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At least 19 recordsLinked to original sources
PubMed2006

Distributed computing methodology for training neural networks in an image-guided diagnostic application.

Distributed computing is a process through which a set of computers connected by a network is used collectively to solve a single problem. In this paper, we propose a distributed computing methodology for training neural networks for the detection of lesions in colonoscopy. Our approach is based on partitioning the training set across multiple processors using a parallel virtual machine. In this way, interconnected computers of varied architectures can be used for the distributed evaluation of the error function and gradient values, and, thus, training neural networks utilizing various learning methods. The proposed methodology has large granularity and low synchronization, and has been implemented and tested. Our results indicate that the parallel virtual machine implementation of the training algorithms developed leads to considerable speedup, especially when large network architectures and training sets are used.

Algorithms↗
PubMed2000

Simulations of flow-induced director structures in nematic liquid crystals through leslie-ericksen equations. I. Computational methodology in two dimensions

A computational treatment of the constitutive equations of nematodynamics, based on the Leslie-Ericksen approach, is presented and discussed for a rotating planar nematic sample subjected to a constant magnetic field. The dynamics of the velocity v and director n fields is taken into account exactly. Coupled partial differential equations suitable to be solved numerically are worked out, in terms of derived functionals of v and n and of their spatial and time derivatives. Time-dependent patterns of the director are obtained using a finite-difference scheme in a spatial polar grid. Several experimental situations are analyzed, corresponding to common experimental setups: continuously rotating samples for different values of the rotational speed; 30 degrees and 90 degrees step-rotation experiments. A comparison is made to existing approximate treatments. Dependence upon the sample dimension is also discussed.

Journal Article↗
PubMedDate not supplied

Modelling and simulation of information systems on computer: methodological advantages.

Modelling and simulation of information systems by the means of miniatures on computer aim at two general objectives: (a) as an aid to design and realization of information systems; and (b) a tool to improve the dialogue between the designer and the users. An operational information system has two components bound by a dynamic relationship, an information system and a behavioural system. Thanks to the behaviour system, modelling and simulation allow the designer to integrate into the projects a large proportion of the system's implicit specification. The advantages of modelling to the information system relate to: (a) The conceptual phase: initial objectives are compared with the results of simulation and sometimes modified. (b) The external specifications: simulation is particularly useful for personalising man-machine relationships in each application. (c) The internal specifications: if the miniatures are built on the concept of process, the global design and the software are tested and also the simulation refines the configuration and directs the choice of hardware. (d) The implementation: stimulation reduces costs, time and allows testing. Progress in modelling techniques will undoubtedly lead to better information systems.

Computers↗
PubMed2006

Computational methodologies for modelling, analysis and simulation of signalling networks.

This article is a critical review of computational techniques used to model, analyse and simulate signalling networks. We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication. In order to avoid an overly abstract and general discussion, we focus on three case studies in the areas of receptor signalling and kinase cascades, cell-cycle regulation and wound healing. We report on a variety of modelling techniques and associated tools, in addition to the traditional approach based on ordinary differential equations (ODEs), which provide a range of descriptive and analytical powers. As the field matures, we expect a wider uptake of these alternative approaches for several reasons, including the need to take into account low protein copy numbers and noise and the great complexity of cellular organisation. An advantage offered by many of these alternative techniques, which have their origins in computing science, is the ability to perform sophisticated model analysis which can better relate predicted behaviour and observations.

Algorithms↗
PubMed2000

Computational methodology for estimating changes in free energies of biomolecular association upon mutation. The importance of bound water in dimer-tetramer assembly for beta 37 mutant hemoglobins.

The computational modeling program HINT (Hydropathic INTeractions), an empirical hydropathic force field that includes hydrogen bonding, Coulombic, and hydrophobic terms, was used to model the free energy of dimer-tetramer association in a series of deoxy hemoglobin beta 37 double mutants. Five of the analyzed mutants (beta 37W --> Y, beta 37W --> A, beta 37W --> G, beta 37W --> E, and beta 37W --> R) have been solved crystallographically and characterized thermodynamically and subsequently made a good test set for the calibration of our method as a tool for free energy prediction. Initial free energy estimates for these mutants were conducted without the inclusion of crystallographically conserved water molecules and systematically underestimated the experimentally calculated loss in free energy observed for each mutant dimer-tetramer association. However, the inclusion of crystallographic waters, interacting at the dimer-dimer interface of each mutant, resulted in HINT free energy estimates that were more accurate with respect to experimental data. To evaluate the ability of our method to predict free energies for de novo protein models, the same beta 37 mutants were computationally generated from native deoxy hemoglobin and similarly analyzed. Our theoretical models were sufficiently robust to accurately predict free energy changes in a localized region around the mutated residue. However, our method did not possess the capacity to generate the long-range secondary structural effects observed in crystallographically solved mutant structures. Final method analysis involved the computational generation of structurally and/or thermodynamically uncharacterized beta 37 deoxy hemoglobin mutants. HINT analysis of these structures revealed that free energy predictions for dimer-tetramer association in these models agreed well with previously observed energy predictions for structurally and thermodynamically characterized beta 37 deoxy hemoglobin mutants.

Biopolymers↗
PubMed1983

Computer methodology for simulation and prediction of alloimmune responses: expected antibody specificities.

The methodology presented here was developed for simulating planned alloimmunization results, with regard to the type and number of expected antibody specificities. The computer program designed for this purpose was adapted to an immunogenetic model using Boolean algebra. It was written to help immunogeneticists avoid handling routine data preceding selection of donor-recipient pairs, specially concerning blood type alloimmunizations in animals: all of the donor-recipient combinations and the expected antibody specificities (their limit number being specified in each particular immunization program) are provided in the print-out.

Animals↗
PubMed1999

Fragmentation of an alkali metal-attached peptide probed by collision-induced dissociation fourier transform mass spectrometry and computational methodology.

Collision-induced dissociation of metal-cationized N-CBZ-Gly-Pro-Gly-Pro-Ala was studied by Fourier transform mass spectrometry. Lithium-, sodium-, potassium- and rubidium-cationized peptide species were generated by matrix-assisted laser desorption/ionization (MALDI) using 2,5-dihydroxybenzoic acid as matrix, together with appropriate metal salts. The experimental mass spectrometric results were interpreted with the aid of Monte Carlo conformational searches using the Amber(*) force field, together with ab initio molecular orbital calculations with Gaussian-94 for the singly lithium- and potassium-cationized peptides. It is concluded that metal coordination plays a key role in guiding the gas-phase fragmentation of the cationized peptide. In contrast to lithium and sodium, potassium and rubidium apparently do not coordinate to the C-terminal carbonyl. When the peptide is cationized with the two smaller alkali metals, losses corresponding to alanine and CBZ are observed, while the coordination of potassium and rubidium results in only CBZ loss upon dissociation.

Amino Acid Sequence↗
PubMed1980

Computed tomography/guided stereotactic surgery: conception and development of a new stereotactic methodology.

Computed tomography (CT) has become the first modality to provide the patient's self-brain map for stereotactic neurosurgery. This paper describes our development of a nearly artifact-free stereotactic frame designed for CT imaging. The surgical procedure is performed within the CT scanner itself. The scanner's computer, via a new software program, spatially integrates the new stereotactic frame with the CT images of the patient and with the scanner gantry to provide rapid coordinate determinations, calculate potential probe trajectories, obtain target accuracy within 1 mm, and observe for any procedural complications. Our initial clinical experience with this system is described.

Brain Neoplasms↗
PubMed1993

[Stable xenon computed tomography. Methodology and clinical application].

According to the principle of the dynamic computed tomography, stable xenon computed tomography allows measurement of the increase in density caused by xenon in the brain tissue. During a period of about 4 min a patient inhales a mixture of xenon (33%) and oxygen. By means of a special software, this method can be used to calculate flowmaps and to determine the local cerebral blood flow in a 1 cm x 1 cm areal. Stable xenon computed tomography is used mainly for cerebral blood flow measurements in patients with cerebrovascular diseases and also allows calculation of cerebral reserve capacity following stimulation of blood flow by the carboanhydrase inhibitor acetazolamide (Diamox).

Acetazolamide↗
PubMed1980

[Computer aerography. Methodology and clinical use exemplified by labio-maxilla-palate clefts (author's transl)].

Computer aerography, which is based on the use of the double-aerometer by Sven Smith, is described as an objective method for clinic-scientific problems. Medical examination of labio-maxilla-palate-cleft patients shows how this procedure, which has a low degree of inconvenience and is also applicable to children, contributes essentially to the settling of clinic-scientific problems. Further scopes are still being tested.

Cleft Lip↗
PubMed1984

Computer based methodology for construction of orthodontic arch wire templates.

This paper presents the details and logic of two Fortran computer programs. The program, BRACKET, is designed to evaluate the constant relationship among teeth and orthodontic brackets to which an arch wire is adapted. The program, WIRE, is used to initially fit brackets to teeth using the constants derived in BRACKETS, based upon a series of orthogonal transformations. Subsequently, an orthodontic arch wire is fitted through the brackets, and the results are displayed using computer graphics. It is anticipated that the system would be useful in the orthodontic clinical setting as an aid in arch wire formation. The graphics produce a template which incorporates essential points to consider in arch wire formation, namely, perimeter length, lateral widths, symmetry, and appropriate arch form for the patient.

Computers↗
PubMed2004

Medical privacy protection based on granular computing.

Based on granular computing methodology, we propose two criteria to quantitatively measure privacy invasion. The total cost criterion measures the effort needed for a data recipient to find private information. The average benefit criterion measures the benefit a data recipient obtains when he received the released data. These two criteria remedy the inadequacy of the deterministic privacy formulation proposed in Proceedings of Asia Pacific Medical Informatics Conference, 2000; Int J Med Inform 2003;71:17-23. Granular computing methodology provides a unified framework for these quantitative measurements and previous bin size and logical approaches. These two new criteria are implemented in a prototype system Cellsecu 2.0. Preliminary system performance evaluation is conducted and reviewed.

Computing Methodologies↗
PubMedDate not supplied

Improvement in Fourier analysis of gated blood-pool studies using single photon emission computed tomography: methodology and clinical feasibility.

We have developed a new method for obtaining reconstructed left ventricular (LV) planar images acquired from multidirectional views using gated blood-pool single photon emission computed tomography (SPECT), and have applied Fourier analysis to these planar images. In this paper, we describe the methodology of our new technique and discuss its feasibility for the detection of LV wall motion abnormalities (WMA) in patients with coronary artery disease (CAD). Sagittal long-axis, horizontal long-axis and short-axis sections of the LV were generated from the reconstructed transaxial tomograms. Sections covering only the LV at the same phase of the cardiac cycle were added to reconstruct planar images. Fourier analysis was then performed to construct phase and amplitude images. In 42 patients with significant WMA, a comparative study concerning the detection of WMA was performed between conventional and SPECT methods. The SPECT method had greater sensitivity in all segments of the LV, with no significant loss in specificity. In particular, the sensitivity of the SPECT method was significantly greater than that of the conventional method for inferior and posterior WMA (91% vs 57%; and 76% vs 35%, respectively). The method described here shows greater clinical effectiveness for the detection of LV WMA in patients with CAD.

Adult↗