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PubMed2003

Accuracy of a system for creating 3D computer models of dental arches.

Three-dimensional imaging of dental tissues will have a major impact in dentistry if the images are accurate. The purpose of this study was to measure the accuracy and precision of a system for creating three-dimensional images of dental arches. Using vinyl polysiloxane impression materials and improved dental stone, we made 10 stone casts of a "dental" standard with known dimensions. The impressions and casts were scanned by means of a Comet 100 optical scanner. Custom software created three-dimensional images (computer models) from the scanned data. Accuracy was defined as the average of the absolute differences between the computer models and the standard. Precision was the standard deviation of accuracy over 10 repeated measures. Software processing improved the accuracy of the scanner data. Accuracy +/- precision for the casts and impressions was 0.024 +/- 0.002 mm and 0.013 +/- 0.003 mm, respectively. The system produced computer models with sufficient accuracy for clinical application.

Algorithms↗

PubMed1999

A computational model for visual selection.

We propose a computational model for detecting and localizing instances from an object class in static gray-level images. We divide detection into visual selection and final classification, concentrating on the former: drastically reducing the number of candidate regions that require further, usually more intensive, processing, but with a minimum of computation and missed detections. Bottom-up processing is based on local groupings of edge fragments constrained by loose geometrical relationships. They have no a priori semantic or geometric interpretation. The role of training is to select special groupings that are moderately likely at certain places on the object but rate in the background. We show that the statistics in both populations are stable. The candidate regions are those that contain global arrangements of several local groupings. Whereas our model was not conceived to explain brain functions, it does cohere with evidence about the functions of neurons in V1 and V2, such as responses to coarse or incomplete patterns (e.g., illusory contours) and to scale and translation invariance in IT. Finally, the algorithm is applied to face and symbol detection.

Algorithms↗

PubMed1987

A computational model of reasoning from the clinical literature.

This paper explores the premise that a formalized representation of empirical studies can play a central role in computer-based decision support. The specific motivations underlying this research include the following propositions: Reasoning from experimental evidence contained in the clinical literature is central to the decisions physicians make in patient care. A computational model, based upon a declarative representation for published reports of clinical studies, can drive a computer program that selectively tailors knowledge of the clinical literature as it is applied to a particular case. The development of such a computational model is an important first step toward filling a void in computer-based decision support systems. Furthermore, the model may help us better understand the general principles of reasoning from experimental evidence both in medicine and other domains. Roundsman is a developmental computer system which draws upon structured representations of the clinical literature in order to critique plans for the management of primary breast cancer. Roundsman is able to produce patient-specific analyses of breast cancer management options based on the 24 clinical studies currently encoded in its knowledge base. The Roundsman system is a first step in exploring how the computer can help to bring a critical analysis of the relevant literature to the physician, structured around a particular patient and treatment decision.

Artificial Intelligence↗

PubMed1999

[Study of the posterior cruciate ligament using a 3D computer model: ligament biometry during flexion, application to surgical replacement of the ligament].

We have developed a 3D computed model of the knee joint, constructed from MRI acquisitions in a living individual. We have used this model to perform an anatomic and biometric study of the posterior cruciate ligament (PCL) during flexion, and an assessment of the optimal location for an intraarticular graft. The method used a 3D computed model constructed from MRI acquisitions during knee flexion (0 to 75 degrees). The range of motion was limited by a positioning device. We took 13 acquisitions from 0 to 75 degrees of flexion. Each acquisition consisted of 21 sagittal cross sections of 3 mm slice thickness. We used the Delaunay reconstruction to obtain a 3D geometric model. A matching process to fix one part of the articulation during the movement, allows for the kinematic analysis of the tibia relative to the fixed femur. This model allows to follow the displacement of a bone point during knee flexion. Knowing the relative displacement of the bone insertions of the ligament, it may be possible to determine the length of the PCL and its bands, to evaluate the length variation during movement, and to determine the optimal location for the insertion of an intraarticular graft, that would lead to the least stretch during flexion. It was found that the mean length of the PCL was 30.2 mm, with the posterior band being 30% longer than the anterior band. During flexion the posterior band increases its length by 10% at 50 degrees flexion, and by 20% at 75 degrees flexion. The anterior band stretches more, to reach 40% elongation at 75 degrees flexion. The best position for insertion of a graft seems to be in the posterolateral portion of the anatomic tibial insertion, and posterior to the anatomic femoral insertion. This method confirms the data in the literature, states precisely the length of the different bands of the PCL, and specifies the points of insertion for a graft, which lead to the least variation in length during flexion.

Biometry↗

PubMed1998

Using computer modeling to help identify patient subgroups in clinical data repositories.

OBJECTIVE: The ability to accurately and efficiently identify patient cases of interest in a hospital information system has many important clinical, research, educational and administrative uses. The identification of cases of interest sometimes can be difficult. This paper describes a two-stage method for searching for cases of interest. DESIGN: First, a Boolean search is performed using coded database variables. The user classifies the retrieved cases as being of interest or not. Second, based on the user-classified cases, a computer model of the patient cases of interest is constructed. The model is then used to help locate additional cases. These cases provide an augmented training set for constructing a new computer model of the cases of interest. This cycle of modeling and user classification continues until halted by the user. MEASUREMENTS: This paper describes a pilot study in which this method is used to identify the records of patients who have venous thrombosis. RESULTS: The results indicate that computer modeling enhances the identification of patient cases of interest.

Bayes Theorem↗

PubMed2001

Computational models of normal and abnormal action potential propagation in cardiac tissue: linking experimental and clinical cardiology.

Computational models have the potential to make a huge impact on our understanding of normal and abnormal cardiac function. The aim of this article is to review tools that have been developed to simulate the electrophysiology of cardiac cells and tissue, and to show how computational models have been used to gain insight into normal and abnormal action potential propagation. Some of the practical problems experienced in the development and application of these models are described, and examples are given.

Action Potentials↗

PubMedDate not supplied

Parallel neural systems for classical conditioning: support from computational modeling.

Classical conditioning has been explained by two main types of theories that postulate different learning mechanisms. Rescorla and Wagner (1972) put forth a theory in which conditioning is based on the ability of the US to drive learning through error correction. Alternatively, Mackintosh (1973) put forth a theory in which the ability of the CS to be associated with the unconditioned stimulus is modulated. We have proposed a reconciliation of these two mechanisms as working in parallel within different neural systems: a cerebellar system for US modulation and a hippocampal system for CS modulation. We developed a computational model of cerebellar function in eyeblink conditioning based on the error correction mechanism of the Rescorla-Wagner rule in which learning-related activity from the cerebellum inhibits the inferior olive, which is the US input pathway to the cerebellum (Gluck et al., 1994). We developed a computational model of the hippocampal region that forms altered representations of conditioned stimuli based on their behavioral outcomes (Gluck & Myers, 1993; Myers et al., 1995). Overall, computational modeling and empirical findings support the idea that, at least in the case of eyeblink conditioning, there may be two different neural systems: the cerebellum which mediates US-based error correction and hippocampus which alters representations of CSs.

Animals↗

PubMedDate not supplied

Computational modelling of blood flow through curved stenosed arteries.

A computational model of three-dimensional blood flow in curved arteries with elliptic stenosis was developed. Two groups of models, (a) different angles of curvature and (b) degrees of stenosis, have been studied under typical conditions for stenosed coronary artery. Useful information on the haemodynamics has been obtained. Results of pressure drop show that the presence of the curvature augments the increased flow resistance due to stenotic lesions. The study also demonstrates the significant presence of secondary flow in a curved artery. In addition, the results have shown that the secondary flow in a curved artery brings about elevated shear stress on the vessel wall. These results indicated that both curvature and stenosis should be considered together by cardiologists to assess or quantify the severity of the stenosis. This study employed a powerful computer-aided design (CAD) package to construct the model and a commercial computational fluid dynamics (CFD) code for the analysis of blood flow in stenosed arteries. The long-term application of this form of research promises to be an effective tool for gaining insights into the pathology of arterial diseases.

Arteries↗

PubMed1993

Regularity of cochlear nucleus stellate cells: a computational modeling study.

This article reports on a computational modeling study designed to investigate the generation of the transient chopper response of cochlear nucleus stellate cells. The model is based on a simulation of the auditory periphery which feeds a generic stellate-cell model. Physiological recordings of transient chopper units in response to short, best frequency, tone bursts show a brief initial period (typically < 10 ms) of rapid rate adaptation as evidenced by a rapid rise in mean interspike interval. Associated with this rate adaptation is a significant increase in firing irregularity. The changes in rate and irregularity have recently been attributed to the activation of noisy inhibitory inputs on the cell [e.g., Banks and Sachs, J. Neurophysiol. 65, 606-629 (1991)]. However, the results show that the transient chopper response pattern can be generated without the need for inhibitory inputs. The transience of the initial chopping pattern is sensitive to the following model parameters: (a) the firing threshold of the cell, (b) the number of excitatory inputs that converge on the cell, and (c) the magnitude of the current delivered to the cell for each active input. The response was also found to be relatively insensitive to changes in the degree of dendritic filtering imposed on the auditory-nerve input. The results of each simulation can be explained by considering the pattern of depolarization the cell receives during the course of a tone burst.

Acoustic Stimulation↗

PubMed1990

The use of selective inhibitors and computer modelling to evaluate the role of specific high affinity cyclic AMP phosphodiesterases in the hormonal regulation of hepatocyte intracellular cyclic AMP concentrations.

Using experimentally derived data for the activities and kinetic constants of hepatocyte cyclic AMP phosphodiesterase isoenzymes together with the derived changes in adenylate cyclase activity, due to stimulation and subsequent desensitization by glucagon, a computer model was established to simulate hepatocyte cyclic AMP metabolism. The established ability of glucagon to activate the 'dense-vesicle' cyclic AMP phosphodiesterase by eliciting its cyclic AMP-dependent phosphorylation was shown on the model to be capable of eliciting a profound reduction in the glucagon-stimulated increase in intracellular cyclic AMP. This was consistent with experimentally derived observations using the compound ICI 118233 which was used to inactivate the 'dense-vesicle' enzyme selectively. The non-hydrolysable adenosine agonist N6 (phenylisopropyl)-adenosine (PIA), which prevents glucagon pre-treatment of hepatocytes blocking the ability of insulin to stimulate the peripheral plasma membrane cyclic AMP phosphodiesterase, is shown here to accentuate the ability of insulin to decrease glucagon-elevated intracellular cyclic AMP concentrations. This effect was obliterated using the compound ICI 63197, a selective inhibitor of the peripheral plasma membrane phosphodiesterase. Computer modelling studies, taking into account experimentally derived actions in insulin in activating the peripheral plasma membrane phosphodiesterase, confirmed the potential of this enzyme to decrease intracellular cyclic AMP concentrations. Modelling of the putative effect of an insulin 'mediator' in activating the two cyclic GMP-stimulated cyclic AMP phosphodiesterase isoenzymes was shown to elicit a decrease in intracellular cyclic AMP concentrations which was comparable to that caused by insulin's action on intact hepatocytes. The relative contribution of each phosphodiesterase form to the metabolism of hepatocyte intracellular cyclic AMP, together with an assessment of the potential effect of inhibition and activation of specific species, was evaluated using the computer model. These experimental and stimulation studies indicate that alterations in the phosphodiesterase activity of the 'dense-vesicle' enzyme, the peripheral plasma membrane enzyme, the cyclic GMP-stimulated cyclic AMP isoforms and the IBMX-insensitive PDE-MQ-II can elicit profound effects upon hepatocyte intracellular cyclic AMP concentrations.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2000

A computational model for the prediction of total knee replacement kinematics in the sagittal plane.

A computational model has been developed using a current generation computer-aided engineering (CAE) package to predict total knee replacement (TKR) kinematic in the sagittal plane. The model includes friction and soft tissue restraint varying according to the flexion angle. The model was validated by comparing the outcomes of anterior-posterior (A-P) laxity tests of two contemporary knee replacements against data obtained from a knee simulating machine. It was also validated against predictions from a computer model reported in the literature. Results show good agreement in terms of A-P displacements. Further tests were performed to determined the influence of the soft tissue restraints varying with flexion angle. This work represents the first attempt to use a sophisticated commercial CAE package to predict TKR motions and the advantages of the modelling procedure chosen are discussed.

Biomechanical Phenomena↗

PubMedDate not supplied

A computer model of lung morphology to analyze SPECT images.

Measurement of the spatial distribution of aerosol deposition in human lungs can be performed using single photon emission computed tomography (SPECT). To relate deposition patterns to real lung structures, a computer model of the airway network has been developed. Computer simulations are presented that are compatible with the analysis of SPECT images. Computational techniques that are consistent with clinical procedures are used to analyze airways by type and number within transverse slices of the lung volume. The computer models serve as customized templates, which when analyzed alongside gamma scintigraphy images, can assist in the interpretation of human test data.

Computer Simulation↗

PubMed1994

Coupling of spinal locomotor networks in larval lamprey revealed by receptor blockers for inhibitory amino acids: neurophysiology and computer modeling.

1. Receptor blockers for inhibitory amino acids were applied to part or all of the spinal cord of larval lamprey during brain stem-initiated locomotor activity. Blocking glycinergic inhibition with strychnine applied to the entire spinal cord converted the locomotor pattern from left-right alternation to synchronous left-right bursting. The results suggest that left and right oscillators are connected by relatively strong reciprocal inhibitory (glycinergic) connections in parallel with weaker reciprocal excitatory connections. This possible organization was supported by results from a computer model consisting of left and right oscillators connected by reciprocal inhibition and excitation in parallel. In addition, the results suggest that reciprocal inhibition is not required for left-right rhythmicity but rather is involved primarily with phasing of left-right activity. 2. Locally blocking glycinergic inhibition with strychnine in the rostral spinal cord resulted in synchronous left-right burst activity in that region of the cord as well as in more caudal areas of the cord in which reciprocal inhibition should still be functional. 3. Blocking glycinergic inhibition in the caudal spinal cord converted the pattern in that region of the cord to left-right synchronous activity. The effects in the ascending direction on the burst patterns in more rostral areas of the spinal cord were less than those mentioned above in the descending direction with application of strychnine to the rostral spinal cord. 4. With glycinergic inhibition or GABAergic inhibition blocked in the entire spinal cord, stable longitudinal coupling along the spinal cord persisted. This and the neurophysiology results mentioned above suggest that the main mechanism for longitudinal coupling between locomotor networks in adjacent regions of the spinal cord is ipsilateral excitatory connections and not crossed inhibitory connections. This possible organization was supported by results from a computer model, which consisted of a pair of oscillators in the more rostral and more caudal spinal cord that could be connected by various types of coupling schemes. 5. The neurophysiological data above suggest that ipsilateral, excitatory coupling is stronger in the descending direction than in the ascending direction. In the computer model, a dominant descending coupling is a necessary requirement to produce positive longitudinal phase lags.

Animals↗

PubMed1976

Subsite mapping of enzymes. Application of the depolymerase computer model to two alpha-amylases.

In the preceding paper (Allen and Thoma, 1976) we developed a depolymerase computer model, which uses a minimization routine to establish a subsite map for a depolymerase. In the present paper we show how the model is applied to experimental data for two alpha-amylases. Michaelis parameters and bond-cleavage frequencies for substrates of chain lengths up to twelve glucosyl units have been reported for Bacillus amyloliquefaciens, and a subsite map has been proposed for this enzyme [Thoma et al. (1971) J. Biol. Chem. 246, 5621-5635]. By applying the computer model to the experimental data, we have arrived at a ten-subsite map. We find that a significant improvement in this map is achieved by allowing the hydrolytic rate coefficient to vary as a function of the number of occupied subsites comprising the enzyme-binding region. The bond-cleavage frequencies, the enzyme is found to have eight subsites. A partial subsite map is arrived at, but the entire binding region cannot be mapped because Michaelis parameters are complicated by transglycosylation reactions. The hydrolytic rate coefficients for this enzyme are not constant.

Amino Acid Sequence↗

PubMed2002

[Computer models of the electrophysiological properties of the heart].

Computer models of the heart can improve the understanding of the electrophysiological processes in healthy and diseased heart. They become more and more important for detailed diagnosis of arrhythmias and for optimization of therapy. Models of myocardium cells known today are described--they are based on the properties of all relevant ion channels in the cell membrane. Then it is demonstrated, how many cells can be joined to form a cell patch and how finally the complete heart can be modelled. A simpler approach is using a so called cellular automation that allows for a significant reduction of calculation time while sacrificing some accordance to reality. Adaptive cellular automations allow for a fast simulation with acceptable accuracy. Using them some results were gained for the simulation of typical arrhythmias, in the field of validation using an animal model and for therapy planning with RF-ablation.

Arrhythmias, Cardiac↗

PubMed1991

3-D computer model of subcortical structures of human brain.

Three-dimensional computer model of thalamus and adjacent formations of human brain has been elaborated on the basis of sagittal slices from the Schaltenbrand-Bailey stereotactic atlas. The model includes 120 morphologically distinguishable structures and consists of more than 16 million points (volume elements) each of them being associated with the particular structure in the brain. The model is stored in the long-term computer memory. A special software has been developed to facilitate utilizing the model obtained. The software facilitates synthesizing arbitrary cross-sections through the brain and provides the correspondence between the stereotactic coordinates of any point and its position on the screen of monitor. The coordinates of the point in the system of stereotactic atlas and the name of the structure, the point belongs to, are also supplied. It is also possible to get magnified images of cross-sections and to get isometrical images. The system enables the neurosurgeon to improve the planning and execution of stereotactic operations, and will also be helpful for education.

Brain↗

PubMed1991

Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling.

The conformation of Escherichia coli 5 S rRNA was investigated using chemical and enzymatic probes. The four bases were monitored at one of their Watson-Crick positions with dimethylsulfate (at C(N-3) and A(N-1], with a carbodiimide derivative (at G(N-1) and U(N-3] and with kethoxal (at G(N-1, N-2]. Position N-7 of purine was probed with diethylpyrocarbonate (at A(N-7] and dimethylsulfate (at G(N-7]. Double-stranded or stacked regions were tested with RNase V1 and unpaired guanine residues with RNase T1. We also used lead(II) that has a preferential affinity for interhelical and loop regions and a high sensitivity for flexible regions. Particular care was taken to use uniform conditions of salt, magnesium, pH and temperature for the different enzymatic chemical probes. Derived from these experimental data, a three dimensional model of the 5 S rRNA was built using computer modeling which integrates stereochemical constraints and phylogenetic data. The three domains of 5 S rRNA secondary structure fold into a Y-shaped structure that does not accommodate long-range tertiary interactions between domains. The three domains have distinct structural and dynamic features as revealed by the chemical reactivity and the lead(II)-induced hydrolysis: domain 2 (loop B/helix III/loop C) displays a rather weak structure and possesses dynamic properties while domain 3 (helix V/region E/helix IV/loop D) adopts a highly structured and overall helical conformation. Conserved nucleotides are not crucial for the tertiary folding but maintain an intrinsic structure in the loop regions, especially via non-canonical pairing (A.G, G.U, G.G, A.C, C.C), which can close the loops in a highly specific fashion. In particular, nucleotides in the large external loop C fold into an organized conformation leading to the formation of a five-membered loop motif. Finally, nucleotides at the hinge region of the Y-shape are involved in a precise array of hydrogen bonds based on a triple interaction between U14, G69 and G107 stabilizing the quasi-colinearity of helices II and V. The proposed tertiary model is consistent with the localization of the ribosomal protein binding sites and possesses strong analogy with the model proposed for Xenopus laevis 5 S rRNA, indicating that the Y-shape model can be generalized to all 5 S rRNAs.

Base Sequence↗

PubMed1999

A computational model of neglect dyslexia.

This paper presents a straightforward theory of neglect (a pre-attentive salience system selects objects' centers for the focus of an attentional "spotlight") as a computational model. This construction permits simulations of model "lesions" and allows checking unequivocally the model's implications. The current model can account for some of the common patterns of observations of neglect dyslexia: that errors increase with word length and that short words may be read as "too long". Most importantly, it also accounts for a dissociation between neglect dyslexia and neglect on line bisection tasks. A two stage model can account for the patterns of performance seen in many neglect subjects, but more important is the demonstration that a theory's implementation as a computational model permits unambiguous evaluation of the theory's implications.

Computer Simulation↗