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PubMed2001

An evaluation of synapse independence.

If, as is widely believed, information is stored in the brain as distributed modifications of synaptic efficacy, it can be argued that the storage capacity of the brain will be maximized if the number of synapses that operate independently is as large as possible. The majority of synapses in the brain are glutamatergic; their independence will be compromised if glutamate released at one synapse can significantly activate receptors at neighboring synapses. There is currently no agreement on whether "spillover" after the liberation of a vesicle will significantly activate receptors at neighboring synapses. To evaluate the independence of central synapses, it is necessary to compare synaptic responses with those generated at neighboring synapses by glutamate spillover. Here, synaptic activation and spillover responses are simulated in a model, based on data for hippocampal synapses, that includes an approximate representation of the extrasynaptic space. Recently-published data on glutamate transporter distribution and properties are incorporated. Factors likely to influence synaptic or spillover responses are investigated. For release of one vesicle, it is estimated that the mean response at the nearest neighboring synapse will be <5% of the synaptic response. It is concluded that synapses can operate independently.

ATP-Binding Cassette Transporters↗
PubMed2001

Computational neuroanatomy: new perspectives for neuroradiology.

Computational neuroanatomy is emerging as an exciting new methodology to characterise shape and neuroanatomical configuration of different brains. It encompasses a triad of techniques: Voxel-based morphometry (VBM), which compares neuroanatomical differences on a voxel by voxel basis, Deformation-based morphometry (DBM), which provides information about global differences in brain shape and Tensor-based morphometry (TBM) which provides information about local shape differences. This review will describe the methodology and clinical applications of these techniques.

Brain↗
PubMed2002

Analysis and 3D reconstruction of heterogeneity in malignant brain tumors: an interdisciplinary case study using a novel computational visualization approach.

OBJECTIVE: To explore how a multidisciplinary approach, combining modern visualization and image processing techniques with innovative experimental studies, can augment the understanding of tumor development. STUDY DESIGN: We analyzed histologic sections of a microscopic brain tumor and reconstructed these slices into a 3D representation. We processed these slices to: (1) identify tumor boundaries, (2) isolate proliferating tumor cells, and (3) segment the tumor into regions based on the density of proliferating cells. We then reconstructed the 3D shape of the tumor using a constrained deformable surface approach. RESULTS: This novel method allows the analyst to (1) see specific properties of histologic slices in the 3D environment with animation, (2) switch 2D "views" dynamically, and (3) see relationships between the 3D structure and structure on a plane. CONCLUSION: Using this method to analyze a specific "case," we were also able to shed light on the limitations of a widely held assumption about the shape of expanding microscopic solid tumors as well as find more indications that such tumors behave as adaptive biosystems. Implications of these case study results, as well as future applications of the method for tumor biology research, are discussed.

Antibodies, Monoclonal↗
PubMed1992

The use of spectral methods in bidomain studies.

A Fourier transform method is developed for solving the bidomain coupled differential equations governing the intracellular and extracellular potentials on a finite sheet of cardiac cells undergoing stimulation. The spectral formulation converts the system of differential equations into a "diagonal" system of algebraic equations. Solving the algebraic equations directly and taking the inverse transform of the potentials proved numerically less expensive than solving the coupled differential equations by means of traditional numerical techniques, such as finite differences; the comparison between the computer execution times showed that the Fourier transform method was about 40 times faster than the finite difference method. By application of the Fourier transform method, transmembrane potential distributions in the two-dimensional myocardial slice were calculated. For a tissue characterized by a ratio of the intra- to extracellular conductivities that is different in all principal directions, the transmembrane potential distribution exhibits a rather complicated geometrical pattern. The influence of the different anisotropy ratios, the finite tissue size, and the stimuli configuration on the pattern of membrane polarization is investigated.

Algorithms↗
PubMed1992

Finite element methods for the biomechanics of soft hydrated tissues: nonlinear analysis and adaptive control of meshes.

This chapter addresses computationally demanding numerical formulations in the biomechanics of soft tissues. The theory of mixtures can be used to represent soft hydrated tissues in the human musculoskeletal system as a two-phase continuum consisting of an incompressible solid phase (collagen and proteoglycan) and an incompressible fluid phase (interstitial water). We first consider the finite deformation of soft hydrated tissues in which the solid phase is represented as hyperelastic. A finite element formulation of the governing nonlinear biphasic equations is presented based on a mixed-penalty approach and derived using the weighted residual method. Fluid and solid phase deformation, velocity, and pressure are interpolated within each element, and the pressure variables within each element are eliminated at the element level. A system of nonlinear, first-order differential equations in the fluid and solid phase deformation and velocity is obtained. In order to solve these equations, the contributions of the hyperelastic solid phase are incrementally linearized, a finite difference rule is introduced for temporal discretization, and an iterative scheme is adopted to achieve equilibrium at the end of each time increment. We demonstrate the accuracy and adequacy of the procedure using a six-node, isoparametric axisymmetric element, and we present an example problem for which independent numerical solution is available. Next, we present an automated, adaptive environment for the simulation of soft tissue continua in which the finite element analysis is coupled with automatic mesh generation, error indicators, and projection methods. Mesh generation and updating, including both refinement and coarsening, for the two-dimensional examples examined in this study are performed using the finite quadtree approach. The adaptive analysis is based on an error indicator which is the L2 norm of the difference between the finite element solution and a projected finite element solution. Total stress, calculated as the sum of the solid and fluid phase stresses, is used in the error indicator. To allow the finite difference algorithm to proceed in time using an updated mesh, solution values must be transferred to the new nodal locations. This rezoning is accomplished using a projected field for the primary variables. The accuracy and effectiveness of this adaptive finite element analysis is demonstrated using a linear, two-dimensional, axisymmetric problem corresponding to the indentation of a thin sheet of soft tissue. The method is shown to effectively capture the steep gradients and to produce solutions in good agreement with independent, converged, numerical solutions.

Adaptation, Physiological↗
PubMed2004

[Knowledge discovery in database and its application in clinical diagnosis].

Nowadays the tremendous amount of data has far exceeded our human ability for comprehension, and this has been particularly true for the medical database. However, traditional statistical techniques are no longer adequate for analyzing this vast collection of data. Knowledge discovery in database and data mining play an important role in analyzing data and uncovering important data patterns. This paper briefly presents the concepts of knowledge discovery in database and data mining, then describes the rough set theory, and gives some examples based on rough set.

Artificial Intelligence↗
PubMed2002

Local energy as a measure of back symmetry in scoliosis.

The Cobb angle has been the most commonly used method in measuring the severity of scoliosis and its progression. However, in recent years a number of researchers have chosen to monitor scoliosis by examining the severity of the surface deformity resulting from the scoliosis. Each of these approaches has been limited by errors introduced in manual location of landmarks. Scoliosis results in an asymmetry of the back. It would be very desirable to have a computer-based method of measuring this asymmetry. This paper investigates the use of wavelets and the concept of local energy to measure asymmetry associated with scoliosis. The local energy model uses wavelet theory to obtain information about shading and boundaries of objects in an image. Edges and sharp discontinuities are areas of high local energy in an image. Features such as scapular prominence, shoulder edges, waist creases and other anomalies that contribute to the scoliotic back asymmetry have high local energy. A preliminary study was completed to determine if this approach was applicable to measurement of back asymmetry. Two-dimensional local energy images were created from photographs of the backs of patients with scoliosis. The local energy was integrated across each image and a left-to right line of symmetry was calculated. This line of symmetry was then correlated with the scoliotic score developed by our group. This technique shows promise of providing an automatic method of measuring scoliosis progression.

Back↗
PubMed2002

Accuracy of rasterstereography versus radiography in idiopathic scoliosis after anterior correction and fusion.

Rasterstereography enables to reduce the number of radiographs in the conservative treatment of idiopathic scoliosis (Cobb angles below 50 degrees). The aim of the present study was to evaluate the use of rasterstereography in severe scoliosis before and after anterior surgery. The results show that the accuracy (as compared to radiographs) is lower in the pre-operative rasterstereographs. However, after operation the Cobb angles were less than 50 degrees in all cases and the accuracy of the rasterstereographs was similar to that of non-operated scolioses. This finding might allow a significant reduction of post-operative radiographs.

Adolescent↗
PubMed2002

In vivo measurement of solid organ visco-elastic properties.

To support the ongoing development of software-based surgical simulation systems, work is underway to acquire the mechanical properties of living tissue. When such simulations include force feedback, visco-elastic properties must be evaluated over a range of frequencies relevant to human perception and motor control. A minimally invasive instrument has been developed which can perform normal indentation on solid organs, and apply and measure deformations over a frequency range from DC to approximately 100Hz. Measurement performance was validated on a series of objects and materials with known properties, and the device was subsequently used in in vivo tests on porcine liver. Results of these validation tests as well as the data extracted from the in vivo experiments are presented. Testing in ongoing, and will be expanded to more completely characterize liver, as well as porcine spleen and other solid organ tissues. While these animal tissue property tests are valuable in and of themselves, they pave the way for the development of instruments and experimental protocols suitable for the measurement of human tissue properties.

Animals↗
PubMed2005

Normalization for Affymetrix GeneChips.

OBJECTIVES: The high density oligonucleotide microarrays from Affymetrix (Affymetrix GeneChips) are very popular in biomedical research. They enable to study the expression of thousands of genes simultaneously. In experiments with multiple arrays, normalization techniques are used to reduce the so-called obscuring variation, i.e. the technical variation that is of non-biological origin. Several different normalization methods have been proposed during the last years. METHODS: We review published results about the comparison of normalization methods proposed for Affymetrix GeneChips. RESULTS: The quantile normalization seems to perform favorably regarding precision (low variance), accuracy (low bias), and practicability (low computing time). However, according to very recent results, this normalization method can have an impact on the biological variability and, therefore, appears to be less than optimal from this point of view. CONCLUSION: Although the quantile normalization may be recommendable, more investigations based on more data sets are needed so that the different normalization methods can be evaluated on widely differing data.

Algorithms↗
PubMed2005

The bell curve.

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Adolescent↗
PubMed1988

The inverse problem in electrocardiography: solutions in terms of equivalent sources.

This paper reviews those inverse electrocardiographic solutions that compute the electrical activity of the heart in terms of equivalent sources such as multipoles or multiple dipoles, as opposed to more realistic source formulations such as epicardial potentials. It treats, in succession, inverse solutions in terms of a single fixed-location dipole, a multipole series, moving dipoles, and, finally, multiple fixed-location dipoles. For each category of solution, simulation studies, animal experiments, and work involving human subjects are reviewed. Finally, more recent work that seeks to compute the cardiac activation isochrones, from the time integrals of the torso potentials during the QRS complex of the electrocardiogram, is described. The paper concludes with a discussion on the future of inverse electrocardiographic solutions in terms of equivalent sources.

Animals↗
PubMedDate not supplied

Computed tomography in nuclear medicine.

Utilizing mathematical techniques and computer processing similar to those employed in x-ray transmission computed tomography and magnetic resonance imaging, cross-sectional images of radiopharmaceutical distribution are demonstrating encouraging maps of organ physiology and pathophysiology. The basic concepts of single photon emission computed tomography (SPECT), and some of its clinical implications, are presented to demonstrate the potential applications of this new modality.

Cerebral Infarction↗
PubMedDate not supplied

Calculating confidence intervals for threshold and post-test probabilities.

We describe a method and a computer program, written in JavaScript, for calculating confidence intervals. The method uses Taylor's series to approximate the standard errors of a post-test probability and threshold probabilities and, from them, to obtain the associated confidence intervals. This method is valid if the variables of interest are stochastically independent.

Adult↗