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Toward Intelligent Vehicle Intrusion Detection Using the Neural Knowledge DNA
PublikacjaIn 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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Smart innovation process enhancement using SOEKS and decisional DNA
PublikacjaProduct innovation always requires a foundation based on both knowledge and experience. The production and innovation process of products is very similar to the evolution process of humans. The genetic information of humans is stored in genes, chromosomes and DNA. Similarly, the information about the products can be stored in a system having virtual genes, chromosomes and decisional DNA (DDNA). The present paper proposes...
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A proposal for knowledge sharing in the e-Decisional community using Decisional DNA
PublikacjaZaproponowano 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
PublikacjaSingle-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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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-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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The interaction of antitumor 1-nitroacridines with DNA in cell-free systems
PublikacjaUzyskano nowe pochodne 1-nitro i 3-nitroakrydyny wykazujące zdolność do specyficznego cięcia DNA w miejscach bezzasadowych. Z użyciem oligonukleotydu z indukowanym miejscem bezzasadowym potwierdzono taką aktywność u obu otrzymanych pochodnych.
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Zastosowanie immobilizowanego białka MutS do wychwytywania fragmentów DNA zawierających niesparowane zasady
PublikacjaBiałko MutS wiąże DNA zawierające błędnie sparowane oraz niesparowane zasady w DNA. Podjęto szereg prób wykorzystania tego białka jako narzędzia do detekcji nieznanych mutacji lub zagęszczania frakcji DNA z niesparowaną zasadą. Dotychczas żadna z metod oparta na użyciu białka MutS nie została wdrożona powszechnie do praktyki laboratoryjnej. Głównym powodem takiego stanu rzeczy jest stosunkowo silne powinowactwo MutS do DNA w pełni...
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Preparation of DNA films for studies under vacuum conditions. The influence of cations in buffer solutions
PublikacjaBadania zostały przeprowadzone w celu określenia optymalnych warunków wymaganych do przygotowania jednolitych filmów superskręconego plazmidowego DNA do wykorzystania w doświadczeniach napromieniowania w warunkach wysokiej próżni. Badania pokazują, że znaczne szkody w DNA powstają w wyniku odpompowywania filmów DNA z roztworów zawierających jedynie czysta wodę.
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Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublikacjaBiałka wiążące się do jednoniciowego DNA (SSB) odgrywają ważną rolę w replikacji, rekombinacji i naprawie DNA u bakterii, archea i eukariota. Ostatnio wzrosło zainteresowanie białkami SSB jako przydatnymi narzędziami w metodach badawczych biologii molekularnej, analitycznych i diagnostycznych. Większość znanych prokariotycznych białek SSB zbudowanych jest z czterech podjednostek (homotetramer) z jedną domeną wiążąca (OB) jednoniciowe...
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Teloxantron inhibits the processivity of telomerase with preferential DNA damage on telomeres
PublikacjaTelomerase reactivation is one of the hallmarks of cancer, which plays an important role in cellular immortalization and the development and progression of the tumor. Chemical telomerase inhibitors have been shown to trigger replicative senescence and apoptotic cell death both in vitro and in vivo. Due to its upregulation in various cancers, telomerase is considered a potential target in cancer therapy. In this study, we identified...
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Introducing the concept of Decisional DNA-Based web content mining
PublikacjaPrzedstawiono koncepcje zastosowania struktury reprezentacji wiedzy opartej na decyzyjnym DNA w procesie wyszukiwania informacji w internecie. Dokonano analizy eksperymentow tak wspomaganego wyszukiwania oraz sformulowano wnioski na temat przyszlych badan prowadzacych do dalszej integracji procesu wyszukiwania z doswiadczeniami zdobytymi w trakcie tego wyszukiwania.
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Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis
PublikacjaMastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublikacjaThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Dane BadawczeThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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Covalent DNA modification by products of myrosinase catalysed glucosinolate degradation in cell-free system
PublikacjaThe bioactive phytochemicals found in Brassica vegetables belonging to glucosinolates (GLS) and especially the products of their degradation isothiocyanates (ITC) and indoles are regarded as the most promising cancer chemopreventive compounds. These secondary metabolites constitute defence system repelling or preventing the development of agrophages attacking brassica plants. The antibiological properties of these compounds suggest...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublikacjaAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Set of Experience and Decisional DNA: Toward Brains for Cyber-physical Systems and Industry of the Future
PublikacjaThe concept of Decisional DNA is decade old. This article introduces the initial idea of Set of Experience Knowledge Structure, its advancement into Decisional DNA, and its potential for real life applications in divers domains. The most current and future research steps into Industry 4.0 are also presented and discussed
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublikacjaMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor
PublikacjaRolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds of thousands of samples are required daily. This work presents the first research to date on direct, real-time and label-free isothermal DNA amplification monitoring using a microcavity in-line...
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Prediction based on integration of Decisional DNA and a feature selection algorithm Relief-F
PublikacjaThe paper presents prediction model based on Decisional DNA and Set of experienced integrated with Relief_F algorithm for feature selection
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Decisional DNA based intelligent knowledge model for flexible manufacturing system
PublikacjaModeling 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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Aplikacja wspomagająca przetwarzanie sekwencji dna: moduł dopasowań
PublikacjaBiologia molekularna jest obecnie bardzo dynamicznie rozwijającą się dziedziną nauki. Wzrost mocy obliczeniowej komputerów pozwala na coraz szybszą i dokładniejszą analizę wielocząsteczkowych biologicznych polimerów. Poniższy artykuł przedstawia jeden z modułów programu AlignGator - modułowego systemu przeznaczonego do analizy DNA. Omawiany moduł pozwala na tworzenie, oraz edycję wielodopasowań. W początkowej części artykułu opisane...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Decisional DNA with embedded Relief-F linear regression for knowledge and experience management
PublikacjaOmowiono zastowania Decyzyjnego DNA, regresji liniowej oraz funkcji RELIEF-F w procesach formalnego modelowania i wspomagania zarzadzania wiedza oraz zarzadzania doswiadczeniem.
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DNA repair is responsible for the presence of oxidatively damaged DNA lesions in urine
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Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublikacjaPyrazine 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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Molecular basis for the DNA damage induction and anticancer activity of asymmetrically substituted anthrapyridazone PDZ-7
Publikacjanthrapyridazones, imino analogues of anthraquinone, constitute a family of compounds with remarkable anti-cancer activity. To date, over 20 derivatives were studied, of which most displayed nanomolar cytotoxicity towards broad spectrum of cancer cells, including breast, prostate and leukemic ones. BS-154, the most potent derivative, had IC50 values close to 1 nM, however, it was toxic in animal studies. Here, we characterize another...
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The Neural Knowledge DNA Based Smart Internet of Things
PublikacjaABSTRACT The Internet of Things (IoT) has gained significant attention from industry as well as academia during the past decade. Smartness, however, remains a substantial challenge for IoT applications. Recent advances in networked sensor technologies, computing, and machine learning have made it possible for building new smart IoT applications. In this paper, we propose a novel approach: the Neural Knowledge DNA based Smart Internet...
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Decisional DNA based framework for representing Virtual Engineering Objects
PublikacjaIn this paper, we propose a frame-work to represent the Virtual Engineering Objects (VEO) utilizing Set of Knowledge Experience Structure (SOEKS) and Decisional DNA. A VEO will enable the discovery of new knowledge in a manufacturing unit and the generation of new rules that drive reasoning. The proposed VEO framework will not only be knowledge based representation but it will also have its associated experience embedded within...
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How acidic amino acid residues facilitate DNA target site selection
PublikacjaDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Effects of metallic silver particles on resonance energy transfer between fluorophores bound to DNA.
PublikacjaZbadano wpływ filmów wysepek metalicznego srebra na rezonansowe przekazywanie energii między fluoroforami związanymi z DNA. Donorem i akceptorem były odpowiednio 4´,6 diamidyno-2-fenylindon i jodek propydyny. Zmierzone dla tego układu czasy zaniku i widma fluorescencji pokazują, że sąsiedztwo cząstek srebra dramatycznie zwiększa promień Forstera, a tym samym i przekazywanie energii w znakowanym DNA.
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Two-photon induced fluorescence of Cy5-DNA in buffer solution and on silver island film
PublikacjaOpisano fluorescencję barwnika CY5 połączonego z DNA w roztworze buforowym na wysepkach srebrowych.
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublikacjaA significant number of DNA-based techniques has been introduced into the field of microorganisms’ characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before...
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DNA and its Metaphors
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Increased concentration of Taq DNA polymerase as a solution for GC-rich templates from clinical and environmental samples
PublikacjaDNA polymerase is an enzyme which plays crucial role in replication and DNA repair. It found application in PCR (polymerase chain reaction) where catalyses process of in vitro DNA synthesis. To meet the demands posed by mod- ern diagnostic, molecular biology or genetic engineering it is necessary to improve DNA polymerases to obtain new or better features useful in these fields. So far implemented modifications in majority are...
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Klasyfikacja dna morskiego na podstawie kątowej zależności cech echa z sonaru wielowiązkowego
PublikacjaPrzedstawiono metodę rozpoznawania i klasyfikacji rodzaju dna morskiego opartą na przetwarzaniu echa z sonaru wielowiązkowego. Metoda ta polega na obliczaniu zbioru parametrów obwiedni ech dla poszczególnych wiązek, podobnie jak w metodach wykorzystujących echosondy jednowiązkowe. Następnie estymowana jest zależność wartości poszczególnych parametrów od kąta wiązki oraz badane jest powiązanie otrzymanej zależności z rodzajem dna...
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Silver nanoparticles induce premutagenic DNA oxidation that can be prevented by phytochemicals from Gentiana asclepiadea
PublikacjaAmong nanomaterials, silver nanoparticles (AgNPs) have the broadest and most commercial applications due to their antibacterial properties, highlighting the need for exploring their potential toxicity and underlying mechanisms of action. Our main aim was to investigate whether AgNPs exert toxicity by inducing oxidative damage to DNA in human kidney HEK 293 cells. In addition, we tested whether this damage could be counteracted...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublikacjaTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Photostability pf Cy3 and Cy5-labeled DNA in the presence of metallic silver particles
PublikacjaZbadano wpływ cząstek metalicznego srebra na fotostabilność oligomerów DNA kowalencyjnie związanych z Cy3 lub Cy5. Zbliżenie fluoroforów do cząstek srebra powodowało zwiększenie intensywności fluorescencji i pojawienie się frakcji emisji bardziej odpornej na wybielanie.
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The influence of the substrate temperature on the preparation of DNA films for studies under vacuum conditions
PublikacjaPrzeanalizowano wpływ temperatury na formowanie warstw DNA. Sprawdzono wpływ stabilizatorów na jakość otrzymanych próbek. Stwierdzono, że optymalnymi warunkami przygotowywania filmów do badań w warunkach próżniowych jest - 10 st. C przy minimalnej zawartości NaOH.
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DNA adduct formation by C-1748, a potent antitumor 4-methyl-1-nitroacridine of lowered toxicity.
Publikacja4-podstawione 1-nitroakrydyny reprezentują nową grupę pochodnych zsyntetyzowanych na Politechnice Gdańskiej. W porównaniu do macierzystych 1-nitroakrydyn związki te wykazują obniżoną toksyczność i podwyższoną aktywność przeciwnowotworową. Wiodąca pochodna 4-metylo-1-nitroakrydyna o symbolu C-1748 jest obecnie w przygotowaniu do I fazy badań klinicznych w leczeniu raka okrężnicy. Wprowadzenie elektrodonorowej grupy metylowej w...
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Toward Smart Innovation Engineering: Decisional DNA-Based Conceptual Approach
PublikacjaABSTRACT 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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Aplikacja wspomagająca przetwarzanie sekwencji dna: moduł edycji chromatogramu
PublikacjaModuł edycji chromatogramu jest częścią większej aplikacji, służącej do wspomagania przetwarzania danych pochodzących z sekwencjonowania DNA. Aplikacja skonstruowana jest z odrębnych, samodzielnych programów, które współpracują dwiema drogami - poprzez popularne formaty plików, co umożliwia wprowadzenie do modułów danych opracowanych częściowo w aplikacjach zewnętrznych, oraz poprzez przesyłanie danych pomiędzy modułami, co usprawnia...
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Decisional-DNA Based Smart Production Performance Analysis Model
Publikacjan order to allocate resources effectively according to the production plan and to reduce disturbances, a framework for smart production performance analysis is proposed in this article. Decisional DNA based knowledge models of engineering objects, processes and factory are developed within the proposed framework. These models are the virtual representation of manufacturing resources, and with help of Internet of Things, are capable...
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DNA methylation in cancer development, diagnosis and therapy-multiple opportunities for genotoxic agents to act as methylome disruptors or remediators
PublikacjaThe role of DNA methylation and recently discovered hydroxymethylation in the function of the human epigenome is currently one of the hottest topics in the life sciences. Progress in this field of research has been further accelerated by the discovery that alterations in the methylome are not only associated with key functions of cells and organisms, such as development, differentiation and gene expression, but may underlie a number...
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From Individual to Collective: Intelligence Amplification with Bio-Inspired Decisional DNA and its Extensions
PublikacjaIn nature, deoxyribonucleic acid (DNA) contains the genetic instructions used in the development and functioning of all known living organisms. The idea behind our vision is to develop an artificial system, an architecture that would support discovering, adding, storing, improving and sharing information and knowledge among agents and organizations through experience. We propose a novel Knowledge Representation (KR) approach in...
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Total DNA Methylation Changes Reflect Random Oxidative DNA Damage in Gliomas
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Total DNA methylation as a biomarker of DNA damage and tumor malignancy in intracranial meningiomas
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Mitochondrial DNA Part B-Resources
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Recent Advances in DNA and Gene Sequences
Czasopisma