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Search Results: 1 - 10 of 5895 matches for " Pavel Sou?ek "
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Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach  [PDF]
Jaroslav Kubrycht, Karel Sigler, Pavel Souek, Ji?í Hude?ek
Computational Molecular Bioscience (CMB) , 2016, DOI: 10.4236/cmb.2016.61001
Abstract: In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.
Virtual Interactomics of Proteins from Biochemical Standpoint
Jaroslav Kubrycht,Karel Sigler,Pavel Souek
Molecular Biology International , 2012, DOI: 10.1155/2012/976385
Abstract: Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations. 1. General Remarks Many important findings in pharmacology, cell biology, and pathobiology have been achieved with the aid of virtual interactomics including computer-aided structural analysis, prediction and in silico simulation of interacting sites, protein complexes, and interaction networks. Virtual interactomics has been developed in the last thirty years, and it is in fact based on gradual bioinformatic processing of experimental data. These data were usually obtained from individual studies of interactions, and various large-scale experimental methods such as the two-hybrid system, phage display library studies reverse interactomics, SPOT arrays or microarray studies, and extended sequence studies [1–7]. In addition to sequence data, three-dimensional (3D) structures are ever more frequently required for interactomic predictions. X-ray crystallography or nuclear magnetic resonance studies represent the most frequent sources of 3D structures, whereas combination of electron microscopy of molecular complexes with X-ray crystallography turns out to be interesting for the same purpose [8–11]. Alternatively, sophisticated 3D structure simulations such as homology modeling or combination of cryoelectron microscopy densities, and
Comparison of chromosomal aberrations frequency and polymorphism of GSTs genes in workers occupationally exposed to cytostatics or anaesthetics
udovít Mu ák, , Erika Hala ová, Tatiana Matáková, Lucia Letková, Ludmila Vodi ková, , Janka Buchancová, Henrieta Hude ková, Oto Osina, Pavel Sou ek, Pavel Vodi ka
Interdisciplinary Toxicology , 2009, DOI: 10.2478/v10102-009-0016-0
Abstract: Authors compared the incidence of chromosomal aberrations (CAs) of workers occupationally exposed to cytostatics (group EXP1) or anaesthetics (group EXP2) in relationship to polymorphism of GSTM1, GSTP1 and GSTT1 genes. The cytogenetic analysis for chromosomal aberrations frequency and for polymorphisms of genes the PCR and PCR-RFLP method were used. Statistically higher frequency of total CAs was detected in both exposed groups: group EXP1 1.90±1.34%; Mann-Whitney U-test, p=0.001; group EXP2 2.53±1.46%, p=0.0008) as compared to control (1.26±0.93%). In group EXP2 was detected statistically higher frequency of aberrations CSA-type as compared to CTA-type. In xenobiotic metabolizing genes for GST higher frequency of total CAs and constituent types chromatid-type aberrations (CTAs) and chromosome-type aberrations (CSAs) of genes GSTM1 and GSTT1 with null genotype was detected. Statistically significant difference was detected only in CSA-type of aberrations in GSTT1 gene. In gene GSTP1 was not detected any difference in frequency of aberrations in presence of the variant allele. Presented results point out importance of individual susceptibility in evaluation of genotoxic agents of anaesthetics or cytostatics.
Long-term sustainability of bio-components production
Souek Ivan,Oci? Ozren J.
Hemijska Industrija , 2012, DOI: 10.2298/hemind110718078s
Abstract: Biofuels play an increasingly important role in motor fuel market. The list of biofuels (bio-components) in accordance with EU legislations contains a number of substances not widely used in the market. Traditionally these include: fatty acid methyl esters (FAME, in the Czech Republic methyl ether of rape seed oil) and bioethanol (also ethyl terc. buthyl ether ETBE, based on bioethanol). The availability and possible utilizations of bio-component fuels in Czech Republic and Serbia are discussed. Additional attention is paid on the identification of the possibilities to improve effectiveness of rape seeds cultivation and utilization of by-products from FAME production (utilization of sew, rape-meal and glycerol) which will allow fulfilment of the sustainability criteria for the first generation biofuels. The new approaches on renewable co-processing are commented. The concept of 3E (emissions, energy demand, and economics) is introduced specifying three main attributes for effective production of FAME production in accordance with legal compliances. Bio-components price change is analyzed in comparison to the price of motor fuels, identifying possible (speculative) crude price break-even point at the level of 149-176 USD/bbl at which point bio-fuels would become economically cost effective for the use by refiners.
Investigation of Gd3Ga5O12 by Micropolarimetry  [PDF]
Pavel Novotny, Marie K?i?ánková, Pavel Bohá?ek
Journal of Analytical Sciences, Methods and Instrumentation (JASMI) , 2013, DOI: 10.4236/jasmi.2013.31003

This paper summarizes the results of investigation of garnets Gd3Ga5O12 (GGG) on the basis of their optical activity. Dispersion of Verdet constant was measured in the visible light range and in a strong magnetic field. The applied technique, namely micropolarimetry, exhibits high resolution which corresponds to the type of polarization microscope used in the investigation.

Mapping Creative Industries in the Zlin Region
Bedná? Pavel,Grebení?ek Pavel
Journal of Competitiveness , 2012,
Abstract: Mapping of creative industries is a crucial basis for assessing the creative economy in regions. It ensures the development of creative clusters and the subsequent identification of stakeholders and networks. The present approach is to transfer creative industries research from global cities and urbanized old industrial regions to peripheral rural regions, in our case with preserved ethnographic traditions and crafts and tradition in design and film production which forms the core activities of the region. The article discusses the methods of secondary data quantitative analysis of the commercial creative industries from publicly available sources and reveals shortcomings in databases in the Czech Republic. The mapping takes into account the contribution of time factor within the definition of the creative industries segments, where it reveals significant differences not only between them but also, it shows differentiation between enterprises with employees and non-employing enterprises. The article serves as a foundation for the facilitation of creative clusters and creative industries development strategies as instruments that support competitiveness at the regional level.
Pavel Polá ek
Journal of Hydrology and Hydromechanics , 2011, DOI: 10.2478/v10098-011-0009-5
Abstract: This paper deals with optimisation and acceleration of the clarification process. It was established that both these objectives are closely inter-related and can be accomplished by the formation of aggregates with a high agitation intensity until the flocculation optimum is reached. This is a new method of formation of aggregates which is called the Inline High Density Suspension (IHDS) formation process. Further, under the IHDS process the aggregates are formed with a single root-mean-square velocity gradient G >> 50 s-1. It was also established that the process of formation of aggregates (expressed by residual e of the observed determinant) passes through a minimum. This minimum is considered to be the flocculation optimum. Furthermore, the agitation intensity (G) was found to be the inherent means influencing compactness and thereby density of the aggregates formed. This proves the vital role of agitation intensity on the morphological and physical properties of aggregates formed. The resultant aggregates formed by the IHDS process are very compact, dense and homogeneous in their size, shape, volume and inner structure. Last but not least, the IHDS process applied to the HR-CSAV type sludge blanket clarifier facilitated its high attainable upflow velocity above of 25 m h-1.
Journal of Central European Agriculture , 2007,
Abstract: One of major concerns of modern agriculture is conservation, evaluation and utilization of genetic resources of agricultural plants. The aim of this research was to evaluate the resistance of leaves and berries of table grape varieties to powdery mildew (Erysiphe necator) under field conditions. During the period 1996-2004, 32 table varieties (viz. 28 interspecific varieties and 4 varieties of Vitis vinifera) were investigated. A high resistance of leaves and berries to powdery mildew has been proved for varieties Augustovskii, Yalovenskii Ustoichivyi, P l skei Muskotály and Pleven Ustoichyvii. It was also possible to confirm a lower degree of resistance to powdery mildew in some hybrids of V.vinifera x V. amurensis. Varieties of V. vinifera showed a low degree of resistance to powdery mildew infestation.
The Clifford Deformation of the Hermite Semigroup
Hendrik De Bie,Bent ?rsted,Petr Somberg,Vladimir Souek
Symmetry, Integrability and Geometry : Methods and Applications , 2013,
Abstract: This paper is a continuation of the paper [De Bie H., rsted B., Somberg P., Sou ek V., Trans. Amer. Math. Soc. 364 (2012), 3875–3902], investigating a natural radial deformation of the Fourier transform in the setting of Clifford analysis. At the same time, it gives extensions of many results obtained in [Ben Sa d S., Kobayashi T., rsted B., Compos. Math. 148 (2012), 1265–1336]. We establish the analogues of Bochner's formula and the Heisenberg uncertainty relation in the framework of the (holomorphic) Hermite semigroup, and also give a detailed analytic treatment of the series expansion of the associated integral transform.
Invariant prolongation of overdetermined PDE's in projective, conformal and Grassmannian geometry
Matthias Hammerl,Petr Somberg,Vladimír Souek,Josef ?ilhan
Mathematics , 2011,
Abstract: This is the second in a series of papers on natural modification of the normal tractor connection in a parabolic geometry, which naturally prolongs an underlying overdetermined system of invariant differential equations. We give a short review of the general procedure developed in [5] and then compute the prolongation covariant derivatives for a number of interesting examples in projective, conformal and Grassmannian geometries.
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