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Search results for: dna
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Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna
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Ancient DNA sequence quality is independent of fish bone weight
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Evolutionary algorithm and decisional DNA for multiple travelling salesman problem
PublicationIn the real world, it is common to face optimization problems that have two or more objectives that must be optimized at the same time, that are typically explained in different units, and are in conflict with one another. This paper presents a hybrid structure that combines set of experience knowledge structures (SOEKS) and evolutionary algorithms, NSGA-II (Non-dominated Sorting Genetic Algorithm II), to solve multiple optimization...
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Interaction of antitumor triazoloacridone C-1305 and its analogs with telomeric DNA
PublicationBadaliśmy oddziaływanie pochodnej triazoloakrydonu C-1305 i jego bliskich analogów strukturalnych z oligonukleotydami zawierającycmi sekwencje telomerowe TTAGGG oraz oligonukleotydami sfałdowanymi w strukturę G-kwadrupleksu. Wykazaliśmy, że spośród badanych związków pochodna C-1305 wykazała największą specyficzność w stosunku do telomerowego DNA. Związek ten stabilizował także strukturę G-kwadrupleksu, podczas gdy jego analogi...
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Detection of Helicobacter rodentium-like DNA in the liver tissue of patients with chronic liver diseases by polymerase chain reaction–denaturing gradient gel electrophoresis and DNA sequence analysis
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Cellular senescence induced by DNA damage and its role in carcinogenesis and chemotherapy
PublicationUszkodzenia DNA indukują w komórce różne procesy, w tym starzenie komórkowe, co może uruchamiać proces karcinogenezy jak i być związane z odpowiedzią na leki przecinowotworowe. Biologiczna rola starzenia komórkowego nie jest jednak jasna. Zasugerowano, że proces starzenia komórkowego może hamować proces karcinogenezy poprzez indukcję nieodwracalnego zahamowania wzrostu przez czynniki genotoksyczne. Indukcja starzenia komórkowego...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Cross sections for electron scattering from selected components of DNA and RNA
PublicationWykorzystując metodę atomów niezależnych obliczono różniczkowe i całkowite przekroje czynne na sprężyste rozproszenie elektronów na wybranych drobinach, będących analogami składników DNA i RNA. Przekroje te obliczono w zakresie energii zderzenia od 50eV do 200 eV dla następujących drobin: C4H8O, C4H8O2, C5H10O2 oraz H3PO4. Przy użyciu metody BEB (binary-ecounter Bethe method) dla powyższych związków obliczono również przekroje...
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Cross section calculations for electron scattering from DNA and RNA bases.
PublicationPoliczono różniczkowy i scałkowany przekrój czynny na rozproszenie sprężyste elektronów (w przybliżeniu atomów niezależnych) na uracylu, cytozynie, guaninie, adeninie i tyminie w zakresie energii od 50-4000 eV. W przybliżeniu modelu BEB policzono również przekroje czynne na jonizację tych molekuł.
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Wybrane metody badania poziomu metylacji DNA w komórkach eukariotycznych
PublicationMetylacja regionów promotorowych jest jednym z głównych mechanizmów regulacji transkrypcji genów u eukariota. W komórkach ssaczych metylacja DNA zachodzi głównie na reszcie cytozyny występującej w dinukleotydach CpG i jest katalizowana przez metylotransferazy DNA (DNMT1, DNMT3A i DNMT3B) (Turek Plewa, Jagodziński 2005). Mapowanie 5 metylocytozyny w DNA genomowym jest jednym z narzędzi do badania wpływu metylacji na tkankowo-specyficzną...
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H2AX phosphorylation, its role in DNA damage response and cancer therapy
PublicationDouble-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may have severe consequences for cell survival, as they lead to chromosome aberrations, genomic instability, or cell death. Various physical, chemical, and biological factors are involved in DSB induction. Cells respond to DNA damage by activating the so-called DNA damage response (DDR), a complex molecular mechanism developed to detect...
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Applying Decisional DNA to Internet of Things: The Concept and Initial Case Study
PublicationIn this article, we present a novel approach utilizing Decisional DNA to help the Internet of Things capture decisional events and reuse them for decision making in future operations. The Decisional DNA is a domain-independent, standard and flexible knowledge representation structure that allows its domains to acquire, store, and share experiential knowledge and formal decision events in an explicit way. We apply this approach...
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Thermodynamic and electrostatic properties of ternary Oxytricha nova TEBP-DNA complex
PublicationZa pomocą metod chemi obliczeniowej badano właściwości molekularne kompleksu telomerowego białka TEBP z Oxytricha nova w kompleksie trójskkładnikowym z DNA o sekwencji telomerowej. Wyliczone wartości energii kompleksowania wskazują specyficznie na jedną z dróg tworzenia kompleksu, gdzie wpierw podjednostka alfa łaczy się z DNA a następnie podjednostka beta dołącza się do takiego dwuskładnikowego kompleksu. Policzone rozkłady molekularnego...
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Gaining knowledge through experience: developing decisional DNA applications in robotics
PublicationOmówiono nowatorskie podejscie do zastosowania wiedzy opartej na doświadczeniu i budowie decyzyjnego DNA w obszarach związanych z robotyką.In this article, we explore an approach that integrates Decisional DNA, a domain-independent, flexible, and standard knowledge representation structure, with robots in order to test the usability and suitability of this novel knowledge representation structure. Core issues in using this Decisional...
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Modyfikacje polimeraz DNA jako rozwiązania problemów w reakcjach PCR
PublicationReakcja PCR już od wielu lat jest podstawowym narzędziem stosowanym w biotechnologii molekularnej. Nadal napotykamy jednak liczne problemy podczas jej przeprowadzania związane z trudnymi matrycami, obecnością inhibitorów itp. Optymalizacja reakcji PCR jest więc niezbędna w celu poprawy wyników. Jednym z rozwiązań tych problemów może być modyfikowanie polimeraz DNA. W powyższym artykule opisano problemy i rozwiązania zależne polimerazy...
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Toward Intelligent Vehicle Intrusion Detection Using the Neural Knowledge DNA
PublicationIn this paper, we propose a novel intrusion detection approach using past driving experience and the neural knowledge DNA for in-vehicle information system security. The neural knowledge DNA is a novel knowledge representation method designed to support discovering, storing, reusing, improving, and sharing knowledge among machines and computing systems. We examine our approach for classifying malicious vehicle control commands...
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A proposal for knowledge sharing in the e-Decisional community using Decisional DNA
PublicationZaproponowano model platformy wspomagającej wymianę wiedzy w społeczeństwie decyzyjnym opartym na decyzyjnym DNA.
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...
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Decisional DNA based intelligent knowledge model for flexible manufacturing system
PublicationModeling an effective mechanism for design and control strategies for the implementation of a flexible manufacturing system (FMS) has been a challenge. Consequently, to overcome this issue various techniques have applied in the past but most of these models are effective only for some specific situation or an element of FMS. In this study, the knowledge representation technique of Decisional DNA (DDNA) is applied to FMS to develop...
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Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublicationPyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure...
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Toward Smart Innovation Engineering: Decisional DNA-Based Conceptual Approach
PublicationABSTRACT Knowledge and experience are essential requirements for product innovation. The presented paper proposes a systematic approach for product innovation support using a Smart Knowledge Management System comprising a Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA). This proposed system is dynamic in nature because it updates itself every time a new decision related to innovation is made. Through this...
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Typing of Scopulariopsis and Microascus fungi by Random Amplified Polymorphic DNA (RAPD)
PublicationOBJECTIVES Scopulariopsis species and their teleomorphs of the genus Microascus are commonly isolated from soil, decaying plant material and indoor environments. Moreover, certain Scopulariopsis and Microascus species are recognised as opportunistic human pathogens. Although most species can be identified by detailed morphological study, phenotypic characters appear to overlap in several cases and morphology seems to be insufficient...
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A Framework for Enhancing Supplier Selection Process by Using SOEKS and Decisional DNA
PublicationAbstract. Supplier selection process is one of the significant stages in supply chain management for industrial manufactured products. It plays an integral role in the success of any manufacturing organization and is an important part starting right from selecting raw material to dispatch of finished products. This paper contributes to enhance the supplier selection process by proposing a multi-criteria decision making framework...
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Experience Based Decisional DNA (DDNA) to Support Sustainable Product Design
PublicationThis paper presents the idea of providing engineering design knowledge to designers working on sustainable product design and development process. The new product development process often requires significant amount of design knowledge which can be saved and recalled by designers during the design process. This knowledge is very important for successful sustainable product development as it can include material selection, product...
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Using Decisional DNA to Enhance Industrial and Manufacturing Design: Conceptual Approach
PublicationDuring recent years, manufacturing organizations are facing market changes such as the need for short product life cycles, technological advancement, intense pressure from competitors and the continuous customers’ expectation for high quality products at lower costs. In this scenario, knowledge and its associated engineering/management of every stage involved in the industrial design has become increasingly important for manufacturing...
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Representing and Managing Experiential Knowledge with Decisional DNA and its Drimos® Extension
PublicationThe Semantic Web concept is proposing a future concept of the WorldWideWeb (WWW) where both humans and man-made systems are able to interconnect and exchange knowledge. One of the challenges of Semantic Web is smart and trusted accommodation of knowledge in artificial systems so it can be unified, enhanced, reused, shared, communicated and distributed with added aptitude. Our research represents an important component of addressing...
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Mitochondrial DNA of Anisakis simplex S.S. as a Potential Tool for Differentiating Populations
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Novel Method of Identifying DNA Methylation Fingerprint of Acute Myeloid Leukaemia
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Induced circularly polarized luminescence for revealing DNA binding with fluorescent dyes
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Regulation of the switch from early to late bacteriophage λ DNA replication
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Diagnosis of Brain Tumors Through Global Specific DNA Methylation Analysis
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Molecular Diagnostics of Brain Tumours by Measuring the 5-Methylcytosine Level in Their DNA
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P04.06 Temozolomide influence on global DNA methylation in glioblastoma cell lines
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Effects of Base π-Stacking on Damage to DNA by Low-Energy Electrons
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High Concentrations of Excised Oxidative DNA Lesions in Human Cerebrospinal Fluid
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Severe oxidatively damaged DNA after cisplatin treatment of cancer patients
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Oxidative DNA damage in cancer patients: a cause or a consequence of the disease development?
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Vitamin C enhances substantially formation of 5-hydroxymethyluracil in cellular DNA
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
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Maintenance and stabilization of mtDNA can be facilitated by the DNA-binding activity of Ilv5p
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Characterization of DNA Polymerase from Thermus thermophilus MAT72 Phage Tt72
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Central carbon metabolism influences fidelity of DNA replication in Escherichia coli
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Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours
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Analysis of differences in the stability of proteins encoded in mitochondrial DNA of model organisms
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Obliczenia numeryczne konstrukcji dna jachtu podczas wejścia na mieliznę
PublicationPozytywne zmiany w dostępie do żeglarstwa, które dokonały się w ostatnim dziesięcioleciu spowodowały wzrost liczby osób uprawiających ten sport. Przepisy, wg których projektowane są jachty nie stawiają żadnych wymagań wytrzymałości konstrukcji na wypadek kolizji jednostki z dnem. Z doświadczenia wiadomo, że wejście jachtu na piaszczystą mieliznę nie musi powodować uszkodzeń, jednak kolizja z podwodną skałą w szkierach szwedzkich...
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Relationship between selected DNA polymorphisms and coronary artery disease complications
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Direct cloning of heavy metal resistance genes from metagenomic DNA
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Przetwarzanie i analiza obrazów sonarowych powierzchni dna basenu portowego
PublicationW artykule przedstawiono problemy związane z poszukiwaniem obiektów zalegających na dnie basenu portowego.
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Trójwymiarowe obrazowanie dna morskiego ze szczególnym uwzględnieniem wód płytkich
PublicationW ostatnim dziesięcioleciu nabrały znaczenia obserwacje szerokokątne (ang. swath scan) przy pomocy sonarów bocznych i sonarów wielowiązkowych. Wynikiem pomiarów dokonywanych przy pomocy sonarów wielowiązkowych jest jednak duża liczba danych geoprzestrzennych o precyzyjnie określonej referencji geograficznej, charakteryzujących się zróżnicowaną dynamiką i posiadających zróżnicowaną rozdzielczość. Stwarza to problemy w procesie...