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Results: We developed a web version of the G4Hunter application. This new web-based server is a
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gene/nucleotide sequence entries from NCBI databases and provides complete characterization of
localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application
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localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application
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number="1/2018",
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[popis] => The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
[popis_orig] => The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
[klicova_slova] => G-quadruplex; bacteria; bioinformatics; deinococcus; G4Hunter
[klicova_slova_orig] => G-quadruplex; bacteria; bioinformatics; deinococcus; G4Hunter
[url] => https://www.mdpi.com/journal/molecules/special_issues/Gquadruplex_Microorganisms#published
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[citace_text] => BARTAS, M.; ČUTOVÁ, M.; BRÁZDA, V.; KAURA, P.; ŠŤASTNÝ, J.; KOLOMAZNÍK, J.; COUFAL, J.; GOSWAMI, P.; ČERVEŇ, J.; PEČINKA, P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. MOLECULES, 2019, vol. 24, no. 9, p. 1-13. ISSN: 1420-3049.
[citace_html] => BARTAS, M.; ČUTOVÁ, M.; BRÁZDA, V.; KAURA, P.; ŠŤASTNÝ, J.; KOLOMAZNÍK, J.; COUFAL, J.; GOSWAMI, P.; ČERVEŇ, J.; PEČINKA, P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. MOLECULES, 2019, vol. 24, no. 9, p. 1-13. ISSN: 1420-3049.
[citace_rtf] =>
[citace_bibtex] => @article{BUT156781,
author="BARTAS, M. and ČUTOVÁ, M. and BRÁZDA, V. and KAURA, P. and ŠŤASTNÝ, J. and KOLOMAZNÍK, J. and COUFAL, J. and GOSWAMI, P. and ČERVEŇ, J. and PEČINKA, P.",
title="The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria",
journal="MOLECULES",
year="2019",
volume="24",
number="9",
pages="1--13",
doi="10.3390/molecules24091711",
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[nazev_en] => The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria
[popis_en] => The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
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[nazev] => Automatic assessment of the cardiomyocyte development stages from confocal microscopy images using deep convolutional networks
[nazev_orig] => Automatic assessment of the cardiomyocyte development stages from confocal microscopy images using deep convolutional networks
[duvernost_udaju_id] => S
[popis] => Computer assisted image acquisition techniques, including confocal microscopy, require efficient tools for an automatic sorting of vast amount of generated image data. The complexity of the classification process, absence of adequate tools, and insufficient amount of reference data has made the automated processing of images challenging. Mastering of this issue would allow implementation of statistical analysis in research areas such as in research on formation of t-tubules in cardiac myocytes. We developed a system aimed at automatic assessment of cardiomyocyte development stages (SAACS). The system classifies confocal images of cardiomyocytes with fluorescent dye stained sarcolemma. We based SAACS on a densely connected convolutional network (DenseNet) topology. We created a set of labelled source images, proposed an appropriate data augmentation technique and designed a class probability graph. We showed that the DenseNet topology, in combination with the augmentation technique is suitable for the given task, and that high-resolution images are instrumental for image categorization. SAACS, in combination with the automatic high-throughput confocal imaging, will allow application of statistical analysis in the research of the tubular system development or remodelling and loss.
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[klicova_slova] => cardiomyocyte development stages; densely connected convolutional network; deep learning; classification of object images; confocal microscopy
[klicova_slova_orig] => cardiomyocyte development stages; densely connected convolutional network; deep learning; classification of object images; confocal microscopy
[url] => https://doi.org/10.1371/journal.pone.0216720
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[citace_text] => ŠKRABÁNEK, P.; ZAHRADNÍKOVÁ, A. Automatic assessment of the cardiomyocyte development stages from confocal microscopy images using deep convolutional networks. PLoS One, 2019, vol. 14, no. 5, p. 1-18. ISSN: 1932-6203.
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[citace_rtf] =>
[citace_bibtex] => @article{BUT157176,
author="Pavel {Škrabánek} and Alexandra {Zahradníková}",
title="Automatic assessment of the cardiomyocyte development stages from confocal microscopy images using deep convolutional networks",
journal="PLoS One",
year="2019",
volume="14",
number="5",
pages="1--18",
doi="10.1371/journal.pone.0216720",
issn="1932-6203",
url="https://doi.org/10.1371/journal.pone.0216720"
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[popis_en] => Computer assisted image acquisition techniques, including confocal microscopy, require efficient tools for an automatic sorting of vast amount of generated image data. The complexity of the classification process, absence of adequate tools, and insufficient amount of reference data has made the automated processing of images challenging. Mastering of this issue would allow implementation of statistical analysis in research areas such as in research on formation of t-tubules in cardiac myocytes. We developed a system aimed at automatic assessment of cardiomyocyte development stages (SAACS). The system classifies confocal images of cardiomyocytes with fluorescent dye stained sarcolemma. We based SAACS on a densely connected convolutional network (DenseNet) topology. We created a set of labelled source images, proposed an appropriate data augmentation technique and designed a class probability graph. We showed that the DenseNet topology, in combination with the augmentation technique is suitable for the given task, and that high-resolution images are instrumental for image categorization. SAACS, in combination with the automatic high-throughput confocal imaging, will allow application of statistical analysis in the research of the tubular system development or remodelling and loss.
[klicova_slova_en] => cardiomyocyte development stages; densely connected convolutional network; deep learning; classification of object images; confocal microscopy
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[nazev] => Multi-objective strategic waste transfer station planning
[nazev_orig] => Multi-objective strategic waste transfer station planning
[duvernost_udaju_id] => S
[popis] => The production of mixed municipal waste changes due to the increase of separation rate, urbanization and other factors. The future changes in the legislation and technology development influences the way the waste is being treated. Thus the method, location and capacity of processing sites are unknown. The realization of future projects can be supported by the developing of transportation infrastructure. Such a feature may be represented by a robust transfer station grid, which can be designed to handle all possible future realizations and technological solutions (establishment of waste treatment facilities). The paper presents an approach utilising a mathematical model for the design of transfer stations. It is formulated as a multi-objective two-stage mixed-integer stochastic programming problem, where the trade-off between the environmental aspect and the economic viability is considered. The model is tested through a case study for the Czech Republic, where the waste treatment of over 6,000 municipalities is analysed. The solutions for different preferences are assessed throughout the principle called out-of-sample stability with 10,000 scenarios. The optimal decision consists of the robust transfer station grid with selected locations and their respective capacity. The particular solution with respect to the potential trade-off suggests to save 1.148 mil of travelled kilometres with only 0.77 mil EUR. The output in the form of decision support can serve possible stakeholders from the field of waste management to plan more sustainable projects.
[popis_orig] => The production of mixed municipal waste changes due to the increase of separation rate, urbanization and other factors. The future changes in the legislation and technology development influences the way the waste is being treated. Thus the method, location and capacity of processing sites are unknown. The realization of future projects can be supported by the developing of transportation infrastructure. Such a feature may be represented by a robust transfer station grid, which can be designed to handle all possible future realizations and technological solutions (establishment of waste treatment facilities). The paper presents an approach utilising a mathematical model for the design of transfer stations. It is formulated as a multi-objective two-stage mixed-integer stochastic programming problem, where the trade-off between the environmental aspect and the economic viability is considered. The model is tested through a case study for the Czech Republic, where the waste treatment of over 6,000 municipalities is analysed. The solutions for different preferences are assessed throughout the principle called out-of-sample stability with 10,000 scenarios. The optimal decision consists of the robust transfer station grid with selected locations and their respective capacity. The particular solution with respect to the potential trade-off suggests to save 1.148 mil of travelled kilometres with only 0.77 mil EUR. The output in the form of decision support can serve possible stakeholders from the field of waste management to plan more sustainable projects.
[klicova_slova] => Multi-objective model; Stochastic programming; Strategic planning; Transfer station; Waste treatment
[klicova_slova_orig] => Multi-objective model; Stochastic programming; Strategic planning; Transfer station; Waste treatment
[url] => https://doi.org/10.1016/j.jclepro.2019.05.167
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[citace_text] => KŮDELA, J.; ŠOMPLÁK, R.; NEVRLÝ, V.; LIPOVSKÝ, T.; SMEJKALOVÁ, V.; DOBROVSKÝ, L. Multi-objective strategic waste transfer station planning. Journal of Cleaner Production, 2019, vol. 230, no. 1 September, p. 1294-1304. ISSN: 0959-6526.
[citace_html] => KŮDELA, J.; ŠOMPLÁK, R.; NEVRLÝ, V.; LIPOVSKÝ, T.; SMEJKALOVÁ, V.; DOBROVSKÝ, L. Multi-objective strategic waste transfer station planning. Journal of Cleaner Production, 2019, vol. 230, no. 1 September, p. 1294-1304. ISSN: 0959-6526.
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[citace_bibtex] => @article{BUT157309,
author="Jakub {Kůdela} and Radovan {Šomplák} and Vlastimír {Nevrlý} and Tomáš {Lipovský} and Veronika {Smejkalová} and Ladislav {Dobrovský}",
title="Multi-objective strategic waste transfer station planning",
journal="Journal of Cleaner Production",
year="2019",
volume="230",
number="1 September",
pages="1294--1304",
doi="10.1016/j.jclepro.2019.05.167",
issn="0959-6526",
url="https://doi.org/10.1016/j.jclepro.2019.05.167"
}
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[nazev_en] => Multi-objective strategic waste transfer station planning
[popis_en] => The production of mixed municipal waste changes due to the increase of separation rate, urbanization and other factors. The future changes in the legislation and technology development influences the way the waste is being treated. Thus the method, location and capacity of processing sites are unknown. The realization of future projects can be supported by the developing of transportation infrastructure. Such a feature may be represented by a robust transfer station grid, which can be designed to handle all possible future realizations and technological solutions (establishment of waste treatment facilities). The paper presents an approach utilising a mathematical model for the design of transfer stations. It is formulated as a multi-objective two-stage mixed-integer stochastic programming problem, where the trade-off between the environmental aspect and the economic viability is considered. The model is tested through a case study for the Czech Republic, where the waste treatment of over 6,000 municipalities is analysed. The solutions for different preferences are assessed throughout the principle called out-of-sample stability with 10,000 scenarios. The optimal decision consists of the robust transfer station grid with selected locations and their respective capacity. The particular solution with respect to the potential trade-off suggests to save 1.148 mil of travelled kilometres with only 0.77 mil EUR. The output in the form of decision support can serve possible stakeholders from the field of waste management to plan more sustainable projects.
[klicova_slova_en] => Multi-objective model; Stochastic programming; Strategic planning; Transfer station; Waste treatment
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[nazev] => Circular economy implementation in waste management network design problem: a case study
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[duvernost_udaju_id] => S
[popis] => The paper presents a new approach to support the strategic decision-making in the area of municipal solid waste management applying modern circular economy principles. A robust two-stage integer non-linear program is developed. The primary goal tends to reduce the waste production. The generated waste should be preferably recycled as much as possible and the resultant residual waste might be used for energy recovery. Only some waste residues are appropriate for landfilling. The aim is to propose the near-optimal waste allocation for its suitable processing as well as waste transportation plan at an operational level. In addition, the key strategical decisions on waste treatment facilities location must be made. Since waste production is very often hard to predict, it is modeled as an uncertain decision-dependent quantity. To support the circular economy ideas, advertising and pricing principles are introduced and applied. Due to the size of available real-world data and complexity of the designed program, the presented model is linearized and uncertainty is handled by a robust optimization methodology. The model, data, and algorithm are implemented in MATLAB and Julia, using the state-of-the-art solvers. The computational result is a set of decisions providing a trade-off between the average performance and the immunization against the worst-case conditions.
[popis_orig] => The paper presents a new approach to support the strategic decision-making in the area of municipal solid waste management applying modern circular economy principles. A robust two-stage integer non-linear program is developed. The primary goal tends to reduce the waste production. The generated waste should be preferably recycled as much as possible and the resultant residual waste might be used for energy recovery. Only some waste residues are appropriate for landfilling. The aim is to propose the near-optimal waste allocation for its suitable processing as well as waste transportation plan at an operational level. In addition, the key strategical decisions on waste treatment facilities location must be made. Since waste production is very often hard to predict, it is modeled as an uncertain decision-dependent quantity. To support the circular economy ideas, advertising and pricing principles are introduced and applied. Due to the size of available real-world data and complexity of the designed program, the presented model is linearized and uncertainty is handled by a robust optimization methodology. The model, data, and algorithm are implemented in MATLAB and Julia, using the state-of-the-art solvers. The computational result is a set of decisions providing a trade-off between the average performance and the immunization against the worst-case conditions.
[klicova_slova] => Circular economy; Robust optimization; Facility location; Waste treatment; Decision-dependent production; Network design
[klicova_slova_orig] => Circular economy; Robust optimization; Facility location; Waste treatment; Decision-dependent production; Network design
[url] => https://doi.org/10.1007/s10100-019-00626-z
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[citace_text] => HRABEC, D.; KŮDELA, J.; ŠOMPLÁK, R.; NEVRLÝ, V.; POPELA, P. Circular economy implementation in waste management network design problem: a case study. Central European Journal of Operations Research, 2019, vol. 1, no. 1, p. 1-18. ISSN: 1435-246X.
[citace_html] => HRABEC, D.; KŮDELA, J.; ŠOMPLÁK, R.; NEVRLÝ, V.; POPELA, P. Circular economy implementation in waste management network design problem: a case study. Central European Journal of Operations Research, 2019, vol. 1, no. 1, p. 1-18. ISSN: 1435-246X.
[citace_rtf] =>
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author="Dušan {Hrabec} and Jakub {Kůdela} and Radovan {Šomplák} and Vlastimír {Nevrlý} and Pavel {Popela}",
title="Circular economy implementation in waste management network design problem: a case study",
journal="Central European Journal of Operations Research",
year="2019",
volume="1",
number="1",
pages="1--18",
doi="10.1007/s10100-019-00626-z",
issn="1435-246X",
url="https://doi.org/10.1007/s10100-019-00626-z"
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[nazev_en] => Circular economy implementation in waste management network design problem: a case study
[popis_en] => The paper presents a new approach to support the strategic decision-making in the area of municipal solid waste management applying modern circular economy principles. A robust two-stage integer non-linear program is developed. The primary goal tends to reduce the waste production. The generated waste should be preferably recycled as much as possible and the resultant residual waste might be used for energy recovery. Only some waste residues are appropriate for landfilling. The aim is to propose the near-optimal waste allocation for its suitable processing as well as waste transportation plan at an operational level. In addition, the key strategical decisions on waste treatment facilities location must be made. Since waste production is very often hard to predict, it is modeled as an uncertain decision-dependent quantity. To support the circular economy ideas, advertising and pricing principles are introduced and applied. Due to the size of available real-world data and complexity of the designed program, the presented model is linearized and uncertainty is handled by a robust optimization methodology. The model, data, and algorithm are implemented in MATLAB and Julia, using the state-of-the-art solvers. The computational result is a set of decisions providing a trade-off between the average performance and the immunization against the worst-case conditions.
[klicova_slova_en] => Circular economy; Robust optimization; Facility location; Waste treatment; Decision-dependent production; Network design
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[nazev] => GAC Application to Corner Detection Based on Eccentricity
[nazev_orig] => GAC Application to Corner Detection Based on Eccentricity
[duvernost_udaju_id] => S
[popis] => The geometric algebra GAC offers the same efficiency for calculations
with arbitrary conic sections as provided by CGA for spheres.
We shall exploit these properties in image processing, particularly in
corner detection. Indeed, the point cluster will be approximated by a
conic section and, consequently, classified as points with ellipse–like or
hyperbola–like neighbourhood. Then, by means of eccentricity, we decide
whether the points form a corner.
[popis_orig] => The geometric algebra GAC offers the same efficiency for calculations
with arbitrary conic sections as provided by CGA for spheres.
We shall exploit these properties in image processing, particularly in
corner detection. Indeed, the point cluster will be approximated by a
conic section and, consequently, classified as points with ellipse–like or
hyperbola–like neighbourhood. Then, by means of eccentricity, we decide
whether the points form a corner.
[klicova_slova] => Geometric algebras, GAC, Corner detection
[klicova_slova_orig] => Geometric algebras, GAC, Corner detection
[url] =>
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[citace_text] => HRDINA, J.; VAŠÍK, P.; NÁVRAT, A. GAC Application to Corner Detection Based on Eccentricity. In Advances in Computer Graphics. Lecture Notes in Computer Science. Switzerland: Springer Nature Switzerland AG 2019, 2019. p. 564-570. ISBN: 978-3-030-22513-1.
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[citace_rtf] =>
[citace_bibtex] => @inproceedings{BUT157415,
author="Jaroslav {Hrdina} and Petr {Vašík} and Aleš {Návrat}",
title="GAC Application to Corner Detection Based on Eccentricity",
booktitle="Advances in Computer Graphics",
year="2019",
series="Lecture Notes in Computer Science",
number="11542",
pages="564--570",
publisher="Springer Nature Switzerland AG 2019",
address="Switzerland",
doi="10.1007/978-3-030-22514-8",
isbn="978-3-030-22513-1"
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[nazev_en] => GAC Application to Corner Detection Based on Eccentricity
[popis_en] => The geometric algebra GAC offers the same efficiency for calculations
with arbitrary conic sections as provided by CGA for spheres.
We shall exploit these properties in image processing, particularly in
corner detection. Indeed, the point cluster will be approximated by a
conic section and, consequently, classified as points with ellipse–like or
hyperbola–like neighbourhood. Then, by means of eccentricity, we decide
whether the points form a corner.
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[nazev] => Colour Image Segmentation by Region Growing Based on Conformal Geometric Algebra
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[duvernost_udaju_id] => S
[popis] => We apply conformal geometric algebra (CGA) to classical algorithms for colour image segmentation. Particularly, we modify stan dard Prewitt quaternionic filter for edge detection and region growing segmentation procedure and use them simultaneously, which is only allowed by common CGA language, more precisely by the notion of flat point in normalised and unnormalised form
[popis_orig] => We apply conformal geometric algebra (CGA) to classical algorithms for colour image segmentation. Particularly, we modify stan dard Prewitt quaternionic filter for edge detection and region growing segmentation procedure and use them simultaneously, which is only allowed by common CGA language, more precisely by the notion of flat point in normalised and unnormalised form
[klicova_slova] => Conformal geometric algebra; Region growing; Flat point
[klicova_slova_orig] => Conformal geometric algebra; Region growing; Flat point
[url] => https://doi.org/10.1007/978-3-030-22514-8 _ 56
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[citace_text] => HRDINA, J.; MATOUŠEK, R.; TICHÝ, R. Colour Image Segmentation by Region Growing Based on Conformal Geometric Algebra. In Advances in Computer Graphics. LNCS. Springer Nature Switzerland AG 2019: Springer, Cham, 2019. p. 564-570. ISBN: 978-3-030-22513-1.
[citace_html] => HRDINA, J.; MATOUŠEK, R.; TICHÝ, R. Colour Image Segmentation by Region Growing Based on Conformal Geometric Algebra. In Advances in Computer Graphics. LNCS. Springer Nature Switzerland AG 2019: Springer, Cham, 2019. p. 564-570. ISBN: 978-3-030-22513-1.
[citace_rtf] =>
[citace_bibtex] => @inproceedings{BUT157433,
author="Jaroslav {Hrdina} and Radomil {Matoušek} and Radek {Tichý}",
title="Colour Image Segmentation by Region Growing Based on Conformal Geometric Algebra",
booktitle="Advances in Computer Graphics",
year="2019",
series="LNCS",
number="11542",
pages="564--570",
publisher="Springer, Cham",
address="Springer Nature Switzerland AG 2019",
doi="10.1007/978-3-030-22514-8\{_}56",
isbn="978-3-030-22513-1",
url="https://doi.org/10.1007/978-3-030-22514-8 _ 56"
}
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[nazev_en] => Colour Image Segmentation by Region Growing Based on Conformal Geometric Algebra
[popis_en] => We apply conformal geometric algebra (CGA) to classical algorithms for colour image segmentation. Particularly, we modify stan dard Prewitt quaternionic filter for edge detection and region growing segmentation procedure and use them simultaneously, which is only allowed by common CGA language, more precisely by the notion of flat point in normalised and unnormalised form
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[nazev] => Trident Snake Robot Motion Simulation in V-Rep
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[popis_orig] => We present a simulation of a trident snake robot motion in two local control models, the original one and its nilpotent approximation. More precisely, we derive the control system from the kinematics of a trident snake robot, calculate its nilpotent approximation and compare these two models by simulating their local motion planning in software V-Rep.
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[identifikator] => ISBN 978-3-030-14984-0
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[citace_text] => BYRTUS, R.; VECHETOVÁ, J. Trident Snake Robot Motion Simulation in V-Rep. In Modelling and Simulation for Autonomous Systems. Information Systems and Applications, incl. Internet/Web, and HCI. Switzerland: Springer International Publishing, 2019. p. 27-42. ISBN: 978-3-030-14984-0.
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[citace_bibtex] => @inproceedings{BUT157494,
author="Roman {Byrtus} and Jana {Vechetová}",
title="Trident Snake Robot Motion Simulation in V-Rep",
booktitle="Modelling and Simulation for Autonomous Systems",
year="2019",
series="Information Systems and Applications, incl. Internet/Web, and HCI",
volume="11472",
number="1",
pages="27--42",
publisher="Springer International Publishing",
address="Switzerland",
doi="10.1007/978-3-030-14984-0\{_}3",
isbn="978-3-030-14984-0"
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