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Search results for: CASP, COVID, EMA, MODEL ACCURACY, PROTEIN STRUCTURE PREDICTION, SARS-COV-2
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PROTEIN SCIENCE
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Stochastic model of the process of starting piston combustion engines and the practical use of the process
PublicationW artykule zaproponowano model procesu rozruchu silników o zapłonie samoczynnym, w formie procesu semimarkowskiego, dyskretnego w stanach i ciągłego w czasie eksploatacji. Stanami tego procesu są: stan zimny silnika (s1), stan ciepły silnika (s2) i stan gorący silnika (s3). Zaproponowano również koncepcję zastosowania opracowanego modelu do określenia ilości substancji szkodliwych, jakie emitowane są w spalinach podczas rozruchu...
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Accuracy of Pretreatment Ultrasonography Assessment of Intra-Abdominal Spread in Epithelial Ovarian Cancer: A Prospective Study
PublicationThe aim of this study was to test the accuracy of ultrasonography performed by gynecological oncologists for the preoperative assessment of epithelial ovarian cancer (EOC) spread in the pelvis and abdominal cavity. A prospective, observational cohort study was performed at a single tertiary cancer care unit. Patients with suspected EOC were recruited and underwent comprehensive transvaginal and abdominal ultrasonography performed...
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Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
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Paweł Burdziakowski dr inż.
PeoplePaweł Burdziakowski, PhD, is a professional in low-altitude aerial photogrammetry and remote sensing, marine and aerial navigation. He is also a licensed flight instructor and software developer. His main areas of interest are digital photogrammetry, navigation of unmanned platforms and unmanned systems, including aerial, surface, underwater. He conducts research in algorithms and methods to improve the quality of spatial measurements...
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Prediction of manoeuvring abilities of 10000 DWT pod-driven coastal tanker
PublicationThis paper aims to present a new approach in the prediction of manoeuvring abilities of pod-driven ships. A new mathematical model of motions based on MMG methodology was developed and a new type of description of forces acting on azimuth drives is presented. Captive model tests of medium-size coastal tanker and pod open water tests were carried out in CTO S.A. (Ship Design and Research Centre S.A.) to obtain hull hydrodynamic derivatives...
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Accuracy analysis of 3D model obtained by photogrammetric method on the example of historic room from Wisłoujście Fortress
PublicationThe article presents a comparison of obtained models of a test object. Close range photogrammetry was used to obtain 3D models. As test object was used one of the rooms located in Wisłoujście Fortress in Gdańsk, Poland. Different models were obtained by using different distribution and number of reference points. Article contains analysis of differences between coordinates of control points obtained from total station measurements...
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Stochastic model of the load spectrum for main engines of sea-going ships
PublicationW artykule przedstawiono możliwość zastosowania procesów semimarkowskich do probabilistycznego opisu widma obciążeń silników o zapłonie samoczynnym, zastosowanych do napędu statków - czyli silników głównych. W rozważaniach uwzględnione zostały charakterystyki zewnętrzne mocy tego rodzaju silników. Umożliwiły one sformułowanie czteroelementowego zbioru stanów procesu obciążeń tego rodzaju silników. Do opisu rzeczywistego procesu...
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Model Assisted Statistics and Applications
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Viscoelastic model of waterhammer in single pipeline - problems and questions
PublicationW artykule dokonano analizy zastosowania lepkosprężystego modelu uderzenia hydraulicznego w pojedynczym przewodzie. Przedstawiono teoretyczne podstawy lepkosprężystego zachowania się materiału przewodu oraz matematyczny opis modelu uderzenia hydraulicznego w rurociągu z tworzywa sztucznego. Przedyskutowano główne problemy pojawiające się przy aplikacji takiego modelu. Nacisk położono na identyfikację parametrów modelu. Przeanalizowano...
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Prediction Model for Hemorrhagic Complications after Laparoscopic Sleeve Gastrectomy: Development of SLEEVE BLEED Calculator
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Rapid antenna design optimization using shape-preserving response prediction
PublicationAn approach to rapid optimization of antennas using the shape-preserving response-prediction (SPRP) technique and coarsediscretization electromagnetic (EM) simulations (as a low-fidelity model) is presented. SPRP allows us to estimate the response of the high-fidelity EM antenna model, e.g., its reflection coefficient versus frequency, using the properly selected set of so-called characteristic points of the low-fidelity model...
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The accuracy of a new approach to order determination for the Modified Prony method in swath mapping application
PublicationThis article presents the performance of a new approach to determine the model order for the modified Prony method applied to swath acoustic mapping. Key requirements for any mapping application are depth determination accuracy and angular resolution. Depth determination accuracy is strictly related to angular accuracy and geometrical relations between receiver and sources of the backscattered signal. Angular resolution determines...
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Mapping of the Covid-19 Vaccine Uptake Determinants From Mining Twitter Data
PublicationOpinion polls on vaccine uptake clearly show that Covid-19 vaccine hesitancy is increasing worldwide. Thus, reaching herd immunity not only depends on the efficacy of the vaccine itself, but also on overcoming this hesitancy of uptake in the population. In this study, we revealed the determinants regarding vaccination directly from people’s opinions on Twitter, based on the framework of the 6As taxonomy. Covid-19 vaccine acceptance...
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Using MusicXML to evaluate accuracy of OMR Systems
PublicationIn this paper a methodology for automatic accuracy evaluation in optical music recognition (OMR) applications is proposed. Presented approach assumes using ground truth images together with digital music scores describing their content. The automatic evaluation algorithm measures differences between the tested score and the reference one, both stored in MusicXML format. Some preliminary test results of this approach are presented...
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Analysis of muscles behaviour. Part II. The computational model of muscles group acting on the elbow joint
PublicationThe purpose of this paper is to present the computational model of muscles' group describing the movements of flexion/extension at the elbow joint in the sagittal plane of the body when the forearm is being kept in the fixed state of supination/pronation. The method ofevaluating the muscle forces is discussed in detail. This method is the basis for the quantitative and qualitative verification of the proposed computational model...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Diagnostic model of compression-ignition engine slide bearings for controlling the changes of their state
PublicationW artykule przedstawiono koncepcję umożliwiającą sterowanie procesami zmian stanów eksploatacyjnych silnika na podstawie modelu diagnostycznego łożysk ślizgowych. Jako model łożyska ślizgowego przyjęty został topologiczny model diagnostyczny, pozwalający na pełne i dokładne wykorzystanie oleju smarowego jako jednego z nośników informacji o stanie technicznym łożyska. Przedstawiona została przykładowa interpretacja stanów eksploatacyjnych...
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Three-dimensional geographically weighted inverse regression (3GWR) model for satellite derived bathymetry using Sentinel-2 observations
PublicationCurrent trends of development of satellite derived bathymetry (SDB) models rely on applying calibration techniques including analytical approaches, neuro-fuzzy systems, regression optimization and others. In most of the cases, the SDB models are calibrated and verified for test sites, that provide favourable conditions for the remote derivation of bathymetry such as high water clarity, homogenous bottom type, low amount of sediment...
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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DL_MG: A Parallel Multigrid Poisson and Poisson–Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution
PublicationThe solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential -- a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the...
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Robust output prediction of differential – algebraic systems – application to drinking water distribution system
PublicationThe paper presents the recursive robust output variable prediction algorithm, applicable for systems described in the form of nonlinear algebraic-differential equations. The algorithm bases on the uncertainty interval description, the system model, and the measurements. To improve the algorithm efficiency, nonlinear system models are linearised along the nominal trajectory. The effectiveness of the algorithm is demonstrated on...
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublicationRadiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g.,...
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Multistage generalized adaptive notch filter with improved accuracy
PublicationGeneralized adaptive notch filters (GANFs) are estimators of coefficients of quasi-periodically time-varying systems. Current state of the art GANFs can deliver highly accurate estimates of system variations’ frequency, but underperform in terms of accuracy of the coefficient estimates. The paper proposes a novel multistage GANF with accuracy improved in this aspect. The processing pipeline consists of three stages. The preliminary...
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Anti-plane surface waves in media with surface structure: Discrete vs. continuum model
PublicationWe present a comparison of the dispersion relations derived for anti-plane surface waves using the two distinct approaches of the surface elasticity vis-a-vis the lattice dynamics. We consider an elastic half-space with surface stresses described within the Gurtin–Murdoch model, and present a formulation of its discrete counterpart that is a square lattice half-plane with surface row of particles having mass and elastic bonds different...
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Electron collisions with methyl-substituted ethylenes: Cross section measurements and calculations for 2-methyl–2-butene and 2,3-dimethyl–2-butene
PublicationWe report electron-scattering cross sections determined for 2-methyl–2-butene [(H3C)HC==C(CH3)2] and 2,3-dimethyl–2-butene [(H3C)2C=C(CH3)2] molecules. Absolute grand-total cross sections (TCSs) were measured for incident electron energies in the 0.5–300 eV range, using a linear electron-transmission technique. The experimental TCS energy dependences for the both targets appear to be very similar with respect to the shape. In each...
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Krzysztof Jan Kaliński prof. dr hab. inż.
PeopleKrzysztof J. Kaliński completed his MSc study at Gdańsk University of Technology (GUT) Faculty of Production Engineering (1980, result – get a first). He obtained PhD at GUT Faculty of Machine Building (1988, result – get a first), DSc at GUT Faculty of Mechanical Engineering (ME) (2002, result – get a first), and professor’s title – w 2013 r. In 2015 r. he became full professor.His research area includes: theoretical and applied...
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Study on the accuracy of axle load spectra used for pavement design
PublicationWeigh-in-Motion (WIM) systems are used in order to reduce the number of overloaded vehicles. Data collected from WIM provide characteristics of vehicle axle loads that are crucial for pavement design as well as for the development of pavement distress prediction models. The inaccuracy of WIM data lead to erroneous estimation of traffic loads and in consequence inaccurate prediction of pavement distress process. The objective of...
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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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ADVANCES IN PROTEIN CHEMISTRY
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JOURNAL OF PROTEIN CHEMISTRY
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Protein overproduction alters exosome secretion in Chinese hamster ovary cells
PublicationDespite the abundance of available cell lines, nearly 70% of all recombinant therapeutic proteins today are produced in Chi-nese hamster ovary (CHO) cells. The impact of protein overproduction on the secretion of exosomes by CHO cells has been investigated here. Increased secretion of extracellular vesicles (EVs) by protein overexpressing CHO cells was demonstrated with protein content assay, nanoparticle tracking analysis, and...
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Changes in the structure of Armenia’s labour resources between 1993 and 2020
PublicationThe article characterises the structure of Armenia’s labour resources in the period between1993 and 2020. It aims to assess the changes on the Armenian labour market by means of a deductive analysis of historical data and observation of changes in the structure of resources based on generally available macroeconomic data. The authors evaluate these processes against the background of demographic and economic changes, by presenting...
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Research on deformations of laser-welded joint of a steel sandwich structure model.
PublicationPrzedstawiono problemy związane z zachowaniem złącza laserowego pod obciążeniem zginającym. Pokazano wyniki badań laboratoryjnych dla określenia mechanizmu pracy złącza i przedyskutowano uzyskane rezultaty.
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Jacek Tejchman prof. dr hab. inż.
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Programmes to Combat the Economic Impact of the COVID-19 Pandemic in Kazakhstan and Ukraine and Unemployment
PublicationThe following article presents economic programmes to combat the negative effects of the COVID-19 pandemic. The analysed programmes were undertaken by the governments of Ukraine and Kazakhstan. They contributed to reducing unemployment in both countries. The findings of Ukrainian researchers focused mainly on estimating losses in the SME sector, especially in the hotel, tourism and transport sectors. Scientific literature in Kazakhstan...
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1,3-Dibenzylimidazolidine-2-thione
PublicationW strukturze 1,3-Dibenzylimidazolidino-2-tionu w ciele stałym pierścień imidazolidy występuje w konformacji skręconej (Twisted). Stwierdzono obecność oddziaływań międzycząsteczkowych (typu π-π stacking) pomiędzy pierścieniami fenylowymi reszt benzylowych.
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Fast and reliable knowledge-based design closure of antennas by means of iterative prediction-correction scheme
PublicationA novel framework for expedited antenna optimization with an iterative prediction-correction scheme is proposed. The methodology is comprehensively validated using three real-world antenna structures: narrow-band, dual-band and wideband, optimized under various design scenarios. The keystone of the proposed approach is to reuse designs pre-optimized for various sets of performance specifications and to encode them into metamodels...
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Analysis of the Accuracy of Pulse Estimation Using Smart Watches
PublicationThe purpose of this paper is to perform an analysis of the accuracy of the pulse estimation by comparing readings from a smartwatch with readings from medical devices. The study required writing applications that allow continuous pulse measurement. As a result, two applications were created for the smartwatch. The first one is dedicated to Android Wear devices, while the other one is compatible with Tizen watches. The next step...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Color prediction from first principle quantum chemistry computations: a case of alizarin dissolved in methanol
PublicationThe electronic spectrum of alizarin (AZ) in methanol solution was measured and used as reference data for color prediction. The visible part of the spectrum was modelled by different DFT functionals within the TD-DFT framework. The results of a broad range of functionals applied for theoretical spectrum prediction were compared against experimental data by a direct color comparison. The tristimulus model of color expressed in terms...
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublicationFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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The Effect of Flexible Pavement Mechanics on the Accuracy of Axle Load Sensors in Vehicle Weigh-in-Motion Systems
PublicationWeigh-in-Motion systems are tools to prevent road pavements from the adverse phenomena of vehicle overloading. However, the effectiveness of these systems can be significantly increased by improving weighing accuracy, which is now insufficient for direct enforcement of overloaded vehicles. Field tests show that the accuracy of Weigh-in-Motion axle load sensors installed in the flexible (asphalt) pavements depends on pavement temperature...
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The accuracy of pulse rate estimation from the sequence of face images
PublicationThe goal of this paper is to analyze the accuracy of pulse rate estimation from the sequence of face images. Simulated and real signals were used to evaluate two pulse rate estimators; one for frequency domain and the second one for time domain using the autocorrelation function. The results show that the mean difference between the reference measurements and estimated pulse rate values are about 2bpm. In the analysis of short...
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Belief in the importance of socially responsible behaviors – the significance of trust and personal experiences with COVID-19
PublicationA vast number of studies have shown that trust is related to socially desirable traits and behaviors. In the present research we have investigated the relationship between generalized trust and beliefs about the importance of socially responsible behaviors (SRB) during the pandemic – namely, following the sanitary regime and getting vaccinated. Basing on the previous findings we assumed that trustful people...
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Solubility of sulfanilamide in binary solvents containing water: Measurements and prediction using Buchowski-Ksiazczak solubility model
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Model Based Monitoring of Dynamic Loads and Remaining Useful Life Prediction in Rolling Mills and Heavy Machinery
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Experimental investigations and prediction of WEDMed surface of nitinol SMA using SinGAN and DenseNet deep learning model
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