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Search results for: ambiguous restraints, coarse-grained models, nmr-assisted protein-structure modeling, unres
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Sequence variants of p21 gene of the MRL/MpJ mouse: a possible association with the deficit of p21 protein and regenerative phenotype.
PublicationThe MRL/MpJ mouse is known for its enhanced regeneration abilities that manifested themselves by scarless ear-hole wound closure. The deficit of p21 found in the MRL is associated with the regenerative capacity as the p21 gene knockout in a mouse strain unrelated to the MRL mouse results in an ear-hole closure effect, similar to that observed in the MRL mouse. Cdkn1a gene encodes p21 protein, a cyclin-dependent kinase inhibitor,...
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Methodology of research on the impact of ITS services on the safety and efficiency of road traffic using transport models
PublicationThe current assessment of the impact of Intelligent Transport System (ITS) services on the level of traffic safety and efficiency is based mainly on expert assessments, statistical surveys or several traffic safety models requiring development. There is no structured, uniform assessment method that would give the opportunity to compare the impact of ITS services and their different configurations. The paper presents the methodology...
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Computer Assisted Language Learning: an International Journal
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International Journal of Computer Assisted Radiology and Surgery
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Knowledge-Based Virtual Modeling and Simulation of Manufacturing Processes for Industry 4.0
PublicationABSTRACT Industry 4.0 aims at providing a digital representation of a production landscape, but the challenges in building, maintaining, optimizing, and evolving digital models in inter-organizational production chains have not been identified yet in a systematic manner. In this paper, various Industry 4.0 research and technical challenges are addressed, and their present scenario is discussed. Moreover, in this article, the novel...
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Type III Responses to Transient Inputs in Hybrid Nonlinear Neuron Models
PublicationExperimental characterization of neuronal dynamics involves recording both of spontaneous activity patterns and of responses to transient and sustained inputs. While much theoretical attention has been devoted to the spontaneous activity of neurons, less is known about the dynamic mechanisms shaping their responses to transient inputs, although these bear significant physiological relevance. Here, we study responses to transient...
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Use of Porosity in Models of Consolidation
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Evaluation of accuracy of surrogate models
PublicationArtykuł przestawia statystyczne podejście do oceny dokładności modeli zastępczych. Prezentowana jest miara dokładności bazująca na dystrybucji błędów w zbiorze testowym. Praca zawiera dyskusję na temat oceny dokładności samego modelu oraz zasadności wyboru kryterium zatrzymującego proces automatycznego tworzenia modelu.
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Graph models of clos networks
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Models in the Research Process of Psoriasis
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Active shape models in practice
PublicationAutorzy wykonali uniwersalny system lokalizacji obiektów zawierający implementację aktywnych modeli kształtu, a przeprowadzone z użyciem tego systemu eksperymenty wykazały powżne wady badanej metody. W pracy przedstawiono zaobserwowane w praktyce problemy związane ze stosowaniem metody aktywnych modeli kształtu (ASM).
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Extended hypoplastic models for soils
PublicationPoprawione i poszerzone wydanie pracy habilitacyjnej nt. hipoplastycznego modelu konstytutywnego gruntów.
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Models of the kinematics of lapping machines.
PublicationPrzedstawiono wyniki analiz symulacyjnych układów kinematycznych docierania jednotarczowego powierzchni płaskich. Analizowano układ standardowy i układy niekonwencjonalne, zmieniając ich parametry geometryczne i kinematyczne. Wytypowano układ optymalny w aspekcie równomierności zużycia tarczy docierającej.
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Digital waveguide models of the panpipes
PublicationW artykule przedstawiono główne cechy syntezy falowodowej. Omówiono cechy instrumentu fletni Pana. Przedyskutowano cechy zaproponowanych dwóch modeli fletni Pana różniących się złożonością obliczeniową. Pokazano szczegóły implementacyjne tych modeli, a także uzyskane wyniki symulacji dźwięków w modelach. Dokonano porównania dźwięków rzeczywistych i uzyskanych w wyniku syntezy falowodowej.
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Asymptotic Expansion Method with Respect to Small Parameter for Ternary Diffusion Models
PublicationTernary diffusion models lead to strongly coupled systems of PDEs. We choose the smallest diffusion coefficient as a small parameter in a power series expansion whose components fulfill relatively simple equations. Although this series is divergent, one can use its finite sums to derive feasible numerical approximations, e.g. finite difference methods (FDMs).
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Application of different building representation techniques in HEC-RAS 2-D for urban flood modeling using the Toce River experimental case
PublicationThis paper presents the impact of the choice of building representation techniques and hydrodynamic models on urban flood simulations using HEC-RAS 2-D for the Toce River physical model. To this end, eight numerical models based on previous laboratory experiments were prepared to simulate unsteady urban flooding on each side of building units. Two simplified building layouts (aligned and staggered) were examined, where models were...
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Optimal shape design of multi-element trawl-doors using local surrogate models
PublicationTrawl-doors have a large influence on the fuel consumption of fishing vessels. Design and optimiza-tion of trawl-doors using computational models are a key factor in minimizing the fuel consump-tion. This paper presents an optimization algorithm for the shape design of trawl-door shapes using computational fluid dynamic (CFD) models. Accurate CFD models are computationally expensive. Therefore, the direct use of traditional optimization...
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The use of mathematical models for diagnosis of activated sludge systems in WWTP
PublicationIn this study diagnosis of activated sludge systems in wastewater treatment plant (WWTP) was investigated. Diagnosis of technical objects can be realized in many ways. One of the divisions of the diagnostic methods include modelling with or without a model of the object. The first of these is the analysis of the symptoms for which, based on the parameter values, the abnormality in the diagnosed objects are sought. Another way is...
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Software modules and application layer's security structure of RSMAD
PublicationThe paper discusses the software modules of Radio System for Monitoring and Acquisition of Data from Traffic Enforcement Cameras (in short RSMAD). The structure of the application layer of the system has also been analysed in details, including: purpose, structure and principles of operation of software modules constituting this system. In addition, the paper presents and discusses the structure of security of application layer...
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Cost-Efficient Bi-Layer Modeling of Antenna Input Characteristics Using Gradient Kriging Surrogates
PublicationOver the recent years, surrogate modeling has been playing an increasing role in the design of antenna structures. The main incentive is to mitigate the issues related to high cost of electromagnetic (EM)-based procedures. Among the various techniques, approximation surrogates are the most popular ones due to their flexibility and easy access. Notwithstanding, data-driven modeling of antenna characteristics is associated with serious...
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Comparative analysis of various transformation techniques for voiceless consonants modeling
PublicationIn this paper, a comparison of various transformation techniques, namely Discrete Fourier Transform (DFT), Discrete Cosine Transform (DCT) and Discrete Walsh Hadamard Transform (DWHT) are performed in the context of their application to voiceless consonant modeling. Speech features based on these transformation techniques are extracted. These features are mean and derivative values of cepstrum coefficients, derived from each transformation....
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Selection of main engines for hopper suction dredgers with the use oobability models
PublicationThis paper presents a new original method of selection of main engines for hopper suction dredgers with regard to probabilistic models. It was proposed to use the normal distribution to describe the operational loads of the main receivers. The principles for determination of parameters of load distribution and design power of the main engines were formulated. Lastly, the principles of selection of the size and number of main engines...
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Influence of chemical structure on physicochemical properties and thermal decomposition of the fully bio-based poly(propylene succinate-co-butylene succinate)s
PublicationIn this work, two polyesters and four copolyesters were studied. All materials were synthesized to obtain the monomers dedicated for thermoplastic polyurethane elastomers. For this type of PUR, the monomers should characterize by appropriate selected physicochemical properties and macromolecular structure distribution, which depends on synthesis conditions. The study of chemical structure with extensive and knowledgeable analysis...
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Reliable computationally-efficient behavioral modeling of microwave passives using deep learning surrogates in confined domains
PublicationThe importance of surrogate modeling techniques has been steadily growing over the recent years in high-frequency electronics, including microwave engineering. Fast metamodels are employed to speedup design processes, especially those conducted at the level of full-wave electromagnetic (EM) simulations. The surrogates enable massive system evaluations at nearly EM accuracy and negligible costs, which is invaluable in parameter...
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Justifying the prolongation of the service life of the bearing structure of a tank car when using Y25 bogies
PublicationThis paper substantiates the use of Y25 bogies under tank cars in order to prolong their service life. The reported study has been carried out for a tank car with rated parameters, as well as the actual ones, registered during full-scale research. Mathematical modeling was performed to determine the basic indicators of the tank car dynamics. The differential equations of motion were solved by a Runge-Kutta method using the Mathcad...
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Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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Influence of dopants on structure of polycrystalline bismuth niobate
PublicationBismuth niobate (BiNbO4) has attracted attention as a low-fired ceramics with promising microwave application potential. BiNbO4 ceramics was fabricated by mixed oxide method and sintered at temperature T<1000˚C. As the sintering aids a small amount of CuO oxide was used. The crystalline structure of the ceramic samples was examined by X-ray diffraction method at room temperature. The Rietveld refinement method was used for analysis...
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Isolation and structure of a covalent cross-link adduct between mitomycin C and DNA
PublicationA DNA cross-link adduct of the antitumor agent mitomycin C (MC) to DNA has been isolated and characterized; the results provide direct proof for bifunctional alkylation of DNA by MC. Exposure of MC to Micrococcus luteus DNA under reductive conditions and subsequent nuclease digestion yielded adducts formed between MC and deoxyguanosine residues. In addition to the two known monoadducts, a bisadduct was obtained. Reductive MC activation...
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Inverse Modeling and Optimization of CSRR-based Microwave Sensors for Industrial Applications
PublicationDesign optimization of multivariable resonators is a challenging topic in the area of microwave sensors for industrial applications. This paper proposes a novel methodology for rapid re-design and parameter tuning of complementary split-ring resonators (CSRRs). Our approach involves inverse surrogate models established using pre-optimized resonator data as well as analytical correction techniques to enable rapid adjustment of geometry...
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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease
PublicationWe previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation...
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On Unsupervised Artificial-Intelligence-Assisted Design of Antennas for High-Performance Planar Devices
PublicationDesign of modern antenna structures is a challenging endeavor. It is laborious, and heavily reliant on engineering insight and experience, especially at the initial stages oriented towards the devel-opment of a suitable antenna architecture. Due to its interactive nature and hands-on procedures (mainly parametric studies) for validating suitability of particular geometric setups, typical antenna development requires many weeks...
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Justification of models of changing project environment for harvesting grain, oilseed and legume crops
PublicationAn analysis of the condition of implementation of projects in agricultural production is carried out. The disadvantages of existing methods and models of planning of the content and time of execution of works in the projects, which mostly do not take into account the changing components of their project environment, are substantiated. The proposed methodology for justifying the models of a changing project environment for harvesting...
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Evaluation of Foundation Input Motions Based on Kinematic Interaction Models
PublicationThe present study was designed to demonstrate the importance of baseslab averaging and embedment effects on the foundation-level input motions due to earthquake excitations. Evaluation of foundation-level input motions based on the most commonly adopted kinematic interaction models are presented. In order to conduct this investigation, original records of horizontal accelerations for two casestudy buildings were utilized. Computed...
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Signal propagation in electromagnetic media described by fractional-order models
PublicationIn this paper, signal propagation is analysed in electromagnetic media described by fractional-order (FO) models (FOMs). Maxwell’s equations with FO constitutive relations are introduced in the time domain. Then, their phasor representation is derived for one-dimensional case of the plane wave propagation. With the use of the Fourier transformation, the algorithm for simulation of the non-monochromatic wave propagation is introduced....
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X-Ray Structure Analysis Online
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Fast Multi-Objective Optimization of Narrow-Band Antennas Using RSA Models and Design Space Reduction
PublicationComputationally efficient technique for multi-objective design optimization of narrow-band antennas is presented. In our approach, the corrected low-fidelity antenna model (obtained through coarse-discretization EM simulations) is enhanced using frequency scaling and response correction, sampled, and utilized to obtain a fast response surface approximation (RSA) antenna surrogate. The RSA model is constructed in the reduced design space....
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GIS-based hydrodynamic modeling for urban flood mitigation in fast-growing regions: a case study of Erbil, Kurdistan Region of Iraq
PublicationFloods threaten urban infrastructure, especially in residential neighborhoods and fast-growing regions. Flood hydrodynamic modeling helps identify flood-prone locations and improve mitigation plans' resilience. Urban floods pose special issues due to changing land cover and a lack of raw data. Using a GIS-based modeling interface, input files for the hydrodynamic model were developed. The physical basin's properties were identified...
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Modeling the global atmospheric transport and deposition of mercury to the Great Lakes
PublicationMercury contamination in the Great Lakes continues to have important public health and wildlife ecotoxicology impacts, and atmospheric deposition is a significant ongoing loading pathway. The objective of this study was to estimate the amount and source-attribution for atmospheric mercury deposition to each lake, information needed to prioritize amelioration efforts. A new global, Eulerian version of the HYSPLIT-Hg model was used...
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Which Curve Fits Best: Fitting ROC Curve Models to Empirical Credit-Scoring Data
PublicationIn the practice of credit-risk management, the models for receiver operating characteristic (ROC) curves are helpful in describing the shape of an ROC curve, estimating the discriminatory power of a scorecard, and generating ROC curves without underlying data. The primary purpose of this study is to review the ROC curve models proposed in the literature, primarily in biostatistics, and to fit them to actual credit-scoring ROC data...
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Inverse and forward surrogate models for expedited design optimization of unequal-power-split patch couplers
PublicationIn the paper, a procedure for precise and expedited design optimization of unequal power split patchcouplers is proposed. Our methodology aims at identifying the coupler dimensions that correspond to thecircuit operating at the requested frequency and featuring a required power split. At the same time, thedesign process is supposed to be computationally efficient. The proposed methodology involves two typesof auxiliary models (surrogates):...
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Examining Quality of Hand Segmentation Based on Gaussian Mixture Models
PublicationResults of examination of various implementations of Gaussian mix-ture models are presented in the paper. Two of the implementations belonged to the Intel’s OpenCV 2.4.3 library and utilized Background Subtractor MOG and Background Subtractor MOG2 classes. The third implementation presented in the paper was created by the authors and extended Background Subtractor MOG2 with the possibility of operating on the scaled version of...
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Evaluation of foundation input motions based on kinematic interaction models
PublicationThe present study was designed to demonstrate the importance of base-slab averaging and embedment effects on the foundation-level input motions due to earthquake excitations. Evaluation of foundation-level input motions based on the most commonly adopted kinematic interaction models are presented. In order to conduct this investigation, original records of horizontal accelerations for two case-study buildings were utilized. Computed...
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Turbulence models impact on the flow and thermal analyses of jet impingement
PublicationAccurate numerical reconstruction of heat and mass transfer processes in particular applications, such a jet impingement, is difficult to obtain even with the use of modern computational methods. In the proposed paper, the flow and thermal phenomena occurring during single minijet impingement on the flat, concave and convex, heated surfaces were considered. Problem of impingement on non-flat surface, still not common and purely...
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
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UV-assisted fluctuation-enhanced gas sensing by ink-printed MoS2 devices
PublicationIn this work, MoS2 flakes were printed on ceramic substrates and investigated toward 1–10 ppm of nitrogen dioxide (NO2), 2–12 ppm of ammonia (NH3), and 2–12 ppm acetone (C3H6O) under UV light (275 nm). The structure of overlapping MoS2 flakes and UV light assistance affected high responsivity to NO2 when DC resistance was monitored, and superior sensitivity to NH3 was obtained from the low-frequency noise spectra. MoS2 exhibited...
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Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublicationAbstract - We present an implicit solvent model for ab initio electronic-structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comput. Chem., 23 (2002) 662). While this model depends on only two parameters, we demonstrate...