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Search results for: AMBIGUOUS RESTRAINTS, COARSE-GRAINED MODELS, NMR-ASSISTED PROTEIN-STRUCTURE MODELING, UNRES
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Key issues in modeling and optimization of lignocellulosic biomass fermentative conversion to gaseous biofuels
PublicationThe industrial-scale production of lignocellulosic-based biofuels from biomass is expected to benefit society and the environment. The main pathways of residues processing include advanced hydrolysis and fermentation, pyrolysis, gasification, chemical synthesis and biological processes. The products of such treatment are second generation biofuels. The degree of fermentation of organic substances depends primarily on their composition...
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Overview of new product development strategies and models
PublicationMotivation: The motivation for the overview presented in this article is to provide a starting point for considering whether existing new product development methodology and its level of detail allows product teams to develop high-quality and business-effective product concepts. Aim: The aim of this article is recognise the current state of research into new product development methodology and to present the strategies and models...
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Bio-based polyester polyols for polyurethane foams - chemical structure of reference sample
Open Research DataPresented dataset includes the results of FTIR and H NMR spectroscopy of bio-based polyester polyol - poly(propylene succinate) (reference sample for materials obtained during MINIATURA 4 project realization).
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Video DATA - Traffic generation modeling for discount shops - Rakoczego Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 21 Rakoczego street in Gdansk. The data covers the day 01.10.2020 at 6:00-10:00. The video camera was installed niearby the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split and the...
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Reliable data-driven modeling of high-frequency structures by means of nested kriging with enhanced design of experiments
PublicationData-driven (or approximation) surrogate models have been gaining popularity in many areas of engineering and science, including high-frequency electronics. They are attractive as a way of alleviating the difficulties pertinent to high computational cost of evaluating full-wave electromagnetic (EM) simulation models of microwave, antenna, and integrated photonic components and devices. Carrying out design tasks that involve massive...
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Limitations of WSSUS modeling of stationary underwater acoustic communication channel
PublicationPerformances of underwater acoustic communication (UAC) systems are strongly related to specific propagation conditions of the underwater channel. Due to their large variability, there is a need for adaptive matching of the UAC systems signaling to the transmission properties of the channel. This requires a knowledge of instantaneous channel characteristics, in terms of the specific parameters of stochastic models. The wide-sense...
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Adaptive Method for Modeling of Temporal Dependencies between Fields of Vision in Multi-Camera Surveillance Systems
PublicationA method of modeling the time of object transition between given pairs of cameras based on the Gaussian Mixture Model (GMM) is proposed in this article. Temporal dependencies modeling is a part of object re-identification based on the multi-camera experimental framework. The previously utilized Expectation-Maximization (EM) approach, requiring setting the number of mixtures arbitrarily as an input parameter, was extended with the...
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Conformational studies of neurohypophyseal hormones analogues with glycoconjugates by NMR spectroscopy
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NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide
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Hybridization-driven gap in U3Bi4Ni3: A 209Bi NMR/NQR study
PublicationZostały przeprowadzone badania jądrowego rezonansu magnetycznego (na jądrach 209Bi) na kryształach U3Bi4Ni3. U3Ni4Bi3 jest tzw. izolatorem typu Kondo.
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Intelligent Decision Forest Models for Customer Churn Prediction
PublicationCustomer churn is a critical issue impacting enterprises and organizations, particularly in the emerging and highly competitive telecommunications industry. It is important to researchers and industry analysts interested in projecting customer behavior to separate churn from non‐churn consumers. The fundamental incentive is a firm’s intent desire to keep current consumers, along with the exorbitant expense of gaining new ones....
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Early Stages of RNA-Mediated Conversion of Human Prions
PublicationPrion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...
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Quantitative structure—retention relationship modeling of the retention behavior of selected antipsychotic drugs in normal-phase thin-layer chromatography
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Mechanisms positioned in a neighbourhood of their singular positions - velocity amplification in the electromagnetic damping. Part 1 - Background of the mechanical structure modeling
PublicationW pracy przedstawiono metodę modelowania dynamiki drgającego hybrydowego układu mechanicznego złożonego z odkształcalnego podukładu ciągłego oraz z połączonego z nim mechanizmu. U układzie pojawiają się drgania części odkształcalnej. By je wytłumić, ich energia zamieniana jest w energię elektryczną (za pomocą prądnicy prądu stałego) i rozpraszana na oporności obecnej w układzie elektrycznym. Aby przyśpieszyć tłumienie, wprowadzony...
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Modeling the application of steel slag in stabilizing expansive soil
PublicationThe objective of this study was to evaluate the suitability of steel slag as an additive to the engineering properties of weak clay soil. Different geotechnical laboratory tests were conducted on both stabilized and natural soils. Steel slag (SS) was added at a rate of 0, 5, 10, 15, 20, and 25% to the soil. Specific gravity, grain size analysis, Atterberg limit test, compaction test, free swell, California bearing ratio (CBR),...
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Comparative testing of numerical models of river ice jams
PublicationIce processes in general, and ice jams in particular, play a dominant role in the hydrologic regime of Canadian rivers, often causing extreme floods and affecting the life cycle of many aquatic, terrestrial, and avian species. Various numerical models have been developed to help simulate the formation and consequences of these very dynamic and often destructive jam events. To test and compare the performance of existing models,...
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A Concept of Modeling and Optimization of Applications in Large Scale Systems
PublicationThe chapter presents the idea that includes modeling and subsequent optimization of application execution on large scale parallel and distributed systems. The model considers performance, reliability and power consumption. It should allow easy modeling of various classes of applications while reflecting key parameters of both the applications and two classes of target systems: clusters and volunteer based systems. The chapter presents...
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Modelling Coarse Particulate Matter PM10 Concentration in the Tricity Area Using GIS
PublicationEnvironmental pollution is an issue of global concern, with Particulate Matter (PM) poisoning being a prime cause of lung cancer. This has led the European Commission to establish strict daily and annual PM concentration limits. The monitoring of air quality in major cities is the responsibility of European Member States. The Tricity, a 414.81 km 2 area in northern Poland, is monitored by a network of only 9 stations operated by...
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Modeling of traffic safety indictors on Polish national road network
PublicationAlthough decreased from 2001 to 2013, Poland’s road deaths improved at a slower rate than the rest of the EU, leaving Poland as one of the worst road safety performing countries in the EU. The national road network in Poland, despite the dynamic transformation and development, still does not conform to the EU safety standards. Similar situation exists in other EU countries, particularly those in Central and Eastern Europe. Safety...
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DESIGN LOGICAL LINGUISTIC MODELS TO CALCULATE NECESSITY IN TRUCKS DURING AGRICULTURAL CARGOES LOGISTICS USING FUZZY LOGIC
Publication: The study is aimed to develop the logic-linguistic models to design a number of rules for the correct calculation of the vehicles needed, taking into account the technical, technological, and weather and climate conditions of the harvesting and transport complex. The article has shown that the construction of the design of logic-linguistic models was not performed earlier to solve the problem of the agro-industrial production...
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Rothe’s method for physiologically structured models with diffusion
PublicationWe consider structured population models with diffusion and dynamic boundary conditions. The respective approximation, called Rothe’s method, produces positive and exponentially bounded solutions. Its solutions converge to the exact solution of the original PDE.
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Adaptive Sampling for Non-intrusive Reduced Order Models Using Multi-Task Variance
PublicationNon-intrusive reduced order modeling methods (ROMs) have become increasingly popular for science and engineering applications such as predicting the field-based solutions for aerodynamic flows. A large sample size is, however, required to train the models for global accuracy. In this paper, a novel adaptive sampling strategy is introduced for these models that uses field-based uncertainty as a sampling metric. The strategy uses...
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Multi-objective optimization of expensive electromagnetic simulation models
PublicationVast majority of practical engineering design problems require simultaneous handling of several criteria. For the sake of simplicity and through a priori preference articulation one can turn many design tasks into single-objective problems that can be handled using conventional numerical optimization routines. However, in some situations, acquiring comprehensive knowledge about the system at hand, in particular, about possible...
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Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublicationToxoplasma gondii is an important zoonotic protozoan that infects a wide variety of vertebrates as intermediate hosts. For this reason, the diagnosis of this disease is very important and requires continuous improvement. One possibility is to use recombinant antigens in serological tests. Apical membrane antigen 1 (AMA1), a protein located in specific secretory organelles (micronemes) of T. gondii, is very interesting in regard...
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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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Instrument detection and pose estimation with rigid part mixtures model in video-assisted surgeries
PublicationLocalizing instrument parts in video-assisted surgeries is an attractive and open computer vision problem. A working algorithm would immediately find applications in computer-aided interventions in the operating theater. Knowing the location of tool parts could help virtually augment visual faculty of surgeons, assess skills of novice surgeons, and increase autonomy of surgical robots. A surgical tool varies in appearance due to...
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Integrate-and-fire models with an almost periodic input function
PublicationWe investigate leaky integrate-and-fire models (LIF models for short) driven by Stepanov and μ-almost periodic functions. Special attention is paid to the properties of the firing map and its displacement, which give information about the spiking behavior of the considered system. We provide conditions under which such maps are well-defined and are uniformly continuous. We show that the LIF models with Stepanov almost periodic...
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Mariusz Kaczmarek dr hab. inż.
PeopleReceived M.Sc., Eng. in Electronics in 1995 from Gdansk University of Technology, Ph.D. in Medical Electronics in 2003 and habilitation in Biocybernetics and Biomedical Engineering in 2017. He was an investigator in about 13 projects receiving a number of awards, including four best papers, practical innovations (7 medals and awards) and also the Andronicos G. Kantsios Award and Siemens Award. Main research activities: the issues...
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Modeling SPMD Application Execution Time
PublicationParallel applications in a Single Process Multiple Data paradigm assume splitting huge amounts of data to multiple processors working in parallel at small data packets. As the individual data packets are not independent, the processors must interact with each other to exchange results of the calculations with their adjacent partners and take these results into account in their own computations. An example of SPMD is geometric parallelism...
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Identification of models and signals robust to occasional outliers
PublicationIn this paper estimation algorithms derived in the sense of the least sum of absolute errors are considered for the purpose of identification of models and signals. In particular, off-line and approximate on-line estimation schemes discussed in the work are aimed at both assessing the coefficients of discrete-time stationary models and tracking the evolution of time-variant characteristics of monitored signals. What is interesting,...
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Identification of models and signals robust to occasional outliers
PublicationIn this paper estimation algorithms derived in the sense of the least sum of absolute errors are considered for the purpose of identification of models and signals. In particular, off-line and approximate on-line estimation schemes discussed in the work are aimed at both assessing the coefficients of discrete-time stationary models and tracking the evolution of time-variant characteristics of monitored signals. What is interesting,...
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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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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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4D Models in World Wide Web
PublicationThe paper presents some results of research curried out within the framework of the European project named "Cultural Heritage Through Time" (CHT2). One of the main project aims were to develop a methodology for sharing multi-temporal information via the Internet (webGIS) for remote analysis of structures and landscapes over time. Reported in this paper results are focused on testing two technologies (Hexagon and Esri) for online...
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Simulation-Driven Antenna Modeling by Means of Response Features and Confined Domains of Reduced Dimensionality
PublicationIn recent years, the employment of full-wave electromagnetic (EM) simulation tools has become imperative in the antenna design mainly for reliability reasons. While the CPU cost of a single simulation is rarely an issue, the computational overhead associated with EM-driven tasks that require massive EM analyses may become a serious bottleneck. A widely used approach to lessen this cost is the employment of surrogate models, especially...
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Expedited Acquisition of Database Designs for Reduced-Cost Performance-Driven Modeling and Rapid Dimension Scaling of Antenna Structures
PublicationFast replacement models have been playing an increasing role in high-frequency electronics, including the design of antenna structures. Their role is to improve computational efficiency of the procedures that normally entail large numbers of expensive full-wave electromagnetic (EM) simulations, e.g., parametric optimization or uncertainty quantification. Recently introduced performance-driven modeling methods, such as the nested...
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The structure, including stereochemistry, of levorin A1
PublicationThe constitution and stereostructure of levorin A1 1, an aromatic heptaeneantifungal antibiotic, was established on the basis of NMR studies, which contained DQFCOSY,ROESY, HSQC and HMBC experiments. Mycosamine moiety was used as an internalchiral probe to determine the absolute configuration of levorin A1 stereogenic centers: 13S,15R, 17S, 18R, 19S, 21R. The relative configuration of the remaining stereogenic centers wasassigned...
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Innovations in Wastewater Treatment: Harnessing Mathematical Modeling and Computer Simulations with Cutting-Edge Technologies and Advanced Control Systems
PublicationThe wastewater treatment landscape in Central Europe, particularly in Poland, has undergone a profound transformation due to European Union (EU) integration. Fueled by EU funding and rapid technological advancements, wastewater treatment plants (WWTPs) have adopted cutting-edge control methods to adhere to EU Water Framework Directive mandates. WWTPs contend with complexities such as variable flow rates, temperature fluctuations,...
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Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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Video DATA - Traffic generation modeling for discount shops - Chrobrego Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 75 Chrobrego street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number...
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Video DATA - Traffic generation modeling for discount shops - Czerska Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 71 Czerska street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number of...
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Video DATA - Traffic generation modeling for discount shops - Gdanska Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 21C Gdanska street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number of...
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Video DATA - Traffic generation modeling for discount shops - Dragana Street
Open Research DataThe data includes video traffic data (vehicles, pedestrians, cyclists) registered at 27 Dragana street in Gdansk. The data covers the day 01.10.2020 at 6:00-22:00. The video camera was installed at the parking area belonging to the discount store Lidl. The data obtained was used in analysis, providing information about the modal split, the number of...
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Rubrene Thin Films with Viably Enhanced Charge Transport Fabricated by Cryo-Matrix-Assisted Laser Evaporation
PublicationAmong organic semiconductors, rubrene (RB; C42H28) is of rapidly growing interest for the development of organic and hybrid electronics due to exceptionally long spin diffusion length and carrier mobility up to 20 cm2V−1s−1 in single crystals. However, the fabrication of RB thin films resembling properties of the bulk remains challenging, mainly because of the RB molecule’s twisted conformation. This hinders the formation of orthorhombic...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublicationEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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The structure of the control system for a dynamically positioned ship
PublicationThe article discusses functions and tasks of dynamic positioning (DP) systems for ships. The analysed issues include ship steering, in particular stabilisation of ship position and direction of motion (real course) at low manoeuvring speeds, and commonly used DP ship models. Requirements imposed by classification societies on DP ships are quoted. A multi-layer structure of the DP control system is presented, with special attention...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Efficient knowledge-based optimization of expensive computational models using adaptive response correction
PublicationComputer simulation has become an indispensable tool in engineering design as they allow an accurate evaluation of the system performance. This is critical in order to carry out the design process in a reliable manner without costly prototyping and physical measurements. However, high-fidelity computer simulations are computationally expensive. This turns to be a fundamental bottleneck when it comes to design automation using numerical...