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At least 487 records · Page 27Linked to original sources
PubMed1987

Computer simulation of the Wolff-Parkinson-White syndrome utilizing a human heart model.

The relationship between the location of an accessory pathway and body surface ECG waveforms was investigated by computer simulation of the WPW syndrome using a human heart model. The 3-dimensional heart model is composed of 50,000 units so as to represent the details of ventricular excitation. Ten typical accessory pathways near the A-V groove were examined, which correspond to Gallagher's classification of the WPW syndrome based on their surgical experience. Twelve-lead ECG waveforms were calculated for these 10 cases and were compared with the clinical observations of Gallagher et al. The polarities of the delta waves at 40 msec after the onset of the QRS were listed. The agreement of our model with the clinical data obtained by Gallagher et al is 87%. Details of changes in the ECG waveforms were also examined by changing ther terminal location of the accessory pathway along the radial and longitudinal directions in the ventricles, and it was found that the ECG waveforms of the limb leads are more sensitive to this difference in the preexcited location than those of the chest leads. The simulated epicardial isochronic patterns also agree with the measurements.

Computer Simulation↗
PubMedDate not supplied

Computer simulation of arcuate keratotomy for astigmatism.

BACKGROUND: The development of refractive corneal surgery involves numerous attempts to isolate the effect of individual factors on surgical outcome. Computer simulation of refractive keratotomy allows the surgeon to alter variables of the technique and to isolate the effect of specific factors independent of other factors, something that cannot easily be done in any of the currently available experimental models. METHODS: We used the finite element numerical method to construct a mathematical model of the eye. The model analyzed stress-strain relationships in the normal corneoscleral shell and after astigmatic surgery. The model made the following assumptions: an axisymmetric eye, an idealized aspheric anterior corneal surface, transversal isotropy of the cornea, nonlinear strain tensor for large displacements, and near incompressibility of the corneoscleral shell. The eye was assumed to be fixed at the level of the optic nerve. The model described the acute elastic response of the eye to corneal surgery. RESULTS: We analyzed the effect of paired transverse arcuate corneal incisions for the correction of astigmatism. We evaluated the following incision variables and their effect on change in curvature of the incised and unincised meridians: length (longer, more steepening of unincised meridian), distance from the center of the cornea (farther, less flattening of incised meridian), depth (deeper, more effect), and the initial amount of astigmatism (small effect). CONCLUSIONS: Our finite element computer model gives reasonably accurate information about the relative effects of different surgical variables, and demonstrates the feasibility of using nonlinear, anisotropic assumptions in the construction of such a computer model. Comparison of these computer-generated results to clinically achieved results may help refine the computer model.

Animals↗
PubMed1992

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase.

Computer simulation approaches can provide a powerful tool for correlating the structure of enzymes with their catalytic activity. One of the most effective ways of simulating enzymatic reactions is provided by the empirical valence bond method. The general applicability of this method has been demonstrated in several enzymatic reactions and it is reexamined here in a study of the initial proton-transfer step in the catalytic reaction of carbonic anhydrase. The simulations produce a rate constant which is in agreement with the observed kinetic data and emphasizes the importance of the electrostatic effect associated with the catalytic zinc ion. The calculations are also used to examine the validity of linear free-energy relationships (LFERs) in enzyme catalysis and to evaluate quantum-mechanical corrections of the calculated rate constant. It is found that LFERs are valid in the present case and it is argued that this reflects the fact that the protein responds linearly to the development of electrostatic forces during the reaction. It is concluded that the present approach can be used to augment experimental studies in establishing the general validity of LFERs. It is noted, however, that such relationships are much more valid for transitions between different resonance structures than for transitions between reactants and product states.

Carbonic Anhydrases↗
PubMed2000

Computer simulation of cytotoxic and vascular effects of radiosurgery in solid and necrotic brain metastases.

PURPOSE: Solid and necrotic brain tumors respond to radiosurgery, although necrotic lesions often contain a significant proportion of hypoxic cells which cannot become reoxygenated during the short overall treatment time of single dose application. In addition to the direct cytotoxic action, delayed vascular occlusion followed by ischemic tumor cell death could contribute to the effect of radiosurgery. MATERIALS AND METHODS: In order to determine the impact of the two possible effects on tumor response, a 3-dimensional computer simulation was developed and fitted to response data obtained from 90 patients who were treated by LINAC radiosurgery for 1-3 brain metastases with median marginal doses of 20 Gy. Complete response rates were as follows: small, solid lesions (diameter 0.4-1 cm), 52% (12/23); large solid lesions (1.1-5.2 cm), 28% (17/60); large necrotic lesions, 12% (6/50). The 3-dimensional computer model simulated the growth of small solid and large, solid or necrotic tumors situated in a vascularized stroma. Oxygen supply, tumor cell division (cell cycle time 5 days), neovascularization, tumor cell kill by single dose irradiation (linear-quadratic model, alpha/beta=10 Gy, oxygen enhancement ratio 3.0) and time-dependent vascular occlusion (alpha/beta=3 Gy) were modeled by Monte-Carlo simulation techniques. RESULTS: In the presence of neovascularization, solid tumors with a hypoxic fraction of 1-2% developed. Without neoangiogenesis, central necrosis occurred, and tumors had a hypoxic fraction of 20-25%. Assuming a pure cytotoxic effect of radiosurgery, neither the dose-response relationship for the solid lesions of different size nor that for the large lesions with solid or necrotic appearance could be reproduced for any given level of radiosensitivity. This was only possible by introducing a vascular effect that led to the occlusion of >/=99% of the vessels at the border of the target volume within 1 year after irradiation. In the presence of the vascular effect, the apparent radiosensitivity of the tumor cells was increased by 50-100%. Calculations of the dose-equivalent for the vascular effect show that it contributes 19-33% of the overall effect of single dose radiosurgery. CONCLUSION: This simulation study suggests that the therapeutic effect of single radiosurgery in malignant brain tumors cannot be understood without the consideration of vascular effects. The computer model might serve as a basis for exploring new treatment modalities that modify both cytotoxic and vascular effects of radiosurgery.

Blood Vessels↗
PubMed1995

Filter wheel equalization for chest radiography: a computer simulation.

A chest radiographic equalization system using lung-shaped templates mounted on filter wheels is under development. Using this technique, 25 lung templates for each lung are available on two computer controlled wheels which are located in close proximity to the x-ray tube. The large magnification factor (> 10X) of the templates assures low-frequency equalization due to the blurring of the focal spot. A low-dose image is acquired without templates using a (generic) digital receptor, the image is analyzed, and the left and right lung fields are automatically identified using software developed for this purpose. The most appropriate left and right lung templates are independently selected and are positioned into the field of view at the proper location under computer control. Once the templates are positioned, acquisition of the equalized radiographic image onto film commences at clinical exposure levels. The templates reduce the exposure to the lung fields by attenuating a fraction of the incident x-ray fluence so that the exposure to the mediastinum and diaphragm areas can be increased without overexposing the lungs. A data base of 824 digitized chest radiographs was used to determine the shape of the specific lung templates, for both left and right lung fields. A second independent data base of 208 images was used to test the performance of the templates using computer simulations. The template shape characteristics derived from the clinical image data base are demonstrated. The detected exposure in the lung fields on conventional chest radiographs was found to be, on average, three times the detected exposure behind the diaphragm and mediastinum.(ABSTRACT TRUNCATED AT 250 WORDS)

Biophysical Phenomena↗
PubMed2001

Computer simulations of lung airway structures using data-driven surface modeling techniques.

Knowledge of human lung morphology is a subject critical to many areas of medicine. The visualization of lung structures naturally lends itself to computer graphics modeling due to the large number of airways involved and the complexities of the branching systems. In this study, a method of generating three-dimensional computer simulations of human lung airway networks using data-driven, surface modeling techniques is presented. By simulating the tubular airway structures and realistic bifurcation shapes, anatomically accurate representations of human lungs are obtained. These computer models are designed for use in computational fluid dynamic applications and particle trajectory analyses, and to be complimentary to medical imaging (gamma scintigraphy) protocols.

Computer Graphics↗
PubMed1989

Computer simulations of figure-ground discrimination in the visual system of the fly.

Figure-ground discrimination and pattern discrimination represent one of the most important problems in computer vision. Based on computational neuronal network model proposed by Reichardt et al. for figure-ground discrimination in the visual system of the fly, entire systematic computer simulations were carried out under nonstationary conditions. Results show that the model network and simulations have predictive power for behavioural experimental results. This paper proposes that motion perception and elementary pattern discrimination in human visual system may be mediated by some kind of figure-ground system with movement detectors as input layer.

Animals↗
PubMed2003

Computer simulation of cytoplasmic pH regulation mediated by the F-type H+-ATPase.

Cytoplasmic pH regulation mediated by the H(+)-ATPase was examined with the aid of computer simulation. The data obtained with our simulation model were consistent with the experimental data and the simulation clarified the following points that may be difficult to be clarified with experimental studies. (1) The change in the enzyme amount controlled by cytoplasmic pH was essential for the pH regulation. (2) No significant change in internal pH was observed in acidic surroundings even if the proton transport activity of the H(+)-ATPase changed greater than sixfold. (3) The cytoplasmic pH homeostasis can be maintained even when the biosynthetic rate of the enzyme decreased by 50%. These results suggested that this regulatory system has an ability to maintain the pH in homeostasis even under harsh conditions that decrease cellular metabolic activities.

Adenosine Triphosphatases↗
PubMed2001

Computer simulation study of the interface width of the liquid/liquid interface.

Four molecular dynamics computer simulations have been performed to study the intrinsic width and the width due to thermal fluctuations of the water/carbon tetrachloride interface. We observed that thermal fluctuations have a capillary wave character. The surface tension calculated by using capillary wave formalism shows a very good agreement with the value obtained from the components of the pressure tensor.

Journal Article↗
PubMed1995

Computer simulation of tablet motion in coating drum.

PURPOSE: The purpose is to develop a new method of finding optimal conditions in tablet coating operations with the use of computer simulation. METHODS: DEM(Discrete Element Method), which calculates trajectories of individual tablets by numerically integrating Newton's equations of motion, was used in this simulation. RESULTS: The effects of tablet size, tablet loading, rotation speed on mean surface time, circulation time, and surface time deviation agree qualitatively with experimental results by other workers. CONCLUSIONS: It is found that DEM is a useful method of predicting tablet motion in a coating drum.

Computer Simulation↗
PubMed1990

The behaviour of common measures of association used to assess a vaccination programme under complex disease transmission patterns--a computer simulation study of malaria vaccines.

Case-control studies have been evoked as important alternatives to randomized clinical trials in the evaluation of infectious disease interventions. Using computer simulations, we compare the behaviour of common measures of association derived from case-control studies in the context of a malaria vaccine programme administered under complex transmission conditions. Several simplifying assumptions of previous workers have been relaxed and the simulated conditions are endemic rather than epidemic. The common estimators of association used in case-control studies remain unbiased only in limited circumstances. The term dependent happenings, first defined by Ross in 1916, is resurrected. Since the number of people becoming infected is dependent on the number of people already infected, control programmes in infectious diseases produce direct as well as indirect effects. Three different study designs with different pairs of comparison populations are defined. The choice of comparison population can be used to differentiate direct from indirect effects. In order to clarify the direct effects of a vaccination programme the comparison groups must be subjected to identical transmission intensities. In contrast, the referent group must remain unaffected by consequences of the intervention to determine indirect effects.

Brazil↗
PubMed2003

Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans.

MOTIVATION: The ultimate goal of bioinformatics is to reconstruct biological systems in the computer. Since biological systems have many levels, it is important to focus on an appropriate level. In our first application of computer modeling to the early development of the nematode Caenorhabditis elegans, we focus on the cellular arrangement in early embryos. This plays a very important role in cell fate determination by cell-cell interaction, and is regarded as a system, one level higher than the system of gene regulation within cells. It is largely restricted by physical conditions that seemed feasible to model by computer. RESULTS: We constructed a computer model of the C.elegans embryo, currently up to the 4-cell stage, using a deformable and dividable triangulated network. The model is based solely on cellular-level dynamics. We found that the optimal ranges of three parameters that affect the elongation of dividing cells led, in computer simulations, to almost the same cellular arrangements as in real embryos. The nature of the model and the relationship with real embryos are discussed.

Animals↗
PubMed2005

Inter- and intraspecific resolution of nrDNA TRFLP assessed by computer-simulated restriction analysis of a diverse collection of ectomycorrhizal fungi.

An assessment of the inter- and intraspecific resolution of 5' nrDNA ITS TRFLP was conducted by computer-simulated restriction analysis of 316 ectomycorrhizal GenBank sequences. Generally, sequences with a similarity of < 90 % could be distinguished with two to three independent enzyme digests, although sequences with similarity > 95 % were likely to remain unresolved. Choice of restriction enzyme strongly influenced resolution, especially when less than three enzymes were used. Although our results showed that 5' nrDNA ITS TRFLP is a powerful tool for distinguishing between species of ectomycorrhizal fungi, closely related species, including species of Rhizopogon, Dermocybe, Hebeloma, and Lactarius produced indistinguishable 5' nrDNA ITS TRFLP--profiles. 5' nrDNA ITS TRFLP may also split a species, and the probability of this occurring reflected intraspecific sequence variation. For groups of closely related species, the use of 3' nrDNA ITS in conjunction with 5' nrDNA ITS produced improved resolution comparable with RFLP analyses. Overall, our results show that nrDNA ITS TRFLP is a valuable addition to the array of molecular tools available to ectomycorrhizal ecologists. However, simple assessments of ectomycorrhizal species diversity based on numbers of unique TRF created with a single restriction enzyme must be viewed with caution, as for each enzyme we examined, identical TRF common to groups of unrelated species were observed. In addition, to maximize the effectiveness of TRFLP in surveys of ectomycorrhizal fungi it will be useful to combine information from at least two independent enzyme digests in order to distinguish and track species in the field.

Basidiomycota↗
PubMed1997

Computer simulations to identify in polyproteins of FMDV OK1 and A12 strains putative nonapeptides with amino acid motifs for binding to BoLA class I A11 and A20 haplotype molecules.

The computer program "Findpatterns" was used to search FMDV- (OK1 and A12 strains) coded structural and nonstructural proteins for the availability of putative proteasome-generated nonapeptides with motifs reported for BoLA class I A11 and A20 haplotypes. These BoLA class I A11 and A20 nonapeptide motifs are identical to motifs of nonapeptides that interact with the peptide binding grooves of HLA class I B35 and B27 haplotypes, respectively. The computer findpattern program was used to analyze the FMDV-coded polyproteins for proteolytically cleavable nonapeptides with motifs for binding to the peptide binding grooves of BoLA class I A11 or 20 haplotypes. The computer simulations revealed that FMDV-infected cells (keratinocytes and antigen presenting cells. e.g., dendritic Langerhans cells in bovines) may be able to present viral nonapeptides to CD8+ cytolytic T cells (CTLs) in a BoLA-restricted manner. The role of the cellular arm of the immune response in the protection of bovines against FMDV is not known. Thus, the present computer analysis may encourage further experiments to develop a new generation of FMDV nonapeptide vaccines to stimulate the anti-FMDV cytolytic T cell response in bovine so this would complement the humoral immune response achieved by immunization with the inactivated virus vaccine.

Amino Acid Sequence↗
PubMed1998

Animats: computer-simulated animals in behavioral research.

The term animat refers to a class of simulated animals. This article is intended as a nontechnical introduction to animat research. Animats can be robots interacting with the real world or computer simulations. In this article, the use of computer-generated animats is emphasized. The scientific use of animats has been pioneered by artificial intelligence and artificial life researchers. Behavior-based artificial intelligence uses animats capable of autonomous and adaptive activity as conceptual tools in the design of usefully intelligent systems. Artificial life proponents view some human artifacts, including informational structures that show adaptive behavior and self-replication, as animats may do, as analogous to biological organisms. Animat simulations may be used for rapid and inexpensive evaluation of new livestock environments or management techniques. The animat approach is a powerful heuristic for understanding the mechanisms that underlie behavior. The simple rules and capabilities of animat models generate emergent and sometimes unpredictable behavior. Adaptive variability in animat behavior may be exploited using artificial neural networks. These have computational properties similar to natural neurons and are capable of learning. Artificial neural networks can control behavior at all levels of an animat's functional organization. Improving the performance of animats often requires genetic programming. Genetic algorithms are computer programs that are capable of self-replication, simulating biological reproduction. Animats may thus evolve over generations. Selective forces may be provided by a human overseer or be part of the simulated environment. Animat techniques allow researchers to culture behavior outside the organism that usually produces it. This approach could contribute new insights in theoretical ethology on questions including the origins of social behavior and cooperation, adaptation, and the emergent nature of complex behavior. Animat studies applied to domestic animals have been few so far, and have involved simulations of space use by swine. I suggest other applications, including modeling animal movement during human handling and the effects of environmental enrichment on the satisfaction of behavioral needs. Appropriate use of animat models in a research program could result in savings of time and numbers of animals required. This approach may therefore come to be viewed as both ethically and economically advantageous.

Animal Welfare↗
PubMed1996

Force transmission and stress distribution in a computer-simulated model of the kidney: an analysis of the injury mechanisms in renal trauma.

Injury mechanisms in renal trauma were investigated by analyzing the stress distributions within a two-dimensional computer-simulated model of the kidney. In biomechanics, damage to biological tissue is primarily caused by stresses resulting in tissue deformation beyond recovery limits. Segmental surface force was applied to the model and the resulting stress distributions were analyzed. Maximum stress concentrations were found at the periphery of the kidney model. Stresses were caused by the combined effect of the applied force and the reaction generated by the liquid-filled inner compartment as a function of its hydrostatic pressure. Maximum stress concentrations corresponded to typical injury sites observed clinically. Our findings suggest that a similar mechanism may play a crucial role in renal trauma. Renal injuries as well as the higher trauma susceptibility of hydronephrotic kidneys and renal cysts could thus be explained. The role of computer models in injury biomechanics research is discussed.

Biomechanical Phenomena↗
PubMed2005

Computational simulations of the total cavo-pulmonary connection: insights in optimizing numerical solutions.

The Fontan procedure is a palliative surgical technique that is used to treat patients with congenital heart defects that include complex lesions such as those with a hypoplastic ventricle. In vitro, in vivo, and computational models of a set of modifications to the Fontan procedure, called the total cavopulmonary connection (TCPC), have been developed. Using these modeling methods, attempts have been made at finding the most energy efficient TCPC circuit. Computational modeling has distinct advantages to other modeling methods. However, discrepancies have been found in validation studies of TCPC computational models. There is little in the literature available to help explain and correct for such discrepancies. Differences in computational results can occur when choosing between steady flow versus transient flow numerical solvers. In this study transient flow solver results were shown to be more consistent with results from previous TCPC in vitro experiments. Using a transient flow solver we found complex fluctuating flow patterns can exist with steady inflow boundary conditions in computational models of the TCPC. To date such findings have not been reported in the literature. Furthermore, our computational modeling results suggest fluctuating flow patterns as well as the magnitudes of these secondary flow structures diminish if the TCPC offset between vena cavae is increased or if flanged connections are added. An association was found between these modifications and improvements in TCPC circuit flow efficiencies. In summary, development of accurate computational simulations in the validation process is critical to efforts in finding the most efficient TCPC circuits, efforts aimed at potentially improving the long term outcome for Fontan patients.

Blood Flow Velocity↗
PubMed2002

Computer simulation of forearm rotation in angular deformities: a new therapeutic approach.

A new computer-assisted simulation of forearm rotation based on orthogonal radiographs of the forearm is introduced. A new computer program called STOOPS was developed based on a new kinematic model describing motion of the radius and ulna in regards to forearm rotation. The computer program allows simulation of angular deformities of the forearm and can predict subsequent rotational impairment. To validate the program, the authors compared the actual pronation of 21 patients with angular deformities with the predicted pronation by STOOPS. The mean difference between the simulated and clinically measured pronation was 5.6 degrees (S.D. 9.4 degrees ). There was no statistically significant difference between the measured and simulated values. Using the computer-assisted simulation may help predict impairment of pronation due to angular deformities. If clinical impairment differs from the computed one, other causes such as lesions to the interosseous membrane or the adjacent joints have to be excluded. If values are similar, correction of the angular deformities should result in improvement of forearm pronation.

Adolescent↗