arXiv subjects

Jan Urban

Publications and source records attributed to Jan Urban.

7 recordsLinked to original sources

arXiv2017

Zampa's systems theory: a comprehensive theory of measurement in dynamic systems

The article outlines in memoriam Prof. Pavel Zampa's concepts of system theory which enable to devise a measurement in dynamic systems independently of the particular system behaviour. From the point of view of Zampa's theory, terms like system time, system attributes, system link, system element, input, output, subsystems, and state variables are defined. In Conclusions, Zampa's theory is discussed together with another mathematical approaches of qualitative dynamics known since the 19th century. In Appendices, we present applications of Zampa's technical approach to measurement of complex dynamical (chemical and biological) systems at the Institute of Complex Systems, University of South Bohemia in Ceske Budejovice.

cs.OH↗

arXiv2016

Super-resolved 3-D imaging of live cells organelles from bright-field photon transmission micrographs

Current biological and medical research is aimed at obtaining a detailed spatiotemporal map of a live cell's interior to describe and predict cell's physiological state. We present here an algorithm for complete 3-D modelling of cellular structures from a z-stack of images obtained using label-free wide-field bright-field light-transmitted microscopy. The method visualizes 3-D objects with a volume equivalent to the area of a camera pixel multiplied by the z-height. The computation is based on finding pixels of unchanged intensities between two consecutive images of an object spread function. These pixels represent strongly light-diffracting, light-absorbing, or light-emitting objects. To accomplish this, variables derived from R\'{e}nyi entropy are used to suppress camera noise. Using this algorithm, the detection limit of objects is only limited by the technical specifications of the microscope setup--we achieve the detection of objects of the size of one camera pixel. This method allows us to obtain 3-D reconstructions of cells from bright-field microscopy images that are comparable in quality to those from electron microscopy images.

q-bio.QM↗

arXiv2015

Measurement in biological systems from the self-organisation point of view

Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological systems as dynamical systems far from not only their chemical equilibrium, but, in most cases, also of their Lyapunov stable states. Thus, in biological experiments, we do not observe states, but distinct trajectories followed by the examined organism. If one of the possible sequences is selected, a minute sub-section of the whole problem is obtained, sometimes in a seemingly highly reproducible manner. But the state of the organism is known only if a complete set of possible trajectories is known. And this is often practically impossible. Therefore, we propose a different framework for reporting and analysis of biological experiments, respecting the view of non-linear mathematics. This view should be used to avoid overoptimistic results, which have to be consequently retracted or largely complemented. An increase of specification of experimental procedures is the way for better understanding of the scope of paths, which the biological system may be evolving. And it is hidden in the evolution of experimental protocols.

q-bio.OT↗

arXiv2015

Point Information Gain and Multidimensional Data Analysis

We generalize the Point information gain (PIG) and derived quantities, i.e. Point information entropy (PIE) and Point information entropy density (PIED), for the case of R\'enyi entropy and simulate the behavior of PIG for typical distributions. We also use these methods for the analysis of multidimensional datasets. We demonstrate the main properties of PIE/PIED spectra for the real data on the example of several images, and discuss possible further utilization in other fields of data processing.

physics.data-an↗

arXiv2012

Blank measurement based time-alignment in LC-MS

Here are presenting the blank based time-alignment (BBTA) as a strong analytical approach for treatment of non-linear shift in time occurring in HPLC-MS data. Need of such tool in recent large dataset produced by analytical chemistry and so-called omics studies is evident. Proposed approach is based on measurement and comparison of blank and analyzed sample evident features. In the first step of BBTA procedure, the number of compounds is reduced by max-to-mean ratio thresholding, which extensively reduce the computational time. Simple thresholding is followed by selection of time markers defined from blank inflex points which are then used for the transformation function, polynomial of second degree, in the example. BBTA approach was compared on real HPLC-MS measurement with Correlation Optimized Warping (COW) method. It was proved to have distinctively shorter computational time as well as lower level of mathematical presumptions. The BBTA is computationally much easier, quicker (more then 1000x) and accurate in comparison with warping. Moreover, markers selection works efficiently without any peak detection. It is sufficient to analyze only baseline contribution in the analyte measurement with sparse knowledge of blank behavior. Finally, BBTA does not required usage of extra internal standards and due to its simplicity it has a potential to be widespread tool in HPLC-MS data treatment.

q-bio.QM↗

arXiv2011

Automatic segmentation of HeLa cell images

In this work, the possibilities for segmentation of cells from their background and each other in digital image were tested, combined and improoved. Lot of images with young, adult and mixture cells were able to prove the quality of described algorithms. Proper segmentation is one of the main task of image analysis and steps order differ from work to work, depending on input images. Reply for biologicaly given question was looking for in this work, including filtration, details emphasizing, segmentation and sphericity computing. Order of algorithms and way to searching for them was also described. Some questions and ideas for further work were mentioned in the conclusion part.

cs.CV↗

arXiv1998

Non-adiabatic molecular Hamiltonian: Canonical transformation coupling electronic and vibrational motions

The coupling of electronic and vibrational motion is studied by two canonical transformations namely normal coordinate transformation and momentum transformation on molecular Hamiltonian. It is shown that by these transformations we can pass from crude approximation to adiabatic approximation and then to non-adiabatic (diabatic) Hamiltonian. This leads to renormalized fermions and renormalized diabatic phonons. Simple calculations on $H_{2}$, $HD$, and $D_{2}$ systems are performed and compared with previous approaches. Problem of electronic quasi-degeneracy is discussed.

physics.chem-ph↗