Search results for: IN SILICO METABOLISM PREDICTION
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Modulation of CYP3A4 activity and induction of apoptosis, necrosis and senescence by the antitumor imidazoacridinone C-1311 in human hepatoma cells
PublicationThere is increasing evidence that the expression level of drug metabolic enzymes affects the final cellular response following drug treatment. Moreover, anti-tumour agents may modulate enzymatic activity and/or cellular expression of metabolic enzymes in tumour cells. We investigated the influence of CYP3A4 overexpression on the cellular response induced by the anti-tumour agent C-1311 in hepatoma cells. C-1311-mediated CYP3A4...
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Lifestyle changes in patients with morbid obesity and type 2 diabetes mellitus during the COVID-19 pandemic
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Employing flowgraphs for forward route reconstruction in video surveillance system
PublicationPawlak’s flowgraphs were utilized as a base idea and knowledge container for prediction and decision making algorithms applied to experimental video surveillance system. The system is used for tracking people inside buildings in order to obtain information about their appearance and movement. The fields of view of the cameras did not overlap. Therefore, when an object was moving through unsupervised areas, prediction was needed...
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A Computationally Efficient Model for Predicting Successful Memory Encoding Using Machine-Learning-based EEG Channel Selection
PublicationComputational cost is an important consideration for memory encoding prediction models that use data from dozens of implanted electrodes. We propose a method to reduce computational expense by selecting a subset of all the electrodes to build the prediction model. The electrodes were selected based on their likelihood of measuring brain activity useful for predicting memory encoding better than chance (in terms of AUC). A logistic...
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Marcin Kulawiak dr hab. inż.
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publication—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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Integration of the sulfate reduction and anammox processes for enhancing sustainable nitrogen removal in granular sludge reactors
PublicationThe Anammox and Sulfate Reduction Ammonium Oxidation processes were compared in two granular sequencing batch reactors operated for 160 days under anammox conditions. It was hypothesized that increasing the concentration of SO42− may positively influence the rate of N removal under anaerobic conditions and it was tested whether SO42− reduction and anammox occur independently or are related to each other. The cooperation of N-S...
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Electrochemistry meets enzymes: Investigation of the biotransformation pathway of C-1311 based on electrochemical simulation in comparison to in vitro methods.
PublicationThe knowledge of the metabolic pathways and the biotransformation of new drugs is one of the major challenges in pharmaceutical research. It is crucial for elucidation of degradation routes of the new biologically active compounds, especially in the area of possible toxicity. Conventional in vitro drug metabolism studies are based on incubating drug candidate with e.g. hepatocytes or, most importantly, liver cell microsomes and...
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Oxylipin profiling for clinical research: Current status and future perspectives
PublicationOxylipins are potent lipid mediators with increasing interest in clinical research. They are usually measured in systemic circulation and can provide a wealth of information regarding key biological processes such as inflammation, vascular tone, or blood coagulation. Although procedures still require harmonization to generate comparable oxylipin datasets, performing comprehensive profiling of circulating oxylipins in large studies...
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Design, synthesis, and molecular docking of new 5-HT reuptake inhibitors based on modified 1,2-dihydrocyclopenta[b] indol-3(4H)-one scaffold
PublicationA new group of serotonin reuptake inhibitors containing 1,2-dihydrocyclopenta[b]indol-3(4H)-one scaffoldwas synthesized, starting from indole 5-((1H-indol-3-yl)(1,3-dioxane-4,6-diones as a key intermediates. Following three transformations including intramolecular cyclization and formation of imines, a series of new ligand for human serotonin transporter was obtained. The ability of these ligands to inhibit human TS3 serotonin transporter...
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Constrained aerodynamic shape optimization using neural networks and sequential sampling
PublicationAerodynamic shape optimization (ASO) involves computational fluid dynamics (CFD)-based search for an optimal aerodynamic shape such as airfoils and wings. Gradient-based optimization (GBO) with adjoints can be used efficiently to solve ASO problems with many design variables, but problems with many constraints can still be challenging. The recently created efficient global optimization algorithm with neural network (NN)-based prediction...
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Electrochemical simulation of metabolic reduction and conjugation reactions of unsymmetrical bisacridine antitumor agents, C-2028 and C-2053
PublicationElectrochemistry (EC) coupled with analysis techniques such as liquid chromatography (LC) and mass spectrometry (MS) has been developed as a powerful tool for drug metabolism simulation. The application of EC in metabolic studies is particularly favourable due to the low matrix contribution compared to in vitro or in vivo biological models. In this paper, the EC(/LC)/MS system was applied to simulate phase I metabolism of the representative...
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3D Computer Model of the Hip Joint Cartilage
PublicationThis paper presents 3D computer model of the hip joint cartilage in the ANSYS program. Model is made on the basis of anatomy and collected data on the material constants of bone and cartilage components. Analysis and comparison of biochemical model, viscoelastic and molecular mixed - aggregation serves to facilitate the creation of the next model of reality, which could be used in the design of joint prostheses. The correctness...
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Hanna Staroszczyk dr hab. inż.
PeopleAbsolwentka Wydziału Inżynierii i Technologii Chemicznej Politechniki Krakowskiej, od 2007 roku pracuje w Katedrze Chemii, Technologii i Biotechnologii Żywności Wydziału Chemicznego Politechniki Gdańskiej. Pracowała w Politechnice Krakowskiej, Akademii Rolniczej w Krakowie, Institute of Food Research w Norwich, Academia Sinica w Tajpej oraz University of Arkansas w Fayetteville. W 2013 roku uzyskała stopień doktora habilitowanego...
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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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The role of intestine and liver in glucuronidation of the imidazo- and triazoloacridinone antitumor agents, C-1311 and C-1305: High affinity substrates for UGT1A10
PublicationCelem przeprowadzonych badań było określenie roli poszczególnych izoform UDP-glukuronylotransferazy (UGT)oraz mikrosomów jelita(HIM)i wątroby (HLM) wyizolowanych od różnych pacjentów w metabolizmie pochodnych akrydonu, związków C-1311 i C-1305. Wykazano, że rodziną UGT katalizującą przemiany C-1305 i C-1311 jest UGT1A, z najwyższą aktywnością wykazywaną przez pozawątrobowy izoenzym UGT1A10. Rozkład aktywności frakcji mikrosomalnych...
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Biotransformation of abused synthetic cannabinoids, JWH-018 and JWH-073, by human cytochromes P450 and UDP-glucuronosyltransferases
PublicationZwiązki oznaczone symbolami JWH-018 i JWH-073 są syntetycznymi pochodnymi kanabinoidów, obecnymi w preparatach o działaniu psychoaktywnym (K2/Spice). Wcześniejsze badań wykazały, że u osób przyjmujących tzw. ''legalną marihuanę'', głównymi produktami biotransformacji obecnymi w moczu były hydroksylowe pochodne obu związków, jak również ich glukuronidy. W związku z tym celem prowadzonych badań było określenie roli poszczególnych...
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Amphotericin B and Its New Derivatives - Mode of Action
PublicationAmphotericin B (AmB) is a well known antifungal and antiprotozoal antibiotic used in the clinic for several decades. Clinicalapplications of AmB, however, are limited by its nephrotoxicity and many other acute side effects which are not acceptable by patientswhen their life is not threaten. In order to improve the therapeutic index of this drug, lipid formulations have been introduced and manyefforts have been made to obtain less...
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Acridinone antitumor agents: C-1311, C-1330 and C-1305 are metabolized by flavin-containing monooxygenase isoenzymes: FMO1, FMO3 and FMO5 with different rates
PublicationRekombinantowe ludzkie monooksygenazy flawinowe: FMO1, FMO3, FMO5 indukują przemiany metaboliczne wybranych do badań pochodnych akrydonu. Biotransformacja związków C-1311, C-1330 i C-1305 przez FMO prowadzi do jednego produktu o strukturze N-tlenku. Wyniki badań wskazują, że najbardziej podatna na przemiany wobec FMO jest pochodna triazoloakrydonu C-1305. Wydaje się więc, że głównymi enzymami pierwszej fazy przemian metabolicznych...
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Genistein: a lysosomal stimulator for treatment of various lysosomal diseases
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The molecular mechanism of genistein action in lysosomal storage diseases: A transcriptomic approach
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Evidence for sex differences in the determinants of homocysteine concentrations
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Disposition of Drugs of Abuse and Their Metabolites in Wastewater as a Method of the Estimation of Drug Consumption
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Genetic Determinants of Vitamin D-Related Disorders; Focus on Vitamin D Receptor
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The Imidazoacridinone Antitumor Drug, C-1311, Is Metabolized by Flavin Monooxygenases but Not by Cytochrome P450s.
PublicationPrezentowane w publikacji wyniki badań mają na celu wyjaśnienie roli enzymów wątrobowych w metabolizmie przeciwnowotworowych pochodnych C-1311 oraz C-1330. Oba związki inkubowane były z frakcją mikrosomalną oraz enzymami rekombinantowymi należącymi do grypy cytochromu P450, FMO oraz UGT. Badania wykazały, że oba związki są metabolizowane przez enzymy frakcji mikrosomalnej, ale nie przez enzymy cytochromu P450. Aktywność enzymatyczna...
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Hyperproteic diet modifies microbiota composition and associated metabolites in rats
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Sulfammox process_task 1
Open Research DataAnaerobic ammonia-oxidizing bacteria have a more comprehensive metabolism thanexpected - there may be other electron acceptors that oxidize ammonium nitrogen under anaerobicconditions, in addition to the well-known nitrite nitrogen, one of which is sulfate in the sulfammoxprocess. Sulfate-containing compounds are part of the medium for the anammox process,...
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Modulation of CYP1A1, CYP1A2 and CYP1B1 expression by cabbage juices and indoles in human breast cell lines
PublicationEpidemiological studies have shown that consumption of cab- bage and sauerkraut is connected with significant reduction of breast cancer incidences. Estrogens are considered a major breast cancer risk factor and their metabolism by P450 enzymes substan- tially contributes to carcinogenic activity. The aim of this study was to investigate the effect of cabbage and sauerkraut juices of differ- ent origin on the expression profile...
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Detoxification of the tricyclic antidepressant opipramol and its analog – IS-noh by UGT enzymes before and after activation by phase I enzymes in rat liver microsomes
PublicationThe present studies were carried out to evaluate the simultaneous one-pot metabolism of opipramol (IS-opi) and analog (IS-noh) by phase I and phase II enzymes present in rat liver microsomes (RLM) as an alternative to separate testing with recombinant enzymes. This approach allows for more time-saving and cost-effective screening of the metabolism of newly discovered drugs. We also considered that the lack of results for phase...
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Evaluation of Response Amplitude Operator of Ship Roll Motions Based on the Experiments in White Noise Waves
PublicationEvaluation of the response amplitude operator (RAO) function for ship wave frequency motions by means of scale model tests in regular waves is a standard procedure conducted by hydrodynamic model testing institutions. The resulting RAO function allows for evaluating sufficiently reliable seakeeping predictions for low to moderate sea states. However, for standard hull forms, correct prediction of roll motion in irregular wave (and...
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Detection of impulsive disturbances in archive audio signals
PublicationIn this paper the problem of detection of impulsive disturbances in archive audio signals is considered. It is shown that semi-causal/noncausal solutions based on joint evaluation of signal prediction errors and leave-one-out signal interpolation errors, allow one to noticeably improve detection results compared to the prediction-only based solutions. The proposed approaches are evaluated on a set of clean audio signals contaminated...
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Impact of Low Switching-to-Fundamental Frequency Ratio on Predictive Current Control of PMSM: A simulation study
PublicationPredictive current control algorithms for permanent magnet synchronous (PMSM) drives rely on an assumption that within short intervals motor currents can be approximated with linear functions. This approximation may result either from discretizing the motor model or from simplifications applied to the continuous-time model. As the linear current approximation has been recognized as inaccurate in case when the drive operates with...
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Analiza bibliometryczna w badaniach dotyczących prognozowania upadłości przedsiębiorstw w Polsce
PublicationCelem opracowania jest ukazanie obrazu piśmiennictwa poświęconego zagadnieniom prognozowania upadłości przedsiębiorstw w Polsce. Jako metodę badawczą zastosowano analizę bibliometryczną. Do analizy wykorzystano bazę Google Scholar oraz narzędzie Publish or Perish 7. Okresem badań objęto lata 1995– 2019. Jako frazy do wyszukiwania publikacji zastosowano: „prognozowanie upadłości”, „prognozowanie zagrożenia finansowego”, „systemy...
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Identification of ship’s hull mathematical model with numerical methods
PublicationThe modern maritime industry is moving toward the development of technology that will allow for full or partial autonomy of ship operation. This innovation places high demands on ship performance prediction techniques at the design stage. The researchwork presented in the article is related to the design stage of the ship and concerns methods for prognosis and evaluation of the specific operational condition of the ship, namely...
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Wireless intelligent audio-video surveillance prototyping system
PublicationThe presented system is based on the Virtex6 FPGA and several supporting devices like a fast DDR3 memory, small HD camera, microphone with A/D converter, WiFi radio communication module, etc. The system is controlled by the Linux operating system. The Linux drivers for devices implemented in the system have been prepared. The system has been successfully verified in a H.264 compression accelerator prototype in which the most demanding...
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New Approaches for Escherichia coli Genotyping
PublicationEasy-to-perform, fast, and inexpensive methods of differentiation of Escherichia coli strains beyond the species level are highly required. Herein two new, original tools for genotyping of E. coli isolates are proposed. The first of the developed method, a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) test uses a highly variable fliC gene, encoding the H antigen as a molecular target. The designing...
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Elimination of impulsive disturbances from archive audio files – comparison of three noise pulse detection schemes
PublicationThe problem of elimination of impulsive disturbances (such as clicks, pops, ticks, crackles, and record scratches) from archive audio recordings is considered and solved using autoregressive modeling. Three classical noise pulse detection schemes are examined and compared: the approach based on open-loop multi-step-ahead signal prediction, the approach based on decision-feedback signal prediction, and the double threshold approach,...
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CYP3A4-dependent cellular response does not relate to CYP3A4-catalysed metabolites of C-1748 and C-1305 acridine antitumor agents in HepG2 cells
PublicationHigh CYP3A4 expression sensitizes tumor cells to certain antitumor agents while for others it can lower their therapeutic ef fi cacy. We have elucidated the in fl uence of CYP3A4 overexpression on the cellular response induced by antitumor acridine derivatives, C-1305 and C-1748, in two hepatocellular carcinoma (HepG2) cell lines, Hep3A4 stably transfected with CYP3A4 isoenzyme, and HepC34 expressing empty vector. The compounds...
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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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Metabolic Profiles of New Unsymmetrical Bisacridine Antitumor Agents in Electrochemical and Enzymatic Noncellular Systems and in Tumor Cells
PublicationNew unsymmetrical bisacridines (UAs) demonstrated high activity not only against a set of tumor cell lines but also against human tumor xenografts in nude mice. Representative UA compounds, named C-2028, C-2045 and C-2053, were characterized in respect to their physicochemical properties and the following studies aimed to elucidate the role of metabolic transformations in UAs action. We demonstrated with phase I and phase II enzymes...
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Efficient uncertainty quantification using sequential sampling-based neural networks
PublicationUncertainty quantification (UQ) of an engineered system involves the identification of uncertainties, modeling of the uncertainties, and the forward propagation of the uncertainties through a system analysis model. In this work, a novel surrogate-based forward propagation algorithm for UQ is proposed. The proposed algorithm is a new and unique extension of the recent efficient global optimization using neural network (NN)-based...
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Investigation of the C-1311 glucuronidation: an electrochemical approach
Open Research DataThis study was undertaken to investigate the glucuronidation of the compound C-1311 (5-diethylaminoethylamino-8-hydroxyimidazoacridinone – the model anticancer acridine derivative) using electrochemistry/mass spectrometry (EC/MS) as a complementary technique to in vitro (liver microsomes) and in silico approaches.
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Plasma free amino acid profiling as metabolomic diagnostic and prognostic biomarker in paediatric cancer patients: a follow‑up study
PublicationAmino acids (AAs) play a crucial role in cancer cell metabolism. Levels of 22 plasma AAs at the time of diagnosis and after treatment were established among 39 pediatric cancer patients and 33 healthy children. Glutamic acid levels decreased and tryptophan levels increased during treatment. Cancer patients presented significantly lower levels of glutamine and leucine post-treatment while levels of 12 other AAs were higher comparing...
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On ship roll resonance frequency
PublicationThe paper deals with the problem of modeling of rolling motion under a variety of excitation parameters. Special emphasis is put on the analysis and prediction of the frequency of the resonant mode of rolling, since it is often an essential issue in terms of motion of a ship related to her safety against capsizing or excessive amplitudes of roll. The research is performed for both free rolling and excited rolling and it is based...
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Elimination of clicks from archive speech signals using sparse autoregressive modeling
PublicationThis paper presents a new approach to elimination of impulsivedisturbances from archive speech signals. The proposedsparse autoregressive (SAR) signal representation is given ina factorized form - the model is a cascade of the so-called formantfilter and pitch filter. Such a technique has been widelyused in code-excited linear prediction (CELP) systems, as itguarantees model stability. After detection of noise pulses usinglinear...
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New semi-causal and noncausal techniques for detection of impulsive disturbances in multivariate signals with audio applications
PublicationThis paper deals with the problem of localization of impulsive disturbances in nonstationary multivariate signals. Both unidirectional and bidirectional (noncausal) detection schemes are proposed. It is shown that the strengthened pulse detection rule, which combines analysis of one-step-ahead signal prediction errors with critical evaluation of leave-one-out signal interpolation errors, allows one to noticeably improve detection results...
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Global Surrogate Modeling by Neural Network-Based Model Uncertainty
PublicationThis work proposes a novel adaptive global surrogate modeling algorithm which uses two neural networks, one for prediction and the other for the model uncertainty. Specifically, the algorithm proceeds in cycles and adaptively enhances the neural network-based surrogate model by selecting the next sampling points guided by an auxiliary neural network approximation of the spatial error. The proposed algorithm is tested numerically...
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Trim Optimisation - Theory and Practice
PublicationForce Technology has been working intensively with trim optimisation tests for almost last 10 years. Focus has primarily been put on the possible power savings and exhaust gases reduction. This paper describes the trim optimisation process for a large cargo vessel. The physics behind changed propulsive power is described and the analyses in order to elaborate the optimum trimmed conditions are presented. Different methods for prediction...
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Chemistry and Nanochemistry 2022.
e-Learning CoursesThe course consists of lectures (15 x 2 hours) and laboratories (5 x 3 hours).The goal of this course is to teach general chemistry and adequately apply it to nano-size systems, their synthesis and analysis. An emphasis is laid on an analysis of electronic structure of molecules and prediction of resulting properties and reasons of consequent behaviour in chemical reactions. The course also encloses laboratory classes, where the...
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Traffic Noise Analysis Applied to Automatic Vehicle Counting and Classification
PublicationProblems related to determining traffic noise characteristics are discussed in the context of automatic dynamic noise analysis based on noise level measurements and traffic prediction models. The obtained analytical results provide the second goal of the study, namely automatic vehicle counting and classification. Several traffic prediction models are presented and compared to the results of in-situ noise level measurements. Synchronized...