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Antibody-Like Phosphorylation Sites. Theme for Studies of Cancer, Aging and Evolution

Computational Molecular Bioscience 2022年第1期12卷 58-83页

作者： jaroslav kubrycht Karel Sigler Department of Physiology Second Faculty of Medicine Charles University Prague Czech Republic Laboratory of Cellular Biology Institute of Microbiology Academy of Sciences of the Czech Republic Prague Czech Republic

Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to ataxia-telangiectasia-mutated kinase known as ATM. In accordance with literature data, inactivation of ATM by mutations can participate in the mechanisms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine receptor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The analyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.

关键词： Ataxia-Telangiectasia-Mutated Kinase (ATM) Carcinogenesis Complementarity Determining Region 1 (CDR1 Hypervariable Region 1) Conserved Domain(s) Deep Evolution Evolution Hypermutation Kinase(s) Phosphorylation Site(s) Plant Immunity Variable Immunoglobulin Domain(s) (IgV)

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Conserved Immunoglobulin Domain Similarities of Higher Plant Proteins

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Computational Molecular Bioscience 2020年第1期10卷 12-44页

The traces of immunoglobulin domain similarities were searched in sequences of higher plants using bioinformatic tools to look for possible early phylogenic structural relationships. 280 thousand sequence IDs, obtained by sixteen types of primary BLAST searches, were differently processed by seventeen selection procedures and an anti-redundant sequence-related approach using JavaScript, PHP, Windows programs and conserved domain searches by means CDD. The resulting seventeen sets of records describing conserved domain similarities of 1323 different sequence IDs yielded a set of next generation (final set) comprising forty-nine records containing superior (“non-refutable”) conserved immunoglobulin domain similarities. The selected sets and their subsets were mapped and subsequently statistically compared with respect to immunoglobulin-related as well as other reciprocal domain linkages. The list of frequently occurring conserved domain similarities concerned first of all domains important for plant and metazoan immunity, e.g. tyrosine kinases accompanying variable immunoglobulin domains in early Metazoa, toll-like receptors, lectin and leucine-rich repeat domains. Detailed description of immunoglobulin domain similarities occurring in the final set was completed by fold analysis of the restricted segments. The data were then discussed with respect to i) immunoglobulin fold evolution, ii) possible structural importance of domains cd14066 (IRAK) and PLN00113 (LRR-associated kinase) for deep evolution of catalytic serine/threonine/tyrosine kinase domains, iii) interatomic, structural and specificity standpoints and iv) traces of antibody-like phosphorylation sites described in our previous paper.

关键词： Conserved Domain Domain Shuffling Deep Evolution Evolution Fold Immunoglobulin Kinase Plant Immunity Resistance

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Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach

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Computational Molecular Bioscience 2016年第1期6卷 1-22页

作者： jaroslav kubrycht Karel Sigler Pavel Souček Jiří Hudeček Department of Physiology Second Faculty of Medicine Charles University Prague Czech Republic Laboratory of Cellular Biology Institute of Microbiology Academy of Sciences of the Czech Republic Prague Czech Republic Toxicogenomics Unit National Institute of Public Health Prague Czech Republic Department of Biochemistry Charles University Prague Czech Republic

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 pa

关键词： Ataxia Telangiectasia-Mutated-Protein (i.e. Kinase ATM Whose Pathogenic Mutation Is Responsible for Early Death of People) Complementarity Determining Region 1 (of Immunoglobulins i.e. CDR1 or Hypervariable Region 1) Database (of Functional Structures) Hypermutation (i.e. Mutation of DNA Sequences Mediated by Enzymes) Immunoglobulin (i.e. Ig or Antibody) Phosphorylation (Enzyme Mediated Modification Concerns Here Mostly Protein Sequences)

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Social networks of reintroduced Przewalski's horses in the Great Gobi B Strictly Protected Area (Mongolia)

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Current Zoology 2024年第2期70卷 182-194页

作者： Anna Bernatkova Ganbaatar Oyunsaikhan jaroslav Simek Martina Komarkova Francisco Ceacero Faculty of Tropical AgriSciences Czech University of Life Sciences PragueCzech Republic Great Gobi B Strictly Protected Area Takhin TalMongolia Zoo Praha U Trojského zamku 120/3PragueCzech Republic

Analyzing social networks is a powerful tool for understanding the ecology of social *** most studies focus on the role of each group member,few compare groups with different *** current population of Przewalski's horses Equus ferus przewalskii at the Great Gobi B Strictly Protected Area(Mongolia)includes groups of wild-born and captive-bred individuals with different experiences with the area(acclimatizing,long-term reintroduced,and wild-born),therefore serving as an ideal natural behavioral *** filmed 11 groups for 141.5 hours in summer 2018(July),late spring 2019(May,June),and autumn 2019(September,October).Affiliative and agonistic interactions were recorded,and social networks were *** tested the influence of origin,experience,season,sex,age,relative time belonging to the group,relat-edness,and dominance rank on different network indices at the individual and group *** found that groups with greater experience in the area are generally better connected than members of the newly formed ***,these strong networks were created by wild-born individuals with very low interaction *** the contrary,inexperienced groups composed of captive-bred individuals displayed many inter actions but created weak social *** results show a trend of behavioral transition from acclimatizing through long-term reintroduced to wild-born groups,supporting that the newly formed groups of released Przewalski's horses need time to display the typical social behavior patterns of wild-born ***-term monitoring of released Przewalski's horses is recommended to promote the success of this reintroduction program.

关键词： Przewalski's horses reintroduction social behavior soft-release.

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Enigmatic thymus: Variations in anatomical localisation of thymic tissue as an easily misdiagnosed congenital anomaly in surgical practice

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World Journal of Clinical Cases 2024年第25期12卷 5646-5652页

作者： Alexander Mayer jaroslav Voller Ivan Varga Fourth Department of Surgery Faculty of MedicineComenius University and University Hospital BratislavaBratislava 81372Slovakia Faculty of Health Care Studies University of Western BohemiaPilsen 30100Czech Republic Institute of Histology and Embryology Faculty of MedicineComenius University in BratislavaBratislava 81372Slovakia

We point out the issue of differential diagnosis regarding the finding of ectopically localised thymic tissue(a thymic cyst)in the *** tissue can be found anywhere along its developmental tract of descent,from the angle of the mandible to the upper *** of the thymic descent can result in ectopically/abnormally localised islets of accessory thymic tissue,which may undergo cystic changes,as described in a case report by Sun et *** anatomical variation of the thymus may be clinically misinterpreted as a neoplasm or other congenital anomalies as a branchial cyst,lymphatic malformation or cystic *** present editorial focuses on the challenge of establishing a diagnosis of ectopically localised tissue of thymus often presented as a lateral cervical mass,especially in the case of cystic variation/degeneration of this thymic *** summarise hypotheses on the origin of such congenital cervical thymic cysts from the point of view of evolutionary history and *** also discuss lesser-known facts about the anatomy,histopathology and developmental biology of the thymus as one of the most enigmatic organs in the human body.

关键词： Thymus Thymic anomalies Thymic ectopy Congenital cervical thymic cyst Embryonic development

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Antimicrobial susceptibility of Enterobacteriaceae causing urinary tract infections： a central military hospital study

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Chinese Medical Journal 2014年第23期127卷 4150-4151页

作者： jaroslav Timko Faculty of Health Care Catholic University in Ruzomberok Institute of Clinical Microbiology of Central Military Hospital - Faculty Hospital Ruzomberok Slovakia

Urinary tract infection （UTI） remains one of the most common bacterial infections seen in hospitalized patients of all ages. Prevalence of UTIs increases with age and is often accompanied by higher resistance rates. The aim of this study was to determine the degree of resistance of most common enterobacterial uropathogens isolated from patients at Central Military Hospital and compare this resistance with the results found by the North America and Europe Study for Monitoring Antimicrobial Resistance Trends （SMART） study during 2009-2010.

关键词： urinary tract infection uropathogens Escherichia coli resistance ampicillin-sulbactam

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Evaluation of granulability and absorbtivity of biomass in agglomeration mixture

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Journal of Central South University 2017年第10期24卷 2260-2265页

作者： Hudák Jozef Lesko jaroslav Semanová Zuzana Frohlichová Mária Findorák Róbert Legemza jaroslav Institute of Metallurgy Faculty of MetallurgyTechnical University of KosiceKosice04200Slovakia

The granulability and absorbtivity of sawdust and coke breeze were *** properties are important within the preparation of agglomeration *** have a significant impact on plynodynamic batch *** of materials to wet is a fundamental condition of granulability of *** and water absorption of wood with liquids is generally significantly affected by their chemical *** important factors affecting the wetting process are undoubtedly the wood moisture content,the value of the surface tension of liquid media and their chemical *** increasing moisture content of wood,the time to equilibrium *** of water absorption and granulability of sawdust was conducted to seek their possible use as a partial replacement of coke dust in the production of the *** have been realized with alder,oak and pine sawdust and reference material-coke *** materials were divided to four classes of granularity:supplied material,1-2 mm,0.5-1 mm and less than 0.5 *** different liquid media were used:water 16°C,water 60°C,soapy water,lime milk and surfactant.

关键词： agglomeration biomass coke breeze granulability absorbtivity

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Classification of Spectra of Emission Line Stars Using Machine Learning Techniques

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International Journal of Automation and computing 2014年第3期11卷 265-273页

作者： Pavla Bromová Petr koda jaroslav Vázn Faculty of Information Technology Brno University of Technology Astronomical Institute of the Academy of Sciences of the Czech Republic

Advances in the technology of astronomical spectra acquisition have resulted in an enormous amount of data available in world-wide telescope archives. It is no longer feasible to analyze them using classical approaches, so a new astronomical discipline,astroinformatics, has emerged. We describe the initial experiments in the investigation of spectral line profiles of emission line stars using machine learning with attempt to automatically identify Be and B[e] stars spectra in large archives and classify their types in an automatic manner. Due to the size of spectra collections, the dimension reduction techniques based on wavelet transformation are studied as well. The result clearly justifies that machine learning is able to distinguish different shapes of line profiles even after drastic dimension reduction.

关键词： Be star stellar spectrum feature extraction dimension reduction discrete wavelet transform classification support vector machines(SVM) clustering.

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Effect of storage conditions on long-term stability of Ag nanoparticles formed via green synthesis

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International Journal of Minerals,Metallurgy and Materials 2017年第10期24卷 1177-1182页

作者： Oksana Velgosova Elena Cizmarova jaroslav Málek Jana Kavulicova Institute of Materials Faculty of Metallurgy Technical University of Kosice Letna 9 042 00 Kosice Slovakia Department of Materials Engineering Faculty of Mechanical Engineering Czech Technical University in Prague Karlovo nám. 13 121 32 Prague 2 Czech Republic Institute of Metallurgy Faculty of Metallurgy Technical University of Kosice Letna 9 042 00 Kosice Slovakia

Spherical Ag nanoparticles(AgNPs) with a diameter of 20 nm or smaller were biologically synthesized using algae Parachlorella kessleri. The effect of storage conditions on the long-term stability of AgNPs was investigated. UV/Vis spectrophotometry, transmission electron microscopy, and dynamic light scattering measurements revealed that the long-term stability of AgNPs was influenced by light and temperature conditions. The most significant loss of stability was observed for the AgNPs stored in daylight at room temperature. The AgNPs stored under these conditions began to lose their stability after approximately 30 d; after 100 d, a substantial amount of agglomerated particles settled to the bottom of the Erlenmeyer flask. The AgNPs stored in the dark at room temperature exhibited better long-term stability. Weak particle agglomeration began at approximately the 100 th day. The AgNPs stored in the dark at about 5℃ exhibited the best long-term stability; the AgNPs stored under such conditions remained spherical, with a narrow size distribution, and stable(no agglomeration) even after 6 months. Zeta-potential measurements confirmed better dispersity and stability of AgNPs stored under these conditions.

关键词： silver nanoparticles stability storage conditions green synthesis Parachlorella kessleri

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Structural and optical properties of nanostructured copper sulfide semiconductor synthesized in an industrial mill

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Frontiers of Chemical Science and Engineering 2019年第1期13卷 164-170页

作者： Marcela Achimovicova Erika Dutkova Erika Tothova Zdenka Bujnakova jaroslav Briancin Satoshi Kitazono Institute of Mineral and Waste Processing Waste Disposal and Geomechanics Clausthal University of Technology Clausthal 38678 Germany Institute of Geotechnics Slovak Academy of Sciences Kosice 04001 Slovakia Nakase Refinery Nihon Seiko Co. Ltd. Yabu-shi Hyogo 667-1111 Japan

Chalcogenide nanostructured semiconductor, copper sulfide (CuS) was prepared from copper and sulfur powders in stoichiometric ratio by a simple, fast, and convenient one-step mechanochemical synthesis after 40 min of milling in an industrial eccentric vibratory mill. The kinetics of the mechanochemical synthesis and the influence of the physical properties of two Cu powder precursor types on the kinetics were studied. The crystal structure, physical properties, and morphology of the product were characterized by X-ray diffraction (XRD), the specific surface area measurements, particle size distribution and scanning electron microscopy. The XRD analysis confirmed the hexagonal crystal structure of the product-CuS (covellite) with the average size of the crystallites 11 nm. The scanning electron microscopy analysis has revealed that the agglomerated grains have a plate-like structure composed of CuS nanoparticles. The thermal analysis was performed to investigate the thermal stability of the mechanochemically synthesized CuS. The optical properties were studied using UV-Vis and photoluminescence spectroscopy. The determined optical band gap energy 1.80 eV responds to the value of the bulk CuS, because of agglomerated nanoparticles. In addition, a mechanism of CuS mechanochemical reaction was proposed, and the verification of CuS commercial production was performed.

关键词： copper sulfide industrial mechanochemical synthesis thermal analysis optical properties

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