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Search results for: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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Improving the prediction of biochar production from various biomass sources through the implementation of eXplainable machine learning approaches
PublicationExamining the game-changing possibilities of explainable machine learning techniques, this study explores the fast-growing area of biochar production prediction. The paper demonstrates how recent advances in sensitivity analysis methodology, optimization of training hyperparameters, and state-of-the-art ensemble techniques have greatly simplified and enhanced the forecasting of biochar output and composition from various biomass...
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The Response of Selected Domestic Capital Markets on the Development of COVID-19 Pandemic – a Broader View
PublicationObjective: The study examines how the record of the first, hundredth, thousandth, ten-thousandth, one-hundred-thousandth, and millionth cases of COVID-19 affected investor behaviour in capital markets. It also looks at whether the month in which the first case was recorded in a given market affected the direction and strength of investor reactions. Lastly, it verifies whether the two announcements made by the WHO related to COVID-19...
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Ship Dynamic Positioning Based on Nonlinear Model Predictive Control
PublicationThe presented work explores the simulation test results of using nonlinear model predictive control algorithm for ship dynamic positioning. In the optimization task, a goal function with a penalty was proposed with a variable prediction step. The results of the proposed control algorithm were compared with backstepping and PID. The effect of estimation accuracy on the control quality with the implemented algorithms was investigated....
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Mathematical model of pennate muscle
PublicationThe purpose of this study is to create a new mathematical model of pennate striated skeletal muscle. This new model describes behaviour of isolated flat pennate muscle in two dimensions (2D) by taking into account that rheological properties of muscle fibres depend on their planar arrangement. A new mathematical model is implemented in two types: 1) numerical model of unipennate muscle (unipennate model); 2) numerical model of...
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Phase Transition in a Sequence-Structure Channel
PublicationWe study an interesting channel which maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein folding from statistical physics. The channel is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. We estimate the conditional entropy between the input sequence and the output fold, giving an upper bound which exhibits an unusual phase transition...
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Improving Accuracy of Contactless Respiratory Rate Estimation by Enhancing Thermal Sequences with Deep Neural Networks
PublicationEstimation of vital signs using image processing techniques have already been proved to have a potential for supporting remote medical diagnostics and replacing traditional measurements that usually require special hardware and electrodes placed on a body. In this paper, we further extend studies on contactless Respiratory Rate (RR) estimation from extremely low resolution thermal imagery by enhancing acquired sequences using Deep...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Dynamic Bankruptcy Prediction Models for European Enterprises
PublicationThis manuscript is devoted to the issue of forecasting corporate bankruptcy. Determining a firm’s bankruptcy risk is one of the most interesting topics for investors and decision-makers. The aim of the paper is to develop and to evaluate dynamic bankruptcy prediction models for European enterprises. To conduct this objective, four forecasting models are developed with the use of four different methods—fuzzy sets, recurrent and...
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On Accuracy Modeling of Gas Turbine Cycles by the In-house COM-GAS Code
PublicationIn this paper, a comparison of accuracy modeling of gas turbine cycles between the basic (classical) model and the in-house COM-GAS code has been presented. The basic model uses a semi-perfect gas and well known projecting assumption. On the other hand, the computational flow mechanics (CFM) basis on a real gas by using thermodynamic tables. The thermodynamic analysis of thermal cycles, simply gas cycle GT8C and gas turbine cycle...
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Consumer Bankruptcy Prediction Using Balanced and Imbalanced Data
PublicationThis paper examines the usefulness of logit regression in forecasting the consumer bankruptcy of households using an imbalanced dataset. The research on consumer bankruptcy prediction is of paramount importance as it aims to build statistical models that can identify consumers in a difficult financial situation that may lead to consumer bankruptcy. In the face of the current global pandemic crisis, the future of household finances...
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Ontology-based text convolution neural network (TextCNN) for prediction of construction accidents
PublicationThe construction industry suffers from workplace accidents, including injuries and fatalities, which represent a significant economic and social burden for employers, workers, and society as a whole.The existing research on construction accidents heavily relies on expert evaluations,which often suffer from issues such as low efficiency, insufficient intelligence, and subjectivity.However, expert opinions provided in construction...
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MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
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Structure and Environment
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublicationThe impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. butylurea (BU) and N,N,N′,N′-tetramethylurea (TMU) were chosen as a tested compounds. The obtained results show that butylurea exerts greater impact on HEWL and its fibrillation than tetramethylurea. Both substances decrease the time of...
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Analysis of a gene expression model
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Radar time budget optimization subject to angle accuracy constraint via cognitive approach
PublicationThe problem of minimizing dwell time in multifunction phased array radar is considered. Target of interest is assumed to fluctuate according to a generalization of Swerling family and the parameters of fluctuation model are assumed to be known. The a'priori position of the target is uncertain. Optimization, whose variables include pulse count and array transmit beampattern, is carried out subject to achieving a desired accuracy...
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Francia 1, 2, 3
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A new marine ecosystem 3D CEMBS model (version 2) for the Baltic Sea
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Application of two-dimensional intensity maps in high-accuracy polarimetry
PublicationWe propose the analysis of 2D intensity contour maps which is based on the optical transmission function for the polarizer-specimen-analyzer system. A small modification of the high-accuracy universal polarimeter (HAUP) technique was used to measure the intensity maps (HAUP maps) and determine the phase retardation, linear dichroism (LD) parameters, and multiple light reflection contribution in uniaxial crystals. We have performed...
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Structure, Physicochemical and Biological Properties of an Aqua (2,2′,2′′-Nitrilotriacetato)-oxidovanadium(IV) Salt with 4-Methylpyridinium Cation
PublicationThe crystal structure of a nitrilotriacetate (nta) oxidovanadi-um(IV) salt with 4-methylpyridinium cation, [4-Me(Py)H]+, of [4-Me(Py)H][VO(nta)(H2O)] stoichiometry was determined. The com-plex comprises a discrete mononuclear [VO(nta)(H2O)]–coordinationentity that can be rarely found among other known compounds con-taining nitrilotriacetate oxidovanadium(IV) moieties. The complex wascharacterized by spectroscopic (IR and EPR) methods,...
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Sławomir Jerzy Ambroziak dr hab. inż.
PeopleSławomir J. Ambroziak was born in Poland, in 1982. He received the M.Sc., Ph.D. and D.Sc. degrees in radio communication from Gdańsk University of Technology (Gdańsk Tech), Poland, in 2008, 2013, and 2020 respectively. Since 2008 he is with the Department of Radiocommunication Systems and Networks of the Gdańsk Tech: 2008-2013 as Research Assistant, 2013-2020 as Assistant Professor, and since 2020 as Associate Professor. He is...
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Low cost real time UAV stereo photogrammetry modelling technique – accuracy considerations
PublicationThe paper presents accuracy considerations regarding three 3D modelling techniques. The tested new consumer type stereo camera (ZED 3D Stereolabs) has been implemented info an aerial mapping system, on board micro air vehicle MAV) and tested object has been mapped using a real-time photogrammetry with original real-time software application. The evaluated results has been compared with model gained with a state of art unmanned...
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2-Methylphenyl 2-methoxyacridine-9-carboxylate
PublicationThe title compound, C22H17NO3, crystallizes in the monoclinic space group P21/c with four molecules per unit cell. The molecules are arranged in centrosymmetric pairs, joined via the C and attached H atoms in the meta position relative to the methoxy group. These pairs are bonded in the crystalline phase as a result of non-specific dispersive interactions, and through a network of C—H⋯O interactions involving the non-bonded O...
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Iminodiacetate complex of cobalt(II) – Structure, physicochemical characteristics, biological properties and catalytic activity for 2-chloro-2-propen-1-ol oligomerization
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Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions
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State Interventionism in Tax System - Example of Action in a COVID-19 Crisis
PublicationThe following article presents and classifies changes in tax systems of selected countries as well as counts them as the response to the emergence of the crisis caused by the COVID-19 pandemic. Such actions were undertaken the context of state interventionism in the tax system. In order to achieve the objective of presenting the state interventionism in the context of tax rates, an analysis of the literature on the phenomenon described,...
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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Induction machine behavioral modeling for prediction of EMI propagation.
PublicationThis paper presents the results of wideband behavioral modeling of an induction machine (IM). The proposed solution enables modeling the IM differential- and common-mode impedance for a frequency range from 1 kHz to 10 MHz. Methods of parameter extraction are derived from the measured IM impedances. The developed models of 1.5 kW and 7.5 kW induction machines are designed using the Saber Sketch scheme editor and simulated in the...
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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublicationThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...
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On trees with equal 2-domination and 2-outer-independent domination numbers
PublicationFor a graph G = (V,E), a subset D \subseteq V(G) is a 2-dominating set if every vertex of V(G)\D$ has at least two neighbors in D, while it is a 2-outer-independent dominating set if additionally the set V(G)\D is independent. The 2-domination (2-outer-independent domination, respectively) number of G, is the minimum cardinality of a 2-dominating (2-outer-independent dominating, respectively) set of G. We characterize all trees...
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Research and Analysis of Accuracy of Location Estimation in Inertial Navigation System
PublicationIn the article the research and analysis of digital signal processing and its influence on accuracy of location estimation in developed inertial navigation system was presented. The purpose of the system is to localize moving people in indoor environment. During research a measuring unit for recording selected movement parameters was made. In the article were also described author’s inertial navigation algorithms.
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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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Discrete-Element bonded-particle Sea Ice model DESIgn, version 1.3a – model description and implementation
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Public Finance in Poland in a COVID Fog: A Look Through the Lens of Fiscal Transparency and Accountability
PublicationAbstract. Goal– The aim of the article is to identify dysfunctional phenomena (implementation of specific mechanisms/solutions and actions taken), generating increased opacity and limit the responsibility/accountability of public f inance in Poland, exacerbated by the COVID-19 crisis. Methods– descriptive analysis, comparative analysis and financial analysis methods were used. Results– fiscal transparency and accountability in...
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Empirical analysis of tree-based classification models for customer churn prediction
PublicationCustomer churn is a vital and reoccurring problem facing most business industries, particularly the telecommunications industry. Considering the fierce competition among telecommunications firms and the high expenses of attracting and gaining new subscribers, keeping existing loyal subscribers becomes crucial. Early prediction of disgruntled subscribers can assist telecommunications firms in identifying the reasons for churn and...
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Depth Determination Accuracy of the Modified Prony Method in a Swath Mapping Application
PublicationThis article presents the performance of the modified Prony method in a swath mapping application. Depth determination accuracy is assessed by processing raw signal acquired by an EdgeTech 6205 swath bathymetry system over flat seafloor. An updated version of the method, proposed previously by the authors, is used to determine the number of signal echoes. The number of signal echoes is essential for performing the low-rank approximation...
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Effect of aggregate structure on fracture process in concrete using 2D lattice model
PublicationArtykuł przedstawia symulacje rys w betonie przy zastosowaniu nowego modelu siatkowego. Zbadano wpływ rozkładu i wielkości kruszywa oraz wpływ strefy kontaktu na nośność i propagacje rys. Obliczenia były dwuwymiarowe.
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Improving the Quality of Magnetic Signature Reproduction by Increasing Flexibility of Multi-Dipole Model Structure and Enriching Measurement Information
PublicationThe paper presents the construction of a multi-dipole model that allows reproducing magneticsignatures of ferromagnetic objects. The virtual object used in the paper is an ellipsoid, which is the sourceof synthetic data. To make the situation more realistic, noise is added to the synthetic data. Two significantimprovements compared to previous work are presented. Three-axial magnetometers are introduced insteadof uniaxial magnetometers....
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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Examining Influence of Distance to Microphone on Accuracy of Speech Recognition
PublicationThe problem of controlling a machine by the distant-talking speaker without a necessity of handheld or body-worn equipment usage is considered. A laboratory setup is introduced for examination of performance of the developed automatic speech recognition system fed by direct and by distant speech acquired by microphones placed at three different distances from the speaker (0.5 m to 1.5 m). For feature extraction from the voice signal...
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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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Synthesis and Structure of Novel Copper(II) Complexes with N,O- or N,N-Donors as Radical Scavengers and a Functional Model of the Active Sites in Metalloenzymes
PublicationToevaluatetheantioxidantactivityofpotentialsyntheticenzymemimetics,wepreparednewfivecopper(II)complexesviaaself‐assemblymethodandnamedthem[Cu(2‐(HOCH2)py)3](ClO4)2(1),[Cu(2‐(HOCH2)py)2(H2O)2]SiF6(2),[Cu2(2‐(HOCH2CH2)py)2(2‐(OCH2CH2)py)2](ClO4)2(3),[Cu(pyBIm)3](BF4)2∙1.5H2O(4)and[Cu(py2C(OH)2)2](ClO4)2(5).ThesyntheticprotocolinvolvedN,O‐ orN,N‐donors:2‐(hydroxymethyl)pyridine(2‐(HOCH2)py),2‐(hydroxyethyl)pyridine(2‐(HOCH2CH2)py),2‐(2‐pyridyl)benzimidazole(pyBIm),di(2‐pyridyl)ke‐tone(py2CO).TheobtainedCu(II)complexeswerefullycharacterisedbyelementalanalysis,FTIR,EPR,UV‐Vis,single‐crystalX‐raydiffractionandHirshfeldsurfaceanalysis.Crystallographicandspectroscopicanalysesconfirmedchromophoresofbothmonomeric({CuN3O3}(1),{CuN2O4}(2),{CuN6}(4),{CuN4O2}(5))anddimericcomplex({CuN2O3}(3)).Mostoftheobtainedspeciespos‐sessedadistortedoctahedralenvironment,exceptdimer3,whichconsistedoftwocoppercentreswithsquarepyramidalgeometries.Thewater‐solublecompounds(1,3and5)wereselectedforbiologicaltesting.Theresultsofthestudyrevealedthatcomplex1insolutionsdisplayedbetterradicalscavengingactivitythancomplexes3,5andfreeligands.Therefore,complex1hasbeenselectedforfurtherstudiestotestitsactivityasanenzymemimetic.Thechosencompoundwastestedontheerythrocytelysateoftwogroupsofpatientsafterundergoingchemotherapyandchemoradiotherapy.Theeffectofthetestedcompound(1)onenzymeactivitylevels(TAS,SODandCAT)suggeststhattheselectedcomplexcanbetreatedasafunctionalmimeticoftheenzymes.
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The surface of a fragment of the structure of an integrated circuit in the semi-contact mode.
Open Research DataThe surface of a fragment of the structure of an integrated circuit. Topographic measurements in the semi-contact mode. NTEGRA Prima (NT-MDT) device. NSG 01 probe.
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Review of Selected Methods for Prediction of Added Resistance in Following Waves
PublicationThe added resistance in waves is a mean value of non-linear, second order reaction of a ship to incoming waves. In the beginning of the 20th century, the experimental methods for investigation of ship hydrodynamics at model scale were developed. They allowed the evaluation of added resistance by measurements in irregular waves (directly) or by measurements in regular waves (in-direct method). The main goal was to find more precise...
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Verification of the theoretical methods for the prediction of resistance of sailing yachts based on model test results of a yacht V.O.60
PublicationWeryfikacja opiera się głównie na serii systematycznych badań modelowych wykonanych w roku 2001 w Laboratorium Hydromechaniki Okrętu WOIO PG. Zademonstrowano prognozy oporu jachtu wykonane trzema metodami z oszacowaniem i dyskusją rozbieżności wyników. Przeprowadzone badania są zorientowane na opracowanie wiarygodnego programu komputerowego dla prognozowania prędkości i innych parametrów ruchu żaglowych, regatowych jachtów oceanicznych...
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Proteolysis of whey protein isolates in nanoemulsion systems: impact of nanoemulsification and additional synthetic emulsifiers
PublicationNanoemulsions are currently of interest in the functional food sector because their small droplet size (100–500 nm) provides a number of potential advantages over conventional emulsions. This study concerned the behavior of nanoemulsions stabilized with whey proteins and two synthetic emulsifiers (Tween 80 and Croduret), and exposed to conditions simulating the human upper gastrointestinal tract. In particular, the effect of synthetic...
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Optimized Deep Learning Model for Flood Detection Using Satellite Images
PublicationThe increasing amount of rain produces a number of issues in Kerala, particularly in urban regions where the drainage system is frequently unable to handle a significant amount of water in such a short duration. Meanwhile, standard flood detection results are inaccurate for complex phenomena and cannot handle enormous quantities of data. In order to overcome those drawbacks and enhance the outcomes of conventional flood detection...
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Structure and electrochemical reactivity of 3-[tris(2-methoxyethoxy)silyl]-propanethiol adsorbed on silver surface
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"Creating a numerical model of noise conditions based on the analysis of traffic volume changes in cities with low and medium structure.
PublicationThe subject of this research study is to analyze noise conditions of the selected area in the city of Gdańsk using data related to traffic volume changes during a day. This is because daily distribution of noise levels is much more helpful for noise control and reduction than traditional maps with Lden levels indicated. Calculations are made with the use of a numerical model developed at the Gdansk Univ. of Technology and implemented...
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"Creating a numerical model of noise conditions based on the analysis of traffic volume changes in cities with low and medium structure.
PublicationThe subject of this research study is to analyze noise conditions of the selected area in the city of Gdańsk using data related to traffic volume changes during a day. This is because daily distribution of noise levels is much more helpful for noise control and reduction than traditional maps with Lden levels indicated. Calculations are made with the use of a numerical model developed at the Gdansk Univ. of Technology and implemented...