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    Wyświetlanie 1-11 z 11
    Tytuł:
    System wspomagania wytwarzania i analiz szczepionek genetycznych
    Genetic vaccine decision support system
    Autorzy:
    Błażewicz, Jacek
    Łukasiak, Piotr
    Powiązania:
    https://bibliotekanauki.pl/articles/1196903.pdf
    Data publikacji:
    2009
    Wydawca:
    Polskie Towarzystwo Przyrodników im. Kopernika
    Opis:
    Genetic vaccines and especially recombinant viral vectors and virus-like particles are considered the most promising vehicles for delivery of antigens in prophylactic and therapeutic vaccines against infectious diseases and cancer. Several potential vaccine design systems exist but their cost-effective development cruelly lacks a standardized evaluation system. Solving the problem Genetic Vaccine Decision Support system (GeVaDSs, http://www.compuvac.org) has been implemented as a part of CompuVac project realized within 6th Framework Program of European Commission. Using GeVaDSs we have successfully developed and standardized methods for evaluation of the efficacy and safety of individual vaccine vectors, in a manner that allows comparison between different vaccine designs, tested in different laboratories, at different time points. With these methods, the efficacy of a unique set of vaccines has been analyzed and compared with an intelligent database. GeVaDSs has allowed to make significant comparisons between different types of vaccines and to initiate novel vaccine design and vaccination regimens. Besides monitoring of T- and B-cell immune responses, GeVaDSs is also aimed at monitoring vaccine "efficacy" and "safety" profiles by analyzing relevant molecular signatures obtained from transcriptomes studies. The "efficacy" and the "safety profile" have been validated, based on analyzing molecular signatures from whole liver and spleen after injection of vaccine vectors. The results of these experiments will drive the development of HCV vaccines. The first HCV vectors generated in single immunization regimen were tested, and interesting results obtained suggest the great potential for the association of our two classes of vectors, viral and VLP derived.
    Źródło:
    Kosmos; 2009, 58, 1-2; 113-125
    0023-4249
    Pojawia się w:
    Kosmos
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Zastosowanie sieci Petriego do modelowania procesów biologicznych
    Applications of Petri nets for modeling of biological processes
    Autorzy:
    Błażewicz, Jacek
    Formanowicz, Dorota
    Formanowicz, Piotr
    Powiązania:
    https://bibliotekanauki.pl/articles/1196917.pdf
    Data publikacji:
    2009
    Wydawca:
    Polskie Towarzystwo Przyrodników im. Kopernika
    Opis:
    Rapid growth of the amount of available biological data made it clear that an analysis of complex biological processes can be made only with the support of mathematics and computer sciences. It is especially important nowadays when the systems biology approach is becoming more and more widely used in biological science. This new way of investigation of biological phenomena allows, at least in principle, to observe complex relationships between different parts of the analyzed system. These interactions may be crucial for the system's nature and behavior, so observing them may lead to important biological discoveries. Probably the most important part of this process consists in building of a formal model of the biological process. One of the promising methods of such an analysis is based on the theory of Petri nets. Models expressed in the language of this theory are very precise on the one hand, and on the other, they are intuitive, which makes their analysis easier in comparison, for example, to models based on ordinary differential equations. In this paper, a brief introduction to the theory of Petri nets is given and its applications for modeling of some exemplary biological processes are shortly discussed. Moreover, some extensions of the classical Petri nets and their biological applications are also presented.
    Źródło:
    Kosmos; 2009, 58, 1-2; 79-88
    0023-4249
    Pojawia się w:
    Kosmos
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Two meta-heuristic algorithms for scheduling on unrelated machines with the late work criterion
    Autorzy:
    Wang, Wen
    Chen, Xin
    Musial, Jędrzej
    Blazewicz, Jacek
    Powiązania:
    https://bibliotekanauki.pl/articles/330022.pdf
    Data publikacji:
    2020
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    late work minimization
    unrelated machines
    tabu search
    genetic algorithm
    minimalizacja opóźnienia
    przeszukiwanie tabu
    algorytm genetyczny
    Opis:
    A scheduling problem in considered on unrelated machines with the goal of total late work minimization, in which the late work of a job means the late units executed after its due date. Due to the NP-hardness of the problem, we propose two meta-heuristic algorithms to solve it, namely, a tabu search (TS) and a genetic algorithm (GA), both of which are equipped with the techniques of initialization, iteration, as well as termination. The performances of the designed algorithms are verified through computational experiments, where we show that the GA can produce better solutions but with a higher time consumption. Moreover, we also analyze the influence of problem parameters on the performances of these metaheuristics.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2020, 30, 3; 573-584
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Computational prediction of non-enzymatic RNA degradation patterns
    Autorzy:
    Rybarczyk, Agnieszka
    Jackowiak, Paulina
    Figlerowicz, Marek
    Blazewicz, Jacek
    Powiązania:
    https://bibliotekanauki.pl/articles/1038733.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    RNA degradation
    non-enzymatic RNA hydrolysis
    branch-and-cut algorithm
    Opis:
    Since the beginning of the 21st century, an increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins). More recently, it has been shown that small regulatory RNAs are also generated as stable intermediates of RNA degradation (the so called RNA fragments originating from tRNA, snRNA, snoRNA etc.). Unfortunately, the mechanisms underlying biogenesis of the RNA fragments remain unclear. It is thought that several factors may be involved in the formation of the RNA fragments. The most important are the specific RNases, RNA-protein interactions and RNA structure. In this work, we focus on the RNA primary and secondary structures as factors influencing the RNA stability and consequently the pattern of RNA fragmentation. Earlier, we identified the major structural factors affecting non-enzymatic RNA degradation. Now, based on these data, we developed a new branch-and-cut algorithm that is able to predict the products of large RNA molecules' hydrolysis in vitro. We also present the experimental data that verify the results generated using this algorithm.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 745-751
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    AmiRNA Designer - new method of artificial miRNA design
    Autorzy:
    Mickiewicz, Agnieszka
    Rybarczyk, Agnieszka
    Sarzynska, Joanna
    Figlerowicz, Marek
    Blazewicz, Jacek
    Powiązania:
    https://bibliotekanauki.pl/articles/1038843.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    artificial miRNA
    RNAi
    gene regulation
    sequence specific
    thermodynamic profiles
    Opis:
    MicroRNAs (miRNAs) are small non-coding RNAs that have been found in most of the eukaryotic organisms. They are involved in the regulation of gene expression at the post-transcriptional level in a sequence specific manner. MiRNAs are produced from their precursors by Dicer-dependent small RNA biogenesis pathway. Involvement of miRNAs in a wide range of biological processes makes them excellent candidates for studying gene function or for therapeutic applications. For this purpose, different RNA-based gene silencing techniques have been developed. Artificially transformed miRNAs (amiRNAs) targeting one or several genes of interest represent one of such techniques being a potential tool in functional genomics. Here, we present a new approach to amiRNA*design, implemented as AmiRNA Designer software. Our method is based on the thermodynamic analysis of the native miRNA/miRNA* and miRNA/target duplexes. In contrast to the available automated tools, our program allows the user to perform analysis of natural miRNAs for the organism of interest and to create customized constraints for the design stage. It also provides filtering of the amiRNA candidates for the potential off-targets. AmiRNA Designer is freely available at http://www.cs.put.poznan.pl/arybarczyk/AmiRNA/.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 1; 71-77
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Exact approaches to late work scheduling on unrelated machines
    Autorzy:
    Liu, Xinbo
    Wang, Wen
    Chen, Xin
    Sterna, Malgorzata
    Blazewicz, Jacek
    Powiązania:
    https://bibliotekanauki.pl/articles/11542692.pdf
    Data publikacji:
    2023
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    late work scheduling
    unrelated machine
    mathematical model
    branch algorithm
    bound algorithm
    dynamic programming
    planowanie pracy
    model matematyczny
    algorytm podziału
    algorytm ograniczeń
    programowanie dynamiczne
    Opis:
    We consider the scheduling problem on unrelated parallel machines in order to minimize the total late work. Since the problem is NP-hard, we propose a mathematical model and two dedicated exact approaches for solving it, based on the branching and bounding strategy and on enumerating combined with a dynamic programming algorithm. The time efficiencies of all three approaches are evaluated through computational experiments.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2023, 33, 2; 285--295
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Assembling the SARS-CoV genome - new method based on graph theoretical approach.
    Autorzy:
    Błażewicz, Jacek
    Figlerowicz, Marek
    Formanowicz, Piotr
    Kasprzak, Marta
    Nowierski, Bartosz
    Styszyński, Rafał
    Szajkowski, Łukasz
    Widera, Paweł
    Wiktorczyk, Mariusz
    Powiązania:
    https://bibliotekanauki.pl/articles/1041512.pdf
    Data publikacji:
    2004
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    algorithm
    assembling
    SARS-CoV
    graphs
    Opis:
    Nowadays, scientists may learn a lot about the organisms studied just by analyzing their genetic material. This requires the development of methods of reading genomes with high accuracy. It has become clear that the knowledge of the changes occuring within a viral genome is indispensable for effective fighting of the pathogen. A good example is SARS-CoV, which was a cause of death of many people and frightened the entire world with its fast and hard to prevent propagation. Rapid development of sequencing methods, like shotgun sequencing or sequencing by hybridization (SBH), gives scientists a good tool for reading genomes. However, since sequencing methods can read fragments of up to 1000 bp only, methods for sequence assembling are required in order to read whole genomes. In this paper a new assembling method, based on graph theoretical approach, is presented. The method was tested on SARS-CoV and the results were compared to the outcome of other widely known methods.
    Źródło:
    Acta Biochimica Polonica; 2004, 51, 4; 983-993
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Translational and structural analysis of the shortest legume ENOD40 gene in Lupinus luteus
    Autorzy:
    Podkowinski, Jan
    Zmienko, Agnieszka
    Florek, Blazena
    Wojciechowski, Pawel
    Rybarczyk, Agnieszka
    Wrzesinski, Jan
    Ciesiolka, Jerzy
    Blazewicz, Jacek
    Kondorosi, Adam
    Crespi, Martin
    Legocki, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1040638.pdf
    Data publikacji:
    2009
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    nitrogen fixation
    transcript structure
    ENOD40
    phylogeny
    Opis:
    Two early nodulin 40 (enod40) genes, ENOD40-1, the shortest legume ENOD40 gene, and ENOD40-2, were isolated from Lupinus luteus, a legume with indeterminate nodules. Both genes were expressed at similar levels during symbiosis with nitrogen-fixing bacteria. ENOD40 phylogeny clustered the L. luteus genes with legumes forming determinate nodules and revealed peptide similarities. The ENOD40-1 small ORF A fused to a reporter gene was efficiently expressed in plant cells, indicating that the start codon is recognized for translation. The ENOD40-1 RNA structure predicted based on Pb(II)-induced cleavage and modeling revealed four structurally conserved domains, an absence of domain 4 characteristic for legumes of indeterminate nodules, and interactions between the conserved region I and a region located upstream of domain 6. Domain 2 contains Mg(II) ion binding sites essential for organizing RNA secondary structure. The differences between L. luteus and Glycine max ENOD40 RNA models suggest the possibility of a switch between two structural states of ENOD40 transcript.
    Źródło:
    Acta Biochimica Polonica; 2009, 56, 1; 89-102
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    New records of isopod species of the Antarctic Specially Managed Area No. 1, Admiralty Bay, South Shetland Islands
    Autorzy:
    Zemko, Karol
    Siciński, Jacek
    Pabis, Krzysztof
    Błażewicz, Magdalena
    Powiązania:
    https://bibliotekanauki.pl/articles/2042155.pdf
    Data publikacji:
    2017
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    Antarctic
    ASMA
    biodiversity
    Crustacea
    glacial fjords
    King George Island
    Źródło:
    Polish Polar Research; 2017, 38, 3; 409-419
    0138-0338
    2081-8262
    Pojawia się w:
    Polish Polar Research
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Diversity and abundance of isopod fauna associated with holdfasts of the brown alga Himantothallus grandifolius in Admiralty Bay, Antarctic
    Autorzy:
    Zemko, Karol
    Pabis, Krzysztof
    Siciński, Jacek
    Błażewicz-Paszkowycz, Magdalena
    Powiązania:
    https://bibliotekanauki.pl/articles/2047139.pdf
    Data publikacji:
    2015
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    Antarctic
    Admiralty Bay
    Isopoda
    macroalgae
    habitat complexity
    Źródło:
    Polish Polar Research; 2015, 4; 405-415
    0138-0338
    2081-8262
    Pojawia się w:
    Polish Polar Research
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Conductive polymer nanocomposites for medical applications
    Autorzy:
    Kuczkowska, Justyna
    Długoń, Elżbieta
    Bezkosty, Patryk
    Nizioł, Jacek
    Błażewicz, Marta
    Sitarz, Maciej
    Powiązania:
    https://bibliotekanauki.pl/articles/1844745.pdf
    Data publikacji:
    2021
    Wydawca:
    Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Polskie Towarzystwo Biominerałów
    Źródło:
    Engineering of Biomaterials; 2021, 24, 163; 118
    1429-7248
    Pojawia się w:
    Engineering of Biomaterials
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
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