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At least 847 records · Page 47Linked to original sources
PubMed1993

Characteristics of endogenous peptides eluted from the class I MHC molecule HLA-B7 determined by mass spectrometry and computer modeling.

Microcapillary HPLC electrospray ionization tandem mass spectrometry was used to sequence 15 peptides eluted from HLA-B7. Sequence alignment implicated four peptide positions in specific interactions with the class I molecule, and their importance was confirmed using synthetic peptides. Because no crystal structure for HLA-B7 was available, computer-assisted modeling was used to understand novel aspects of peptide binding specificity and to accurately predict the effect of defined changes in peptide structure. The results demonstrate that mass-spectrometric sequencing coupled with computer-assisted modeling can be used in the absence of a crystal structure to make accurate predictions concerning requirements for peptide binding to class I molecules. These techniques may be valuable to predict or engineer T cell epitopes.

Amino Acid Sequence↗
PubMed1999

A computer model of myocardial disarray in simulating ECG features of hypertrophic cardiomyopathy.

Hypertrophic cardiomyopathy (HCM) was simulated with a computer heart model having a realistic shape and rotating fiber orientation in order to elucidate possible mechanisms for abnormal ECG findings. The disarray of myocardial muscle in HCM was simulated by assigning random fiber direction and isotropic electrophysiologic properties to abnormal hypertrophic regions, in contrast to the anisotropic modeling for normal myocardium. With these models, main ECG features including abnormal Q wave and QS pattern were reproduced and were comparable with clinical findings. This study suggests that the change in anisotropy in the hypertrophic myocardium is likely to be the main factor responsible to the ECG features of HCM.

Anisotropy↗
PubMed2002

Cysteine mutagenesis and computer modeling of the S6 region of an intermediate conductance IKCa channel.

Cysteine-scanning mutagenesis (SCAM) and computer-based modeling were used to investigate key structural features of the S6 transmembrane segment of the calcium-activated K(+) channel of intermediate conductance IKCa. Our SCAM results show that the interaction of [2-(trimethylammonium)ethyl] methanethiosulfonate bromide (MTSET) with cysteines engineered at positions 275, 278, and 282 leads to current inhibition. This effect was state dependent as MTSET appeared less effective at inhibiting IKCa in the closed (zero Ca(2+) conditions) than open state configuration. Our results also indicate that the last four residues in S6, from A283 to A286, are entirely exposed to water in open IKCa channels, whereas MTSET can still reach the 283C and 286C residues with IKCa maintained in a closed state configuration. Notably, the internal application of MTSET or sodium (2-sulfonatoethyl) methanethiosulfonate (MTSES) caused a strong Ca(2+)-dependent stimulation of the A283C, V285C, and A286C currents. However, in contrast to the wild-type IKCa, the MTSET-stimulated A283C and A286C currents appeared to be TEA insensitive, indicating that the MTSET binding at positions 283 and 286 impaired the access of TEA to the channel pore. Three-dimensional structural data were next generated through homology modeling using the KcsA structure as template. In accordance with the SCAM results, the three-dimensional models predict that the V275, T278, and V282 residues should be lining the channel pore. However, the pore dimensions derived for the A283-A286 region cannot account for the MTSET effect on the closed A283C and A286 mutants. Our results suggest that the S6 domain extending from V275 to V282 possesses features corresponding to the inner cavity region of KcsA, and that the COOH terminus end of S6, from A283 to A286, is more flexible than predicted on the basis of the closed KcsA crystallographic structure alone. According to this model, closure by the gate should occur at a point located between the T278 and V282 residues.

Animals↗
PubMedDate not supplied

Only two-phase models, computed independently for males and females, are appropriate to describe fetal head growth.

OBJECTIVE: To establish an accurate mathematical model describing fetal head growth, taking into account gender differences and changes in growth rate during gestation. METHODS: Ultrasound measurements of head circumference and biparietal diameter were made on 1,336 normal fetuses (684 males and 652 females) in the Maternité Régionale de Nancy (France). A new two-phase model, taking into account an alteration in growth kinetics at 30 gestational weeks, was computed independently for male and female data. The accuracy of this model was tested and compared with three current mathematical models: a linear-quadratic, a linear-cubic, and the Rossavik and Deter (1984) models. RESULTS: In all models, including ours, the coefficients of determination (R(2)) were high (> or =0.999), so long as male and female data were computed separately. However, the standard error estimates (SEE) of our two-phase model were much lower (0.13 < or = SEE < or = 0.57) than the SEE of the three other models when computed over the whole gestational period (0.49 < or = SEE < or = 2.69); nevertheless, when these three other models were computed for these two successive periods, their SEE decreased, and data fitting was improved. CONCLUSION: Only two-phase mathematical models, computed independently for male and female data, accurately describe the kinetics of fetal head growth. They should be used to calculate growth standards and to perform an exact diagnosis of impaired growth.

Cephalometry↗
PubMedDate not supplied

[Computer model of a human body].

The theory of combined designing was made use of to construct a global computer-based model of human organism--it provides for determining different treatment schemes, it can be used to define negative side-effects of treatment and it helps the doctor in choosing a more rational therapy technique for an actual patient.

Decision Making, Computer-Assisted↗
PubMed1992

A computational model of four regions of the cerebellum based on feedback-error learning.

We propose a computationally coherent model of cerebellar motor learning based on the feedback-error-learning scheme. We assume that climbing fiber responses represent motor-command errors generated by some of the premotor networks such as the feedback controllers at the spinal-, brain stem- and cerebral levels. Thus, in our model, climbing fiber responses are considered to convey motor errors in the motor-command coordinates rather than in the sensory coordinates. Based on the long-term depression in Purkinje cells each corticonuclear microcomplex in different regions of the cerebellum learns to execute predictive and coordinative control of different types of movements. Ultimately, it acquires an inverse model of a specific controlled object and complements crude control by the premotor networks. This general model is developed in detail as a specific neural circuit model for the lateral hemisphere. A new experiment is suggested to elucidate the coordinate frame in which climbing fiber responses are represented.

Animals↗
PubMed1990

Effect on a cariogenic challenge of saliva/plaque exchange via a thin salivary film studied by mathematical modelling.

Computer models can be powerful tools for studying complex interacting processes. The computer model of events in dental plaque during a cariogenic challenge described here simulates diffusion and metabolism of substrate, plus coupled diffusion/reaction of fourteen other species, charged and uncharged, including acidic metabolic products and fixed buffers. Its extension to deal with the effects of poor contact with bulk saliva when the plaque is presumed covered by a thin salivary film is here considered. Site-specific mixing rates between film and salivary pool were modelled phenomenologically, using data from the literature. Fast mixing was assumed during an initial carbohydrate intake phase (2 min sugar rinse), followed by site-dependent mixing and logarithmic clearance. The analysis also suggested a possible way of estimating local salivary film thickness. Increasing the halving time for exchange between film and bulk saliva was shown to prolong the pH minimum greatly, and to increase mineral loss. The respective roles of fixed buffers as stores of protons and of mobile buffers (especially bicarbonate) as exporters of protons from the inner plaque were emphasised.

Buffers↗
PubMed2001

Information transfer in metabolic pathways. Effects of irreversible steps in computer models.

Various metabolic models have been studied by computer simulation in an effort to understand why allowing for the reversibility of the reaction catalysed by pyruvate kinase, normally considered as irreversible for all practical purposes, significantly altered the behaviour of the model of glycolysis in Trypanosoma brucei [Eisenthal, R. & Cornish-Bowden, A. (1998) J. Biol. Chem. 273, 5500-5505]. Studies of several much simpler models indicate that the enzymes catalysing early steps in a pathway must receive information about the concentrations of the metabolites at the end of the pathway if a model is to be able to reach a steady state; treating all internal steps as reversible is just one way of ensuring this. Feedback inhibition provides a much better way, and as long as feedback loops are present in a model it makes almost no difference to the behaviour whether the intermediate steps with large equilibrium constants are treated as irreversible. In the absence of feedback loops, ordinary product inhibition of all the enzymes in the chain can also transfer information; this is efficient for regulating fluxes but very inefficient for regulating intermediate concentrations. More complicated patterns of regulation, such as activation of a competing branch or forcing flux through a parallel route, can also serve to some degree as ways of passing information around an irreversible step. However, they normally do so less efficiently than inhibition, because the extent to which an enzyme or a pathway can be activated always has an upper limit (which may be below what is required), whereas most enzymes are inhibited completely at saturating concentrations of inhibitor.

Animals↗
PubMed2004

A computational model of a class of gene networks with positive and negative controls.

This article proposes a computational framework for modelling the logical behavior of a class of gene networks. We characterize the basic behavior of genes in terms of a state-and-transition structure, and model the individual genes as language-generating automata. We consider positive and negative controls as the interaction mechanisms among the genes, and treat such controls as constraints (also expressed in automata) imposed on the behavior of the gene network. By computing the intersection of the languages generated by the gene models and the constraints, we obtain the complete set of pathways in a gene network. Implications and possible improvement of this work are discussed.

Computational Biology↗
PubMed2004

Human respiratory tract cancer risks of inhaled formaldehyde: dose-response predictions derived from biologically-motivated computational modeling of a combined rodent and human dataset.

Formaldehyde inhalation at 6 ppm and above causes nasal squamous cell carcinoma (SCC) in F344 rats. The quantitative implications of the rat tumors for human cancer risk are of interest, since epidemiological studies have provided only equivocal evidence that formaldehyde is a human carcinogen. Conolly et al. (Toxicol. Sci. 75, 432-447, 2003) analyzed the rat tumor dose-response assuming that both DNA-reactive and cytotoxic effects of formaldehyde contribute to SCC development. The key elements of their approach were: (1) use of a three-dimensional computer reconstruction of the rat nasal passages and computational fluid dynamics (CFD) modeling to predict regional dosimetry of formaldehyde; (2) association of the flux of formaldehyde into the nasal mucosa, as predicted by the CFD model, with formation of DNA-protein cross-links (DPX) and with cytolethality/regenerative cellular proliferation (CRCP); and (3) use of a two-stage clonal growth model to link DPX and CRCP with tumor formation. With this structure, the prediction of the tumor dose response was extremely sensitive to cell kinetics. The raw dose-response data for CRCP are J-shaped, and use of these data led to a predicted J-shaped dose response for tumors, notwithstanding a concurrent low-dose-linear, directly mutagenic effect of formaldehyde mediated by DPX. In the present work the modeling approach used by Conolly et al. (ibid.) was extended to humans. Regional dosimetry predictions for the entire respiratory tract were obtained by merging a three-dimensional CFD model for the human nose with a one-dimensional typical path model for the lower respiratory tract. In other respects, the human model was structurally identical to the rat model. The predicted human dose response for DPX was obtained by scale-up of a computational model for DPX calibrated against rat and rhesus monkey data. The rat dose response for CRCP was used "as is" for the human model, since no preferable alternative was identified. Three sets of baseline parameter values for the human clonal growth model were obtained through separate calibrations against respiratory tract cancer incidence data for nonsmokers, smokers, and a mixed population of nonsmokers and smokers, respectively. Additional risks of respiratory tract cancer were predicted to be negative up to about one ppm for all three cases when the raw CRCP data from the rat were used. When a hockey-stick-shaped model was fit to the rat CRCP data and used in place of the raw data, positive maximum likelihood estimates (MLE) of additional risk were obtained. These MLE estimates were lower, for some comparisons by as much as 1,000-fold, than MLE estimates from previous cancer dose-response assessments for formaldehyde. Breathing rate variations associated with different physical activity levels did not make large changes in predicted additional risks. In summary, this analysis of the human implications of the rat SCC data indicates that (1) cancer risks associated with inhaled formaldehyde are de minimis (10(-6) or less) at relevant human exposure levels, and (2) protection from the noncancer effects of formaldehyde should be sufficient to protect from its potential carcinogenic effects.

Animals↗
PubMed1993

Description of a computer model of forest onchocerciasis transmission and its application to field scenarios of vector control and chemotherapy.

This paper describes a computer simulation model for onchocerciasis (SIMON). Using epidemiological and entomological data from a specific hyperendemic village in the forest area of Sierra Leone, the model is used to examine the effect of vector and chemotherapeutic control strategies, both separately and in combination, as well as the risk to an uninfected population caused by immigrant, infected Simulium damnosum and humans. The model suggests that, in this village, the human population of about 420 requires an average annual input of about 200 mature fecund, female Onchocerca volvulus per year to maintain a skin-snip prevalence of just under 70%. SIMON also predicts that 99% effective vector control would lead to eradication of all adult worms in 18 years, and that abandoning control before 14 years could lead to recrudescence. Chemotherapy with ivermectin at six-month intervals reaching 90% of eligible persons (effective 66%) might take 29 years to achieve eradication because of continuing transmission, particularly in the early years, but it would probably be possible to abandon treatments after 18 years because the residual worm population would no longer be self-sustaining. Combined ivermectin and vector control, both at reduced levels, could be as effective as 99% vector control. Immigrant infected flies are likely to pose a greater threat to an uninfected human population than small numbers of infected persons. The model suggests that, at levels of infection undetectable by skin-snip, the parasite could linger in the human population for 30 or more years sustained by sporadic transmission.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed1986

Characterization of two classes of cardiac glycosine binding sites in rat heart and brain membrane preparations, using quantitative computer modelling.

Cardiac glycoside binding to rat heart and brain membrane preparations was measured by a rapid filtration technique. Data were analysed using quantitative computer analysis. The experimental results were consistent with a model in which cardiac glycoside-specific binding occurs at two independent classes of sites. The high-affinity sites in heart membranes were characterized by dissociation constants (Kd) of 40, 50, and 61 nmol/l for ouabain, digoxin and digitoxin, respectively, and the lower-affinity sites were characterized by Kd of 2.3 mumol/l, 67 nmol/l and 71 nmol/l for ouabain, digoxin and digitoxin, respectively. Comparable results were obtained using brain membranes. Potassium ions inhibit [3H]-ouabain binding in a dose-dependent manner with an IC50 of 500 mumol/l. Quantitative computer modeling indicated that potassium inhibits ouabain binding to approximately the same extent at both classed of binding sites, consistent with the hypothesis that the two classes of binding sites for cardiac glycosides might be associated with the Na+K+-ATPase.

Animals↗
PubMed1993

A Computational Model of the Simplest Motor Program.

A computational procedure (program) is defined to generate control signals for the motoneuron pools of agonist and antagonist muscles that will move a limb segment from one stationary position to another. The program accounts for the ability to move different distances with different inertial loads and for the influence of instructions concerning movement speed and accuracy. These motor commands allow the program to produce EMG patterns as well as force and kinematic trajectories that are consistent with much of the data found in the literature of these movements. The program is premised on the notion that kinematically defined tasks are accomplished by programming commands to the motoneuron pools, based on only a few cognitively recognized kinematic and dynamic features of the task. Most of the features found in EMG and kinematic patterns can be considered consequences of the program's algorithmic procedures rather than specifically planned features of those movements.

Journal Article↗