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Search results for: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublicationDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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Studies of the Modelling Accuracy of Steam Turbine Control Systems for Diagnostic Tests of Automatic Synchronizers
PublicationOne of the important factors that affect the reliable operation of the power system and the rapid restitution after disaster is a quick and effective combining synchronous electric power facilities to operate in parallel. Hence, diagnostics of automatic synchronizers at every stage of their life, from building a prototype, through the whole life, until removing such devices from the operation, is an extremely important and responsible...
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Crystal structure, chemical bonding, and physical properties of layered AIrSn2 (A = Sr and Ba)
PublicationWe report the experimental and theoretical investigation of structure, chemical bonding interactions, and physical properties of new ternary stannides AIrSn2 (A = Sr and Ba). AIrSn2 (A = Sr and Ba) crystallizes in the orthorhombic Re3B-type structure with the space group Cmcm (No. 64). According to single-crystal X-ray diffraction results, the structure of AIrSn2 (A = Sr and Ba) can be considered as a Zintl-type compound with heterogeneous...
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Entropy of water calculated from harmonic approximation: estimation of the accuracy of method
PublicationSome molecular dynamics simulations were performed for liquid TIP4P and SPC water at a constant density (1.00 g/cm(3)) and within the temperature range of 5-90 degrees C. By using harmonic approximation, both the entropy of water S-H and the specific heat c(v) were calculated, and the results were compared to literature data. It was found that harmonic approximation overestimates absolute entropy of TIP4P water by 5.6 J/mol K (similar...
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Increasing the conductivity of V2O5-TeO2 glass by crystallization: structure and charge transfer studies
PublicationIn the present paper, V 2 O 5 -TeO 2 glass was prepared by the melt-quenching technique. Crystallization of glass with a vanadium content higher than 35%mol results in an increase in electrical conductivity by a few orders of magnitude and a decrease in activation energy from ~0.40 to ~0.12 eV. In this work, a critical review of existing charge transfer models was presented on the example of V 2 O 5 -TeO 2 glass and glass–ceramics....
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A Computationally Efficient Model for Predicting Successful Memory Encoding Using Machine-Learning-based EEG Channel Selection
PublicationComputational cost is an important consideration for memory encoding prediction models that use data from dozens of implanted electrodes. We propose a method to reduce computational expense by selecting a subset of all the electrodes to build the prediction model. The electrodes were selected based on their likelihood of measuring brain activity useful for predicting memory encoding better than chance (in terms of AUC). A logistic...
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COVID-19 immunizations in occupational medicine
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Triage during the COVID-19 pandemic
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COVID-19 As A Hurdle In OCD Diagnosis
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Functional and spatial structure analysis – Gdańsk-Lower City (Dolne Miasto) district case study, study proposal no 2, February 2021
Open Research DataThe data presents results of work within the studies of the conditions of the district in the context of the city, Gdańsk-Lower City (Dolne Miasto) district, study proposal no 2, from February 2021. The goal of the research process was to present the functional and spatial structure analysis of the area located in Gdańsk-Lower City (Dolne Miasto) district...
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Testing HIADAC high impedance analyzer in Trento University laboratory on Baunier's RC model using 2 wire probe
Open Research DataThe dataset presents impedance spectrum of Baunier's RC model. This object was used to test high-impedance analyzer for diagnostic of anticorossion coatings (HIADAC) realized in the frame of Eureka project E!3174. The impedance spectrum frequency range (1 mHz – 100 kHz) was selected in order to test the whole measureement range of the analyzer. In...
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Performance Modeling and Prediction of Real Application Workload in a Volunteer-based System
PublicationThe goal of this paper is to present a model that predicts the real workload placed on a volunteer based system by an application, with incorporation of not only performance but also availability of volunteers. The application consists of multiple data packets that need to be processed. Knowing the computational workload demand of a single data packet we show how to estimate the application workload in a volunteer based system. Furthermore,...
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Prediction of consumer electricity needs based on Internet weather forecasts
PublicationElectrical energy is considered both as an important driver for producing and transporting goods in companies, as well as a good in itself which requires planning and management for generating and delivering it to consumers in proper time and amounts. Weather information can be considered to convey part of the data on energy delivery needs of consumers. Free meteorological data sources on the Web do not offer consistent data to...
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins
PublicationWater properties may significantly affect protein stability. Osmolytes are compounds that intrinsically affect water in many different ways and thus can influence proteins with this type of indirect mechanism. In this study, we characterize water properties in ternary solutions: model–water–osmolyte, with two model molecules: N-methylacetamide (NMA) and dimethyl sulfoxide (DMSO) and two osmolytes: glycine betaine (TMG)and urea....
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Finite element modelling of a historic church structure in the context of a masonry damage analysis
PublicationThe paper includes a case study of modelling a real historic church using the finite element method (FEM) based on laser scans of its geometry. The main goal of the study was the analysis of the causes of cracking and crushing of masonry walls. An FEM model of the structure has been defined in ABAQUS. A non-linear dynamic explicit analysis with material model including damage plasticity has been performed. A homogenization procedure...
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ESG investing during the Covid-19 crisis. Evidence from Central European Stock Exchanges
PublicationAs COVID-19 turned into a global pandemic, world markets gradually began to recover after initial dynamic declines. Restrictions, and their subsequent loosening, were, and are, not without significance for the financial markets. These particular circumstances provide a unique opportunity to contribute to the literature by focusing on the potential resilience of ESG (environmental, social and governance) investing in an era of crisis....
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Review of Research into Enterprise Bankruptcy Prediction in Selected Central and Eastern European Countries
PublicationIn developed countries, the first studies on forecasting bankruptcy date to the early 20th century. In Central and Eastern Europe, due to, among other factors, the geopolitical situation and the introduced economic system, this issue became the subject of researcher interest only in the 1990s. Therefore, it is worthwhile to analyze whether these countries conduct bankruptcy risk assessments and what their level of advancement is....
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C-1311 (Symadex), a potential anti-cancer drug, intercalates into DNA between A and G moieties. NMR-derived and MD-refined stereostructure of the d(GAGGCCTC) 2 :C-1311 complex
PublicationImidazoacridinone C-1311 (Symadex®) is an antitumor agent which has been recommended for Phase II clinical trials a few years ago. Previously, it was shown experimentally that during the initial stage of its action C-1311 forms stable intercalation complexes with DNA duplexes. Herein, a NMR-derived stereostructure of d(GAGGCCTC)2:C-1311 complex was reported. The ligand was found locating itself between A and G moieties, forming...
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Conceptual fuzzy model of the polish internet mortgage market
PublicationThe aim of this paper is to present the conceptual structure of basic fuzzy model representing Polish Internet mortgage market. The paper starts with introduction describing the market complexities and challenges, and description of previously created rule based model. Then the steps of the process of proposed model fuzzyfication are presented. Final part of the paper consists of conclusions and directions for future research.
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In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublicationDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
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Gender as a moderator between Present-Hedonistic time perspective and depressive symptoms or stress during COVID-19 lock-down
PublicationAlthough numerous studies have addressed the impact of the COVID-19 lock-downs on psychological distress, scarce data is available relating to the role of Present-Hedonistic (PH) time perspective and gender differences in the development of depressive symptoms and stress during the period of strict social distancing. We hypothesized that gender would moderate the relationship between PH and depressiveness or stress levels, such...
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A simple modification to improve the accuracy of methylation-sensitive restriction enzyme quantitative polymerase chain reaction
PublicationDNA digestion with endonucleases sensitive to CpG methylation such as HpaII followed by polymerase chain reaction (PCR) quantitation is commonly used in molecular studies as a simple and inexpensive solution for assessment of region-specific DNA methylation. We observed that the results of such analyses were highly overestimated if mock-digested samples were applied as the reference.We determined DNA methylation levels in several...
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Geometrically nonlinear FEM analysis of 6-parameter resultant shell theory based on 2-D Cosserat constitutive model
PublicationWe develop the elastic constitutive law for the resultant statically and kinematically exact, nonlinear, 6-parameter shell theory. The Cosserat plane stress equations are integrated through-the- thickness under assumption of the Reissner-Mindlin kinematics. The resulting constitutive equations for stress resultant and couple resultants are expressed in terms of two micropolar constants: the micropolar modulus Gc and the micropolar...
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Sounding of Layered Marine Bottom - Model Investigations
PublicationThe necessary actions connected with interpretations of examining of physical properties of sea bottom structure is developing of proper procedure of modeling of the layered structure. The implementation of the acoustic waves for the determination of seabed stratification requires a precise diagnosis of the topic from both the theoretical and practical side. Little differences between the parameters of sediments, as well as irregular...
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Structure of Small Platinum Clusters Revised
PublicationW pracy opisano wyniki obliczeń metodą DFT struktury 2-15 atomowych klastrów platyny.
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Kriging-assisted hybrid reliability design and optimization of offshore wind turbine support structure based on a portfolio allocation strategy
PublicationIn recent years, offshore wind power generation technology has developed rapidly around the world, making important contributions to the further development of renewable energy. When designing an Offshore Wind Turbine (OWT) system, the uncertainties in parameters and different types of constraints need to be considered to find the optimal design of these systems. Therefore, the Reliability-Based Design Optimization (RBDO) method...
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Application Isssues of the Semi-Markov Reliability Model
PublicationPredicting the reliability of marine internal combustion engines, for instance, is of particular importance, as it makes it possible to predict their future reliability states based on the information on the past states. Correct reliability prediction is a complex process which consists in processing empirical results obtained from operating practice, complemented by analytical considerations. The process of technical state changes...
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Crystal structure and physical properties of new Ca2TGe3 (T = Pd and Pt) germanides
PublicationThe crystallographic, electronic transport and thermal properties of Ca2PdGe3 and Ca2PtGe3 are reported. The compounds crystalize in an ordered variant of the AlB2 crystal structure, in space group P6/mmm, with the lattice parameters a = 8.4876(4) Å/8.4503(5) Å and c = 4.1911(3) Å/4.2302(3) Å for Ca2PdGe3 and Ca2PtGe3, respectively. The resistivity data exhibit metallic behavior with residual-resistivity-ratios (RRR) of 13 for...
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Prediction of the motion stability of three-wheel mobile robot
PublicationW pracy rozważa się projektowanie i realizację trajektorii ruchu 3-kołowego robota mobilnego, z uwzględnieniem jego kinematyki i dynamiki. Kołowe roboty mobilne zaliczane są do układów nieholonomicznych, w przypadku których przyjęte ograniczenia (więzy) dotyczą chwilowych prędkości punktów charakterystycznych układu. Model matematyczny obiektu przedstawiono w postaci skończonej liczby nieliniowych równań różniczkowych kinematyki...
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SHM System of the Roof Structure of Sports Arena “Olivia”
PublicationThe paper presents a structural health monitoring system of the Sports Arena “Olivia” in Gdansk, Poland. The system was installed because of doubts about the roof stability due to observed buckling of the steel truss members. The SHM system was based on nonlinear FEM models used for detection of type of near failure modes of the roof. The application of detailed FEM model in current state updated on data from in situ loading testes...
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Synthesis and molecular structure of novel 2-(alkylthio)-4-chloro-N-(4,5-dihydro-5-oxo-1H-1,2,4-triazol-3-yl)-5-methylbenzenesulfonamideswith potential anticancer activity
PublicationOtrzymano 15 nowych związków: 2-(alkilotio)-4-chloro-N-(4,5-dihydro-5-oxo-1H-1,2,4-triazol-3-yl)-5-metylobenzenosulfonamidów, dla których opracowano nową metodę syntezy. Dla jednej pochodnej wyznaczono strukturę rentgenowską. Związek nr 36 wykazuje wysoką aktywność przeciwnowotworową w stosunku do 13 linii komórek nowotworowych o poziomie GI_50 w zakresie stężeń 1,9-3,0 μM.
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Crystal and molecular structure of bis(O,O'-diethyldithiophosphato-S,S')nickel(II): A redetermination
PublicationDoniesienie przedstawia ponownie wyznaczoną strukturę tytułowego, centrosymetrycznego kompleksu, [Ni{S2P(OC2H5)2}2]. Centralny rdzeń (S2P)2 jest płaski, co potwierdza wcześniejsze wyniki uzyskane przez McConnell'a i Kastalsky'ego, przy czym odchylenia standardowe są około siedmiokrotnie mniejsze oraz wyznaczono wszystkie pozycje atomów wodoru. W strukturze krystalicznej zaobserwowano róznież parę krótkich kontaktów HH (2.33 Å).
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Synthesis, Structure, and Spectroscopic Properties of Calcium Thiophenecarboxylate Polymers. Structural Comparison with Analogous Lead Complexes
PublicationThree novel calcium coordination polymers [Ca(2tpCOO)2(2mpa)(H2O)]n (1), [Ca(3tpCOO)2(2mpa)(H2O)]n (2), and {[Ca(3tpacCOO)2(H2O)2]⋅⋅⋅H2O}n (3) (2tpCOO− or 3tpCOO− – thiophene-2- or thiophene-3-carboxylate, 3tpacCOO− – thiophene-3-acetate, 2mpa – 2-methylpropanal), were synthesised using a self-assembly method. The obtained polymers were characterised using SC-XRD, FTIR, UV-Vis DRS, thermogravimetric and luminescence analyses. The...
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Optimization of Chemical Functionalities of Indole-2-carboxamides To Improve Allosteric Parameters for the Cannabinoid Receptor 1 (CB1)
Publication5-Chloro-3-ethyl-N-(4-(piperidin-1-yl)phenethyl)-1H-indole-2-carboxamide (1; ORG27569) is a prototypical allosteric modulator for the cannabinoid type 1 receptor (CB1). Here, we reveal key structural requirements of indole-2-carboxamides for allosteric modulation of CB1: a critical chain length at the C3-position, an electron withdrawing group at the C5-position, the length of the linker between the amide bond and the phenyl ring...
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Proteinase release from activated neutrophils in mechanically ventilated patients with non-COVID-19 and COVID-19 pneumonia
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Rare earth ions doped K 2 Ta 2 O 6 photocatalysts with enhanced UV–vis light activity
PublicationNew rare earth-doped K2Ta2O6 photocatalysts were successfully synthesized by hydrothermal method. The effect of dopant type (Y,Yb,Ho,Pr,Er) and amount of rare earth precursor (2,4,8 and 10 mol%) on the physicochemical and photocatalytic properties of RE-K2Ta2O6 have been investigated. All as-prepared materials were characterized by UV–vis diffuse reflectance spectroscopy, Brunauer-Emmett-Teller specific surface area measurement,...
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Chemometrics for Selection, Prediction, and Classification of Sustainable Solutions for Green Chemistry—A Review
PublicationIn this review, we present the applications of chemometric techniques for green and sustainable chemistry. The techniques, such as cluster analysis, principal component analysis, artificial neural networks, and multivariate ranking techniques, are applied for dealing with missing data, grouping or classification purposes, selection of green material, or processes. The areas of application are mainly finding sustainable solutions...
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Copper(II) Complexes with 1-(Isoquinolin-3-yl)heteroalkyl-2-ones: Synthesis, Structure and Evaluation of Anticancer, Antimicrobial and Antioxidant Potential
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PROTEIN ENGINEERING DESIGN & SELECTION
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The Rayleigh model of the multipath fading channel
Open Research DataThe dataset contains the results of simulations that are part of the research on modelling the multipath fading in the communication channel. The Rayleigh fading envelope is generated using the Monte-Carlo simulation (MCS) in the LabVIEW programming environment.
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Jacek Tomków dr hab. inż.
PeopleEducation:1. 2018 - Ph.D. of Technical Sciencesin field of Materials Engineeringthesis: Influence of underwater welding conditions on cold cracking of high strength low alloy steel 2. 2012 - Master of Science Engineer, Gdansk University of Technologyin the field of: Mechanical Engineeringwith specialization in: Manufacturing Engineering and Computer Aided Manufacturing Processesthesis: Non-destructive testing of welding joints...
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World Research Journal of Peptide and Protein
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Advances in Protein Chemistry and Structural Biology
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Current Topics in Peptide and Protein Research
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International Journal of Peptide and Protein Research
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AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
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Geometrical accuracy of the objects in the axial run-out conditions
PublicationW pracy omówiono wpływ wartości bicia osiowego ostrzy pił tarczowych i parametrów obróbki na dokładność geometryczną powierzchni uzyskiwanych podczas procesu przecinania.
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Sawing accuracy on the twin shaft multi-rip saw
PublicationW pracy przedstawiono analizę i wyniki badań doświadczalnych dokładności przecinania na dwuwrzecionowej pilarce tarczowej. Zaprezentowano warianty struktury geometryczno-ruchowej dwuwrzecionowej pilarki tarczowej, jak również warunki pracy dolnych górnych pił pilarki.
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Accuracy analysis of the radio location service in the sea environment
PublicationW artykule przedstawiono koncepcję systemu bezpieczeństwa na morzu w oparciu o istniejące systemy komórkowe. Scharakteryzowano problem lokalizowania terminala ruchomego przez sieć w warunkach morskich. Przedstawiono wyniki badań przeprowadzonych w warunkach rzeczywistych w odniesieniu do efektywności lokalizowania terminala na morzu. Przedstawiono wnioski, wypływające z przeprowadzonych analiz.