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Results for “computational modelling”

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At least 199 records · Page 11Linked to original sources

PubMed1996

Sensory gating in a computer model of the CA3 neural network of the hippocampus.

We have developed a unique computer model of the CA3 region of the hippocampus that simulates the P50 auditory evoked potential response to repeated stimuli in order to study the neuronal circuits involved in a sensory processing deficit associated with schizophrenia. Our computer model of the CA3 hippocampal network includes recurrent activation from within the CA3 region as well as input from the entorhinal cortex and the medial septal nucleus. We used the model to help us determine if the cortical and septal inputs to the CA3 hippocampus alone are responsible for the gating of auditory evoked activity, or if the strong recurrent activity within the CA3 region contributes to this phenomenon. The model suggests that the medial septal input is critical for normal gating; however, to a large extent the activity of the medial septal input can be replaced by simulated stimulation of the hippocampal neurons by a nicotinic agonist. The model is thus consistent with experimental data that show that nicotine restores gating of the N40 evoked potential in fimbria-fornix lesioned rats and of the P50 evoked potential in schizophrenic patients.

Animals↗

PubMed1985

Shell computer model of cardiac electropotential changes.

A discrete process computer model has been developed to simulate the electropotential changes of heart musculature and the operation of the cardiac conduction system. The model is implemented on an ICL-4/72 computer and is oriented to cardiac rhythm studies, allowing practically all rhythm pathologies, including pacemaker applications, to be simulated. The paper describes in detail the principles on which the model is based, compares the model with other models of the same system and shows concisely some results of simulation experiments in the form of computer generated ECG records.

Atrioventricular Node↗

PubMed2003

Using computational modeling to study the impact of workplace characteristics on patient safety outcomes.

How do patient characteristics, organization characteristics and patient care unit characteristics interact to affect quality, safety, and cost outcomes? What changes can nurse managers make on their units that will optimize outcomes for their patients? To answer these questions, we are collecting data from 35 nursing units in 12 hospitals in Arizona, and using the results as a basis for computational modeling. Although it has been used in clinical research, until now computational modeling has had little application to healthcare or nursing organizations. In this poster session, we describe our application of Orgahead, a computational modeling program.

Models, Nursing↗

PubMed1986

Computer modeling of actinomycin D interactions with double-helical DNA.

We have performed molecular mechanical calculations on intercalation complexes of actinomycin D with a series of base-paired hexanucleoside pentaphosphates; d(GCGCGC)2, d(GCCGGC)2, d(GCATGC)2, d(GCTAGC)2 and d(ATGCAT)2. Our results are in good agreement with previous experimental work on sequence selectivity. The results provide a rationalization for the strong preference of actinomycin D to intercalate on the 3' side of guanine residues, consistent with previously proposed models. Finally, the computed structures for d(ATGCAT)2-actinomycin D complexes have been compared with two-dimensional nuclear magnetic resonance nuclear Overhauser effect experimental results. To our knowledge, this is the first extensive comparison of molecular mechanical model structures for a drug-DNA complex with experimental solution phase data. We find generally good agreement between our computational models and the experimental solution phase structures.

Computers↗

PubMed2006

Computational modeling of arterial wall growth. Attempts towards patient-specific simulations based on computer tomography.

The present manuscript documents our first experiences with a computational model for stress-induced arterial wall growth and in-stent restenosis related to atherosclerosis. The underlying theoretical framework is provided by the kinematics of finite growth combined with open system thermodynamics. The computational simulation is embedded in a finite element approach in which growth is essentially captured by a single scalar-valued growth factor introduced as internal variable on the integration point level. The conceptual simplicity of the model enables its straightforward implementation into standard commercial finite element codes. Qualitative studies of stress-induced changes of the arterial wall thickness in response to balloon angioplasty or stenting are presented to illustrate the features of the suggested growth model. First attempts towards a patient-specific simulation based on realistic artery morphologies generated from computer tomography data are discussed.

Aorta↗

PubMed1995

Validation of a computer model of haemorrhage and transcapillary refill.

A computer model is described which uses blood volume deficit and its duration to simulate the first two hours of haemorrhage, including an estimation of the blood volume added by Starlings transcapillary refill mechanism. Computer prediction of the haematocrit was compared with published data on haemorrhage in animals. There was close correlation with data on the haemodilution caused by Starling's transcapillary refill mechanism in conscious swine (r = 0.84).

Animals↗

PubMed1989

Three-dimensional computer model of the heart: fibrillation induced by extrastimulation.

We present a three-dimensional (3D) computer model that simulates electrical activity in the heart during fibrillation. A real dog heart is discretized to form 1473 interconnected cubic elements. The model exhibits normal activation and recovery from pacing. Five or more extrastimuli induce a self-sustaining tachyarrhythmia that soon degenerates into a fibrillatory rhythm. The extrastimuli increase the excitability of the myocardial cell population. The result is a rapid re-excitation of cells that allows for only a partial recovery of cell action potential. This suggests that a dispersion of refractory states of the cell population is the cause of fibrillation in this computer model.

Animals↗

PubMed2003

Dopaminergic modulation of the P50 auditory-evoked potential in a computer model of the CA3 region of the hippocampus: its relationship to sensory gating in schizophrenia.

We modeled the neuronal circuits that may underlie a sensory-processing deficit associated with schizophrenia. Schizophrenic patients have small P50 auditory-evoked responses to click stimuli compared to normal subjects. The P50 auditory-evoked response is a positive waveform recorded in the EEG approximately 50 ms after the auditory click stimulus. In addition to relatively small amplitudes, schizophrenic patients do not gate or suppress the P50 auditory-evoked response to the second of two paired-click stimuli spaced 0.5 s apart. Neuropleptic medication, which decreases dopaminergic neuronal transmission, increases the amplitude of the P50 auditory-evoked response but does not improve gating. Normal subjects have large P50 auditory-evoked responses to click stimuli when compared to unmedicated schizophrenic patients, and they gate their response to paired click stimuli or have smaller P50 auditory-evoked response amplitudes to the second of two click stimuli spaced 0.5 s apart. Schizophrenic patients do not gate and have similar response amplitudes to both clicks. We hypothesized that the small amplitudes of unmedicated schizophrenic subjects were due to a state of occlusion whereby excessive background noise in local circuits reduced the ability of cells to respond synchronously to sensory input, thereby reducing the amplitude of the P50 waveform in the EEG. Because the P50 auditory-evoked potential amplitudes increased with neuroleptic medication, which reduces dopaminergic neuronal transmission, we hypothesized a role for dopamine in modulating the signal-to-noise (S/N) in the local circuits responsible for sensory gating. To test the hypothesis that modulation of the S/N ratio reduces sensory gating, we developed a model of the effects of dopaminergic neuronal transmission that modulates the S/N in neuronal circuits. The model uses the biologically relevant computer model of the CA3 region of the hippocampus developed in the companion paper [Moxon et al. (2003) Biol Cybern, this volume]. Modified Hebb cell assemblies represented the response of the network to the click stimulus. The results of our model showed that excessive dopaminergic input impaired the ability of cells to respond synchronously to sensory input, which reduced the amplitudes of the P50 evoked responses.

Acoustic Stimulation↗

PubMed1991

An evaluation of eight computer models of mammalian inner hair-cell function.

Eight computer models of auditory inner hair cells have been evaluated. From an extensive literature on mammalian species, a subset of well-reported auditory-nerve properties in response to tone-burst stimuli were selected and tested for in the models. This subset included tests for: (a) rate-level functions for onset and steady-state responses; (b) two-component adaptation; (c) recovery of spontaneous activity; (d) physiological forward masking; (e) additivity; and (f) frequency-limited phase locking. As models of hair-cell functioning are increasingly used as the front end of speech-recognition devices, the computational efficiency of each model was also considered. The evaluation shows that no single model completely replicates the subset of tests. Reasons are given for our favoring the Meddis model [R. Meddis, J. Acoust. Soc. Am. 83, 1056-1063 (1988)] both in terms of its good agreement with physiological data and its computational efficiency. It is concluded that this model is well suited to provide the primary input to speech recognition devices and models of central auditory processing.

Animals↗

PubMed2005

Computational model of hole transport in DNA.

A computational model based on the molecular dynamics (MD) simulation for the hole transport in DNA has been developed and applied to study hole current in DNA strands consisting of different numbers of GC pairs. The approach is based on the hopping mechanism which is thermally activated. The calculations show that the hole hopping intensifies with the temperature and the transport rate increases in agreement with the experimental evidence. It is also determined that the degree of structural ordering in the DNA strand enhances the hole conductivity and reasons are provided why this may occur.

Base Pairing↗

PubMed2001

Computational models of cells and tissues: machines, agents and fungal infection.

Computational models have been of interest in biology for many years and have represented a particular approach to trying to understand biological processes and phenomena from a systems point of view. Much of the early work was rather abstract and high level and probably seemed to many to be of more philosophical than practical value. There have, however, been some advances in the development of more realistic models and the current state of computer science research provides us with new opportunities through both the emergence of models that can model seriously complex systems and also the support that modern software can give to the modelling process. This paper describes a few of the early simple models and then goes on to look at some new ideas in the area with a particular application drawn from the world of mycology. Some general principles relating to how new and emerging computational techniques can help to represent and understand extremely complex models conclude the paper.

Computational Biology↗

PubMed1995

Computer models: killing mosquitoes with information.

This paper looks at the relationship between man and mosquitoes from the perspective of coevolution. From this perspective, the primacy of information processing in vector control programs becomes acutely evident. A composite mosquito control program is developed and illustrated to show the benefits derived from incremental increases in information. The use of computer modeling is seen as the next logical step to be taken by vector control personnel to add the next increment of efficiency and effectiveness. This step could well lead to significant reductions or perhaps the elimination of the need for pesticide use. The author encourages the use of computer modeling in teams as the means to learn across disciplines. The feasibility of this approach has been greatly enhanced by the availability of off-the-shelf modeling programs. The author appeals to university and vector control professionals to support students and staff in learning computer modeling techniques.

Animals↗

PubMed2000

Computational modeling of the baroreflex arc: nucleus tractus solitarius.

In this study, we examine the utility of computational modeling in understanding nervous system function. We start by examining the reasons for, and major approaches to, computational modeling. We then chose a modeling approach and applied different variations to understanding nucleus tractus solitarius (NTS) neuronal responses to various baroreceptive stimuli. We examine the results in light of our objectives and with regard to the known parameters of the system under investigation. Our results demonstrate that modeling can be a useful tool in analysis of (and examination of underlying mechanisms for) NTS behavior on many levels.

Animals↗

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↗

PubMed2004

Mutation, fitness, viral diversity, and predictive markers of disease progression in a computational model of HIV type 1 infection.

The aim of this study was to develop a computational model of HIV infection able to simulate the natural history of the disease and to test predictive parameters of disease progression. We describe the results of a numerical simulation of the cellular and humoral immune response to HIV-1 infection as an adaptive pathway in a "bit-string" space. A total of 650 simulations of the HIV-1 dynamics were performed with a modified version of the Celada-Seiden immune system model. Statistics are in agreement with epidemiological studies showing a log normal distribution for the time span between infection and the development of AIDS. As predictive parameters of disease progression we found that HIV-1 accumulates "bit" mutations mainly in the peptide sequences recognized by cytotoxic CD8 T cells, indicating that cell-mediated immunity plays a major role in viral control. The viral load set point was closely correlated with the time from infection to development of AIDS. Viral divergence from the viral quasispecies that was present at the beginning of infection in long-term nonprogressors (LTNP) was found to be similar to that found in rapid progressors at the time CD4 T cells drop below the critical value of 200 cells/microl. In contrast, the diversity indicated by the number of HIV strains present at the same time was higher for rapid and normal progressors compared to LTNP, suggesting that the early immune response can make the difference. This computational model may help to define the predictive parameters of HIV dynamics and disease progression, with potential applications in therapeutic and vaccine simulations.

Biomarkers↗

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↗