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Search results for: DNA–PROTEIN RECOGNITION
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Changes in Epigenetic Patterns Related to DNA Replication in Vicia faba Root Meristem Cells under Cadmium-Induced Stress Conditions
PublicationExperiments on Vicia faba root meristem cells exposed to 150 µM cadmium chloride (CdCl2) were undertaken to analyse epigenetic changes, mainly with respect to DNA replication stress. Histone modifications examined by means of immunofluorescence labeling included: (1) acetylation of histone H3 on lysine 56 (H3K56Ac), involved in transcription, S phase, and response to DNA damage during DNA biosynthesis; (2) dimethylation of histone...
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Genome-wide DNA methylation profiling of the regenerative MRL/MpJ mouse and two normal strains
PublicationAims We aimed to identify the pivotal differences in the DNA methylation profiles between the regeneration capable MRL/MpJ mouse and reference mouse strains. Materials and Methods Global DNA methylation profiling was performed in ear pinnae, bone marrow, spleen, liver, heart from uninjured adult females of the MRL/MpJ and C57BL/6J and BALB/c. Results and conclusion A number of differentially methylated regions distinguishing between...
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Automatic Watercraft Recognition and Identification on Water Areas Covered by Video Monitoring as Extension for Sea and River Traffic Supervision Systems
PublicationThe article presents the watercraft recognition and identification system as an extension for the presently used visual water area monitoring systems, such as VTS (Vessel Traffic Service) or RIS (River Information Service). The watercraft identification systems (AIS - Automatic Identification Systems) which are presently used in both sea and inland navigation require purchase and installation of relatively expensive transceivers...
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Luminescence recognition material as an INHIBIT logic gate in presence of Pb2+ and Cu2+ ions in aqueous solutions
PublicationA recognition material consisting of silica xerogel with amino-modified surface selectively recognizes Pb2+ and Cu2+ (but only in presence of Pb2+ ions) in aqueous solutions of other metal ions. The analytical action of the material is based on a significant change in luminescence emission spectra of the material after chemisorption of Pb2+ ions. In the presence of Pb2+ in octahedral coordination environment, a new broad and strong...
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Influence of G2 arrest on the cytotoxicity of DNA topoisomerase inhibitorstoward human carcinoma cells with different p53 status
PublicationRola bloku G2 w efekcie cytotoksycznym inhibitorów DNA topoizomeraz w stosunku do ludzkich komórek rakowych różniących się funkcjonalnością białka p53.
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Decisional-DNA-Based Digital Twin Implementation Architecture for Virtual Engineering Objects
PublicationDigital twin (DT) is an enabling technology that integrates cyber and physical spaces. It is well-fitted for manufacturing setup since it can support digitalized assets and data analytics for product and process control. Conventional manufacturing setups are still widely used all around the world for the fabrication of large-scale production. This article proposes a general DT implementation architecture for engineering objects/artifacts...
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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Effects of Salvia officinalis and Thymus vulgaris on oxidant-induced DNA damage and antioxidant status in HepG2 cells
PublicationSalvia officinalis (SO) and Thymus vulgaris (TV) are medicinal plants well known for their curative powers. However, the molecular mechanisms responsible for these abilities of sage and thyme have not been fully understood yet. In this study we investigated the composition and the quantitative estimation of plant extracts, the protective effects of plant extracts against hydrogen peroxide- and 2,3-dimethoxy-1,4 naphthoquinone-induced...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublicationThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Smart Embedded Systems with Decisional DNA Knowledge Representation
PublicationEmbedded systems have been in use since the 1970s. For most of their history embedded systems were seen simply as small computers designed to accomplish one or a few dedicated functions; and they were usually working under limited resources i.e. limited computing power, limited memories, and limited energy sources. As such, embedded systems have not drawn much attention from researchers, especially from those in the artificial...
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Numerical calculations of behaviour of ship double-bottom structure during grounding
PublicationIdeą projektu CORET jest dodanie do obecnej konstrukcji dna podwójnego statku specjalnych powłok polimerowo-betonowych w celu zwiększenia odporności na rozszczelnienie podczas kolizji, czy wejścia na mieliznę. Aby poprawnie zaprojektować te bariery ochronne konieczne jest przeprowadzenie symulacji numerycznej. Tworzenie modelu numerycznego konstrukcji podczas kolizji jest bardzo złożone i wymaga wykonania symulacji pomocniczych...
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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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Algorytm budowy reprezentacji przedziałowej grafu jako heurystyka dla problemu mapowania DNA
PublicationW pracy dokonano analizy przydatności algorytmu Corneil'a budowy reprezentacji przedziałowej grafu jako heurystyki dla problemu tworzenia map fizycznych DNA. Prezentowana analiza dotyczy dwóch osobno rozpatrywanych przypadków, w których do danych wzorcowych wprowadzamy odpowiednio błędy negatywne (reprezentujące niedobór informacji) oraz błędy pozytywne (reprezentujące fałszywe informacje). Rozpatrywany algorytm zachowuje się znacznie...
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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublicationIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
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Termodynamika oddziaływań i przejść strukturalnych DNA w układach wodnych na podstawie symulacji metodą dynamiki molekularnej
PublicationKwas deoksyrybonukleinowy jest jednym z najistotniejszych elementów każdej żywej komórki ze względu na rolę głównego nośnika informacji genetycznej. Posiada on instrukcje potrzebne do wzrostu, budowy, funkcjonowania oraz namnażania się wielu żywych organizmów, w tym także wirusów. Okazuje się, że w zależności od warunków środowiskowych, DNA może przyjmować wiele różnych struktur drugorzędowych, z których większość stanowi formy...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Tailoring Diffusional Fields in Zwitterion/Dopamine Copolymer Electropolymerized at Carbon Nanowalls for Sensitive Recognition of Neurotransmitters
PublicationThe importance of neurotransmitter sensing in the diagnosis and treatment of many psychological illnesses and neurodegenerative diseases is non-negotiable. For electrochemical sensors to become widespread and accurate, a long journey must be undertaken for each device, from understanding the materials at the molecular level to real applications in biological fluids. We report a modification of diamondized boron-doped carbon nanowalls...
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Language material for English audiovisual speech recognition system developmen . Materiał językowy do wykorzystania w systemie audiowizualnego rozpoznawania mowy angielskiej
PublicationThe bi-modal speech recognition system requires a 2-sample language input for training and for testing algorithms which precisely depicts natural English speech. For the purposes of the audio-visual recordings, a training data base of 264 sentences (1730 words without repetitions; 5685 sounds) has been created. The language sample reflects vowel and consonant frequencies in natural speech. The recording material reflects both the...
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Manufacturing collective intelligence by the means of Decisional DNA and virtual engineering objects, process and factory
PublicationEngineering collective intelligence is paramount in current industrial times. This research proposes and presents case studies for collective knowledge structures required in the industry field. Knowledge structures such as Set of Experience and Decisional DNA are extended into more advanced knowledge structures for manufacturing processes. These structures are called Virtual Engineering Object, Virtual Engineering Process and...
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Multidimensional Scaling Analysis Applied to Music Mood Recognition
PublicationThe paper presents two experiments aimed at categorizing mood associated with music. Two parts of a listening test were designed and carried out with a group of students, most of whom where users of online social music services. The initial experiment was designed to evaluate the extent to which a given label describes the mood of the particular music excerpt. The second subjective test was conducted to collect the similarity data...
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Buzz-based recognition of the honeybee colony circadian rhythm
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Gait Recognition: A Challenging Task for MEMS Signal Identification
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Versatile pattern recognition system based on Fisher criterion
PublicationZaprezentowano system rozpoznawania obrazów w postaci bitmap. Zaimplementowany algorytm ekstrakcji cech jest uniwersalny i może być używany do różnych obrazów. Cały system bazuje na kryterium Fishera.
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Automatic recognition of the arterial input function in MRI studies
PublicationArtykuł prezentuje opis automatycznej metody detekcji tętniczej funkcji wejście (AIF). Metoda została porównana z klinicznie pomierzonymi seriami obrazów DSC-MRI.
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Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface
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Recognition of input items to the logistic operations in accommodation services
PublicationIn this study the authors set themselves the aim to analyze the elements of the entrance to the accommodation services in terms of logistics. Therefore, providers of this type of services were examined. This allowed to carry out analyses also with including the variety of accommodation services
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A Framework for Training and Testing of Complex Pattern Recognition Systems
PublicationW pracy przedstawiono szkielet aplikacji stworzony po to, by uprościć konstruowanie systemów rozpoznawania obrazów oraz zapewnić środowisko testowe umożliwiające ocenę algorytmów przy użyciu dużych zestawów danych. Jasno zdefiniowana architektura wraz z wieloma gotowymi do użycia modułami pozwala skoncentrować się na implementacji najważniejszych algorytmów. Szkielet wspiera tworzenie modułów, który mogą być wielokrotnie używane,...
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Camera-based Automatic System for Tool Measurements and Recognition
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Machine learning applied to bi-heterocyclic drugs recognition
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Automatic Image and Speech Recognition Based on Neural Network
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Audiovisual speech recognition for training hearing impaired patients
PublicationPraca przedstawia system rozpoznawania izolowanych głosek mowy wykorzystujący dane wizualne i akustyczne. Modele Active Shape Models zostały wykorzystane do wyznaczania parametrów wizualnych na podstawie analizy kształtu i ruchu ust w nagraniach wideo. Parametry akustyczne bazują na współczynnikach melcepstralnych. Sieć neuronowa została użyta do rozpoznawania wymawianych głosek na podstawie wektora cech zawierającego oba typy...
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Mutual recognition of certification systems: The case of SERMO and ACLES
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Towards Recognition of Spatial Relations between Entities for Polish
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Evaluation of Knowledge-Based Recognition of Spatial Expressions for Polish
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Buzz-based recognition of the honeybee colony circadian rhythm
PublicationHoneybees are one of the highly valued pollinators. Their work as individuals is appreciated for crops pollination and honey production. It is believed that work of an entire bee colony is intense and almost continuous. The goal of the work presented in this paper is identification of bees circadian rhythm with a use of sound-based analysis. In our research as a source of information on bee colony we use their buzz that have been...
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UV-induced electron transfer between triethylamine and 5-bromo-2′-deoxyuridine. A puzzle concerning the photochemical debromination of labeled DNA
Publication5-Bromo-2'-deoxyuridine (BrdU) photosensitizes DNA to strand break formation. However, this type of photodamage is completely quenched by the presence of triethylamine (TEA) which originates from RP-HPLC purification commonly employed by oligonucleotide providers. While the presence of TEA in oligonucleotide samples does not interfere with PCR or other molecular biology applications, the mechanism of photochemical reaction proceeding...
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Comparison of immune response in sheep immunized with DNA vaccine encoding Toxoplasma gondii GRA7 antigen in different adjuvant formulations
PublicationPraca przedstawia badania dotyczące odpowiedzi immunologicznej owiec immunizowanych plazmidowym DNA kodującym antygen granul GRA7 Toxoplasma gondii w trzech różnych formulacjach adjuvanta. Sześćdziesiąt owiec było szczepionych domięśniowo z DNa plazmidów. Dwanaście otrzymało liposomową formę plazmidu pVAXIgGRA7, 12 formulację z Emulsigen P plazmidu pVAXIgGRA7 1 12 formulację z Emulsigen D plazmidu pVAXIgGRA7. Wszystkie zwierzęta...
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Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode
PublicationThis work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10−18 to 10−8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10−14 M for PD-L1 (S/N = 3.3) and at a concentration of 10−14...
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Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA): Past, Present and Future
PublicationThis article reviews research work on set of experience knowledge structure (SOEKS)-decisional DNA (DDNA) done in the past, ongoing, and planned for the future. Firstly, the concept of the knowledge representation technique of SOEKS-DDNA is discussed, and then an attempt is made to organize the past research related with it in chronological order. This work focuses on the review on SOEKS-DDNA, its application in different domains,...
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Transport of Particles in Intestinal Mucus under Simulated Infant and Adult Physiological Conditions: Impact of Mucus Structure and Extracellular DNA
PublicationThe final boundary between digested food and the cells that take up nutrients in the small intestine is a protective layer of mucus. In this work, the microstructural organization and permeability of the intestinal mucus have been determined under conditions simulating those of infant and adult human small intestines. As a model, we used the mucus from the proximal (jejunal) small intestines of piglets and adult pigs. Confocal...
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Beyond Antioxidant Activity: Redox Properties of Catechins May Affect Changes in the DNA Methylation Profile—The Example of SRXN1 Gene
PublicationThe role of catechins in the epigenetic regulation of gene expression has been widely studied; however, if and how this phenomenon relates to the redox properties of these polyphenols remains unknown. Our earlier study demonstrated that exposure of the human colon adenocarcinoma HT29 cell line to these antioxidants affects the expression of redox-related genes. In particular, treatment with (−)-epigallocatechin (EGC) downregulated...
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Polysaccharide–Protein Complexes in a Coarse-Grained Model
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ANALYSIS OF THE p53 PROTEIN GENE EXPRESSION MODEL
PublicationWe study the asymptotic behaviour of the solutions of the p53-Mdm2 model proposed by Monk (2003). The p53 gene is crucial for cellular inhibition of the angiogenesis process, while Mdm2 is a negative regulator of the p53 tumor-suppressor. We investigate the stability of the positive steady state and perform some numerical experiments.
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Apple pectin complexes with whey protein isolate
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Some applications of thermophiles and their enzymes for protein processing
PublicationPrzedstawiono charakterystykę, właściwości oraz możliwości zastosowań enzymów proteolitycznych wytwarzanych przez termofile. Zaletą tych biokatalizatorów jest między innymi duża odporność na działanie rozpuszczalników organicznych, detergentów i innych czynników denaturujących białka oraz mała wrażliwość na zmiany pH. Dokonano też przeglądu czynników powodujących dużą stabilność proteaz z termofili.
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Pea Protein for Hempseed Oil Nanoemulsion Stabilization
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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One-tube cell lysis and DNA extraction procedure for PCR based detection of Mycobacterium ulcerans in aquatic insects, molluscs and fish.
PublicationMycobacterium ulcerans jest bakterią wywołującą choroby skóry u ludzi i zwierząt. W trakcie prowadzonych badań opracowano prostą w wykonaniu metodę ekstrakcji DNA Mycobacterium ulcerans z próbek środowiskowych oraz klinicznych. Opracowana metoda izolacji DNA może być przydatna w badaniu źródeł infekcji oraz dróg szerzenia się Mycobacterium ulcerans.
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Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities.
PublicationCelem pracy było scharakteryzowanie odziaływania związku C-1305 z DNA w porównaniu do innych inhibitorów topoizomerazy II. Badania pokazują, że C-1305 odziaływuje preferencyjnie z parami CG, interkaluje do DNA i zaburza sąsiednie otoczenie w bardzo charakterystyczny sposób, który nie został zaobserwowany u pozostałych 22 badanych związków.