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Wyniki wyszukiwania dla: —TRANSFER LEARNING, DEEP LEARNING, PROTEIN STRUCTURE, FUNCTION, AND INTERACTION PREDICTION, SEQUENCE MODELLING
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublikacjaWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology
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Monitoring the BTEX Volatiles during 3D Printing with Acrylonitrile Butadiene Styrene (ABS) Using Electronic Nose and Proton Transfer Reaction Mass Spectrometry
PublikacjaWe describe a concept study in which the changes of concentration of benzene, toluene, ethylbenzene, and xylene (BTEX) compounds and styrene within a 3D printer enclosure during printing with different acrylonitrile butadiene styrene (ABS) filaments were monitored in real-time using a proton transfer reaction mass spectrometer and an electronic nose. The quantitative data on the concentration of the BTEX compounds, in particular...
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Efkleidis Katsaros
OsobyEfklidis Katsaros received the B.Sc. degree in mathematics from the Aristotle University of Thessaloniki, Greece, in 2016, and the M.Sc. degree (cum laude) in data science: statistical science from Leiden University, The Netherlands, in 2019. He is currently pursuing the Ph.D. degree in deep video multi-task learning with the Department of Biomedical Engineering, Gdańsk University of Technology, Poland. Since 2020, he has been...
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Numerical simulation of screw displacement pile interaction with non-cohesive soil
PublikacjaA trial numerical simulation of screw displacement pile interaction with non-cohesive subsoil during the transfer of compression load. The simulation was carried out in an axisymmetric system. The technological phases of pile installation in the ground were numerically modelled using equivalent processes which provided similar effects to real technical actions. The results of the numerical calculations were verified by comparing...
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Balanced Spider Monkey Optimization with Bi-LSTM for Sustainable Air Quality Prediction
PublikacjaA reliable air quality prediction model is required for pollution control, human health monitoring, and sustainability. The existing air quality prediction models lack efficiency due to overfitting in prediction model and local optima trap in feature selection. This study proposes the Balanced Spider Monkey Optimization (BSMO) technique for effective feature selection to overcome the local optima trap and overfitting problems....
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Edyta Gołąb-Andrzejak dr hab.
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublikacjaThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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Supramolecular deep eutectic solvents and their applications
PublikacjaIn recent years, the growing awareness of the harmfulness of chemicals to the environment has resulted in the development of green and sustainable technologies. The compromise between economy and environmental requirements is based on the development of new efficient and green solutions. Supramolecular deep eutectic solvents (SUPRADESs), a new deep eutectic solvent (DES) subclass characterized by inclusion properties, are a fresh...
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Dipole-bound anions supported by charge-transfer interaction: valence- and dipole-bound anionic states of H3N→BF3
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Interactive Prototypes in Teaching User-Centred Design and Business Process Modelling
PublikacjaThis publication describes experiences gathered during the use of interactive prototyping in two areas: design of user interfaces for a touch screen information kiosk and interactive prototyping of business processes. Prototyping is promoted here as a technique useful for both visualizing design concepts and for stimulating communication within relevant teams. Developing interactive prototypes of use interfaces is discussed here...
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Primary role identification in e-mail networks using pattern subgraphs and sequence diagrams
PublikacjaSocial networks often forms very complex structures that additionally change over time. Description of actors' roles in such structures requires to take into account this dynamics reflecting behavioral characteristics of the actors. A role can be defined as a sequence of different types of activities. Various types of activities are modeled by pattern subgraphs, whereas sequences of these activities are modeled by sequence diagrams....
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EXPERIMENTAL AND THEORETICAL FLOW OF THE FORCES IN DEEP BEAMS WITH CANTILEVAR
PublikacjaThis article presents the results of experimental research carried out on deep beams with cantilever which was loaded throughout the depth. The main deep beam was directly simply supported on the one side. On the other side the deep beam was suspended in another deep member situated at right angles. All deep beams created a spatial arrangement. The paper is focused on the analysis of the cracks morphology and flow of the internal...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublikacjaMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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Protein transphosphorylation during the mutual interaction between phytochrome a and a nuclear isoform of nucleoside diphosphate kinase is regulated by red light
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublikacjaInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublikacjaEfficient 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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FDTD-Compatible Green's function based on scalar discrete Green's function and multidimensional Z-transform
PublikacjaIn this contribution, a new formulation of the discrete Green's function (DGF) is presented for the finitedifference time-domain (FDTD) grid. Recently, dyadic DGF has been derived from the impulse response of the discretized scalar wave equation (i.e., scalar DGF) with the use of the multidimensional Z-transform. Its software implementation is straightforward because only elementary functions are involved and a single function...
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Olgun Aydin Dr
OsobyOlgun Aydin finished his PhD by publishing a thesis about Deep Neural Networks. He works as a Senior Data Scientist in PwC Poland, gives lectures in Gdansk University of Technology in Poland and member of WhyR? Foundation. Olgun is a very big fan of R and author of the book called “R Web Scraping Quick Start Guide” , two video courses are called “Deep Dive into Statistical Modelling using R” and “Applied Machine Learning and Deep...
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Improving Accuracy of Contactless Respiratory Rate Estimation by Enhancing Thermal Sequences with Deep Neural Networks
PublikacjaEstimation 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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Rating Prediction with Contextual Conditional Preferences
PublikacjaExploiting contextual information is considered a good solution to improve the quality of recommendations, aiming at suggesting more relevant items for a specific context. On the other hand, recommender systems research still strive for solving the cold-start problem, namely where not enough information about users and their ratings is available. In this paper we propose a new rating prediction algorithm to face the cold-start...
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A Closed Bipolar Electrochemical Cell for the Interrogation of BDD Single Particles: Electrochemical Advanced Oxidation
PublikacjaA closed bipolar electrochemical cell containing two conductive boron-doped diamond (BDD) particles of size 250 – 350 m, produced by high-pressure high-temperature (HPHT) synthesis, has been used to demonstrate the applicability of single BDD particles for electrochemical oxidative degradation of the dye, methylene blue (MB). The cell is fabricated using stereolithography 3D printing and the BDD particles are located at either...
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Adaptive estimation of the transformer stray capacitances for DC–DC converter modelling
PublikacjaNew low cost and accurate estimation method of transformer stray capacitances for wide band DC–DC converter modelling and design is proposed. The Wiener filter (WF) method is applied to estimate the transformer impedance – referred to the selected transformer winding configurations. Laboratory tests are used to adapt the filter, that is to find optimal impedance which minimises mean square error between measured, noise perturbed...
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Natural convective heat transfer from isothermal cuboids
PublikacjaThe paper presents results of theoretical and experimental investigations of the convective heat transfer from isothermal cuboid. The analytical solution was performed taking into account complete boundary layer length and the manner of its propagation around isothermal cuboid. It arises at horizontal bottom surface and grows on vertical lateral surface of the block. After changing its direction, the boundary layer occurs above...
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A Fast Method of Separation of the Noisy Background from the Head-Cross Section in the Sequence of MRI Scans
PublikacjaThe paper presents a new method of removing the noisy background from the sequence of magnetic resonance imaging (MRl) scans. The sequence of scans is required in order to monitor a passage of a contrast agent through the brain tissue. The scans contain the noisy head-cross data and also the noisy background data. The latter has to be removed and excluded from a further analysis. It is achieved by applying some basic morphological...
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Butyrylcholinesterase signal sequence self-aggregates and enhances amyloid fibril formation in vitro
PublikacjaAlzheimer’s disease (AD) pathogenesis has been attributed to extracellular aggregates of amyloid β (Aβ) plaques and neurofibrillary tangles in the human brain. It has been reported that butyrylcholinesterase (BChE) also accumulates in the brain Aβ plaques in AD. We have previously found that the BChE substitution in 5′UTR caused an in-frame N-terminal extension of 41 amino acids of the BChE signal peptide. The resultant variant...
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Interaction of Novel Ionic Liquids with Soils
PublikacjaWith the constant development of new ionic liquids, the understanding of the chemical fate of these compounds also needs to be updated. To this effect, in this contribution, the interaction of a number of novel ionic liquids with soils was determined. Therefore, three novel headgroups (ammonium, phosphonium or pyrrolidinium) with single or quaternary substitution were tested on a variety of soils with high to low organic matter...
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Citizenship Teaching and Learning
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum 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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Electromagnetic interference frequencies prediction model of flyback converter for snubber design
PublikacjaSnubber design for flyback converters usually requires experimental prototype measurements or simulation based on accurate and complex models. In this study simplified circuit modelling of a flyback converter has been described to dimension snubbers in early stage of design process. Simulation based prediction of the transistor and diode ringing frequencies has been validated by measurements in a prototype setup. In that way obtained...
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Experimental and predicted physicochemical properties of monopropanolamine-based deep eutectic solvents
PublikacjaIn this work, the novel deep eutectic solvents (DESs) based on 3-amino-1-propanol (AP) as hydrogen bond donor (HBD) and tetrabutylammonium bromide (TBAB) or tetrabutylammonium chloride (TBAC) or tetraethylammonium chloride (TEAC) as hydrogen bond acceptors (HBAs) were synthesized with different molar ratios of 1:4, 1:6 and 1:8 salt to AP. Fourier Transform Infrared Spectroscopy measurements were performed to provide an evidence...
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Experimental and predicted physicochemical properties of monopropanolamine-based deep eutectic solvents
PublikacjaIn this work, the novel deep eutectic solvents (DESs) based on 3-amino-1-propanol (AP) as hydrogen bond donor (HBD) and tetrabutylammonium bromide (TBAB) or tetrabutylammonium chloride (TBAC) or tetraethylammonium chloride (TEAC) as hydrogen bond acceptors (HBAs) were synthesized with different molar ratios of 1: 4, 1: 6 and 1: 8 salt to AP. Fourier Transform Infrared Spectroscopy measurements were performed to provide an evidence...
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The pattern of verbal, visuospatial and procedural learning in Richardson variant of progressive supranuclear palsy in comparison to Parkinson’s disease
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Detection of Cystic Fibrosis Symptoms Based on X-Ray Images Using Machine Learning- Pilot Study
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Early Predictors of Learning a Foreign Language in Pre-school – Polish as a First Language, English as a Foreign Language
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NLITED - New Level of Integrated Techniques for Daylighting Education: Preliminary Data on the Use of an E-learning Platform
PublikacjaProject NLITED – New Level of Integrated Techniques for Daylighting Education - is an educational project for students and professionals. The project's objective is to create and develop an online eLearning platform with 32 eModules dedicated to daylight knowledge. The project also offers e-learners two summer school training where the theory is put into practice. The platform was launched on January 31, 2022. The paper...
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Universal Predictors of Dental Students’ Attitudes towards COVID-19 Vaccination: Machine Learning-Based Approach
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Technological vs. Non-Technological Mindsets: Learning From Mistakes, and Organizational Change Adaptability to Remote Work
PublikacjaThe permanent implementation of the change in working methods, e.g., working in the virtual space, is problematic for some employees and, as a result, for management leaders. To explore this issue deeper, this study assumes that mindset type: technological vs. non-technological, may influence the organizational adaptability to change. Moreover, the key interest of this research is how non-technological mindsets...
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Numerical Modelling of Structures with Uncertainties
PublikacjaThe nature of environmental interactions, as well as large dimensions and complex structure of marine offshore objects, make designing, building and operation of these objects a great challenge. This is the reason why a vast majority of investment cases of this type include structural analysis, performed using scaled laboratory models and complemented by extended computer simulations. The present paper focuses on FEM modelling...
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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublikacjaThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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[NCh-bio] Advances in Biotechnology: Protein Folding and Assembly
Kursy Online{mlang pl} Dyscyplina: nauki chemiczne Zajęcia obowiązkowe dla doktorantów I i II roku z obszaru biotechnologii Prowadzący: dr hab. Gracjana Klein-Raina, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: chemical sciences Obligatory course for 1st and 2nd-year PhD students from biotechnology area Academic teachers: dr hab. Gracjana Klein-Raina, prof. PG Total hours of training: 15 teaching...
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Polymeric materials in medicine – structure and desing 2023/24
Kursy Online -
Deep Instance Segmentation of Laboratory Animals in Thermal Images
PublikacjaIn this paper we focus on the role of deep instance segmentation of laboratory rodents in thermal images. Thermal imaging is very suitable to observe the behaviour of laboratory animals, especially in low light conditions. It is an non-intrusive method allowing to monitor the activity of animals and potentially observe some physiological changes expressed in dynamic thermal patterns. The analysis of the recorded sequence of thermal...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublikacjaOsmolytes 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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Numerical Study of Turbulent Flow and Heat Transfer of Nanofluids in Pipes
PublikacjaIn this work, Nusselt number and friction factor are calculated numerically for turbulent pipe flow (Reynolds number between 6000 and 12000) with constant heat flux boundary condition using nanofluids. The nanofluid is modelled with the single-phase approach and the simulation results are compared with experimental data. Ethylene glycol and water, 60:40 EG/W mass ratio, as base fluid and SiO2 nanoparticles are used as nanofluid...
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ColorNephroNet: Kidney tumor malignancy prediction using medical image colorization
PublikacjaRenal tumor malignancy classification is one of the crucial tasks in urology, being a primary factor included in the decision of whether to perform kidney removal surgery (nephrectomy) or not. Currently, tumor malignancy prediction is determined by the radiological diagnosis based on computed tomography (CT) images. However, it is estimated that up to 16% of nephrectomies could have been avoided because the tumor that had been...
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Proline, glutamic acid, and leucine rich protein 1 (PELP1) expression in deep paravertebral muscles in idiopathic scoliosis girls
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A simplified energy dissipation based model of heat transfer for subcooled flow boiling
PublikacjaIn the paper a model is presented based on energetic considerations for subcooled flow boiling heat transfer. The model is the extension of authors own model developed earlier for saturated flow boiling and condensation. In the former version of the model we used the heat transfer coefficient for the liquid single-phase as a reference level, due to the lack of the appropriate model for heat transfer coefficient for the subcooled...