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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublikacjaCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn 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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Au nanostructures coated with a ultrathin film of Al2O3 - measurements and FDTD simulations
Dane BadawczeGold plasmonic platforms have been coated with an ultra-thin films of aluminium oxide. Optical measurements, showing the influence of the thickness of Al2O3 on plasmon resonance position. The observed red-shift of the resonance location with the increase of the thickness of the Al2O3 film, can be explained by the change in the dielectric function of...
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Dispiro[cyclopropane-1,50-endo-tricyclo-[5.2.1.02,6]deca-3,8-diene-100,100-cyclopropane]
PublikacjaThe title compound, C14H16, is built up from three fivememberedrings. Two of the five-membered rings display anenvelope conformation and the third one is almost planar(r.m.s. deviation = 0.014 A ° ).
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Plaque of Dorothy and John Brandes in St. Mary's Church in Gdańsk
Dane BadawczeThe data set concerns epigraphy. It refers to the plaque placed in St. Mary’s Church in Gdańsk, that is dedicated to John Brandes, highly influential citizen of Gdańsk, whose official career was crowned with the function of mayor, and his wife Dorothy née Zimmermann. The plaque was placed in the church in 1586. Data set contains two photos of the plaque,...
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Improved-Efficacy EM-Driven Optimization of Antenna Structures Using Adaptive Design Specifications and Variable-Resolution Models
PublikacjaOptimization-driven parameter tuning is an essential step in the design of antenna systems. Although in many cases it is still conducted through parametric studies, rigorous numerical methods become a necessity if truly optimum designs are sought for, and the problem intricacies (number of variables, multiple goals, constraints) make the interactive approaches insufficient. The two practical considerations of electromagnetic (EM)-driven...
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Acoustic heating produced in resonators filled by a newtonian fluid
PublikacjaAcoustic heating in resonators is studied. The governing equation of acoustic heating is derived by means of the special linear combination of conservation equations in differential form, allowing the reduction of all acoustic terms in the linear part of the final equation, but preserving terms belonging to the thermal mode responsible for heating. This equation is instantaneous and includes nonlinear acoustic terms that form a...
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Agnieszka Pladzyk dr hab. inż.
OsobyAgnieszka Pladzyk (ur. w Piszu) jest chemikiem, pracownikiem Katedry Chemii Nieorganicznej na Wydziale Chemicznym PG, gdzie zajmuje się projektowaniem, syntezą nowych samoorganizujących się jedno- i wielordzeniowych układów opartych na metalach przejściowych i związkach krzemosiarkowych. Badania te nakierowane są na poszukiwanie nowych prekursorów materiałów funkcjonalnych o właściwościach magnetycznych, luminescencyjnych i katalitycznych. W...
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Sialadenoma papilliferum - Female, 15 - Tissue image [7040247104956411]
Dane BadawczeThis is the histopathological image of PALATE tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Tropospheric delays derived from GNSS observations during the derecho event in Poland of 11th August 2017
Dane BadawczePropagation of global navigation satellite systems (GNSS) radio signals is disturbed by the current state of the Earth's atmosphere. For this reason, advances processing of GNSS signals can be used for investigation of the atmospheric condition. In case of troposphere, the GNSS signals allow for obtain information of tropospheric delay, which is mainly...
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Data-driven, probabilistic model for attainable speed for ships approaching Gdańsk harbour
PublikacjaThe growing demand for maritime transportation leads to increased traffic in ports. From this arises the need to observe the consequences of the specific speed ships reach when approaching seaports. However, usually the analyzed cases refer only to the statistical evaluation of the studied phenomenon or to the empirical modelling, ignoring the mutual influence of variables such as ship type, length or weather conditions. In this...
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Building modernization located in the conservation protection zone in the aspect of technical conditions
PublikacjaThe paper presents a description of the technical condition of the building after many years of operation and analyzes the impact of the current use and the lack of regular periodic repairs on the technical efficiency of the building. The influence of the technical solutions applied during the construction of the building on the current limitations related to the planned, target change in the way of use was discussed. Variant conceptual...
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Fixed point indices of iterated smooth maps in arbitrary dimension
PublikacjaWe give a complete description of possible sequences ofindices of iterations of f at an isolated fixed point, answering inaffirmative the Chow, Mallet-Paret and Yorke conjecture posed in[S.N. Chow, J. Mallet-Parret, J.A. Yorke, A periodic point index whichis a bifurcation invariant, in: Geometric Dynamics, Rio de Janeiro,1981, in: Lecture Notes in Math., vol. 1007, Springer, Berlin, 1983,pp. 109-131].
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Electrocatalytic Gas Sensor with Reference Layer
PublikacjaThis paper presents studies of gas sensors prepared in ceramic technology with Nasicon as a solid electrolyte. Sensors work in the voltammetric mode thus based on the excitation of a sensor with a periodic potential signal while current response is recorded. The main aim is to investigate a Bi8Nb2O17 reference layer influence on sensor properties. Sensors I-V characteristics in different concentration of nitrogen dioxide have been...
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Acoustic field and the entropy mode induced by it in a waveguide filled with some non-equilibrium gases
PublikacjaThe non-linear propagation of an acoustic beam in a rectangular waveguide is considered. The medium of sound propagation, is a gas where thermodynamically non-equilibrium processes take place: such as exothermic chemical reactions or excitation of vibrational degrees of a molecule’s freedom. The incident and reflected compounds of the acoustic field do not interact in the leading order in the case of periodic weakly nonlinear sound...
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The finite-difference simulation of x-rays propagation through a system of lenses
PublikacjaThe propagation of X-ray waves through an optical system consisting of 33 aluminum X-ray refractive lenses is considered. For solving the problem, a finite-difference method is suggested and investigated. It is shown that very small steps of the difference grid are necessary for reliable computation of propagation of X-ray waves through the system of lenses. It is shown that the wave phase is a function very quickly increasing...
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Weakly connected Roman domination in graphs
PublikacjaA Roman dominating function on a graph G=(V,E) is defined to be a function f :V → {0,1,2} satisfying the condition that every vertex u for which f(u) = 0 is adjacent to at least one vertex v for which f(v)=2. A dominating set D⊆V is a weakly connected dominating set of G if the graph (V,E∩(D×V)) is connected. We define a weakly connected Roman dominating function on a graph G to be a Roman dominating function such that the set...
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Thermal Self-Action of Acoustic Beams Containing Several Shock Fronts
PublikacjaThermal self-action of an acoustic beam with one discontinuity or several shock fronts is studied in a Newtonian fluid. The stationary self-action of a single sawtooth wave with discontinuity (or some integer number of these waves), symmetric or asymmetric, is considered in the cases of self-focusing and self- defocusing media. The results are compared with the non-stationary thermal self-action of the periodic sound. Thermal self-action...
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Top personal income tax rates (PIT) in EU countries (in%).
Dane BadawczeWhen analyzing the historical PIT rates, it should be noted that in 2000 the average rate was almost 45%. The highest income tax (approx. 60%) was imposed in Belgium, Denmark, as well as in the Netherlands and France. On the other hand, the lowest (25%) rates were recorded in Estonia and Latvia, which were not yet members of the European Union. In the...
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The α-µ model of the multipath fading channel
Dane BadawczeThe dataset contains the results of simulations that are part of the research on modelling the multipath fading in the communication channel. The envelope of the α-µ fading process is generated using the Monte-Carlo simulation (MCS) in the LabVIEW programming environment.
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More Just Measure of Fairness for Sharing Network Resources
PublikacjaA more just measure of resource distribution in computer networks is proposed. Classic functions evaluate fairness only “on average”. The proposed new fairness score function ensures that no node is left without resources while on average everything looks good. It is compared with well-known and widely adopted function proposed by Jain, Chiu and Hawe and another one recently proposed fairness function by Chen and Zhang. The function...
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Epitaph of Ferber family in St. Mary's Church in Gdańsk
Dane BadawczeThe data set concerns epigraphy. It refers to the epitaph placed in St. Mary’s Church in Gdańsk, that is dedicated to one of the greatest family in Gdańsk – family Ferber, and one of its member – Konstantin Ferber, whose official career was crowned with the function of mayor of city. The epitaph was erected by his brother John Ferber, the juror, councilor...
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A New Approach of Solidification Analysis in Modular Latent Thermal Energy Storage Unit Based on Image Processing
PublikacjaThe solidification process of RT18HC in a cylindrical shell and tube storage unit has been studied using a new methodology based on image processing. The main idea of the algorithm is to label the region of solidification and use statistical functions to calculate the dimensions of the solidification front over time. Said analysis includes two methods. The first method is to measure the solid fraction changes during solidification....
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Assessment of Environmental Loads in the Life Cycle of a Retail and Service Building
PublikacjaIn order to achieve the European Union’s climate and energy goals, investments are required, mainly in the areas of energy efficiency, renewable energy sources and infrastructure. Buildings are responsible for almost half of total energy consumption, and nearly 80% of them are energy and ecologically inefficient. The policy of European countries is increasingly more focused on facilities with the highest potential in the areas...
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Badania wytrzymałościowe zgrzein łączących pręty zbrojeniowe o średnicy Ø30mm
PublikacjaZakres badań dotyczy oceny wytrzymałościowej zgrzein doczołowych, wykonanych metodą zwarciową. Elementami zgrzewanymi były pręty zbrojeniowe o średnicy Ø30mm. Badania związane są z okresową kontrolą stabilności parametrów zgrzewarki, szczególnie w odniesieniu do górnych, dopuszczalnych przez producenta zakresów parametrów zgrzewania oraz analizą wyników i porównaniu rezultatów prób wytrzymałościowych uzyskanych w 2019 i 2020 w...
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Hydraulics and hydrology 2022
Kursy OnlineFor the purpose of this course we are interested in the engineering aspect of hydrology, or what might call engineering hydrology. From this point of view we are mainly concerned with quantifying amounts of water at various locations as function of time for surface water applications. Solving engineering problems using hydrologic principles.
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Hydraulics and hydrology
Kursy OnlineFor the purpose of this course we are interested in the engineering aspect of hydrology, or what might call engineering hydrology. From this point of view we are mainly concerned with quantifying amounts of water at various locations as function of time for surface water applications. Solving engineering problems using hydrologic principles.
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Techniki zwiększania efektywności metody elementów skończonych poprzez redukcję dziedziny obliczeniowej z wykorzystaniem własności geometrii struktur
PublikacjaWspółczesna elektronika ze względu na swój szybki rozwój wymaga od nas efektywnego modelowania zjawisk polowych. Celem rozprawy jest zwiększanie efektywności metody elementów skończonych poprzez redukcję dziedziny obliczeniowej z wykorzystaniem własności geometrii struktur oraz jej hybrydyzację z użyciem technik analitycznych. Rozprawa zawiera przegląd stanu wiedzy na temat dostępnych obecnie technik modelowania jak również opis...
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Dynamics of Field Line Mappings in Magnetic Flux Tubes
PublikacjaWe study the topological constraints on the dynamics of magnetic field lines in flux tubes. Our approach is based on the application of the topological invariant: fixed point index. We consider periodic flux tubes and find various restrictions on the field lines that come from the sequence of fixed point indices of iterations. We also analyze the case of a tube with a cylindrical obstacle, deducing some special dynamical properties...
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Complexes of silanethiolate ligands: Synthesis, structure, properties and application
PublikacjaThe purposeful syntheses of silanethiolate complexes started approximately in the mid-eighties of the 20th century but no summary of the synthetic efforts has been reported till now. The synthetic methods and the resulting complexes have some common features, which are emphasized throughout the review. Thereby specific difficulties during synthesis are outlined and the structures, properties and possible applications of the resulting...
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Determination of chlorine concentration using single temperature modulated semiconductor gas sensor
PublikacjaA periodic temperature modulation using sinusoidal heater voltage was applied to a commercial SnO2 semiconductor gas sensor. Resulting resistance response of the sensor was analyzed using a feature extraction method based on Fast Fourier Transformation (FFT). The amplitudes of the higher harmonics of the FFT from the dynamic nonlinear responses of measured gas were further utilized as an input for Artificial Neural...
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Rating mathematical models for first-pass of tracer in pCT lung studies
PublikacjaThis paper presents a comparison of model based on the Gauss function and the most commonly used Gamma-variate model in perfusion computed tomography (pCT) lung studies. It also verifies whether used model affects value of blood volume parameter. Three mean concentration-time curves were created from actual pCT measurements: arterial input function, blood vessels in lungs and lung parenchyma. On the basis of these mean curves we...
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Forecast of basic fuel prices in imports to Poland (constant prices in USD in 2007)
Dane BadawczeThis dataset presents price growth forecasts for conventional energy sources. It should be noted that the Ministry of Economy forecasts a more than two-fold increase in oil prices (although these forecasts may be greatly underestimated) over 23 years, an almost two-fold increase in natural gas prices and a 40% increase in coal prices.
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Complex Root Finding Algorithm Based on Delaunay Triangulation
PublikacjaA simple and flexible algorithm for finding zeros of a complex function is presented. An arbitrary-shaped search region can be considered and a very wide class of functions can be analyzed, including those containing singular points or even branch cuts. The proposed technique is based on sampling the function at nodes of a regular or a self-adaptive mesh and on the analysis of the function sign changes. As a result, a set of candidate points...
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Infiltrating duct and lobular carcinoma - Female, 72 - Tissue image [7240729592878081]
Dane BadawczeThis is the histopathological image of BREAST tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Hyalinizing trabecular tumor - Female, 46 - Tissue image [11010630088571531]
Dane BadawczeThis is the histopathological image of THYROID GLAND tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Acinic cell adenocarcinoma - Male, 56 - Tissue image [6280729578141741]
Dane BadawczeThis is the histopathological image of PAROTID GLANID tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Other mycoses, not elsewhere classified - Female, 40 - Tissue image [6290730011493361]
Dane BadawczeThis is the histopathological image of ACCESSORY SINUSES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Mucoepidermoid carcinoma - Female, 63 - Tissue image [6010730010702581]
Dane BadawczeThis is the histopathological image of BASE OF TONGUE tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Other specified mycoses - Female, 41 - Tissue image [6290730011482201]
Dane BadawczeThis is the histopathological image of ACCESSORY SINUSES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Computing dynamical curlicues
Dane BadawczeA curlicue is a piece-wise linear curve in the complex plane which can be generated by an arbitrary sequence of real numbers u_n. It can be interpreted as a trajectory of a particle in the plane which starts in the origin at time t=0 and moves with a constant velocity, changing its direction at instances t=0,1,2,3,..., where the new direction is given...
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Alternative convolution approach to friction in unsteady pipe flow
PublikacjaIn the paper some aspects of the unsteady friction in pipe flow expressed by the convolution are analyzed. This additional term introduced into the motion equation involves the accelerations of fluid occurring in the past and a weighting function. The essence of such approach is to assume the appropriate form of weighting function. However, until now no fully reliable formula for this function has been found. To avoid some inconveniences...
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Mining Knowledge of Respiratory Rate Quantification and Abnormal Pattern Prediction
PublikacjaThe described application of granular computing is motivated because cardiovascular disease (CVD) remains a major killer globally. There is increasing evidence that abnormal respiratory patterns might contribute to the development and progression of CVD. Consequently, a method that would support a physician in respiratory pattern evaluation should be developed. Group decision-making, tri-way reasoning, and rough set–based analysis...