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End-to-end service survivability under attacks on networks
PublikacjaW artykule zaproponowano model znajdowania przeżywalnych i odpornych na ataki połączeń od końca do końca dla sieci o topologii bezskalowej. Głównymi założeniami są: zróżnicowanie sposobu zapewniania przeżywalności połączeń w zależności od klasy ruchu oraz omijanie przez ścieżki aktywne węzłów, narażonych na ataki (tzw. centrów). Wprowadzono nową metrykę dla wyznaczania ścieżek, proporcjonalną do wymaganej jakości obsługi połączeń,...
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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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Identification and properties of the Deinococcus grandis andDeinococcus proteolyticus single-stranded DNA binding proteins (SSB)
PublikacjaW celu poznania właściwości biochemicznych białek SSB pochodzących z Deinococcus grandis (DgrSSB) i Deinococcus proteolyticus (DprSSB) sklonowano zaamplifikowane w reakcji PCR geny ssb w systemie ekspresyjnym Escherichia coli. Geny składają się z 891(DgrSSB) i 876 (DprSSB) nukleotydów kodujących odpowiednio 296 i 291 reszt aminokwasowych o teoretycznie wyznaczonej masie cząsteczkowej dla białek, równej 32,29 i 31,33 kDa. Sekwencja...
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Bacterial SSB-like proteins of family Deinococcaceae - indentification, isolation, obtaining, purification and molecular characteristic
PublikacjaWiększość poznanych białek SSB jest aktywna w formie homotetramerycznej. Od 2002 roku znane są białka organizmów ekstremofilnych. Scharakteryzowano białka mikroorganizmów rodziny Deinococaceae. Uzyskane termostabilne białka stanowią atrakcyjną alternatywę w stosunku do znanych białek SSB w metodach diagnostyki molekularnej, technikach biologii molekularnej i analityce.
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Protective Effect of Black Tea Against Ethanol-Induced Oxidative Modifications of Liver Proteins and Lipids
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Discrimination of normal oral mucosa from oral cancer by mass spectrometry imaging of proteins and lipids
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Lon Protease Is Important for Growth under Stressful Conditions and Pathogenicity of the Phytopathogen, Bacterium Dickeya solani
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Extracellular Matrix Proteins Expression Profiling in Chemoresistant Variants of the A2780 Ovarian Cancer Cell Line
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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
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Investigations of changes in the arabinogalactan proteins (AGPs) structure, size and composition during the fruit ripening process
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Ovocystatin Induced Changes in Expression of Alzheimer’s Disease Relevant Proteins in APP/PS1 Transgenic Mice
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Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublikacjaThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
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Efficient removal of dyes and proteins by nitrogen-doped porous graphene blended polyethersulfone nanocomposite membranes
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Virtual screening for small molecular non-covalent binders of the SARS-CoV-2 main protease
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Human sperm proteins identified by 2-dimensional electrophoresis and mass spectrometry and their relevance to a transcriptomic analysis
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The Immunogenic and Immunoprotective Activities of Recombinant Chimeric T. gondii Proteins Containing AMA1 Antigen Fragments
PublikacjaToxoplasmosis, one of the most common parasitoses worldwide, is potentially dangerous for individuals with a weakened immune system, but specific immunoprophylaxis intended for humans is still lacking. Thus, efforts have been made to create an efficient universal vaccine for both animals and humans to overcome the shortcomings of currently used treatment methods and protect all hosts against toxoplasmosis. The current work represents...
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Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublikacjaInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
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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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The biological role of prolyl oligopeptidase and the procognitive potential of its peptidic inhibitors from food proteins
PublikacjaProlyl oligopeptidase (POP) is a conserved serine protease belonging to proline-specific peptidases. It has both enzymatic and non-enzymatic activity and is involved in numerous biological processes in the human body, playing a role in e.g., cellular growth and differentiation, inflammation, as well as the development of some neurodegenerative and neuropsychiatric disorders. This article describes the physiological and pathological...
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus-expression and purification
PublikacjaSklonowano w system ekspresyjny pET-30LIC Escherichia coli gen kodujący białka SSB-podobne Thermus thermophilus i T. aquaticus. Oczyszczono do homogenności białka SSB-podobne, a uzyskane preparaty umożliwiają wykonanie badań strukturalnych w/w białek.
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus - expression and purification
PublikacjaBiałka SSB są niezbędne do życia każdemu organizmowi. W tej pracy prezentujemy wyniki otrzymania i oczyszczania białek SSB Thermus thermophilus i T. aquaticus. Dotąd były znane białka SSB jedynie o budowie homotetrameru lub heterotrimeru. Białka SSB Thermus thermophilus i T. aquaticus stanowią nową klasę białek SSB - białek homodimerycznych. Ponadto dowiedziono, iż białka te są użyteczne w reakcji PCR.
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Relationship between seawater pollution and qualitative changes in the extracted proteins from mussels Mytilus galloprovincialis
PublikacjaCelem badań było znalezienie wiarygodnego bioznacznika dla oceny poziomu zanieczyszczenia wody morskiej. W tym celu porównano:-zawartość żelaza (Fe) oraz miedzi (Cu)-białek-poziomu aktywności przeciwutleniającejmałży (Mytilus galloprovincialis)zebranych z rejonów zanieczyszczonych i niezanieczyszczonych bułgarskiej strefy ekonomicznej Morza Czarnego.W badanich wykorzystano takie techniki analityczne jak: -spektroskopia w podczerwieni...
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Urine headspace analysis in medical diagnostics
PublikacjaThe analysis of the volatile organic compounds in the bodily fluids such as urine may provide useful information on the patients’ general health. The potential application of urine headspace analysis could facilitate the diagnostics of various diseases such as metabolic disorders, urinary tract diseases and gastrointestinal conditions. Described in this paper are the currently available techniques of urine sample analysis as well...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublikacjaAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Evolution of functionally important compartments of proteins – what can we learn from studying epoxide hydrolases?
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Photoactive Protochlorophyllide-Enzyme Complexes Reconstituted with PORA, PORB and PORC Proteins of A. thaliana: Fluorescence and Catalytic Properties
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The Major Heat Shock Proteins, Hsp70 and Hsp90, in 2-Methoxyestradiol-Mediated Osteosarcoma Cell Death Model
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Fibronectin-, vitronectin- and laminin-binding proteins at the cell walls of Candida parapsilosis and Candida tropicalis pathogenic yeasts
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One Step Beyond: Design of Substrates Spanning Primed Positions of Zika Virus NS2B-NS3 Protease
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Influence of milk, milk fractions and milk proteins on the growth and viability of mastitis-causing Staphylococcus aureus strain
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublikacjaWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublikacjaBACKGROUND: In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.RESULTS: We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino...
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Impact of the depletion of high-abundance proteins in blood plasma/serum on the proteome of these media in growing farm animals
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Borrelia burgdorferi BmpA-BBK32 and BmpA-BBA64: New Recombinant Chimeric Proteins with Potential Diagnostic Value
PublikacjaCurrently, the diagnosis of Lyme disease is based mostly on two-tiered serologic testing. In the new generation of immunoenzymatic assays, antigens comprise whole-cell lysates of members of the Borrelia burgdorferi sensu lato (s.l.) species complex, with the addition of selected recombinant proteins. Due to the high diversity of members of the B. burgdorferi s.l. genospecies and the low degree of conservation among the amino acid...
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Stripe order and magnetic anisotropy in the S=1 antiferromagnet BaMoP2O8
PublikacjaMagnetic behavior of yavapaiite-type BaMoP2O8 with the spatially anisotropic triangular arrangement of the S=1Mo4+ ions is explored using thermodynamic measurements, neutron diffraction, and density-functional band-structure calculations. A broad maximum in the magnetic susceptibility around 46 K is followed by the stripe antiferromagnetic order with the propagation vector k=(12,12,12) formed below TN≃21 K. This stripe phase is...
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DEGRADATION OF GFRP MARINE LAMINATES WITH NANO PARTICLE MODIFIED COATINGS
PublikacjaWater absorption and surface blistering behaviour was studied for polyester-matrix laminates with SiO2 nanoparticle reinforced gel coats. Accelerated water immersion tests at 37°C showed that addition of 10% nanoparticles increases blisters incubation time by ca. 50% compared to 5% and 0% nanoparticles composites.
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Improvement of Imperfect String Matching Based on Asymetric n-Grams
PublikacjaTypical approaches to string comparing treats them as either different or identical without taking into account the possibility of misspelling of the word. In this article we present an approach we used for improvement of imperfect string matching that allows one to reconstruct potential string distortions. The proposed method increases the quality of imperfect string matching, allowing the lookup of misspelled words without significant...
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WIKI-WS as a C2 NIWA Web Service Management Platform
PublikacjaThe Wiki-WS platform was implemented within the C2 NIWA project for production purposes. Wiki-WS stands for developing, managing and maintaining web services. The production deployment needed implementation of several functional improvements and establishing a strong security 7 safety policy. The WikiWS platform has to be used as an educational environmement for developing web sevices and production environment for execution of...
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Cost Effective Corrosion and Fatigue Monitoring for Marine Transport Products
PublikacjaW artykule omówiono genezę i główne założenia projektu badawczego "Cost Effective Corrosion and Fatigue Monitoring for Transport Products'' o kryptonimie CORFAT, realizowanego w ramach VII Programu Ramowego Unii Europejskiej. Przedstawiono cele i metodykę badań, zalety nowej nowej metodyki monitorowania statków, zadania projektu, zalety i ograniczenia metody Emisji Akustycznej (EA), opis innych metod badań nieniszczących (NNDT)....
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"Shadow" method application within endoscopic examinations of marine engines
PublikacjaThe paper deals with diagnostic issues concerning endoscopic examinations of the working spaces within marine diesel and gas turbine engines. In the beginning, the endoscopy apparatus being on the laboratory equipment of the Department of Ship Power Plants of Gdansk University of Technology in Poland has been characterized. The endoscopy considerations have been focused on theoretical bases of a digital image processing and especially...
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"Shadow" method application within endoscopic examinations of marine engines
PublikacjaThe paper deals with diagnostic issues concerning endoscopic examinations of the working spaces within marine diesel and gas turbine engines. In the beginning, the endoscopy apparatus being on the laboratory equipment of the Department of Ship Power Plants of Gdansk University of Technology in Poland has been characterized. The endoscopy considerations have been focused on theoretical bases of a digital image processing and especially...
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The thermal effort during marine steam turbine flooding with water
PublikacjaThe work discussed an extreme case of cooling a steam turbine. The ship's steam turbine was used as an example. In marine transport units with low-speed engines dominate, however, there are also units with steam turbines. An example of analysed marine steam turbine is shown in Fig. 1. When considering the issue of cooling steam turbines, it is necessary to estimate the extreme conditions that may occur during operation of the turbine....
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Criteria for evaluation and selection of the best offer for the Contract Engineer service
PublikacjaThe purpose of the legal regulations regarding public procurement in EU countries is to ensure effective funds' spending. When assessing and selecting the best offer, the contracting entities have at their disposal many different criteria, including non-price criteria. Their proper selection and application is necessary to ensure the high quality of the ordered product, delivery or service. Making an order for intellectual services,...
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Selected Problems of Experimental Testing Marine Stern Tube Bearings
PublikacjaThis paper presents typical methods for conducting experimental tests on main shaft slide bearings. There are described their possible testing capabilities, advantages, drawbacks and limitations. Various testing methods were analyzed to find a solution able of providing a wide range of possible investigations at possibly acceptable limitations.
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Towards Digital Anti-Corruption Typology for Public Service Delivery
PublikacjaDigital anti-corruption refers to a family of digital technology tools that are used to fight corruption. Many such tools have not performed well in practice due to their non-alignment with forms of corruption they are supposed to fight against and persistence of corruption-enabling conditions. The aim of this paper is to contribute to filling this gap by offering a typology of digital anti-corruption in public service delivery...
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Power flow in typical series-parallel hybrid filters topologies
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Adenosine triphosphate in the marine boundary layer in the southern Baltic Sea
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Optimization of multiple model neural tracking filter for marine targets
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Coil Design for Wireless Power Transfer with Series-Parallel Compensation
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