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At least 343 records · Page 19Linked to original sources
PubMed1997

Manuo-ocular coordination in target tracking. I. A model simulating human performance.

During eye tracking of a self-moved target, human subjects' performance differs from eye-alone tracking of an external target. Typical latency between target and eye motion onsets is shorter, ocular smooth pursuit (SP) saturation velocity increases and the maximum target motion frequency at which the SP system functions correctly is higher. Based on a previous qualitative model, a quantitative model of the coordination control between the arm motor system and the SP system is presented and evaluated here. The model structure maintains a high level of parallelism with the physiological system. It contains three main parts: the eye motor control (containing a SP branch and a saccadic branch), the arm motor control and the coordination control. The coordination control is achieved via an exchange of information between the arm and the eye sensorimotor systems, mediated by sensory signals (vision, proprioception) and motor command copy. This cross-talk results in improved SP system performance. The model has been computer simulated and the results have been compared with human subjects' behavior observed during previous experiments. The model performance is seen to quantitatively fit data on human subjects.

Hand↗
PubMed2006

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

Biochemical Phenomena↗
PubMed1989

Transient response of rod outer segment cGMP phosphodiesterase to actinic light pulses. II. Detailed quantitative kinetic model.

In the accompanying article (Schmidt, J.A., and Yguerabide, J. (1989) J. Biol. Chem. 264, 19790-19803), we presented a minimal quantitative kinetic model with one rate-limiting step for the transient response of rod outer segment (ROS) phosphodiesterase (PDE) to stimulating light pulses of low fractional bleach (linear response range) and showed that the model was in excellent quantitative agreement with experimental results. The model characterizes the PDE response in terms of the specific rate constant of the rate-limiting step, kL, the lifetime of photoactivated rhodopsin, tau R, and the lifetime of activated PDE, tau P, but makes no predictions on how these kinetic parameters should depend on the concentrations of the various reactive species involved in the PDE response to light and does not reveal the nature of the rate-limiting step. However, we established by curve fitting experimental data to theoretical expressions from the model that kL increases hyperbolically with [GTP], tau R decreases with [GTP], and tau P is independent of GTP. In this report we present three detailed kinetic models which make specific quantitative predictions on how the kinetic parameters of the minimal model should depend on nucleotide and G protein concentrations and test the models against experimental data. Each model consists of one rate-limiting step. The first detailed model postulates that the rate-limiting step is the dissociation of R*GT into R* and GT (T stands for GTP). The second model postulates that the rate-limiting step is the binding of GTP to R*G, and the third model postulates that the rate-limiting step is the encounter rate of R* and G on the ROS disc membrane. We find that only the first detailed model is consistent with the experimental results as characterized by the minimal model. Using this detailed model we (a) define kL and tau R in terms of more fundamental equilibrium and rate parameters, (b) develop a theory for the systematic evaluation of amplification or gain of the PDE light response from light-stimulated GTP-binding data as well as v(t) versus t graphs, and (c) clarify methods which have been used in the past to evaluate gain experimentally.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed1993

Problems, pitfalls, perspectives and potentials of quantitative theoretical models for cellular radiation action.

The problem of quantitative mathematical models in cellular radiation biology is discussed in a general way. It is emphasized that there are a number of stages, starting from the spatial pattern of energy deposition and ending with repair/misrepair processes which all need to be incorporated. Since different types of radiation commonly yield very similar dose-response curves a model which is only valid for one special case cannot claim general applicability. Interaction experiments with ultraviolet and ionizing radiation are discussed in this context. Also the role of different experimental systems (microorganisms versus mammalian cells) has to be taken into account. A number of current model approaches are discussed within this context, and it is shown that most of them do not satisfy the criterion of universal applicability and can therefore not claim to give a 'true' picture of biological reality. Shouldered survival curves are taken as an example to illustrate these points in a more specific way.

Animals↗
PubMed2005

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

Quantitative free energy computation involves both using a model that is sufficiently faithful to the experimental system under study (accuracy) and establishing statistically meaningful measures of the uncertainties resulting from finite sampling (precision). In order to examine the accuracy of a range of common water models used for protein simulation for their solute/solvent properties, we calculate the free energy of hydration of 15 amino acid side chain analogs derived from the OPLS-AA parameter set with the TIP3P, TIP4P, SPC, SPC/E, TIP3P-MOD, and TIP4P-Ew water models. We achieve a high degree of statistical precision in our simulations, obtaining uncertainties for the free energy of hydration of 0.02-0.06 kcal/mol, equivalent to that obtained in experimental hydration free energy measurements of the same molecules. We find that TIP3P-MOD, a model designed to give improved free energy of hydration for methane, gives uniformly the closest match to experiment; we also find that the ability to accurately model pure water properties does not necessarily predict ability to predict solute/solvent behavior. We also evaluate the free energies of a number of novel modifications of TIP3P designed as a proof of concept that it is possible to obtain much better solute/solvent free energetic behavior without substantially negatively affecting pure water properties. We decrease the average error to zero while reducing the root mean square error below that of any of the published water models, with measured liquid water properties remaining almost constant with respect to our perturbations. This demonstrates there is still both room for improvement within current fixed-charge biomolecular force fields and significant parameter flexibility to make these improvements. Recent research in computational efficiency of free energy methods allows us to perform simulations on a local cluster that previously required large scale distributed computing, performing four times as much computational work in approximately a tenth of the computer time as a similar study a year ago.

Amino Acids↗
PubMed2006

A quantitative kinetic model for ATP-induced intracellular Ca2+ oscillations.

A quantitative kinetic model is proposed to simulate the ATP-induced intracellular Ca(2+) oscillations. The quantitative effect of ATP concentration upon the oscillations was successfully simulated. Our simulation results support previous experimental explanations that the Ca(2+) oscillations are mainly due to interaction of Ca(2+) release from the endoplasmic reticulum (ER) and the ATP-dependent Ca(2+) pump back into the ER, and the oscillations are prolonged by extracellular Ca(2+) entry that maintains the constant Ca(2+) supplies to its intracellular stores. The model is also able to simulate the sudden disappearance phenomenon of the Ca(2+) oscillations observed in some cell types by taking into account of the biphasic characteristic of the Ca(2+) release from the endoplasmic reticulum (ER). Moreover, the model simulation results for the Ca(2+) oscillations characteristics such as duration, peak [Ca(2+)](cyt), and average interval, etc., lead to prediction of some possible factors responsible for the variations of Ca(2+) oscillations in different types of cells.

Adenosine Triphosphate↗
PubMed2005

Quantifying hydrogen bonding in QSAR and molecular modeling.

Quantitative descriptions of hydrogen bonding for use in QSAR and molecular modeling by means of H-bond descriptors have been analyzed in detail in this paper. Ten new H-bond surface and enthalpy integral descriptors were proposed. The usefulness of these new descriptors, as well as previously developed descriptors was verified using a set of 154 drugs for which data for intestinal absorption in humans were available. The results showed that descriptors such as the number of H-bond acceptor and donor atoms and polar surface area (PSA) did not sufficiently describe the actual H-bonding ability of atoms in molecules. Thus, to enable successful modeling it was necessary to introduce descriptors directly related to the experimental thermodynamics of hydrogen bonding.

Humans↗
PubMed2006

Predicting solubility of anthracene in non-aqueous solvent mixtures using a combination of Jouyban-Acree and Abraham models.

Quantitative structure property relationships were proposed to calculate the binary interaction terms of the Jouyban-Acree model using coefficients of Abraham solvational models. The applicability of the proposed methods for reproducing solubility data of anthracene in binary solvents has been evaluated using 56 solubility data sets collected from the literature. The mean percentage deviation (MPD) of experimental and calculated solubilities, using predicted mole fraction solubility of anthracene in solvents 1 and 2, has been computed as a measure of accuracy and the MPD of the proposed methods were 5.5 and 4.2%. The accuracy of the method was compared with that of a previously reported method where the MPD was 14.4% and the mean differences between proposed and previous methods was statistically significant. To provide a predictive model, solubility of anthracene was computed using Abraham solvational models and employed to predict the solubility in binary solvents using derived model constants of Jouyban-Acree model and the obtained MPDs were 37.9 and 22.2%, respectively.

Algorithms↗
PubMed2025

A single-locus quantitative genetic model incorporating DNA methylation.

We describe a single-locus quantitative genetic model that incorporates effects due to DNA methylation. Extending Fisher's decomposition of the genotypic value, we distinguish two quantities to predict an individual's phenotypic or genetic values: the "basic genetic value" and the "expressed genetic value". We show how these quantities relate to the concept of breeding value and derive their corresponding formulas, along with those for phenotypic variance and covariance between relatives. The resulting parameters are influenced by several factors, including the population distribution of DNA methylation levels, the functional relationship between methylation and phenotype, the magnitudes of genetic and methylation effects, and allele frequencies. We show that under the conditions modeled, the presence of DNA methylation does not bias estimated breeding values.

DNA Methylation↗
PubMed1994

Developmental quantitative genetic models of evolutionary change.

Discussions about evolutionary change in developmental processes or morphological structures are predicated on specific quantitative genetic models whose parameters predict whether evolutionary change can occur, its relative rate and direction, and if correlated change will occur in other related and unrelated structures. The appropriate genetic model should reflect the relevant genetical and developmental biology of the organisms, yet be simple enough in its parameters so that deductions can be made and hypotheses tested. As a consequence, the choice of the most appropriate genetic model for polygenically controlled traits is a complex tissue and the eventual choice of model is often a compromise between completeness of the model and computational expediency. Herein, we discuss several developmental quantitative genetic models for the evolution of development and morphology. The models range from the classical direct effects model to complex epigenetic models. Further, we demonstrate the algebraic equivalency of the Cowley and Atchley epigenetic model and Wagner's developmental mapping model. Finally, we propose a new multivariate model for continuous growth trajectories. The relative efficacy of these various models for understanding evolutionary change in developmental and morphological traits is discussed.

Animals↗
PubMed2001

Development of a generalized, quantitative physicochemical model of CYP3A4 inhibition for use in early drug discovery.

PURPOSE: To examine the structure-activity relationships for the inhibition of the activity of recombinant human CYP3A4 and to establish a generalized, quantitative physicochemical model for use in early drug discovery. METHODS: Inhibition of the activity of recombinant human CYP3A4 (erythromycin N-demethylase) by 30 diverse chemicals was studied using enhanced throughput methodology. RESULTS: There was a general, strong correlation between the IC50 value determined against erythromycin N-demethylase activity and lipophilicity (LogD7.4) (r2 = 0.68, p <0.0001). This relationship was strengthened further by subdividing the structures studied into two distinct subpopulations of chemistry within the dataset. These could be identified by the absence (r2 = 0.80, p <0.0001) or presence (r2 = 0.69, p <0.0001) of a sterically uninhindered N-containing heterocycle, more specifically a pyridine, imidazole, of triazole function. The presence of these structural motifs increased the potency of CYP3A4 inhibition by approximately 10-fold for a given lipophilicity (LogD7.4.value). More detailed analyses of AstraZeneca compounds demonstrated that the inhibitory potency of the pyridine structure can be attenuated through direct steric effects or electronic substitution resulting in a modulation of the pKa of the pyridine nitrogen, thereby influencing its ability to interact with the CYP heme. CONCLUSIONS: A generalized, quantitative model is proposed for the inhibition of the major drug metabolizing enzyme, CYP3A4. This model indicates the importance of lipophilicity and rationalizes increased potency arising through additional interactions with the heme iron. These general relationships were shown to be applicable to a selection of compounds of interest to several early research projects.

Algorithms↗
PubMed1988

A model for quantitation of peritumoral brain edema.

A model system is described which is suitable for quantitation of peritumoral brain edema. The temporal development of peritumoral brain edema in dexamethasone-treated rabbits and untreated controls was evaluated following the implantation of VX2 carcinoma cells into the frontal lobe of New Zealand White rabbits. A colorimetric assay of Evans blue (EB) extravasation was used to quantitate edema. Animals receiving a sham tumor injection contained an equal amount of EB compared to control animals. Dexamethasone was found to significantly reduce the extravasation of EB in rabbits with VX2 brain tumors and to delay the onset of neurologic deficits. These results are consistent with events occurring in patients with brain tumors. Studies of new drugs or physiologic aspects of peritumoral edema can be conducted with this model system.

Animals↗
PubMed2005

A poultry-processing model for quantitative microbiological risk assessment.

A poultry-processing model for a quantitative microbiological risk assessment (QMRA) of campylobacter is presented, which can also be applied to other QMRAs involving poultry processing. The same basic model is applied in each consecutive stage of industrial processing. It describes the effects of inactivation and removal of the bacteria, and the dynamics of cross-contamination in terms of the transfer of campylobacter from the intestines to the carcass surface and the environment, from the carcasses to the environment, and from the environment to the carcasses. From the model it can be derived that, in general, the effect of inactivation and removal is dominant for those carcasses with high initial bacterial loads, and cross-contamination is dominant for those with low initial levels. In other QMRA poultry-processing models, the input-output relationship between the numbers of bacteria on the carcasses is usually assumed to be linear on a logarithmic scale. By including some basic mechanistics, it is shown that this may not be realistic. As nonlinear behavior may affect the predicted effects of risk mitigations; this finding is relevant for risk management. Good knowledge of the variability of bacterial loads on poultry entering the process is important. The common practice in microbiology to only present geometric mean of bacterial counts is insufficient: arithmetic mean are more suitable, in particular, to describe the effect of cross-contamination. The effects of logistic slaughter (scheduled processing) as a risk mitigation strategy are predicted to be small. Some additional complications in applying microbiological data obtained in processing plants are discussed.

Algorithms↗
PubMed1985

Quantitative genetic models of female choice based on "arbitrary" male characters.

Multivariate, quantitative genetic models are developed for the evolution of female mating preferences in situations where males contribute only their gametes to their progeny. Although female mating preferences may not be directly subject to selection, they can evolve via genetic correlations with other characters that are undergoing evolutionary change. The first set of models examines the evolutionary origin of mating preferences directed at one or more traits that may or may not be expressed only in males. When several selected characters possess additive genetic variance, an indirect selective force exists for the evolution of multivariate mating preferences. The magnitude of this force is proportional to the covariance between a female's relative preference for a given male's phenotype and the expected viability of his progeny. The contribution of any single character to this covariance determines its potential value as a mate choice criterion. The pattern of genetic and phenotypic covariation may cause selectively unimportant traits to be useful in mate choice. In the extreme, selectively neutral characters may become the objects of mating preferences, if they are relatively immune to random environmental variation and genetically correlated with selectively important characters. The second set of models examines the dynamic evolution of such a selectively neutral ("arbitrary") character that is both the object of a mating preference and genetically correlated with a third trait that affects viability. The outcome of evolution in this three character system is highly indeterminate. As in other sexual selection models, there exists a line of neutral equilibria wherein the mean of the criterion character matches the mean level of mating preference within the population, while the viability trait equilibrates at the phenotypic value conferring maximum viability. This line of equilibria, however, is not likely to be stable unless females choose mates according to absolute mating preferences. Thus, mating preferences that initially may arise as a mean of increasing offspring viability may nevertheless lead to indeterminate and potentially maladaptive evolutionary outcomes.

Animals↗
PubMed2005

Minimum information requested in the annotation of biochemical models (MIRIAM).

Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The lack of a standard description format, lack of stringent reviewing and authors' carelessness are the main causes for incomplete model descriptions. With today's increased interest in detailed biochemical models, it is necessary to define a minimum quality standard for the encoding of those models. We propose a set of rules for curating quantitative models of biological systems. These rules define procedures for encoding and annotating models represented in machine-readable form. We believe their application will enable users to (i) have confidence that curated models are an accurate reflection of their associated reference descriptions, (ii) search collections of curated models with precision, (iii) quickly identify the biological phenomena that a given curated model or model constituent represents and (iv) facilitate model reuse and composition into large subcellular models.

Biochemistry↗
PubMed2004

Pharmacological manipulations of ATP-dependent potassium channels and adenosine A1 receptors do not impact hippocampal ischemic preconditioning in vivo: evidence in a highly quantitative gerbil model.

Ischemic preconditioning models have been characterized in brain, heart, and other tissues, and previous pharmacologic studies have suggested an involvement of adenosine and ATP dependent potassium (KATP) channels in such tolerance phenomena. This question was reexamined in a reproducible gerbil model in which the duration of ischemic depolarization defined the severity of preconditioning and test insults. Agents studied were glibenclamide, a blocker of KATP channels; 1,3-dipropyl-8-cyclopentylxanthine (DPCPX), an adenosine A1 receptor antagonist; and N6-cyclopentyladenosine (CPA), an A1 agonist. Intraventricular glibenclamide injections aggravated neuron damage after brief priming insults, in parallel with a dose-dependent prolongation of ischemic depolarization. However, the depolarization thresholds for ischemic neuronal injury were identical in vehicle- and glibenclamide-treated animals, and glibenclamide did not affect preconditioning when equivalent insult severity was maintained during priming insults. Neither DPCPX nor CPA had any effect on the onset or duration of depolarization after intraperitoneal injection in this model, and neither drug affected neuron damage. In the case of CPA, it was necessary to maintain temperature for 4 to 6 hours of recirculation to avoid significant confounding hypothermia. These results fail to support a direct involvement of A1 receptors or KATP channels during early stages in the development of ischemic tolerance in vivo, and emphasize the need for robust, well-controlled, and quantitative models in such studies.

Adenosine↗
PubMed2006

A bottom-up approach to gene regulation.

The ability to construct synthetic gene networks enables experimental investigations of deliberately simplified systems that can be compared to qualitative and quantitative models. If simple, well-characterized modules can be coupled together into more complex networks with behaviour that can be predicted from that of the individual components, we may begin to build an understanding of cellular regulatory processes from the 'bottom up'. Here we have engineered a promoter to allow simultaneous repression and activation of gene expression in Escherichia coli. We studied its behaviour in synthetic gene networks under increasingly complex conditions: unregulated, repressed, activated, and simultaneously repressed and activated. We develop a stochastic model that quantitatively captures the means and distributions of the expression from the engineered promoter of this modular system, and show that the model can be extended and used to accurately predict the in vivo behaviour of the network when it is expanded to include positive feedback. The model also reveals the counterintuitive prediction that noise in protein expression levels can increase upon arrest of cell growth and division, which we confirm experimentally. This work shows that the properties of regulatory subsystems can be used to predict the behaviour of larger, more complex regulatory networks, and that this bottom-up approach can provide insights into gene regulation.

Arabinose↗
PubMedDate not supplied

Quantitative risk modeling in aseptic manufacture.

Expedient risk assessment of aseptic manufacturing processes offers unique opportunities for improved and sustained assurance of product quality. Contemporary risk assessments applied to aseptic manufacturing processes, however, are commonly handicapped by assumptions and subjectivity, leading to inexactitude. Quantitative risk modeling augmented with Monte Carlo simulations represents a novel, innovative, and more efficient means of risk assessment. This technique relies upon fewer assumptions and removes subjectivity to more swiftly generate an improved, more realistic, quantitative estimate of risk. The fundamental steps and requirements for an assessment of the risk of bioburden ingress into aseptically manufactured products are described. A case study exemplifies how quantitative risk modeling and Monte Carlo simulations achieve a more rapid and improved determination of the risk of bioburden ingress during the aseptic filling of a parenteral product. Although application of quantitative risk modeling is described here purely for the purpose of process improvement, the technique has far wider relevance in the assisted disposition of batches, cleanroom management, and the utilization of real-time data from rapid microbial monitoring technologies.

Algorithms↗