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At least 973 records · Page 54Linked to original sources
PubMed1978

Characterization of increased synthesis of acute phase proteins from plasma concentration measurements: a system analysis of the ideal situation with use of computer simulation.

A method for characterizing the secretion of acute phase proteins in vivo from serial plasma concentration measurements is presented. By using a simple two-compartment model it was found that descriptive parameters could be derived from the time course of the increased plasma concentration of the protein. It was assumed that the secretion of an acute phase protein is adequately described by: (i) the start time t1; (ii) the end time t2; (iii) the magnitude of increased flux of the protein from synthetic sites to the extracellular space, described by a turnover index, S. The influence of sampling interval and analytical precision on the reliability of the estimated parameter values was investigated in the ideal situation by using computer simulation. It was found that informative estimates of the secretion rate of an acute phase protein could be obtained provided a fairly high analytical precision with a coefficient of variation less than or equal to 0.01 and using a sampling interval between 0.5--2 h.

Adrenocorticotropic Hormone↗
PubMed1979

Prediction of infarct size from serial CK determinations: evaluation by clinical studies and computer simulation.

To assess reduction of infarct size by therapeutic intervention, a high predictive accuracy is mandatory. The CK release in the circulation (CKr) was studied in 12 consecutive patients after uncomplicated myocardial infarction, admitted within 5 h after onset of symptoms. Despite improvement of existing methods, such as a more frequent sampling, CK-MB determination instead of total CK determination and use of a gamma-exponential instead of a log-normal curve-fitting technique, the correlation between CKr predicted from measurements within 7 h after the start of CK rise and CKr calculated after completion of the CK curve remained poor. Computer simulations were done to investigate measurement errors as a cause of this failure. Normally distributed noise, with standard deviations ranging from 0.2% to 8.0% of peak CK-MB, was added to the first points of an ideal gamma-exponential CK-MB curve and predictions were made from these "noisy" points. A small noise already produced a great variation in prediction: 0.8% noise resulted in a deviation of predicted CKr from calculated CKr ranging from --20 to +6%. It is concluded that adequate prediction of infarct size from serial CK determinations in the first 7 h after onset of the CK rise must fail if the precision of the biochemical determination is not less than 0.4%.

Clinical Enzyme Tests↗
PubMed1984

Decrease in the ability of CFU-s in shielded marrow to be recruited into cell cycle after multiple irradiations: experimental results and computer simulations.

Nine doses of 1.5 Gy given to mice with one shielded leg result in very similar perturbations in shielded marrow (CFU-s kinetics whatever the source of radiation (X or gamma rays). At the time of the ninth irradiation, the size of the shielded CFU-s compartment is reduced to 75% of control level. After 15 min it decreases to 47% and, 1 day later, remains below the pre-ninth irradiation level (62% of control level) in spite of two significant peaks of CFU-s in DNA synthesis, at 1 and 8 hr after the ninth irradiation. For acceptable fitting to experimental data, computer simulations make it necessary to assume that a fraction of shielded marrow CFU-s is not capable of entering the cell cycle after the treatment. This is not explainable by defects in the stimulators of CFU-s proliferation secreted by shielded haemopoietic tissue because their production and their efficacy are demonstrated to be normal after the nine exposures. The incomplete recovery of the shielded CFU-s pool from proliferating CFU-s can be attributed to a loss in CFU-s by differentiation at birth.

Animals↗
PubMed2005

Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases.

The use of computers to simulate the functions of complex biological macromolecules is essential to achieve a microscopic description of biological processes and to model and interpret experimental data. Here we apply theoretical computational approaches to investigate the fidelity of T7 DNA polymerase, divided into discrete steps that include contributions from substrate binding, pK(a) shifts, and rate constants for the PO bond-breaking and bond-making processes. We begin by defining the discrimination between right and wrong nucleotides in terms of the free energy landscape for the dNMP incorporation reaction. We then use the linear response approximation and the empirical valence bond methods to obtain converging results for the contribution of the binding and chemical steps to the overall fidelity. These approaches are successful in reproducing general trends in the observed polymerase incorporation fidelity. The calculations demonstrate the potential for further integration of theoretical and experimental studies to analyze high- and low-fidelity DNA polymerases.

Base Pairing↗
PubMed1985

Computer simulations indicate that electrical field effects contribute to the shape of the epileptiform field potential.

In the presence of convulsant drugs such as picrotoxin, neurons in the hippocampal-slice preparation generate synchronized depolarizing bursts. This synchrony occurs on a time scale of tens of milliseconds and is produced by excitatory synaptic interactions between neurons. The synaptic interactions themselves occur on a time scale of tens of milliseconds. The "epileptiform" local-field potential during such synchronized bursts is comb-shaped ("ringing"), whereas the field potential expected if action potentials in neighboring neurons were uncorrelated is noisy and not comb-shaped. This suggests that individual action potentials are locally synchronized on a time scale of 1 ms. We have previously shown, using computer simulations, that electrical interactions--mediated by currents flowing in the extracellular medium--can plausibly explain action-potential synchronization in experiments where chemical synapses are blocked. The present simulations demonstrate that electrical interactions can also account for action-potential synchronization--and thus the "ringing" shape of the field potential--during epileptiform bursts, where excitatory synapses are functional. The field potential is thus a modulating influence on, as well as a reflection of, underlying neuronal transmembrane events.

Action Potentials↗
PubMed2005

Uniform shear flow in dissipative gases: computer simulations of inelastic hard spheres and frictional elastic hard spheres.

In the preceding paper, we have conjectured that the main transport properties of a dilute gas of inelastic hard spheres (IHSs) can be satisfactorily captured by an equivalent gas of elastic hard spheres (EHSs), provided that the latter are under the action of an effective drag force and their collision rate is reduced by a factor (1+alpha)/2 (where alpha is the constant coefficient of normal restitution). In this paper we test the above expectation in a paradigmatic nonequilibrium state, namely, the simple or uniform shear flow, by performing Monte Carlo computer simulations of the Boltzmann equation for both classes of dissipative gases with a dissipation range 0.5 < or = alpha < or = 0.95 and two values of the imposed shear rate a. It is observed that the evolution toward the steady state proceeds in two stages: a short kinetic stage (strongly dependent on the initial preparation of the system) followed by a slower hydrodynamic regime that becomes increasingly less dependent on the initial state. Once conveniently scaled, the intrinsic quantities in the hydrodynamic regime depend on time, at a given value of alpha, only through the reduced shear rate a*(t) is proportional to a/square root(T(t)), until a steady state, independent of the imposed shear rate and of the initial preparation, is reached. The distortion of the steady-state velocity distribution from the local equilibrium state is measured by the shear stress, the normal stress differences, the cooling rate, the fourth and sixth cumulants, and the shape of the distribution itself. In particular, the simulation results seem to be consistent with an exponential overpopulation of the high-velocity tail. These properties are common to both the IHS and EHS systems. In addition, the EHS results are in general hardly distinguishable from the IHS ones if alpha approximately > 0.7, so that the distinct signature of the IHS gas (higher anisotropy and overpopulation) only manifests itself at relatively high dissipations.

Journal Article↗
PubMed1980

Infanticide and fertility among Eskimos: a computer simulation.

Until recently, certain Eskimo groups were reported to practice female infanticide in the belief that the time spent suckling a girl would delay the mother's next opportunity to bear a son, males being preferred to females because of their future role as providers in a hunting economy. From sex ratios in census data, rates of female infanticide of up to 66% for some groups have been inferred, leading some ethnographers to conclude that these groups were headed for extinction. Eskimo beliefs regarding the effects of infanticide on fertility, however, are in accord with the results of research on the relation of fertility and lactation: The cessation of lactation following infanticide would significantly shorten the expected interval until the next birth. Given this fact and available field data regarding the parameters of Eskimo population growth, the present computer simulation indicates that Eskimo populations could sustain a rate of 30% female infanticide and still survive. Higher reported rates are explained as the combined result of female infanticide plus the tendency of ethnographers to overestimate the ages of juvenile females relative to juvenile males.

Computers↗
PubMed1984

Theoretical models and computer simulations of neural learning systems.

It has been generally assumed for a long time that learning is accomplished in the central nervous system (CNS) by modifying strengths of ties between neurons. Various mechanisms may contribute to this process, but it is not known which are the specific mechanisms, and what are the rules by which they operate. Theoretical models, which are based on that general assumption are introduced. The purpose of the models is to suggest plausible ways by which learned information may be stored in the neural network, and be retrieved when it is needed. The networks in the models consist of four basic subunits, in accordance with identified units in the CNS: sensing, response, feeling, and control, plus association areas. The suggested operation rules are based on established operation rules of individual neurons, and assumed rules when neurons in groups are considered. Computer simulations are done, to check the consistency of the models, and to illustrate how they work. They simulate how an hypothetical kitten learns part of its environment, and show how relevant information may be stored and retrieved in its neuronal network. The suggested mechanisms could be examined in experiments, albeit not easy ones to conduct.

Animals↗
PubMed1995

Dynamics of family size and composition: a computer simulation study with reference to rural India.

"This study attempts to understand the dynamics that produce the persistent observation of a strong positive correlation between family size and extent of landholdings in predominantly agrarian economies [in India]. Such a correlation can arise from different types of demographic configurations including the rules of family formation. For example, big landholdings may be associated with large families, despite the lack of differentials across holdings of different size in fertility and mortality, simply because these families may remain undivided for long periods. In the absence of conclusive data to analyse this relationship in the Indian case, this study sets up a computer simulation model for studying the results of alternative demographic configurations."

Asia↗
PubMed1981

Computer simulation of protein self-association during small-zone gel filtration. Estimation of equilibrium constants.

A simulation is developed that qualitatively describes the small-zone-gel-filtration behaviour of a reversibly associating protein. The results reflect the dependence of the apparent molecular weight of a reversibly associating protein on the equilibrium constant (KD) and initial concentration of the protein as well as the column length. The behaviour of a protein on an individual column is characterized and thus a means is provided for estimation of KD. The procedure is extended to describe the behaviour of a mixture of two proteins capable of heterologous as well as homologous association. This computer simulation has been applied in association studies of immunoglobulin light chains [Stevens, Westholm, Solomon & Schiffer (1980) Proc. Natl. Acad. Sci. 77, 1144--1148]. The KD value determined for the Bence--Jones protein Au (10(5) M-1) is close to the value (6.6 X 10(4) M-1) determined by other methods [Maeda, Steffen & Engel (1978) Biophys. Chem. 9, 57-64].

Bence Jones Protein↗
PubMed2006

Computational simulation of the input-output relationship in hippocampal pyramidal cells.

The precise mapping of how complex patterns of synaptic inputs are integrated into specific patterns of spiking output is an essential step in the characterization of the cellular basis of network dynamics and function. Relative to other principal neurons of the hippocampus, the electrophysiology of CA1 pyramidal cells has been extensively investigated. Yet, the precise input-output relationship is to date unknown even for this neuronal class. CA1 pyramidal neurons receive laminated excitatory inputs from three distinct pathways: recurrent CA1 collaterals on basal dendrites, CA3 Schaffer collaterals, mostly on oblique and proximal apical dendrites, and entorhinal perforant pathway on distal apical dendrites. We implemented detailed computer simulations of pyramidal cell electrophysiology based on three-dimensional anatomical reconstructions and compartmental models of available biophysical properties from the experimental literature. To investigate the effect of synaptic input on axosomatic firing, we stochastically distributed a realistic number of excitatory synapses in each of the three dendritic layers. We then recorded the spiking response to different stimulation patterns. For all dendritic layers, synchronous stimuli resulted in trains of spiking output and a linear relationship between input and output firing frequencies. In contrast, asynchronous stimuli evoked non-bursting spike patterns and the corresponding firing frequency input-output function was logarithmic. The regular/irregular nature of the input synaptic intervals was only reflected in the regularity of output inter-burst intervals in response to synchronous stimulation, and never affected firing frequency. Synaptic stimulations in the basal and proximal apical trees across individual neuronal morphologies yielded remarkably similar input-output relationships. Results were also robust with respect to the detailed distributions of dendritic and synaptic conductances within a plausible range constrained by experimental evidence. In contrast, the input-output relationship in response to distal apical stimuli showed dramatic differences from the other dendritic locations as well as among neurons, and was more sensible to the exact channel densities.

Action Potentials↗
PubMed1982

The simple model of adipocyte hexose transport. Kinetic features, effect of insulin, and network thermodynamic computer simulations.

Kinetic studies of the rat adipocyte hexose transport system were performed using the integrated rate approach and these compared to the simple carrier model of transport. Equilibrium exchange 3-O-methylglucose entry and exit studies showed directional symmetry with Km = overall dissociation constants = 8-10 mM. Comparison of zero-trans and equilibrium exchange entry also revealed similar Km and Vmax values. Insulin pretreatment increased the maximal rate of transport at 20 mM 3-O-methylglucose about 5- to 6-fold with each procedure. Studies of glucose-induced steady state 3-O-methylglucose countertransport provided evidence that carrier permeability and not carrier-substrate dissociation was rate limiting for overall transport. These data, therefore, indicate equal mobility of the loaded and unloaded carriers. Network thermodynamic computer simulations of the simple carrier model using kinetic parameters derived from zero-trans experiments provided good fits of actual data. The effect of insulin was best represented by an increase in total number of carrier units. It is concluded that the adipocyte hexose carrier displays bidirectional symmetry, limitation of transport by carrier movement rather than substrate-carrier interaction, equal rates of movement of loaded and unloaded carriers, and adherence to a simple carrier model in which insulin increases the total number of carrier units.

3-O-Methylglucose↗
PubMed1998

Computer simulation of inspiratory nasal airflow and inhaled gas uptake in a rhesus monkey.

There is increasing evidence that inspiratory airflow patterns play a major role in determining the location of nasal lesions induced in rats by reactive, water-soluble gases such as formaldehyde and chlorine. Characteristic lesion patterns have also been seen in inhalation toxicity studies conducted in rhesus monkeys, the nasal anatomy of which resembles that of humans. To examine the hypothesis that regions of high airflow-dependent uptake and lesions occur in similar nasal locations in the primate, airflow and gas uptake patterns were simulated in an anatomically accurate computer model of the right nasal airway of a rhesus monkey. The results of finite-element simulations of steady-state inspiratory nasal airflow for the full range of resting physiological flow rates are reported. Simulated airflow patterns agreed well with experimental observations, exhibiting secondary flows in the anterior nose and streamlined flow posteriorly. Simulated airflow results were used to predict gas transport to the nasal passage walls using formaldehyde as an example compound. Results from the uptake simulations were compared with published observations of formaldehyde-induced nasal lesions in rhesus monkeys and indicated a strong correspondence between airflow-dependent transport patterns and local lesion sites. This rhesus computer model will provide a means for confirming the extrapolation of toxicity data between species by extrapolating rat simulation results to monkeys and comparing these predictions with primate lesion data.

Air Movements↗
PubMed1992

Computer simulation of arterial flow with applications to arterial and aortic stenoses.

A computer model for simulating pressure and flow propagation in the human arterial system is developed. The model is based on the one-dimensional flow equations and includes nonlinearities arising from geometry and material properties. Fifty-five arterial segments, representing the various major arteries, are combined to form the model of the arterial system. Particular attention is paid to the development of peripheral pressure and flow pulses under normal flow conditions and under conditions of arterial and aortic stenoses. Results show that the presence of severe arterial stenoses significantly affects the nature of the distal pressure and flow pulses. Aortic stenoses also have a profound effect on central and peripheral pressure pulse formation. Comparison with the published experimental data suggests that the model is capable of simulating arterial flow under normal flow conditions as well as conditions of stenotic obstructions in a satisfactory manner.

Aortic Valve Stenosis↗