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Search results for: COVID-19 MOLECULAR DOCKING MULTI-EPITOPES VACCINESMM-PBSA/MM-GBSA ANALYSIS SARS-COV-2 VARIANTS
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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Multi-objective design of miniaturized impedance transformers by domain segmentation
PublicationFast multi-objective design optimization of compact microstrip impedance transformers is discussed. Our approach exploits approximation models constructed using sampled coarse- mesh EM simulation data in a partitioned design space and response correction techniques for design refinement. Demonstra
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DNA variants in Helicobacter pylori infected patients with chronic gastritis, dysplasia and gastric cancer
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DNA Variants in Helicobacter Pylori Infected Patients with Chronic Gastritis, Dysplasia and Gastric Cancer
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Drug transporter expression profiling in chemoresistant variants of the A2780 ovarian cancer cell line
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Association between Age at Diagnosis of Graves' Disease and Variants in Genes Involved in Immune Response
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Syntheses and structures of the first terminal phosphanylphosphido complex of hafnium [cp2hf(cl){η1-(me3si)p-p(net2)2}] and the firstzirconocene-phosphanylphosphinidene dimer [cp2zr{μ2-p-p(net2)2}2zrcp2]
PublicationReactions of (Et2N)2P-P(SiMe3)Li with [Cp2MCl2] (M= Zr, Hf) in toluene or pentane yield the related terminal phosphanylphosphido complexes [Cp2M(Cl){η1-(Me3Si)P-P(NEt2)2}]. The solid statestructure of [Cp2Hf(Cl){η1-(Me3Si)P-P(NEt2)2}] was established by single crystal X-ray diffraction. The reaction of (Et2N)2P-P(SiMe3)Li with [Cp2ZrCl2] in THF or DME solutions leads to the formationof deep red crystals of the first neutral diamagnetic...
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Low-cost multi-objective design of compact microwave structures using domain patching
PublicationA good compromise between size and electrical performance is an important design consideration for compact microwave structures. Comprehensive information about size/performance trade-offs can be obtained through multi-objective optimization. Due to considerable electromagnetic (EM) cross-couplings in highly compressed layouts, the design process has to be conducted at the level of high-fidelity EM analysis which is computationally...
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Structural Insights into Autoreactive Determinants in Thyroid Peroxidase Composed of Discontinuous and Multiple Key Contact Amino Acid Residues Contributing to Epitopes Recognized by Patients’ Autoantibodies
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Multi-criterion decision making in distributed systems by quantum evolutionary algorithms
PublicationDecision making by the AQMEA (Adaptive Quantum-based Multi-criterion Evolutionary Algorithm) has been considered for distributed computer systems. AQMEA has been extended by a chromosome representation with the registry of the smallest units of quantum information. Evolutionary computing with Q-bit chromosomes has been proofed to characterize by the enhanced population diversity than other representations, since individuals represent...
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Electron-impact dissociation of molecular hydrogen: benchmark cross sections
PublicationWe present a joint experimental and theoretical investigation of a fundamental process in atomic and molecular physics: electron impact excitation of molecular hydrogen’s (H2) most dominant transition (X1Σg+ → b3Σu+). Excitation of this state is by far the main channel that causes the dissociation of H2 into H + H atoms at low energies. The Convergent Close-Coupling (CCC) calculations predicted significant, more than factor of...
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From Scores to Predictions in Multi-Label Classification: Neural Thresholding Strategies
PublicationIn this paper, we propose a novel approach for obtaining predictions from per-class scores to improve the accuracy of multi-label classification systems. In a multi-label classification task, the expected output is a set of predicted labels per each testing sample. Typically, these predictions are calculated by implicit or explicit thresholding of per-class real-valued scores: classes with scores exceeding a given threshold value...
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Synthesis and structural characterization of novel 2-benzimidazolylthioureas: adducts of natural isothiocyanatesand 2-amino-1-methylbenzimidazole
PublicationNa drodze syntezy chemicznej uzyskano addukty naturalnych izotiocyjanianów - alilu, benzylu i fenyloetylu i 2-amino-1-metylobenzoimidazolu. W następstwie optymalizacji warunków reakcji, poszczególne 2-benzimidazolilotiomoczniki otrzymano produkty z umiarkowanymi wydajnościami. Strukturę molekularną i krystaliczną produktów scharakteryzowano przy użyciu metod spektroskopowych i X-ray. Analiza uzyskanych widm pozwoliła stwierdzić,...
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublicationStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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A multi-criteria decision model for the introduction of electric storage multiple units on the partially electrified Gdynia-Hel railway
Publication: In this article a multi-criteria study of the use of independently powered electric multiple units on the partially electrified Gdynia Główna - Hel line was carried out. The use of (currently used) diesel and, as an alternative, electric and electric multiple units with an electric energy storage was considered. The analysis was carried out on the basis of three criteria for assessing the route service options, i.e. environmental,...
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Enhancement of lift and drag performances of a NACA0012 airfoil by multi-DBD plasma actuator with additional floating interelectrodes
PublicationIt is clear that the improvement of aircraft aerodynamic performances is currently and will continue to be a significant area of research for the aeronautical industry. The current study is focused on theenhancement of aerodynamic airfoil performances by using a multi-DBD plasma actuator mounted around the model leading-edge. Experiments have been conducted at the University of Orleans, in the 2 m x 2 m test section of a large...
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Pyrolysis of poly(2-propylheptyl acrylate)
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE 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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Topochemical, Single‐Crystal‐to‐Single‐Crystal [2+2] Photocycloadditions Driven by Chalcogen‐Bonding Interactions
PublicationThe face-to-face association of (E)-1,2-di(4-pyridyl)ethylene (bpen) molecules into rectangular motifs stabilized for the first time by chalcogen bonding (ChB) interactions is shown to provide photoreactive systems leading to cyclobutane formation through single-crystal-to-single-crystal [2+2] photodimerizations. The chelating chalcogen bond donors are based on original aromatic, ortho-substituted bis(selenocyanato)benzene derivatives...
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The new investing effectiveness evaluation multi-criteria method in modern supply systems
PublicationThe important problem in the processes of modelling and programming the development of sustainable energy sector is the multi-criteria manner of assessing the effectiveness of investments. The goal of this paper is to show how to take into account the impact of investments in multidimensional modelling decision-making processes. This goal can be achieved through the development, presentation, and use of a new multi-criteria method...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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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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An application of multi-agent system for ship’s power systems design
PublicationDesign process of transport ship power system consists of structure (topology) and component elements selection. Compliance with the requirements for static components does not guarantee optimal dynamic characteristics of entire power system. Design steps are difficult to formalize and as a consequence to this reason expert and multi-agent systems are used for solving selected design issues. In the paper distributed multi-agent...
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History-based dynamic weight voting for multi-agent systems
PublicationTaking decision in multi-agent systems may involve voting. Two basic voting protocols are surveyed in the paper. Then, a new history-based dynamic weight voting is proposed. This voting protocol allows for identification of the agents which contribute to the correct system decision. The proposed solution is contrasted with majority voting and with weighted average voting, to show its advantages
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Compact broadband multi-way 1:6 power divider
PublicationThis paper introduces a design flow of a microstrip multi-way 1:6 power divider incorporating photonic bandgap (PBG) structures. Themethod proposed has enabled the achievement of considerable miniaturization (15%) together with transmission characteristics enhancement(141% bandwidth). Measured results show significant similarity to theoretical characteristics, which proves the attractiveness of presented design methodology.
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Solving highly-dimensional multi-objective optimization problems by means of genetic gender
PublicationPaper presents a computational optimization study using a genetic gender approach for solving multi-objective optimization problems of detection observers. In this methodology the information about an individual gender of all the considered solutions is applied for the purpose of making distinction between different groups of objectives. This information is drawn out of the fitness of individuals and applied during a current parental...
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Solving highly-dimensional multi-objective optimization problems by means of genetic gender
PublicationPaper presents a computational optimization study using a genetic gender approach for solving multi-objective optimization problems of detection observers. In this methodology the information about an individual gender of all the considered solutions is applied for the purpose of making distinction between different groups of objectives. This information is drawn out of the fitness of individuals and applied during a current parental...
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Expedited Simulation-Driven Multi-Objective Design Optimization of Quasi-Isotropic Dielectric Resonator Antenna
PublicationMajority of practical engineering design problems require simultaneous handling of several criteria. Although many of design tasks can be turned into single-objective problems using sufficient formulations, in some situations, acquiring comprehensive knowledge about possible trade-offs between conflicting objectives may be necessary. This calls for multi-objective optimization that aims at identifying a set of alternative, Pareto-optimal...
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Multi-Beam Antenna for Ka-Band CubeSat Connectivity Using 3-D Printed Lens and Antenna Array
PublicationIn this paper, the design of a passive multi-beam lens antenna is proposed for the CubeSat space communication system as an alternative application of a 2-D microstrip antenna array that has originally been designed for a 39 GHz 5 G MU-MIMO system. The half-ellipsoid lens is 3-D printed using stereolithography (SLA) technology. The antenna prototype is capable of selecting the main beam between 16 different directions with a gain...
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Selective Harmonic Elimination PWM For a Cascaded Multi-level Inverter
PublicationThis paper deals with the selective harmonic elimination pulse width modulation (SHE-PWM) technique. This technique is used for the elimination of selected dominant low order harmonics in the multi-level inverter output voltage. The presence of these harmonics is the essential drawback of such kind of inverters; especially when it is used for the control of different AC drivers. The SHE-PWM is based...
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Bandwidth-size design trade-offs for compact spline-parameterised patch couplers by means of electromagnetic-driven multi-objective optimisation
PublicationBroad bandwidth and small size are the key performance figures for contemporary microwave couplers. These requirements are conflicting, i.e. improvement of one generally leads to degradation of the other assuming fixed topology of the circuit at hand. From a designer's perspective, the knowledge about available design trade-offs is indispensable as it permits for tailoring the circuit for particular applications as well as comparing...
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Implementation of multi-operand addition in FPGA using high-level synthesis
PublicationThe paper presents the results of high-level synthesis (HLS) of multi-operand adders in FPGA using the Vivado Xilinx environment. The aim was to estimate the hardware amount and latency of adders described in C-code. The main task of the presented experiments was to compare the implementations of the carry-save adder (CSA) type multi-operand adders obtained as the effect of the HLS synthesis and those based on the basic component...
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Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublicationThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
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Synthesis and hydrogen evolving catalysis of a panchromatic photochemical molecular device
PublicationA dinuclear hydrogen evolution photocatalyst [(tbbpy)2Os(tpphz)PtI2](PF6)2 (tbbpy = 4,4′-tert-butyl-2,2′-bipyridine; tpphz = tetrapyrido[3,2-a:2′,3′-c:2′′,3′′-h:2′′′,3′′′-j]phenazine) is synthesized in order to make use of the broader range of visible light absorption mitigated by the osmium center. In a first step, the activity of the complex for hydrogen evolution is investigated by evaluating the role of different electron donors...
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The melatonin-producing system is fully functional in retinal pigment epithelium (ARPE-19)
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
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Chitosan-Based Membranes as Gentamicin Carriers for Biomedical Applications — Influence of Chitosan Molecular Weight
PublicationOver the past decade, much attention has been paid to chitosan as a potential drug carrier because of its non-toxicity, biocompatibility, biodegradability and antibacterial properties. The effect of various chitosan characteristics on its ability to carry different antibiotics is discussed in the literature. In this work, we evaluated the influence of the different molecular weights of this polymer on its potential as an antibacterial...
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Analysis of Roughness, the Material Removal Rate, and the Acoustic Emission Signal Obtained in Flat Grinding Processes
PublicationIn this work, the analysis of the acoustic emission (AE) signal in grinding processes is addressed. The proposed analysis method decomposes the acoustic signal into three frequency ranges. The total energy of each range is determined, as well as the highest frequency. Different grinding experiments were carried out, according to a full factorial design of experiments (DOE), in which feed speed, depth of cut, and transversal step...
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Head movement compensation algorithm in multi-display communication by gaze
PublicationAn influence of head movements on the gaze estimation accuracy when using a head mounted eye tracking system is discussed in the paper. This issue has been examined for a multi-display environment. It was found that head movement (rotation) to some extent does not influence on the gaze estimation accuracy seriously. Acceptable results were obtained when using eye-tracker to communicate with a computer via in two displays simultaneously.
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Spatial differentiation of road safety in Europe based on NUTS-2 regions
PublicationRoad safety varies significantly across the regions in Europe. To understand the factors behind this differentiation and the effects they have, data covering 263 NUTS-2 (Nomenclature of Territorial Units for Statistics) regions across Europe (European Union and Norway) have been analysed. The assessment was made using Geographically Weighted Regression (GWR). As a dependent variable the Road Fatality Rate (RFR – number of fatalities...
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Torque Transmitted by Multi-plate Wet Clutches in Relation to Number of Friction Plates and Their Dimensions
PublicationIn the paper results of experimental tests on multi-plate wet clutch torque capacity for various diameters and numbers of friction plates are presented. Construction of an apparatus for laboratory tests of wet clutch engagement, drag torque and maximum torque is shown. Methodology of maximum torque capacity experiment and hydraulic circuit diagram, which supplies a motor and an actuator for the experiment are described. Analytically...
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Multi-Channel Virtual Instrument for Measuring Temperature—A Case Study
PublicationThe article presents the hardware and software configuration of the developed multi-channel temperature measurement system as well as calibration procedures and measurement results verifying the properties of measurement channels. The system has been developed and dedicated primarily for measuring the temperature distribution in a laboratory model simulating underground power lines. With the adopted configuration of the analog...
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Surface sliding in human abdominal wall numerical models: Comparison of single-surface and multi-surface composites
PublicationDetermining mechanical properties of abdominal soft tissues requires a coupled experimental-numerical study, but first an appropriate numerical model needs to be built. Precise modeling of human abdominal wall mechanics is difficult because of its complicated multi-layer composition and large variation between specimens. There are several approaches concerning simplification of numerical models, but it is unclear how far one could...
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Crystal Growth, Structure, and Magnetism of the 2D Spin 1/2 Triangular Lattice Material Rb3Yb(PO4)2
PublicationThe single-crystal growth, crystal structure, heat capacity, and anisotropic magnetization characterization of Rb3Yb- (PO4)2, a Yb-based triangular lattice material, are presented. Single-crystal X-ray diffraction shows that Rb3Yb(PO4)2 exhibits [Yb(PO4)]∞ layers, with the Yb in an ordered plane of equilateral triangles. One phosphate group oxygen that is not a near neighbor of the magnetic Yb displays positional disorder. The...
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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublicationMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach
PublicationThe knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular,...
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Experimental investigation of thermal energy storage in shell-and-multi-tube unit with nano-enhanced phase change material
PublicationThis paper deals with thermal energy storage with use of nanoparticle enhanced phase change material in shell-and-multitube unit. The experiments are conducted under atmospheric pressure. Paraffin wax and two different fatty acids are used as base phase change material. Graphite and multi-walled carbon nanotubes serve as nanoparticles. Graphite nanoparticles are tested at the concentrations of 0.1%, 1% and 5% by weight, while multi-walled...
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Preference-based evolutionary multi-objective optimization in ship weather routing
PublicationIn evolutionary multi-objective optimization (EMO) the aim is to find a set of Pareto-optimal solutions. Such approach may be applied to multiple real-life problems, including weather routing (WR) of ships. The route should be optimal in terms of passage time, fuel consumption and safety of crew and cargo while taking into account dynamically changing weather conditions. Additionally it must not violate any navigational constraints...