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Search results for: single-stranded dna binding domain
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Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations
PublicationCalculations are reported for electron and positron scattering from isolated cytosine and thymine, where the two pyrimidinic single-ring DNA bases, in the gas-phase at energies near the elastic threshold, they reveal the special features of the dipole-driven scattering states. All molecules examined exhibit, in fact, supercritical (>1.67 D) permanent dipoles which can therefore also support, below threshold, excited bound compound...
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On root finding algorithms for complex functions with branch cuts
PublicationA simple and versatile method is presented, which enhances the complex root finding process by eliminating branch cuts and branch points in the analyzed domain. For any complex function defined by a finite number of Riemann sheets, a pointwise product of all the surfaces can be obtained. Such single-valued function is free of discontinuity caused by branch cuts and branch points. The roots of the new function are the same as the...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublicationAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...
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A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model
PublicationWe have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the...
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Estimation of time-frequency complex phase-based speech attributes using narrow band filter banks
PublicationIn this paper, we present nonlinear estimators of nonstationary and multicomponent signal attributes (parameters, properties) which are instantaneous frequency, spectral (or group) delay, and chirp-rate (also known as instantaneous frequency slope). We estimate all of these distributions in the time-frequency domain using both finite and infinite impulse response (FIR and IIR) narrow band filers for speech analysis. Then, we present...
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Nonlinear electrical properties of glass-ceramics nanocomposites containing ferroelectric nanocrystallites of Bi2VO5.5
PublicationNonlinear A.C. impedance measurements were conducted in the 50BiV-50SrBAlO nanocomposite as a function of frequency, temperature and A.C. voltage. This material is ferroelectric below temperature of 730 K, and above 730 K is a good ion-conductor. For this nanocomposite a low A.C. voltage of 1 V rms is enough to observe high nonlinearities. The origin of these nonlinear effects depends on the temperature and frequency. In the high...
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Synthesis, structural and spectroscopic properties of asymmetric schiff bases derived from 2,3-diaminopyridine
PublicationTwo Schiff base derivatives, 4-(2-amino-3-pyridyliminomethyl)phenol (I) and 3-(2-amino-3- pyridyliminomethyl)nitrobenzene (II ), were synthesised and characterised by spectroscopy. The structure of I was determined by single crystal X-ray diffraction studies. The asymmetric Schiff base derived from 2,3-diaminopyridine selectively recognise transition and heavy metal cations, and some anion. Ligands I and II form stable complexes...
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Call and Connections Times in ASON/GMPLS Architecture
PublicationIt is assumed that demands of information soci- ety could be satisfied by architecture ASON/GMPLS comprehended as Automatically Switched Optical Network (ASON) with Generalized Multi-Protocol Label Switching (GMPLS) protocols. Introduction this solution must be preceded by performance evaluation to guarantee society expectations. Call and connections times are in ASON/GMPLS architecture important for real-time applications. Practical...
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Resonance Frequency Calculation of a Multilayer and Multipatch Spherical Microstrip Structure Using a Hybrid Technique
PublicationThis communication offers a rigorous analysis of the resonance frequency problem of a spherical microstrip structure mounted on a multilayer, dielectric-coated metallic sphere, with an electrically small radius. The structure consists of single or multiple metallic patches with arbitrary shapes. A full-wave analysis is employed with the use of proposed hybrid approach, combining the finite-difference technique with a spectral domain...
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Anticancer imidazoacridinone C-1311 inhibits hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) and angiogenesis
PublicationAntitumor imidazoacridinone C-1311 is a DNA-reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor. Here, we demonstrate the mechanism of C-1311 inhibitory action on novel targets: hypoxia-inducible factor-1α (HIF-1α), vascular-endothelial growth factor (VEGF), and angiogenesis. In a cell-free system, C-1311 prevented HIF-1α binding to an oligonucleotide encompassing a canonical hypoxia-responsive element (HRE),...
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Synthesis, crystal structure and spectroscopic characterization of new anionic iridium(III) complexes and their interaction with biological targets
PublicationThe synthesis and characterisation of new anionic iridium(II) complexes (NH4)2[IrCl4(κ2N,N’-H2biim)]2 · 5H2O (1) and ((CH3)2NH2)[IrCl4(κ2N,N’-PyBIm)] · H2O (2) are presented in this article. Spectroscopic methods (1H, 13C and 15N NMR, FTIR, UV-Vis) were used to characterize these new complexes. Solid-state structural analysis (SC-XRD) of complexes 1 and 2 shows a slightly distorted octahedral geometry of Ir(III) ions, which is...
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Evaluation and cellular responses of modulators of TRF1/TRF2 protein’s function as potential anticancer drugs interfering with telomeric shelterin’s function
PublicationA number of proteins that interact with telomeres have been identified in human cells, indicating the high plasticity of human nucleoprotein complex organization. The most important complex is the "shelterin" complex, which consists of six proteins: TRF1, TRF2, TIN2, POT1, TPP1. The TRF1 and TRF2 directly bind to telomeric double-stranded DNA and the TIN2 protein. The TIN2 protein also binds to the TPP1 protein, stabilizing the...
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Evaluation of Three Peptide Immobilization Techniques on a QCM Surface Related to Acetaldehyde Responses in the Gas Phase
PublicationThe quartz-crystal microbalance is a sensitive and universal tool for measuring concentrations of various gases in the air. Biochemical functionalization of the QCM electrode allows a label-free detection of specific molecular interactions with high sensitivity and specificity. In addition, it enables a real-time determination of its kinetic rates and affinity constants. This makes QCM a versatile bioanalytical screening tool for...
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Desensitization of glucosamine-6-phosphate synthase to inhibition by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase, known also as L-Glutamine: D-fructose-6-phosphate amidotransferase, catalyzes the first committed step in the pathway leading to the ultimate formation of UDP-GlcNAc. The final product of this pathway is an activated precursor of numerous macromolecules containing amino sugars, including chitin and mannproteins in fungi, peptidoglycan and lipopolysaccharides in bacteria, and glycoproteins...
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Results from a Genome-Wide Association Study (GWAS) in Mastocytosis Reveal New Gene Polymorphisms Associated with WHO Subgroups
PublicationMastocytosis is rare disease in which genetic predisposition is not fully understood. The aim of this study was to analyze associations between mastocytosis and single nucleotide polymorphisms (SNPs) by a genome-wide association study (GWAS) approach. A total of 234 patients were enrolled in our study, including 141 with cutaneous mastocytosis (CM; 78 children and 63 adults) and 93 with systemic mastocytosis (SM, all adults)....
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Multi-objective antenna design by means of sequential domain patching
PublicationA simple yet robust methodology for rapid multiobjective design optimization of antenna structures has been presented. The key component of our approach is sequential domain patching of the design space which is a stencil-based search that aims at creating a path that connects the extreme Pareto-optimal designs, obtained by means of single-objective optimization runs. The patching process yields the initial approximation of the...
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Analysis of radiation and scattering problems with the use of hybrid techniques based on the discrete Green's function formulation of the FDTD method
PublicationIn this contribution, simulation scenarios are presented which take advantage of the hybrid techniques based on the discrete Green's function formulation of the finite-difference time-domain (DGF-FDTD) method. DGF-FDTD solutions are compatible with the finite-difference grid and can be applied for perfect hybridization of the FDTD method. The following techniques are considered: (i) DGF-FDTD for antenna simulations, (ii) DGF-based...
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Low-coherence sensors with nanolayers for biomedical sensing
PublicationIn this paper, we describe the fiber optic low-coherence sensors using thin film. We investigated their metrological parameters. Presented sensors were made with the use of standard telecommunication single mode optical fiber (SMF28). Different materials were applied to obtain thick layers, such as boron doped diamond, silver and gold. The thickness of layers used in the experiments ranged from 100 nm to 300 nm. Measurements were...
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Molecular basis of essentiality of early critical steps in the lipopolysaccharide biogenesis in Escherichia coli K-12: requirement of MsbA, cardiolipin, LpxL, LpxM and GcvB
PublicationTo identify the physiological factors that limit the growth of Escherichia coli K-12 strains synthesizing minimal lipopolysaccharide (LPS), we describe the first construction of strains devoid of the entire waa locus and concomitantly lacking all three acyltransferases (LpxL/LpxM/LpxP), synthesizing minimal lipid IVA derivatives with a restricted ability to grow at around 21 °C. Suppressors restoring growth up to 37 °C of Δ(gmhD-waaA)...
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A novel cold-active beta-D-galactosidase from the Paracoccus sp. 32d - gene cloning, purification and characterization
PublicationBeta-D-galactosidase (EC 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. Cold-active beta-D-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (I) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (II) convert lactose to glucose and galactose which...
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The Ellenbogen's “Matter as Software” Concept for Quantum Computer Implementation. C60 and X@C60 Molecules as Available Molecular Building Blocks (MBBs) for Tip-Based Nanofabrication (TBN) of Quantum Computing Devices
PublicationThe TBN bottom-up strategy of building quantum devices from C60 and X@C60 MBBs is proposed as an extension of the Ellenbogen's “Matter as Software” idea to quantum information processing. The capped SW or DW CNT STM tip is considered as device for manipulating C60 and X@C60 molecules. In this article, the possibility of using easily available on the market C60 Fullerene and endohedral X@C60 molecules together with commercial CNT...
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublicationA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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Reduced-Cost Two-Level Surrogate Antenna Modeling using Domain Confinement and Response Features
PublicationElectromagnetic (EM) simulation tools have become indispensable in the design of contemporary antennas. Still, the major setback of EM-driven design is the associated computational overhead. This is because a single full-wave simulation may take from dozens of seconds up to several hours, thus, the cost of solving design tasks that involve multiple EM analyses may turn unmanageable. This is where faster system representations (surrogates)...
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Induced-fit binding of laccase to gold and carbon electrodes for the biological fuel cell applications
PublicationAnalogues of laccase natural substrates (syringic, veratric, ferulic, vanillic, isovanillic, 3,5-dimethoxybenzoic aldehydes) were employed to bind and orient laccase molecules in a way which facilitates adsorption of the catalyst molecules and their electrical connection with the conductive support. Laccase was bound efficiently to these substrates both on gold and carbon electrodes forming, respectively, 2D and 3D films sensitive...
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Towards an experience based collective computational intelligence for manufacturing
PublicationKnowledge based support can play a vital role not only in the new fast emerging information and communication technology based industry, but also in traditional manufacturing. In this regard, several domain specific research endeavors have taken place in the past with limited success. Thus, there is a need to develop a flexible domain independent mechanism to capture, store, reuse, and share manufacturing knowledge. Consequently,...
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Experience-based Intelligence Augmentation with Decisional DNA: Upcoming direction
PublicationIntelligence amplification systems and technologies have gained significant interest from academia and industry during the past few decades. One of the main reasons behind this trend is the fact that most experts agree that truly intelligent artificial system is yet to be developed. The question increasing often asked is this: Is full replication of human intelligence desirable key aim in intelligence related technology and research?...
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Simulation model for assessment of IMS-based NGN call processing performance
PublicationIn current telecommunications it is assumed that demands of information society for quickly delivered services will be satisfied by Next Generation Network (NGN) architecture, which includes IP Multimedia Subsystem (IMS) elements. To guarantee Quality of Service (QoS), proper design and dimensioning of NGN is absolutely necessary, for which appropriate models have to be proposed. As NGN architecture is very complicated, the most...
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System for characterisation and multidimensional imaging of seafloor using multibeam sonar data
PublicationMultibeam sonars are widely used in applications like high resolution bathymetry measurements, underwater object detection and imaging, etc. Also, they are the promising tool in seafloor characterisation and classification, having several advantages over conventional single beam echosounders. The proposed approach to seafloor classification relies on the combined use of three different techniques. In each of them, a set of descriptors...
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Message Inter-Arrival and Inter-Departure Time Distributions in IMS/NGN Architecture
PublicationCurrently is it assumed that requirements of the information society for delivering multimedia services will be satisfied by the Next Generation Network (NGN) architecture, which includes elements of the IP Multimedia Subsystem (IMS) solution. In order to guarantee Quality of Service (QoS), NGN has to be appropriately designed and dimensioned. Therefore, proper traffic models should be proposed and applied. This requires determination...
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Fast bubble dynamics and sizing
PublicationSingle bubble sizing is usually performed by measuring the resonant bubble response using the Dual Frequency Ultrasound Method. However, in practice, the use of millisecond-duration chirp-like waves yields nonlinear distortions of the bubble oscillations. In comparison with the resonant curve obtained under harmonic excitation, it was observed that the bubble dynamic response shifted by up to 20 percent of the resonant frequency...
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Simulation model of IMS/NGN call processing performance
PublicationIn current telecommunications it is assumed that demands of the information society for quickly delivered services will be satisfied by the Next Generation Network (NGN) architecture, which includes IP Multimedia Subsystem (IMS) elements. To guarantee Quality of Service (QoS), proper design and dimensioning of NGN is absolutely necessary, for which appropriate models have to be proposed. As the NGN architecture is very complicated,...
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Method of Monitoring of the Grinding Process with Lapping Kinematics Using Audible Sound Analysis
PublicationUtilising microphones as audible sound sensors for monitoring a single-side grinding process with lapping kinematics is presented in the paper. The audible sound generated during grinding depended on the cutting properties of electroplated tools with D107 diamond grains and different thicknesses of the nickel bond. The tool wear affected the obtained technological effects such as material removal rate and the surface roughness...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Hybrid quantum-classical approach for atomistic simulation of metallic systems
PublicationThe learn-on-the-fly (LOTF) method [G. Csanyi et al., Phys. Rev. Lett. 93, 175503 (2004)] serves to seamlessly embed quantum-mechanical computations within a molecular-dynamics framework by continual local retuning of the potential's parameters so that it reproduces the quantum-mechanical forces. In its current formulation, it is suitable for systems where the interaction is short-ranged, such as covalently bonded semiconductors....
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Swapping Space for Time: An Alternative to Time-Domain Interferometry
PublicationYoung's double-slit experiment [1] requires two waves produced simultaneously at two different points in space. In quantum mechanics the waves correspond to a single quantum object, even as complex as a big molecule. An interference is present as long as one cannot tell for sure which slit is chosen by the object. The more we know about the path, the worse the interference. In the paper we show that quantum mechanics allows for...
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Multiple sound sources localization in real time using acoustic vector sensor
PublicationMethod and preliminary results of multiple sound sources localization in real time using the acoustic vector sensor were presented in this study. Direction of arrival (DOA) for considered source was determined based on sound intensity method supported by Fourier analysis. Obtained spectrum components for considered signal allowed to determine the DOA value for the particular frequency independently. The accuracy of the developed...
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Call Control Evaluation in ASON/GMPLS Architecture
PublicationThe Automatically Switched Optical Network (ASON) utilizing Generalized Multi–Protocol Label Switching (GMPLS) protocols named as ASON/GMPLS is one of the propositions of Next Generation Network. The basic assumption of ASON control plane is a separation of call control from connection control. The control plane is divided into call control and connection control components. Presented work regards the problem of call control evaluation...
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Approximation of Message Inter-Arrival and Inter-Departure Time Distributions in IMS/NGN Architecture Using Phase-Type Distributions
PublicationCurrently it is assumed that requirements of the information society for delivering multimedia services will be satisfied by the Next Generation Network (NGN) architecture, which includes elements of the IP Multimedia Subsystem (IMS) solution. In order to guarantee Quality of Service (QoS), NGN has to be appropriately designed and dimensioned. Therefore, proper traffic models should be proposed and applied. This requires determination...
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Multiple sound sources localization in free field using acoustic vector sensor
PublicationMethod and preliminary results of multiple sound sources localization in free field using the acoustic vector sensor were presented in this study. Direction of arrival (DOA) for considered source was determined based on sound intensity method supported by Fourier analysis. Obtained spectrum components for considered signal allowed to determine the DOA value for the particular frequency independently. The accuracy of the developed...
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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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IFI16 Impacts Metabolic Reprogramming during Human Cytomegalovirus Infection
PublicationCellular lipid metabolism plays a pivotal role in human cytomegalovirus (HCMV) infection, as increased lipogenesis in HCMV-infected cells favors the envelopment of newly synthesized viral particles. As all cells are equipped with restriction factors (RFs) able to exert a protective effect against invading pathogens, we asked whether a similar defense mechanism would also be in place to preserve the metabolic compartment from HCMV...
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The effects of gas exposure on the graphene/AlGaN/GaN heterostructure under UV irradiation
PublicationThis work demonstrates a graphene/AlGaN/GaN sensing device with two-dimensional electron gas (2DEG) toward nitrogen dioxide (NO2), tetrahydrofuran, and acetone detection under UV light irradiation. We propose combining measurements of the DC characteristics with a fluctuation-enhanced sensing method to provide insight into the gas detection mechanisms in the synergistic structure of highly stable GaN and gas-sensitive graphene....
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A Semiautomatic Experience-Based Tool for Solving Product Innovation Problem
PublicationIn this paper we present the idea of Smart Innovation Engineering (SIE) System and its implementation methodology. The SIE system is semi-automatic system that helps in carrying the process of product innovation. It collects the experiential knowledge from the formal decisional events. This experiential knowledge is collected from the group of similar products having some common functions and features. The SIE system behaves like...
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Smart Innovation Engineering Using Set of Experience and Decisional DNA
PublicationKnowledge-based Engineering Systems are founded upon integration of knowledge into computer systems and are one of the core requirements for the future Industry 4.0. Since the fourth industrial revolution is passing through the developing phase, implementation of Cyber-Physical Production Systems require more realistic approach. Knowledge Management and Knowledge Engineering plays an important role in manufacturing industries facing...
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Traffic model for evaluation of call processing performance parameters in IMS-based NGN
PublicationIn the modern world requirements for accurate and fast information distribution are becoming more and more important, which creates a strong necessity for appropriate telecommunication network architecture. Proposition of such an architecture is the Next Generation Network (NGN) concept, which in order to guarantee Quality of Service (QoS), should be correctly designed and dimensioned. For this reason proper traffic models must...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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Traffic Model of IMS/NGN Architecture with Transport Stratum Based on MPLS Technology
PublicationGrowing expectations for a fast access to information create strong demands for a universal telecommunication network architecture, which provides various services with strictly determined quality. Currently it is assumed that these requirements will be satisfied by Next Generation Network (NGN), which consists of two stratums and includes IP Multimedia Subsystem (IMS) elements. To guarantee Quality of Service (QoS) all NGN stratums...
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Damage detection in a bolted lap joint using guided waves
PublicationThe paper presents the experimental investigation of guided waves application to the condition assessment of prestressed bolted connections and a concept of new quantitative indicator. The main goal of the research was the analysis of the influence of the contact conditions changes to the characteristics of a propagating disturbance. The experimental tests were carried out for a single bolted lap joint. The excitation and acquisition...
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Multi-objective optimization of microwave couplers using corrected domain patching
PublicationPractical design of microwave components and circuits is a compromise between various, often conflicting objectives. In case of compact structures, the trade-offs are typically concerned with the circuit size and its electrical performance. Comprehensive information about the best possible trade-offs can be obtained by means of multi-objective optimization. In this paper, we propose a computationally efficient technique for identifying...