the decision-making thereof. The model was tested using empirical examples with data from real business environment.

Nailfold capillaroscopic report: qualitative and quantitative methods

Directory of Open Access Journals (Sweden)

S. Zeni

2011-09-01

Full Text Available Nailfold capillaroscopy (NVC is a simple and non-invasive method used for the assessment of patients with Raynaud’s phenomenon (RP and in the differential diagnosis of various connective tissue diseases. The scleroderma pattern abnormalities (giant capillaries, haemorrages and/or avascular areas have a positive predictive value for the development of scleroderma spectrum disorders. Thus, an analytical approach to nailfold capillaroscopy can be useful in quantitatively and reproducibly recording various parameters. We developed a new method to assess patients with RP that is capable of predicting the 5-year transition from isolated RP to RP secondary to scleroderma spectrum disorders. This model is a weighted combination of different capillaroscopic parameters (giant capillaries, microhaemorrages, number of capillaries that allows physicians to stratify RP patients easily using a relatively simple diagram to deduce prognosis.

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.

Accuracy of quantitative visual soil assessment

Science.gov (United States)

van Leeuwen, Maricke; Heuvelink, Gerard; Stoorvogel, Jetse; Wallinga, Jakob; de Boer, Imke; van Dam, Jos; van Essen, Everhard; Moolenaar, Simon; Verhoeven, Frank; Stoof, Cathelijne

2016-04-01

Visual soil assessment (VSA) is a method to assess soil quality visually, when standing in the field. VSA is increasingly used by farmers, farm organisations and companies, because it is rapid and cost-effective, and because looking at soil provides understanding about soil functioning. Often VSA is regarded as subjective, so there is a need to verify VSA. Also, many VSAs have not been fine-tuned for contrasting soil types. This could lead to wrong interpretation of soil quality and soil functioning when contrasting sites are compared to each other. We wanted to assess accuracy of VSA, while taking into account soil type. The first objective was to test whether quantitative visual field observations, which form the basis in many VSAs, could be validated with standardized field or laboratory measurements. The second objective was to assess whether quantitative visual field observations are reproducible, when used by observers with contrasting backgrounds. For the validation study, we made quantitative visual observations at 26 cattle farms. Farms were located at sand, clay and peat soils in the North Friesian Woodlands, the Netherlands. Quantitative visual observations evaluated were grass cover, number of biopores, number of roots, soil colour, soil structure, number of earthworms, number of gley mottles and soil compaction. Linear regression analysis showed that four out of eight quantitative visual observations could be well validated with standardized field or laboratory measurements. The following quantitative visual observations correlated well with standardized field or laboratory measurements: grass cover with classified images of surface cover; number of roots with root dry weight; amount of large structure elements with mean weight diameter; and soil colour with soil organic matter content. Correlation coefficients were greater than 0.3, from which half of the correlations were significant. For the reproducibility study, a group of 9 soil scientists and 7

On the usability of quantitative modelling in operations strategy decission making

NARCIS (Netherlands)

Akkermans, H.A.; Bertrand, J.W.M.

1997-01-01

Quantitative modelling seems admirably suited to help managers in their strategic decision making on operations management issues, but in practice models are rarely used for this purpose. Investigates the reasons why, based on a detailed cross-case analysis of six cases of modelling-supported

Establishment of reproducible osteosarcoma rat model using orthotopic implantation technique.

Science.gov (United States)

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

2009-05-01

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

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

A custom-built PET phantom design for quantitative imaging of printed distributions

International Nuclear Information System (INIS)

Markiewicz, P J; Angelis, G I; Kotasidis, F; Green, M; Matthews, J C; Lionheart, W R; Reader, A J

2011-01-01

This note presents a practical approach to a custom-made design of PET phantoms enabling the use of digital radioactive distributions with high quantitative accuracy and spatial resolution. The phantom design allows planar sources of any radioactivity distribution to be imaged in transaxial and axial (sagittal or coronal) planes. Although the design presented here is specially adapted to the high-resolution research tomograph (HRRT), the presented methods can be adapted to almost any PET scanner. Although the presented phantom design has many advantages, a number of practical issues had to be overcome such as positioning of the printed source, calibration, uniformity and reproducibility of printing. A well counter (WC) was used in the calibration procedure to find the nonlinear relationship between digital voxel intensities and the actual measured radioactive concentrations. Repeated printing together with WC measurements and computed radiography (CR) using phosphor imaging plates (IP) were used to evaluate the reproducibility and uniformity of such printing. Results show satisfactory printing uniformity and reproducibility; however, calibration is dependent on the printing mode and the physical state of the cartridge. As a demonstration of the utility of using printed phantoms, the image resolution and quantitative accuracy of reconstructed HRRT images are assessed. There is very good quantitative agreement in the calibration procedure between HRRT, CR and WC measurements. However, the high resolution of CR and its quantitative accuracy supported by WC measurements made it possible to show the degraded resolution of HRRT brain images caused by the partial-volume effect and the limits of iterative image reconstruction. (note)

Impact of implementation choices on quantitative predictions of cell-based computational models

Science.gov (United States)

Kursawe, Jochen; Baker, Ruth E.; Fletcher, Alexander G.

2017-09-01

'Cell-based' models provide a powerful computational tool for studying the mechanisms underlying the growth and dynamics of biological tissues in health and disease. An increasing amount of quantitative data with cellular resolution has paved the way for the quantitative parameterisation and validation of such models. However, the numerical implementation of cell-based models remains challenging, and little work has been done to understand to what extent implementation choices may influence model predictions. Here, we consider the numerical implementation of a popular class of cell-based models called vertex models, which are often used to study epithelial tissues. In two-dimensional vertex models, a tissue is approximated as a tessellation of polygons and the vertices of these polygons move due to mechanical forces originating from the cells. Such models have been used extensively to study the mechanical regulation of tissue topology in the literature. Here, we analyse how the model predictions may be affected by numerical parameters, such as the size of the time step, and non-physical model parameters, such as length thresholds for cell rearrangement. We find that vertex positions and summary statistics are sensitive to several of these implementation parameters. For example, the predicted tissue size decreases with decreasing cell cycle durations, and cell rearrangement may be suppressed by large time steps. These findings are counter-intuitive and illustrate that model predictions need to be thoroughly analysed and implementation details carefully considered when applying cell-based computational models in a quantitative setting.

Quantitative analysis of a wind energy conversion model

International Nuclear Information System (INIS)

Zucker, Florian; Gräbner, Anna; Strunz, Andreas; Meyn, Jan-Peter

2015-01-01

A rotor of 12 cm diameter is attached to a precision electric motor, used as a generator, to make a model wind turbine. Output power of the generator is measured in a wind tunnel with up to 15 m s −1 air velocity. The maximum power is 3.4 W, the power conversion factor from kinetic to electric energy is c p = 0.15. The v 3 power law is confirmed. The model illustrates several technically important features of industrial wind turbines quantitatively. (paper)

Quantitative Systems Pharmacology: A Case for Disease Models.

Science.gov (United States)

Musante, C J; Ramanujan, S; Schmidt, B J; Ghobrial, O G; Lu, J; Heatherington, A C

2017-01-01

Quantitative systems pharmacology (QSP) has emerged as an innovative approach in model-informed drug discovery and development, supporting program decisions from exploratory research through late-stage clinical trials. In this commentary, we discuss the unique value of disease-scale "platform" QSP models that are amenable to reuse and repurposing to support diverse clinical decisions in ways distinct from other pharmacometrics strategies. © 2016 The Authors Clinical Pharmacology & Therapeutics published by Wiley Periodicals, Inc. on behalf of The American Society for Clinical Pharmacology and Therapeutics.

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

Science.gov (United States)

Anderson, Ryan; Clegg, Samuel M.; Frydenvang, Jens; Wiens, Roger C.; McLennan, Scott M.; Morris, Richard V.; Ehlmann, Bethany L.; Dyar, M. Darby

2017-01-01

Accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “sub-model” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. The sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing.

Science.gov (United States)

Wu, Zujian; Pang, Wei; Coghill, George M

2015-01-01

Both qualitative and quantitative model learning frameworks for biochemical systems have been studied in computational systems biology. In this research, after introducing two forms of pre-defined component patterns to represent biochemical models, we propose an integrative qualitative and quantitative modelling framework for inferring biochemical systems. In the proposed framework, interactions between reactants in the candidate models for a target biochemical system are evolved and eventually identified by the application of a qualitative model learning approach with an evolution strategy. Kinetic rates of the models generated from qualitative model learning are then further optimised by employing a quantitative approach with simulated annealing. Experimental results indicate that our proposed integrative framework is feasible to learn the relationships between biochemical reactants qualitatively and to make the model replicate the behaviours of the target system by optimising the kinetic rates quantitatively. Moreover, potential reactants of a target biochemical system can be discovered by hypothesising complex reactants in the synthetic models. Based on the biochemical models learned from the proposed framework, biologists can further perform experimental study in wet laboratory. In this way, natural biochemical systems can be better understood.

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

DEFF Research Database (Denmark)

Lassen, Martin L; Muzik, Otto; Beyer, Thomas

2017-01-01

The purpose of this study was to test the feasibility of migrating a quantitative brain imaging protocol from a positron emission tomography (PET)-only system to an integrated PET/MR system. Potential differences in both absolute radiotracer concentration as well as in the derived kinetic paramet...

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.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

Science.gov (United States)

Addona, Terri A; Abbatiello, Susan E; Schilling, Birgit; Skates, Steven J; Mani, D R; Bunk, David M; Spiegelman, Clifford H; Zimmerman, Lisa J; Ham, Amy-Joan L; Keshishian, Hasmik; Hall, Steven C; Allen, Simon; Blackman, Ronald K; Borchers, Christoph H; Buck, Charles; Cardasis, Helene L; Cusack, Michael P; Dodder, Nathan G; Gibson, Bradford W; Held, Jason M; Hiltke, Tara; Jackson, Angela; Johansen, Eric B; Kinsinger, Christopher R; Li, Jing; Mesri, Mehdi; Neubert, Thomas A; Niles, Richard K; Pulsipher, Trenton C; Ransohoff, David; Rodriguez, Henry; Rudnick, Paul A; Smith, Derek; Tabb, David L; Tegeler, Tony J; Variyath, Asokan M; Vega-Montoto, Lorenzo J; Wahlander, Åsa; Waldemarson, Sofia; Wang, Mu; Whiteaker, Jeffrey R; Zhao, Lei; Anderson, N Leigh; Fisher, Susan J; Liebler, Daniel C; Paulovich, Amanda G; Regnier, Fred E; Tempst, Paul; Carr, Steven A

2010-01-01

Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low µg/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma. PMID:19561596

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

Science.gov (United States)

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

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

Original methods of quantitative analysis developed for diverse samples in various research fields. Quantitative analysis at NMCC

International Nuclear Information System (INIS)

Sera, Koichiro

2003-01-01

Nishina Memorial Cyclotron Center (NMCC) has been opened for nationwide-common utilization of positron nuclear medicine (PET) and PIXE since April 1993. At the present time, nearly 40 subjects of PIXE in various research fields are pursued here, and more than 50,000 samples have been analyzed up to the present. In order to perform quantitative analyses of diverse samples, technical developments in sample preparation, measurement and data analysis have been continuously carried out. Especially, a standard-free method for quantitative analysis'' made it possible to perform analysis of infinitesimal samples, powdered samples and untreated bio samples, which could not be well analyzed quantitatively in the past. The standard-free method'' and a ''powdered internal standard method'' made the process for target preparation quite easier. It has been confirmed that results obtained by these methods show satisfactory accuracy and reproducibility preventing any ambiguity coming from complicated target preparation processes. (author)

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.

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.

77 FR 41985 - Use of Influenza Disease Models To Quantitatively Evaluate the Benefits and Risks of Vaccines: A...

Science.gov (United States)

2012-07-17

... models to generate quantitative estimates of the benefits and risks of influenza vaccination. The public...] Use of Influenza Disease Models To Quantitatively Evaluate the Benefits and Risks of Vaccines: A... Influenza Disease Models to Quantitatively Evaluate the Benefits and Risks of Vaccines: A Technical Workshop...

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.

Expert judgement models in quantitative risk assessment

Energy Technology Data Exchange (ETDEWEB)

Rosqvist, T. [VTT Automation, Helsinki (Finland); Tuominen, R. [VTT Automation, Tampere (Finland)

1999-12-01

Expert judgement is a valuable source of information in risk management. Especially, risk-based decision making relies significantly on quantitative risk assessment, which requires numerical data describing the initiator event frequencies and conditional probabilities in the risk model. This data is seldom found in databases and has to be elicited from qualified experts. In this report, we discuss some modelling approaches to expert judgement in risk modelling. A classical and a Bayesian expert model is presented and applied to real case expert judgement data. The cornerstone in the models is the log-normal distribution, which is argued to be a satisfactory choice for modelling degree-of-belief type probability distributions with respect to the unknown parameters in a risk model. Expert judgements are qualified according to bias, dispersion, and dependency, which are treated differently in the classical and Bayesian approaches. The differences are pointed out and related to the application task. Differences in the results obtained from the different approaches, as applied to real case expert judgement data, are discussed. Also, the role of a degree-of-belief type probability in risk decision making is discussed.

Expert judgement models in quantitative risk assessment

International Nuclear Information System (INIS)

Rosqvist, T.; Tuominen, R.

1999-01-01

Expert judgement is a valuable source of information in risk management. Especially, risk-based decision making relies significantly on quantitative risk assessment, which requires numerical data describing the initiator event frequencies and conditional probabilities in the risk model. This data is seldom found in databases and has to be elicited from qualified experts. In this report, we discuss some modelling approaches to expert judgement in risk modelling. A classical and a Bayesian expert model is presented and applied to real case expert judgement data. The cornerstone in the models is the log-normal distribution, which is argued to be a satisfactory choice for modelling degree-of-belief type probability distributions with respect to the unknown parameters in a risk model. Expert judgements are qualified according to bias, dispersion, and dependency, which are treated differently in the classical and Bayesian approaches. The differences are pointed out and related to the application task. Differences in the results obtained from the different approaches, as applied to real case expert judgement data, are discussed. Also, the role of a degree-of-belief type probability in risk decision making is discussed

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…

Handgrip force steadiness in young and older adults: a reproducibility study.

Science.gov (United States)

Blomkvist, Andreas W; Eika, Fredrik; de Bruin, Eling D; Andersen, Stig; Jorgensen, Martin

2018-04-02

Force steadiness is a quantitative measure of the ability to control muscle tonus. It is an independent predictor of functional performance and has shown to correlate well with different degrees of motor impairment following stroke. Despite being clinically relevant, few studies have assessed the validity of measuring force steadiness. The aim of this study was to explore the reproducibility of handgrip force steadiness, and to assess age difference in steadiness. Intrarater reproducibility (the degree to which a rating gives consistent result on separate occasions) was investigated in a test-retest design with seven days between sessions. Ten young and thirty older adults were recruited and handgrip steadiness was tested at 5%, 10% and 25% of maximum voluntary contraction (MVC) using Nintendo Wii Balance Board (WBB). Coefficients of variation were calculated from the mean force produced (CVM) and the target force (CVT). Area between the force curve and the target force line (Area) was also calculated. For the older adults we explored reliability using intraclass correlation coefficient (ICC) and agreement using standard error of measurement (SEM), limits of agreement (LOA) and smallest real difference (SRD). A systematic improvement in handgrip steadiness was found between sessions for all measures (CVM, CVT, Area). CVM and CVT at 5% of MVC showed good to high reliability, while Area had poor reliability for all percentages of MVC. Averaged ICC for CVM, CVT and Area was 0.815, 0.806 and 0.464, respectively. Averaged ICC on 5%, 10%, and 25% of MVC was 0.751, 0.667 and 0.668, respectively. Measures of agreement showed similar trends with better results for CVM and CVT than for Area. Young adults had better handgrip steadiness than older adults across all measures. The CVM and CVT measures demonstrated good reproducibility at lower percentages of MVC using the WBB, and could become relevant measures in the clinical setting. The Area measure had poor reproducibility

Quantitative model of New Zealand's energy supply industry

Energy Technology Data Exchange (ETDEWEB)

Smith, B. R. [Victoria Univ., Wellington, (New Zealand); Lucas, P. D. [Ministry of Energy Resources (New Zealand)

1977-10-15

A mathematical model is presented to assist in an analysis of energy policy options available. The model is based on an engineering orientated description of New Zealand's energy supply and distribution system. The system is cast as a linear program, in which energy demand is satisfied at least cost. The capacities and operating modes of process plant (such as power stations, oil refinery units, and LP-gas extraction plants) are determined by the model, as well as the optimal mix of fuels supplied to the final consumers. Policy analysis with the model enables a wide ranging assessment of the alternatives and uncertainties within a consistent quantitative framework. It is intended that the model be used as a tool to investigate the relative effects of various policy options, rather than to present a definitive plan for satisfying the nation's energy requirements.

A general mixture model for mapping quantitative trait loci by using molecular markers

NARCIS (Netherlands)

Jansen, R.C.

1992-01-01

In a segregating population a quantitative trait may be considered to follow a mixture of (normal) distributions, the mixing proportions being based on Mendelian segregation rules. A general and flexible mixture model is proposed for mapping quantitative trait loci (QTLs) by using molecular markers.

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...

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

Quantitative modeling of gene networks of biological systems using fuzzy Petri nets and fuzzy sets

Directory of Open Access Journals (Sweden)

Raed I. Hamed

2018-01-01

Full Text Available Quantitative demonstrating of organic frameworks has turned into an essential computational methodology in the configuration of novel and investigation of existing natural frameworks. Be that as it may, active information that portrays the framework's elements should be known keeping in mind the end goal to get pertinent results with the routine displaying strategies. This information is frequently robust or even difficult to get. Here, we exhibit a model of quantitative fuzzy rational demonstrating approach that can adapt to obscure motor information and hence deliver applicable results despite the fact that dynamic information is fragmented or just dubiously characterized. Besides, the methodology can be utilized as a part of the blend with the current cutting edge quantitative demonstrating strategies just in specific parts of the framework, i.e., where the data are absent. The contextual analysis of the methodology suggested in this paper is performed on the model of nine-quality genes. We propose a kind of FPN model in light of fuzzy sets to manage the quantitative modeling of biological systems. The tests of our model appear that the model is practical and entirely powerful for information impersonation and thinking of fuzzy expert frameworks.

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

3D Bioprinting of Tissue/Organ Models.

Science.gov (United States)

Pati, Falguni; Gantelius, Jesper; Svahn, Helene Andersson

2016-04-04

In vitro tissue/organ models are useful platforms that can facilitate systematic, repetitive, and quantitative investigations of drugs/chemicals. The primary objective when developing tissue/organ models is to reproduce physiologically relevant functions that typically require complex culture systems. Bioprinting offers exciting prospects for constructing 3D tissue/organ models, as it enables the reproducible, automated production of complex living tissues. Bioprinted tissues/organs may prove useful for screening novel compounds or predicting toxicity, as the spatial and chemical complexity inherent to native tissues/organs can be recreated. In this Review, we highlight the importance of developing 3D in vitro tissue/organ models by 3D bioprinting techniques, characterization of these models for evaluating their resemblance to native tissue, and their application in the prioritization of lead candidates, toxicity testing, and as disease/tumor models. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method.

Science.gov (United States)

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-02-01

To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil.

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

Comparison of conventional, model-based quantitative planar, and quantitative SPECT image processing methods for organ activity estimation using In-111 agents

International Nuclear Information System (INIS)

He, Bin; Frey, Eric C

2006-01-01

Accurate quantification of organ radionuclide uptake is important for patient-specific dosimetry. The quantitative accuracy from conventional conjugate view methods is limited by overlap of projections from different organs and background activity, and attenuation and scatter. In this work, we propose and validate a quantitative planar (QPlanar) processing method based on maximum likelihood (ML) estimation of organ activities using 3D organ VOIs and a projector that models the image degrading effects. Both a physical phantom experiment and Monte Carlo simulation (MCS) studies were used to evaluate the new method. In these studies, the accuracies and precisions of organ activity estimates for the QPlanar method were compared with those from conventional planar (CPlanar) processing methods with various corrections for scatter, attenuation and organ overlap, and a quantitative SPECT (QSPECT) processing method. Experimental planar and SPECT projections and registered CT data from an RSD Torso phantom were obtained using a GE Millenium VH/Hawkeye system. The MCS data were obtained from the 3D NCAT phantom with organ activity distributions that modelled the uptake of 111 In ibritumomab tiuxetan. The simulations were performed using parameters appropriate for the same system used in the RSD torso phantom experiment. The organ activity estimates obtained from the CPlanar, QPlanar and QSPECT methods from both experiments were compared. From the results of the MCS experiment, even with ideal organ overlap correction and background subtraction, CPlanar methods provided limited quantitative accuracy. The QPlanar method with accurate modelling of the physical factors increased the quantitative accuracy at the cost of requiring estimates of the organ VOIs in 3D. The accuracy of QPlanar approached that of QSPECT, but required much less acquisition and computation time. Similar results were obtained from the physical phantom experiment. We conclude that the QPlanar method, based

Immunohistochemical Markers for Quantitative Studies of Neurons and Glia in Human Neocortex

DEFF Research Database (Denmark)

Lyck, Lise; Dalmau, Ishar; Chemnitz, John

2007-01-01

Reproducible visualisation of neurons and glia in human brain is essential for quantitative studies of the cellular changes in neurological disease. However, immunohistochemistry in human brain specimens is often compromised due to prolonged fixation. To select cell-lineage specific antibodies fo...

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

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

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.

Quantitative imaging reveals heterogeneous growth dynamics and treatment-dependent residual tumor distributions in a three-dimensional ovarian cancer model

Science.gov (United States)

Celli, Jonathan P.; Rizvi, Imran; Evans, Conor L.; Abu-Yousif, Adnan O.; Hasan, Tayyaba

2010-09-01

Three-dimensional tumor models have emerged as valuable in vitro research tools, though the power of such systems as quantitative reporters of tumor growth and treatment response has not been adequately explored. We introduce an approach combining a 3-D model of disseminated ovarian cancer with high-throughput processing of image data for quantification of growth characteristics and cytotoxic response. We developed custom MATLAB routines to analyze longitudinally acquired dark-field microscopy images containing thousands of 3-D nodules. These data reveal a reproducible bimodal log-normal size distribution. Growth behavior is driven by migration and assembly, causing an exponential decay in spatial density concomitant with increasing mean size. At day 10, cultures are treated with either carboplatin or photodynamic therapy (PDT). We quantify size-dependent cytotoxic response for each treatment on a nodule by nodule basis using automated segmentation combined with ratiometric batch-processing of calcein and ethidium bromide fluorescence intensity data (indicating live and dead cells, respectively). Both treatments reduce viability, though carboplatin leaves micronodules largely structurally intact with a size distribution similar to untreated cultures. In contrast, PDT treatment disrupts micronodular structure, causing punctate regions of toxicity, shifting the distribution toward smaller sizes, and potentially increasing vulnerability to subsequent chemotherapeutic treatment.

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

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...

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

Energy Technology Data Exchange (ETDEWEB)

Zhou, Jian-Ying; Chen, Lijun; Zhang, Bai; Tian, Yuan; Liu, Tao; Thomas, Stefani N.; Chen, Li; Schnaubelt, Michael; Boja, Emily; Hiltket, Tara; Kinsinger, Christopher; Rodriguez, Henry; Davies, Sherri; Li, Shunqiang; Snider, Jacqueline E.; Erdmann-Gilmore, Petra; Tabb, David L.; Townsend, Reid; Ellis, Matthew; Rodland, Karin D.; Smith, Richard D.; Carr, Steven A.; Zhang, Zhen; Chan, Daniel W.; Zhang, Hui

2017-09-21

The identification of protein biomarkers requires large-scale analysis of human specimens to achieve statistical significance. In this study, we evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics strategy using one channel for universal normalization across all samples. A total of 307 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating 107 one-dimensional (1D) LC-MS/MS datasets and 8 offline two-dimensional (2D) LC-MS/MS datasets (25 fractions for each set) for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assess the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we developed a quantification confidence score based on the quality of each peptide-spectrum match (PSM) to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS datasets collected over a 16 month period.

Qualitative and quantitative combined nonlinear dynamics model and its application in analysis of price, supply–demand ratio and selling rate

International Nuclear Information System (INIS)

Zhu, Dingju

2016-01-01

The qualitative and quantitative combined nonlinear dynamics model proposed in this paper fill the gap in nonlinear dynamics model in terms of qualitative and quantitative combined methods, allowing the qualitative model and quantitative model to perfectly combine and overcome their weaknesses by learning from each other. These two types of models use their strengths to make up for the other’s deficiencies. The qualitative and quantitative combined models can surmount the weakness that the qualitative model cannot be applied and verified in a quantitative manner, and the high costs and long time of multiple construction as well as verification of the quantitative model. The combined model is more practical and efficient, which is of great significance for nonlinear dynamics. The qualitative and quantitative combined modeling and model analytical method raised in this paper is not only applied to nonlinear dynamics, but can be adopted and drawn on in the modeling and model analysis of other fields. Additionally, the analytical method of qualitative and quantitative combined nonlinear dynamics model proposed in this paper can satisfactorily resolve the problems with the price system’s existing nonlinear dynamics model analytical method. The three-dimensional dynamics model of price, supply–demand ratio and selling rate established in this paper make estimates about the best commodity prices using the model results, thereby providing a theoretical basis for the government’s macro-control of price. Meanwhile, this model also offer theoretical guidance to how to enhance people’s purchasing power and consumption levels through price regulation and hence to improve people’s living standards.

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.

Quantitative analysis of volatile organic compounds using ion mobility spectra and cascade correlation neural networks

Science.gov (United States)

Harrington, Peter DEB.; Zheng, Peng

1995-01-01

Ion Mobility Spectrometry (IMS) is a powerful technique for trace organic analysis in the gas phase. Quantitative measurements are difficult, because IMS has a limited linear range. Factors that may affect the instrument response are pressure, temperature, and humidity. Nonlinear calibration methods, such as neural networks, may be ideally suited for IMS. Neural networks have the capability of modeling complex systems. Many neural networks suffer from long training times and overfitting. Cascade correlation neural networks train at very fast rates. They also build their own topology, that is a number of layers and number of units in each layer. By controlling the decay parameter in training neural networks, reproducible and general models may be obtained.

Human mobility: Models and applications

Science.gov (United States)

Barbosa, Hugo; Barthelemy, Marc; Ghoshal, Gourab; James, Charlotte R.; Lenormand, Maxime; Louail, Thomas; Menezes, Ronaldo; Ramasco, José J.; Simini, Filippo; Tomasini, Marcello

2018-03-01

Recent years have witnessed an explosion of extensive geolocated datasets related to human movement, enabling scientists to quantitatively study individual and collective mobility patterns, and to generate models that can capture and reproduce the spatiotemporal structures and regularities in human trajectories. The study of human mobility is especially important for applications such as estimating migratory flows, traffic forecasting, urban planning, and epidemic modeling. In this survey, we review the approaches developed to reproduce various mobility patterns, with the main focus on recent developments. This review can be used both as an introduction to the fundamental modeling principles of human mobility, and as a collection of technical methods applicable to specific mobility-related problems. The review organizes the subject by differentiating between individual and population mobility and also between short-range and long-range mobility. Throughout the text the description of the theory is intertwined with real-world applications.

Comparison of blood flow models and acquisitions for quantitative myocardial perfusion estimation from dynamic CT

International Nuclear Information System (INIS)

Bindschadler, Michael; Alessio, Adam M; Modgil, Dimple; La Riviere, Patrick J; Branch, Kelley R

2014-01-01

Myocardial blood flow (MBF) can be estimated from dynamic contrast enhanced (DCE) cardiac CT acquisitions, leading to quantitative assessment of regional perfusion. The need for low radiation dose and the lack of consensus on MBF estimation methods motivates this study to refine the selection of acquisition protocols and models for CT-derived MBF. DCE cardiac CT acquisitions were simulated for a range of flow states (MBF = 0.5, 1, 2, 3 ml (min g) −1 , cardiac output = 3, 5, 8 L min −1 ). Patient kinetics were generated by a mathematical model of iodine exchange incorporating numerous physiological features including heterogenenous microvascular flow, permeability and capillary contrast gradients. CT acquisitions were simulated for multiple realizations of realistic x-ray flux levels. CT acquisitions that reduce radiation exposure were implemented by varying both temporal sampling (1, 2, and 3 s sampling intervals) and tube currents (140, 70, and 25 mAs). For all acquisitions, we compared three quantitative MBF estimation methods (two-compartment model, an axially-distributed model, and the adiabatic approximation to the tissue homogeneous model) and a qualitative slope-based method. In total, over 11 000 time attenuation curves were used to evaluate MBF estimation in multiple patient and imaging scenarios. After iodine-based beam hardening correction, the slope method consistently underestimated flow by on average 47.5% and the quantitative models provided estimates with less than 6.5% average bias and increasing variance with increasing dose reductions. The three quantitative models performed equally well, offering estimates with essentially identical root mean squared error (RMSE) for matched acquisitions. MBF estimates using the qualitative slope method were inferior in terms of bias and RMSE compared to the quantitative methods. MBF estimate error was equal at matched dose reductions for all quantitative methods and range of techniques evaluated. This

Quantitative histopathology in the prognostic evaluation of patients with transitional cell carcinoma of the urinary bladder

DEFF Research Database (Denmark)

Sasaki, M; Sørensen, Flemming Brandt; Fukuzawa, S

1993-01-01

BACKGROUND: Morphologic grading of malignancy is considered to be of prognostic value in patients with transitional cell carcinomas of the urinary bladder (TCC). This qualitative approach is, however, associated with low reproducibility. Grading of malignancy can be carried out on a reproducible......, quantitative scale. METHODS: A retrospective, prognostic study of 110 patients treated for TCC in clinical Stages Ta-T4 (median follow-up time, 6 years) was performed, evaluating various grading techniques. Unbiased estimates of the volume-weighted mean nuclear volume (nuclear vV), nuclear volume fraction...... of nuclear vV are prognostically superior to morphologic grading of malignancy in noninvasive TCC, whereas both morphologically and quantitatively based malignancy grading are without prognostic value in invasive TCC....

Quantitative histopathology in the prognostic evaluation of patients with transitional cell carcinoma of the urinary bladder

DEFF Research Database (Denmark)

Sasaki, M; Sørensen, Flemming Brandt; Fukuzawa, S

1993-01-01

BACKGROUND: Morphologic grading of malignancy is considered to be of prognostic value in patients with transitional cell carcinomas of the urinary bladder (TCC). This qualitative approach is, however, associated with low reproducibility. Grading of malignancy can be carried out on a reproducible......, quantitative scale.METHODS: A retrospective, prognostic study of 110 patients treated for TCC in clinical Stages Ta-T4 (median follow-up time, 6 years) was performed, evaluating various grading techniques. Unbiased estimates of the volume-weighted mean nuclear volume (nuclear vV), nuclear volume fraction...... of nuclear vV are prognostically superior to morphologic grading of malignancy in noninvasive TCC, whereas both morphologically and quantitatively based malignancy grading are without prognostic value in invasive TCC....

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.

The Diagnostic Reproducibility of Tomosynthesis for the Correlation between Acromiohumeral Distance and Rotator Cuff Size or Type.

Science.gov (United States)

Song, Yoonah; Lee, Seunghun; Lee, Bong Gun; Joo, Young Bin; Song, Soon-Young

2018-01-01

To correlate the acromiohumeral distance (AHD) using tomosynthesis and rotator cuff (RC) pathology and various anatomical indices and to assess the diagnostic reproducibility of tomosynthesis for the evaluation of subacromial impingement. A retrospective review of 63 patients with clinically suspected subacromial impingement was conducted. Two musculoskeletal radiologists independently measured the following quantitative data: the AHD on plain radiographs and the AHD at three compartments (anterior, middle, and posterior) using tomosynthesis, computed tomography (CT) arthrography, or magnetic resonance (MR) arthrography. To investigate the association between the AHD and RC pathology and various anatomical indices, we reviewed the arthroscopic operation record as the referenced standard. The size of rotator cuff tear (RCT) in full-thickness tears displayed a significant inverse correlation with the middle and the posterior tomosynthetic AHDs ( p tomosynthesis, and CT or MR arthrography ( p tomosynthesis is reproducible compared with other modalities.

Quantitative theory of driven nonlinear brain dynamics.

Science.gov (United States)

Roberts, J A; Robinson, P A

2012-09-01

Strong periodic stimuli such as bright flashing lights evoke nonlinear responses in the brain and interact nonlinearly with ongoing cortical activity, but the underlying mechanisms for these phenomena are poorly understood at present. The dominant features of these experimentally observed dynamics are reproduced by the dynamics of a quantitative neural field model subject to periodic drive. Model power spectra over a range of drive frequencies show agreement with multiple features of experimental measurements, exhibiting nonlinear effects including entrainment over a range of frequencies around the natural alpha frequency f(α), subharmonic entrainment near 2f(α), and harmonic generation. Further analysis of the driven dynamics as a function of the drive parameters reveals rich nonlinear dynamics that is predicted to be observable in future experiments at high drive amplitude, including period doubling, bistable phase-locking, hysteresis, wave mixing, and chaos indicated by positive Lyapunov exponents. Moreover, photosensitive seizures are predicted for physiologically realistic model parameters yielding bistability between healthy and seizure dynamics. These results demonstrate the applicability of neural field models to the new regime of periodically driven nonlinear dynamics, enabling interpretation of experimental data in terms of specific generating mechanisms and providing new tests of the theory. Copyright © 2012 Elsevier Inc. All rights reserved.

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

Directory of Open Access Journals (Sweden)

Martin L. Lassen

2017-07-01

Full Text Available The purpose of this study was to test the feasibility of migrating a quantitative brain imaging protocol from a positron emission tomography (PET-only system to an integrated PET/MR system. Potential differences in both absolute radiotracer concentration as well as in the derived kinetic parameters as a function of PET system choice have been investigated. Five healthy volunteers underwent dynamic (R-[11C]verapamil imaging on the same day using a GE-Advance (PET-only and a Siemens Biograph mMR system (PET/MR. PET-emission data were reconstructed using a transmission-based attenuation correction (AC map (PET-only, whereas a standard MR-DIXON as well as a low-dose CT AC map was applied to PET/MR emission data. Kinetic modeling based on arterial blood sampling was performed using a 1-tissue-2-rate constant compartment model, yielding kinetic parameters (K1 and k2 and distribution volume (VT. Differences for parametric values obtained in the PET-only and the PET/MR systems were analyzed using a 2-way Analysis of Variance (ANOVA. Comparison of DIXON-based AC (PET/MR with emission data derived from the PET-only system revealed average inter-system differences of −33 ± 14% (p < 0.05 for the K1 parameter and −19 ± 9% (p < 0.05 for k2. Using a CT-based AC for PET/MR resulted in slightly lower systematic differences of −16 ± 18% for K1 and −9 ± 10% for k2. The average differences in VT were −18 ± 10% (p < 0.05 for DIXON- and −8 ± 13% for CT-based AC. Significant systematic differences were observed for kinetic parameters derived from emission data obtained from PET/MR and PET-only imaging due to different standard AC methods employed. Therefore, a transfer of imaging protocols from PET-only to PET/MR systems is not straightforward without application of proper correction methods.Clinical Trial Registration:www.clinicaltrialsregister.eu, identifier 2013-001724-19

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.

Recent trends in social systems quantitative theories and quantitative models

CERN Document Server

Hošková-Mayerová, Šárka; Soitu, Daniela-Tatiana; Kacprzyk, Janusz

2017-01-01

The papers collected in this volume focus on new perspectives on individuals, society, and science, specifically in the field of socio-economic systems. The book is the result of a scientific collaboration among experts from “Alexandru Ioan Cuza” University of Iaşi (Romania), “G. d’Annunzio” University of Chieti-Pescara (Italy), "University of Defence" of Brno (Czech Republic), and "Pablo de Olavide" University of Sevilla (Spain). The heterogeneity of the contributions presented in this volume reflects the variety and complexity of social phenomena. The book is divided in four Sections as follows. The first Section deals with recent trends in social decisions. Specifically, it aims to understand which are the driving forces of social decisions. The second Section focuses on the social and public sphere. Indeed, it is oriented on recent developments in social systems and control. Trends in quantitative theories and models are described in Section 3, where many new formal, mathematical-statistical to...

Quantitative chromatography in the analysis of labelled compounds 1. Quantitative paper chromotography of amino acids by A spot comparison technique

International Nuclear Information System (INIS)

Barakat, M.F.; Farag, A.N.; El-Gharbawy, A.A.

1974-01-01

For the determination of the specific activity of labelled compounds separated by paper sheet chromatography, it was found essential to perfect the quantitative aspect of the paper chromatographic technique. Actually, so far paper chromatography has been used as a separation tool mainly and its use in quantification of the separated materials is by far less studied. In the present work, the quantitative analysis of amino acids by paper sheet chromatography has been carried out by methods, depending on the use of the relative spot area values for correcting the experimental data obtained. The results obtained were good and reproducible. The main advantage of the proposed technique is its extreme simplicity. No complicated equipment of procedures are necessary

Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: The comparison of two quantitative methods

DEFF Research Database (Denmark)

Usaite, Renata; Wohlschlegel, James; Venable, John D.

2008-01-01

The quantitative proteomic analysis of complex protein mixtures is emerging as a technically challenging but viable systems-level approach for studying cellular function. This study presents a large-scale comparative analysis of protein abundances from yeast protein lysates derived from both wild......-type yeast and yeast strains lacking key components of the Snf1 kinase complex. Four different strains were grown under well-controlled chemostat conditions. Multidimensional protein identification technology followed by quantitation using either spectral counting or stable isotope labeling approaches...... labeling strategy. The stable isotope labeling based quantitative approach was found to be highly reproducible among biological replicates when complex protein mixtures containing small expression changes were analyzed. Where poor correlation between stable isotope labeling and spectral counting was found...

Evaluation of aluminum pit corrosion in oak ridge research reactor pool by quantitative imaging and thermodynamic modeling

International Nuclear Information System (INIS)

Jang, Ping-Rey; Arunkumar, Rangaswami; Lindner, Jeffrey S.; Long, Zhiling; Mott, Melissa A.; Okhuysen, Walter P.; Monts, David L.; Su, Yi; Kirk, Paula G.; Ettien, John

2007-01-01

The Oak Ridge Research Reactor (ORRR) was operated as an isotope production and irradiation facility from March 1958 until March 1987. The US Department of Energy permanently shut down and removed the fuel from the ORRR in 1987. The water level must be maintained in the ORRR pool as shielding for radioactive components still located in the pool. The U.S. Department of Energy's Office of Environmental Management (DOE EM) needs to decontaminate and demolish the ORRR as part of the Oak Ridge cleanup program. In February 2004, increased pit corrosion was noted in the pool's 6 mm (1/4'')-thick aluminum liner in the section nearest where the radioactive components are stored. If pit corrosion has significantly penetrated the aluminum liner, then DOE EM must accelerate its decontaminating and decommissioning (D and D) efforts or look for alternatives for shielding the irradiated components. The goal of Mississippi State University's Institute for Clean Energy Technology (ICET) was to provide a determination of the extent and depth of corrosion and to conduct thermodynamic modeling to determine how further corrosion can be inhibited. Results from the work will facilitate ORNL in making reliable disposition decisions. ICET's inspection approach was to quantitatively estimate the amount of corrosion by using Fourier - transform profilometry (FTP). FTP is a non-contact 3- D shape measurement technique. By projecting a fringe pattern onto a target surface and observing its deformation due to surface irregularities from a different view angle, the system is capable of determining the height (depth) distribution of the target surface, thus reproducing the profile of the target accurately. ICET has previously demonstrated that its FTP system can quantitatively estimate the volume and depth of removed and residual material to high accuracy. The results of our successful initial deployment of a submergible FTP system into the ORRR pool are reported here as are initial thermodynamic

Condylar position analysis with a new electronic condylar position measuring instrument E-CPM: influence of different examiners and a working bite on reproducibility.

Science.gov (United States)

Vahle-Hinz, K; Rybczynski, A; Jakstat, H; Ahlers, M O

2009-01-01

Condylar position analysis facilitates a quantitative comparison of the condylar position with and without a bite record, different records and changed influencing factors. Handling by the examiner when positioning the model is a significant factor with regard to the accuracy of the examination. Measurement accuracy could be improved when positioning the models by using special working bites, hence the objective of the experiments described in this study consisted in examining the extent to which the measuring results are influenced by different examiners and by using working bites. In the first trial, one examiner performed ten measurements without and with an interposed working bite for five model pairs in each case. In the second trial, nine examiners (three specialized dentists, three dental assistants, three students) performed ten measurements in each case without and with an interposed working bite. The three-dimensional position was read digitally with the E-CPM (Gamma Dental, Klosterneuburg/Vienna, Austria), recorded by means of spreadsheet software (Microsoft Excel) and diagnostic software (CMDfact, CMD3D module, dentaConcept, Hamburg), and evaluated with graphing software (Sigma Plot, Systat Software, USA). In the first trial, it was shown that the reproducibility of mounting was improved markedly (p <0.01) by using bite records in the form of working bites. In the second trial, it was shown that the mean error increased significantly (p <0.01) when several examiners performed the measurements compared with the results of one examiner alone. No significantly different results occurred (p < 0.01) in the comparison of the different groups of examiners with different educational and training backgrounds. This applied for the mounting methods without and with working bite. On the other hand, the reproducibility of mounting improved distinctly (p<0.01) in every group of examiners when working bites were used. Reproducibility of condylar position analysis was

A quantitative risk-based model for reasoning over critical system properties

Science.gov (United States)

Feather, M. S.

2002-01-01

This position paper suggests the use of a quantitative risk-based model to help support reeasoning and decision making that spans many of the critical properties such as security, safety, survivability, fault tolerance, and real-time.

Quantitative capillary electrophoresis and its application in analysis of alkaloids in tea, coffee, coca cola, and theophylline tablets.

Science.gov (United States)

Li, Mengjia; Zhou, Junyi; Gu, Xue; Wang, Yan; Huang, Xiaojing; Yan, Chao

2009-01-01

A quantitative CE (qCE) system with high precision has been developed, in which a 4-port nano-valve was isolated from the electric field and served as sample injector. The accurate amount of sample was introduced into the CE system with high reproducibility. Based on this system, consecutive injections and separations were performed without voltage interruption. Reproducibilities in terms of RSD lower than 0.8% for retention time and 1.7% for peak area were achieved. The effectiveness of the system was demonstrated by the quantitative analysis of caffeine, theobromine, and theophylline in real samples, such as tea leaf, roasted coffee, coca cola, and theophylline tablets.

Hippocampal volume change measurement: Quantitative assessment of the reproducibility of expert manual outlining and the automated methods FreeSurfer and FIRST

NARCIS (Netherlands)

Mulder, E.R.; de Jong, R.A.; Knol, D.L.; van Schijndel, R.A.; Cover, K.S.; Visser, P.J.; Barkhof, F.; Vrenken, H.

2014-01-01

Background: To measure hippocampal volume change in Alzheimer's disease (AD) or mild cognitive impairment (MCI), expert manual delineation is often used because of its supposed accuracy. It has been suggested that expert outlining yields poorer reproducibility as compared to automated methods, but

Tip-Enhanced Raman Voltammetry: Coverage Dependence and Quantitative Modeling.

Science.gov (United States)

Mattei, Michael; Kang, Gyeongwon; Goubert, Guillaume; Chulhai, Dhabih V; Schatz, George C; Jensen, Lasse; Van Duyne, Richard P

2017-01-11

Electrochemical atomic force microscopy tip-enhanced Raman spectroscopy (EC-AFM-TERS) was employed for the first time to observe nanoscale spatial variations in the formal potential, E 0' , of a surface-bound redox couple. TERS cyclic voltammograms (TERS CVs) of single Nile Blue (NB) molecules were acquired at different locations spaced 5-10 nm apart on an indium tin oxide (ITO) electrode. Analysis of TERS CVs at different coverages was used to verify the observation of single-molecule electrochemistry. The resulting TERS CVs were fit to the Laviron model for surface-bound electroactive species to quantitatively extract the formal potential E 0' at each spatial location. Histograms of single-molecule E 0' at each coverage indicate that the electrochemical behavior of the cationic oxidized species is less sensitive to local environment than the neutral reduced species. This information is not accessible using purely electrochemical methods or ensemble spectroelectrochemical measurements. We anticipate that quantitative modeling and measurement of site-specific electrochemistry with EC-AFM-TERS will have a profound impact on our understanding of the role of nanoscale electrode heterogeneity in applications such as electrocatalysis, biological electron transfer, and energy production and storage.

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

Directory of Open Access Journals (Sweden)

Colin eHorne

2016-02-01

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

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.

Genomic value prediction for quantitative traits under the epistatic model

Directory of Open Access Journals (Sweden)

Xu Shizhong

2011-01-01

Full Text Available Abstract Background Most quantitative traits are controlled by multiple quantitative trait loci (QTL. The contribution of each locus may be negligible but the collective contribution of all loci is usually significant. Genome selection that uses markers of the entire genome to predict the genomic values of individual plants or animals can be more efficient than selection on phenotypic values and pedigree information alone for genetic improvement. When a quantitative trait is contributed by epistatic effects, using all markers (main effects and marker pairs (epistatic effects to predict the genomic values of plants can achieve the maximum efficiency for genetic improvement. Results In this study, we created 126 recombinant inbred lines of soybean and genotyped 80 makers across the genome. We applied the genome selection technique to predict the genomic value of somatic embryo number (a quantitative trait for each line. Cross validation analysis showed that the squared correlation coefficient between the observed and predicted embryo numbers was 0.33 when only main (additive effects were used for prediction. When the interaction (epistatic effects were also included in the model, the squared correlation coefficient reached 0.78. Conclusions This study provided an excellent example for the application of genome selection to plant breeding.

Tropospheric jet response to Antarctic ozone depletion: An update with Chemistry-Climate Model Initiative (CCMI) models

Science.gov (United States)

Son, Seok-Woo; Han, Bo-Reum; Garfinkel, Chaim I.; Kim, Seo-Yeon; Park, Rokjin; Abraham, N. Luke; Akiyoshi, Hideharu; Archibald, Alexander T.; Butchart, N.; Chipperfield, Martyn P.; Dameris, Martin; Deushi, Makoto; Dhomse, Sandip S.; Hardiman, Steven C.; Jöckel, Patrick; Kinnison, Douglas; Michou, Martine; Morgenstern, Olaf; O’Connor, Fiona M.; Oman, Luke D.; Plummer, David A.; Pozzer, Andrea; Revell, Laura E.; Rozanov, Eugene; Stenke, Andrea; Stone, Kane; Tilmes, Simone; Yamashita, Yousuke; Zeng, Guang

2018-05-01

The Southern Hemisphere (SH) zonal-mean circulation change in response to Antarctic ozone depletion is re-visited by examining a set of the latest model simulations archived for the Chemistry-Climate Model Initiative (CCMI) project. All models reasonably well reproduce Antarctic ozone depletion in the late 20th century. The related SH-summer circulation changes, such as a poleward intensification of westerly jet and a poleward expansion of the Hadley cell, are also well captured. All experiments exhibit quantitatively the same multi-model mean trend, irrespective of whether the ocean is coupled or prescribed. Results are also quantitatively similar to those derived from the Coupled Model Intercomparison Project phase 5 (CMIP5) high-top model simulations in which the stratospheric ozone is mostly prescribed with monthly- and zonally-averaged values. These results suggest that the ozone-hole-induced SH-summer circulation changes are robust across the models irrespective of the specific chemistry-atmosphere-ocean coupling.

[A quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse].

Science.gov (United States)

Zhang, Yu; Chen, Yuzhen; Hu, Chunguang; Zhang, Huaning; Bi, Zhenwang; Bi, Zhenqiang

2015-05-01

To construct a quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse and to find out effective interventions to reduce salmonella contamination. We constructed a modular process risk model (MPRM) from evisceration to chilling in Excel Sheet using the data of the process parameters in poultry and the Salmomella concentration surveillance of Jinan in 2012. The MPRM was simulated by @ risk software. The concentration of salmonella on carcass after chilling was 1.96MPN/g which was calculated by model. The sensitive analysis indicated that the correlation coefficient of the concentration of salmonella after defeathering and in chilling pool were 0.84 and 0.34,which were the primary factors to the concentration of salmonella on carcass after chilling. The study provided a quantitative assessment model structure for salmonella on carcass in poultry slaughterhouse. The risk manager could control the contamination of salmonella on carcass after chilling by reducing the concentration of salmonella after defeathering and in chilling pool.

MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis.

Science.gov (United States)

Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

2016-01-01

Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Both Ki-67 and MCM-2 are markers of proliferation which are closely linked to grade. Therefore, they

A semi-quantitative model for risk appreciation and risk weighing

DEFF Research Database (Denmark)

Bos, Peter M.J.; Boon, Polly E.; van der Voet, Hilko

2009-01-01

Risk managers need detailed information on (1) the type of effect, (2) the size (severity) of the expected effect(s) and (3) the fraction of the population at risk to decide on well-balanced risk reduction measures. A previously developed integrated probabilistic risk assessment (IPRA) model...... provides quantitative information on these three parameters. A semi-quantitative tool is presented that combines information on these parameters into easy-readable charts that will facilitate risk evaluations of exposure situations and decisions on risk reduction measures. This tool is based on a concept...... detailed information on the estimated health impact in a given exposure situation. These graphs will facilitate the discussions on appropriate risk reduction measures to be taken....

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...

[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.

A quantitative model to assess Social Responsibility in Environmental Science and Technology.

Science.gov (United States)

Valcárcel, M; Lucena, R

2014-01-01

The awareness of the impact of human activities in society and environment is known as "Social Responsibility" (SR). It has been a topic of growing interest in many enterprises since the fifties of the past Century, and its implementation/assessment is nowadays supported by international standards. There is a tendency to amplify its scope of application to other areas of the human activities, such as Research, Development and Innovation (R + D + I). In this paper, a model of quantitative assessment of Social Responsibility in Environmental Science and Technology (SR EST) is described in detail. This model is based on well established written standards as the EFQM Excellence model and the ISO 26000:2010 Guidance on SR. The definition of five hierarchies of indicators, the transformation of qualitative information into quantitative data and the dual procedure of self-evaluation and external evaluation are the milestones of the proposed model, which can be applied to Environmental Research Centres and institutions. In addition, a simplified model that facilitates its implementation is presented in the article. © 2013 Elsevier B.V. All rights reserved.

Functional linear models for association analysis of quantitative traits.

Science.gov (United States)

Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

2013-11-01

Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. © 2013 WILEY

A multicenter reproducibility study of single-voxel 1H-MRS of the medial temporal lobe

International Nuclear Information System (INIS)

Traeber, Frank; Block, Wolfgang; Guer, Okan; Schild, Hans H.; Freymann, Nikolaus; Heun, Reinhard; Jessen, Frank; Kucinski, Thomas; Hammen, Thilo; Ende, Gabriele; Pilatus, Ulrich; Hampel, Harald

2006-01-01

Proton magnetic resonance spectroscopy ( 1 H-MRS) has provided evidence for a reduction of N-acetyl-aspartate (NAA) in the medial temporal lobe (MTL) in cerebral disorders such as Alzheimer's Disease. Within the 1 H-MRS study of the German Research Network on Dementia, we determined the multicenter reproducibility of single-voxel 1 H-MRS of the MTL. At five sites with 1.5T MR systems, single-voxel 1 H spectra from the MTL of an identical healthy subject were measured. The same subject was also examined at one of the sites five times to assess intracenter stability. The protocol included water-suppressed spectra with TE 272 ms and TE 30 ms and unsuppressed spectra for absolute quantification of metabolite concentrations. The intracenter reproducibility of absolute NAA concentration, expressed as coefficient of variation (CV), was 1.8%. CV for the concentrations of creatine (Cr), choline (Cho), and myoinositol (MI) and for the ratios NAA/Cr, NAA/Cho, and MI/NAA varied by 11-16%. Intercenter CV was 3.9% for NAA and were below 10% for all other metabolites and metabolic ratios. Our study demonstrates that quantitative assessment of NAA with single-voxel MRS can be performed with high intercenter reproducibility. This is the basis for applying 1 H-MRS in large-scale early recognition and treatment studies in MTL affecting disorders. (orig.)

Parameter determination for quantitative PIXE analysis using genetic algorithms

International Nuclear Information System (INIS)

Aspiazu, J.; Belmont-Moreno, E.

1996-01-01

For biological and environmental samples, PIXE technique is in particular advantage for elemental analysis, but the quantitative analysis implies accomplishing complex calculations that require the knowledge of more than a dozen parameters. Using a genetic algorithm, the authors give here an account of the procedure to obtain the best values for the parameters necessary to fit the efficiency for a X-ray detector. The values for some variables involved in quantitative PIXE analysis, were manipulated in a similar way as the genetic information is treated in a biological process. The authors carried out the algorithm until they reproduce, within the confidence interval, the elemental concentrations corresponding to a reference material

Quantitative proteomic analysis of human lung tumor xenografts treated with the ectopic ATP synthase inhibitor citreoviridin.

Directory of Open Access Journals (Sweden)

Yi-Hsuan Wu

Full Text Available ATP synthase is present on the plasma membrane of several types of cancer cells. Citreoviridin, an ATP synthase inhibitor, selectively suppresses the proliferation and growth of lung cancer without affecting normal cells. However, the global effects of targeting ectopic ATP synthase in vivo have not been well defined. In this study, we performed quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ and provided a comprehensive insight into the complicated regulation by citreoviridin in a lung cancer xenograft model. With high reproducibility of the quantitation, we obtained quantitative proteomic profiling with 2,659 proteins identified. Bioinformatics analysis of the 141 differentially expressed proteins selected by their relative abundance revealed that citreoviridin induces alterations in the expression of glucose metabolism-related enzymes in lung cancer. The up-regulation of enzymes involved in gluconeogenesis and storage of glucose indicated that citreoviridin may reduce the glycolytic intermediates for macromolecule synthesis and inhibit cell proliferation. Using comprehensive proteomics, the results identify metabolic aspects that help explain the antitumorigenic effect of citreoviridin in lung cancer, which may lead to a better understanding of the links between metabolism and tumorigenesis in cancer therapy.

Quantitative and qualitative assessment of structural magnetic resonance imaging data in a two-center study

International Nuclear Information System (INIS)

Chalavi, Sima; Simmons, Andrew; Dijkstra, Hildebrand; Barker, Gareth J; Reinders, AAT Simone

2012-01-01

Multi-center magnetic resonance imaging (MRI) studies present an opportunity to advance research by pooling data. However, brain measurements derived from MR-images are susceptible to differences in MR-sequence parameters. It is therefore necessary to determine whether there is an interaction between the sequence parameters and the effect of interest, and to minimise any such interaction by careful choice of acquisition parameters. As an exemplar of the issues involved in multi-center studies, we present data from a study in which we aimed to optimize a set of volumetric MRI-protocols to define a protocol giving data that are consistent and reproducible across two centers and over time. Optimization was achieved based on data quality and quantitative measures, in our case using FreeSurfer and Voxel Based Morphometry approaches. Our approach consisted of a series of five comparisons. Firstly, a single-center dataset was collected, using a range of candidate pulse-sequences and parameters chosen on the basis of previous literature. Based on initial results, a number of minor changes were implemented to optimize the pulse-sequences, and a second single-center dataset was collected. FreeSurfer data quality measures were compared between datasets in order to determine the best performing sequence(s), which were taken forward to the next stage of testing. We subsequently acquired short-term and long-term two-center reproducibility data, and quantitative measures were again assessed to determine the protocol with the highest reproducibility across centers. Effects of a scanner software and hardware upgrade on the reproducibility of the protocols at one of the centers were also evaluated. Assessing the quality measures from the first two datasets allowed us to define artefact-free protocols, all with high image quality as assessed by FreeSurfer. Comparing the quantitative test and retest measures, we found high within-center reproducibility for all protocols, but lower

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.

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

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.

Reproducibility of in-vivo diffusion tensor cardiovascular magnetic resonance in hypertrophic cardiomyopathy

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McGill Laura-Ann

2012-12-01

Full Text Available Abstract Background Myocardial disarray is an important histological feature of hypertrophic cardiomyopathy (HCM which has been studied post-mortem, but its in-vivo prevalence and extent is unknown. Cardiac Diffusion Tensor Imaging (cDTI provides information on mean intravoxel myocyte orientation and potentially myocardial disarray. Recent technical advances have improved in-vivo cDTI, and the aim of this study was to assess the interstudy reproducibility of quantitative in-vivo cDTI in patients with HCM. Methods and results A stimulated-echo single-shot-EPI sequence with zonal excitation and parallel imaging was implemented. Ten patients with HCM were each scanned on 2 different days. For each scan 3 short axis mid-ventricular slices were acquired with cDTI at end systole. Fractional anisotropy (FA, mean diffusivity (MD, and helix angle (HA maps were created using a cDTI post-processing platform developed in-house. The mean ± SD global FA was 0.613 ± 0.044, MD was 0.750 ± 0.154 × 10-3 mm2/s and HA was epicardium −34.3 ± 7.6°, mesocardium 3.5 ± 6.9° and endocardium 38.9 ± 8.1°. Comparison of initial and repeat studies showed global interstudy reproducibility for FA (SD = ± 0.045, Coefficient of Variation (CoV = 7.2%, MD (SD = ± 0.135 × 10-3 mm2/s, CoV = 18.6% and HA (epicardium SD = ± 4.8°; mesocardium SD = ± 3.4°; endocardium SD = ± 2.9°. Reproducibility of FA was superior to MD (p = 0.003. Global MD was significantly higher in the septum than the reference lateral wall (0.784 ± 0.188 vs 0.750 ± 0.154 x10-3 mm2/s, p  Conclusions To the best of our knowledge, this is the first study to assess the interstudy reproducibility of DTI in the human HCM heart in-vivo and the largest cDTI study in HCM to date. Our results show good reproducibility of FA, MD and HA which indicates that current technology yields robust in-vivo measurements that have potential clinical value. The

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

Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women

Energy Technology Data Exchange (ETDEWEB)

Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M. [University of California, San Francisco, Musculoskeletal and Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States)

2012-07-15

The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 {+-} 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. (orig.)

Quantitative aspects and dynamic modelling of glucosinolate metabolism

DEFF Research Database (Denmark)

Vik, Daniel

. This enables comparison of transcript and protein levels across mutants and upon induction. I find that unchallenged plants show good correspondence between protein and transcript, but that treatment with methyljasmonate results in significant differences (chapter 1). Functional genomics are used to study......). The construction a dynamic quantitative model of GLS hydrolysis is described. Simulations reveal potential effects on auxin signalling that could reflect defensive strategies (chapter 4). The results presented grant insights into, not only the dynamics of GLS biosynthesis and hydrolysis, but also the relationship...

Minimum joint space width (mJSW) of patellofemoral joint on standing ''skyline'' radiographs: test-retest reproducibility and comparison with quantitative magnetic resonance imaging (qMRI)

Energy Technology Data Exchange (ETDEWEB)

Simoni, Paolo; Jamali, Sanaa; Alvarez Miezentseva, Victoria [CHU de Liege, Diagnostic Imaging Departement, Domanine du Sart Tilman, Liege (Belgium); Albert, Adelin [CHU de Liege, Biostatistics Departement, Domanine du Sart Tilman, Liege (Belgium); Totterman, Saara; Schreyer, Edward; Tamez-Pena, Jose G. [Qmetrics Technologies, Rochester, NY (United States); Zobel, Bruno Beomonte [Campus Bio-Medico University, Diagnostic Imaging Departement, Rome (Italy); Gillet, Philippe [CHU de Liege, Orthopaedic surgery Department, Domanine du Sart Tilman, Liege (Belgium)

2013-11-15

To assess the intraobserver, interobserver, and test-retest reproducibility of minimum joint space width (mJSW) measurement of medial and lateral patellofemoral joints on standing ''skyline'' radiographs and to compare the mJSW of the patellofemoral joint to the mean cartilage thickness calculated by quantitative magnetic resonance imaging (qMRI). A couple of standing ''skyline'' radiographs of the patellofemoral joints and MRI of 55 knees of 28 volunteers (18 females, ten males, mean age, 48.5 {+-} 16.2 years) were obtained on the same day. The mJSW of the patellofemoral joint was manually measured and Kellgren and Lawrence grade (KLG) was independently assessed by two observers. The mJSW was compared to the mean cartilage thickness of patellofemoral joint calculated by qMRI. mJSW of the medial and lateral patellofemoral joint showed an excellent intraobserver agreement (interclass correlation (ICC) = 0.94 and 0.96), interobserver agreement (ICC = 0.90 and 0.95) and test-retest agreement (ICC = 0.92 and 0.96). The mJSW measured on radiographs was correlated to mean cartilage thickness calculated by qMRI (r = 0.71, p < 0.0001 for the medial PFJ and r = 0.81, p < 0.0001 for the lateral PFJ). However, there was a lack of concordance between radiographs and qMRI for extreme values of joint width and KLG. Radiographs yielded higher joint space measures than qMRI in knees with a normal joint space, while qMRI yielded higher joint space measures than radiographs in knees with joint space narrowing and higher KLG. Standing ''skyline'' radiographs are a reproducible tool for measuring the mJSW of the patellofemoral joint. The mJSW of the patellofemoral joint on radiographs are correlated with, but not concordant with, qMRI measurements. (orig.)

Methodologies for Quantitative Systems Pharmacology (QSP) Models: Design and Estimation.

Science.gov (United States)

Ribba, B; Grimm, H P; Agoram, B; Davies, M R; Gadkar, K; Niederer, S; van Riel, N; Timmis, J; van der Graaf, P H

2017-08-01

With the increased interest in the application of quantitative systems pharmacology (QSP) models within medicine research and development, there is an increasing need to formalize model development and verification aspects. In February 2016, a workshop was held at Roche Pharma Research and Early Development to focus discussions on two critical methodological aspects of QSP model development: optimal structural granularity and parameter estimation. We here report in a perspective article a summary of presentations and discussions. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

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

Application of a nitrocellulose immunoassay for quantitation of proteins secreted in cultured media

International Nuclear Information System (INIS)

LaDuca, F.M.; Dang, C.V.; Bell, W.R.

1986-01-01

A macro immunoassay was developed to quantitate proteins (antigens) secreted in the culture media of primary rat hepatocytes. Dilutions of protein standards and undiluted spent culture media were applied to numbered sheets of nitrocellulose (NC) paper by vacuum filtration (in volumes up to 1 ml) through a specially designed macrofiltration apparatus constructed of plexiglas. Sequential incubation of the NC with bovine serum albumin blocking buffer, monospecific antibody, and 125 I Protein A enabled quantitation of protein concentration by determination of NC bound radioactivity. Linear and reproducible standard curves were obtained with fibrinogen, albumin, transferrin, and haptoglobin. A high degree of coefficient of correlation between radioactivity (cmp) and protein concentration was found. Intra- and inter-test reproducibility was excellent. By using monospecific antibodies, single proteins (i.e., fibrinogen), as low as 32 ng/ml, could be quantified in heterogeneous protein mixtures and in spent culture media. The assay was sensitive to the difference of fibrinogen secretion under nonstimulatory (serum-free hormonally define medium, SFHD) and stimulatory (SFHD plus hydrocortisone) culture conditions. The procedure and techniques described are applicable to the quantitation of any protein in a suitable buffer

The qualitative and quantitative accuracy of DFT methods in computing 1J(C–F), 1J(C–N) and nJ(F–F) spin–spin coupling of fluorobenzene and fluoropyridine molecules

International Nuclear Information System (INIS)

Adeniyi, Adebayo A.; Ajibade, Peter A.

2015-01-01

The qualitative and quantitative quality of DFT methods combined with different basis sets in computing the J-coupling of the types 1 J(C–F) and n J(F–F) are investigated for the fluorobenzene and fluoropyridine derivatives. Interestingly, all of the computational methods perfectly reproduced the experimental order for n J(F–F) but many failed to reproduce the experimental order for 1 J(C–F) coupling. The functional PBEPBE gives the best quantitative values that are closer to the experimental spin–spin coupling when combined with the basis sets aug-cc-pVDZ and DGDZVP but is also part of the methods that fail to perfectly reproduce the experimental order for the 1 J(C–F) coupling. The basis set DGDZVP combined with all the methods except with PBEPBE perfectly reproduces the 1 J(C–F) experimental order. All the methods reproduce either the positive or the negative sign of the experimental spin–spin coupling except for the basis set 6-31+G(d,p) which fails to reproduce the experimental positive value of 3 J(F–F) regardless of what type of DFT methods was used. The values of the FC term is far higher than all other Ramsey terms in the one bond 1 J(C–F) coupling but in the two, three and four bonds n J(F–F) the values of PSO and SD are higher. - Graphical abstract: DFT methods were used to compute the J-coupling of molecules benf, benf2, benf2c, benf2c2, pyrf, pyrfc and pyrfc2, and are presented. Right combination of DFT functional with basis set can reproduce high level EOM-CCSD and experimental J-coupling results. All the methods can reproduce the qualitative order of the experimental J-coupling but not all reproduce the quantitative. The best quantitative results were obtained from PBEPBE combined with the high basis set aug-cc-pVDZ Also, PBEPBE combines with lower basis set DGDZVP to give a highly similar value. - Highlights: • DFT methods were used to compute the J-coupling of the molecules. • Right combination of DFT functional with basis

Reproducibility of a semi-automatic method for 6-point vertebral morphometry in a multi-centre trial

International Nuclear Information System (INIS)

Guglielmi, Giuseppe; Stoppino, Luca Pio; Placentino, Maria Grazia; D'Errico, Francesco; Palmieri, Francesco

2009-01-01

Purpose: To evaluate the reproducibility of a semi-automated system for vertebral morphometry (MorphoXpress) in a large multi-centre trial. Materials and methods: The study involved 132 clinicians (no radiologist) with different levels of experience across 20 osteo-centres in Italy. All have received training in using MorphoXpress. An expert radiologist was also involved providing data used as standard of reference. The test image originate from normal clinical activity and represent a variety of normal, under and over exposed films, indicating both normal anatomy and vertebral deformities. The image was represented twice to the clinicians in a random order. Using the software, the clinicians initially marked the midpoints of the upper and lower vertebrae to include as many of the vertebrae (T5-L4) as practical within each given image. MorphoXpress performs the localisation of all morphometric points based on statistical model-based vision system. Intra-operator as well inter-operator measurement of agreement was calculated using the coefficient of variation and the mean and standard deviation of the difference of two measurements to check their agreement. Results: The overall intra-operator mean differences in vertebral heights is 1.61 ± 4.27% (1 S.D.). The overall intra-operator coefficient of variation is 3.95%. The overall inter-operator mean differences in vertebral heights is 2.93 ± 5.38% (1 S.D.). The overall inter-operator coefficient of variation is 6.89%. Conclusions: The technology tested here can facilitate reproducible quantitative morphometry suitable for large studies of vertebral deformities

Comparison of semi-quantitative and quantitative dynamic contrast-enhanced MRI evaluations of vertebral marrow perfusion in a rat osteoporosis model.

Science.gov (United States)

Zhu, Jingqi; Xiong, Zuogang; Zhang, Jiulong; Qiu, Yuyou; Hua, Ting; Tang, Guangyu

2017-11-14

This study aims to investigate the technical feasibility of semi-quantitative and quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in the assessment of longitudinal changes of marrow perfusion in a rat osteoporosis model, using bone mineral density (BMD) measured by micro-computed tomography (micro-CT) and histopathology as the gold standards. Fifty rats were randomly assigned to the control group (n=25) and ovariectomy (OVX) group whose bilateral ovaries were excised (n=25). Semi-quantitative and quantitative DCE-MRI, micro-CT, and histopathological examinations were performed on lumbar vertebrae at baseline and 3, 6, 9, and 12 weeks after operation. The differences between the two groups in terms of semi-quantitative DCE-MRI parameter (maximum enhancement, E max ), quantitative DCE-MRI parameters (volume transfer constant, K trans ; interstitial volume, V e ; and efflux rate constant, K ep ), micro-CT parameter (BMD), and histopathological parameter (microvessel density, MVD) were compared at each of the time points using an independent-sample t test. The differences in these parameters between baseline and other time points in each group were assessed via Bonferroni's multiple comparison test. A Pearson correlation analysis was applied to assess the relationships between DCE-MRI, micro-CT, and histopathological parameters. In the OVX group, the E max values decreased significantly compared with those of the control group at weeks 6 and 9 (p=0.003 and 0.004, respectively). The K trans values decreased significantly compared with those of the control group from week 3 (pquantitative DCE-MRI, the quantitative DCE-MRI parameter K trans is a more sensitive and accurate index for detecting early reduced perfusion in osteoporotic bone.

Quantitative modelling of HDPE spurt experiments using wall slip and generalised Newtonian flow

NARCIS (Netherlands)

Doelder, den C.F.J.; Koopmans, R.J.; Molenaar, J.

1998-01-01

A quantitative model to describe capillary rheometer experiments is presented. The model can generate ‘two-branched' discontinuous flow curves and the associated pressure oscillations. Polymer compressibility in the barrel, incompressible axisymmetric generalised Newtonian flow in the die, and a

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.

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)

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network.

Directory of Open Access Journals (Sweden)

Felipe Leal Valentim

Full Text Available Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1 mutation has a larger impact on APETALA1 (AP1, which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1 by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.

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.

High-resolution morphological and biochemical imaging of articular cartilage of the ankle joint at 3.0 T using a new dedicated phased array coil: in vivo reproducibility study

International Nuclear Information System (INIS)

Welsch, Goetz H.; Trattnig, Siegfried; Mamisch, Tallal C.; Weber, Michael; Horger, Wilhelm; Bohndorf, Klaus

2008-01-01

The objective of this study was to evaluate the feasibility and reproducibility of high-resolution magnetic resonance imaging (MRI) and quantitative T2 mapping of the talocrural cartilage within a clinically applicable scan time using a new dedicated ankle coil and high-field MRI. Ten healthy volunteers (mean age 32.4 years) underwent MRI of the ankle. As morphological sequences, proton density fat-suppressed turbo spin echo (PD-FS-TSE), as a reference, was compared with 3D true fast imaging with steady-state precession (TrueFISP). Furthermore, biochemical quantitative T2 imaging was prepared using a multi-echo spin-echo T2 approach. Data analysis was performed three times each by three different observers on sagittal slices, planned on the isotropic 3D-TrueFISP; as a morphological parameter, cartilage thickness was assessed and for T2 relaxation times, region-of-interest (ROI) evaluation was done. Reproducibility was determined as a coefficient of variation (CV) for each volunteer; averaged as root mean square (RMSA) given as a percentage; statistical evaluation was done using analysis of variance. Cartilage thickness of the talocrural joint showed significantly higher values for the 3D-TrueFISP (ranging from 1.07 to 1.14 mm) compared with the PD-FS-TSE (ranging from 0.74 to 0.99 mm); however, both morphological sequences showed comparable good results with RMSA of 7.1 to 8.5%. Regarding quantitative T2 mapping, measurements showed T2 relaxation times of about 54 ms with an excellent reproducibility (RMSA) ranging from 3.2 to 4.7%. In our study the assessment of cartilage thickness and T2 relaxation times could be performed with high reproducibility in a clinically realizable scan time, demonstrating new possibilities for further investigations into patient groups. (orig.)

Optimization of Ecg Gating in Quantitative Femoral Angiography

International Nuclear Information System (INIS)

Nilsson, S.; Berglund, I.; Erikson, U.; Johansson, J.; Walldius, G.

2003-01-01

Purpose: To determine which phase of the heart cycle would yield the highest reproducibility in measuring atherosclerosis-related variables such as arterial lumen volume and edge roughness. Material and Methods: 35 patients with hypercholesterolemia underwent select ive femoral angiography, repeated four times at 10-min intervals. The angiographies were performed with Ecg-gated exposures. In angiographies 1 and 2 the delay from R-wave maximum to each exposure was 0.1 s, in angiographies 3 and 4 the delay was 0.1, 0.3, 0.5 or 0.7 s or the exposures were performed 1/s without Ecg gating. Arterial lumen volume and edge roughness were measured in a 20-cm segment of the superficial femoral artery using a computer-based densitometric method. Measurement reproducibility was determined by comparing angiographies 1-2 and angiographies 3-4. Results: When measuring arterial lumen volume and edge roughness of a 20-cm segment of the femoral artery, reproducibility was not dependent on Ecg gating. In measuring single arterial diameters and cross-sectional areas, the reproducibility was better when exposures were made 0.1 s after the R-wave maximum than when using other settings of the Ecg gating device or without Ecg gating. Conclusion: The influence of pulsatile flow upon quantitative measurement in femoral angiograms seems to be the smallest possible in early systole, as can be demonstrated when measuring single diameters and cross-sectional areas. In variables based on integration over longer segments, measurement reproducibility seems to be independent of phase

Optimization of Ecg Gating in Quantitative Femoral Angiography

Energy Technology Data Exchange (ETDEWEB)

Nilsson, S.; Berglund, I.; Erikson, U. [Univ. Hospital, Uppsala (Sweden). Dept. of Oncology, Radiology and Clinical Immunology; Johansson, J.; Walldius, G. [Karolinska Hospital, Stockholm (Sweden). King Gustav V Research Inst.

2003-09-01

Purpose: To determine which phase of the heart cycle would yield the highest reproducibility in measuring atherosclerosis-related variables such as arterial lumen volume and edge roughness. Material and Methods: 35 patients with hypercholesterolemia underwent select ive femoral angiography, repeated four times at 10-min intervals. The angiographies were performed with Ecg-gated exposures. In angiographies 1 and 2 the delay from R-wave maximum to each exposure was 0.1 s, in angiographies 3 and 4 the delay was 0.1, 0.3, 0.5 or 0.7 s or the exposures were performed 1/s without Ecg gating. Arterial lumen volume and edge roughness were measured in a 20-cm segment of the superficial femoral artery using a computer-based densitometric method. Measurement reproducibility was determined by comparing angiographies 1-2 and angiographies 3-4. Results: When measuring arterial lumen volume and edge roughness of a 20-cm segment of the femoral artery, reproducibility was not dependent on Ecg gating. In measuring single arterial diameters and cross-sectional areas, the reproducibility was better when exposures were made 0.1 s after the R-wave maximum than when using other settings of the Ecg gating device or without Ecg gating. Conclusion: The influence of pulsatile flow upon quantitative measurement in femoral angiograms seems to be the smallest possible in early systole, as can be demonstrated when measuring single diameters and cross-sectional areas. In variables based on integration over longer segments, measurement reproducibility seems to be independent of phase.

Solvable stochastic dealer models for financial markets

Science.gov (United States)

Yamada, Kenta; Takayasu, Hideki; Ito, Takatoshi; Takayasu, Misako

2009-05-01

We introduce solvable stochastic dealer models, which can reproduce basic empirical laws of financial markets such as the power law of price change. Starting from the simplest model that is almost equivalent to a Poisson random noise generator, the model becomes fairly realistic by adding only two effects: the self-modulation of transaction intervals and a forecasting tendency, which uses a moving average of the latest market price changes. Based on the present microscopic model of markets, we find a quantitative relation with market potential forces, which have recently been discovered in the study of market price modeling based on random walks.

Prognostic, quantitative histopathologic variables in lobular carcinoma of the breast

DEFF Research Database (Denmark)

Ladekarl, M; Sørensen, Flemming Brandt

1993-01-01

BACKGROUND: A retrospective investigation of 53 consecutively treated patients with operable lobular carcinoma of the breast, with a median follow-up of 6.6 years, was performed to examine the prognostic value of quantitative histopathologic parameters.METHODS: The measurements were performed...... of disease, vv(nuc), MI, and NI were of significant independent, prognostic value. On the basis of the multivariate analyses, a prognostic index with highly distinguishing capacity between prognostically poor and favorable cases was constructed.CONCLUSION: Quantitative histopathologic variables are of value...... for objective grading of malignancy in lobular carcinomas. The new parameter--estimates of the mean nuclear volume--is highly reproducible and suitable for routine use. However, larger and prospective studies are needed to establish the true value of the quantitative histopathologic variables in the clinical...

Prognostic, quantitative histopathologic variables in lobular carcinoma of the breast

DEFF Research Database (Denmark)

Ladekarl, M; Sørensen, Flemming Brandt

1993-01-01

BACKGROUND: A retrospective investigation of 53 consecutively treated patients with operable lobular carcinoma of the breast, with a median follow-up of 6.6 years, was performed to examine the prognostic value of quantitative histopathologic parameters. METHODS: The measurements were performed...... of disease, vv(nuc), MI, and NI were of significant independent, prognostic value. On the basis of the multivariate analyses, a prognostic index with highly distinguishing capacity between prognostically poor and favorable cases was constructed. CONCLUSION: Quantitative histopathologic variables are of value...... for objective grading of malignancy in lobular carcinomas. The new parameter--estimates of the mean nuclear volume--is highly reproducible and suitable for routine use. However, larger and prospective studies are needed to establish the true value of the quantitative histopathologic variables in the clinical...

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

Wires in the soup: quantitative models of cell signaling

Science.gov (United States)

Cheong, Raymond; Levchenko, Andre

2014-01-01

Living cells are capable of extracting information from their environments and mounting appropriate responses to a variety of associated challenges. The underlying signal transduction networks enabling this can be quite complex, necessitating for their unraveling by sophisticated computational modeling coupled with precise experimentation. Although we are still at the beginning of this process, some recent examples of integrative analysis of cell signaling are very encouraging. This review highlights the case of the NF-κB pathway in order to illustrate how a quantitative model of a signaling pathway can be gradually constructed through continuous experimental validation, and what lessons one might learn from such exercises. PMID:18291655

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.

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

DEFF Research Database (Denmark)

Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S.

2017-01-01

analysis, new methods for the effective use of the ever more readily available and abundant -omics data (i.e. transcriptomics, proteomics and metabolomics) are urgently needed.Results: The jQMM library presented here provides an open-source, Python-based framework for modeling internal metabolic fluxes......, it introduces the capability to use C-13 labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale C-13 Metabolic Flux Analysis (2S-C-13 MFA). In addition, the library includes a demonstration of a method that uses proteomics data to produce actionable...... insights to increase biofuel production. Finally, the use of the jQMM library is illustrated through the addition of several Jupyter notebook demonstration files that enhance reproducibility and provide the capability to be adapted to the user's specific needs.Conclusions: jQMM will facilitate the design...

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

A quantitative analysis of instabilities in the linear chiral sigma model

International Nuclear Information System (INIS)

Nemes, M.C.; Nielsen, M.; Oliveira, M.M. de; Providencia, J. da

1990-08-01

We present a method to construct a complete set of stationary states corresponding to small amplitude motion which naturally includes the continuum solution. The energy wheighted sum rule (EWSR) is shown to provide for a quantitative criterium on the importance of instabilities which is known to occur in nonasymptotically free theories. Out results for the linear σ model showed be valid for a large class of models. A unified description of baryon and meson properties in terms of the linear σ model is also given. (author)

Evaluating quantitative and qualitative models: An application for nationwide water erosion assessment in Ethiopia

NARCIS (Netherlands)

Sonneveld, B.G.J.S.; Keyzer, M.A.; Stroosnijder, L

2011-01-01

This paper tests the candidacy of one qualitative response model and two quantitative models for a nationwide water erosion hazard assessment in Ethiopia. After a descriptive comparison of model characteristics the study conducts a statistical comparison to evaluate the explanatory power of the

Evaluating quantitative and qualitative models: an application for nationwide water erosion assessment in Ethiopia

NARCIS (Netherlands)

Sonneveld, B.G.J.S.; Keyzer, M.A.; Stroosnijder, L.

2011-01-01

This paper tests the candidacy of one qualitative response model and two quantitative models for a nationwide water erosion hazard assessment in Ethiopia. After a descriptive comparison of model characteristics the study conducts a statistical comparison to evaluate the explanatory power of the

The quantitative modelling of human spatial habitability

Science.gov (United States)

Wise, J. A.

1985-01-01

A model for the quantitative assessment of human spatial habitability is presented in the space station context. The visual aspect assesses how interior spaces appear to the inhabitants. This aspect concerns criteria such as sensed spaciousness and the affective (emotional) connotations of settings' appearances. The kinesthetic aspect evaluates the available space in terms of its suitability to accommodate human movement patterns, as well as the postural and anthrometric changes due to microgravity. Finally, social logic concerns how the volume and geometry of available space either affirms or contravenes established social and organizational expectations for spatial arrangements. Here, the criteria include privacy, status, social power, and proxemics (the uses of space as a medium of social communication).

Quantitative Imaging in Cancer Evolution and Ecology

Science.gov (United States)

Grove, Olya; Gillies, Robert J.

2013-01-01

Cancer therapy, even when highly targeted, typically fails because of the remarkable capacity of malignant cells to evolve effective adaptations. These evolutionary dynamics are both a cause and a consequence of cancer system heterogeneity at many scales, ranging from genetic properties of individual cells to large-scale imaging features. Tumors of the same organ and cell type can have remarkably diverse appearances in different patients. Furthermore, even within a single tumor, marked variations in imaging features, such as necrosis or contrast enhancement, are common. Similar spatial variations recently have been reported in genetic profiles. Radiologic heterogeneity within tumors is usually governed by variations in blood flow, whereas genetic heterogeneity is typically ascribed to random mutations. However, evolution within tumors, as in all living systems, is subject to Darwinian principles; thus, it is governed by predictable and reproducible interactions between environmental selection forces and cell phenotype (not genotype). This link between regional variations in environmental properties and cellular adaptive strategies may permit clinical imaging to be used to assess and monitor intratumoral evolution in individual patients. This approach is enabled by new methods that extract, report, and analyze quantitative, reproducible, and mineable clinical imaging data. However, most current quantitative metrics lack spatialness, expressing quantitative radiologic features as a single value for a region of interest encompassing the whole tumor. In contrast, spatially explicit image analysis recognizes that tumors are heterogeneous but not well mixed and defines regionally distinct habitats, some of which appear to harbor tumor populations that are more aggressive and less treatable than others. By identifying regional variations in key environmental selection forces and evidence of cellular adaptation, clinical imaging can enable us to define intratumoral

A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks.

Directory of Open Access Journals (Sweden)

Teeraphan Laomettachit

Full Text Available To understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a "standard component" modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with "standard components" can capture in quantitative detail many essential properties of cell cycle control in budding yeast.

Evaluation of ViroCyt® Virus Counter for Rapid Filovirus Quantitation

Directory of Open Access Journals (Sweden)

Cynthia A. Rossi

2015-03-01

Full Text Available Development and evaluation of medical countermeasures for diagnostics, vaccines, and therapeutics requires production of standardized, reproducible, and well characterized virus preparations. For filoviruses this includes plaque assay for quantitation of infectious virus, transmission electron microscopy (TEM for morphology and quantitation of virus particles, and real-time reverse transcription PCR for quantitation of viral RNA (qRT-PCR. The ViroCyt® Virus Counter (VC 2100 (ViroCyt, Boulder, CO, USA is a flow-based instrument capable of quantifying virus particles in solution. Using a proprietary combination of fluorescent dyes that stain both nucleic acid and protein in a single 30 min step, rapid, reproducible, and cost-effective quantification of filovirus particles was demonstrated. Using a seed stock of Ebola virus variant Kikwit, the linear range of the instrument was determined to be 2.8E+06 to 1.0E+09 virus particles per mL with coefficient of variation ranging from 9.4% to 31.5% for samples tested in triplicate. VC particle counts for various filovirus stocks were within one log of TEM particle counts. A linear relationship was established between the plaque assay, qRT-PCR, and the VC. VC results significantly correlated with both plaque assay and qRT-PCR. These results demonstrated that the VC is an easy, fast, and consistent method to quantify filoviruses in stock preparations.

Evaluation of ViroCyt® Virus Counter for Rapid Filovirus Quantitation

Directory of Open Access Journals (Sweden)

Cynthia A. Rossi

2015-02-01

Full Text Available Development and evaluation of medical countermeasures for diagnostics, vaccines, and therapeutics requires production of standardized, reproducible, and well characterized virus preparations. For filoviruses this includes plaque assay for quantitation of infectious virus, transmission electron microscopy (TEM for morphology and quantitation of virus particles, and real-time reverse transcription PCR for quantitation of viral RNA (qRT-PCR. The ViroCyt® Virus Counter (VC 2100 (ViroCyt, Boulder, CO, USA is a flow-based instrument capable of quantifying virus particles in solution. Using a proprietary combination of fluorescent dyes that stain both nucleic acid and protein in a single 30 min step, rapid, reproducible, and cost-effective quantification of filovirus particles was demonstrated. Using a seed stock of Ebola virus variant Kikwit, the linear range of the instrument was determined to be 2.8E+06 to 1.0E+09 virus particles per mL with coefficient of variation ranging from 9.4% to 31.5% for samples tested in triplicate. VC particle counts for various filovirus stocks were within one log of TEM particle counts. A linear relationship was established between the plaque assay, qRT-PCR, and the VC. VC results significantly correlated with both plaque assay and qRT-PCR. These results demonstrated that the VC is an easy, fast, and consistent method to quantify filoviruses in stock preparations.

Technical Note: Description and assessment of a nudged version of the new dynamics Unified Model

Directory of Open Access Journals (Sweden)

O. Morgenstern

2008-03-01

Full Text Available We present a "nudged" version of the Met Office general circulation model, the Unified Model. We constrain this global climate model using ERA-40 re-analysis data with the aim of reproducing the observed "weather" over a year from September 1999. Quantitative assessments are made of its performance, focusing on dynamical aspects of nudging and demonstrating that the "weather" is well simulated.

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

A multicenter reproducibility study of single-voxel {sup 1}H-MRS of the medial temporal lobe

Energy Technology Data Exchange (ETDEWEB)

Traeber, Frank; Block, Wolfgang; Guer, Okan; Schild, Hans H. [University of Bonn, Department of Radiology, Bonn (Germany); Freymann, Nikolaus; Heun, Reinhard; Jessen, Frank [University of Bonn, Department of Psychiatry, Bonn (Germany); Kucinski, Thomas [University of Hamburg, Department of Neuroradiology, Hamburg (Germany); Hammen, Thilo [University of Erlangen, Department of Psychiatry, Erlangen (Germany); Ende, Gabriele [Central Institute of Mental Health, NMR Research in Psychiatry, Mannheim (Germany); Pilatus, Ulrich [University of Frankfurt, Department of Neuroradiology, Frankfurt (Germany); Hampel, Harald [University of Munich, Department of Psychiatry, Munich (Germany)

2006-05-15

Proton magnetic resonance spectroscopy ({sup 1}H-MRS) has provided evidence for a reduction of N-acetyl-aspartate (NAA) in the medial temporal lobe (MTL) in cerebral disorders such as Alzheimer's Disease. Within the {sup 1}H-MRS study of the German Research Network on Dementia, we determined the multicenter reproducibility of single-voxel {sup 1}H-MRS of the MTL. At five sites with 1.5T MR systems, single-voxel {sup 1}H spectra from the MTL of an identical healthy subject were measured. The same subject was also examined at one of the sites five times to assess intracenter stability. The protocol included water-suppressed spectra with TE 272 ms and TE 30 ms and unsuppressed spectra for absolute quantification of metabolite concentrations. The intracenter reproducibility of absolute NAA concentration, expressed as coefficient of variation (CV), was 1.8%. CV for the concentrations of creatine (Cr), choline (Cho), and myoinositol (MI) and for the ratios NAA/Cr, NAA/Cho, and MI/NAA varied by 11-16%. Intercenter CV was 3.9% for NAA and were below 10% for all other metabolites and metabolic ratios. Our study demonstrates that quantitative assessment of NAA with single-voxel MRS can be performed with high intercenter reproducibility. This is the basis for applying {sup 1}H-MRS in large-scale early recognition and treatment studies in MTL affecting disorders. (orig.)

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

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.

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

Directory of Open Access Journals (Sweden)

Daniel Nigusse Tollosa

2017-11-01

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

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

Science.gov (United States)

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

2017-11-17

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

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

Quantitative Analysis of cardiac SPECT

International Nuclear Information System (INIS)

Nekolla, S.G.; Bengel, F.M.

2004-01-01

The quantitative analysis of myocardial SPECT images is a powerful tool to extract the highly specific radio tracer uptake in these studies. If compared to normal data bases, the uptake values can be calibrated on an individual basis. Doing so increases the reproducibility of the analysis substantially. Based on the development over the last three decades starting from planar scinitigraphy, this paper discusses the methods used today incorporating the changes due to tomographic image acquisitions. Finally, the limitations of these approaches as well as consequences from most recent hardware developments, commercial analysis packages and a wider view of the description of the left ventricle are discussed. (orig.)

Alpha-transfer reactions and the pairing-vibration model

International Nuclear Information System (INIS)

Betts, R.R.

1977-01-01

The pairing-vibration model with isospin is extended to include α-transfer reactions. Selection rules and expressions for transition strengths are derived and compared with experimental results for A = 40--66 nuclei. The selection rules are found to be followed quite well in the examples studied. The systematics of ground-state transition strengths are qualitatively quite well reproduced although the quantitative agreement is poor. When the changing nature of the pairing quanta is incorporated using two-particle transfer data the agreement becomes quantitatively good. Evidence is presented for clustering other than that due to pairing in 40 Ca and 44 Ti

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....

Modeling logistic performance in quantitative microbial risk assessment.

Science.gov (United States)

Rijgersberg, Hajo; Tromp, Seth; Jacxsens, Liesbeth; Uyttendaele, Mieke

2010-01-01

In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage times, temperatures, gas conditions, and their distributions) are determined. However, the logistic chain with its queues (storages, shelves) and mechanisms for ordering products is usually not taken into account. As a consequence, storage times-mutually dependent in successive steps in the chain-cannot be described adequately. This may have a great impact on the tails of risk distributions. Because food safety risks are generally very small, it is crucial to model the tails of (underlying) distributions as accurately as possible. Logistic performance can be modeled by describing the underlying planning and scheduling mechanisms in discrete-event modeling. This is common practice in operations research, specifically in supply chain management. In this article, we present the application of discrete-event modeling in the context of a QMRA for Listeria monocytogenes in fresh-cut iceberg lettuce. We show the potential value of discrete-event modeling in QMRA by calculating logistic interventions (modifications in the logistic chain) and determining their significance with respect to food safety.

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.

Quantitative and Functional Requirements for Bioluminescent Cancer Models.

Science.gov (United States)

Feys, Lynn; Descamps, Benedicte; Vanhove, Christian; Vermeulen, Stefan; Vandesompele, J O; Vanderheyden, Katrien; Messens, Kathy; Bracke, Marc; De Wever, Olivier

2016-01-01

Bioluminescent cancer models are widely used but detailed quantification of the luciferase signal and functional comparison with a non-transfected control cell line are generally lacking. In the present study, we provide quantitative and functional tests for luciferase-transfected cells. We quantified the luciferase expression in BLM and HCT8/E11 transfected cancer cells, and examined the effect of long-term luciferin exposure. The present study also investigated functional differences between parental and transfected cancer cells. Our results showed that quantification of different single-cell-derived populations are superior with droplet digital polymerase chain reaction. Quantification of luciferase protein level and luciferase bioluminescent activity is only useful when there is a significant difference in copy number. Continuous exposure of cell cultures to luciferin leads to inhibitory effects on mitochondrial activity, cell growth and bioluminescence. These inhibitory effects correlate with luciferase copy number. Cell culture and mouse xenograft assays showed no significant functional differences between luciferase-transfected and parental cells. Luciferase-transfected cells should be validated by quantitative and functional assays before starting large-scale experiments. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property

OpenAIRE

Side, Domenico Delle; Nassisi, Vincenzo; Pennetta, Cecilia; Alifano, Pietro; Di Salvo, Marco; Talà, Adelfia; Chechkin, Aleksei; Seno, Flavio; Trovato, Antonio

2017-01-01

We present an effective dynamical model for the onset of bacterial bioluminescence, one of the most studied quorum sensing-mediated traits. Our model is built upon simple equations that describe the growth of the bacterial colony, the production and accumulation of autoinducer signal molecules, their sensing within bacterial cells, and the ensuing quorum activation mechanism that triggers bioluminescent emission. The model is directly tested to quantitatively reproduce the experimental distri...

Quantitative model of the effects of contamination and space environment on in-flight aging of thermal coatings

Science.gov (United States)

Vanhove, Emilie; Roussel, Jean-François; Remaury, Stéphanie; Faye, Delphine; Guigue, Pascale

2014-09-01

The in-orbit aging of thermo-optical properties of thermal coatings critically impacts both spacecraft thermal balance and heating power consumption. Nevertheless, in-flight thermal coating aging is generally larger than the one measured on ground and the current knowledge does not allow making reliable predictions1. As a result, a large oversizing of thermal control systems is required. To address this issue, the Centre National d'Etudes Spatiales has developed a low-cost experiment, called THERME, which enables to monitor the in-flight time-evolution of the solar absorptivity of a large variety of coatings, including commonly used coatings and new materials by measuring their temperature. This experiment has been carried out on sunsynchronous spacecrafts for more than 27 years, allowing thus the generation of a very large set of telemetry measurements. The aim of this work was to develop a model able to semi-quantitatively reproduce these data with a restraint number of parameters. The underlying objectives were to better understand the contribution of the different involved phenomena and, later on, to predict the thermal coating aging at end of life. The physical processes modeled include contamination deposition, UV aging of both contamination layers and intrinsic material and atomic oxygen erosion. Efforts were particularly focused on the satellite leading wall as this face is exposed to the highest variations in environmental conditions during the solar cycle. The non-monotonous time-evolution of the solar absorptivity of thermal coatings is shown to be due to a succession of contamination and contaminant erosion by atomic oxygen phased with the solar cycle.

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-01-15

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

Systematic heterogenization for better reproducibility in animal experimentation.

Science.gov (United States)

Richter, S Helene

2017-08-31

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

The QUASAR reproducibility study, Part II: Results from a multi-center Arterial Spin Labeling test-retest study

DEFF Research Database (Denmark)

Petersen, Esben Thade; Mouridsen, Kim; Golay, Xavier

2010-01-01

Quantitative STAR labeling of Arterial Regions or QUASAR), a method providing user independent quantification of CBF in a large test-retest study across sites from around the world, dubbed "The QUASAR reproducibility study". Altogether, 28 sites located in Asia, Europe and North America participated...... and a total of 284 healthy volunteers were scanned. Minimal operator dependence was assured by using an automatic planning tool and its accuracy and potential usefulness in multi-center trials was evaluated as well. Accurate repositioning between sessions was achieved with the automatic planning tool showing...

The QUASAR reproducibility study, Part II: Results from a multi-center Arterial Spin Labeling test-retest study

DEFF Research Database (Denmark)

Petersen, Esben; Mouridsen, Kim; Golay, Xavier

2009-01-01

Quantitative STAR labeling of Arterial Regions or QUASAR), a method providing user independent quantification of CBF in a large test-retest study across sites from around the world, dubbed "The QUASAR reproducibility study". Altogether, 28 sites located in Asia, Europe and North America participated...... and a total of 284 healthy volunteers were scanned. Minimal operator dependence was assured by using an automatic planning tool and its accuracy and potential usefulness in multi-center trials was evaluated as well. Accurate repositioning between sessions was achieved with the automatic planning tool showing...

Integration of CFD codes and advanced combustion models for quantitative burnout determination

Energy Technology Data Exchange (ETDEWEB)

Javier Pallares; Inmaculada Arauzo; Alan Williams [University of Zaragoza, Zaragoza (Spain). Centre of Research for Energy Resources and Consumption (CIRCE)

2007-10-15

CFD codes and advanced kinetics combustion models are extensively used to predict coal burnout in large utility boilers. Modelling approaches based on CFD codes can accurately solve the fluid dynamics equations involved in the problem but this is usually achieved by including simple combustion models. On the other hand, advanced kinetics combustion models can give a detailed description of the coal combustion behaviour by using a simplified description of the flow field, this usually being obtained from a zone-method approach. Both approximations describe correctly general trends on coal burnout, but fail to predict quantitative values. In this paper a new methodology which takes advantage of both approximations is described. In the first instance CFD solutions were obtained of the combustion conditions in the furnace in the Lamarmora power plant (ASM Brescia, Italy) for a number of different conditions and for three coals. Then, these furnace conditions were used as inputs for a more detailed chemical combustion model to predict coal burnout. In this, devolatilization was modelled using a commercial macromolecular network pyrolysis model (FG-DVC). For char oxidation an intrinsic reactivity approach including thermal annealing, ash inhibition and maceral effects, was used. Results from the simulations were compared against plant experimental values, showing a reasonable agreement in trends and quantitative values. 28 refs., 4 figs., 4 tabs.

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction

Directory of Open Access Journals (Sweden)

Cobbs Gary

2012-08-01

Full Text Available Abstract Background Numerous models for use in interpreting quantitative PCR (qPCR data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Results Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

Science.gov (United States)

Cobbs, Gary

2012-08-16

Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of

On the Bengtsson-Frauendorf cranked-quasiparticle model

International Nuclear Information System (INIS)

Pal, K.F.; Nagarajan, M.A.; Rowley, N.

1989-01-01

The cranked-quasiparticle model of Bengtsson and Frauendorf (non-self-consistent HFB) is compared with some exact calculations of particles moving in a cranked, deformed mean field but interacting via rotationally invariant two-body forces. In order to make the exact calculations manageable, a single shell is used but despite this small basis the quasiparticle model is shown to have a high degree of success. The usual choice of pair gap is discussed and shown to be good. The general structures of band crossings in the exact calculations are well reproduced and some crossing frequencies are given quantitatively though the odd-particle systems require blocking. Interaction strengths are not well reproduced though some qualitative features, e.g. oscillations, are obtained. These interactions are generally underestimated, an effect which causes the HFB yrast band to behave less collectively than it should. (orig.)

Predictive value of EEG in postanoxic encephalopathy: A quantitative model-based approach.

Science.gov (United States)

Efthymiou, Evdokia; Renzel, Roland; Baumann, Christian R; Poryazova, Rositsa; Imbach, Lukas L

2017-10-01

The majority of comatose patients after cardiac arrest do not regain consciousness due to severe postanoxic encephalopathy. Early and accurate outcome prediction is therefore essential in determining further therapeutic interventions. The electroencephalogram is a standardized and commonly available tool used to estimate prognosis in postanoxic patients. The identification of pathological EEG patterns with poor prognosis relies however primarily on visual EEG scoring by experts. We introduced a model-based approach of EEG analysis (state space model) that allows for an objective and quantitative description of spectral EEG variability. We retrospectively analyzed standard EEG recordings in 83 comatose patients after cardiac arrest between 2005 and 2013 in the intensive care unit of the University Hospital Zürich. Neurological outcome was assessed one month after cardiac arrest using the Cerebral Performance Category. For a dynamic and quantitative EEG analysis, we implemented a model-based approach (state space analysis) to quantify EEG background variability independent from visual scoring of EEG epochs. Spectral variability was compared between groups and correlated with clinical outcome parameters and visual EEG patterns. Quantitative assessment of spectral EEG variability (state space velocity) revealed significant differences between patients with poor and good outcome after cardiac arrest: Lower mean velocity in temporal electrodes (T4 and T5) was significantly associated with poor prognostic outcome (pEEG patterns such as generalized periodic discharges (pEEG analysis (state space analysis) provides a novel, complementary marker for prognosis in postanoxic encephalopathy. Copyright © 2017 Elsevier B.V. All rights reserved.

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...

Tuning plasmons layer-by-layer for quantitative colloidal sensing with surface-enhanced Raman spectroscopy.

Science.gov (United States)

Anderson, William J; Nowinska, Kamila; Hutter, Tanya; Mahajan, Sumeet; Fischlechner, Martin

2018-04-19

Surface-enhanced Raman spectroscopy (SERS) is well known for its high sensitivity that emerges due to the plasmonic enhancement of electric fields typically on gold and silver nanostructures. However, difficulties associated with the preparation of nanostructured substrates with uniform and reproducible features limit reliability and quantitation using SERS measurements. In this work we use layer-by-layer (LbL) self-assembly to incorporate multiple functional building blocks of collaborative assemblies of nanoparticles on colloidal spheres to fabricate SERS sensors. Gold nanoparticles (AuNPs) are packaged in discrete layers, effectively 'freezing nano-gaps', on spherical colloidal cores to achieve multifunctionality and reproducible sensing. Coupling between layers tunes the plasmon resonance for optimum SERS signal generation to achieve a 10 nM limit of detection. Significantly, using the layer-by-layer construction, SERS-active AuNP layers are spaced out and thus optically isolated. This uniquely allows the creation of an internal standard within each colloidal sensor to enable highly reproducible self-calibrated sensing. By using 4-mercaptobenzoic acid (4-MBA) as the internal standard adenine concentrations are quantified to an accuracy of 92.6-99.5%. Our versatile approach paves the way for rationally designed yet quantitative colloidal SERS sensors and their use in a variety of sensing applications.

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.

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

Science.gov (United States)

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

2012-05-01

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

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....

High performance liquid chromatographic assay for the quantitation of total glutathione in plasma

Science.gov (United States)

Abukhalaf, Imad K.; Silvestrov, Natalia A.; Menter, Julian M.; von Deutsch, Daniel A.; Bayorh, Mohamed A.; Socci, Robin R.; Ganafa, Agaba A.

2002-01-01

A simple and widely used homocysteine HPLC procedure was applied for the HPLC identification and quantitation of glutathione in plasma. The method, which utilizes SBDF as a derivatizing agent utilizes only 50 microl of sample volume. Linear quantitative response curve was generated for glutathione over a concentration range of 0.3125-62.50 micromol/l. Linear regression analysis of the standard curve exhibited correlation coefficient of 0.999. Limit of detection (LOD) and limit of quantitation (LOQ) values were 5.0 and 15 pmol, respectively. Glutathione recovery using this method was nearly complete (above 96%). Intra-assay and inter-assay precision studies reflected a high level of reliability and reproducibility of the method. The applicability of the method for the quantitation of glutathione was demonstrated successfully using human and rat plasma samples.

Quantitative Methods in Supply Chain Management Models and Algorithms

CERN Document Server

Christou, Ioannis T

2012-01-01

Quantitative Methods in Supply Chain Management presents some of the most important methods and tools available for modeling and solving problems arising in the context of supply chain management. In the context of this book, “solving problems” usually means designing efficient algorithms for obtaining high-quality solutions. The first chapter is an extensive optimization review covering continuous unconstrained and constrained linear and nonlinear optimization algorithms, as well as dynamic programming and discrete optimization exact methods and heuristics. The second chapter presents time-series forecasting methods together with prediction market techniques for demand forecasting of new products and services. The third chapter details models and algorithms for planning and scheduling with an emphasis on production planning and personnel scheduling. The fourth chapter presents deterministic and stochastic models for inventory control with a detailed analysis on periodic review systems and algorithmic dev...

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.

Comparison of ASL and DCE MRI for the non-invasive measurement of renal blood flow: quantification and reproducibility

Energy Technology Data Exchange (ETDEWEB)

Cutajar, Marica; Hales, Patrick W.; Clark, Christopher A.; Gordon, Isky [UCL Institute of Child Health, Imaging and Biophysics Unit, London (United Kingdom); Thomas, David L. [UCL Institute of Neurology, Department of Brain Repair and Rehabilitation, London (United Kingdom); Banks, T. [Great Ormond Street Hospital, Department of Radiology, London (United Kingdom)

2014-06-15

To investigate the reproducibility of arterial spin labelling (ASL) and dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) and quantitatively compare these techniques for the measurement of renal blood flow (RBF). Sixteen healthy volunteers were examined on two different occasions. ASL was performed using a multi-TI FAIR labelling scheme with a segmented 3D-GRASE imaging module. DCE MRI was performed using a 3D-FLASH pulse sequence. A Bland-Altman analysis was used to assess repeatability of each technique, and determine the degree of correspondence between the two methods. The overall mean cortical renal blood flow (RBF) of the ASL group was 263 ± 41 ml min{sup -1} [100 ml tissue]{sup -1}, and using DCE MRI was 287 ± 70 ml min{sup -1} [100 ml tissue]{sup -1}. The group coefficient of variation (CV{sub g}) was 18 % for ASL and 28 % for DCE-MRI. Repeatability studies showed that ASL was more reproducible than DCE with CV{sub g}s of 16 % and 25 % for ASL and DCE respectively. Bland-Altman analysis comparing the two techniques showed a good agreement. The repeated measures analysis shows that the ASL technique has better reproducibility than DCE-MRI. Difference analysis shows no significant difference between the RBF values of the two techniques. (orig.)

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.

Quantitative computational models of molecular self-assembly in systems biology.

Science.gov (United States)

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Statistical analysis of probabilistic models of software product lines with quantitative constraints

DEFF Research Database (Denmark)

Beek, M.H. ter; Legay, A.; Lluch Lafuente, Alberto

2015-01-01

We investigate the suitability of statistical model checking for the analysis of probabilistic models of software product lines with complex quantitative constraints and advanced feature installation options. Such models are specified in the feature-oriented language QFLan, a rich process algebra...... of certain behaviour to the expected average cost of products. This is supported by a Maude implementation of QFLan, integrated with the SMT solver Z3 and the distributed statistical model checker MultiVeStA. Our approach is illustrated with a bikes product line case study....

Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark® for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens

Directory of Open Access Journals (Sweden)

Jeffrey S. Larson

2010-01-01

Full Text Available We report here the results of the analytical validation of assays that measure HER2 total protein (H2T and HER2 homodimer (H2D expression in Formalin Fixed Paraffin Embedded (FFPE breast cancer tumors as well as cell line controls. The assays are based on the VeraTag technology platform and are commercially available through a central CAP-accredited clinical reference laboratory. The accuracy of H2T measurements spans a broad dynamic range (2-3 logs as evaluated by comparison with cross-validating technologies. The measurement of H2T expression demonstrates a sensitivity that is approximately 7–10 times greater than conventional immunohistochemistry (IHC (HercepTest. The HERmark assay is a quantitative assay that sensitively and reproducibly measures continuous H2T and H2D protein expression levels and therefore may have the potential to stratify patients more accurately with respect to response to HER2-targeted therapies than current methods which rely on semiquantitative protein measurements (IHC or on indirect assessments of gene amplification (FISH.

Quantitative modelling and analysis of a Chinese smart grid: a stochastic model checking case study

DEFF Research Database (Denmark)

Yuksel, Ender; Nielson, Hanne Riis; Nielson, Flemming

2014-01-01

Cyber-physical systems integrate information and communication technology with the physical elements of a system, mainly for monitoring and controlling purposes. The conversion of traditional power grid into a smart grid, a fundamental example of a cyber-physical system, raises a number of issues...... that require novel methods and applications. One of the important issues in this context is the verification of certain quantitative properties of the system. In this paper, we consider a specific Chinese smart grid implementation as a case study and address the verification problem for performance and energy...... consumption.We employ stochastic model checking approach and present our modelling and analysis study using PRISM model checker....

Two-phase 1D+1D model of a DMFC: development and validation on extensive operating conditions range

Energy Technology Data Exchange (ETDEWEB)

Casalegno, A.; Marchesi, R.; Parenti, D. [Dipartimento di Energetica, Politecnico di Milano (Italy)

2008-02-15

A two-phase 1D+1D model of a direct methanol fuel cell (DMFC) is developed, considering overall mass balance, methanol transport in gas phase through anode diffusion layer, methanol and water crossover. The model is quantitatively validated on an extensive range of operating conditions, 24 polarisation curves. The model accurately reproduces DMFC performance in the validation range and, outside this, it is able to predict values under feasible operating conditions. Finally, the estimations of methanol crossover flux are qualitatively and quantitatively similar to experimental measures and the main local quantities' trends are coherent with results obtained with more complex models. (Abstract Copyright [2008], Wiley Periodicals, Inc.)

Relative validity and reproducibility of a food frequency questionnaire to assess dietary fiber intake in Danish adults.

Science.gov (United States)

Vuholm, Stine; Lorenzen, Janne K; Kristensen, Mette

2014-01-01

Differences in habitual dietary fiber intake may modify effects of dietary fiber interventions, thus measurement of habitual dietary fiber intake is relevant to apply in intervention studies on fiber-rich foods, and food frequency questionnaire (FFQ) is a commonly used method. Rye bread is the major contributor of dietary fiber in the Danish population, and a nation-specific FFQ is therefore needed. The aim of this study was to assess the relative validity and reproducibility of a self-administered quantitative FFQ designed to assess total dietary fiber intake among Danish adults. In order to assess the relative validity of the FFQ, a total of 125 participants completed both a 7-day weighed dietary recording (DR) and an FFQ consisting of 60 questions. To evaluate the reproducibility of the FFQ, a sub-group of 12 participants subsequently completed an FFQ approximately 6 months later. Estimates of mean dietary fiber intake were 24.9±9.8 and 28.1±9.4 g/day when applying the FFQ and DR, respectively, where FFQ estimates were ~12% lower (pfiber intake of the two methods was r=0.63 (pfiber intake (g/day), adequate ranking of subjects according to their dietary fiber intake, and good reproducibility. The FFQ is therefore believed to be a valuable tool for epidemiology and screening in human interventions, where intake of dietary fibers is of specific interest.

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...

[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

Quantitative analysis of negative bias illumination stress-induced instability mechanisms in amorphous InGaZnO thin-film transistors

International Nuclear Information System (INIS)

Kim, Yong Sik; Bae, Min Kyung; Kong, Dong Sik; Jung, Hyun Kwang; Kim, Jae Hyeong; Kim, Woo Joon; Hur, In Seok; Kim, Dong Myong; Kim, Dae Hwan

2011-01-01

The physical origins of the negative bias illumination stress (NBIS)-induced threshold voltage shift (ΔV T ) in amorphous InGaZnO (a-IGZO) thin-film transistors (TFTs) under ambient light from a backlight unit are quantitatively and systematically investigated. Furthermore, a methodology for extracting the instability parameters is proposed and demonstrated. For the quantitative analysis, the subgap density-of-states (DOS)-based DC I-V model is intensively used. The NBIS time-evolution of the measured I DS -V GS characteristics is reproduced very well via the proposed methodology and instability parameters. Consequently, photo-excited electron detrapping, followed by ionization of oxygen vacancies (V O +2 ) and field-enhanced V O +2 diffusion, followed by hole trapping into the gate insulator, are found to be the dominant mechanisms in NBIS-induced instability of a-IGZO TFTs.

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).

ReproPhylo: An Environment for Reproducible Phylogenomics.

Directory of Open Access Journals (Sweden)

Amir Szitenberg

2015-09-01

Full Text Available The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This 'single file' approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.

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 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.

Relative Validity and Reproducibility of a Food-Frequency Questionnaire for Estimating Food Intakes among Flemish Preschoolers

Directory of Open Access Journals (Sweden)

Inge Huybrechts

2009-01-01

Full Text Available The aims of this study were to assess the relative validity and reproducibility of a semi-quantitative food-frequency questionnaire (FFQ applied in a large region-wide survey among 2.5-6.5 year-old children for estimating food group intakes. Parents/guardians were used as a proxy. Estimated diet records (3d were used as reference method and reproducibility was measured by repeated FFQ administrations five weeks apart. In total 650 children were included in the validity analyses and 124 in the reproducibility analyses. Comparing median FFQ1 to FFQ2 intakes, almost all evaluated food groups showed median differences within a range of ± 15%. However, for median vegetables, fruit and cheese intake, FFQ1 was > 20% higher than FFQ2. For most foods a moderate correlation (0.5-0.7 was obtained between FFQ1 and FFQ2. For cheese, sugared drinks and fruit juice intakes correlations were even > 0.7. For median differences between the 3d EDR and the FFQ, six food groups (potatoes & grains; vegetables Fruit; cheese; meat, game, poultry and fish; and sugared drinks gave a difference > 20%. The largest corrected correlations (>0.6 were found for the intake of potatoes and grains, fruit, milk products, cheese, sugared drinks, and fruit juice, while the lowest correlations (<0.4 for bread and meat products. The proportion of subjects classified within one quartile (in the same/adjacent category by FFQ and EDR ranged from 67% (for meat products to 88% (for fruit juice. Extreme misclassification into the opposite quartiles was for all food groups < 10%. The results indicate that our newly developed FFQ gives reproducible estimates of food group intake. Overall, moderate levels of relative validity were observed for estimates of food group intake.

Pulsed amperometric detection at glassy carbon electrodes: A new waveform for sensitive and reproducible determination of electroactive compounds.

Science.gov (United States)

Nardiello, Donatella; Palermo, Carmen; Natale, Anna; Quinto, Maurizio; Centonze, Diego

2015-09-24

In this work, the application of a new pulsed amperometric detection (PAD) waveform at a glassy carbon electrode, operating in typical chromatographic mobile phases, is proposed for the sensitive and reproducible determination of arylethanolaminic and phenolic moiety based compounds (e.g. beta-agonists and polyphenols). Preliminary experiments by cyclic voltammetry were carried out to investigate the electrochemical behaviour and to select the detection and cleaning electrode potentials. The proposed potential-time profile was designed to prevent the carbon electrode fouling under repeated analyses, thus ensuring a reproducible and sensitive quantitative determination, without the need of any mechanical or chemical electrode cleaning procedure. The waveform electrochemical parameters, including detection and delay times, were optimized in terms of sensitivity, limit of detection and response stability. The optimized waveform allowed the sensitive and stable detection of model compounds, such as clenbuterol and caffeic acid, that showed detection limits of 0.1 μg L(-1) and 14 μg L(-1), quantification limits of 0.4 μg L(-1) and 46 μg L(-1), and linearity up to 100 μg L(-1) (r = 0.9993) and 10 mg L(-1) (r = 0.9998), respectively. Similar results were obtained for other compounds of the same classes, with precision values under repeatability conditions ranging from 3.0 to 5.9%. The proposed method can be then considered as an excellent alternative to the post-column detection of beta-agonists, phenols and polyphenols. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

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

Quantitative determination of pneumococcal capsular polysaccharide serotype 14 using a modification of phenol-sulfuric acid method.

Science.gov (United States)

Cuesta, Gabriela; Suarez, Norma; Bessio, Maria I; Ferreira, Fernando; Massaldi, Hugo

2003-01-01

The capsular polysaccharide of Streptococcus pneumoniae, serotype 14, is part of every pneumococcal vaccine presently in the market or under development. A strategy for the quantitative determination of this polysaccharide by the phenol-sulfuric acid method is described. The modality of acid addition is shown to be the critical step for obtaining reproducible test results between different technicians. Raising the incubation temperature above 80 degrees C increased the consistency of the method by more than 60% regardless of the acid addition modality, but at the expense of some loss of sensitivity. Incubation at 110 degrees C was found necessary to obtain reproducible results within 3% for this technique, which was used to follow the enrichment of the polysaccharide during the last steps of purification. A model mixture of the component polysaccharide sugars provided an adequate and economic standard to construct the calibration curve for this assay, with absorbance reading either in the reaction tubes or in a microplate. A similar procedure may be applied to the determination of other bacterial polysaccharides as well.

Towards reproducible experimental studies for non-convex polyhedral shaped particles

Directory of Open Access Journals (Sweden)

Wilke Daniel N.

2017-01-01

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

Towards reproducible experimental studies for non-convex polyhedral shaped particles

Science.gov (United States)

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

2017-06-01

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

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

Science.gov (United States)

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

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

Science.gov (United States)

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

2012-01-01

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

Quantitative myocardial perfusion PET combined with coronary anatomy derived from CT angiography. Validation of a new fusion and visualisation software

International Nuclear Information System (INIS)

Fricke, Harald; Weise, Reiner; Burchert, Wolfgang; Fricke, Eva; Elsner, Andreas; Bolte, Matthias; Domik, Gitta; Hoff, Joerg van den

2009-01-01

Aim: Dynamic perfusion PET offers a clinical relevant advantage over myocardial perfusion scintigraphy due to its ability to measure myocardial blood flow quantitatively. This leads to an improved detection of multivessel disease and the possibility to assess not only the culprit lesion but lower grade stenoses as well. For appropriate revascularization, perfusion defects must be matched to coronary lesions. It has been shown that image fusion of morphological and functional images is superior to side-by-side analysis. Still, software for quantitative perfusion PET combined with CT angiography is rare. In this paper we present a new software tool for image fusion and visualization of quantitative perfusion PET and coronary morphology derived from CT angiography. Methods: In our software, a PET uptake image is used for manual co-registration. Co-registration results are then applied to the functional data derived from compartment modelling. To evaluate the reproducibility of the manual co-registration, we calculated the deviation between a series of manual co-registrations performed on nine pairs of unregistered PET and CT datasets by five trained participants. Two dimensional transfer functions were used to highlight the coronary arteries from the CT study in the combined data sets. Results: The average Euclidian distances for three references points were between 3.7 and 4.1 mm. The maximum distance was 10.6 mm. By the use of the two dimensional transfer functions, coronary anatomy could be easily visualised either by user-interaction or automatically by use of neuronal networks. Conclusions: With this approach it is possible to combine quantitative perfusion PET with coronary anatomy derived from CT angiography. Our first experiences indicate that manual image fusion with our tool is reproducible and that visualisation of the combined datasets is achieved within short time. (orig.)

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.

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.

An optimized framework for quantitative magnetization transfer imaging of the cervical spinal cord in vivo.

Science.gov (United States)

Battiston, Marco; Grussu, Francesco; Ianus, Andrada; Schneider, Torben; Prados, Ferran; Fairney, James; Ourselin, Sebastien; Alexander, Daniel C; Cercignani, Mara; Gandini Wheeler-Kingshott, Claudia A M; Samson, Rebecca S

2018-05-01

To develop a framework to fully characterize quantitative magnetization transfer indices in the human cervical cord in vivo within a clinically feasible time. A dedicated spinal cord imaging protocol for quantitative magnetization transfer was developed using a reduced field-of-view approach with echo planar imaging (EPI) readout. Sequence parameters were optimized based in the Cramer-Rao-lower bound. Quantitative model parameters (i.e., bound pool fraction, free and bound pool transverse relaxation times [ T2F, T2B], and forward exchange rate [k FB ]) were estimated implementing a numerical model capable of dealing with the novelties of the sequence adopted. The framework was tested on five healthy subjects. Cramer-Rao-lower bound minimization produces optimal sampling schemes without requiring the establishment of a steady-state MT effect. The proposed framework allows quantitative voxel-wise estimation of model parameters at the resolution typically used for spinal cord imaging (i.e. 0.75 × 0.75 × 5 mm 3 ), with a protocol duration of ∼35 min. Quantitative magnetization transfer parametric maps agree with literature values. Whole-cord mean values are: bound pool fraction = 0.11(±0.01), T2F = 46.5(±1.6) ms, T2B = 11.0(±0.2) µs, and k FB  = 1.95(±0.06) Hz. Protocol optimization has a beneficial effect on reproducibility, especially for T2B and k FB . The framework developed enables robust characterization of spinal cord microstructure in vivo using qMT. Magn Reson Med 79:2576-2588, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method

OpenAIRE

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-01-01

Objective: To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. Methods: TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Results: Both assays provided good linearity, accuracy, reproducibility and selectivity for dete...

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.

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

Evolutionary models of early-type contact binary SV Centauri

Energy Technology Data Exchange (ETDEWEB)

Nakamura, Y; Saio, H [Tohoku Univ., Sendai (Japan). Faculty of Science; Sugimoto, Daiichiro

1978-12-01

Models of the early-type contact binary system SV Centauri are computed with a binary-star evolution program. The effects of mass exchange, i.e., the effects of mass acceptance as well as mass loss, are properly included. With the initial masses of the component stars as 12.4 and 8.0 M sub(solar mass), the following observed configurations are well reproduced; the component stars are definitely in contact and the rate of mass exchange is 4 x 10/sup -4/ M sub(solar mass)yr/sup -1/. The more massive component is less luminous and has a lower effective temperature. Such features are also reproduced quantitatively. Agreement of the computed models with observation indicates that the binary system SV Cen is actually in the phase of rapid mass exchange preceding the mass-ratio reversal.

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.

Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

Science.gov (United States)

Han, Lide; Yang, Jian; Zhu, Jun

2007-06-01

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

Effects of ROI definition and reconstruction method on quantitative outcome and applicability in a response monitoring trial

International Nuclear Information System (INIS)

Krak, Nanda C.; Boellaard, R.; Hoekstra, Otto S.; Hoekstra, Corneline J.; Twisk, Jos W.R.; Lammertsma, Adriaan A.

2005-01-01

Quantitative measurement of tracer uptake in a tumour can be influenced by a number of factors, including the method of defining regions of interest (ROIs) and the reconstruction parameters used. The main purpose of this study was to determine the effects of different ROI methods on quantitative outcome, using two reconstruction methods and the standard uptake value (SUV) as a simple quantitative measure of FDG uptake. Four commonly used methods of ROI definition (manual placement, fixed dimensions, threshold based and maximum pixel value) were used to calculate SUV (SUV [MAN] , SUV 15 mm , SUV 50 , SUV 75 and SUV max , respectively) and to generate ''metabolic'' tumour volumes. Test-retest reproducibility of SUVs and of ''metabolic'' tumour volumes and the applicability of ROI methods during chemotherapy were assessed. In addition, SUVs calculated on ordered subsets expectation maximisation (OSEM) and filtered back-projection (FBP) images were compared. ROI definition had a direct effect on quantitative outcome. On average, SUV [MAN] , SUV 15 mm , SUV 50 and SUV 75 , were respectively 48%, 27%, 34% and 15% lower than SUV max when calculated on OSEM images. No statistically significant differences were found between SUVs calculated on OSEM and FBP reconstructed images. Highest reproducibility was found for SUV 15 mm and SUV [MAN] (ICC 0.95 and 0.94, respectively) and for ''metabolic'' volumes measured with the manual and 50% threshold ROIs (ICC 0.99 for both). Manual, 75% threshold and maximum pixel ROIs could be used throughout therapy, regardless of changes in tumour uptake or geometry. SUVs showed the same trend in relative change in FDG uptake after chemotherapy, irrespective of the ROI method used. The method of ROI definition has a direct influence on quantitative outcome. In terms of simplicity, user-independence, reproducibility and general applicability the threshold-based and fixed dimension methods are the best ROI methods. Threshold methods are in

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...

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

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.

A suite of models to support the quantitative assessment of spread in pest risk analysis

NARCIS (Netherlands)

Robinet, C.; Kehlenbeck, H.; Werf, van der W.

2012-01-01

In the frame of the EU project PRATIQUE (KBBE-2007-212459 Enhancements of pest risk analysis techniques) a suite of models was developed to support the quantitative assessment of spread in pest risk analysis. This dataset contains the model codes (R language) for the four models in the suite. Three

Quantitative analysis of Ni2+/Ni3+ in Li[NixMnyCoz]O2 cathode materials: Non-linear least-squares fitting of XPS spectra

Science.gov (United States)

Fu, Zewei; Hu, Juntao; Hu, Wenlong; Yang, Shiyu; Luo, Yunfeng

2018-05-01

Quantitative analysis of Ni2+/Ni3+ using X-ray photoelectron spectroscopy (XPS) is important for evaluating the crystal structure and electrochemical performance of Lithium-nickel-cobalt-manganese oxide (Li[NixMnyCoz]O2, NMC). However, quantitative analysis based on Gaussian/Lorentzian (G/L) peak fitting suffers from the challenges of reproducibility and effectiveness. In this study, the Ni2+ and Ni3+ standard samples and a series of NMC samples with different Ni doping levels were synthesized. The Ni2+/Ni3+ ratios in NMC were quantitatively analyzed by non-linear least-squares fitting (NLLSF). Two Ni 2p overall spectra of synthesized Li [Ni0.33Mn0.33Co0.33]O2(NMC111) and bulk LiNiO2 were used as the Ni2+ and Ni3+ reference standards. Compared to G/L peak fitting, the fitting parameters required no adjustment, meaning that the spectral fitting process was free from operator dependence and the reproducibility was improved. Comparison of residual standard deviation (STD) showed that the fitting quality of NLLSF was superior to that of G/L peaks fitting. Overall, these findings confirmed the reproducibility and effectiveness of the NLLSF method in XPS quantitative analysis of Ni2+/Ni3+ ratio in Li[NixMnyCoz]O2 cathode materials.

Quantitative stress measurement of elastic deformation using mechanoluminescent sensor: An intensity ratio model

Science.gov (United States)

Cai, Tao; Guo, Songtao; Li, Yongzeng; Peng, Di; Zhao, Xiaofeng; Liu, Yingzheng

2018-04-01

The mechanoluminescent (ML) sensor is a newly developed non-invasive technique for stress/strain measurement. However, its application has been mostly restricted to qualitative measurement due to the lack of a well-defined relationship between ML intensity and stress. To achieve accurate stress measurement, an intensity ratio model was proposed in this study to establish a quantitative relationship between the stress condition and its ML intensity in elastic deformation. To verify the proposed model, experiments were carried out on a ML measurement system using resin samples mixed with the sensor material SrAl2O4:Eu2+, Dy3+. The ML intensity ratio was found to be dependent on the applied stress and strain rate, and the relationship acquired from the experimental results agreed well with the proposed model. The current study provided a physical explanation for the relationship between ML intensity and its stress condition. The proposed model was applicable in various SrAl2O4:Eu2+, Dy3+-based ML measurement in elastic deformation, and could provide a useful reference for quantitative stress measurement using the ML sensor in general.

Thermodynamic modeling of the Mg-Al-Ca system

Energy Technology Data Exchange (ETDEWEB)

Janz, A.; Groebner, J. [Clausthal University of Technology, Institute of Metallurgy, Robert-Koch-Str. 42, D-38678 Clausthal-Zellerfeld (Germany); Cao, H.; Zhu, J.; Chang, Y.A. [Department of Materials Science and Engineering, University of Wisconsin, 1509 University Ave., Madison, WI 53706 (United States); Schmid-Fetzer, R. [Clausthal University of Technology, Institute of Metallurgy, Robert-Koch-Str. 42, D-38678 Clausthal-Zellerfeld (Germany)], E-mail: schmid-fetzer@tu-clausthal.de

2009-02-15

A thermodynamic model has been developed that provides a quantitative description for a wide area of the Mg-Al-Ca system. All available experimental data plus new key experiments using differential scanning calorimetry/differential thermal analysis have been considered to create a dataset which reproduces the primary crystallizing phases, the extensive ternary solubilities of binary phases and the ternary C36 Laves phase. This enables validated thermodynamic calculations in various areas of this ternary system.

Quantitative Modeling of Acid Wormholing in Carbonates- What Are the Gaps to Bridge

KAUST Repository

Qiu, Xiangdong; Zhao, Weishu; Chang, Frank; Dyer, Steve

2013-01-01

Conventional wormhole propagation models largely ignore the impact of reaction products. When implemented in a job design, the significant errors can result in treatment fluid schedule, rate, and volume. A more accurate method to simulate carbonate matrix acid treatments would accomodate the effect of reaction products on reaction kinetics. It is the purpose of this work to properly account for these effects. This is an important step in achieving quantitative predictability of wormhole penetration during an acidzing treatment. This paper describes the laboratory procedures taken to obtain the reaction-product impacted kinetics at downhole conditions using a rotating disk apparatus, and how this new set of kinetics data was implemented in a 3D wormholing model to predict wormhole morphology and penetration velocity. The model explains some of the differences in wormhole morphology observed in limestone core flow experiments where injection pressure impacts the mass transfer of hydrogen ions to the rock surface. The model uses a CT scan rendered porosity field to capture the finer details of the rock fabric and then simulates the fluid flow through the rock coupled with reactions. Such a validated model can serve as a base to scale up to near wellbore reservoir and 3D radial flow geometry allowing a more quantitative acid treatment design.

Image analysis and modeling in medical image computing. Recent developments and advances.

Science.gov (United States)

Handels, H; Deserno, T M; Meinzer, H-P; Tolxdorff, T

2012-01-01

Medical image computing is of growing importance in medical diagnostics and image-guided therapy. Nowadays, image analysis systems integrating advanced image computing methods are used in practice e.g. to extract quantitative image parameters or to support the surgeon during a navigated intervention. However, the grade of automation, accuracy, reproducibility and robustness of medical image computing methods has to be increased to meet the requirements in clinical routine. In the focus theme, recent developments and advances in the field of modeling and model-based image analysis are described. The introduction of models in the image analysis process enables improvements of image analysis algorithms in terms of automation, accuracy, reproducibility and robustness. Furthermore, model-based image computing techniques open up new perspectives for prediction of organ changes and risk analysis of patients. Selected contributions are assembled to present latest advances in the field. The authors were invited to present their recent work and results based on their outstanding contributions to the Conference on Medical Image Computing BVM 2011 held at the University of Lübeck, Germany. All manuscripts had to pass a comprehensive peer review. Modeling approaches and model-based image analysis methods showing new trends and perspectives in model-based medical image computing are described. Complex models are used in different medical applications and medical images like radiographic images, dual-energy CT images, MR images, diffusion tensor images as well as microscopic images are analyzed. The applications emphasize the high potential and the wide application range of these methods. The use of model-based image analysis methods can improve segmentation quality as well as the accuracy and reproducibility of quantitative image analysis. Furthermore, image-based models enable new insights and can lead to a deeper understanding of complex dynamic mechanisms in the human body

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

Improved quantitation and reproducibility in multi-PET/CT lung studies by combining CT information.

Science.gov (United States)

Holman, Beverley F; Cuplov, Vesna; Millner, Lynn; Endozo, Raymond; Maher, Toby M; Groves, Ashley M; Hutton, Brian F; Thielemans, Kris

2018-06-05

Matched attenuation maps are vital for obtaining accurate and reproducible kinetic and static parameter estimates from PET data. With increased interest in PET/CT imaging of diffuse lung diseases for assessing disease progression and treatment effectiveness, understanding the extent of the effect of respiratory motion and establishing methods for correction are becoming more important. In a previous study, we have shown that using the wrong attenuation map leads to large errors due to density mismatches in the lung, especially in dynamic PET scans. Here, we extend this work to the case where the study is sub-divided into several scans, e.g. for patient comfort, each with its own CT (cine-CT and 'snap shot' CT). A method to combine multi-CT information into a combined-CT has then been developed, which averages the CT information from each study section to produce composite CT images with the lung density more representative of that in the PET data. This combined-CT was applied to nine patients with idiopathic pulmonary fibrosis, imaged with dynamic 18 F-FDG PET/CT to determine the improvement in the precision of the parameter estimates. Using XCAT simulations, errors in the influx rate constant were found to be as high as 60% in multi-PET/CT studies. Analysis of patient data identified displacements between study sections in the time activity curves, which led to an average standard error in the estimates of the influx rate constant of 53% with conventional methods. This reduced to within 5% after use of combined-CTs for attenuation correction of the study sections. Use of combined-CTs to reconstruct the sections of a multi-PET/CT study, as opposed to using the individually acquired CTs at each study stage, produces more precise parameter estimates and may improve discrimination between diseased and normal lung.

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

Validity and reproducibility of a food frequency questionnaire focused on the Mediterranean diet for the Quebec population.

Science.gov (United States)

Cantin, J; Latour, E; Ferland-Verry, R; Morales Salgado, S; Lambert, J; Faraj, M; Nigam, A

2016-02-01

Validated dietary assessment methods specific to population and food habits are needed to conduct randomized clinical trials evaluating the efficacy of the Mediterranean diet in primary and secondary prevention of cardiovascular disease. Therefore, the aim of our study was to assess the reproducibility and the relative validity of a French language semi-quantitative food frequency questionnaire (FFQ) focused on the Mediterranean diet within the population of Quebec. Fifty-three participants aged 19-86 years with and without coronary heart disease were recruited, and randomized in 3 groups in a crossover design where the sequence of administration of two FFQs and a dietary record (DR) differed in each group. The FFQ includes 157 food items and was designed to measure food intake over one month. It was administered twice 3-5 weeks apart to assess reproducibility and was compared to a 12-day DR to assess validity. For reproducibility (n = 47), intraclass correlation coefficients (ICCs) for energy and 33 nutrients ranged from 0.38 to 0.91 (mean 0.63). For validity, the Pearson's correlation coefficients between the DR and the FFQ pre-DR ranged from 0.26 to 0.84 (mean 0.55) and ICCs ranged from 0.25 to 0.84 (mean 0.54). As for the DR and the FFQ post-DR, the Pearson's correlation coefficients ranged from 0.36 to 0.83 (mean 0.55) and the ICCs ranged from 0.36 to 0.83 (mean 0.53). This FFQ demonstrates good reproducibility and validity for most key nutrients of the Mediterranean diet for the Quebec population. Copyright © 2015 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples.

Science.gov (United States)

Zellner, Maria; Babeluk, Rita; Diestinger, Michael; Pirchegger, Petra; Skeledzic, Senada; Oehler, Rudolf

2008-09-01

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.

Applying quantitative adiposity feature analysis models to predict benefit of bevacizumab-based chemotherapy in ovarian cancer patients

Science.gov (United States)

Wang, Yunzhi; Qiu, Yuchen; Thai, Theresa; More, Kathleen; Ding, Kai; Liu, Hong; Zheng, Bin

2016-03-01

How to rationally identify epithelial ovarian cancer (EOC) patients who will benefit from bevacizumab or other antiangiogenic therapies is a critical issue in EOC treatments. The motivation of this study is to quantitatively measure adiposity features from CT images and investigate the feasibility of predicting potential benefit of EOC patients with or without receiving bevacizumab-based chemotherapy treatment using multivariate statistical models built based on quantitative adiposity image features. A dataset involving CT images from 59 advanced EOC patients were included. Among them, 32 patients received maintenance bevacizumab after primary chemotherapy and the remaining 27 patients did not. We developed a computer-aided detection (CAD) scheme to automatically segment subcutaneous fat areas (VFA) and visceral fat areas (SFA) and then extracted 7 adiposity-related quantitative features. Three multivariate data analysis models (linear regression, logistic regression and Cox proportional hazards regression) were performed respectively to investigate the potential association between the model-generated prediction results and the patients' progression-free survival (PFS) and overall survival (OS). The results show that using all 3 statistical models, a statistically significant association was detected between the model-generated results and both of the two clinical outcomes in the group of patients receiving maintenance bevacizumab (p<0.01), while there were no significant association for both PFS and OS in the group of patients without receiving maintenance bevacizumab. Therefore, this study demonstrated the feasibility of using quantitative adiposity-related CT image features based statistical prediction models to generate a new clinical marker and predict the clinical outcome of EOC patients receiving maintenance bevacizumab-based chemotherapy.

Mapping quantitative trait loci in a selectively genotyped outbred population using a mixture model approach

NARCIS (Netherlands)

Johnson, David L.; Jansen, Ritsert C.; Arendonk, Johan A.M. van

1999-01-01

A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, are selectively genotyped. Maximum likelihood estimation of model parameters is obtained from an Expectation-Maximization (EM) algorithm facilitated by

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

Variable selection in near infrared spectroscopy for quantitative models of homologous analogs of cephalosporins

Directory of Open Access Journals (Sweden)

Yan-Chun Feng

2014-07-01

Full Text Available Two universal spectral ranges (4550–4100 cm-1 and 6190–5510 cm-1 for construction of quantitative models of homologous analogs of cephalosporins were proposed by evaluating the performance of five spectral ranges and their combinations, using three data sets of cephalosporins for injection, i.e., cefuroxime sodium, ceftriaxone sodium and cefoperazone sodium. Subsequently, the proposed ranges were validated by using eight calibration sets of other homologous analogs of cephalosporins for injection, namely cefmenoxime hydrochloride, ceftezole sodium, cefmetazole, cefoxitin sodium, cefotaxime sodium, cefradine, cephazolin sodium and ceftizoxime sodium. All the constructed quantitative models for the eight kinds of cephalosporins using these universal ranges could fulfill the requirements for quick quantification. After that, competitive adaptive reweighted sampling (CARS algorithm and infrared (IR–near infrared (NIR two-dimensional (2D correlation spectral analysis were used to determine the scientific basis of these two spectral ranges as the universal regions for the construction of quantitative models of cephalosporins. The CARS algorithm demonstrated that the ranges of 4550–4100 cm-1 and 6190–5510 cm-1 included some key wavenumbers which could be attributed to content changes of cephalosporins. The IR–NIR 2D spectral analysis showed that certain wavenumbers in these two regions have strong correlations to the structures of those cephalosporins that were easy to degrade.

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.

Reproducibility of Left Ventricular Mass by Echocardiogram in the ELSA-Brasil

Directory of Open Access Journals (Sweden)

Alexandre Pereira Tognon

2015-02-01