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Results for “quantitative model”

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At least 865 records · Page 48Linked to original sources
PubMed1997

T cell repertoire formation displays characteristics of qualitative models of thymic selection.

The use of T cell receptor elements varies between mouse strains, reflecting a balance between positive and negative selection. The presence of H-2E biases V alpha and V beta usage through major histocompatibility class II isotype preferences of V elements, and mammary tumor virus-dependent, negative selection. Quantitative models of thymic selection predict that negative selection equates to 'excess' positive selection, whereas qualitative models suggest that positive and negative selection are opposing forces. This report attempts to distinguish between the models by assessing whether, at the level of the T cell repertoire, positive and negative selection have quantitative or qualitative characteristics. The data show that the effect of bearing V alpha and V beta regions which are both preferentially (or negatively) selected in the presence of H-2E is additive or synergistic, whilst positive stimuli counteract negative ones. The data thus provide support for qualitative models of thymic selection.

Animals↗
PubMed1998

Impact of diabetic retinopathy screening on a British district population: case detection and blindness prevention in an evidence-based model.

OBJECTIVES: To quantify case detection and blindness prevention attainable through screening for diabetic retinopathy in a district population. DESIGN: Literature review including a pooled estimate of screening test sensitivity, and quantitative modelling, including sensitivity analyses. SETTING AND PATIENTS: The diabetic population of a typical district health authority or health board. MAIN RESULTS: Evidence suggests that in a British general practice based diabetic population, prevalence of retinopathy requiring treatment would be between 1% and 6%; annual incidence of blindness among diabetics with retinopathy requiring treatment would be between 6% and 9%; sensitivity of screening tests in detecting retinopathy requiring treatment would be between 50% and 88%; and treatment could prevent 77% of expected cases of blindness. Of those screened, about 4% would be correctly detected as requiring treatment during an initial screening round, but this yield could decrease to about 1% in subsequent annual screening rounds. Of those treated, about 6% would be prevented from going blind within a year of treatment and 34% within 10 years of treatment. CONCLUSIONS: Screening and early treatment of diabetic retinopathy can prevent substantial disability. The effectiveness and efficiency of screening could be enhanced by improving the performance of current tests or increasing use of mydriatic retinal photography, and by increasing uptake, particularly among diabetics at greatest risk.

Blindness↗
PubMed2001

LiBr. 2H(2)O Crystallization Inhibition in the Presence of Additives.

Experiments have been performed to measure the effect of additives on the crystallization temperature of concentrated LiBr solutions cooled at a rate of 20 degrees C/h. The measured crystallization temperatures correspond not to the temperatures of equilibrium solubility but to the critical temperature for heterogeneous nucleation of the hydrated LiBr salt on the glass wall of the test tube containing the sample solution. Various additives at concentrations from 250 to 1500 ppm have been investigated. Some soluble additives further decreased the experimental crystallization temperature by as much as 13 degrees C, corresponding to 22 degrees C below the equilibrium solubility. Large decreases in the crystallization temperature can be correlated with large values of complexation constants of the additive for either the Li(+) or the Br(-) ion in solution. Solution complexation, however, is not sufficient to explain the magnitude of the decrease in the crystallization temperature. The only phenomenon capable of quantitatively explaining the magnitude of the decrease in the crystallization temperature is the change in the crystal/solution interfacial energy due to adsorption of the additive on the surface of the prenucleation embryos. A quantitative model of the crystal/solution interfacial energy due to adsorption has been developed using both the Langmuir and Gibbs adsorption equations, allowing the quantitative prediction of crystallization temperatures with additive concentration. Copyright 2001 Academic Press.

Journal Article↗
PubMed2002

An efficient method for studying short-term plasticity with random impulse train stimuli.

In this article, we introduce an efficient method that models quantitatively nonlinear dynamics associated with short-term plasticity (STP) in biological neural systems. It is based on the Voterra-Wiener modeling approach adapted for special stimulus/response datasets. The stimuli are random impulse trains (RITs) of fixed amplitude and Poisson distributed, variable interimpulse intervals. The class of stimuli, we use can be viewed as a hybrid between the paired impulse approach (variable interimpulse interval between two input impulses) and the fixed frequency approach (impulses repeated at fixed intervals, varying in frequency from one stimulus dataset to the next). The responses are sequences of population spike amplitudes of variable size and are assumed to be contemporaneous with the corresponding impulses in the RITs they are evoked by. The nonlinear dynamics of the mechanisms underlying STP are captured by kernels used to create compact STP models with predictive capabilities. Compared to similar methods in the literature, the method presented in this article provides a comprehensive model of STP with considerable improvement in prediction accuracy and requires shorter experimental data collection time.

Action Potentials↗
PubMed2006

Fast and robust method for the determination of microstructure and composition in butadiene, styrene-butadiene, and isoprene rubber by near-infrared spectroscopy.

In the tire industry, synthetic styrene-butadiene rubber (SBR), butadiene rubber (BR), and isoprene rubber (IR) elastomers are essential for conferring to the product its properties of grip and rolling resistance. Their physical properties depend on their chemical composition, i. e., their microstructure and styrene content, which must be accurately controlled. This paper describes a fast, robust, and highly reproducible near-infrared analytical method for the quantitative determination of the microstructure and styrene content. The quantitative models are calculated with the help of pure spectral profiles estimated from a partial least squares (PLS) regression, using (13)C nuclear magnetic resonance (NMR) as the reference method. This versatile approach allows the models to be applied over a large range of compositions, from a single BR to an SBR-IR blend. The resulting quantitative predictions are independent of the sample path length. As a consequence, the sample preparation is solvent free and simplified with a very fast (five minutes) hot filming step of a bulk polymer piece. No precise thickness control is required. Thus, the operator effect becomes negligible and the method is easily transferable. The root mean square error of prediction, depending on the rubber composition, is between 0.7% and 1.3%. The reproducibility standard error is less than 0.2% in every case.

Journal Article↗
PubMed2006

Modified 'Joyce model' of opioid dependence/withdrawal.

By comprehensive and detailed measurement of the time course of withdrawal signs in rats, Joyce et al. (J. Theo. Biol. 240:531-537, 2006) recently provided a creative quantitative model of the onset of drug dependence based on the requirement of protein synthesis. Because the initial model fit the data imperfectly over the full time course, those authors postulated that additional features would be needed. We report excellent fit of the data (R(2)=0.96) by adding: (1) a transient early phase, and (2) a delay in the buildup of protein.

Analgesics, Opioid↗
PubMed2004

Competitive clonal hematopoiesis in mouse chimeras explained by a stochastic model of stem cell organization.

Many current experimental results show the necessity of new conceptual approaches to understand hematopoietic stem cell organization. Recently, we proposed a novel theoretical concept and a corresponding quantitative model based on microenvironment-dependent stem cell plasticity. The objective of our present work is to subject this model to an experimental test for the situation of chimeric hematopoiesis. Investigating clonal competition processes in DBA/2-C57BL/6 mouse chimeras, we observed biphasic chimerism development with initially increasing but long-term declining DBA/2 contribution. These experimental results were used to select the parameters of the mathematical model. To validate the model beyond this specific situation, we fixed the obtained parameter configuration to simulate further experimental settings comprising variations of transplanted DBA/2-C57BL/6 proportions, secondary transplantations, and perturbation of stabilized chimeras by cytokine and cytotoxic treatment. We show that the proposed model is able to consistently describe the situation of chimeric hematopoiesis. Our results strongly support the view that the relative growth advantage of strain-specific stem cells is not a fixed cellular property but is sensitively dependent on the actual state of the entire system. We conclude that hematopoietic stem cell organization should be understood as a flexible, self-organized rather than a fixed, preprogrammed process.

Animals↗
PubMed2005

Modeling intercellular interactions during carcinogenesis.

By modulating the microenvironment of malignant or premalignant cells, inhibitory or stimulatory signals from nearby cells can play a key role in carcinogenesis. However, current commonly used quantitative models for induction of cancers by ionizing radiation focus on single cells and their progeny. Intercellular interactions are neglected or assumed to be confined to unidirectional radiation bystander effect signals from cells of the same tissue type. We here formulate a parsimoniously parameterized two-stage logistic (TSL) carcinogenesis model that incorporates some effects of intercellular interactions during the growth of premalignant cells. We show that for baseline tumor rates, involving no radiation apart from background radiation, this TSL model gives acceptable fits to a number of data sets. Specifically, it gives the same baseline hazard function, using the same number of adjustable parameters, as does the commonly used two-stage clonal expansion (TSCE) model, so it is automatically applicable to the many data sets on baseline cancer that have been analyzed using the TSCE model. For perturbations of baseline rates due to radiation, the models differ. We argue from epidemiological and laboratory evidence, especially results for the atomic bomb survivors, that for radiation carcinogenesis the TSL model gives results at least as realistic as the TSCE or similar models, despite involving fewer adjustable parameters in many cases.

Carcinogenicity Tests↗
PubMed2006

Structure-permeation relationships for the non-invasive transdermal delivery of cationic peptides by iontophoresis.

Transdermal iontophoresis enables the controlled, non-invasive administration of peptide therapeutics. The aims of this study were (i) to evaluate the effect of amino acid sequence and the spatial distribution of peptide physicochemical properties on electrotransport, and (ii) to develop a quantitative model to predict peptide transport rates. Experimental results showed that the distribution of molecular properties over the peptide surface significantly affected iontophoretic delivery: different arrangements of the same residues resulted in different transport behavior. Computational studies generated three-dimensional quantitative structure-permeation relationships (3D-QSPR) based on 3D descriptors. The model predicted that iontophoresis was favored by peptide hydrophilicity but hindered by voluminous, localized hydrophobicity. Molecular characteristics that favor electrotransport are the converse of those required for passive diffusion across biological membranes. The data represent the first analysis of peptide electrotransport in terms of the spatial distribution of molecular properties and provide insight into the ab initio prediction of transdermal iontophoretic peptide delivery.

Administration, Cutaneous↗
PubMedDate not supplied

Required parental investment and mating patterns: a quantitative analysis in the context of evolutionarily stable strategies.

Much social psychological research has been dedicated to understanding mating strategies from the standpoint of genetic-fitness payout (e.g., Simpson and Gangestad, 2000). The current work is designed to provide a coherent, quantitative model for predicting different classes of mating strategies in both males and females. Specifically, the framework developed in this paper is an elaboration of Dawkins' (1989) quantitative assessment of different male and female mating strategies. Dawkins suggests that the prevalence of different strategies employed should be predictable in terms of evolutionary stable strategies. In the current work, a quantitative analysis predicting the prevalence of different mating strategies within each sex was conducted. The mathematical functions derived suggest that variability in the costs associated with raising offspring affects the expected prevalence of mating strategies differently for males and females. According to the present model, variability in female strategies should be less affected by changes in parental investment (PI) than variability in male strategies. Important predictions regarding male and female mating strategies across cultures are discussed.

Biological Evolution↗
PubMedDate not supplied

A neuromorphic model for achromatic and chromatic surface representation of natural images.

This study develops a neuromorphic model of human lightness perception that is inspired by how the mammalian visual system is designed for this function. It is known that biological visual representations can adapt to a billion-fold change in luminance. How such a system determines absolute lightness under varying illumination conditions to generate a consistent interpretation of surface lightness remains an unsolved problem. Such a process, called 'anchoring' of lightness, has properties including articulation, insulation, configuration, and area effects. The model quantitatively simulates such psychophysical lightness data, as well as other data such as discounting the illuminant, and lightness constancy and contrast effects. The model retina embodies gain control at retinal photoreceptors, and spatial contrast adaptation at the negative feedback circuit between mechanisms that model the inner segment of photoreceptors and interacting horizontal cells. The model can thereby adjust its sensitivity to input intensities ranging from dim moonlight to dazzling sunlight. A new anchoring mechanism, called the Blurred-Highest-Luminance-As-White rule, helps simulate how surface lightness becomes sensitive to the spatial scale of objects in a scene. The model is also able to process natural color images under variable lighting conditions, and is compared with the popular RETINEX model.

Adaptation, Ocular↗
PubMedDate not supplied

Pharmacophore modeling and in silico screening for new P450 19 (aromatase) inhibitors.

Cytochrome P450 19 (P450 19, aromatase) constitutes a successful target for the treatment of breast cancer. This study analyzes chemical features common to P450 19 inhibitors to develop ligand-based, selective pharmacophore models for this enzyme. The HipHop and HypoRefine algorithms implemented in the Catalyst software package were employed to create both common feature and quantitative models. The common feature model for P450 19 includes two ring aromatic features in its core and two hydrogen bond acceptors at the ends. The models were used as database search queries to identify active compounds from the NCI database.

Algorithms↗
PubMed2003

Prediction of dihydrofolate reductase inhibition and selectivity using computational neural networks and linear discriminant analysis.

A data set of 345 dihydrofolate reductase inhibitors was used to build QSAR models that correlate chemical structure and inhibition potency for three types of dihydrofolate reductase (DHFR): rat liver (rl), Pneumocystis carinii (pc), and Toxoplasma gondii (tg). Quantitative models were built using subsets of molecular structure descriptors being analyzed by computational neural networks. Neural network models were able to accurately predict log IC(50) values for the three types of DHFR to within +/-0.65 log units (data sets ranged approximately 5.5 log units) of the experimentally determined values. Classification models were also constructed using linear discriminant analysis to identify compounds as selective or nonselective inhibitors of bacterial DHFR (pcDHFR and tgDHFR) relative to mammalian DHFR (rlDHFR). A leave-N-out training procedure was used to add robustness to the models and to prove that consistent results could be obtained using different training and prediction set splits. The best linear discriminant analysis (LDA) models were able to correctly predict DHFR selectivity for approximately 70% of the external prediction set compounds. A set of new nitrogen and oxygen-specific descriptors were developed especially for this data set to better encode structural features, which are believed to directly influence DHFR inhibition and selectivity.

Animals↗
PubMed1994

Modeling eukaryotic transcriptional activation.

In recent years, many components involved in promoter-specific transcriptional activation in eukaryotes have been identified and characterized. We argue that a proper understanding of transcriptional activation will require quantitative modeling and we outline some of the considerations that such modeling will need to take into account.

Animals↗
PubMed2001

A general model for ontogenetic growth.

Several equations have been proposed to describe ontogenetic growth trajectories for organisms justified primarily on the goodness of fit rather than on any biological mechanism. Here, we derive a general quantitative model based on fundamental principles for the allocation of metabolic energy between maintenance of existing tissue and the production of new biomass. We thus predict the parameters governing growth curves from basic cellular properties and derive a single parameterless universal curve that describes the growth of many diverse species. The model provides the basis for deriving allometric relationships for growth rates and the timing of life history events.

Animals↗
PubMed2005

Oxygen-sensitive contrast in blood for steady-state free precession imaging.

Steady-state free precession (SSFP) methods have gained widespread recognition for their ability to provide fast scans at high signal-to-noise ratio. This paper demonstrates that such methods are also capable of reflecting functional information, particularly blood oxygenation state. It is well known that SSFP signals show substantial sensitivity to small off-resonance frequency variations. However, that mechanism cannot explain the oxygen-sensitive contrast in blood that was observed with steady-state methods using phase-cycled radiofrequency pulses. From theoretical and experimental models it is demonstrated that the mechanism responsible for such contrast originates from the motion of spins through local field inhomogeneities in and around deoxygenated red blood cells. In addition, this work shows that it is critical to choose the scan parameters carefully for robust oxygen-sensitive contrast. Finally, it is demonstrated that it is possible to build a quantitative model that incorporates the Luz-Meiboom model, which had been used in the past to estimate quantitative measures of vascular blood oxygen levels. It is envisioned that this method could be instrumental in real-time imaging focused on detecting diseases where the oxygen state of blood is impaired.

Chi-Square Distribution↗
PubMed1995

Addition of side chain interactions to modified Lifson-Roig helix-coil theory: application to energetics of phenylalanine-methionine interactions.

We introduce here i, i + 3 and i, i + 4 side chain interactions into the modified Lifson-Roig helix-coil theory of Doig et al. (1994, Biochemistry 33:3396-3403). The helix/coil equilibrium is a function of initiation, propagation, capping, and side chain interaction parameters. If each of these parameters is known, the helix content of any isolated peptide can be predicted. The model considers every possible conformation of a peptide, is not limited to peptides with only a single helical segment, and has physically meaningful parameters. We apply the theory to measure the i, i + 4 interaction energies between Phe and Met side chains. Peptides with these residues spaced i, i + 4 are significantly more helical than controls where they are spaced i, i + 5. Application of the model yields delta G for the Phe-Met orientation to be -0.75 kcal.mol-1, whereas that for the Met-Phe orientation is -0.54 kcal.mol-1. These orientational preferences can be explained, in part, by rotamer preferences for the interacting side chains. We place Phe-Met i, i + 4 at the N-terminus, the C-terminus, and in the center of the host peptide. The model quantitatively predicts the observed helix contents using a single parameter for the side chain-side chain interaction energy. This result indicates that the model works well even when the interaction is at different locations in the helix.

Amino Acid Sequence↗