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At least 613 records · Page 34Linked to original sources
PubMed1998

A molecular dynamics computer simulation study of nucleotide analogues. Comparison of the hydration pattern of dithymidine phosphate with those of the dithymidine methylphosphonate diastereomers.

The hydration pattern of thymidyl(3'->5') thymidine 1 and those of Rp and Sp diastereomers of the corresponding methylphosphonate analogue 2, have been studied using Molecular Dynamics (MD) computer simulation. It was found that the methylphosphonate modification leads to significant changes in the coordination of water molecules around the internucleotidic linkage and these, in turn, affect the hydration pattern of other parts of the molecule. The most notable differences between Rp and Sp diastereomers 2a and 2b were found to occur at the deoxyribose moieties of the nucleosid-5'-yl units.

Computer Simulation↗
PubMed2006

Computer simulation of the linear and nonlinear optical susceptibilities of p-nitroaniline in cyclohexane, 1,4-dioxane, and tetrahydrofuran in quadrupolar approximation. II. Local field effects and optical susceptibilitities.

This is the second part of a study to elucidate the local field effects on the nonlinear optical properties of p-nitroaniline (pNA) in three solvents of different multipolar character, that is, cyclohexane (CH), 1,4-dioxane (DI), and tetrahydrofuran (THF), employing a discrete description of the solutions. By the use of liquid structure information from molecular dynamics simulations and molecular properties computed by high-level ab initio methods, the local field and local field gradients on p-nitroaniline and the solvent molecules are computed in quadrupolar approximation. To validate the simulations and the induction model, static and dynamic (non)linear properties of the pure solvents are also computed. With the exception of the static dielectric constant of pure THF, a good agreement between computed and experimental refractive indices, dielectric constants, and third harmonic generation signals is obtained for the solvents. For the solutions, it is found that multipole moments up to two orders higher than quadrupole have a negligible influence on the local fields on pNA, if a simple distribution model is employed for the electric properties of pNA. Quadrupole effects are found to be nonnegligible in all three solvents but are especially pronounced in the 1,4-dioxane solvent, in which the local fields are similar to those in THF, although the dielectric constant of DI is 2.2 and that of the simulated THF is 5.4. The electric-field-induced second harmonic generation (EFISH) signal and the hyper-Rayleigh scattering signal of pNA in the solutions computed with the local field are in good to fair agreement with available experimental results. This confirms the effect of the "dioxane anomaly" also on nonlinear optical properties. Predictions based on an ellipsoidal Onsager model as applied by experimentalists are in very good agreement with the discrete model predictions. This is in contrast to a recent discrete reaction field calculation of pNA in 1,4-dioxane, which found that the predicted first hyperpolarizability of pNA deviated strongly from the predictions obtained using Onsager-Lorentz local field factors.

Aniline Compounds↗
PubMed1993

Estimates by computer simulation of genetic distances from comparisons of RNAse A mismatch cleavage patterns.

The RNAse A mismatch cleavage method was used to analyze genomic variability in RNA and DNA systems. However, there is no method which relates the digestion patterns observed to the extent of genetic variation. Here we report computer simulations which provide a simple estimator of genetic distances from the comparison of RNAse A digestion patterns. The results show that the number of non-shared fragments is proportional to the number of mutations between each pair of sequences compared. This prediction is supported by the comparison of the RNAse A mismatch patterns and the nucleotide sequences of a set of influenza A (H3N2) hemagglutinin genes. The procedure allows a quantitative and reliable use of the RNAse A mismatch cleavage method.

Computer Simulation↗
PubMed1991

Applications of a computer simulation model of the natural history of CD4 T-cell number in HIV-infected individuals.

Data from the Multicenter AIDS Cohort Study (MACS) of 1637 gay men, recruited in 1984 and 1985 in Los Angeles and followed at 6-monthly intervals, are used to develop a computer simulation model of the typical pattern of CD4 T-cell number changes in HIV-infected AIDS-free subjects. The empirical model incorporates the following features: (1) within-person and between-person variability in CD4 measurements; (2) variation in the rates of decline of CD4 values; (3) variation in the level of CD4 at which clinical AIDS is diagnosed, and (4) greater absolute variation in CD4 values in men with high CD4 levels compared with men with low CD4 values. Three applications of the model to assist in the design and interpretation of clinical trials are given. Further applications to clinical trials and to estimate the current and future spectrum of HIV-mediated immunological disease in the USA, as measured by the CD4 values, are discussed.

Biomarkers↗
PubMed1991

Computer simulation analysis of morphological patterns in human melanocytic skin tumours.

Tumour cell proliferation and particularly tumour cell motility are considered to be essential pre-requisites for invasive tumour growth. Despite abundant in vitro data on tumour cell motility, the behaviour of tumour cells in complex human tumour tissues is yet unknown. In this study, estimates of proliferation and motility are statistically derived from morphological tumour patterns in human melanocytic skin tumours. Two-dimensional, discrete, random computer simulations of tumour growth were carried out in order to determine the influence of tumour cell proliferation and motility on morphological patterns. A set of binary morphological criteria turned out to facilitate a significant estimate of the relative probabilities of motility and proliferation (CART analysis). When the same morphological criteria were applied to H & E stained slides of 45 melanocytic skin tumours, benign common nevi showed a predominance of motility, whereas primary and metastatic malignant melanoma revealed a predominance of proliferation. The direct assessment of the number of proliferating cells by Ki-67 staining shows a steep increase from benign nevi to primary and metastatic melanoma. These data provide first evidence that in benign common nevi the overall motility exceeds the very low degree of proliferation, whereas in malignant melanocytic tumours proliferation considerably exceeds tumour cell motility.

Cell Division↗
PubMed1999

How accurate is visual assessment of synchronicity in myocardial motion? An In vitro study with computer-simulated regional delay in myocardial motion: clinical implications for rest and stress echocardiography studies.

Asynchronicity in echocardiographic images is normally assessed visually. No prior quantitative studies have determined the limitations of this approach. To quantify visual recognition of myocardial asynchronicity in echocardiographic images, computer-simulated delay phantom loops were generated from a 3.3 MHz digital image data from a normal left ventricular short-axis heart cycle acquired at 55 frames per second. Six expert observers visually assessed 30 abnormal and 3 normal loops with differing computer-induced delay patterns on 3 occasions and in this optimally simulated environment could recognize only single delays of 89 ms or more. This was improved to 71 ms or more by use of side-by-side (normal versus abnormal) comparative review. Thus visual assessment of clinically important regional delay in rest or stress echo images is limited.

Computer Simulation↗
PubMed1997

Computer simulation to support policy making in the control of pseudorabies.

A further integration of international markets makes a coordinated policy against contagious animal infections increasingly important. In the future, stricter demands are to be expected concerning the control and eradication of such infections. To anticipate these demands, a computer simulation model is created in which scenarios can be evaluated with respect to epidemiological and economic effects of the infections and control strategies. In this paper, the simulation model is described for Pseudorabies in swine. In the model, the population of herds is subdivided into two main herd types: breeding and finishing. Each herd is in one of 24 states per herd type. The states are based on (1) the reproduction ratio R which is the number of secondary cases caused by one infectious herd, (2) the prevalence for each value of R and (3) the expected number of infectious animals in an infectious herd within each prevalence range and for each R. The different values of R are based on experiments and field data in which different vaccination strategies were used. The transition matrix with the probabilities of every transition from one state to another is calculated on a weekly base. With this matrix the distribution of herds over states from week to week is derived. To include a dynamic element in the transition probabilities, the number of newly infectious herds per week is a function of animal and other contacts, including aerial, material and personal contacts. Calculations show that the infection in the Dutch swine population will not disappear without vaccination. With a vaccination scheme in which sows are vaccinated 3 times per year and fattening pigs 1 time per cycle the infection will ultimately be eradicated, but 2 vaccinations per cycle for fattening pigs are needed to eradicate the infection within an acceptable timespan (i.e. 2 to 3 years). The latter strategy will become compulsory in the Netherlands from October 1st 1995.

Animals↗
PubMed1999

Evaluation of spurious results in the infrared measurement of CO2 isotope ratios due to spectral effects: a computer simulation study.

The application of infrared spectroscopy to the measurement of carbon isotope ratio breath tests is a promising alternative to conventional techniques, offering relative simplicity and lower costs. However, when designing such an instrument one should be conscious of several spectral effects that may be misinterpreted as changes in the isotope concentration and which therefore lead to spurious results. Through a series of computer simulations which model the behaviour of the CO2 absorption spectrum, the risk these effects pose to reliable measurement of 13CO2/12CO2 ratios and the measures required to eliminate them are evaluated. The computer model provides a flexible high-resolution spectrum of the four main isotopomer fundamental transitions and fifteen of their most significant hotband transitions. It is demonstrated that the infrared source, infrared windows and breath sample itself all exhibit strong temperature induced errors but pressure effects do not produce significant errors. We conclude that for reliable measurement of 13CO2/12CO2 ratios using infrared spectroscopy no pressure controls are required. window effects are eliminated using windows wedged at a minimum angle of 0.8-2.2 mrad, depending on the material, and the temperature sensitivity of source and gas cells necessitates stabilization to an accuracy of at least 0.2 K.

Biophysical Phenomena↗
PubMed2005

Computer simulation for ergonomic improvements in laparoscopic surgery.

It is the aim of this study to reduce the stress and strain of the medical staff during laparoscopic operations, and, simultaneously, to increase the safety and efficiency of an integrated operation room (OR) by an ergonomic redesign. This was attempted by a computer simulation approach using free modelling of the OR and 3D human models (manikins). After defining ergonomically "ideal" postures, optimal solutions for key elements of an ergonomic design of the OR (position and height of the image displays, height of the OR table and the Mayo stand) could be evaluated with special regard to the different individual body size of each member of the team. These data should be useful for the development of team adapted, user friendly integrated OR suites of the future.

Computer Simulation↗
PubMed1994

Importance of collateral vessels in aortic coarctation: computer simulation at rest and exercise using transmission line elements.

Coarctation of the aorta causes arterial hypertension in the upper body and a low blood pressure downstream. Collateral blood vessels compensate by reducing the downstream pressure drop. To study the effect of various coarctation and collateral properties, we designed a computer model of the arterial circulation. The model contains a flow source and a library of subroutines for the lines and connectors. Distributed friction and wall viscoelasticity effects are included. Computer simulation was performed, using published values for vessel dimensions, in an arterial model with a coarctation and one lumped collateral. Rest and two levels of exercise (by increased heart rate) were studied. Without a collateral, we found the downstream pressure of the model was extremely dependent on the size of the coarctation. A collateral vessel reduced the pressure difference between the up- and downstream circulations. For a severe coarctation, the length and the diameter of the collateral were the main factors determining the downstream pressure and flow, whereas wall stiffness of the collateral had little influence. The relationship between mean pressure drop and cardiac output in coarctation was also dependent on the peripheral resistance in different flow beds, especially during exercise.

Aortic Coarctation↗
PubMed2006

Using a speech perception neural network computer simulation to contrast neuroanatomic versus neuromodulatory models of auditory hallucinations.

A number of studies suggest that schizophrenia may arise from overzealous pruning of synapses that are an extension of normal developmental pruning during adolescence. Moreover, there has been a long history of studies suggesting that this disorder arises from alterations in the dopaminergic neuromodulatory systems. In order to further assess and compare these two hypotheses, a computer simulation of some aspects of speech perception was developed utilizing a recurrent, backpropagation model of working memory previously reported by Elman . This system was found to produce spontaneous percepts simulating hallucinated speech when the working memory component either was excessively pruned or when neuronal responses were modulated to simulatea hyperdopaminergic system. These hallucinogenic systems also demonstrated disruptions in processing input information when "phonetic information" was degraded. The perceptual performance of these systems were compared to that of actual hallucinating patients and normal controls while tracking (repeating while simultaneously listening to) speech that was phonetically degraded. We found that the neural network simulation producing the best match to speech tracking performance of human hallucinators was an overpruned system with compensatory hypodopaminergic adjustments. These data suggest that the primary pathophysiology of schizophrenia arises from curtailed connectivity in working memory systems and that dopaminergic alterations reflect secondary compensatory adjustments.

Adolescent↗
PubMed2006

Variations of the 'grand-piano sign' during total knee replacement. A computer-simulation study.

The appearance of the 'grand-piano sign' on the anterior resected surface of the femur has been considered to be a marker for correct femoral rotational alignment during total knee replacement. Our study was undertaken to assess quantitatively the morphological patterns on the resected surface after anterior femoral resection with various angles of external rotation, using a computer-simulation technique. A total of 50 right distal femora with varus osteoarthritis in 50 Korean patients were scanned using computerised tomography. Computer image software was used to simulate the anterior femoral cut, which was applied at an external rotation of 0 degrees, 3 degrees and 6 degrees relative to the posterior condylar axis, and parallel to the surgical and clinical epicondylar axes in each case. The morphological patterns on the resected surface were quantified and classified as the 'grand-piano sign', 'the boot sign' and the 'butterfly sign'. The surgeon can use the analogy of these quantified sign patterns to ensure that a correct rotational alignment has been obtained intra-operatively.

Adult↗
PubMed2003

A computer simulation of human walking in persons with joint contractures.

Joint contractures decrease the patient's ability to walk, but usually other parts of the body compensate the affected joint contractures. When we restore the gait performance in paraplegic patients by means of functional electrical stimulation, however, we cannot expect complications of compensation. A computer simulation was done to clarify how the contractures affect the gait pattern when no complications of compensation were expected. A seven-segment link mechanical model was used for simulation of human walking in the sagittal plane. In turn, using a personal computer stance and swing-leg joint contractures of the ankle, knee, and/or hip were simulated. When stance-leg contracture was simulated, step length became short with increasing hip flexion contracture. The trunk was tilted backward during knee flexion or ankle plantarflexion contracture simulation. When the swing-leg contracture was simulated, step length became short with increasing knee flexion contracture. We found that hip or knee flexion contracture of < or = 15 degrees, or ankle plantarflexion contracture of < 0 degrees was required to maintain positive step length and forward movement of the center of gravity. These findings suggest that 15 degrees of hip and knee flexion contracture, and 0 degrees of ankle plantarflexion contracture are critical when gait restoration is performed by functional electrical stimulation.

Ankle↗
PubMed1994

Computer simulations of the effects of different synaptic input systems on the steady-state input-output structure of the motoneuron pool.

1. The effects of different types of synaptic input on the steady-state input-output relations of the mammalian motoneuron pool were investigated by the use of computer simulations. The properties of the simulated motor units and their synaptic inputs were based as closely as possible on the experimental data from studies in the cat hindlimb. 2. Three basic types of synaptic input systems were simulated: postsynaptic, presynaptic, and neuromodulatory. The effects of these inputs on three aspects of the system input-output structure were studied: gain, precision, and motor-unit type utilization. 3. The gain analyses were based on a simulation of the steady-state homonymous Ia input. The gain of this steady-state Ia "reflex" was found to be determined largely by the slope of the pool input-output function. Precision was evaluated in two ways, from the amplitudes of the quantal steps due to motor-unit recruitment and from the sensitivity of the input-output function to noise. The pattern of motor-unit type utilization allowed indirect assessment of fatigue resistance: the larger the percentage of force generated by FF units, the lower the fatigue resistance. 4. A uniformly distributed input (i.e., one that generates equal input in all motoneurons) generates outputs that are solely determined by the intrinsic properties of the motor units. Thus the gain, precision, and motor-unit type patterns generated by a uniform input were used as the basis with which the effects of all other input systems were compared. 5. Postsynaptic excitatory inputs with nonuniform distributions within the pool did influence gain. The greatest effect was the increase mediated by the rubrospinal excitatory input (27% increase at 30% of maximal force). However, this input also greatly decreased both fatigue resistance and precision, due to increased activation of FF units at low force levels. In contrast, the Ia input slightly decreased gain (12% decrease at 30% of maximum force) while slightly increasing fatigue resistance and precision. 6. The simulated neuromodulatory input was based on the monoaminergic reticulospinal effect on motoneurons. Gain was generally increased by the monoaminergic input. However, the magnitude of the increase strongly depended on whether the monoaminergic effects were largest on S units (giving a 20% increase at 30% of maximum force), equal on all types (52%), or largest on FF units (102%). Presynaptic inhibition reduced gain with no effect whatsoever on fatigue resistance or precision. 7. Therefore Ia reflex gain was modifiable by all three types of input: postsynaptic, presynaptic, and neuromodulatory.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1995

Using the standard staircase to measure the point of subjective equality: a guide based on computer simulations.

In experiments that measure a point of subjective equality, it is necessary to employ a psychophysical technique that measures the 50% point (P50) on the psychometric function. The standard staircase is an attractive candidate, because its simplicity makes it easy to understand and implement. However, Pentland (1980, Perception & Psychophysics, 28, 377-379) found his own maximum likelihood method (Best PEST) to be considerably less variable than the standard staircase. Here, computer simulations were used to study the effects of manipulating several parameters of the standard staircase in order to try to find a variant that would be competitive with the performance of Best PEST. A graphical summary of some of the standard staircase implementations that were found to be most stable is presented in order that investigators may choose easily the parameters best suited to their requirements. A comparison with an implementation of Pentland's Best PEST failed to replicate Pentland's finding, suggesting that investigators should have no misgivings about the standard staircase in experiments that measure a point of subjective equality.

Algorithms↗
PubMed1997

Formation of the branching pattern of blood vessels in the wall of the avian yolk sac studied by a computer simulation.

The present study was performed to provide data to support the notion previously believed but not proved experimentally or theoretically, that blood vessels are formed by the selection of capillaries in the network. In an attempt to understand the mechanism of formation of blood vessel branching structures, the transformation of a capillary network to a branching system in the wall of quail yolk sac was successively recorded by a series of photographs, and a computer simulation was carried out for the process of in vivo vascularization based on the photographs. The simulation demonstrated that a positive feedback system participated in the formation of a branching structure. That is, vessels which had been much used were enlarged, whereas less used vessels were reduced in their size and finally extinguished. The enlarged vessels became major components of the branching system. As the body of an embryo grew, it was observed that polygonal capillary networks enlarged, which led each polygon of the network to divide into a few finer polygons. Then, some of the capillary vessels were again selected and formed a branching system. This process repeated during the body growth, indicating that the vascular system developed adaptively to the body growth. A region where the growth was fast, received much blood flow and produced finer networks of capillaries. Thus, it was experimentally demonstrated for the first time that capillaries in the network are successively selected by a positive feedback mechanism and form blood vessels.

Animals↗
PubMed1995

Application of R-charts to detection of random errors: a computer simulation study.

The application of R-charts to quality control in clinical chemistry was investigated. These charts are widely used in statistical process control and plot the range (ie the difference between the highest and the lowest values) of a set of controls. A set of five control serums was considered. A computer simulation program was developed for this investigation. It showed a power function that is remarkably insensitive to systematic errors. Consequently these charts may be a useful tool in discriminating between systematic and random errors, helping the trouble-shooting significantly, if used concurrently with Levey-Jennings' charts. Nevertheless, as several control samples are necessary, this technique is not cost-effective for short analytical runs.

Bias↗
PubMed2002

Development of efficient threshold strategies for frequency doubling technology perimetry using computer simulation.

PURPOSE: To develop new test procedures for frequency-doubling technology (FDT) perimetry that improve performance beyond those currently used. METHODS: Two novel threshold estimation procedures were evaluated: a rapid, efficient binary search technique (REBS) and a maximum-likelihood estimation (ZEST) procedure. A computerized visual field simulation model was developed to determine the accuracy and efficiency of these procedures. This model was constructed using previously derived characteristics of FDT perimetry from both normal observers (n = 506) and those with glaucomatous visual field loss (n = 352). The computer simulation program was used to determine the best parameters for the two new procedures and the effect of variability and response errors on algorithm performance. Comparisons were made to the performance of the modified binary search (MOBS) procedure used in the current commercial implementation of the FDT perimeter. RESULTS: Both the optimized REBS and ZEST procedures approximately halved the time required for FDT threshold testing without loss of accuracy or reproducibility. CONCLUSIONS: With suitable parameter choices, comparable performance was achieved using either ZEST or REBS. Simulation results indicate that accurate thresholds can be measured with an optimized ZEST or REBS procedure in approximately half the time required by traditional estimation methods.

Aged↗