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Search results for: j-domain proteins
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The measurement of conformational stability of proteins adsorbed on siloxanes
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Molecular basis of TRF proteins and their interactions with peptides
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Coarse-Grained Models of Proteins: Theory and Applications
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Computational techniques for efficient conformational sampling of proteins
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Chemometria praktyczna : zinterpretuj wyniki swoich pomiarów / J. Mazerski.
PublicationWbrew swojej nazwie chemometria nie zajmuje się sposobami i teorią wykonywania pomiarów wielkości chemicznych ani nie ogranicza się tylko do chemii, nawet szeroko pojętej. Chemometria jest dziedziną nauki i techniki zajmującą się wydobywaniem użytecznej informacji z wielowymiarowych danych pomiarowych, wykorzystującą metody statystyki i matematyki.Chemometria różni się od statystyki nie tylko charakterem zestawu analizowanych danych,...
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Akwarelą pod strzechy. Krenz J.: Cykl 5 akwarel.
PublicationAkwarelą pod strzechy. wystawa zbiorowa, poplenerowa Stowarzyszenia Akwarelistów Polskich prezentowana w Muzeum - Kaszubski Park Etnograficzny im. Teodory i Izydora Gulgowskich we Wdzydzach Kiszewskich.
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Budownictwo przemysłowe : Obliczanie i konstrukcja silosów / J. Tejchman.
PublicationSkrypt zawiera podstawowe informacje na temat silosów z przedmiotu Budownictwo przemysłowe. Tytuły rozdziałów są następujące: obliczenia teoretyczne naporu materiałów sypkich, obliczanie naporu materiałów sypkich według normy niemieckiej, obliczanie naporu materiałów sypkich według Eurokodu, pomiar właściwości materiałów sypkich, obliczenia statyczne silosów, obliczenia silosów żelbetowych metodą elementów skończonych, mechanizmy...
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Accelerated multi-objective design optimization of antennas by surrogate modeling and domain segmentation
PublicationMulti-objective optimization yields indispensable information about the best possible design trade-offs of an antenna structure, yet it is challenging if full-wave electromagnetic (EM) analysis is utilized for performance evaluation. The latter is a necessity for majority of contemporary antennas as it is the only way of achieving acceptable modeling accuracy. In this paper, a procedure for accelerated multi-objective design of...
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Accurate Modeling of Antenna Structures by Means of Domain Confinement and Pyramidal Deep Neural Networks
PublicationThe importance of surrogate modeling techniques has been gradually increasing in the design of antenna structures over the recent years. Perhaps the most important reason is a high cost of full-wave electromagnetic (EM) analysis of antenna systems. Although imperative in ensuring evaluation reliability, it entails considerable computational expenses. These are especially pronounced when carrying out EM-driven design tasks such...
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Concrete-domain reasoning techniques in knowledge cartography
PublicationWiele zjawisk w świecie rzeczywistym opisujemy korzystając z liczb i symboli. W ramach naszej pracy jako punkt wyjścia traktujemy podejście kartograficzne opracowane na potrzeby wnioskowania z ontologii opartych na logice opisowej i pozwalające na efektywne przetwarzanie baz wiedzy zwierających dużą liczbę osobników. Niniejszy artykuł przedstawia rozszerzenie podejścia kartograficznego pozwalające na wnioskowanie z wartości symbolicznych,...
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Enterprise Information Management in Cultural Heritage Domain
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A distributed scheme for inter-domain routing optimization
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Macromodels in the frequency domain analysis of microwave resonators.
PublicationW artykule zaprezentowana jest technika włączania makromodeli do metod siatkowych sformułowanych w dziedzinie częstotliwości.W odróżnieniu do poprzednich, nowy schemat nie wprowadza zależności częstotliwościowej do macierzy systemowej i dzięki temu może być użyta w analizie rezonatorów. Testy numeryczne pokazują wzrost dokładności obliczeń w szerokim zakresie częstotliwości, przy czym właściwości zbieżności iteracyjnego algorytmu...
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Crystal structures of the DsbG disulfide isomerase reveal an unstable disulfide
PublicationDsb proteins control the formation and rearrangement of disulfide bonds during the folding of secreted and membrane proteins in bacteria. DsbG, a member of this family, has disulfide bond isomerase and chaperone activity. Here, we present two crystal structures of DsbG at 1.7- and 2.0-Angstrom resolution that are meant to represent the reduced and oxidized forms, respectively. The oxidized structure, however, reveals a mixture...
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LSA Is not Dead: Improving Results of Domain-Specific Information Retrieval System Using Stack Overflow Questions Tags
PublicationThe paper presents the approach to using tags from Stack Overflow questions as a data source in the process of building domain-specific unsupervised term embeddings. Using a huge dataset of Stack Overflow posts, our solution employs the LSA algorithm to learn latent representations of information technology terms. The paper also presents the Teamy.ai system, currently developed by Scalac company, which serves as a platform that...
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Low-cost multi-objective design of compact microwave structures using domain patching
PublicationA good compromise between size and electrical performance is an important design consideration for compact microwave structures. Comprehensive information about size/performance trade-offs can be obtained through multi-objective optimization. Due to considerable electromagnetic (EM) cross-couplings in highly compressed layouts, the design process has to be conducted at the level of high-fidelity EM analysis which is computationally...
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Variable‐fidelity modeling of antenna input characteristics using domain confinement and two‐stage Gaussian process regression surrogates
PublicationThe major bottleneck of electromagnetic (EM)-driven antenna design is the high CPU cost of massive simulations required by parametric optimization, uncertainty quantification, or robust design procedures. Fast surrogate models may be employed to mitigate this issue to a certain extent. Unfortunately, the curse of dimensionality is a serious limiting factor, hindering the construction of conventional data-driven models valid over...
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Investigating Analytics Dashboards’ Support for the Value-based Healthcare Delivery Model
PublicationImproving the value of care is one of the essential aspects of Value-Based Healthcare (VBHC) model today. VBHC is a new HC delivery model which is centered on patient health outcomes and improvements. There is anecdotal evidence that the use of decision aid tools like dashboards can play a significant role in the successful implementation of VBHC models. However, there has been little or no systematic studies and reviews to establish...
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Two bacterial small heat shock proteins, IbpA and IbpB, form a functional heterodimer
PublicationSmall heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones which in stress conditions bind to unfolded protein substrates and prevent their irreversible aggregation. Substrates trapped in sHsps-containing aggregates are efficiently refolded into native structures by ATP-dependent Hsp70 and Hsp100 chaperones. Most γ-proteobacteria possess a single sHsp (IbpA), while in a subset of Enterobacterales, as...
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J. Pawlik TESTOWY
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Attenuation of Hyperglycemia in Diabetic Rats Assisted by Immobilized Probiotic in Sodium Alginate
PublicationDiabetes mellitus type 2 (DM2) is the most common chronic disease worldwide, characterized mainly by increased glucose concentration in the blood and affecting several organs’ functionality. The daily consumption of probiotic bacteria can help control diabetes and reduce the damage caused. Cell immobilization techniques are a powerful tool that provides physical cell protection to such probiotic bacteria against gastrointestinal...
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Recent advances in high-frequency modeling by means of domain confinement and nested kriging
PublicationDevelopment of modern high-frequency components and circuits is heavily based on full-wave electromagnetic (EM) simulation tools. Some phenomena, although important from the point of view of the system performance, e.g., EM cross-coupling effects, feed radiation in antenna arrays, substrate anisotropy, cannot be adequately accounted for using simpler means such as equivalent network representations. Consequently, the involvement...
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A vector-enzymatic DNA fragment amplification-expression technology for construction of artificial, concatemeric DNA, RNA and proteins for novel biomaterials, biomedical and industrial applications
PublicationA DNA fragment amplification/expression technology for the production of new generation biomaterials for scientific, industrial and biomedical applications is described. The technology enables the formation of artificial Open Reading Frames (ORFs) encoding concatemeric RNAs and proteins. It recruits the Type IIS SapI restriction endonuclease (REase) for an assembling of DNA fragments in an ordered head-to-tail-orientation. The...
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Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublicationInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
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Low-cost data-driven modelling of microwave components using domain confinement and PCA-based dimensionality reduction
PublicationFast data-driven surrogate models can be employed as replacements of computationally demanding full-wave electromagnetic simulations to facilitate the microwave design procedures. Unfortunately, practical application of surrogate modelling is often hindered by the curse of dimensionality and/or considerable nonlinearity of the component characteristics. This paper proposes a simple yet reliable approach to cost-efficient modelling...
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J. FE modelling of cracks in concrete elements within continuum mechanics.
PublicationW artykule przedstawiono wyniki symulacji rys zakrzywionych w elementach betonowych w warunkach mieszanego sposobu obciążenia. Symulacje wykonano przy zastosowaniu 3 różnych modeli: modelu sprężysto-plastycznego, modelu w ramach mechaniki zniszczeniowej i modelu z rysami obracającymi się.
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Fast Multi-Objective Aerodynamic Optimization Using Sequential Domain Patching and Multifidelity Models
PublicationExploration of design tradeoffs for aerodynamic surfaces requires solving of multi-objective optimization (MOO) problems. The major bottleneck here is the time-consuming evaluations of the computational fluid dynamics (CFD) model used to capture the nonlinear physics involved in designing aerodynamic surfaces. This, in conjunction with a large number of simulations necessary to yield a set of designs representing the best possible...
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Denaturation of proteins by surfactants studied by the Taylor dispersion analysis
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The construction of bifunctional fusion proteins consisting of MutS and GFP
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The construction of bifunctional fusion proteins consisting of MutS and GFP
PublicationSkonstruowano białka chimeryczne zawierające białko MutS z Thermus thermophilus i białko zielonej fluoresceiny GFP z Aequorea victoria, posiadające dla łatwiejszego oczyszczania domeny oligo-histydynowe na N- lub C-końcu. Fuzyjne białka rozpoznawały niekomplementarności w DNA podobnie do MutS T. thermophilus. Fluorescencyjne białka rozpoznające niekomplementarne DNA mogą być użyteczne w wykrywaniu jednonukleotydowych polimorfizmów...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Time domain validation of ultracapacitor fractional order model
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Understanding the containment of public spaces: upgrading public domain
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Model-Based Testing of Embedded Systems in the Automotive Domain
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Lexicon Based Algorithm for Domain Ontology Merging and Alignment
PublicationMore and more systems contain some kind of knowledge describing their field of operation. Such knowledge in many cases is stored as an ontology. A need arises for ability to quickly match those ontologies to enable interoperability of such systems. The paper presents a lexicon based algorithm for merging and aligning of OWL ontologies. The proposed similarity levels are being presented and the proposed algorithm is being described....
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Cross-domain applications of multimodal human-computer interfaces
PublicationDeveloped multimodal interfaces for education applications and for disabled people are presented, including interactive electronic whiteboard based on video image analysis, application for controlling computers with mouth gestures and audio interface for speech stretching for hearing impaired and stuttering people and intelligent pen allowing for diagnosing and ameliorating developmental dyslexia. The eye-gaze tracking system named...
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Internet of Robotic Things: Its Domain, Methodologies, and Applications
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Application of gaze tracking technology to quality of experience domain
PublicationA new methodological approach to study subjective assessment results employing gaze tracking technology is shown. Notions of Human-Computer Interaction (HCI) and Quality of Experience (QoE) are shortly introduced in the context of their common application. Then, the gaze tracking system developed at the Multimedia Systems Department (MSD) of Gdansk University of Technology (GUT) is presented. A series of audio-visual subjective...
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Time-domain prosodic modifications for text-to-speech synthesizer
PublicationAn application of prosodic speech processing algorithms to Text-To-Speech synthesis is presented. Prosodic modifications that improve the naturalness of the synthesized signal are discussed. The applied method is based on the TD-PSOLA algorithm. The developed Text-To-Speech Synthesizer is used in applications employing multimodal computer interfaces.
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Numerical conditioning of delta-domain Lyapunov and Riccati equations
PublicationW pracy rozważono problem uwarunkowania dyskretno czasowych równań Lapunowa oraz równań Riccatiego - to znaczy problem wrażliwości rozwiązań takich równań na odchyłki ich parametrów od nominalnych wartości. Zdefiniowano odpowiedni "różniczkowy" wskaźnik uwarunkowania oraz podano efektywną metodę szacowania jego wartości. Udowodniono teoretycznie - a także przekonująco zilustrowano na drodze numerycznej - twierdzenie głoszące, iż...
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Robust pole placement in delta domain for SISO plans
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A new anisotropic bending model for nonlinear shells: Comparison with existing models and isogeometric finite element implementation
PublicationA new nonlinear hyperelastic bending model for shells formulated directly in surface form is presented, and compared to four existing prominent bending models. Through an essential set of elementary nonlinear bending test cases, the membrane and bending stresses of each model are examined analytically. Only the proposed bending model passes all the test cases, while the other bending models either fail or only pass the test cases for...
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Patch size setup and performance/cost trade-offs in multi-objective antenna optimization using domain patching technique
PublicationA numerical study concerning multi-objective optimization of antenna structures using sequential domain patching (SDP) technique has been presented. We investigate the effect of various setups of the patch size on the operation of the SDP algorithm and possible trade-offs concerning the quality of the Pareto set found by SDP and the computational cost of the optimization process. Our considerations are illustrated using a UWB monopole...
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Mycobacterium tuberculosis Complex and Mycobacterial Heat Shock Proteins in Lymph Node Tissue from Patients with Pulmonary Sarcoidosis
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Synthesis and physical properties of the 10.6 K ferromagnet NdIr3
PublicationThe magnetic, transport, and thermodynamic properties of NdIr3 are reported. Its PuNi3-type crystal structure (space group R−3m), with lattice parameters a= 5.3262(1)Å and c=26.2218(3)Å, was confirmed by powder x-ray diffraction. Our measurements indicate that NdIr3 exhibits a previously unreported paramagnetic to ferromagnetic phase transition below TC=10.6 K(determined by using the Arrott plot). The magnetic susceptibility obeys...
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TIME-DOMAIN NUMERICAL EVALUATION OF SHIP RESISTANCE AND MOTION IN REGULAR WAVES BY USING THE CFD URANS METHOD
PublicationTaking into account the International Maritime Organisation’s (IMO) strategy to radically reduce the GHG emitted by the shipping industry towards zero emission operation, today's assessment of ship behaviour in waves, its seakeeping characteristics and resistance and their interrelation with fuel consumption and emissions are one of the most attended research subject. There are three methods to conduct this analysis, which are...