Biomedical subjects

J Pánek

Publications and source records attributed to J Pánek.

4 recordsLinked to original sources

PubMed1999

Point pattern matching in the analysis of two-dimensional gel electropherograms.

In the automation of proteome analysis, matching of two-dimensional (2-D) electropherograms represents a bottleneck in the process. Here we present a point pattern recognition approach to the matching of spots in 2-D electropherograms. The algorithm is based on a comparison of spot neighborhoods, converted to point patterns between reference and compared gels. The neighborhood was characterized by a syntactic descriptor which minimized the influence of spot displacements. A combined criterion utilizing the similarity of point patterns and a metric definition of position similarity was derived. The efficiency and accuracy of the algorithm was tested on a set of 69 gels with different levels of similarity. For a typical gel the accuracy of matching was higher than 98% and the number of correctly identified spots was higher than 95%.

Algorithms↗

PubMed1997

Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis.

MOTIVATION: The principal motivation was to design an environment for the development of image-analysis applications which would allow the integration of independent modules into one frame and make available tools for their build-up, running, management and mutual communication. RESULTS: The system was designed as modular, consisting of the core and work modules. The system core focuses on overall management and provides a library of classes for build-up of the work modules, their user interface and data communication. The work modules carry practical implementation of algorithms and data structures for the solution of a particular problem, and were implemented as dynamic-link libraries. They are mutually independent and run as individual threads, communicating with each other via a unified mechanism. The environment was designed to simplify the development and testing of new algorithms or applications. An example of implementation for the particular problem of the analysis of two-dimensional (2D) gel electrophoretograms is presented. The environment was designed for the Windows NT operating system with the use of Microsoft Foundation Class Library employing the possibilities of C++ programming language. AVAILABILITY: Available on request from the authors.

Computer Graphics↗

PubMed1993

Quantitative analysis of gel electrophoretograms by image analysis and least squares modeling.

A computer-aided quantitative method for a complex analysis of gel electrophoretograms is presented. The analysis consists of several steps: (i) determination of the background image by methods of mathematical morphology and its subtraction from the gel image, (ii) selection of an appropriate part of the gel lane including curved lanes and lanes with a nonuniform width, (iii) computation of the lane densitogram by averaging several lane-parallel scans, (iv) decomposition of the lane densitogram into component bands using a data selecting algorithm and Marquardt's minimizer. Several different functions for component bands are utilized. It is shown that the densitogram can be decomposed into component bands with reasonable accuracy only if an appropriate model function is chosen. The algorithms are tested on several different gel electrophoretograms which show typical features as a nonuniform background, curved lanes, an asymmetrical band shape and a superposition of small bands on the shoulders of big ones. It is shown that overlapped bands are best approximated by an asymmetrical Gausian curve and an asymmetrical Gauss-Cauchy function. Linear response to the serial dilution of the protein sample is tested.

DNA, Bacterial↗

PubMed1990

Interactions of oxidized lipids with protein. Part XVI. Interactions of oxidized ethyl linoleate with collagen.

The reaction of ethyl linoleate with collagen proceeded at 60 degrees C following the first order kinetics but during the hydroperoxide decomposition the rate constant of the first order decomposition was substantially lower than that of the second order decomposition. Contrary to cellulose, collagen catalyzed the hydroperoxide decomposition. The amount of total oxidation products rose rapidly at the stage of rapid hydroperoxide formation, and slowly afterwards. The browning reaction was fasted in the stage of maximum hydroperoxide content, and both ether-insoluble and ether-soluble pigments were formed, the latter low in nitrogen. The amount of lipid oligomers increased mainly in the reaction stage following the hydroperoxide maximum. Soluble collagen was converted into insoluble forms by the reaction with oxidized lipids. Basic amino acids were blocked by reaction with oxidized lipids but the bonds formed became resistant to acid hydrolysis only in the stage following the hydroperoxide maximum. Changes of sensory profiles could be explained by reactions of flavour-active carbonylic oxidation products with protein.

Amino Acids↗