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At least 1,297 records · Page 72Linked to original sources
PubMed1991

A distributed image-processing system for measurements of intracellular calcium in living cells.

During the last decade, image-processing techniques have been introduced as a valuable tool in biologically oriented research. In combination with novel fluorescent probes, these techniques permit assessment of subcellular distributions of several intracellularly important cations, such as free calcium ions and protons. Typically, systems used for image processing are located centrally around the experimental setup. This configuration has drawbacks, mainly because the laborious extraction and processing of data that generally follow an experimental session limits the access to the system for other investigators. We describe here the principles of a distributed image processing system, based on IBM-compatible personal computers (PCs), that without extra hardware can cope with all the necessary image processing involved in imaging of intracellular cations. The potential of the PC as an image processor, however, reaches beyond this specific application and many image processing tasks can be carried out successfully on a standard PC. Thus, the centrally located dedicated image processor is used only for image acquisition in the experimental situation. This in turn optimizes the utilization of expensive resources and increases efficiency. The mouse-operated software is described in detail, so that interested investigators can extract useful parts for integration into their own applications and experimental environment.

Animals↗
PubMed1991

A pharmacodynamic approach to optimizing insulin therapy.

We have developed a program for simulation and optimization of insulin therapy in patients with insulin-dependent diabetes. The program, denoted GLUCOJECT, is based on a physiologic model of minimal complexity, which describes the pharmacokinetics of absorption and clearance of subcutaneous insulin and the dynamics of glucose utilization as dependent on both prevailing glucose and insulin levels. With self-monitored glucose values and insulin doses collected with one of several commercially available memory meters, GLUCOJECT reconstructs an average or 'typical' daily plasma glucose and insulin profile and displays them in a graph. The program then calculates the expected rate of glucose utilization, which permits calculation of the rate of glucose entry into plasma from both endogenous (hepatic) and exogenous (dietary) sources. In turn, this allows one to calculate an 'ideal' plasma insulin profile required to maintain a relatively constant 'ideal' plasma glucose level. GLUCOJECT can evaluate several different insulin regimens involving various combinations of short-, intermediate- and long-acting insulins, and select the one(s) most closely approximating the ideal or optimal insulin profile, using a least-squares criterion. For any optimized insulin regimen, GLUCOJECT calculates and displays the predicted time course of plasma glucose. These features make the program attractive as an educational tool for both patients and health care professionals and could potentially assist in the management of patients with insulin-dependent diabetes.

Blood Glucose↗
PubMed1993

Semi-automatic computer construction of three-dimensional shapes for the finite element method.

Precise estimation of spatio-temporal distribution of ions (or other constitutives) in three-dimensional geometrical configuration plays a major role in biology. Since a direct experimental information regarding the free intracellular Ca2+ spatio-temporal distribution is not available to date, mathematical models have been developed. Most of the existing models are based on the classical numerical method of finite-difference (FD). Using this method one is limited when dealing with complicated geometry, general boundary conditions and variable or non-linear material properties. These difficulties are easily solved when the finite-element-method (FEM) is employed. The first step in the implementation of the FEM procedure is the mesh generation which is the single most tedious, time consuming task and vulnerable to mistake. In order to overcome these limitations we developed a new interface called AUTOMESH. This tool is used as a preprocessor program which generates two- and three-dimensional meshes for some known and often-used shapes in neurobiology. AUTOMESH creates an appropriate mesh by using the mesh generator commercial tool of FIDAP.

Calcium↗
PubMed1994

An architecture for EEG signal processing and interpretation during sleep (ESPIS).

The project's aim is to develop a dedicated workstation in order to process multiple channels of electrophysiological signals in real-time during sleep. In ESPIS we are aiming to define both an architecture and an environment for EEG signal interpretation in medicine based on computer science gold standards (Unix, XWindow, Motif). Signal processing and pattern recognition analysis are provided by parallel processing on a specific developed acquisition architecture (DSP) based on transputers. The main result is a high performance prototype demonstrating signal interpretation during sleep which has already been tested in a medical environment. The overall specifications allow this biomedical device to be extended to other types of medical signals.

Algorithms↗
PubMed1995

IntroStat: a hypertext-based design for an electronic textbook to introduce biomedical statistics.

A hypertext-based system called IntroStat has been developed to introduce fundamental methods of biomedical statistics. The system has been developed on a Macintosh II using HyperCard. It is written mainly in Hypertalk, a scripting language of HyperCard. Being an electronic textbook of probability and statistics, the system features computational capabilities. At the end of the sections describing basic methods of statistics, pages are provided where a user may enter data and try the methods right there. Some means for branching are provided for easy access to a page of interest, including branching by contents, by index, and by keyword reference. The system design is proposed as a model of an electronic textbook for biomedical statistics.

Biometry↗
PubMed1996

A flexible high-precision video system for digital recording of motor acts through lightweight reflex markers.

This paper describes and evaluates the digital MacReflex system for wireless recording of movements in three dimensions. Up to seven high resolution infra-red sensitive CCD video cameras with electronic shutters register the positions of maximally 40 stroboscopically illuminated retro-reflective tape markers. The system is equipped with real-time video processors for computation of position co-ordinates for the markers and for optimised data transmission and storage. Data are output to any type of computer through a standard serial interface, which also provides possibilities for simultaneous A/D-sampling. Dynamic manipulation of the recorded signals in three-dimensional plots is provided by standard software and transformation and evaluation of recorded data are performed in standard software. The described equipment is found to offer a flexible and easily operated solution for recording of movements with high resolution.

Computer Graphics↗
PubMed1996

OpenLabs advanced instrument workstation services.

The advanced instrument workstation (AIW) is one of a number of system modules developed in the OpenLabs project, offering advanced services that complement the basic services available from laboratory information systems (LIS) in general. The AIW services relate to instrument interfacing, user interfacing, quality control, calibration verification, patient result validation, local and remote fault diagnosis and maintenance, and external quality assessment (EQA) by external organisations.

Clinical Laboratory Information Systems↗
PubMed1996

Patient result validation services.

Patient result validation is a vital final stage of laboratory quality assurance and is usually the responsibility of senior laboratory staff. Computerised validation systems have recently been introduced to autovalidate data meeting certain pre-defined criteria, thereby allowing senior staff to focus on problematic cases. This article describes the patient results validation service module developed for an advanced instrument workstation in the OpenLabs project. Using knowledge-based techniques, the module provides a range of locally configurable advanced validation procedures (e.g., internal consistency checks, delta checks, and checks for selected specific errors) in addition to the standard reference range and pathological limits checks offered by many laboratory information systems.

Artificial Intelligence↗
PubMed1991

The use of personal computers in hospital infection control.

The storage, retrieval and analysis of hospital infection data is best performed by using computers. Many laboratory mainframe systems have infection control modules and there are some commercial programs for personal computers (PCs). An alternative is to use business and statistical PC software. Because of their large customer base these programs are reliable and easy to use yet extremely sophisticated and flexible, and they can be easily customized for use in infection control. Many combinations of software and hardware are available but the ones described here have been used successfully for several years at the Prince of Wales Hospital in Hong Kong.

Computer Graphics↗
PubMed1989

Animation: a useful tool for protein molecular dynamicists, applied to hydrogen bonds in the active site of elastase.

Massive amounts of coordinate data result from molecular dynamics calculations. The animation program MDKINO is a simple but powerful tool for previewing or reviewing the results. In recent simulations of elastase, we have examined hydrogen bonding patterns, conformational changes involving shifts in ring positions and rotations of amino acid side chains, electric fields in interatomic space, and electric forces acting on chosen nuclei. Animation is also useful for checking on the stability of calculations in progress. Simple programming techniques achieve acceptable levels of animation with readily available hardware (PS330 or PS390 display with a serial interface to a laboratory VAX). In about half an hour, it is possible to make and watch a color stereo "movie" of a selected subsystem of a simulation (up to 1,000 frames of about 100 atoms each).

Binding Sites↗
PubMed1991

Implementing knot-theoretical characterization methods to analyze the backbone structure of proteins: application to CTF L7/L12 and carboxypeptidase A inhibitor proteins.

In this work we apply a recently developed method for characterizing the shape of the tertiary structure of proteins. The approach is based on a combination of graph- and knot-theoretical characterizations of Cartesian projections of the space curve describing the protein backbone. The proposed technique reduces the essential shape features to a topologically based code formed by a sequence of knot symbols and polynomials. These polynomials are topological invariants that describe the overcrossing and knotting patterns of curves derived from the molecular space curve. These descriptors are algorithmically computed. The procedure is applied to describe the structure of the carboxy terminal fragment of the L7/L12 chloroplast ribosomal protein (CTF L7/L12) and the potato carboxypeptidase A inhibitor protein (PCI), which has a set of three disulfide bridges. In the former case, we describe the protein's shape features in terms of its alpha-helices, and a backbone simplified by considering helices without internal structure. An extension of the methodology to describe disulfide bridges is discussed and applied to PCI. Changes in the knot-theoretical characterization due to possible uncertainties in the resolution of the X-ray structure, as well as the inclusion of low-frequency motions of the backbone, are also discussed.

Carboxypeptidases↗
PubMed1991

Visualization of structural similarity in proteins.

Two new methods for the visualization of structural similarity in proteins with known three-dimensional structures are presented. They are based on the degree of equivalence of alpha-carbon pairs in two proteins. The quantitative measure for residue equivalence is the comparison score generated using the sequence and structure alignment method of Taylor and Orengo, which is based on the comparison of interatomic distances (and other properties that can be defined on a residue basis). The first method uses information on corresponding alpha-carbon positions to display vectors joining these structurally equivalent residues. These vectors can be defined as target constraints, and their minimization "bends" the two proteins toward a common average structure. In the average structure the corresponding residues virtually superpose, while insertions and deletions become clearly visible. The second method uses the comparison scores to perform a weighted least-squares fit of the two structures. It is further used to color code the two structures according to the score value, i.e., their similarity, on a continuous scale from red to blue. Examples of the methods for the comparison of flavodoxin, chemotaxis Y protein and L-arabinose-binding protein are given.

Amino Acid Sequence↗
PubMed1991

FORME: an interactive package for protein backbone deformation.

The FORME package presented herein is designed for modeling purposes: It allows interactive deformation of the protein backbone. General formalism on transformations is introduced and the operators of stretching inside an "acceptance area" and stretching with end-block invariance (i.e., governed by a translational moving) are described. A discussion is presented on the choice of strategy to achieve an interactive deformation tool. Perspectives about complex transformations are presented.

Computer Graphics↗
PubMed1992

Object Command Language: a formalism to build molecular models and to analyze structural parameters in macromolecules, with applications to nucleic acids.

We have written a programming language OCL (Object Command Language) to solve, in a general way, two recurring problems that arise during the construction of molecular models and during the geometrical characterization of macromolecules: how to move precisely and reproducibly any part of a molecular model in any user-defined local reference axes; and how to calculate standard or user-defined structural parameters that characterize the complex geometries of any macromolecule. OCL endows the user with three main capabilities: the definition of subsets of the macromolecule, called objects in OCL, with a formalism from elementary set theory or lexical analysis; the definition of sequences of elementary geometrical operations, called procedures in OCL, enabling one to build arbitrary three-dimensional (3D) orthonormal reference frames, to be associated with previously defined objects; and the transmission of these definitions to programs that allow one to display, to modify and to analyze interactively the molecular structure, or to programs that perform energy minimizations or molecular dynamics. Several applications to nucleic acids are presented.

Computer Graphics↗
PubMed1993

Fast algorithm for exact rendering of space-filling molecular models with shadows.

An algorithm for accurate rendering of space-filling molecular models with shadows is presented. The intensity of light and cast shadows are computed to generate realistic pictures. Arbitrary numbers of light sources, which may be at infinite or finite distances can be applied. Hidden-surface removal, lighting, and shadowing are presented in detail.

Algorithms↗
PubMed1995

Interfacing electrochromic spectacles to computer IO ports.

Many important properties of molecules depend on their precise three-dimensional (3D) structure. It is therefore useful to be able to view a molecule in 3D on a 2D computer screen when manipulating it. An inexpensive method for viewing in 3D using liquid crystal glasses and a PC is presented. The methodology used is easily extended to other computers and workstations.

Computer Graphics↗
PubMed1995

Development of quantitative structure property relationships for poly(arylene ether)s.

The technique of quantitative structure-activity relationships (QSAR) is well accepted by the drug design community. The analogous technique of quantitative structure-property relationships (QSPR) has applications in the field of polymer chemistry. A variety of molecular modeling and molecular orbital techniques was used to find molecular descriptors that could be used to derive an empirical equation to describe the glass transition temperature of two related classes of poly(arylene ether)s. The derived equation was then used to predict the thermal characteristics of another polymer of the same type.

Computer Graphics↗