Autor: Blazewicz, Jacek - Prolib Integro

Skocz do pozycji: 1.

Tytuł:: System wspomagania wytwarzania i analiz szczepionek genetycznych
Genetic vaccine decision support system
Autorzy:: Błażewicz, Jacek
Łukasiak, Piotr
Wydawca:: Polskie Towarzystwo Przyrodników im. Kopernika
Powiązania:: https://bibliotekanauki.pl/articles/1196903.pdf Link otwiera się w nowym oknie
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.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 2.

Tytuł:: Zastosowanie sieci Petriego do modelowania procesów biologicznych
Applications of Petri nets for modeling of biological processes
Autorzy:: Błażewicz, Jacek
Formanowicz, Dorota
Formanowicz, Piotr
Wydawca:: Polskie Towarzystwo Przyrodników im. Kopernika
Powiązania:: https://bibliotekanauki.pl/articles/1196917.pdf Link otwiera się w nowym oknie
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.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 3.

Tytuł:: Two meta-heuristic algorithms for scheduling on unrelated machines with the late work criterion
Autorzy:: Wang, Wen
Chen, Xin
Musial, Jędrzej
Blazewicz, Jacek
Tematy:: late work minimization
unrelated machines
tabu search
genetic algorithm
minimalizacja opóźnienia
przeszukiwanie tabu
algorytm genetyczny; Pokaż więcej
Wydawca:: Uniwersytet Zielonogórski. Oficyna Wydawnicza
Powiązania:: https://bibliotekanauki.pl/articles/330022.pdf Link otwiera się w nowym oknie
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.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 4.

Tytuł:: Computational prediction of non-enzymatic RNA degradation patterns
Autorzy:: Rybarczyk, Agnieszka
Jackowiak, Paulina
Figlerowicz, Marek
Blazewicz, Jacek
Tematy:: RNA degradation
non-enzymatic RNA hydrolysis
branch-and-cut algorithm; Pokaż więcej
Wydawca:: Polskie Towarzystwo Biochemiczne
Powiązania:: https://bibliotekanauki.pl/articles/1038733.pdf Link otwiera się w nowym oknie
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.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 5.

Tytuł:: AmiRNA Designer - new method of artificial miRNA design
Autorzy:: Mickiewicz, Agnieszka
Rybarczyk, Agnieszka
Sarzynska, Joanna
Figlerowicz, Marek
Blazewicz, Jacek
Tematy:: artificial miRNA
RNAi
gene regulation
sequence specific
thermodynamic profiles; Pokaż więcej
Wydawca:: Polskie Towarzystwo Biochemiczne
Powiązania:: https://bibliotekanauki.pl/articles/1038843.pdf Link otwiera się w nowym oknie
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/.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 6.

Tytuł:: Exact approaches to late work scheduling on unrelated machines
Autorzy:: Liu, Xinbo
Wang, Wen
Chen, Xin
Sterna, Malgorzata
Blazewicz, Jacek
Tematy:: late work scheduling
unrelated machine
mathematical model
branch algorithm
bound algorithm
dynamic programming
planowanie pracy
model matematyczny
algorytm podziału
algorytm ograniczeń
programowanie dynamiczne; Pokaż więcej
Wydawca:: Uniwersytet Zielonogórski. Oficyna Wydawnicza
Powiązania:: https://bibliotekanauki.pl/articles/11542692.pdf Link otwiera się w nowym oknie
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.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 7.

Tytuł:: Online and semi-online scheduling on two hierarchical machines with a common due date to maximize the total early work
Autorzy:: Xiao, Man
Liu, Xiaoqiao
Li, Weidong
Chen, Xin
Sterna, Malgorzata
Blazewicz, Jacek
Tematy:: online scheduling
semi online scheduling
early work
hierarchical scheduling
competitive ratio; Pokaż więcej
Wydawca:: Uniwersytet Zielonogórski. Oficyna Wydawnicza
Powiązania:: https://bibliotekanauki.pl/articles/59123802.pdf Link otwiera się w nowym oknie
Opis:: In this study, we investigate several online and semi-online scheduling problems related to two hierarchical machines with a common due date to maximize the total early work. For the pure online case, we design an optimal online algorithm with a competitive ratio of √2. Additionally, for the cases when the largest processing time is known, we give optimal algorithms with a competitive ratio of 6/5 if the largest job is a lower-hierarchy one, and of √5 − 1 if the largest job is a higher-hierarchy one.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 8.

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
Tematy:: algorithm
assembling
SARS-CoV
graphs; Pokaż więcej
Wydawca:: Polskie Towarzystwo Biochemiczne
Powiązania:: https://bibliotekanauki.pl/articles/1041512.pdf Link otwiera się w nowym oknie
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.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 9.

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
Tematy:: nitrogen fixation
transcript structure
ENOD40
phylogeny; Pokaż więcej
Wydawca:: Polskie Towarzystwo Biochemiczne
Powiązania:: https://bibliotekanauki.pl/articles/1040638.pdf Link otwiera się w nowym oknie
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.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 10.

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
Tematy:: Antarctic
ASMA
biodiversity
Crustacea
glacial fjords
King George Island; Pokaż więcej
Wydawca:: Polska Akademia Nauk. Czytelnia Czasopism PAN
Powiązania:: https://bibliotekanauki.pl/articles/2042155.pdf Link otwiera się w nowym oknie
Dostawca treści:: Biblioteka Nauki

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