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Wyniki wyszukiwania dla: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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Underground Water Level Prediction in Remote Sensing Images Using Improved Hydro Index Value with Ensemble Classifier
PublikacjaThe economic sustainability of aquifers across the world relies on accurate and rapid estimates of groundwater storage changes, but this becomes difficult due to the absence of insitu groundwater surveys in most areas. By closing the water balance, hydrologic remote sensing measures offer a possible method for quantifying changes in groundwater storage. However, it is uncertain to what extent remote sensing data can provide an...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublikacjaSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublikacjaEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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The behavioural model of graphene field-effect transistor
PublikacjaThe behavioural model of a graphene field-effect transistor (GFET) is proposed. In this approach the GFET element is treated as a “black box” with only external terminals available and without considering the physical phenomena directly. The presented circuit model was constructed to reflect steady-states characteristics taking also into account GFET capacitances. The authors’ model is defined by a relatively small number of equations...
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Experimental guinea pig model of dermatophytosis: a simple and useful tool for the evaluation of new diagnostics and antifungals
PublikacjaCelem badań było opracowanie prostego modelu zwierzęcego (świnki morskie) odpowiedniego do sprawdzania systemów diagnostycznych oraz terapii infekcji dermatofitów. Następujące zmienne były analizowane: przygotowanie skóry przez golenie versus użycie taśmy, testowy szczep Microsporum canis czy Trichophyton mentagrophytes jako czynnik etiologiczny, sposób inokulacji. Przebieg infekcji był oceniany poprzez ocenę zaczerwienienia i...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublikacjaEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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A novel luminescent chemical sensor for the determination of Pb 2+ and Cu 2+ ions
PublikacjaSilica xerogel surface grafted with aminopropyl (PrNH2) groups was additionally treated by cetyltrimethylammonium bromide (CTAB) surfactant and ascorbic acid (asc) in alkaline solution. This material symbolized as SiO2-PrNH2-CTAB/asc, proved to be a stable luminescent material, exhibited an emission band peaked at 393 nm under excitation wavelength 335 nm. Time evolution of the band intensity suggests changes of defect concentration...
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The Use of Cluster Analysis to Evaluate the Impact of COVID-19 Pandemic on Daily Water Demand Patterns
PublikacjaProper determination of unitary water demand and diurnal distribution of water consumption (water consumption histogram) provides the basis for designing, dimensioning, and all analyses of water supply networks. It is important in the case of mathematical modelling of flows in the water supply network, particularly during the determination of nodal water demands in the context of Extended Period Simulation (EPS). Considering the...
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2-Methoxyestradiol and Hydrogen Peroxide as Promising Biomarkers in Parkinson’s Disease
PublikacjaEstrogens function in numerous physiological processes including controlling brain cell growth and differentiation. 2-Meth- oxestradiol (2-ME2), a 17β-estradiol (E2) metabolite, is known for its anticancer effects as observed both in vivo and in vitro. 2-ME2 affects all actively dividing cells, including neurons. The study aimed to determine whether 2-ME2 is a potentially cancer-protective or rather neurodegenerative agent in a...
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The Concept of Accuracy Analysis of the Vertical Displacements Gained from the Hydrostatic Levelling Systems’ Measurements
PublikacjaAbstract: Nowadays, hydrostatic levelling is a widely used method for the vertical displacements’ determinations of objects such as bridges, viaducts, wharfs, tunnels, high buildings, historical buildings, special engineering objects (e.g., synchrotron), sports and entertainment halls. The measurements’ sensors implemented in the hydrostatic levelling systems (HLSs) consist of the reference sensor (RS) and sensors located on the...
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Crystal structure and physical properties of a novel ternary compound La15MoxGe9
PublikacjaWe present the synthesis, structural characterization and physical properties measurements of a new compound, La15MoxGe9 in Mn5Si3-type derived structure with interstitial Mo. The sample was synthesized by arc-melting method. La15MoxGe9 crystallizes in non-centrosymmetric hexagonal structure P63mc (#186) with lattice parameters a = b = 15.495(5) Å and c = 6.917(2) Å. The refinement on single X-ray diffraction data show that interstitial...
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Novel 2-alkythio-4-chloro-N-[imino(heteroaryl)methyl]benzenesulfonamide Derivatives: Synthesis, Molecular Structure, Anticancer Activity and Metabolic Stability
PublikacjaA series of novel 2-alkythio-4-chloro-N-[imino-(heteroaryl)methyl]benzenesulfonamide derivatives, 8–24, were synthesized in the reaction of the N-(benzenesulfonyl)cyanamide potassium salts 1–7 with the appropriate mercaptoheterocycles. All the synthesized compounds were evaluated for their anticancer activity in HeLa, HCT-116 and MCF-7 cell lines. The most promising compounds, 11–13, molecular hybrids containing benzenesulfonamide...
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Non-isolating 2-bondage in graphs
PublikacjaA 2-dominating set of a graph G=(V,E) is a set D of vertices of G such that every vertex of V(G)D has at least two neighbors in D. The 2-domination number of a graph G, denoted by gamma_2(G), is the minimum cardinality of a 2-dominating set of G. The non-isolating 2-bondage number of G, denoted by b_2'(G), is the minimum cardinality among all sets of edges E' subseteq E such that delta(G-E') >= 1 and gamma_2(G-E') > gamma_2(G)....
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Colloidal aspects of protein digestion
Publikacja.
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Stabilizing agents and protein stability
PublikacjaBiałka są kluczowymi elementami żywych organizmów, jak również efektywnymi katalizatorami w biotechnologii i medycynie. Szybki rozwój wielu gałęzi biotechnologii wiąże się z coraz większym zapotrzebowaniem na produkty białkowe charakteryzujące się wysoką stabilnością. Jednym ze sposobów osiągnięcia większej stabilności białek jest wykorzystanie małych związków organicznych, tzw. osmolitów. Do tej grupy związków należą aminokwasy,...
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Alternative and New Protein Sources
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The Positioning Accuracy of BAUV Using Fusion of Data from USBL System and Movement Parameters Measurements
PublikacjaThe article presents a study of the accuracy of estimating the position coordinates of BAUV (Biomimetic Autonomous Underwater Vehicle) by the extended Kalman filter (EKF) method. The fusion of movement parameters measurements and position coordinates fixes was applied. The movement parameters measurements are carried out by on-board navigation devices, while the position coordinates fixes are done by the USBL (Ultra Short Base...
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Age, frequency of volunteering, and Present-Hedonistic time perspective predict donating items to people in need, but not money to combat COVID-19 during lock-down
PublikacjaRestrictions due to COVID-19 necessitated staying at home, but in some cases, encouraged charitable behavior, e.g., donating items to people in need (e.g., clothes, food), or money to support combatting COVID-19. Drawing on the previous findings regarding helping during disastrous situations and roles of time perspective in helping behaviors, the study tested the predictive value of age, gender, previous volunteering, altruistic...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublikacjaApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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The analysis of the accuracy of spatial models using photogrammetric software: Agisoft Photoscan and Pix4D
PublikacjaThis article was created as a result of research conducted within the master thesis. The purpose of the measurements was to analyze the accuracy of the positioning of points by computer programs. Selected software was a specialized computer software dedicated to photogrammetric work. For comparative purposes it was decided to use tools with similar functionality. As the basic parameters that affect the results selected the resolution...
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Ductile fracture prediction in thin metallic plates subjected to explosions
PublikacjaPraca dotyczy modelowania zniszczenia ciągłego. Zaprezentowano wyniki eksperymentów przeprowadzonych na płytach metalowych poddanych eksplozjom oraz wyniki jednoosiowych prób laboratoryjnych. Opisano przyjęty model prawa konstytutywnego oraz kryteriów zniszczenia. Przedstawiono identyfikację parametrów materiałowych dla przyjętego modelu. Zaprezentowano model numeryczny oraz wyniki symulacji które następnie porównano z wynikami...
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Simple 2-D Direction-of-Arrival Estimation Using an ESPAR Antenna
PublikacjaIn this letter, it has been shown how an electronically steerable parasitic array radiator (ESPAR) antenna can be used for 2-D direction-of-arrival (DoA) estimation employing received signal strength (RSS) values only. The proposed approach relies on changes in RSS values recorded at the antenna output port observed for different vertical and horizontal directions, while antenna’s main beam sweeps 360° area around the ESPAR antenna. Based...
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DYNAMIC RESPONSE OF FORUM GDANSK STRUCTURE DUE TO RAIL TRAFFIC
PublikacjaThe paper presents the study of the impact of vibration induced by the movement of the railway rolling stock on the Forum Gdańsk structure. This object is currently under construction and is located over the railway tracks in the vicinity of the Gdańsk Główny and Gdańsk Śródmieście railway stations. The analysis covers the influence of vibrations on the structure itself and on the people within. The in situ measurements on existing...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Reactive imines: Addition of 2-aminopyrimidine to the imine bond and isolation of the aminal from the equilibrium mixture aminal/imine
PublikacjaThe reaction between o-vanillin and 2-aminopyrimidine leads to the formation of a single crystalline product: aminal, 1, which results from the reaction of the initially formed imine with 2-aminopyrimidine. The reaction was followed by the NMR spectroscopy. VT NMR studies prove that in solution two major species are observed: aminal and imine and their ratio depends on the time or/and temperature with the imine content increasing...
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Accuracy assessment of mobile satellite measurements in relation to the geometrical layout of rail tracks
PublikacjaThe paper presents the campaigns of mobile satellite measurements, carried out in 2009–2015 on the railway and tram lines. The accuracy of the measurement method has been analysed on the basis of the results obtained in both horizontal and vertical planes. The track axis deviation from the defined geometric shape has been analysed in the areas clearly defined in terms of geometry, i.e. on the straight sections and sections with...
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Effective Air Quality Prediction Using Reinforced Swarm Optimization and Bi-Directional Gated Recurrent Unit
PublikacjaIn the present scenario, air quality prediction (AQP) is a complex task due to high variability, volatility, and dynamic nature in space and time of particulates and pollutants. Recently, several nations have had poor air quality due to the high emission of particulate matter (PM2.5) that affects human health conditions, especially in urban areas. In this research, a new optimization-based regression model was implemented for effective...
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Discussion on “Dynamic soil-structure interaction: A three-dimensional numerical approach and its application to the Lotung case study”. Poor performance of the HSS model
PublikacjaThe Hardening Soil Small (HSS) is a constitutive model being extension to the well established Hardening Soil Model (HS) accounting for the nonlinearity of small strain stiffness. It is implemented in commercial finite element computer codes for geotechnical analyses and used widely in research and design. The article deals with a problem known as overshooting after very small load reversals. It induces much higher stiffness than...
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Automated Reduced Model Order Selection
PublikacjaThis letter proposes to automate generation of reduced-order models used for accelerated -parameter computation by applying a posteriori model error estimators. So far,a posteriori error estimators were used in Reduced Basis Method (RBM) and Proper Orthogonal Decomposition (POD) to select frequency points at which basis vectors are generated. This letter shows how a posteriori error estimators can be applied to automatically select...
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In the search for experimental and quantumchemical evidence for zwitterionic nature of (2 E )-3-[4-(dimethylamino)phenyl]-2-nitroprop-2-enenitrile – An extreme example of donor–π–acceptor push–pull molecule
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublikacjaHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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Accuracy Investigations of Turbine Blading Neural Models Applied to Thermal and Flow Diagnostics
PublikacjaPossibility of replacing computional fluid dynamics simulations by a neural model for fluid flow and thermal diagnostics of steam turbines is investigated. Results of calculations of velocity magnitude of steam for 3D model of the stator of steam turbine is presented.
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System of monitoring of the Forest Opera in Sopot structure and roofing
PublikacjaThe authors present a solution realized in Forest Opera (name in Polish: Opera Leśna) in Sopot (Poland) in connection with the modernization and construction of a new roof. The complicated structure of the roof of the facility and the used covering in form of membrane made of technical fabric required (for security reasons) to install the unit of devices allowing for the continuous geodetic monitoring of the facility. Monitoring...
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublikacjaThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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The Synthesis of 3-Amino-pyrazine-2-carbohydrazide and 3-Amino-N'-methylpyrazine-2-carbohydrazide Derivatives
PublikacjaW poszukiwaniu biologicznie aktywnych związków otrzymano szereg pochodnych 3-Amino-pirazyno-2-karbohydrazydu i 3-Amino-N'-metylopirazyno-2-karbohydrazydu w wyniku reakcji hydrazydu aminopirazynoinowegokwasu z izocyjanianami, aldehydami, ketonami, CS2 i kwasem mrówkowym.
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Survival time prognosis under a Markov model of cancer development
PublikacjaIn this study we look at a breast cancer data set of women from Pomerania region collected in year 1987-1992 in the Medical University of Gdańsk. We analyze the clinical risk factors in conjunction with Markov model of cancer development. We evaluate Artificial Neural Network (ANN) survival time prediction via a simulation study.
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Lateral forces determine dimensional accuracy of the narrow‑kerf sawing of wood
PublikacjaThe shrinking global forest area limits the supply of industrially usable raw resources. This, in combination with the ever‑increasing consumption of timber due to population growth can lead to the lack of a positive balance between the annual volumetric growth and consumption of wood. An important innovation toward increasing environmental and economic sustainability of timber production is to reduce the volume of wood residues...
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Remote communication in Scrum teams - a COVID-19 preventive measure or work time optimisation?
PublikacjaThe article presents the impact of remote work, resulting from the COVID-19 pandemic, on the functioning of Scrum teams. Attempts have been made to analyse the positive and negative aspects of remote work. The article also looks at the impact of remote work on the level of communication and efficiency of Scrum teams. For this purpose, the author conducted research on a sample of 40 organisations that declared to use Scrum methodology,...
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Electrochemical simulation of metabolism for antitumor-active imidazoacridinone C-1311 and in silico prediction of drug metabolic reactions
PublikacjaThe metabolism of antitumor-active 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) has been investigated widely over the last decade but some aspects of molecular mechanisms of its metabolic transformation are still not explained. In the current work, we have reported a direct and rapid analytical tool for better prediction of C-1311 metabolism which is based on electrochemistry (EC) coupled on-line with electrospray...
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Prediction of energy consumption and evaluation of affecting factors in a full-scale WWTP using a machine learning approach
PublikacjaTreatment of municipal wastewater to meet the stringent effluent quality standards is an energy-intensive process and the main contributor to the costs of wastewater treatment plants (WWTPs). Analysis and prediction of energy consumption (EC) are essential in designing and operating sustainable energy-saving WWTPs. In this study, the effect of wastewater, hydraulic, and climate-based parameters on the daily consumption of EC by...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublikacjaDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublikacjaDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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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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Reconstruction of 3D structure of positive corona streamer by local methods
PublikacjaThe computer algorithms were used for reconstruction of streamer 3D structure. We propose the 3D tree structure model of corona discharge streamer composed with nodes and edges between chosen couples of nodes, which enables easy computation of some important parameters ofstreamers. The 3D model can be derived directly from two projection images by global methods like evolutionary searching or particle simulations. In this paper...
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Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublikacjaIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
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Quality Control of Bacterial Extracellular Vesicles with Total Protein Content Assay, Nanoparticles Tracking Analysis, and Capillary Electrophoresis
PublikacjaExtracellular vesicles (EVs) were isolated from Pectobacterium zantedeschiae culturing media using direct ultracentrifugation (UC), iodixanol cushion ultracentrifugation (ICUC), and iodixanol density gradient ultracentrifugation (IDGUC) techniques. The isolates were characterized with total protein content assay (bicinchoninic acid assay, BCA), nanoparticles tracking analysis (NTA), and capillary electrophoresis (CE). A satisfactory...
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Deposition of phosphate coatings on titanium within scaffold structure
PublikacjaPurpose: Existing knowledge about the appearance, thickness, and chemical composition of phosphate coatings on titanium inside porous structures is insufficient. Such knowledge is important for the design and fabrication of porous implants. Methods: Metallic scaffolds were fabricated by selective laser melting of 316L stainless steel powder. Phosphate coatings were deposited on Ti sensors placed either outside the scaffolds or...
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Minimal 2-dominating sets in Trees
PublikacjaWe provide an algorithm for listing all minimal 2-dominating sets of a tree of order n in time O(1.3247^n). This leads to that every tree has at most 1.3247^n minimal 2-dominating sets. We also show that thisbound is tight.
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Investigating COVID-19 active pharmaceutical ingredients (APIs) degradation using Peroxydisulfate/FeMnOx binary metal oxide/Ultrasound System
PublikacjaDegradation of Favipiravir using a hybrid system of peroxydisulfate, FeMnOx binary metal oxide, and ultrasound irradiation was studied. A novel catalyst was synthesized with deep eutectic solvent (DES). The effects of DES type on catalytic performance was evaluated and the catalysts were characterized using XRD, SEM, BET, XPS, and EDS. DES-based catalysts exhibited higher efficiency due to structure change, surface area enhancement...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...