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Search results for: residue arithmetic
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy 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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A study on the protection of methionine and the reduction of methionine sulfoxide in methionine-containing analogues of the growth-modeling factor Gly-His-Lys
PublicationThe protection of methionine and the reduction of methionine sulfoxide in methionine-containing analogues of Gly-His-Lys are described. The peptides were synthesized by a solid-phase method using the standard Fmoc procedure. Simultaneous deprotection of the peptide side chain and liberation from the resin were achieved using an appropriate TFA cocktail. The TFA cocktail was selected to minimize oxidation of the methionine residue....
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Structural features responsible for control of the eukaryotic GlcN-6-P synthase activity
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. As UDP-GlcNAc, the final product of the hexosamine path, constitutes one of the essential substrates for assembly of bacterial and fungal cell walls, the enzyme is an interesting target for antimicrobial therapy.The structure of E. coli enzyme, known since 2001, forms a dimer of two identical...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Functionalized azobenzocrown ethers as sensor materials—The synthesis and ion binding properties
PublicationNew 13- and 16-membered azobenzocrown ethers with aromatic amino, amide, ether–ester or ether–amide residue in para position to an azo moiety were obtained. Acid–base properties and ion binding ability of the colored compounds were studied by spectroscopic methods: UV–vis, fluorimetry and 1H NMR spectroscopy. Selected azobenzocrowns were tested as ionophores in ion-selective membrane electrodes (ISEs) – classic and miniature all...
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Ionic liquids in extraction techniques: Determination of pesticides in food and environmental samples
PublicationThe intensive use of pesticides in agricultural practices has promoted the appearance of environmentaland public health problems. Due to that, scientists face challenges with developing simple, fast, sensitive,selective, and low-cost methods dedicated to determining pesticide residues in food and environmentalsamples. Following thefifth principle of Green Analytical Chemistry, chemists are searching for greeneralternatives for...
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Implementation of Extended Kalman Filter with Optimized Execution Time for Sensorless Control of a PMSM Using ARM Cortex-M3 Microcontroller
PublicationThis paper addresses the implementation and optimization of an Extended Kalman Filter (EKF) for the Permanent Magnet Synchronous Motor (PMSM) sensorless control using an ARM Cortex-M3 microcontroller. A various optimization levels based on arithmetic calculation reduction was implemented in ARM Cortex-M3 microcontroller. The execution time of EKF estimator was reduced from 260.4 μs to 37.7 μs without loss of accuracy. To further...
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Improved model of isothermal and incompressible fluid flow in pipelines versus the Darcy–Weisbach equation and the issue of friction factor
PublicationIn this article, we consider the modelling of stationary incompressible and isothermal one-dimensional fluid flow through a long pipeline. The approximation of the average pressure in the developed model by the arithmetic mean of inlet and outlet pressures leads to the known empirical Darcy–Weisbach equation. Most importantly, we also present another improved approach that is more accurate because the average pressure is estimated...
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A new quaternion-based encryption method for DICOM images
PublicationIn this paper, a new quaternion-based lossless encryption technique for digital image and communication on medicine (DICOM) images is proposed. We have scrutinized and slightly modified the concept of the DICOM network to point out the best location for the proposed encryption scheme, which significantly improves speed of DICOM images encryption in comparison with those originally embedded into DICOM advanced encryption standard...
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GPU-Accelerated Finite-Element Matrix Generation for Lossless, Lossy, and Tensor Media [EM Programmer's Notebook]
PublicationThis paper presents an optimization approach for limiting memory requirements and enhancing the performance of GPU-accelerated finite-element matrix generation applied in the implementation of the higher-order finite-element method (FEM). It emphasizes the details of the implementation of the matrix-generation algorithm for the simulation of electromagnetic wave propagation in lossless, lossy, and tensor media. Moreover, the impact...
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Microwave assisted liquefaction with crude glycerol as a potential method of brewer's spent grain utylization
PublicationBrewer's spent grain was applied as a low-cost industrial type of lignocellulose biomass in a liquefaction and solvent: biomass ratio on the efficiency of the process, chemical structure and basic properties of obtained prepared polyols and soil residues shed light on the biomass degradation mechanism through application of microwaves and further reaction of degradation products with solvent particles.
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The speciation of selected heavy metals in sewage sludge stabilized in reed basins
PublicationThe aim of the work was to determine influence of time on organic matter content, nutrients concentrations as well as speciation of selected heavy metals (Cd, Pb, Ni, Cr, Cu and Zn) in sewage sludge stabilized in reed basins during 7-15 years. The analyzed sewage sludge was collected from reed basins from four municipal WWTPs located in Denmark serving from 9 000 to 40 000 pe in Vallo, Rudkøbing, Nakskov and Helsinge. Sewage...
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Design of new cholinesterase inhibitors based on phosphorus analogs of tacrine as potential anti-Alzheimer’s disease agents
PublicationBased on the analysis of the determined free binding energy (using the AutoDock Vina 1.1.2 docking program), the most potent cholinesterase inhibitors were selected. Moreover, studies of 3D visualization of the results of molecular modeling led to the identification of potential sites for the interaction of new potential inhibitors with amino acid residues building active sites of investigated cholinesterases.
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Generalized Dold sequences on partially-ordered sets
PublicationDold sequences constitute an important class of integer sequences that play an important role in combinatorics, number theory, topology and dynamical systems. We generalize the notion of Dold sequence for the case of partially ordered sets and describe their properties. In particular we give two alternative descriptions of generalized Dold sequences: by some class of elementary sequences as well as by different...
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Surface Roughness Evaluation in Thin EN AW-6086-T6 Alloy Plates after Face Milling Process with Different Strategies
PublicationLightweight alloys made from aluminium are used to manufacture cars, trains and planes. The main parts most often manufactured from thin sheets requiring the use of milling in the manufacturing process are front panels for control systems, housing parts for electrical and electronic components. As a result of the final phase of the manufacturing process, cold rolling, residual stresses remain in the surface layers, which can influence...
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Conserved motifs of MutL proteins
PublicationtThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...
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Influence of friction stir welding technological parameters on the properties of the joints of selected aluminum alloys
PublicationThe purpose of this dissertation was to determine the effect of friction stir welding technological parameters on the properties of selected aluminum alloy joints, with consideration of the residual stresses and dislocation density in the joints. The goal of the present work was also to produce defect-free joints with high mechanical and electrochemical properties. In the dissertation, similar welds of AA6082 alloy and dissimilar...
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Simple colorimetric copper(II) sensor – spectral characterization and possible applications
PublicationNew o-hydroxyazocompound L bearing pyrrole residue was obtained in the simple synthetic protocol. The structure of L was confirmed and analyzed by X-ray diffraction. It was found that new chemosensor can be successfully used as copper(II) selective spectrophotometric regent in solution and can be also applied for the preparation of sensing materials generating selective color signal upon interaction with copper(II). Selective colorimetric...
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Comparison of Average Energy Slope Estimation Formulas for One-dimensional Steady Gradually Varied Flow
PublicationTo find the steady flow water surface profile, it is possible to use Bernoulli’s equation, which is a discrete form of the differential energy equation. Such an approach requires the average energy slope between cross-sections to be estimated. In the literature, many methods are proposed for estimating the average energy slope in this case, such as the arithmetic mean, resulting in the standard step method, the harmonic mean and...
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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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An Attempt to Create Speech Synthesis Model That Retains Lombard Effect Characteristics
PublicationThe speech with the Lombard effect has been extensively studied in the context of speech recognition or speech enhancement. However, few studies have investigated the Lombard effect in the context of speech synthesis. The aim of this paper is to create a mathematical model that allows for retaining the Lombard effect. These models could be used as a basis of a formant speech synthesizer. The proposed models are based on dividing...
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A review of phosphorus recovery methods at various steps of wastewater treatment and sewage sludge management. The concept of “no solid waste generation” and analytical methods
PublicationPhosphorus deposits around the world are rapidly depleting, therefore phosphorus recovery methods are gaining more and more interest both in science and industry. This article presents the main methods of phosphorus recovery from sewage sludge. The described approaches are divided in two groups: phosphorus recovery from sewage sludge and leachate, and recovery of phosphorus from sewage sludge ashes. The latter seems to have more...
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Expert opinion on the effectiveness of protection against electric shock in case of fault in an installation for electric vehicles charging
PublicationThe opinion concerns the use of residual current devices for protection against electric shock by automatic disconnection of supply in a Norwegian installation intended for charging of electric vehicles.
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Sensitivity analysis of critical loads of I-columns
PublicationThe first order variation of critical buckling load of thin-walled columns with bisymmetric open cross-section due to some variations of the design variables such as: cross-section dimensions, or material characteristics is derived. The influence of the residual welding stresses is taken into account. In the numerical examples dealing with I-column the functions describing the effect of the variation of the dimensions of the flange...
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Structural, functional, and stability change predictions in human telomerase upon specific point mutations,
PublicationOverexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation,...
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Laser Beam as a Precision Tool to Increase Fatigue Resistance in an Eyelet of Undercarriage Drag Strut
PublicationThe article contains the results of tests on a laser-processed eyelet of undercarriage drag strut to increase its fatigue strength. Laser processing concentrated on both sides around the hole of eye for connecting the undercarriage drag strut caused that the material in this area withstood more than twice the number of load cycles established for this material. In order to determine the reasons for the increase in fatigue strength,...
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Electric shock hazard in circuits with variable-speed drives
PublicationThe conventional approach to electrical safety under fault condition in typical power systems considers earth fault currents of sinusoidal waveform and frequency of 50/60 Hz. However, in circuits with variable-speed drives, there is earth fault current flow with harmonics, and these harmonics influence the threshold of ventricular fibrillation. The paper presents earth fault current waveforms in circuits with variable-speed drives...
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A memory efficient and fast sparse matrix vector product on a Gpu
PublicationThis paper proposes a new sparse matrix storage format which allows an efficient implementation of a sparse matrix vector product on a Fermi Graphics Processing Unit (GPU). Unlike previous formats it has both low memory footprint and good throughput. The new format, which we call Sliced ELLR-T has been designed specifically for accelerating the iterative solution of a large sparse and complex-valued system of linear equations arising...
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A highly-efficient technique for evaluating bond-orientational order parameters
PublicationWe propose a novel, highly-efficient approach for the evaluation of bond-orientational order parameters (BOPs). Our approach exploits the properties of spherical harmonics and Wigner 3jj-symbols to reduce the number of terms in the expressions for BOPs, and employs simultaneous interpolation of normalised associated Legendre polynomials and trigonometric functions to dramatically reduce the total number of arithmetic operations....
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Secure Quaternion Feistel Cipher for DICOM Images
PublicationAn improved and extended version of a quaternion-based lossless encryption technique for digital image and communication on medicine (DICOM) images is proposed. We highlight and address several security flaws present in the previous version of the algorithm originally proposed by Dzwonkowski et al. (2015). The newly proposed secure quater- nion Feistel cipher (S-QFC) algorithm...
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Azo and azoxythiacrown ethers: synthesis and properties
PublicationA series of 16- and 18-membered azo- and azoxythiacrown ethers have been synthesized by reductive macrocyclization of the respective bis(nitrophenoxy)oxaalkanes. The aromatic residues located in the polyether region of the molecule were introduced to macrocyclic skeletons and their affinities toward different groups of metal cations in ion-selective electrodes were described. X-ray structures for one dinitropodand and one azoxybenzothiacrown...
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Simulation of the remanence influence on the transient states in a single-phase multiwinding transformer
PublicationThis paper presents the mathematical model of a single-phase multi-winding core type transformer taking into account magnetic hysteresis phenomenon based on the feedback Preisach model (FPM). The set of loop differential equations was developed for a K-th winding transformer model where the flux linkages of each winding includes flux Φ common to all windings as a function of magneto motive force Θ of all windings. The first purpose...
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Verification and Benchmarking in MPA Coprocessor Design Process
PublicationThis paper presents verification and benchmarking required for the development of a coprocessor digital circuit for integer multiple-precision arithmetic (MPA). Its code is developed, with the use of very high speed integrated circuit hardware description language (VHDL), as an intellectual property core. Therefore, it can be used by a final user within their own computing system based on field-programmable gate arrays (FPGAs)....
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1,3,4-Thiadiazole-based diamides: Synthesis and complexation properties
PublicationAromatic diamides, derivative of 2,6-pyridinedicarboxylic acid and isophthalic acid, bearing 1,3,4-thiadiazole residue were prepared with satisfactory yields in conventional procedures and microwave stimulated reactions. X-ray structure of N,N-bis (1,3,4-thiadiazol-2-yl)-2,6-pyridinedicarboxamide (2) DMSO solvate (2DMSO) was described. Selective zinc(II), lanthanum(III), terbium(III) and L-tyrosine recognition was found for N,N-bis(1,3,4-thiadiazol-2-yl)-2,6-pyridinedicarboxamide...
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Determination of pharmaceuticals in fish: method optimization and occurrence in different species from Mediterranean rivers
PublicationThe multi-residue analytical method developed, based on accelerated solvent extraction, gel permeation chromatography purification and UPLC-MS/MS analysis allowed the simultaneous determination of 21 pharmaceuticals. Recoveries obtained for most of the target compounds were higher than 50%. The application of UPLC-MS/MS operating in the MRM mode, with two transitions monitored for each compound, provided good sensitivity and selectivity....
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Binuclear Co(II), Zn(II) and Cd(II) tri-tert-butoxysilanethiolates. Synthesis, crystal structure and spectroscopic studies.
PublicationA series of Co(II), Zn(II) and Cd(II) complexes have been synthesized in reaction of respective metal tri-tert-butoxysilanethiolates with pyrazine 1 and 2 and 1,2-bis(2-pyridyl)ethylene 3–5. All compounds have been characterized by single-crystal X-ray structure determination, elemental analysis, FT-IR and thermogravimetry. Obtained complexes are bimetallic with the formula of [M{SSi(OtBu)3}2(μ-L)]2 and metal ions bridged by N,N′-spacer....
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Vascular stents - materials and manufacturing technologies
PublicationThe objective of this article is to present materials and technology for the manufacture of vascular stents with appropriate design requirements. The use of the right material is very important in implantology. A biomaterial introduced into the circulatory system must be biocompatible and hemocompatible. At the same time, it should not initiate toxic, mutagenic, or immunological reactions. Currently, 316L stainless steel (316L...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublicationNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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Three-Dimensional Fractography for Conventional and Additive Manufactured Steels After Bending-Torsion Fatigue
PublicationIn this study, fracture surface topography parameters were measured to investigate the effects of multiaxial loading. In order to assess the metrological aspects of fracture for notched specimens made of high-strength steels processed by both conventional and additively manufacturing (AM) techniques, an optical surface profilometer was used. Three bending moment to torsion moment ratios (B/T) were studied, i.e. 2, 1 and 2/3. The...
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Roller burnishing
PublicationThe paper shows the process of roller burnishing as a method of finishing machine components. Based on own research the author presents the effects of the roller burnishing process to increase the hardness and residual stress as well as the wear and fatigue strength of burnishing components.
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Generic invariant measures for iterated systems of interval homeomorphisms
PublicationIt is well known that iterated function systems generated by orientation preserving homeomorphisms of the unit interval with positive Lyapunov exponents at its ends admit a unique invariant measure on (0, 1) provided their action is minimal. With the additional requirement of continuous differentiability of maps on a fixed neighbourhood of {0,1} { 0 , 1 } , we present a metric in the space of such systems which renders it complete....
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Tuning matrix-vector multiplication on GPU
PublicationA matrix times vector multiplication (matvec) is a cornerstone operation in iterative methods of solving large sparse systems of equations such as the conjugate gradients method (cg), the minimal residual method (minres), the generalized residual method (gmres) and exerts an influence on overall performance of those methods. An implementation of matvec is particularly demanding when one executes computations on a GPU (Graphics...
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Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-D-Galactosidase from Arthrobacter sp. 32cB
PublicationB-Galactosidase from Arthrobacter sp. 32cB (ArthbetaDG) is a cold-adapted enzyme able to catalyze hydrolysis of beta-D-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthbetaDG D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to...
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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A new Toxoplasma gondii chimeric antigen containing fragments of SAG2, GRA1, and ROP1 proteins—impact of immunodominant sequences size on its diagnostic usefulness
PublicationThis study presents the first evaluation of new Toxoplasma gondii recombinant chimeric antigens containing three immunodominant regions of SAG2, GRA1, and one of two ROP1 fragments differing in length for the serodiagnosis of human toxoplasmosis. The recombinant chimeric antigens SAG2-GRA1-ROP1L (with large fragment of ROP1, 85-396 amino acid residues) and SAG2-GRA1-ROP1S (with a small fragment of ROP1, 85-250 amino acid residues)...
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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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Investigation of long-range dependencies in the stochastic part of daily GPS solutions
PublicationThe long-range dependence (LRD) of the stochastic part of GPS-derived topocentric coordinates change (North, East, Up) results with relatively high autocorrelation values with a focus on self-similarity. One of the reasons for such self-similarity in the GPS time series are noises that are commonly recognised to prevail in the form of the flicker noise model. To prove the self-similarity of the stochastic part of GPS time series...
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Influence of laser processing of the low alloy medium carbon structural steel on the development of the fatigue crack
PublicationThe paper contains the results of the structural analysis, hardness tests and fatigue tests conducted for the medium carbon structural steel with low content of Cr and Ni after its processing with CO2 laser beam. Pre-cracks were made in the round compact tension (RCT) specimen used for fatigue test. Next, four paths, parallel to each other, were melted on both sides of the samples using a laser beam. The paths were perpendicular...
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The biological role of prolyl oligopeptidase and the procognitive potential of its peptidic inhibitors from food proteins
PublicationProlyl 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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One-step recovery of REE oxalates in electro-leaching of spent NdFeB magnets
PublicationRecovery of rare-earth elements (REEs) from spent NdFeB magnets is receiving great attention because of high amount of neodymium and potential risk of environmental pollution. In this study, a novel environment-friendly hydrometallurgical route is proposed for efficient recovery of REEs during electrochemical leaching with sulfuric and oxalic acids. With proper adjustment of the electrolyte composition and operating conditions,...