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Results for “Experimental validation”

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At least 145 records · Page 8Linked to original sources

PubMed2005

Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes.

Allosteric RNAs operate as molecular switches that alter folding and function in response to ligand binding. A common type of natural allosteric RNAs is the riboswitch; designer RNAs with similar properties can be created by RNA engineering. We describe a computational approach for designing allosteric ribozymes triggered by binding oligonucleotides. Four universal types of RNA switches possessing AND, OR, YES and NOT Boolean logic functions were created in modular form, which allows ligand specificity to be changed without altering the catalytic core of the ribozyme. All computationally designed allosteric ribozymes were synthesized and experimentally tested in vitro. Engineered ribozymes exhibit >1,000-fold activation, demonstrate precise ligand specificity and function in molecular circuits in which the self-cleavage product of one RNA triggers the action of a second. This engineering approach provides a rapid and inexpensive way to create allosteric RNAs for constructing complex molecular circuits, nucleic acid detection systems and gene control elements.

Allosteric Site↗

PubMed2005

Dynamic characterization of hysteresis elements in mechanical systems. II. Experimental validation.

The industrial demand for machine tools with ever increasing speed and accuracy calls for a closer look at the physical phenomena that are present at small movements of those machine's slides. One of these phenomena, and probably the most dominant one, is the dependence of the friction force on displacement that can be described by a rate-independent hysteresis function with nonlocal memory. The influence of this highly nonlinear effect on the dynamics of the system has been theoretically analyzed in Part I of this paper. This part (II) aims at verifying these theoretical results on three experimental setups. Two setups, consisting of linearly driven rolling element guideways, have been built to specifically study the hysteretic friction behavior. The experiments performed on these specially designed setups are then repeated on one axis of an industrial pick-and-place device, driven by a linear motor and guided by commercial guideways. The results of the experiments on all the setups agree qualitatively well with the theoretically predicted ones and point to the inherent difficulty of accurate quantitative identification of the hysteretic behavior. They further show that the hysteretic friction behavior has a direct bearing on the dynamics of machine tools and its presence should therefore be carefully considered in the dynamic identification process of these systems.

Computers↗

PubMed2026

Experimental validation of an AI-driven digital healthcare platform for oral health behavior and plaque assessment among vietnamese children.

BACKGROUND: Oral health among children in developing countries, including Vietnam, remains a significant public health concern. Innovative approaches leveraging artificial intelligence AI-based digital health platforms may offer effective strategies for managing dental plaque and promoting better oral hygiene behaviors among school-aged children. This study aimed to evaluate the effectiveness of an AI-driven oral healthcare platform (Denti-i Vietnam) in improving oral hygiene and behavioral outcomes among Vietnamese primary school students. METHODS: A total of 204 primary school students aged 8-10 years in Hanoi, Vietnam, participated in this experimental study. Participants were randomly assigned to an intervention group (n = 107), which used the AI-driven oral healthcare platform, and a comparison group (n = 97), which received traditional oral health education via pamphlets. Oral health behaviors, dental plaque levels (Simplified Oral Hygiene Index; OHI-S), and caries indices (dft/DMFT) were assessed at baseline and after the intervention period. RESULTS: The intervention group demonstrated a significant reduction in the OHI-S score compared to baseline (2.49 ± 0.60 to 1.70 ± 0.76, p < 0.001), particularly in the debris component, indicating enhanced plaque control. Notable improvements were also observed in oral hygiene behaviors, including increased frequency of toothbrushing before and after breakfast (p < 0.01) and more frequent parental assistance during brushing (p = 0.03). Furthermore, parental awareness of dental caries significantly increased in the intervention group (p = 0.001). CONCLUSIONS: The AI-driven oral healthcare platform significantly improved both oral hygiene behaviors and plaque control among Vietnamese primary school children. These findings suggest that AI-driven digital health tools can serve as practical and scalable solutions for promoting oral health in developing countries.

Humans↗

PubMed2005

Experimental validation of a critical domain size in reaction-diffusion systems with Escherichia coli populations.

In a one-variable, finite size reaction-diffusion system, the existence of a minimal domain size required for the existence of a non-zero steady state is predicted, provided that the reaction-diffusion variable has a fixed value of zero at the boundaries of the domain (Dirichlet boundary conditions). This type of reaction diffusion model can be applied in population biology, in which the finite domain of the system represents a refuge where individuals can live normally immersed in a desert, or region where the conditions are so unfavourable that individuals cannot live in it. Building on a suggestion by Kenkre and Kuperman, and using non-chemotactic E. coli populations and a quasi-one-dimensional experimental design, we were able to find a minimal size (approximately 0.8 cm) for a refuge immersed in a region irradiated with intense UV light. The observed minimal size is in reasonable agreement with theory.

Biofilms↗

PubMedDate not supplied

Improved sensitivity to cerebral hemodynamics during brain activation with a time-gated optical system: analytical model and experimental validation.

Time domain (TD) diffuse optical measurement systems are being applied to neuroimaging, where they can detect hemodynamics changes associated with cerebral activity. We show that TD systems can provide better depth sensitivity than the more traditional continuous wave (CW) systems by gating late photons, which carry information about deep layers of the brain, and rejecting early light, which is sensitive to the superficial physiological signal clutter. We use an analytical model to estimate the contrast due to an activated region of the brain, the instrumental noise of the systems, and the background signal resulting from superficial physiological signal clutter. We study the contrast-to-noise ratio and the contrast-to-background ratio as a function of the activation depth and of the source-detector separation. We then present experimental results obtained with a time-gated instrument on the motor cortex during finger-tapping exercises. Both the model and the experimental results show a similar contrast-to-noise ratio for CW and TD, but that estimation of the contrast is experimentally limited by background fluctuations and that a better contrast-to-background ratio is obtained in the TD case. Finally, we use the time-gated measurements to resolve in depth the brain activation during the motor stimulus.

Artifacts↗

PubMed2006

Steady state analysis and experimental validation of a model for hepatic high-density lipoprotein transport.

Transport of high-density lipoprotein (HDL) in the hepatocyte plays a fundamental role in reverse cholesterol transport and regulation of plasma HDL levels. On the basis of a recently developed kinetic model, the steady state distribution of HDL was analyzed. Fractional fluorescence of labeled HDL in the basolateral membrane, sorting endosomes (SE), the subapical compartment/ apical recycling compartment, the biliary canaliculus and in late endosomes and lysosomes (LE/LYS) including expected standard deviation is predicted. Improved parameter estimation was obtained by including kinetic data of apical endocytosis of fluorescent markers for LE/LYS, asialoorosomucoid and Rhodamine-dextran, in the regression. Predicted values using the refined kinetic parameters are in good agreement with experimental values of compartmental steady state fluorescence of Alexa488-HDL in polarized hepatic HepG2 cells. From calculated steady state fluxes, it is suggested that export of HDL from basolateral SE is the key step for determining the transport of HDL through the hepatocyte. The analysis provides testable predictions for high-throughput fluorescence microscopy screening experiments on potential inhibitors of hepatic HDL processing. By quantitative fluorescence imaging and model analysis, it is shown that the phosphoinositide kinase inhibitor wortmannin prevents apical transport of fluorescent HDL from basolateral SE. The results support that endosomes of polarized hepatic cells have different sorting functions and that apical endocytosis is an integrative trafficking step in hepatocytes.

Androstadienes↗

PubMed2005

Theoretical and experimental validation of a dual-frequency excitation method for spatial control of cavitation.

Inertial cavitation has been implicated as the primary mechanism for a host of emerging applications. In all these applications, the main concern is to induce cavitation in perfectly controlled locations in the field; this means specifically to be able to achieve the cavitation threshold at the geometrical focus of the transducer without stimulating its near field. In this study, we develop dual-frequency methods to preferentially lower the cavitation threshold at the focus relative to the rest of the field. Two families of dual-frequency driving waveforms are evaluated in a bubble model incorporating rectified diffusion. Results are then verified by experiment. Finally, the performance of the rest of acoustic field in suppressing cavitation when cavitation is induced at the focus is investigated theoretically and checked experimentally. This study shows that dual-frequency phased arrays could be used to precisely control cavitation. The cavitation threshold is proved to be 1.2 times higher in the near field than at the focus. The concept of cavitation field is introduced and complements cavitation studies concentrating on the focal behaviour only.

Computer Simulation↗

PubMed1984

Gas transport during high-frequency ventilation: theoretical model and experimental validation.

We present a theoretical model of gas transport through the dead space during high-frequency ventilation (HFV) with volumes less than dead space volume. The analysis is based on the axial distribution of transit times of gas moving through the dead space. The model predicts that for tidal volumes (V) much less than dead space (VD), gas exchange will be proportional to the product of frequency (f) and V2. If gas transport is analyzed in terms of Fick's law, then the effective diffusion coefficient (Deff) can be shown to be equal to fV2 times a constant, whose value equals the square of the coefficient of dispersion of axial transit times through the dead space (sigma t/t)2. Experimental results in straight tubes fit the predictions of this model quite well. A (sigma t/t) through the entire dead space of about 30% is more than sufficient to account for gas exchange during HFV in physical models or in intact animals. An axial dispersion of this magnitude can be measured directly from a typical Fowler dead space determination in healthy subjects.

Animals↗

PubMed2005

Epileptic transitions: model predictions and experimental validation.

The essence of epilepsy is that a patient displays (long) periods of normal EEG activity (i.e., nonepileptiform) intermingled occasionally with epileptiform paroxysmal activity. The mechanisms of transition between these two types of activity are not well understood. To provide more insight into the dynamics of the neuronal networks leading to seizure generation, the authors developed a computational model of thalamocortical circuits based on relevant patho(physiologic) data. The model exhibits bistability, i.e., it features two operational states, ictal and interictal, that coexist. The transitions between these two states occur according to a Poisson process. An alternative scenario for transitions can be a random walk of network parameters that ultimately leads to a paroxysmal discharge. Predictions of bistable computational model with experimental results from different types of epilepsy are compared.

Adolescent↗

PubMed1996

Role of erythrocytes in leukocyte-endothelial interactions: mathematical model and experimental validation.

The binding of circulating cells to the vascular wall is a central process in inflammation, metastasis, and therapeutic cell delivery. Previous in vitro studies have identified the adhesion molecules on various circulating cells and the endothelium that govern the process under static conditions. Other studies have attempted to simulate in vivo conditions by subjecting adherent cells to shear stress as they interact with the endothelial cells in vitro. These experiments are generally performed with the cells suspended in Newtonian solutions. However, in vivo conditions are more complex because of the non-Newtonian flow of blood, which is a suspension consisting of 20-40% erythrocytes by volume. The forces imparted by the erythrocytes in the flow can contribute to the process of cell adhesion. A number of experimental and theoretical studies have suggested that the rheology of blood can influence the binding of circulating leukocytes by increasing the normal and axial forces on leukocytes or the frequency of their collision with the vessel wall, but there have been no systematic investigations of these phenomena to date. The present study quantifies the contribution of red blood cells (RBCs) in cell capture and adhesion to endothelial monolayers using a combination of mathematical modeling and in vitro studies. Mathematical modeling of the flow experiments suggested a physical mechanism involving RBC-induced leukocyte dispersion and/or increased normal adhesive contact. Flow chamber studies performed with and without RBCs in the suspending medium showed increases in wall collision and binding frequencies, and a decrease in rolling velocity in the presence of erythrocytes. Increased fluid viscosity alone did not influence the binding frequency, and the differences could not be attributed to large near-wall excesses of the lymphocytes. The results indicate that RBCs aid in the transport and initial engagement of lymphocytes to the vascular wall, modifying the existing paradigm for immune cell surveillance of the vascular endothelium by adding the erythrocyte as an essential contributor to this process.

Biophysical Phenomena↗

PubMed1995

Experimental validation of Monte Carlo dose calculations about a high-intensity Ir-192 source for pulsed dose-rate brachytherapy.

Despite widespread use of high-intensity Ir-192 remotely afterloaded sources, no published measured or calculated dose-rate tables for currently used source designs are available. For a pulsed dose-rate Ir-192 source, both transverse axis (0.5-10 cm) and two-dimensional polar dose-rate profiles (1.5, 3, and 5 cm) were measured with thermoluminescent dosimetry in a solid water phantom. Dose rates were normalized to measured air-kerma strength, and the source geometry was verified by pinhole autoradiography and transmission radiography. At each measurement point, dose rates were calculated by a Monte Carlo photon transport (MCPT) code, which realistically modeled the experimental phantom, source, and detector geometry. Agreement between MCPT absolute dose-rate calculations and measurements averaged 3% and was less than 5%, demonstrating that Monte Carlo simulation is an accurate and powerful tool for two-dimensional dosimetric characterization of high activity Ir-192 sources.

Brachytherapy↗

PubMed2005

Anchor profiles of HLA-specific peptides: analysis by a novel affinity scoring method and experimental validation.

The study of intermolecular interactions is a fundamental research subject in biology. Here we report on the development of a quantitative structure-based affinity scoring method for peptide-protein complexes, named PepScope. The method operates on the basis of a highly specific force field function (CHARMM) that is applied to all-atom structural representations of peptide-receptor complexes. Peptide side-chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. A de novo approach to estimate dehydration energies was developed, based on the simulation of individual amino acids in a solvent box filled with explicit water molecules. Transferability of the method was demonstrated by its application to the hydrophobic HLA-A2 and -A24 receptors, the polar HLA-A1, and the sterically ruled HLA-B7 receptor. A combined theoretical and experimental study on 39 anchor substitutions in FxSKQYMTx/HLA-A2 and -A24 complexes indicated a prediction accuracy of about two thirds of a log-unit in Kd. Analysis of free energy contributions identified a great role of desolvation and conformational strain effects in establishing a given specificity profile. Interestingly, the method rightly predicted that most anchor profiles are less specific than so far assumed. This suggests that many potential T-cell epitopes could be missed with current prediction methods. The results presented in this work may therefore significantly affect T-cell epitope discovery programs applied in the field of peptide vaccine development.

Amino Acid Sequence↗

PubMed2001

In vitro selection of allosteric ribozymes: theory and experimental validation.

In vitro selection techniques offer powerful and versatile methods to isolate nucleic acid sequences with specific activities from huge libraries. We describe an in vitro selection strategy for the de novo selection of allosteric self-cleaving ribozymes responding to pefloxacin and other quinolone derivatives. Within 16 selection cycles, highly sensitive clones responding to drug levels in the sub-micromolar range were obtained. The morpholine moiety of the quinolone derivatives was required for inhibition of the self-cleavage of the selected ribozymes: modifications of the aromatic system were tolerated better than modifications of the morpholine ring. We also present a theoretical model that analyzes the predicted fraction of ribozymes with a given binding constant and cleavage rate recovered after each selection cycle. This model precisely predicts the actual experimental values obtained with the selection procedure. It can thus be used to determine the optimal conditions for an in vitro selection of an allosteric ribozyme with a desired dissociation constant and cleavage rate for a given application.

Allosteric Regulation↗

PubMed1980

The amino acid requirements of chicks: experimental validation of model-calculated requirements.

The amino acid requirements of broiler chicks, on a weekly or biweekly basis, were calculated according to a model presented previously (Hurwitz et al., 1978). Based on the present results, the model has been somewhat modified. The model requirements provided the basis for computer-designed diets which were fed to chicks of different ages and were composed to others computed on the basis of NRC (1971, 1977) requirements. In all cases the model-based diets, which were considerably lower in protein, supported weight gains equivalent to those obtained on NRC-based diets. The relatively poorer feed efficiency observed in the first trial with chicks fed the model-based diets, could be alleviated by equalizing both energy and lipid concentrations in the experimental diets. Thus, equal growth and feed efficiency were obtained with the model and NRC (1971)-based diets, for 2- to 10-week-old chicks. The possible reasons for the slightly higher abdominal fat content of the chicks fed the model-based diets are discussed.

Amino Acids↗

PubMed2005

Efficient energy based modeling and experimental validation of liquid filling in planar micro-fluidic components and networks.

This paper presents a model that describes how liquid flow fills micro-fluidic components and networks. As an alternative to computational fluid dynamic (CFD) simulations, we use a constrained energy minimization approach. This approach is based on two assumptions that hold in many micro-fluidic devices: (i) The length scales are small, and we consider slow filling rates, hence fluid momentum and viscous terms are small compared to surface tension forces, consequently the liquid/gas interfaces can be viewed as a succession of quasi-steady equilibrium configurations. (ii) Any equilibrium configuration corresponds to a surface tension energy minima which is constrained by the device shape and the volume of liquid in the device. The model is developed for planar micro-fluidic devices, is based on a fundamental physical principle, and shows accurate agreement with experimental data. It takes us only a few minutes to evaluate the model for a planar component of any shape using the Surface Evolver software, and this is significantly less then the computer run time required for CFD simulations. Moreover, once a library of component models has been created (which takes less than an hour of computer time) it then takes only seconds to simulate different network architectures with thousands of components. This fast "reconfigure the network and simulate in seconds" capability is essential for the design of truly complex networks that will enable the next generation of passive, micro-fluidic, lab-on-a-chip systems.

Computer Simulation↗

PubMed1998

A sequence based computational identification of a Drosophila developmentally regulated TATA-less RNA polymerase II promoter and its experimental validation.

Many RNA polymerase II promoters lack the characteristic TATA box sequence located -25/-30 nucleotides upstream from the transcription start. In Drosophila, half of the promoters identified so far are TATA-deficient. The yemanuclein-alpha gene whose promoter activity is restricted to oogenesis, falls in this class. A number of upstream and downstream promoter elements have been identified for some TATA-less promoters. The yem-alpha promoter contains none of the consensus elements identified so far. Our work was based on the assumption that the physical parameters of the DNA could be used to predict the location of the yem-alpha promoter. A sequence based computational analysis allowed us to determine the characteristic changes of DNA curvature and helix stability in the presumptive regulatory region. Our experimental data were in good agreement with the computational analysis. We have started to investigate the general value of this approach by analyzing other promoters.

Animals↗

PubMed1995

Cell orientation response to cyclically deformed substrates: experimental validation of a cell model.

We have developed a stochastic model that describes the orientation response of bipolar cells grown on a cyclically deformed substrate. The model was based on the following hypotheses regarding the behavior of individual cells: (a) the mechanical signal responsible for cell reorientation is the peak to peak surface strain along the cell's major axis (p-p axial strain); (b) each cell has an axial strain threshold and the threshold is normally distributed in the cell population; (c) the cell will avoid any direction where the p-p axial strain is above its threshold; and (d) the cell will randomly orient within the range of directions where the p-p axial strains are less than the cell's threshold. These hypotheses were tested by comparing model predictions with experimental observations from stretch experiments conducted with human melanocytes. The cells were grown on elastic rectangular culture dishes subjected to unidirectional cyclic (1 Hz) stretching with amplitudes of 0, 4, 8, and 12%. After 24 h of stimulation, the distribution of cell orientations was determined by measuring the orientations of 300-400 randomly selected cells. The 12% stretch experiment was used to determine the mean, 3.5%, and the standard deviation, 1.0% of the strain threshold for the cell population. The Kolmogorov-Smirnov test was then used to determine if the orientation distributions predicted by the model were different from experimentally measured distributions for the 4 and 8% stretches. No significant differences were found between the predicted and experimental distributions (4%: p = 0.70; and 8%: p = 0.71). These results support the hypothesis that cells randomly orient, but avoid directions where the p-p axial strains are above their thresholds.

Algorithms↗

PubMed2006

Experimental validation of a T2rho transverse relaxation model using LASER and CPMG acquisitions.

The transverse relaxation rate (R2=1/T2) of many biological tissues are altered by endogenous magnetized particles (i.e., ferritin, deoxyhemoglobin), and may be sensitive to the pathological progression of neurodegenerative disorders associated with altered brain-iron stores. R2 measurements using Carr-Purcell-Meiboom-Gill (CPMG) acquisitions are sensitive to the refocusing pulse interval (2taucp), and have been modeled as a chemical exchange (CE) process, while R2 measurements using a localization by adiabatic selective refocusing (LASER) sequence have an additional relaxation rate contribution that has been modeled as a R2rho process. However, no direct comparison of the R2 measured using these two sequences has been described for a controlled phantom model of magnetized particles. The three main objectives of this study were: (1) to compare the accuracy of R2 relaxation rate predictions from the CE model with experimental data acquired using a conventional CPMG sequence, (2) to compare R2 estimates obtained using LASER and CPMG acquisitions, and (3) to determine whether the CE model, modified to account for R2rho relaxation, adequately describes the R2 measured by LASER for a full range of taucp values. In all cases, our analysis was confined to spherical magnetic particles that satisfied the weak field regime. Three phantoms were produced that contained spherical magnetic particles (10 microm diameter polyamide powders) suspended in Gd-DTPA (1.0, 1.5, and 2.0 mmol/L) doped gel. Mono-exponential R2 measurements were made at 4T as a function of refocusing pulse interval. CPMG measurements of R2 agreed with CE model predictions while significant differences in R2 estimates were observed between LASER and CPMG measurements for short taucp acquisitions. The discrepancy between R2 estimates is shown to be attributable to contrast enhancement in LASER due to T2rho relaxation.

Calibration↗