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At least 829 records · Page 46Linked to original sources

PubMed1989

Determination of enzyme or binding constants using generalized linear models, with particular reference to Michaelis-Menten models.

The estimation of Michaelis-Menten pharmacokinetic parameters in patients with epilepsy receiving phenytoin continues to be a vexing problem. The various approximate methods suggested in the literature have serious shortcomings, primarily due to the role of the error term in the statistical model. In this report we present an accurate statistical approach using the Generalized Linear Interactive Modeling (GLIM) computer package developed by the Numerical Algorithms Group, Oxford, U.K. There are several advantages to this model: a meaningful error term can be maintained by means of a link function, the model can incorporate within-subject and between-subject variables, and additional potential explanatory variables can be added to the model. The method is applied to predicting serum phenytoin levels of pregnant women monitored at monthly intervals during pregnancy and for two to five months after pregnancy. Michaelis-Menten parameters are estimated for each women and compared.

Adult↗

PubMed1992

A compartment model for percutaneous absorption: compatibility of lag time and steady-state flux with diffusion model.

The lag times and steady-state flux predicted by a specific case of the compartment model, which was recently proposed to generate finite-dose percutaneous permeation pharmacokinetics, are compared with those predicted by the diffusion model. When the intercompartmental transfer rate constants are defined so that the three statistical moments of the compartmental model (the mean residence times of a drug in the vehicle and that in the skin and the variance of residence time in the vehicle) are identical to those in the diffusion model, the lag times and steady-state flux values predicted by the two models are the same.

Animals↗

PubMed1996

Structure-based modeling of the ligand binding domain of the human cell surface receptor CD23 and comparison of two independently derived molecular models.

CD23, a type II membrane receptor protein, recognizes four different ligands via its extracellular C-type lectin domain: immunoglobulin E (IgE), CD21, and the beta 2-integrins CD11b and CD11c. CD23 specifically interacts in a calcium-dependent manner, "lectin-like" with carbohydrate moieties expressed on CD21 and CD11b/c, but also "lectin-unlike" with protein epitopes on IgE. As a first step in analyzing the multiple binding specificities associated with CD23 in more detail, we report a detailed molecular model of the lectin-like domain of human CD23 (hCD23). The model was built based on information provided by X-ray structures of mannose binding protein (MBP) and E-selectin, both of which are members of the calcium-dependent (C-type) lectin superfamily. Sequence-structure comparisons suggest that hCD23 is structurally more similar to MBP than to E-selectin. The hCD23 model is compared to an independently derived model. Although the CD23-carbohydrate and CD23-protein interactions are both calcium dependent, analysis of the model suggests the presence of distinct binding sites for these ligands.

Amino Acid Sequence↗

PubMed2003

The importance of explicit chain representation in protein folding models: an examination of Ising-like models.

A class of models that represents a protein chain as a sequence of "folded" and "unfolded" residues has recently been used to correlate rates and mechanisms of protein folding with the protein native structure. In order to better understand the conditions under which these "Ising-like" models apply, we compare results from this model to those obtained from an off-lattice model which uses the same potential function. We find that Ising-like models by construction impose folding via a highly sequential nucleation-condensation mechanism, which in turn leads to more rugged energy landscapes, fewer "pathways" to the native state, and in the specific case examined here, the cold shock protein A from Escherichia coli, a qualitative difference in the most likely order of events in folding.

Amino Acids↗

PubMed2003

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling.

We participated in the fold recognition and homology sections of CASP5 using primarily in-house software. The central feature of our structure prediction strategy involved the ability to generate good sequence-to-structure alignments and to quickly transform them into models that could be evaluated both with energy-based methods and manually. The in-house tools we used include: a) HMAP (Hybrid Multidimensional Alignment Profile)-a profile-to-profile alignment method that is derived from sequence-enhanced multiple structure alignments in core regions, and sequence motifs in non-structurally conserved regions. b) NEST-a fast model building program that applies an "artificial evolution" algorithm to construct a model from a given template and alignment. c) GRASP2-a new structure and alignment visualization program incorporating multiple structure superposition and domain database scanning modules. These methods were combined with model evaluation based on all atom and simplified physical-chemical energy functions. All of these methods were under development during CASP5 and consequently a great deal of manual analysis was carried out at each stage of the prediction process. This interactive model building procedure has several advantages and suggests important ways in which our and other methods can be improved, examples of which are provided.

Algorithms↗

PubMed2004

Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.

The treatment of hydration effects in protein dynamics simulations varies in model complexity and spans the range from the computationally intensive microscopic evaluation to simple dielectric screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase. Molecular dynamics (MD) simulations were used to sample potential energy surfaces of the two basins with solvent treated by means of explicit and implicit methods. Implicit solvent methods studied include the generalized Born (GB) model, atomic solvation potential (ASP), and the distance-dependent dieletric constant. By using the linear response approximation (LRA), the explicit solvent calculations determined a free-energy difference that is in excellent agreement with the experimental estimate, while rescoring the protein conformations with GB or the Poisson equation showed inconsistent and inferior results. While the approach of rescoring conformations from explicit water simulations with implicit solvent models is popular among many applications, it perturbs the energy landscape by changing the solvent contribution to microstates without conformational relaxation, thus leading to non-optimal solvation free energies. Calculations applying MD with a GB solvent model produced results of comparable accuracy as observed with LRA, yet the electrostatic free-energy terms were significantly different due to optimization on a potential energy surface favored by an implicit solvent reaction field. The simpler methods of ASP and the distance-dependent scaling of the dielectric constant both produced considerable distortions in the protein internal free-energy terms and are consequently unreliable.

Acetylcholinesterase↗

PubMed1995

Homology modeling of histidine-containing phosphocarrier protein and eosinophil-derived neurotoxin: construction of models and comparison with experiment.

Homology modeling methods have been used to construct models of two proteins--the histidine-containing phosphocarrier protein (HPr) from Mycoplasma capricolum and human eosinophil-derived neurotoxin (EDN). Comparison of the models with the subsequently determined X-ray crystal structures indicates that the core regions of both proteins are reasonably well reproduced, although the template structures are closer to the X-ray structures in these regions--possible enhancements are discussed. The conformations of most of the side chains in the core of HPr are well reproduced in the modeled structure. As expected, the conformations of surface side chains in this protein differ significantly from the X-ray structure. The loop regions of EDN were incorrectly modeled--reasons for this and possible enhancements are discussed.

Algorithms↗

PubMed2002

Selection models and pattern-mixture models to analyse longitudinal quality of life data subject to drop-out.

Longitudinally observed quality of life data with large amounts of drop-out are analysed. First we used the selection modelling framework, frequently used with incomplete studies. An alternative method consists of using pattern-mixture models. These are also straightforward to implement, but result in a different set of parameters for the measurement and drop-out mechanisms. Since selection models and pattern-mixture models are based upon different factorizations of the joint distribution of measurement and drop-out mechanisms, comparing both models concerning, for example, treatment effect, is a useful form of a sensitivity analysis.

Aged↗

PubMed2006

Repeated events survival models: the conditional frailty model.

Repeated events processes are ubiquitous across a great range of important health, medical, and public policy applications, but models for these processes have serious limitations. Alternative estimators often produce different inferences concerning treatment effects due to bias and inefficiency. We recommend a robust strategy for the estimation of effects in medical treatments, social conditions, individual behaviours, and public policy programs in repeated events survival models under three common conditions: heterogeneity across individuals, dependence across the number of events, and both heterogeneity and event dependence. We compare several models for analysing recurrent event data that exhibit both heterogeneity and event dependence. The conditional frailty model best accounts for the various conditions of heterogeneity and event dependence by using a frailty term, stratification, and gap time formulation of the risk set. We examine the performance of recurrent event models that are commonly used in applied work using Monte Carlo simulations, and apply the findings to data on chronic granulomatous disease and cystic fibrosis.

Algorithms↗

PubMedDate not supplied

Time series for modelling counts from a relapsing-remitting disease: application to modelling disease activity in multiple sclerosis.

Many chronic diseases are relapsing-remitting diseases, in which subjects alternate between periods with increasing and decreasing disease activity; relapsing-remitting multiple sclerosis is an example. This paper proposes two classes of models for sequences of counts observed from a relapsing-remitting disease. In the first, the relapsing-remitting nature of the data is modelled by a Poisson time series with a periodic trend in the mean. In this approach, the mean is expressed as a function of a sinusoidal trend and past observations of the time series. An algorithm that uses GLIM is developed, and it results in maximum-likelihood estimation for the amplitude, frequency and autoregressive effects. In the second class of models, the relapsing-remitting behaviour is described by a Poisson time series in which changes in the mean follow a latent Markov chain. An EM algorithm is developed for maximum-likelihood estimation for this model. The two models are illustrated and compared with data from a study evaluating the use of serial magnetic resonance imaging as a measure of disease activity in relapsing-remitting multiple sclerosis.

Algorithms↗

PubMedDate not supplied

Inferring systemic exposure from a pharmacokinetic screen: model-free and model-based approaches.

To infer patterns of average systemic exposure and to estimate individual exposures in phase III clinical trials of a new anxiolytic, two statistical methodologies were applied and compared: non-linear mixed-effect modelling, and a model-free approach based on quartiles of dose-normalized plasma concentrations of the drug. Although the model-based approach provides more quantitative insight about relationships between average exposure and demographic covariates, the model-free approach provides qualitatively similar results about average clearance and quantitatively similar results about individual exposures, and the model-free approach is easy and inexpensive to implement.

Adult↗

PubMed2001

Immunohistochemical expression of molecular markers in an avian model: a potential model for preclinical evaluation of agents for ovarian cancer chemoprevention.

OBJECTIVE: A significant obstacle confronting the evaluation of potential chemopreventive compounds in ovarian carcinoma is the absence of an animal model of spontaneous ovarian carcinogenesis. A potential model of adenocarcinoma has been described in the laying hen (Gallus domesticus). The purpose of this study was to evaluate the immunohistochemical expression of available antibodies that have been utilized in chemoprevention studies in this potential model of epithelial carcinoma. METHODS: Two hundred 2-year-old hens were sacrificed at Auburn University in accordance with IUACUC guidelines. Of these hens, 8 animals were thought grossly to have ovarian carcinoma and ascites. The tumors from these 8 hens were fixed in neutral-buffered formalin and processed to paraffin blocks. Hematoxylin and eosin stains were used to document the histologic presence of adenocarcinoma. Immunohistochemical evaluation for expression of antigen was performed using the following antibodies: CA125, CEA, cytokeratin, EGFR, erbB-2, Ki-67, Lewis Y, p27, PCNA, Tag 72, TGF-alpha, Muc 1, and Muc 2. RESULTS: Upon microscopic examination by a pathologist eight specimens were documented as adenocarcinomas. Several antibodies to antigens that are frequently expressed in human ovarian cancer were cross-reactive in the laying hen. Of these, cytokeratin AE1/AE3, pan cytokeratin, EGFR, Lewis Y, CEA, Tag 72, and erbB-2 stained the chicken carcinomas. EGFR and p185erbB-2 stained diffusely, and cytokeratin AE1/AE3, pan cytokeratin, Lewis Y, CEA, and Tag 72 were focally positive in the tumor. The aforementioned antibodies which have been useful as surrogate endpoints in chemoprevention trials and which also stained the chicken carcinomas included PCNA, p27, and TGF-alpha Antibodies that were not cross-reactive include CA 125, Ki-67, Muc 1, and Muc 2. CONCLUSION: The data presented in this pilot study support the potential utility of an avian model of spontaneously arising adenocarcinoma in which to study chemopreventive agents. More importantly, the influence of chemoprevention protocols on the expression of relevant antigens can be determined using available antibodies that are cross-reactive in this model. Thus, changes in the phenotypic expression of surrogate endpoint biomarkers as identified by cross-reactive antibodies can aid in the development of chemoprevention trials for human ovarian cancer.

Adenocarcinoma↗

PubMed2001

A biokinetic model to describe consequences of inhibition/stimulation in DNA-proofreading and repair-1. Development of the model.

A biokinetic model is described which deals with the mathematical consequences of the inhibition or stimulation of DNA proofreading. It demonstrates the development of the number of DNA mismatch-dependent cells (e.g. cells with a malignant phenotype), where such mismatches arise by the in situ interaction of various substances with nucleotides of the DNA. The model can test for consequences by a logic gating on an "if-then" type of analysis in relation to the separate and consecutive processes of proofreading and repair. In particular, the consequences are considered in cases where either (i) the efficacy of proofreading and repair are reduced/prevented (inhibited) or (ii) are increased by some form of stimulation. On the chosen kinetic parameters, the model is accessible to manipulation as new data arising from further investigations become available and are introduced. The model is based on recently published data which show that an increased "mutant fraction" (see note on terms) arises in DNA replication when intracellular nucleotide pools show "asymmetries" (see note on terms). Extraordinarily high mutant fractions can be predicted/have been recorded in the presence of proofreading inhibitors. The model expresses data in mathematical terms of the competition between the development of mismatch-dependent cells and those with authentic genetic information. (Feedback and metastasis-effects and those of wild-type replicates are included.) A computerized (numerical) integration of the corresponding set of differential equations is offered. (A diskette with the program CANCER.xls is available upon request.)

Animals↗

PubMed2005

Modelling motor cortex stimulation for chronic pain control: electrical potential field, activating functions and responses of simple nerve fibre models.

This computer modelling study on motor cortex stimulation (MCS) introduced a motor cortex model, developed to calculate the imposed electrical potential field characteristics and the initial response of simple fibre models to stimulation of the precentral gyrus by an epidural electrode, as applied in the treatment of chronic, intractable pain. The model consisted of two parts: a three-dimensional volume conductor based on tissue conductivities and human anatomical data, in which the stimulation-induced potential field was computed, and myelinated nerve fibre models allowing the calculation of their response to this field. A simple afferent fibre branch and three simple efferent fibres leaving the cortex at different positions in the precentral gyrus were implemented. It was shown that the thickness of the cerebrospinal fluid (CSF) layer between the dura mater and the cortex below the stimulating electrode substantially affected the distribution of the electrical potential field in the precentral gyrus and thus the threshold stimulus for motor responses and the therapeutic stimulation amplitude. When the CSF thickness was increased from 0 to 2.5 mm, the load impedance decreased by 28%, and the stimulation amplitude increased by 6.6 V for each millimetre of CSF. Owing to the large anode-cathode distance (10 mm centre-to-centre) in MCS, the cathodal fields in mono- and bipolar stimulation were almost identical. Calculation of activating functions and fibre responses showed that only nerve fibres with a directional component parallel to the electrode surface were excitable by a cathode, whereas fibres perpendicular to the electrode surface were excitable under an anode.

Chronic Disease↗

PubMed2002

A conceptual model for defining and assessing land management units using a fuzzy modeling approach in GIS environment.

Appropriate land management decisions are important for current and future use of the land to ensure its sustainability. This requires that land management units (LMUs) be specified to enable the identification of specific parameters employed in decision making processes. This paper presents the development of a conceptual model, within geographic information systems (GIS), for defining and assessing LMUs from available biophysical information. The model consists of two main components (sub-models): land quality-based suitability analysis and soil erosion estimation. Using a fuzzy set methodology, the first sub-model was constructed to derive a land suitability index (LSI) for a cropping land utilization type. The LSI thus highlights the suitability grades of every pixel in the study area on a continuous basis. A submodel of soil erosion was established based on the Revised Universal Soil Loss Equation (RUSLE) utilising the same spatial data bases employed for structuring the LSI. Using a soil loss tolerance principle, a fuzzy membership function of average annual soil loss (called soil loss index, SLI) was established, leading to compatibility between LSI and SLI for data integration. LMUs were then derived from various combinations of LSI and SLI. The methodology developed shows the significance of the model for refining available land suitability evaluation systems, which take no account of expected land degradation (from erosion) due to a nominated land use. It also provides a valuable guideline for cost-effective GIS applications in the identification and assessment of homogeneous land units, using available spatial information sets, at a finer scale.

Conservation of Natural Resources↗

PubMed2004

A new interpretation of the Keller-Segel model based on multiphase modelling.

In this paper an alternative derivation and interpretation are presented of the classical Keller-Segel model of cell migration due to random motion and chemotaxis. A multiphase modelling approach is used to describe how a population of cells moves through a fluid containing a diffusible chemical to which the cells are attracted. The cells and fluid are viewed as distinct components of a two-phase mixture. The principles of mass and momentum balance are applied to each phase, and appropriate constitutive laws imposed to close the resulting equations. A key assumption here is that the stress in the cell phase is influenced by the concentration of the diffusible chemical. By restricting attention to one-dimensional cartesian geometry we show how the model reduces to a pair of nonlinear coupled partial differential equations for the cell density and the chemical concentration. These equations may be written in the form of the Patlak-Keller-Segel model, naturally including density-dependent nonlinearities in the cell motility coefficients. There is a direct relationship between the random motility and chemotaxis coefficients, both depending in an inter-related manner on the chemical concentration. We suggest that this may explain why many chemicals appear to stimulate both chemotactic and chemokinetic responses in cell populations. After specialising our model to describe slime mold we then show how the functional form of the chemical potential that drives cell locomotion influences the ability of the system to generate spatial patterns. The paper concludes with a summary of the key results and a discussion of avenues for future research.

Body Patterning↗

PubMed1997

Artificial implementation of auditory neurons: a comparison of biologically motivated models and a new transfer function oriented model.

Auditory perception neurons, also called inner hair cells (IHCs) because of their physical shape, transform the mechanical movements of the basilar membrane into electrical impulses. The impulse coding of the IHC is the main information carrier in the auditory process and is the basis for improvements in cochlear implants as well as for low-rate, high-quality speech processing and compression. This paper compares biologically motivated models (Meddis, Cooke, Payton) with a newly developed model which is transfer function oriented. The new model has only three reservoirs and the parameters can be controlled through five small ROM tables. This model is compared with the often used Meddis model in terms of accuracy, system parameter flexibility, and hardware effort in an FPGA implementation.

Auditory Pathways↗

PubMed2006

Melanin granule models for the processes of laser-induced thermal damage in pigmented retinal tissues. I. Modeling of laser-induced heating of melanosomes and selective thermal processes in retinal tissues.

The computer modeling was applied for investigation of the processes of laser-induced tissue damage. The melanin granule models for the processes of laser-induced thermal damage and the results of computer modeling of the optical, thermophysical, and thermochemical processes during selective laser interaction with melanoprotein granules (melanosomes) in retinal pigment epithelium are presented in this paper. Physical-mathematical model and system of equations are formulated which describe thermal interaction processes for "short" laser pulses of duration t (p)<10(-6) s and for " long' pulses of duration t(p) > 10(-6) s. Results of numerical simulation of the processes give the space-time distributions of temperature and degrees of thermodenaturation of the protein molecules inside and around melanosomes and in the volume of irradiated tissues. Energy absorption, heat transfer and thermochemical (thermodenaturation, coagulation) processes occurring during the interaction of laser pulses with pigmented spherical and spheroidal granules in heterogeneous tissues are theoretically investigated. The possibility for selective interaction of short laser pulses with pigmented granules is discussed which results in the formation of denaturation microregions inside and near the pigmented granules (granular thermodenaturation) without origination of a continuous macroscopic thermodenaturation lesion in tissue. Analytical model of heating of single spherical and spheroidal granule under laser pulse is presented. Simple equations for time dependencies of particle temperature are obtained. The presented results are of essential interest for laser applications in and can be used for investigation of laser interaction with pigmented tissues in different fields of laser medicine.

Computer Simulation↗