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Search results for: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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A structure and simulation-driven design of compact CPW-fed UWB antenna
PublicationIn this letter, a structure of a miniaturized ultra-wideband CPW-fed antenna and its design proce-dure are presented. The antenna is a modified version of the design previously proposed in the literature, with additional degrees of freedom introduced in order to improve the structure flexibility. The small size is achieved by executing a rigorous optimization procedure that consists of two stages: (i) smart random search carried...
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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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A material model of asphalt mixtures based on Monte Carlo simulations
PublicationThe paper aims to numerically reflect mineral-asphalt mixture structure by a standard FEM software. Laboratory test results are presented due to bending tests of circular notched elements. The result scatter is relatively high. An attempt was made to form a random aggregate distribution in order to obtain various results corresponding to laboratory tests. The material structure calibration, its homogenization and finite element...
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CONTROL OF THE WAVES IN A TOWING TANK WITH THE USE OF A BLACK-BOX MODEL
PublicationThe paper describes an adaptive control system of the waves, implemented in the Ship Design and Research Centre, CTO S.A. The purpose of generating the waves in the towing tank is the modelling of the environmental conditions during hydrodynamic model tests. The tests are performed on scale models of towed or free running ships, anchored structures like oil rigs or bottommounted structures, e.g. wind turbines. In the towing tank...
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Improved RSS-Based DoA Estimation Accuracy in Low-Profile ESPAR Antenna Using SVM Approach
PublicationIn this paper, we have shown how the overall performance of direction-of-arrival (DoA) estimation using lowprofile electronically steerable parasitic array radiator (ESPAR) antenna, which has been proposed for Internet of Things (IoT) applications, can significantly be improved when support vector machine (SVM) approach is applied. Because the SVM-based DoA estimation method used herein relies solely on received signal strength...
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Novel 5-Substituted 2-(Aylmethylthio)-4-chloro-N-(5-aryl-1,2,4-triazin-3-yl)benzenesulfonamides: Synthesis, Molecular Structure, Anticancer Activity, Apoptosis-Inducing Activity and Metabolic Stability
PublicationA series of novel 5-substituted 2-(arylmethylthio)-4-chloro-N-(5-aryl-1,2,4-triazin-3-yl) benzenesulfonamide derivatives 27–60 have been synthesized by the reaction of aminoguanidines with an appropriate phenylglyoxal hydrate in glacial acetic acid. A majority of the compounds showed cytotoxic activity toward the human cancer cell lines HCT-116, HeLa and MCF-7, with IC50 values below 100 M. It was found that for the analogues 36–38...
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Effect of chemical structure on complexation efficiency of aromatic drugs with cyclodextrins: The example of dibenzazepine derivatives
PublicationIt is widely believed that the hydrophobic effect governs the binding of guest molecules to cyclodextrins (CDs). However, it is also known that high hydrophobicity of guest molecules does not always translate to the formation of stable inclusion complexes with CDs. Indeed, a plethora of other factors can play a role in the efficiency of guest–CD interactions, rendering structure-based prediction of the complexation efficiency with...
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Continuation classes for a non-linear Leslie population model with 2 varying parameters
Open Research DataThis dataset contains selected results of rigorous numerical computations conducted in the framework of the research described in the paper "A database schema for the analysis of global dynamics of multiparameter systems" by Z. Arai, W. Kalies, H. Kokubu, K. Mischaikow, H. Oka, P. Pilarczyk, published in SIAM Journal on Applied Dynamical Systems (SIADS),...
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Role of miR-15b/16–2 cluster network in endometrial cancer: An in silico pathway and prognostic analysis
PublicationEndometrial cancer (EC) is the second most common cancer in women. A large number of human cancers exhibit dysregulation of microRNA expression including EC. MiR-15b/16–2 is one of the best-known miRNA clusters that is expressed in many types of cancer tissues. Herein, we analyzed the expression of individual miR-15b/16–2 cluster members, its paralogues, and their target network analysis, as well as their prognostic significance...
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Assessing the Risk in Urban Public Transport for Epidemiologic Factors
PublicationPandemics have presented new challenges for public transport organisers and operators. New diseases (e.g., influenza H1N1, severe acute respiratory syndrome—SARS, as well as, more recently, SARS-CoV-2) increase the need for new protection measures to prevent epidemic outbreaks in public transport infrastructure. The authors’ goal is to present a set of actions in the area of public transport that are adjusted to different levels...
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Reply to “Comment on ‘Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions'” by B. P. van Eijck and J. Kroon
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A simplified behavioral MOSFET model based on parameters extraction for circuit simulations.
PublicationThe paper presents results on behavior modeling of general purpose Metal-Oxide Semiconductor Field-Effect Transistor (MOSFET) for simulation of power electronics systems requiring accuracy both in steady-state and in switching conditions. Methods of parameters extraction including nonlinearity of parasitic capacitances and steady-state characteristics are based on manufacturer data sheet and externally measurable characteristics....
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IMPACT OF THE FINANCING STRUCTURE ON EFFICIENCY OF HEALTHCARE SYSTEMS IN THE FORMER EASTERN BLOC COUNTRIES
PublicationOut-of-pocket expenditures are a significant barrier in accessing health services. This paper aims to analyse the structure of financing system in the context of the performance indicators of healthcare systems. The study was conducted for the 28 countries of the former Eastern bloc in the years 2000 and 2013, based on data from the World Health Organization. In the DEA-CCR input-oriented model, inputs are the percentage share...
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Nonlinear Model of Synchronous Generator for Autonomous Electrical Power Systems Analysis
PublicationThis paper presents the nonlinear lookup table model for synchronous generator (SG) analysis. The saturation effects of the SG magnetic circuit have been considered. The saturated characteristic of the SG magnetic circuit are based on the open circuit saturation curve for magnetizing inductances. The model has been implemented into the Synopsys/Saber software using the MAST modelling language. To implement the no-load voltage characteristic...
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An Algorithm for Listing All Minimal 2-Dominating Sets of a Tree
PublicationWe provide an algorithm for listing all minimal 2-dominating sets of a tree of order n in time O(1.3248n) . This implies that every tree has at most 1.3248 n minimal 2-dominating sets. We also show that this bound is tigh.
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Dehydration converts DsbG crystal diffraction from low to high resolution
PublicationDiffraction quality crystals are essential for crystallographic studies of protein structure, and the production of poorly diffracting crystals is often regarded as a dead end in the process. Here we show a dramatic improvement of poorly diffracting DsbG crystals allowing high-resolution diffraction data measurement. Before dehydration, the crystals are fragile and the diffraction pattern is streaky, extending to 10 Å resolution....
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublicationWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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The structure of demand and its economic consequences for urban transport
PublicationThe structure of demand for urban transport services, determined by the share of passengers entitled to free and reduced fares, is an important factor influencing its economic condition. The aim of this article is to present the results of research into the structure of demand for urban transport as well as its economic consequences. The article begins by considering the nature of the determinants and consequences of the public...
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Graphs with equal domination and 2-distance domination numbers
PublicationW publikacji scharakteryzowane są wszystkie te drzewa i grafy jednocykliczne, w których liczba dominowania oraz liczba 2-dominowania na odległość są sobie równe.
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Edge coloring of graphs of signed class 1 and 2
PublicationRecently, Behr (2020) introduced a notion of the chromatic index of signed graphs and proved that for every signed graph (G, σ) it holds that ∆(G) ≤ χ′(G,σ) ≤ ∆(G) + 1, where ∆(G) is the maximum degree of G and χ′ denotes its chromatic index. In general, the chromatic index of (G, σ) depends on both the underlying graph G and the signature σ. In the paper we study graphs G for which χ′(G, σ) does not depend on σ. To this aim we...
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Model of Rules for IT Organization Evolution
PublicationThe aim of this paper is to introduce the Model of Rules for IT Organization Evolution which shall be in compliance with the Generic IT Organization Evolution Model. Due to its general nature, a set of practical adjustments is proposed in order to adapt the Generic Model to the IT Service Management domain. Further, two sets of rules describing the evolution of the IT Service Management area are defined based on two types of rules...
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Examination method of the effect of the incidence angle of laser beam on distance measurement accuracy to surfaces with different colour and roughness
PublicationInterest in the influence of the incidence angle of a laser beam to distance measurements can be seen in many areas of science and technology: geodesy, glaciology, archaeology, machine automation, and others. This paper presents results of measurements of the effect of the incidence angle of a laser beam to distance measurements to the surfaces of different colour and roughness by Topcon's electro-optical total station with an...
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Customization of UWB 3D-RTLS Based on the New Uncertainty Model of the AoA Ranging Technique
PublicationThe increased potential and effectiveness of Real-time Locating Systems (RTLSs) substantially influence their application spectrum. They are widely used, inter alia, in the industrial sector, healthcare, home care, and in logistic and security applications. The research aims to develop an analytical method to customize UWB-based RTLS, in order to improve their localization performance in terms of accuracy and precision. The analytical...
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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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On the electronic structure of methyl butyrate and methyl valerate
PublicationWe present novel results of the analysis of the electronic structure of two aliphatic esters: methyl butyrate and methyl valerate. High-resolution photoabsorption spectra were collected and analyzed over the energy range 4.0–10.8 eV and showed for both the molecules not only a clear band of the HOMO to LUMO transition, but also vibronic structure associated with the first Rydberg-valence transition. Photoelectron spectra recorded...
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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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Resonant Frequencies in Microstrip Structure with Omega Medium Substrate
PublicationThe paper presents the research on a rectangular microstrip structure with multilayer substrate containing dielectric and omega medium layers. The effect of pseudochiral medium layer location in the substrate and its thickness on the resonant frequency of the rectangular microstrip structure is investigated. The numerical analysis of investigated structures is based on expansion of electric and magnetic fields. Utilizing the continuity...
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Lattice filter based multivariate autoregressive spectral estimation with joint model order and estimation bandwidth adaptation
PublicationThe problem of parametric, autoregressive model based estimation of a time-varying spectral density function of a multivariate nonstationary process is considered. It is shown that estimation results can be considerably improved if identification of the autoregressive model is carried out using the two-sided doubly exponentially weighted lattice algorithm which combines results yielded by two one-sided lattice algorithms running...
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Modelling of localization of deformation in quasi-brittle materials with a continuum and discrete model
PublicationW artykule przedstawiono wyniki obliczeń lokalizacji odkształceń w materiałach kruchych przy zastosowaniu 2 modeli w ramach mechaniki ośrodka ciągłego i jednego modelu w ramach ośrodka dyskretnego. W przypadku pierwszy zastosowano model sprężysto-plastyczny i model zniszczeniowy rozszerzony o długość charakterystyczną mikrostruktury. W przypadku drugim przyjęto model rusztowy złożony z beleczek.
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Measurement Campaign and Mathematical Model Construction for the Ship Zodiak Magnetic Signature Reproduction
PublicationThe paper presents the partial work done within the framework of the EDA Siramis II project focused on magnetic signature reproduction of ships. Reproduction is understood here as the ability to determine the magnetic anomaly of the local Earth magnetic field in any direction and at any measurement depth due to the presence of the analysed object. The B-91 type hydrographic ship Zodiak was selected as the real case study. The work...
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The Undisrupted Growth of the Airbnb Phenomenon between 2014–2020. The Touristification of European Cities before the COVID-19 Outbreak
PublicationAs a result of the Airbnb eruption, not only has the character of the short-term rental market been completely transformed, but the decades long growth in tourism has also been further accelerated. Therefore, due to the new demands of the tourism economy, the major shift in the usage of historic city centers occurred–the process of ‘touristification’, that results in the emergence of its new, unsustainable form. Despite the significance...
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Novel N-(aryl/heteroaryl)-2-chlorobenzenesulfonamide derivatives: synthesis and anticancer activity evaluation
PublicationA new series of N-(aryl/heteroaryl)-2-chlorobenzenesulfonamide derivatives 4-21 have been synthesized, and evaluated at the National Cancer Institute (USA) for their in vitro activities against a panel of 60 different human cancer cell lines. Among them, compounds 16, 20 and 21 exhibited remarkable cytotoxic activity against numerous human cancer cell lines. We found that sulfonamide derivative 21 appeared to be more selective...
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Evaluating Pornography Problems Due to Moral Incongruence Model
PublicationIntroduction To date, multiple models of problematic pornography use have been proposed, but attempts to validate them have been scarce. Aim In our study, we aimed to evaluate the Pornography Problems due to Moral Incongruence model proposing that self-appraisals of pornography addiction stem from (i) general dysregulation, (ii) habits of use, and (iii) moral incongruence between internalized norms and behavior. We investigated...
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Interrelations between Travel Patterns and Urban Spatial Structure of the Largest Russian Cities
PublicationThe study presented within this dissertation involves the analysis of the relationship between urban spatial structure and travel patterns in the largest Russian cities. It is an empirical investigation of how the spatial structure, formed during the Soviet and post-Soviet periods, affects the travel patterns in the largest cities of contemporary Russia. It aims to determine what measures, both urban structure and transportation...
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Verification of the Analytical Traffic Model of a Multidomain IMS/NGN Using the Simulation Model
PublicationIn this paper we verify the previously proposed analytical traffic model of a multidomain Next Generation Network (NGN), which is standardized for delivering multimedia services based on the IP Multimedia Subsystem (IMS). For this reason a proper simulation model used, in which not theoretical queuing system models but the operation of real network elements and standardized call scenarios are accurately implemented. Consequently,...
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Laboratory Determination of Burger's Model Parameters for Visco-elastic Analysis of Road Pavement Materials
PublicationBurger's Model is one of those models that describes performance of asphalt mixtures. Its parameters can be used in road construction analysis based on visco-elastic properties in wide variety of temperatures using dedicated programs (e.g. Veroad) or in Finite Element Method (FEM). Parameters of Burger's Model can be used for example in prediction of low temperature cracking in low winter temperatures or permanent deformation...
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Membrane model of human abdominal wall. Simulations vs. in vivo measurements
PublicationThe study presents a methodology of defining a numerical model of human abdominal wall based on the experimentally registered data of the abdomen geometry due to variations of the intraabdominal pressure. The abdominal wall is modelled here as a simple homogeneous membrane structure made of linear orthotropic material The displacements registered during the increase of pressure are compared with the re-sults of the model static...
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Packing Three-Vertex Paths in 2-Connected Cubic Graphs
PublicationW pracy rozważano problem rozmieszczanie ścieżek P3 w 2-spójnych grafach 3-regularnych. Pokazano, że w 2-spójnym grafie 3-regularnym o n wierzchołkach można zawsze pokryć 9/11 n wierzchołków przez ścieżki P3; podano także odpowiednie oszacowania górne.
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MULTI-CRITERIA MODEL IN MULTIFUNCTIONAL BUILDING SYSTEM DESIGN PROCESS
PublicationThe paper presents a multi-criteria approach in multifunctional building system design process. The aim is to develop a theory relative to the engineering system of multifunctional with a mathematical representation defined by a holistic network for the lifecycle of the designed object. The idea of work was to define the structure of a complex system. Background for the presented field is to develop a design strategy for multifunctional...
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Clinical anatomy of the spatial structure of the right ventricular outflow trac
PublicationBackground. The right ventricular outflow tract (RVOT) is located above the supraventricular crest and reaches the level of the pulmonary valve. Detailed knowledge of the RVOT spatial structure and its morphology is extremely important for cardiac invasive therapeutic procedures. Objectives. To examine the spatial structure of the RVOT using virtual models of the right ventricle (RV) interior obtained post mortem. Material and...
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COVID-19 in Pediatric Intensive Care Units in Poland, PAPITCO-19 Study (Polish Analysis of PICU Trends during COVID-19)
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Module structure in Conley theory with some applications
PublicationA multiplicative structure in the cohomological versjon of Conley index is described . In the case of equivariant flows we apply the normalization procedure known from equivariant degree theory and we propose a new continuation invariant. The theory is then applied to obtain a mountain pass type theorem. Another application is a result on multiple bifurcations for some elliptic PDE.
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Representation of magnetic hysteresis in tape wound core using feedback Preisach model
PublicationThis paper presents a mathematical model for the hysteresis phenomenon in ferromagnetic tape wound core. The feedback scalar Preisach model of hysteresis is used to simulate magnetic behavior of the grain oriented silicon strip of ET114-27 type. Determination of B-H hysteretic curve is based on measurement of the initial magnetization curve and the main hysteresis loop. The Preisach distribution function (PDF) of ET114-27 material...
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5-Bromo-2′-deoxycytidine—a potential DNA photosensitizer
PublicationA double-stranded oligonucleotide, 80 base pairs in length, was multiply labeled with 5-bromo-2′-deoxycytidine (BrdC) using polymerase chain reaction (PCR). The modified oligonucleotide was irradiated with 300 nm photons and its damage was assayed by employing DHPLC, LC-MS and denaturing polyacrylamide gel electrophoresis (PAGE). Two types of damage were demonstrated, namely, single strand breaks (SSBs) and intrastrand cross-links...
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Spurious Modes in Model Order Reduction in Variational Problems in Electromagnetics
PublicationIn this work, we address an everlasting issue in 2 model order reduction (MOR) in electromagnetics that has 3 remained unnoticed until now. Contrary to what has been 4 previously done, we identify for the very first time spurious 5 modes in MOR for time-harmonic Maxwell’s equations and 6 propose a methodology to remove their negative influence on the 7 reduced order model (ROM) response. These spurious modes 8 have nonzero resonance...
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Novel structure and design of compact UWB slot antenna
PublicationIn this paper, a novel structure of a compact UWB slot antenna is presented along with a simulation-driven design optimization algorithm for adjusting geometry parameters of the device. Our primary objective is to obtain small footprint of the structure while maintaining its acceptable electrical performance. It is achieved by introducing sufficiently large number of geometry degrees of freedom, including increased number of parameterized...
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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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Road noise mapping in the city area: measurements compared to model-based estimations
PublicationThe paper presents an approach to the verification of noise prediction models in selected localization in the city of Gdansk. The experiments described include a comparison between environmentalmeasurement results performed in the terrain and the noise level prediction results. The NMPB-96 (Nouvelle Méthode de Prévision du Bruit) and Harmonoise models outcomes provide the subject ofthe analysis. The proposed solution of continuous...
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On the Structure of Time in Computational Semantics of a Variable-Step Solver for Hybrid Behavior Analysis
PublicationHybrid dynamic systems combine continuous and discrete behavior. Often, computational approaches are employed to derive behaviors that approximate the analytic solution. An important part of this is the approximation of differential equation behavior by numerical integration. The accuracy and computational efficiency of the integration usually depend on the complexity of the method and its implicated approximation errors, especially...