Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “computational modeling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed1998

A computer model of gas exchange during cardiopulmonary resuscitation.

This paper presents a computer model of gas exchange during cardiopulmonary resuscitation (CPR) that permits independent adjustment of inspired air content (16% O2 and 4.5% CO2 present in mouth-to-mouth (MTM) ventilation or ambient air), shunt, deadspace, diffusion impairment, cardiac output, and ventilation. The model contains 15500 acini, each with its own blood supply. Gas exchange occurs at each perfused and ventilated acinus. Arterial P(O2) and P(CO2) are calculated from the summed arterial blood flow using standard formulae. The model and simulations show that MTM ventilation provides inadequate oxygenation when the victim is at high altitude or has diffusion impairment. They also show that analysis of inspired and expired gas concentrations to measure gas exchange primarily measures wash in and wash out of gas when cardiac output is low and that this explains the negative oxygen consumption and carbon dioxide production measured in a previous study.

Carbon Dioxide↗
PubMed1995

An evaluation of the accuracy of ageing horses by their dentition: can a computer model be accurate?

The prediction of the age of a horse from its dentition has been widely accepted as an accurate technique, but recent reports have questioned this belief. In this study the dental features of 434 thoroughbreds of known age were documented and a multiple regression equation was calculated from the 13 dental features which had the highest correlation with true age. The accuracy of the ages assessed by a computer model were compared with the ages estimated by experienced equine clinicians. There was little difference between the accuracy of the computer model and the human observers, and neither method provided an acceptable level of accuracy for ageing horses from their dentition.

Age Determination by Teeth↗
PubMed1992

Initial results for automated computational modeling of patient-specific electromagnetic hyperthermia.

Developments in finite-difference time-domain (FD-TD) computational modeling of Maxwell's equations, super-computer technology, and computed tomography (CT) imagery open the possibility of accurate numerical simulation of electromagnetic (EM) wave interactions with specific, complex, biological tissue structures. One application of this technology is in the area of treatment planning for EM hyperthermia. In this paper, we report the first highly automated CT image segmentation and interpolation scheme applied to model patient-specific EM hyperthermia. This novel system is based on sophisticated tools from the artificial intelligence, computer vision, and computer graphics disciplines. It permits CT-based patient-specific hyperthermia models to be constructed without tedious manual contouring on digitizing pads or CRT screens. The system permits in principle near real-time assistance in hyperthermia treatment planning. We apply this system to interpret actual patient CT data, reconstructing a 3-D model of the human thigh from a collection of 29 serial CT images at 10 mm intervals. Then, using FD-TD, we obtain 2-D and 3-D models of EM hyperthermia of this thigh due to a waveguide applicator. We find that different results are obtained from the 2-D and 3-D models, and conclude that full 3-D tissue models are required for future clinical usage.

Computer Simulation↗
PubMed1991

A massively parallel computer model of propagation through a two-dimensional cardiac syncytium.

A computer model of electrical propagation through a two-dimensional (2D) sheet of cardiac tissue has been developed to run on the massively parallel processor Connection Machine (CM-2) computer. The transmembrane ionic currents in each of 16,384 (128 x 128) 100 x 100 microns 2 patches of cardiac tissue are described by modified Beeler-Reuter membrane equations. These equations, along with the parabolic differential equation derived from 2D cable theory, are solved in parallel to study normal and abnormal 2D propagation. The sheet is paced with planar waves at a basic cycle length of 500 msec (control). When a premature ectopic stimulus of sufficient strength and appropriate timing is then applied to a local region of the syncytium, one of two types of reentry is observed: (a) stable figure-of-eight reentry, or (b) unstable but self-sustaining "fibrillation-like" reentry. During this fibrillatory activity, action potential durations are 79.8 +/- 36.8 msec (control = 244.9 +/- 0.9 msec) and coupling intervals average 96.7 +/- 31.3 msec (control = 500 +/- 0 msec). We also observed that passive electrotonically-induced depolarization of already refractory tissue extended the refractory period of that tissue, and that the duration of this extension depended on the magnitude of the electrotonic effect.

Action Potentials↗
PubMed1997

Computed model of gadolinium enhanced MRI of breast disease.

OBJECTIVE: Investigation has shown that the most useful MRI finding for the detection of breast cancer is enhancement following in travenous contrast. However, many widely different imaging protocols have been used. The purpose of this study is to explicate factors that affect the signal intensity of breast lesions after intravenous gadolinium. METHODS AND MATERIALS: A computer model was developed using equations based on published data. The effect of gadolinium on breast tissues was calculated using the model with appropriate values for baseline tissue relaxation times, relaxivity of gadolinium at the given field strength and concentration of gadolinium based on published data, for the TR, TE, flip angle and field strength of several published sequences used for enhanced breast MRI. RESULTS: The computer model allows comparison of the performance of different sequences, which can be displayed graphically. These vary in their performance, largely dependent on T1 weighting. Enhancement is also affected by the baseline of the T1 of the lesion and sensitivity of the sequence to gadolinium. Malignant lesions demonstrate greater observed enhancement than predicted when assuming symmetric distribution of contrast, indicating there is greater accumulation of gadolinium, accounting for the differential enhancement between benign and malignant lesions. CONCLUSIONS: MRI sequences vary greatly in their demonstration of enhancement after intravenous gadolinium contrast. Numerical diagnostic criteria such as % signal intensity change must be interpreted with care when using a different sequence than that on which the criterion was developed. There is preferentially greater accumulation of contrast in malignant lesions, whether due to angiogenesis or altered permeability.

Algorithms↗
PubMed1987

Analysis of the dosage controversy in recess-resect and Faden surgery with the Robinson computer model of eye movements.

In recess-resect surgery, the dosage depends on the preoperative angle of squint and on the ratio between squint-angle reduction and dosage that the surgeon has found in previous surgery. Recommendations pertaining to this ratio vary widely among authors. Some say a recession does more than a resection, while others believe the opposite is true. Finally, most find a lower ratio at smaller preoperative angles of squint. We investigated the matter, using our modified version of the Robinson computer model of eye movements. We calculated the amounts of surgery needed to reduce 10, 15, 20, 25, and 30 degree angles of squint to zero. The increase of the ratio at large angles of squint was indeed predicted by the model. The decrease at small angles of squint, however, was not predicted by the model. We found it impossible to model the decrease of the ratio at small preoperative angles of squint. The ratios for recess and resect surgery were approximately similar. We present an inventory of the possible causes of the discrepancies. In addition, we calculated the effects of Faden surgery and found that the predictions of the computer model correspond closely to reality.

Computers↗
PubMed1999

Construction and optimisation of a computer model for a bacterial membrane.

The main steps in the construction of a computer model for a bacterial membrane are described. The membrane has been built of 72 lipid molecules, 54 of which being 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidylethanolamine (POPE) and 18--1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidyl-rac-glycerol (POPG) molecules (thus in the proportion of 3:1). The membrane was hydrated with 1955 water molecules (approximately 27 water molecules per lipid). To neutralise the electronic charge (-e) on each POPG molecule, 18 sodium ions (Na+) were added to the membrane close to the POPG phosphate groups. The atomic charges on the POPE and POPG headgroups were obtained from ab initio quantum mechanical restrained electrostatic potential fitting (RESP) (Bayly et al., 1993, J. Phys. Chem. 97, 10269) using the GAMESS program at the 6-31G* level (Schmidt et al., 1993, J. Comput. Chem. 14, 1347). The model constructed in this way provided an initial structure for subsequent molecular dynamics simulation studies intended to elucidate the atomic level interactions responsible for the structure and dynamics of the bacterial membrane.

Bacteria↗
PubMed1993

Heterogeneity in retinal disease and the computational model of the human-rod response.

Abnormal rod-receptor activity can be quantitatively assessed in humans by fitting a computational model of the rod's response to the leading edge of the a wave of the electroretinogram. One purpose of the present study was to compare two procedures for fitting the model to the electroretinogram. A computationally simpler method gives comparable results to the more labor-intensive method used previously. This finding holds for both normal observers and patients with retinodegenerative disease that affects the receptors unevenly. A second purpose of the present study was to consider the effects of a heterogeneous disease process on the parameters of the model. a waves from a heterogeneous retina are computer simulated and are fitted with the receptor model. This analysis suggests that the model will overestimate the change in the healthiest rods and will underestimate the percentage of the rods that are significantly affected.

Adult↗
PubMed1986

Computer models and images of the cutaneous surface.

This article describes how computer models of the skin can be used to obtain objective information about surface-altering events. Although alterations produced by various forms of therapy are being emphasized, more needs to be known about alterations produced by aging, environmental factors, and disease. The term "automated optical surfometry" has been applied to the method described in this chapter. (The term "optical profilometry" has also been used. Because this designation was applied at an earlier time to a method that is entirely different, the use of the word "optical surfometry" appears to be preferable as well as more accurate). Space limitations made it possible to allude only briefly to some of the other techniques that are being used to learn more about the configuration and dynamics of the surface of the skin. The development of imaging and modeling methods for topographic studies of the skin owe their origins in large measure to the advent of inexpensive computer technology.

Adolescent↗
PubMed2004

Intracoronary administration of FGF-2: a computational model of myocardial deposition and retention.

This study uses a computational model to characterize the myocardial deposition and retention of basic fibroblast growth factor (FGF-2) at the cellular level after intracoronary (IC) administration of exogenous FGF-2. The model is applied to the in situ conditions present within the myocardium of a dog for which the plasma pharmacokinetics resulting from IC injection of FGF-2 were recorded. Our estimates show that the processes involved in FGF-2 signaling are not diffusion limited; rather, the response time is determined by the reaction time of FGF-2 binding to cell surface receptors. Additionally, the processes of receptor secretion and internalization are found to play crucial roles in the FGF-2 dynamics; future experiments are required to quantify these processes. The model predictions obtained in this study suggest that IC administration of FGF-2 via either a single bolus or repetitive injections causes a transient increase (time scale of hours) in myocardial FGF-2 concentration if the endogenous level of free interstitial FGF-2 is low enough to allow permeation of FGF-2 molecules from the microvascular to the interstitial spaces. The model shows that the majority (64%) of the extracellular FGF-2 ligands are located within the interstitium, and similar fractions are found in the basement membrane and extracellular matrix. Among the FGF-2 molecules found within the interstitium, 2% are free and 98% are bound to interstitial heparan sulfate proteoglycans. These results support the theory of extracellular control of the bioavailability of FGF-2 via dynamic storage of FGF-2 within the basement membrane and extracellular matrix.

Animals↗
PubMed2004

A computational model of the human left-ventricular epicardial myocyte.

A computational model of the human left-ventricular epicardial myocyte is presented. Models of each of the major ionic currents present in these cells are formulated and validated using experimental data obtained from studies of recombinant human ion channels and/or whole-cell recording from single myocytes isolated from human left-ventricular subepicardium. Continuous-time Markov chain models for the gating of the fast Na(+) current, transient outward current, rapid component of the delayed rectifier current, and the L-type calcium current are modified to represent human data at physiological temperature. A new model for the gating of the slow component of the delayed rectifier current is formulated and validated against experimental data. Properties of calcium handling and exchanger currents are altered to appropriately represent the dynamics of intracellular ion concentrations. The model is able to both reproduce and predict a wide range of behaviors observed experimentally including action potential morphology, ionic currents, intracellular calcium transients, frequency dependence of action-potential duration, Ca(2+)-frequency relations, and extrasystolic restitution/post-extrasystolic potentiation. The model therefore serves as a useful tool for investigating mechanisms of arrhythmia and consequences of drug-channel interactions in the human left-ventricular myocyte.

Algorithms↗
PubMed2005

Texture synthesis and perception: using computational models to study texture representations in the human visual system.

Traditionally, texture perception has been studied using artificial textures made of random dots or repeated shapes. At the same time, computer algorithms for natural texture synthesis have improved dramatically. We seek to unify these two fields through a psychophysical assessment of a particular computational model, providing insight into which statistics are most vital for natural texture perception. We employ Portilla and Simoncelli's texture synthesis algorithm, a parametric model that mimics computations carried out in human vision. We find an intriguing interaction between texture type (periodic, structured, or 3-D textures) and image statistics (autocorrelation function and filter magnitude correlations), suggesting different representations may be employed for these texture families under pre-attentive viewing.

Adult↗
PubMed2006

Development of tinnitus-related neuronal hyperactivity through homeostatic plasticity after hearing loss: a computational model.

Tinnitus, the perception of a sound in the absence of acoustic stimulation, is often associated with hearing loss. Animal studies indicate that hearing loss through cochlear damage can lead to behavioral signs of tinnitus that are correlated with pathologically increased spontaneous firing rates, or hyperactivity, of neurons in the auditory pathway. Mechanisms that lead to the development of this hyperactivity, however, have remained unclear. We address this question by using a computational model of auditory nerve fibers and downstream auditory neurons. The key idea is that mean firing rates of these neurons are stabilized through a homeostatic plasticity mechanism. This homeostatic compensation can give rise to hyperactivity in the model neurons if the healthy ratio between mean and spontaneous firing rate of the auditory nerve is decreased, for example through a loss of outer hair cells or damage to hair cell stereocilia. Homeostasis can also amplify non-auditory inputs, which then contribute to hyperactivity. Our computational model predicts how appropriate additional acoustic stimulation can reverse the development of such hyperactivity, which could provide a new basis for treatment strategies.

Acoustic Stimulation↗
PubMed2005

Uncertainty analysis for computer model projections of hurricane losses.

Projecting losses associated with hurricanes is a complex and difficult undertaking that is wrought with uncertainties. Hurricane Charley, which struck southwest Florida on August 13, 2004, illustrates the uncertainty of forecasting damages from these storms. Due to shifts in the track and the rapid intensification of the storm, real-time estimates grew from 2 to 3 billion dollars in losses late on August 12 to a peak of 50 billion dollars for a brief time as the storm appeared to be headed for the Tampa Bay area. The storm hit the resort areas of Charlotte Harbor near Punta Gorda and then went on to Orlando in the central part of the state, with early poststorm estimates converging on a damage estimate in the 28 to 31 billion dollars range. Comparable damage to central Florida had not been seen since Hurricane Donna in 1960. The Florida Commission on Hurricane Loss Projection Methodology (FCHLPM) has recognized the role of computer models in projecting losses from hurricanes. The FCHLPM established a professional team to perform onsite (confidential) audits of computer models developed by several different companies in the United States that seek to have their models approved for use in insurance rate filings in Florida. The team's members represent the fields of actuarial science, computer science, meteorology, statistics, and wind and structural engineering. An important part of the auditing process requires uncertainty and sensitivity analyses to be performed with the applicant's proprietary model. To influence future such analyses, an uncertainty and sensitivity analysis has been completed for loss projections arising from use of a Holland B parameter hurricane wind field model. Uncertainty analysis quantifies the expected percentage reduction in the uncertainty of wind speed and loss that is attributable to each of the input variables.

Journal Article↗
PubMed2001

A computational model of dendrite elongation and branching based on MAP2 phosphorylation.

We introduce a new computational model of dendritic development in neurons. In contrast to previous models, our model explicitly includes cellular mechanisms involved in dendritic development. It is based on recent experimental data which indicates that the phosphorylation state of microtubule-associated protein 2 (MAP2) may play a key role in controlling dendritic elongation and branching (Audesirk et al., 1997). Dephosphorylated MAP2 favours elongation by promoting microtubule polymerization and bundling, whilst branching is more likely to occur when MAP2 is phosphorylated and microtubules are spaced apart. In the model, the rate of elongation and branching is directly determined by the ratio of phosphorylated to dephosphorylated MAP2. This is regulated by calmodulin-dependent protein kinase II (CaMKII) and calcineurin, which are both dependent on the intracellular calcium concentration. Results from computer simulations of the model suggest that the wide variety of branching patterns observed among different cell types may be generated by the same underlying mechanisms and that elongation and branching are not necessarily independent processes. The model predicts how the branching pattern will change following manipulations with calcium, CaMKII and MAP2 phosphorylation.

Animals↗
PubMed1983

Computer modeling of muscle phosphofructokinase kinetics.

The kinetics of the phosphofructokinase reaction were studied by computer modeling. A general random order, two-state allosteric model, of which the Monod--Wyman--Changeux model is a limiting case, was found to most accurately reproduce the experimental observations of Pettigrew & Frieden (1979 a,b). A simplified model with Hill coefficients was found to fit almost as well. In these models substrates bind preferentially to and stabilize the enzyme in the R state, and ATPH3-, the inhibitory species, binds preferentially to and stabilizes the enzyme in the T state. Enzymatic activity is regulated by conversion from the R to the T state, which is effected by protonation, especially of the uncomplexed enzyme, but the experimental data are inadequate for accurate estimation of the pKa of the enzyme. Random order binding of substrates is an important cause of sigmoidal kinetics. Additional experiments that would aid in the discrimination among rival models are described.

Adenosine Triphosphate↗
PubMed2003

Frontal and parietal participation in problem solving in the Tower of London: fMRI and computational modeling of planning and high-level perception.

This study triangulates executive planning and visuo-spatial reasoning in the context of the Tower of London (TOL) task by using a variety of methodological approaches. These approaches include functional magnetic resonance imaging (fMRI), functional connectivity analysis, individual difference analysis, and computational modeling. A graded fMRI paradigm compared the brain activation during the solution of problems with varying path lengths: easy (1 and 2 moves), moderate (3 and 4 moves) and difficult (5 and 6 moves). There were three central findings regarding the prefrontal cortex: (1) while both the left and right prefrontal cortices were equally involved during the solution of moderate and difficult problems, the activation on the right was differentially attenuated during the solution of the easy problems; (2) the activation observed in the right prefrontal cortex was highly correlated with individual differences in working memory (measured independently by the reading span task); and (3) different patterns of functional connectivity were observed in the left and right prefrontal cortices. Results obtained from the superior parietal region also revealed left/right differences; only the left superior parietal region revealed an effect of difficulty. These fMRI results converged upon two hypotheses: (1) the right prefrontal area may be more involved in the generation of a plan, whereas the left prefrontal area may be more involved in plan execution; and (2) the right superior parietal region is more involved in attention processes while the left homologue is more of a visuo-spatial workspace. A 4CAPS computational model of the cognitive processes and brain activation in the TOL task integrated these hypothesized mechanisms, and provided a reasonably good fit to the observed behavioral and brain activation data. The multiple research approaches presented here converge on a deepening understanding of the combination of perceptual and conceptual processes in this type of visual problem solving.

Adolescent↗
PubMed2005

Assessment of different computational models for generation of x-ray spectra in diagnostic radiology and mammography.

Different computational methods based on empirical or semi-empirical models and sophisticated Monte Carlo calculations have been proposed for prediction of x-ray spectra both in diagnostic radiology and mammography. In this work, the x-ray spectra predicted by various computational models used in the diagnostic radiology and mammography energy range have been assessed by comparison with measured spectra and their effect on the calculation of absorbed dose and effective dose (ED) imparted to the adult ORNL hermaphroditic phantom quantified. This includes empirical models (TASMIP and MASMIP), semi-empirical models (X-rayb&m, X-raytbc, XCOMP, IPEM, Tucker et al., and Blough et al.), and Monte Carlo modeling (EGS4, ITS3.0, and MCNP4C). As part of the comparative assessment, the K x-ray yield, transmission curves, and half value layers (HVLs) have been calculated for the spectra generated with all computational models at different tube voltages. The measured x-ray spectra agreed well with the generated spectra when using X-raytbc and IPEM in diagnostic radiology and mammography energy ranges, respectively. Despite the systematic differences between the simulated and reference spectra for some models, the student's t-test statistical analysis showed there is no statistically significant difference between measured and generated spectra for all computational models investigated in this study. The MCNP4C-based Monte Carlo calculations showed there is no discernable discrepancy in the calculation of absorbed dose and ED in the adult ORNL hermaphroditic phantom when using different computational models for generating the x-ray spectra. Nevertheless, given the limited flexibility of the empirical and semi-empirical models, the spectra obtained through Monte Carlo modeling offer several advantages by providing detailed information about the interactions in the target and filters, which is relevant for the design of new target and filter combinations and optimization of radiological imaging protocols.

Computer Simulation↗