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Results for “data reproducibility”

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At least 469 records · Page 26Linked to original sources
PubMed2006

Solar photocatalytic degradation of reactive blue 4 using a Fresnel lens.

The heterogeneous photocatalytic degradation of reactive blue 4 dye (RB4) solutions under Fenton reagent and TiO(2) assisted by concentrated solar light irradiation using a Fresnel lens has been studied. Multivariate experimental design was applied to study the kinetic process. The efficiency of photocatalytic degradation was determined from the analysis of color and total organic carbon (TOC) removal. Factorial experimental design allowed to determine the influence of four parameters (pH and initial concentrations of TiO(2), Fe(II) and H(2)O(2)) on the value of the decoloration kinetic rate constant. Experimental data were fitted using neural networks (NNs). The mathematical model reproduces experimental data within 86% of confidence and allows the simulation of the process for any value of parameters in the experimental range studied. Also, a measure of the saliency of the input variables was made based upon the connection weights of the neural networks, allowing the analysis of the relative relevance of each variable with respect to the others. Results showed that acidic pHs (pH=3.6) are preferred for the complete dye decoloration. The optimum catalyst concentration is 1.2g TiO(2)/l. The use of a low cost catalyst and its activation using a Fresnel lens to concentrate solar energy significantly accelerates the degradation process when compared with direct solar radiation alone and can offer an economical and practical alternative for the destruction of environmental organic compounds.

Hydrogen Peroxide↗
PubMed2000

Direct single-step surface plasmon resonance analysis of interactions between small peptides and immobilized monoclonal antibodies.

Surface plasmon resonance (SPR) methods have been optimized to permit direct kinetic analysis of the antigenic peptide analytes interacting with immobilized monoclonal antibodies (mAbs). High reproducibility and a significant correlation between SPR and previous ELISA data on the same set of antibodies and peptides were observed. The kinetic data obtained provide further insight into the structure of the main antigenic site of foot-and-mouth disease virus (FMDV).

Amino Acid Sequence↗
PubMed2001

Simulation of atmospheric PAH emissions from diesel engines.

Simulation of atmospheric PAH emissions in a typical European passenger car diesel engine at steady conditions or under a certification cycle is made using in-house software. It is based on neural fitting of experimental data from eight different fuels tested under five operating steady conditions (reproducing modes of the European transient urban/extraurban certification cycle). The software allows the determination of PAH emissions as a function of the fuel composition parameters (aromatic content, cetane index, gross heat power, nitrogen and sulphur content) and operation conditions (torque and engine speed). The mathematical model reproduces experimental data with a maximum error of 20%. This tool is very useful, since changes in parameters can be made without experimental cost and the trend in modifications in PAH emissions is immediately obvious.

Air Pollutants↗
PubMed2004

Number of spanning clusters at the high-dimensional percolation thresholds.

A scaling theory is used to derive the dependence of the average number k of spanning clusters at threshold on the lattice size L. This number should become independent of L for dimensions d<6 and vary as ln L at d=6 . The predictions for d>6 depend on the boundary conditions, and the results there may vary between L(d-6) and L0. While simulations in six dimensions are consistent with this prediction [after including corrections of order ln(ln L)], in five dimensions the average number of spanning clusters still increases as ln L even up to L=201 . However, the histogram P(k) of the spanning cluster multiplicity does scale as a function of kX(L), with X(L) =1+const/L, indicating that for sufficiently large L the average k will approach a finite value: a fit of the five-dimensional multiplicity data with a constant plus a simple linear correction to scaling reproduces the data very well. Numerical simulations for d>6 and for d=4 are also presented.

Journal Article↗
PubMed1996

Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions.

Molecular dynamics (MD) simulations of short peptides in water were performed to establish whether it is possible to reproduce experimental data from chemical shift measurements by nuclear magnetic resonance spectroscopy. Three different tetrapeptides were studied. The first, YTGP (Tyr-Thr-Gly-Pro), shows an electrostatic interaction between the aromatic ring of Tyr and the backbone amide hydrogen atom of Gly. The second, YTAP (Tyr-Thr-Ala-Pro), cannot make such an interaction because of steric hindrance of the Ala side chain and hence does not show a well-defined conformation. The third, FTGP (Phe-Thr-Gly-Pro), is shown to alternate between two different conformations. It is demonstrated that small differences in chemical shift, corresponding to these slightly different conformations, can be quantitatively modeled in MD simulations when using the proper force-field parameters and water model Explicit inclusion of hydrogen atoms o the aromatic rings is essential for a proper description of electrostatic interactions, but the choice of the water model is equally important. We found that a combination of the SPC/E water model and a revised GROMOS87 force field gives close agreement with experiment, while the same and other force fields in combination with SPC or TIP3P water did not reproduce the NMR data at all. Simulations of a longer peptide from bovine pancreatic trypsin inhibitor, containing the YTGP sequence, did show the interaction between the aromatic ring and the amide hydrogen, but not as pronounced as the simulations of shorter periods.

Amides↗
PubMed2006

Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray.

The gene expression profile of bovine bone marrow stromal cells undergoing adipogenesis was established using a custom cDNA microarray. Cells that were treated with adipogenic stimulants and those that were not were collected at each of the six time points, and gene expression differences between the treated and untreated samples within each time point were compared using a microarray. Statistical analyses revealed that 158 genes showed a minimum fold change of 2 in at least one of the five post-differentiation time points. These genes are involved in various cellular pathways and functions, including lipogenesis, glycolysis, cytoskeleton remodelling, extracellular matrix, transcription as well as various signalling pathways such as insulin, calcium and wingless signalling. The experiment also identified 17 differentially expressed (DE) microarray elements with no assigned function. Quantitative real-time PCR was employed to validate eight DE genes, and the PCR data were found to reproduce the microarray data for these eight genes. Subsequent gene ontology annotation was able to provide a global overview of the molecular function of DE genes during adipogenesis. This analysis was able to indicate the importance of different gene categories at various stages of adipogenic conversion, thereby providing further insights into the molecular changes during bovine adipogenesis.

Adipogenesis↗
PubMed2005

Investigation of extraction and clean-up procedures used in the quantification and stable isotopic characterisation of PAHs in contaminated urban soils.

Four different extraction methods, soxhlet, soxtherm, sonication and accelerated solvent extraction (ASE), were used to isolate the 16 priority pollutant PAHs from a certified reference soil (LGC 6140) and from a contaminated soil (BG CLR 17). Based on SIM-GC-MS results, all methods were found to give accurate and highly reproducible concentration data. There was, however, significant between-method and sometimes within-method variability in the stable carbon isotope signatures obtained for individual PAHs from the contaminated soil (BG CLR 17) using GC-C-IRMS. When two clean-up procedures, silica/dichloromethane and alumina/hexane/toluene, were used to remove co-extracted material, however, it was found that ASE gave the more consistent and reproducible stable carbon isotope data. These findings are likely to be of importance for the characterisation of natural and anthropogenic organic matter and, in particular, in source identification and apportionment studies.

Carbon Isotopes↗
PubMed2005

Adomian's decomposition method for electromagnetically induced transparency.

We developed the Adomian's decomposition method to work for the electromagnetically induced transparency (EIT) problem. The method is general and capable to solve the coupled nonlinear partial differential equations for a light pulse passing through a three-level -type coherent medium. This EIT system is described by the coupled Maxwell-Schrödinger equations and optical Bloch equations. In the weak probe field case, the results agree with perturbation solutions and experimental data. In the stronger probe field case while perturbation may fail, our results reproduce experimental data well. With the techniques of spatial and time partitions, we extend the decomposition method that will be versatile for the investigation of the light pulse propagating through a coherent atomic medium.

Journal Article↗
PubMed2006

Contemporary intravesical treatment options for urothelial carcinoma of the bladder.

To provide a comprehensive review of intravesical treatment options for non-muscle-invasive bladder cancer, we performed a search of the PubMed database for articles between 1980 and 2006 that reported on intravesical agents for treating this disease. Data were compiled and analyzed, emphasizing findings from large multicenter trials, studies providing reproducible results, data that could be confirmed by cross-referencing the literature, and phase I or II studies for pertinent novel agents. A critical analysis of evidence shows that: 1) treatment with Bacillus Calmette-Guérin (BCG), including a maintenance schedule (with or without interferon-alpha), is the most effective therapy for limiting recurrence, is the only therapy that reduces the incidence of progression, and overall is superior to chemotherapy; 2) mitomycin C, gemcitabine, anthracyclines, and thiotepa provide similar benefits for preventing recurrence in patients with minimal effect on progression; and 3) using chemotherapeutic agents immediately after transurethral resection (when use of BCG is contraindicated because of the risk for systemic absorption) reduces the recurrence rate by up to 50% and seems to be the ideal method of chemotherapy. Although various clinical factors dictate which agent is most appropriate for an individual patient, the current literature supports a single perioperative dose of intravesical mitomycin C followed, in appropriate cases, by induction and maintenance therapy with intravesical BCG.

Adjuvants, Immunologic↗
PubMed1990

Reproducibility of hearing threshold measurements. Supplementary data on bone-conduction and speech audiometry.

The reproducibility of bone-conduction pure-tone audiometry and speech recognition thresholds has been tested in groups of normal-hearing subjects. Each person was tested twice during the same day, and the test-retest difference was calculated. The reproducibility is presented as the standard deviation of this difference. Bone-conduction threshold measurements have a high degree of test-retest precision, whereas air-bone gaps show a large range of distribution in these normal-hearing subjects. This makes the interpretation of such gaps spurious when values are below 20-30 dB. Speech recognition threshold has the highest degree of test-retest precision of all audiometric tests, and this is probably due to the steep slope of the psychometric function at 50% intelligibility. A more detailed graphic presentation of the 50% point of intersection will bring the reproducibility down to less than 2.5 dB.

Adult↗
PubMed1995

Influence of the test area on the mechanical properties of skin.

BACKGROUND: New advances in bioengineering have provided commercially available devices for measuring the mechanical properties of skin in vivo. Reproducibility of data and methodological approaches have not yet been thoroughly studied. OBJECTIVE: To study the reproducibility and the influence of the area of the test site on the values of biomechanical variables yielded in a normal population. METHOD: A 500-mbar suction was transmitted to the skin through Cutometer probes equipped with a 2- or 8-mm opening. RESULTS: The best reproducibility was obtained for the maximum distension of skin and for the biological elasticity. The values of the standard biomechanical ratios were almost the same for both probes. Linear correlations were found between parameters of elasticity. CONCLUSION: The Cutometer is a reliable device. A high degree of correlation exists between biomechanical variables related to elasticity. Under a suction of 500 mbar, both the 2- and 8-mm probes give results which correlate statistically in a large population. However, the two probes do not measure precisely the same aspect of skin mechanics. The 2-mm probe measures the capacity of superficial skin folding, and the 8-mm probe explores the biomechanical properties of the dermis itself and of its slipping mobility on the hypodermis. The biomechanical parameters which appear the most clinically relevant for a normal-looking skin are the maximum distension and the biological elasticity.

Adult↗
PubMed2003

Global nutritional profiling for mutant and chemical mode-of-action analysis in filamentous fungi.

We describe a method for gene function discovery and chemical mode-of-action analysis via nutrient utilization using a high throughput Nutritional Profiling platform suitable for filamentous microorganisms. We have optimized the growth conditions for each fungal species to produce reproducible optical density growth measurements in microtiter plates. We validated the Nutritional Profiling platform using a nitrogen source utilization assay to analyze 21 Aspergillus nidulans strains with mutations in the master nitrogen regulatory gene, areA. Analysis of these data accurately reproduced expected results and provided new data to demonstrate that this platform is suitable for fine level phenotyping of filamentous fungi. Next, we analyzed the differential responses of two fungal species to a glutamine synthetase inhibitor, illustrating chemical mode-of-action analysis. Finally, a comparative phenotypic study was performed to characterize carbon catabolite repression in four fungal species using a carbon source utilization assay. The results demonstrate differentiation between two Aspergillus species and two diverse plant pathogens and provide a wealth of new data on fungal nutrient utilization. Thus, these assays can be used for gene function and chemical mode-of-action analysis at the whole organism level as well as interspecies comparisons in a variety of filamentous fungi. Additionally, because uniform distribution of growth within wells is maintained, comparisons between yeast and filamentous forms of a single organism can be performed.

Aminobutyrates↗
PubMed2001

Temporal gene expression analysis of monolayer cultured rat hepatocytes.

The use of cultured primary hepatocytes within toxicology has proven to be a valuable tool for researchers, however, questions remain with regard to functional differences observed in these hepatocytes relative to the intact liver. Cultured hepatocytes have typically been described as dedifferentiated, a classification based upon the investigation of a few key cellular processes or hepatocellular markers. In the present study, parallel expression monitoring of approximately 8700 rat genes was used to characterize mRNA changes over time in hepatocyte cultures using Affymetrix microarrays. We isolated and labeled mRNA from whole rat livers, hepatocyte-enriched cell pellets, and primary cultured hepatocytes (4, 12, 24, 48, and 72 h postplating), and hybridized these samples to microarrays. From these data, several pairwise and temporal gene expression comparisons were made. Gene expression changes were confirmed by RT/PCR and by performing replicate experiments and repeated hybridizations using a rat toxicology sub-array that contained a 900-gene subset of the 8700-gene rat genomic microarray. PCR data qualitatively reproduced the temporal patterns of gene expression observed with microarrays. Cluster analysis of time course data using self-organizing maps (SOM) revealed a classic hepatocyte dedifferentiation response. Functional grouping of genes with similar transcriptional patterns showed time-dependent regulation of phase I and phase II metabolizing enzymes. In general, cytochrome P450 mRNA expression was repressed, but expression of phase II metabolizing enzymes varied by class (upregulation of glucuronidation, downregulation of sulfation). Potential metabolic targets for toxic insult, such as glutathione metabolism, gluconeogenesis, and glycolysis, were also affected at the transcriptional level. Progressive induction of several genes associated with the cellular cytoskeleton and extracellular matrix was observed in accord with physical changes in cell shape and connectivity associated with cellular adhesion. Finally, many transcriptional changes of genes involved in critical checkpoints throughout the hepatocyte cell cycle and differentiation process were observed. In total, these data establish a more comprehensive understanding of hepatocellular dedifferentiation and reveal many novel aspects of physiological and morphological hepatocyte adaptation. An assembly of all transcripts that demonstrated differential expression in this study can be found in the Supporting Information.

Animals↗
PubMed2006

Reproducibility and transferability of topological data: experimental charge density study of two modifications of L-alanyl-L-tyrosyl-L-alanine.

Two crystalline modifications of the tripeptide L-Ala-L-Tyr-L-Ala, which have different solvent molecules in the crystal structure (water and ethanol for modifications 1 and 2), were the subject of experimental charge density studies based on high resolution X-ray data collected at ultra-low temperatures of 9 K (1) and 20 K (2), respectively. The molecular structures and the intermolecular interactions were found to be rather similar in the two crystal lattices, so that this study allowed the reproducibility of the charge density of a given molecule in different (but widely comparable) crystalline environments to be examined. With respect to bond topological and atomic properties, the agreement between the two modifications of the title tripeptide was in the same range as found from the comparison with the previously reported results of tri-L-alanine. It follows that the reproducibility and transferability of quantitative topological data are comparable and that within the accuracy of experimental charge density work the replacement of the central amino acid residue L-Ala by L-Tyr has no significant influence, neither on bond nor on the atomic properties of the oligopeptide main chain. Intermolecular interactions in the form of hydrogen bonds were characterized quantitatively and qualitatively by topological criteria and by mapping the charge density distribution on the Hirshfeld surface.

Alanine↗
PubMedDate not supplied

Radiographic assessment of the extracranial internal carotid artery.

The accuracy of new (non-invasive) techniques of carotid artery assessment is classically established by comparing the results of the method under study with those of conventional contrast angiography. It is, therefore, important to establish the reproducibility of data acquired from contrast angiograms. Categories of carotid lesion must be chosen such that good reproducibility is likely both on an inter and intra-observer basis. This paper suggests that the smallest useful number of categories be used. It a two category discriminating system (less than 25% and greater than or equal to 25% stenosis), inter-observer agreement was found to be 95% and intra-observer agreement 96%. The principal observer variation occurred at the 0% and greater than 0% level of discrimination and this should be avoided in future studies comparing new arterial assessment techniques with conventional angiography.

Angiography↗
PubMed2000

Use of an ultrahigh-speed laser scanner for constructing three-dimensional shapes of dentition and occlusion.

STATEMENT OF PROBLEM: Acquisition of the 3-dimensional shape of dental casts is useful for quantitative evaluation of the diagnosis and treatment of occlusion. PURPOSE: This study demonstrated the acquisition of data through the use of an ultrahigh-speed laser scanner and an originally developed goniometer, the use of these tools to measure the entire 3-dimensional shape of the dental cast from multiple directions, and the connection of the data measurements to reconstruct the cast's occlusion with the use of a computer. MATERIAL AND METHODS: A commercially available apparatus that emits a line laser and completes 1 scan in only 0.6 seconds was used. To compensate for the unmeasured region, the cast was measured from 4 directions on the original goniometer, and the connection of data to obtain the entire image was carried out. Further, the reconstruction of the occlusion between the upper and lower casts was attempted by transferring the upper cast data to the lower cast. RESULTS: By the data connection, the entire shape of the upper and lower casts was constructed, and the characteristic structure was reproduced. The data connections were satisfactory for the flat surfaces but less accurate for the inclined surfaces. Reconstruction of the occlusion between the upper and lower casts was accomplished. It was then possible to visualize the occlusion from arbitrary directions and sections with computer graphics. CONCLUSION: The construction of the entire 3-dimensional shape of a dental cast and the reconstruction of the occlusion were accomplished using an ultrahigh-speed measurement system and original goniometer. These results will be useful for clinical applications such as computerized diagnoses and treatment of occlusion, and for the replacement of the stone casts in the dental office by computerized data.

Calibration↗
PubMed2005

Inferences on the common coefficient of variation.

The coefficient of variation is often used as a measure of precision and reproducibility of data in medical and biological science. This paper considers the problem of making inference about the common population coefficient of variation when it is a priori suspected that several independent samples are from populations with a common coefficient of variation. The procedures for confidence interval estimation and hypothesis testing are developed based on the concepts of generalized variables. The coverage properties of the proposed confidence intervals and type-I errors of the proposed tests are evaluated by simulation. The proposed methods are illustrated by a real life example.

Blood↗