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Search results for: DE-CISIONAL DNA
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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Open Research DataThe 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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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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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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The interaction of antitumor 1-nitroacridines with DNA in cell-free systems
PublicationUzyskano 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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Cień Boga w ogrodzie filozofa. Parc de La Villette w Paryżu w kontekście filozofii chôry
PublicationKsiążka „Cień Boga w ogrodzie filozofa. Parc de La Villette w Paryżu w kontekście filozofii chôry” przedstawia filozoficzne dyskusje, jakie towarzyszyły projektowaniu rozległego parku w paryskiej dzielnicy La Villette. Na teoretyczne założenia parku złożyły się teksty Bernarda Tschumiego, w których kwestionował on tradycyjne sposoby tworzenia dzieła architektury postulując w zamian zastosowanie długiego szeregu...
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Zastosowanie immobilizowanego białka MutS do wychwytywania fragmentów DNA zawierających niesparowane zasady
PublicationBiałko 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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The Shadow of God in the Garden of the Philosopher. The Parc de La Villette in Paris in the Context of Philosophy of Chôra. Part I-V
PublicationThe book Shadow of God in the Philosopher's Garden. Parcde La Villette in Paris in the context of the philosophy of chôra presents the philosophical discussions that accompanied the design of the extensive park in the Parisian district of La Villette. The core of the park's theoretical framework were texts by Bernard Tschumi, in which he questioned the traditional ways of creating...
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Preparation of DNA films for studies under vacuum conditions. The influence of cations in buffer solutions
PublicationBadania 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
PublicationBiałka 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
PublicationTelomerase 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
PublicationPrzedstawiono 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
PublicationMastocytosis 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?
PublicationThe 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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Covalent DNA modification by products of myrosinase catalysed glucosinolate degradation in cell-free system
PublicationThe 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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Common variants of DNA repair genes and malignant melanoma
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn 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
PublicationThe 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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Prediction based on integration of Decisional DNA and a feature selection algorithm Relief-F
PublicationThe paper presents prediction model based on Decisional DNA and Set of experienced integrated with Relief_F algorithm for feature selection
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy 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
PublicationRolling 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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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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Variation de l’épaisseur du placage de déroulage des bois et son influence sur les caractéristiques mécaniques des panneaux LVL
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Understanding Sustainable Knowledge-Sharing in Agile Projects: Utilizing Follow-the-Sun Technique (FTS) in Virtual Teams
PublicationIn Agile IT projects, promoting effective knowledge sharing is essential not only for achieving success but also for supporting Sustainable Development Goals (SDGs). However, Companies using virtual teams may face challenges in coordinating work, particularly when teams are distributed across different time zones, ultimately hindering their ability to consistently share knowledge. This can lead to delays and inefficiencies, ultimately...
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Sustainable Knowledge Sharing Model for IT Agile Projects
PublicationIn order to overcome work environment challenges and remain competitive in the market, organisations must adapt. An organisation's competitiveness can be improved through knowledge sharing; however, improvement without responsibility can have a negative impact on the sociotechnical environment which people cannot fully comprehend. According to researchers, business involvement in sustainable development goals remains minimal [51]....
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Human Feedback and Knowledge Discovery: Towards Cognitive Systems Optimization
PublicationCurrent computer vision systems, especially those using machine learning techniques are data-hungry and frequently only perform well when dealing with patterns they have seen before. As an alternative, cognitive systems have become a focus of attention for applications that involve complex visual scenes, and in which conditions may vary. In theory, cognitive applications uses current machine learning algorithms, such as deep learning,...
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Visual content representation and retrieval for Cognitive Cyber Physical Systems
PublicationCognitive Cyber Physical Systems have gained significant attention from academia and industry during the past few decade. One of the main reasons behind this interest is the potential of such technologies to revolutionize human life since they intend to work robustly under complex visual scenes, which environmental conditions may vary, adapting to a comprehensive range of unforeseen changes, and exhibiting prospective behavior...
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Visual Content Representation for Cognitive Systems: Towards Augmented Intelligence
PublicationCognitive Vision Systems have gained significant attention from academia and industry during the past few decades. One of the main reasons behind this interest is the potential of such technologies to revolutionize human life since they intend to work robustly under complex visual scenes (which environmental conditions may vary), adapting to a comprehensive range of unforeseen changes, and exhibiting prospective behavior. The combination...
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From Knowledge based Vision Systems to Cognitive Vision Systems: A Review
PublicationComputer vision research and applications have their origins in 1960s. Limitations in computational resources inherent of that time, among other reasons, caused research to move away from artificial intelligence and generic recognition goals to accomplish simple tasks for constrained scenarios. In the past decades, the development in machine learning techniques has contributed to noteworthy progress in vision systems. However,...
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Flexible Knowledge–Vision–Integration Platform for Personal Protective Equipment Detection and Classification Using Hierarchical Convolutional Neural Networks and Active Leaning
PublicationThis work is part of an effort to develop of a Knowledge-Vision Integration Platform for Hazard Control (KVIP-HC) in industrial workplaces, adaptable to a wide range of industrial environments. The paper focuses on hazards resulted from the non-use of personal protective equipment (PPE). The objective is to test the capability of the platform to adapt to different industrial environments by simulating the process of randomly selecting...
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Aplikacja wspomagająca przetwarzanie sekwencji dna: moduł dopasowań
PublicationBiologia 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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Rysunki Parku Krajobrazowego Mata de Busaco w Portugalii
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Voluntariness of social insurance for entrepreneurs – de lege ferenda postulates
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated 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
PublicationOmowiono 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
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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Molecular basis for the DNA damage induction and anticancer activity of asymmetrically substituted anthrapyridazone PDZ-7
Publicationnthrapyridazones, 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
PublicationABSTRACT 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
PublicationIn 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
PublicationDespite 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.
PublicationZbadano 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
PublicationOpisano fluorescencję barwnika CY5 połączonego z DNA w roztworze buforowym na wysepkach srebrowych.
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DNA and its Metaphors
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublicationA 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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Jacek Krenz dr hab. inż. arch.
PeopleJacek Krenz, born in 1948 in Poznań, Poland, is an academic architect and painter. He is a professor at Gdańsk University of Technology, Faculty of Architecture, taught also at University of Fine Arts in Poznań – both in Poland – and at Universidade da Beira Interior in Covilhã, Portugal. Charter member of The Polish Watercolour Society. He is a co-founder of the Wdzydze Artists’ Village in Kaszuby, Poland, where he works in his...
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WETI - DE - Elements of Linear Algebra 2018/19 (M.Musielak)
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Increased concentration of Taq DNA polymerase as a solution for GC-rich templates from clinical and environmental samples
PublicationDNA 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
PublicationPrzedstawiono 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
PublicationAmong 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
PublicationTarget 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...