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At least 469 records · Page 26Linked to original sources
PubMed2003

Computer simulation of the delivery of etanidazole to brain tumor from PLGA wafers: comparison between linear and double burst release systems.

This paper presents the computer simulation results on the delivery of Etanidazole (radiosensitizer) to the brain tumor and examines several factors affecting the delivery. The simulation consists of a 3D model of tumor with poly(lactide-co-glycolide) (PLGA) wafers with 1% Etanidazole loading implanted in the resected cavity. A zero-order release device will produce a concentration profile in the tumor which increases with time until the drug in the carrier is depleted. This causes toxicity complications during the later stages of drug treatment. However, for wafers of similar loading, such release results in a higher drug penetration depth and therapeutic index as compared to the double drug burst profile. The numerical accuracy of the model was verified by the similar results obtained in the two-dimensional and three-dimensional models.

Animals↗
PubMed1993

A computer simulation of the reactions between hydroxyapatite and fluoride in aqueous acidic solutions.

A precipitation reaction between hydroxyapatite (HAp) and fluoride solution was analyzed by computer simulation. The system comprised excess HAp and 0.05-0.2 M acetic buffer solutions containing 0.5-2.0 mM potassium fluoride. The amounts of HAp dissolved and calcium salts precipitated and activities of all the species present in the solution were calculated during the process. In the systems, calcium fluoride was initially precipitated when applying the fluoride solution to HAp, followed by precipitation of fluorapatite (FAp) and re-dissolution of the previously precipitated calcium fluoride at a critical pH at which the ion activity product exceeded the solubility product of FAp. The critical pH was increased with pH of the buffer, whereas it was scarcely affected by fluoride ion concentration, and it was necessary to introduce phosphate ions in advance into the buffer for predominant precipitation of FAp in this system.

Algorithms↗
PubMed2002

On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study.

The interaction of DNA with the polyamine spermine(4+) (Spm(4+)), sodium ions, and water molecules has been studied using molecular dynamics computer simulations in a system modeling a DNA crystal. The simulation model consisted of three B-DNA decamers in a periodic hexagonal cell, containing 1200 water molecules, 8 Spm(4+), 32 Na(+), and 4 Cl(-) ions. The present paper gives a more detailed account of a recently published report of this system and compares results on this mixed Spm(4+)/Na(+)-cation system with an molecular dynamics simulation carried out for the same DNA decamer under similar conditions with only sodium counterions (Korolev et al., J. Mol. Biol. 308:907). The presence of Spm(4+) makes significant influence on the DNA hydration and on the interaction of the sodium ions with DNA. Spermine pushes water molecules out of the minor groove, whereas Na(+) attracts and organizes water around DNA. The major binding site of the Spm(4+) amino groups and the Na(+) ions is the phosphate group of DNA. The flexible polyamine spermine displays a high presence in the minor groove but does not form long-lived and structurally defined complexes. Sodium ions compete with Spm(4+) for binding to the DNA bases in the minor groove. Sodium ions also have several strong binding sites in the major groove. The ability of water molecules, Spm(4+), and Na(+) to modulate the local structure of the DNA double helix is discussed.

Base Sequence↗
PubMed1989

Computer-simulation methods in human linkage analysis.

In human linkage analysis, many statistical problems without analytical solution could be solved by ad hoc Monte Carlo procedures were efficient computer-simulation methods available for members of family pedigrees. In this paper, a general method is described for randomly generating genotypes at one or more marker loci, given observed phenotypes at loci linked among themselves and with the markers. The method is based on a well-known expansion of the multivariate probability of genotypes, given phenotypes, into a product of conditional univariate probabilities that may be viewed as corresponding to conditionally independent univariate random variables. This representation allows a recursive evaluation of the univariate probabilities that can be implemented in a surprisingly simple manner by carrying out successive "risk calculations" with respect to marker genotypes, given observed phenotypes and marker genotypes already generated. Potential applications to various unresolved problems are discussed. The method is applied to 28 published families analyzed for genetic linkage between hereditary motor and sensory neuropathy I and the Duffy (FY) blood group locus and confirms heterogeneity of hereditary motor and sensory neuropathy I. An implementation of the simulation methods developed in the LINKAGE program package will be available later in 1989.

Chromosomes, Human↗
PubMed1999

Conformational analyses by 1H NMR and computer simulations of cyclic hexapeptides related to somatostatin containing acidic and basic peptoid residues.

We report the conformational analysis by 1H NMR in DMSO and computer simulations involving distance geometry and molecular dynamics simulations at 300K of peptoid analogs of the cyclic hexapeptide c-[Phe11-Pro6-Phe7-D-Trp8-Lys9-Thr10]. The analogs c-[Phe11-Nasp6-Phe7-D-Trp8-Lys9-Thr10](1), c-[Phe11-Ndab6Phe7-D-Trp8-Lys9-Thr10] (2) and c-[Phen11-Nlys6-Phe7-D-Trp8-Lys9-Thr10](3) where Nasp denotes N-(2-carboxyethyl) glycine, Ndab N-(2-aminoethyl) glycine and Nlys N-(4-aminobutyl) glycine are subject to conformational studies. The results of free and restrained molecular dynamics simulations at 300K are reported and give insight into the conformational behaviour of these analogs. The compounds show two sets of nuclear magnetic resonance signals corresponding to the cis and trans orientations of the peptide bond between residues 11 and 6. The backbone conformation of the cis isomers that we believe are the bioactive isomers of the three compounds are very similar to each other while there are larger variations amongst the trans isomers. The binding data to the isolated receptors show that the introduction of the Nlys residue in analog 3 leads to an enhancement of binding potency to the hsst5 receptor compared with analog 2 while maintaining identical binding potency to the hsst2 receptor. The Nasp6 analog 1 binds weakly to the hsst2 and is essentially inactive towards the other receptors. Comparison of the conformations and binding activities of these three analogs indicates that the Nlys residue extends sufficiently far to allow binding to a negatively charged binding domain on the hsst5 receptor. According to this model, the Ndab analog 2 cannot extend far enough to allow for binding to the receptor pocket. The loss of activity observed for the Nasp6 compound 1 indicates that the presence of a negatively charged residue in position 6 is unfavorable for binding to the hsst receptors.

Amino Acid Sequence↗
PubMed1997

Estimation of economic values of indices for reproductive performance in dairy herds using computer simulation.

Relationships between measures for reproductive performance and net revenue were studied using data that had been generated by a stochastic model in a computer simulation program for Ontario dairy herds. These measures included projected calving interval, involuntary culling rate, and adjusted calving interval. Adjusted calving interval was calculated by dividing the projected calving interval for pregnant cows by the fraction of the cows that were not culled for reproductive failure. The regression of adjusted calving interval on net revenue had an R2 of 0.72, which was higher than the R2 of 0.59 obtained by the regression of projected calving interval on net revenue. Hence, the estimation of financial losses from suboptimal reproductive performance was more accurate when adjusted calving interval was used as a measure of this performance than when projected calving interval was used. This difference is because projected calving interval did not consider cows that were culled for reproductive reasons, but those cows contributed to a reduction in profit because of suboptimal reproductive performance. The highest R2 (0.78) was obtained with a model that included projected calving interval and involuntary culling rate. However, use of that model might not be practical because herd operators differ in their ability to distinguish between involuntary and voluntary culling. The mean reduction in net revenue from a 1-d increase in adjusted calving interval was estimated at $4.7 (Canadian) per cow. This economic value was not significantly affected by level of adjusted calving interval, carcass price, feed costs, cost of a replacement heifer, or milk price.

Animals↗
PubMed2005

Computer simulations of high-pass filtering in zebrafish larval muscle fibres.

Larval somatic muscle of the zebrafish, Danio rerio, like that of some other organisms, responds to a sustained depolarization with one, and only one, action potential. Here, we report computer simulations, using the NEURON simulation programme, of sodium and potassium currents of somatic muscle of larval Danio rerio to investigate their possible contribution to once-only firing. Our computer model incorporated simulated sodium and potassium ion channels based on steady-state and kinetic parameters derived from a recent electrophysiological study. The model responded to sustained depolarizations with a single action potential at all levels of depolarization above threshold. By varying several parameters of the sodium and potassium currents systematically, the minimum changes necessary to produce repetitive firing were found to be a positive shift in the half-inactivation and a negative shift in the half-activation potentials for the sodium current, accompanied by a slowing of the rate of inactivation to half of the experimentally observed values. This suggests that once-only spiking can be attributed to the steady-state values of activation and inactivation of the sodium current, along with a slower rate of inactivation. Mapping of the resultant firing properties against steady-state and kinetic ion channel parameters revealed a high safety factor for once-only firing and showed that the time constant of inactivation of the sodium current was the key determinant of once-only or repetitive firing. The rapidly inactivating potassium current does not influence once-only firing or the maximum rate of firing in response to periodic excitation in these simulations. Although a contribution of other currents to produce once-only firing has not been excluded, this model suggests that the properties of the sodium current are sufficient to account for once-only firing.

Action Potentials↗
PubMed1997

What can be measured from surface electrogastrography. Computer simulations.

The aims of this study were to investigate the detectability of the propagation of the gastric slow wave from the cutaneous electrogastrogram (EGG) and the patterns of the EGG when the gastric slow waves are uncoupled. A mathematical model was established based on the volume conductor theory to simulate the transfer of the serosal gastric slow wave from the stomach to the abdominal surface. A number of computer simulations were conducted using the model, and the periodic cross-correlation function was used to estimate the phase shift between the four channels. It was found that the propagation of the gastric slow wave was detectable from the multichannel EGG signals. The detectability of the propagation was, however, associated with a number of factors, such as the thickness of the abdominal wall and the propagation velocity of the serosal slow wave. The amplitude of the EGG was found to be associated with the coupling/uncoupling and propagation velocity of the gastric slow wave. The amplitude of the EGG increased when the propagation velocity of the gastric slow wave increased. The amplitude of the EGG was substantially decreased when the gastric slow waves were uncoupled. The uncoupling of the gastric slow wave at a frequency of 3 cpm produced dysrhythmias in the EGG, including tachygastria, bradygastria, and arrhythmia. The power spectra of simulated different positional EGG signals showed similar patterns when the gastric slow wave was coupled and different and unpredictable patterns when the gastric slow wave was uncoupled. In conclusion, multichannel EGG recordings may be necessary to obtain more information on gastric slow waves from the abdominal electrodes. The propagation and coupling or uncoupling of the gastric slow wave may be detected from multichannel EGG recordings.

Computer Simulation↗
PubMed2000

Computer simulations of particle deposition in the developing human lung.

An age-dependent theoretical model has been developed to predict PM dosimetry in children's lungs. Computer codes have been written that describe the dimensions of individual airways and the geometry of branching airway networks within developing lungs. Breathing parameters have also been formulated as functions of subject age. Our computer simulations suggest that particle size, age, and activity level markedly affect deposition patterns of inhaled air pollutants. For example, the predicted lung deposition fraction is 38% in an adult but is nearly twice as high (73%) in a 7-month-old for 2-micron particles inhaled during heavy breathing. Tracheobronchial (TB) and pulmonary (or alveolated airways, P) deposition patterns may also be calculated using the model. Due to different clearance processes in the TB and P airways (i.e., mucociliary transport and macrophage action, respectively), the determination of compartmental dose is important for PM risk assessment analyses. Furthermore, the results of such simulations may aid in the setting of regulatory standards for air pollutants, as the data provide a scientific basis for estimating dose delivered to a designated sensitive subpopulation (children).

Adolescent↗
PubMed1980

A computer simulation of physiological factors contributing to hyperventilation and breathlessness in cardiac patients.

A computer model of human respiration is of value for teaching the basic principles of respiratory physiology to students. An extension of this educational use is in the theoretical exploration of the relative importance of individual factors which may be contributing to disordered function in common clinical problems. For example, when a cardiac patient becomes breathless with increase in ventilation during exercise there are alterations in many physiological variables. The influence of their individual contributions on the total ventilation and thence possibly on breathlessness is often difficult to estimate. We present a theoretical analysis using MACPUF, a digital computer simulation of circulation and gas exchange which can be used to extimate the quantitative contribution of relevant physiological variables by altering them singly and in combination. Alterations in dead space, physiological shunt and pulmonary compliance individually produce only small increases in ventilation. Increased neurogenic drive (e.g. from lung reflexes triggered by pulmonary congestion) is a potentially important but very variable factor. A more important influence on ventilation appears when cardiac output is reduced and anaerobic metabolism simulated, causing changes in blood gas tensions and acidaemia which then change ventilation. Any increase in ventilation becomes more significant as a cause of breathlessness when ventilatory capacity is reduced, which in cardiac patients it not infrequently is.

Cardiac Output↗
PubMed1987

Hemodynamic evaluation of arterial stenoses by computer simulation.

A new method to assess the hemodynamic severity of arterial stenoses was proposed and evaluated. It is based on a previously developed finite element computer simulation model for laminar-separated flow in arteries of axially varying cross-section; the present modification allows use of angiographic stenosis shapes acquired by automatic edge-detection algorithms. The method was validated by comparing its results with published experimental and theoretic results for ideal stenosis shapes. At moderate flowrates (Reynolds number = 500), poststenosis flow separation was predicted for moderately severe (75% area reduction) but not for mild (25%) stenoses. For high flowrates (Reynolds number = 900) in a severe stenosis (89%), stagnation and reversed flow were predicted and the experimental nondimensional pressure drop of 48.5 was correctly determined. Bernoulli's Equation, which neglects viscosity, predicted a drop of only 40. For a severe stenosis (89%), even at low Reynolds numbers (50), reversed flow agreeing with other theoretic solutions was predicted. Predictions are especially useful at low flow rates, where experiments are difficult to conduct. The height of the curve on the graph of nondimensional pressure gradient vs. Reynolds number reflects the hemodynamic severity of a particular stenosis; these curves were predicted for moderate and severe ideal stenoses and agree with experiments. A similar analysis is applied to an actual human coronary artery stenosis, and the results are demonstrated to have use in assessing interventions during angiography.

Arterial Occlusive Diseases↗
PubMed1989

Programmed electrical stimulation at potential ventricular reentry circuit sites. Comparison of observations in humans with predictions from computer simulations.

The purpose of this study was to define specific types of resetting responses to programmed electrical stimulation during human ventricular tachycardia and to use computer simulations of reentry circuits to assess the possible mechanisms and pacing site location relative to the reentry circuit for each type of response. The effects of scanning single stimuli at 35 left ventricular endocardial sites during sustained monomorphic ventricular tachycardia in 12 patients were studied. In considering alterations in QRS configuration and the delay between the stimulus and the advanced QRS, we identified three types of resetting responses to scanning stimuli consistent with stimulation at sites in or near the reentry circuit at 12 abnormal endocardial sites in eight patients. Type 1: all capturing stimuli were followed after a delay by early QRS complexes that had the same configuration as the tachycardia complexes. Type 2: late stimuli reset tachycardia as in type 1 but early stimuli reset the tachycardia after altering the QRS configuration. Type 3: late stimuli reset tachycardia as in type 1, but early stimuli advanced tachycardia with a short stimulus to QRS delay without altering the QRS configuration. In the simulations, premature depolarization of sites in the circuit produced orthodromic and antidromic wavefronts. The orthodromic wavefront propagated through the circuit and exited the circuit at the same site as did the previous tachycardia wavefronts and advanced the tachycardia without altering the configuration of the advanced QRS. The antidromic wavefront of relatively late stimuli was confined within or near the circuit by collision with the orthodromic wavefront of the preceding tachycardia beat and failed to alter ventricular activation distant from the circuit. Therefore, the QRS configuration after the stimulus was unchanged. A type 1 response occurred when all capturing stimuli produced this effect. However, with increasing stimulus prematurity, the antidromic wavefront propagated farther before colliding with an orthodromic wavefront, and under some conditions, it exited the circuit from a site other than the original circuit "exit," and altered the ventricular activation sequence distant from the circuit and, therefore, the QRS configuration, producing a type 2 pattern. The type 3 pattern occurred when the antidromic wavefront of early premature beats captured the original circuit exit. The effect of a stimulus was dependent on the stimulus prematurity, the relative conduction times from the stimulation site to the potential sites of "exit" from the circuit, and the timing of the excitable gap at the stimulation site.(ABSTRACT TRUNCATED AT 400 WORDS)

Cardiac Pacing, Artificial↗
PubMed1992

Computer simulation of the conformational behaviour of angiotensinogen (6-13) renin substrate.

The conformational behaviour of the biologically active angiotensinogen (6-13) fragment has been investigated by computer simulations. A large sample of conformers has been generated using the Monte-Carlo procedure, then analysed using classification and partition methods. Seven families can describe the conformational distribution. About 40% of conformers are fully extended, 28% are folded at the C-terminal His6-Pro7-Phe8-His9 level and the others are folded at different levels. The study highlights the extreme flexibility of the angiotensinogen fragment.

Amino Acid Sequence↗
PubMed1993

Stress shielding and bone resorption in THA: clinical versus computer-simulation studies.

"Stress shielding" of bone around noncemented prosthetic hip stems causes long-term adaptive bone resorption which threatens the integrity of the fixation. Recently, computer-simulation models based on adaptive bone-remodeling theory in combination with finite-element methods have been developed. These models can be used to predict the extent of long-term resorption. In this paper a comparison is presented between the results of these predictions and those of precise measurements in retrieval hip-replacement specimens reported by Engh and associates (1992). It is shown that certainly the predictions and the actual clinical findings are subject to the same trends. Under certain assumptions, these results even match precisely. It is also shown that both clinical results and simulation predictions can be approximated by a simple formula, in which the amount of bone loss is related to the ratio between stem stiffness and preoperative bone density.

Aged↗
PubMed1988

Acoustic effects in in-the-ear hearing aid response: results from a computer simulation.

The response of a hearing aid depends on the design of the instrument and on the characteristics of the individual ear. In this paper a computer simulation of an in the ear (ITE) hearing aid is used to determine the effects on the hearing aid response caused by variations in the size of the ear canal, the magnitude of the eardrum impedance, and the vent size and damping. The simulation results indicate that, for an unvented hearing aid, changes in the size of the ear canal or the eardrum impedance shift the average sound pressure level at the eardrum but have relatively small effects on the overall shape of the frequency response. A vented instrument presents a more complicated situation since the vent modifies the low-frequency response in a predictable manner but can have unexpectedly pronounced effects at high frequencies due to the acoustic feedback.

Acoustic Impedance Tests↗
PubMedDate not supplied

Qualitative probability versus quantitative probability in clinical diagnosis: a study using a computer simulation.

The use of Bayes' theorem as a diagnostic tool in clinical medicine normally requires an input of exact probability estimates. However, humans tend to think in categories ("likely," "unlikely," etc.) rather than in terms of exact probability. A computer simulation of the presenting features of a case of pelvic infection has been used to compare the effects of quantitative and qualitative probability estimates on the diagnostic accuracy of Bayes' theorem. For the commoner conditions (prior probability greater than or equal to 0.2) the use of a two- or three-category system is virtually equivalent to the use of exact probability. However, uncommon conditions (prior probability less than or equal to 0.03) are completely ignored by the qualitative system. It is concluded that the use of simple categories of probability is acceptable for a Bayesian diagnostic system provided that the target conditions have a relatively high prior probability.

Artificial Intelligence↗
PubMed1992

[Computer simulation of the 10-year outcome of a cohort of heroin addicts in Ile-de-France].

The aim of this study is to develop a computer simulation model to describe imaginary cohorts of heroin users in the Ile de France (greater Paris) region. Because of the lack of well-designed cohort studies in France, this model is based on epidemiological data found in various different studies. The results of the simulation reveal horrifying outcomes in ten years' time: in the more optimistic scenario (an annual non-Aids mortality rate of 1%, an annual rate of permanent addiction curtailment of 10% and a syringe exchange rate of 10%), only 50% of heroin users curtail their consumption permanently without being HIV carriers after 10 years, 16% are HIV carriers and 10% have died. In conclusion, medical care should play an important part in the management of drug users, and secondary prevention aimed at reducing the health problems involved in heroin use should be intensified.

Acquired Immunodeficiency Syndrome↗