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Search results for: DNA–PROTEIN RECOGNITION
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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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Smart Innovation Engineering Using Set of Experience and Decisional DNA
PublicationKnowledge-based Engineering Systems are founded upon integration of knowledge into computer systems and are one of the core requirements for the future Industry 4.0. Since the fourth industrial revolution is passing through the developing phase, implementation of Cyber-Physical Production Systems require more realistic approach. Knowledge Management and Knowledge Engineering plays an important role in manufacturing industries facing...
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PROTEIN ENGINEERING DESIGN & SELECTION
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World Research Journal of Peptide and Protein
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Advances in Protein Chemistry and Structural Biology
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Current Topics in Peptide and Protein Research
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International Journal of Peptide and Protein Research
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AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
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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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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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Bożena Kostek prof. dr hab. inż.
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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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Ahmer Bin Hafeez
PeopleI have experience in Microbiology & Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. Currently, my interest lies in translatable omics studies and drug discovery against novel protein targets involved in cancer and infectious diseases and Host-Pathogen PPIs. My aim involves the use of computational methods for the identification of novel targets and to...
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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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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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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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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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Buzz-based recognition of the honeybee colony circadian rhythm
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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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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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Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface
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Gait Recognition: A Challenging Task for MEMS Signal Identification
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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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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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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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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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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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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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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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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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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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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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Minimum inhibitory concentrations (MICs) determination of selected human topoisomerase II alpha and bacterial DNA gyrase inhibitors against fungal strains
Open Research DataThe datasets contain the results of determining the MIC (Minimal Inhibitory Concentration) value of known compounds* (inhibitors of human topoisomerase II alpha and bacterial DNA gyrase) against C. albicans SC5314, C. glabrata ATCC 90030, C. krusei ATCC 6258 and C. parapsilosis ATCC 22019 and Saccharomyces cerevisiae ATCC 9763 by the modified M27-A3...
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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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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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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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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...