Search results for: NANOPARTICLE-PROTEIN AGGREGATION
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Molecular simulation study of cooperativity in hydrophobic association
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AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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Wettability of Horizontal Stainless Steel Tube by Nanofluid Droplets
PublicationThe goal of the present work was the experimental determination of the contact angle of three nanofluids, i.e. water-Al2O3, water-Cu and water-TiO2 on horizontal stainless steel tube of 1.6 mm OD. Of particular interest was the effect of nanoparticle concentration (0.01%, 0.1%, and 1% by weight) on droplet contact angle.
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Wettability of Horizontal Stainless Steel Tube by Nanofluid Droplets
PublicationThe goal of the present work was the experimental determination of the contact angle of three nanofluids, i.e. water-Al2O3, water-Cu and water-TiO2 on horizontal stainless steel tube of 1.6 mm OD. Of particular interest was the effect of nanoparticle concentration (0.01%, 0.1%, and 1% by weight) on droplet contact angle.
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DEGRADATION OF GFRP MARINE LAMINATES WITH NANO PARTICLE MODIFIED COATINGS
PublicationWater 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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Text-mining Similarity Approximation Operators for Opinion Mining in BI tools
PublicationThe concept of the Text-mining Similarity Approximation Operators for Opinion Mining as extensions to Natural Language Interface Database is defined. The new operators: “keywords of” dimension; subsetting operator “about C is q”; aggregation operator “by similar C” are proposed. These operators are based on the Latent Semantic Analysis and Social Network Analysis
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain AAEC191A/pCC90 D54-STOP-PBS, PBS+0.2% glucose, PBS+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain AAEC191A/pCC90 D54-STOP-LB, LB+0.2% glucose, LB+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough 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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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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Aravind Ayyolath
PeopleI am interested in the biology of bacterial stress response and its growth under stress conditions. Our lab focuses on two aspects; protein folding and lipopolysaccharide biosynthesis and we address them with Escherichia coli models. Our recent studies have provided more evidence regarding several genes involved in the survival of bacteria under stress. I am also interested in disease biology and also in identifying proper therapeutic...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain AAEC191A/pCC90 Dra D-mut-PBS, PBS+0.2% glucose, PBS+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain AAEC191A/pCC90 Dra D-mut-LB, LB+0.2% glucose, LB+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain BL21(DE3)/pCC90 D54-STOP-LB, LB+0.2% glucose, LB+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain BL21(DE3)/pCC90 D54-STOP-PBS, PBS+0.2% glucose, PBS+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Free convection of water-Al2O3 nanofluid from horizontal porous coated tube
PublicationThe main aim of the present study was to investigate the influence of nanoparticles on heat transfer coefficients during free convection of water-Al2O3 nanofluid from horizontal porous coated tube under atmospheric pressure for nanoparticle concentration of 0.01% by weight. Contrary to published data present study concerns on free convection of nanofluids in extensive, quiescent fluid.
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Representing and appraising Toulmin model arguments in trust cases
PublicationThe paper presents a Toulmin-based argument model used in trust cases, which allows to argue various properties of IT systems. Argument patterns encountered in trust cases are discussed together with some real-life examples. A method of argument appraisal is introduced together with the corresponding aggregation mechanism. Practical applications of trust cases in industrial and research projects are outlined.
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Nano-structured Pt embedded in acidic salts of heteropolymolybdate matrices: MS EXAFS study
PublicationA structural study of Pt nano-catalysts is presented in the paper. The innovation in the case of the considered catalytic materials resides in the use a meso-microporous inorganic matrix of heteropolyacid salt of composition X2.5H0.5YMo12O40 where X = Rb, Cs and Y = P, Si as a catalyst support. Metallic nanoparticles were created by platinum ions reduction in a hot H2/Argon stream and were mainly located into matrix pores. As the...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Data on solutions of Hes1 system
Open Research DataHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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Characterization of a cryptic plasmid pSFKW33 from Shewanella sp. 33b
PublicationA cryptic plasmid pSFKW33 from psychrotrophic bacterium Shewanella sp. 33B, an isolate from the Gulf of Gdansk (the Baltic Sea), was sequenced and characterized. It is an 8021 bpcircular molecule with 38% GC content, which shows a distinctive nucleotide sequence without homology to other known plasmids. The nucleotide sequence analysis predicts eight open reading frames. The deduced amino acid sequence of ORF-1 shared significant...
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Micelle formation of Tween 20 nonionic surfactant in imidazolium ionic liquids
PublicationAggregation behavior of polyoxyethylene (POE)-type nonionic surfactant Tween 20 in imidazolium ionic liquids with varying chain length and different anions, such as tetrafluoroborate, hexafluorophosphate, bis(trifluoromethanesulfonyl)imide, and trifluoromethanesulfonate, was investigated by means of surface tension, conductivity and dynamic light scattering measurements. The role of the chain length, anion size as well as interactions...
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain BL21(DE3)/pCC90 Dra D-mut-PBS, PBS+0.2% glucose, PBS+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain BL21(DE3)/pCC90 Dra D-mut-LB, LB+0.2% glucose, LB+0.5% glucose
Open Research DataMicrobial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition...
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Low-frequency noise in Au-decorated graphene–Si Schottky barrier diode at selected ambient gases
PublicationWe report results of the current–voltage characteristics and low-frequency noise in Au nanoparticle (AuNP)-decorated graphene–Si Schottky barrier diodes. Measurements were conducted in ambient air with addition of either of two organic vapors, tetrahydrofuran [(CH2)4O; THF] and chloroform (CHCl3), as also during yellow light illumination (592nm), close to the measured particle plasmon polariton frequency of the Au nanoparticle...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen SAG1-SAG2-AMA1F
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Construction, production and evaluation of the diagnostic utility of a recombinant Toxoplasma gondii chimeric antigen SAG1-SAG2-MAG1L
Open Research DataThe intracellular parasite Toxoplasma gondii has the ability to infect a wide range of warm-blooded animals, including humans. Currently, diagnosis of toxoplasmosis is based mainly on the use of the native antigens in enzyme immunoassay which allow for detection of IgG, IgM and IgA antibody classes. However, in some cases the performed studies give...
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Zarządzanie tożsamością w organizacjach na różnych poziomach zagregowania
PublicationNiniejszy artykuł stanowi naukową refleksję nad pojęciem tożsamości grupowej, odnoszonej do przedsiębiorstw oraz ich agregatów, określanych przez autorkę mianem „organizacji na wyższych poziomach zagregowania”. Głównym celem artykułu jest przegląd literatury z zakresu tożsamości przedsiębiorstwa, a na tej podstawie próba ustalenia czym jest taka tożsamość i co się na nią składa. Na wstępie autorka przedstawia definicje tożsamości...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Can sodium 1-alkylsulfonates participate in the sodium dodecyl sulfate micelle formation?
PublicationThe aggregation behavior of sodium dodecyl sulfate (SDS) was studied in an aqueous solution in the presence of increasing concentrations of selected sodium 1-alkylsulfonates, namely sodium 1-octanesulfonate, sodium 1-decanesulfonate, and sodium 1-dodecanesufonate. The critical micelle concentration (CMC) of SDS was determined by conductivity and fluorescence intensity measurements. The steady-state fluorescence quenching experiments...
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Overproduction of CaMet15p native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: O-acetylhomoserine sulfhydrylase (Met15p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of CaStr2p native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: cystathionine-γ-synthase (CaStr2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of homoserine O-acetyltransferase (CaMet2p) native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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The generalization by simplification operator with the Simplify Building tool of objects representing groups of buildings in Gdańsk district - scale 1:10000. Data from OSM
Open Research DataThe process of automatic generalization is one of the elements of spatial data preparation for the purpose of creating digital cartographic studies. The presented data include a part of the process of generalization of building groups obtained from the Open Street Map databases (OSM) [1].
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Induction of immune responses in sheep by vaccination with liposome-entrapped DNA complexes encoding Toxoplasma gondii MIC3 gene
PublicationToxoplasma gondii is a parasite that has been extensively studied due to its medical and veterinary importance in terminating pregnancies. Consequently, a satisfactory vaccine is required to control itsadverse effects on pregnant animals. The microneme protein, MIC3, is a major adhesion protein that binds to the surface of host cells and parasites, and is therefore a potential vaccine against T. gondii.The viability of MIC3 as...
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublicationThe impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. butylurea (BU) and N,N,N′,N′-tetramethylurea (TMU) were chosen as a tested compounds. The obtained results show that butylurea exerts greater impact on HEWL and its fibrillation than tetramethylurea. Both substances decrease the time of...
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SmallAngle Neutron Scattering Study of the Structure of Mixed Micellar Solutions Based on Nonionic and Two Cationic Surfactants
PublicationThe aggregation in mixed water systems based on nonionic surfactant, i.e., heptaethylene glycol monotetradecyl ether (C14E7), and cationic surfactants, i.e., cetyltrimethylammonium bromide (CTAB), and cetyltrimethylammonium chloride (CTAC) has been investigated using the smallangle neutron scattering method. The preliminary results of the study of the behavior of C14E7 aqueous solutions (for a concentration of 0.17%) when adding...
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Medical Image Dataset Annotation Service (MIDAS)
PublicationMIDAS (Medical Image Dataset Annotation Service) is a custom-tailored tool for creating and managing datasets either for deep learning, as well as machine learning or any form of statistical research. The aim of the project is to provide one-fit-all platform for creating medical image datasets that could easily blend in hospital's workflow. In our work, we focus on the importance of medical data anonimization, discussing the...
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Surface active fatty acid ILs: Influence of the hydrophobic tail and/or theimidazolium hydroxyl functionalization on aggregates formation
PublicationNine structurally-related fatty acid ionic liquids have been prepared and their thermal behavior as well as their ability to self-assemble in water has been investigated. The thermal properties were studied by thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC), while the aggregation behavior was analyzed by tensiometry, isothermal titration calorimetry (ITC), conductometry, dynamic light scattering (DLS),...
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Bodybuilders and high-level meat consumers’ behavior towards rabbit, beef, chicken, turkey, and lamb meat: A comparative review
PublicationIn bodybuilders’ diets, protein plays a crucial role in supporting muscle growth and repairing damaged muscle tissue. These individuals meet their protein needs by combining dietary sources with supplements. Animal-based proteins are often preferred over plant-based proteins because they are believed to better support muscle protein synthesis. This review explores the meat consumption patterns of bodybuilders and high-level meat...
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The development of an indirect ELISA for the detection of goose parvovirus antibodies using specific VP3 subunits as the coating antigen
PublicationIn Poland, the leader in goose production in Europe, goose parovirus infection, or Derzsy’s disease (DD), must be reported to the veterinary administration due to the serious economic and epizootic threat to waterfowl production. Prophylactic treatment for DD includes attenuated live or inactivated vaccines. Moreover, the control of DD includes the monitoring of maternal derived antibody (MDA) levels in the offspring and antibody...
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Pilicides effectively hinder chaperone-usher interactions in all Gram-negative bacteria
PublicationThe chaperone-usher pathway of adhesive structures biogenesis is highly conserved in all Gram-negative bacteria. Pili are polymers of thousands protein subunits that possess conserved immunoglobuline-like structure denoted by lack of the seventh G strand. The effect of this structural defect is a hydrophobic acceptor cleft. The folding of protein subunits is strictly dependent on the action of specific periplasmic chaperone protein...
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The generalization of objects representing groups of buildings in the Kartuzy district by simplification operator with the Simplify Building tool - scale 1:10000. Data from OSM.
Open Research DataThe process of automatic generalization is one of the elements of spatial data preparation for the purpose of creating digital cartographic studies. The presented data include a part of the process of generalization of building groups obtained from the Open Street Map databases (OSM) [1].
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Spectroscopic properties of Rhodamine B entrapped in hybrid porous nanolayers at high dye concentration
PublicationThe preparation procedure and characterization of Rhodamine B entrapped in zirconia, silica and mixed silica–zirconia nanolayers is described. The nanolayers were produced by the sol–gel spin-coating technique. The pronounced effect of the dye concentration on the absorption and fluorescence spectra as well as on time-resolved fluorescence spectra was found. The results show that the aggregation of Rhodamine B is stronger in silica...
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The circle object detection with the use of Msplit estimation
PublicationThe paper presents the use of Msplit(q) - estimation in the filtration and aggregation of point clouds containing a known number of elliptical shapes with preliminary unknown - locations and dimensions. These theoretical solutions may have practical relevance especially in the modelling of terrestrial laser scanning data of objects that have similar shape to circles. Mentioned shapes can be scanned of tree trunks, columns, gutters,...
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Deep Eutectic Solvents as Agents for Improving the Solubility of Edaravone: Experimental and Theoretical Considerations
PublicationIn this study, both practical and theoretical aspects of the solubility of edaravone (EDA) in Deep Eutectic Solvents (DESs) were considered. The solubility of edaravone in some media, including water, can be limited, which creates the need for new efficient and environmentally safe solvents. The solubility of EDA was measured spectrophotometrically and the complex intermolecular interactions within the systems were studied with...