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Search results for: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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Modeling and Accuracy Assessment of Determining the Coastline Course Using Geodetic, Photogrammetric and Satellite Measurement Methods: Case Study in Gdynia Beach in Poland
PublicationThe coastal environment represents a resource from both a natural and economic point of view, but it is subject to continuous transformations due to climate change, human activities, and natural risks. Remote sensing techniques have enormous potential in monitoring coastal areas. However, one of the main tasks is accurately identifying the boundary between waterbodies such as oceans, seas, lakes or rivers, and the land surface....
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The influence of Be addition on the structure and thermal properties of alkali-silicate glasses
PublicationBe-Na-(Li)-Si oxide glasses containing up to 15 mol% of BeO were prepared. Their structure was characterized by X-ray powder diffraction and Raman as well as infrared spectroscopic techniques, while their chemical compositions were examined by Inductively Coupled Plasma Optical Emission Spectrometry. All materials were found to be amorphous and contain Al contaminations from minor dissolution of the alumina crucibles. The results...
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Hybrid Reduced Model of Continuous System
PublicationThe paper introduces an alternative method of modelling and modal reduction of continuous systems. Presented method is a hybrid one. It combines the advantages of modal decomposition method and the rigid finite element method. In the proposed method continuous structure is divided into one-dimensional continuous elements. For each 1D element modal decomposition and reduction is applied. Interactions between substructures are...
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Texture or Linker? Competitive Patterning of Receptor Assembly toward Ultra-Sensitive Impedimetric Detection of Viral Species at Gold-Nanotextured Titanium Surfaces
PublicationIn this work, we study the electrodes with a periodic matrix of gold particles pattered by titanium dimples and modified by 3-mercaptopropionic acid (MPA) followed by CD147 receptor grafting for specific impedimetric detection of SARS-CoV-2 viral spike proteins. The synergistic DFT and MM/MD modeling revealed that MPA adsorption geometries on the Au–Ti surface have preferential and stronger binding patterns through the carboxyl...
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Prediction of the stability during optimal control of the 3-wheel mobile platform
PublicationW pracy przedstawiono metodę badania stabilności sterowania optymalnego 3-kołową platformą mobilną podczas realizacji zadanej trajektorii ruchu. Badany robot posiada więzy nieholonomiczne. Model matematyczny robota 3-kołowego opisano za pomocą skończonej liczby nieliniowych równań różniczkowych. Stąd, prognozowanie ruchu takiego obiektu wymaga zastosowania efektywnych algorytmów.
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Synthesis of 3-(2-Alkylthio-4-chloro-5-methylbenzenesulfonyl)-2-(1-phenyl-3-arylprop-2-enylideneamino)guanidine Derivatives with Pro-Apoptotic Activity against Cancer Cells
PublicationThe untypical course of reaction between chalcones and benzenesulfonylaminoguanidines led to the new 3-(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-2-(1-phenyl-3-arylprop-2- enylideneamino)guanidine derivatives 8–33. The new compounds were tested in vitro for their impact on the growth of breast cancer cells MCF-7, cervical cancer cells HeLa and colon cancer cells HCT-116 by MTT assay. The results revealed that the activity of...
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OBTAINING FLUID FLOW PATTERN FOR TURBINE STAGE WITH NEURAL MODEL.
PublicationIn the paper possibility of applying neural model to obtaining patterns of proper operation for fluid flow in turbine stage for fluid-flow diagnostics is discussed. Main differences between Computational Fluid Dynamics (CFD) solvers and neural model is given, also limitations and advantages of both are considered. Time of calculations of both methods was given, also possibilities of shortening that time with preserving the accuracy...
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Objectivity in the non-Markovian spin-boson model
PublicationObjectivity constitutes one of the main features of the macroscopic classical world. An important aspect of the quantum-to-classical transition issue is to explain how such a property arises from the microscopic quantum theory. Recently, within the framework of open quantum systems, there has been proposed such a mechanism in terms of the so-called spectrum broadcast structures. These are multipartite quantum states of the system...
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Fuctional structure of diagnostic system for wheeled tractors
PublicationAn application of computer controlled fuel injection systems in vehicle engines and growing demands concerning toxic substances emission and fuel consumption was a main reason for OBD (On Board Diagnosis) development. In spite of a great technological development, only some tractors are equipped in diagnostic systems. On board diagnosis is strongly connected with emission demands and does not concern other important vehicle functions.In...
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Model-free and Model-based Reinforcement Learning, the Intersection of Learning and Planning
PublicationMy doctoral dissertation is intended as the compound of four publications considering: structure and randomness in planning and reinforcement learning, continuous control with ensemble deep deterministic policy gradients, toddler-inspired active representation learning, and large-scale deep reinforcement learning costs.
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On the derivatives $\partial^{2}P_{\nu}(z)/\partial\nu^{2}$ and $\partial Q_{\nu}(z)/\partial\nu$ of the Legendre functions with respect to their degrees
PublicationWe provide closed-form expressions for the degree-derivatives $[\partial^{2}P_{\nu}(z)/\partial\nu^{2}]_{\nu=n}$ and $[\partial Q_{\nu}(z)/\partial\nu]_{\nu=n}$, with $z\in\mathbb{C}$ and $n\in\mathbb{N}_{0}$, where $P_{\nu}(z)$ and $Q_{\nu}(z)$ are the Legendre functions of the first and the second kind, respectively. For $[\partial^{2}P_{\nu}(z)/\partial\nu^{2}]_{\nu=n}$, we find that % \begin{displaymath} \frac{\partial^{2}P_{\nu}(z)}{\partial\nu^{2}}\bigg|_{\nu=n} =-2P_{n}(z)\Li_{2}\frac{1-z}{2}+B_{n}(z)\ln\frac{z+1}{2}+C_{n}(z), \end{displaymath} % where...
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Study of Integer Spin S = 1 in the Polar Magnet β-Ni(IO3)2
PublicationPolar magnetic materials exhibiting appreciable asymmetric exchange interactions can potentially host new topological states of matter such as vortex-like spin textures; however, realizations have been mostly limited to half-integer spins due to rare numbers of integer spin systems with broken spatial inversion lattice symmetries. Here, we studied the structure and magnetic properties of the S = 1 integer spin polar magnet β-Ni(IO3)2...
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Prediction of the fatigue lifetime of PUR structural elements using a combined experimental-numerical approach
PublicationThis paper presents a method for estimating the fatigue life of polyurethane elastomeric components. A rubber replacement - polyurethane of hardness 80ShA commonly used in vibration damping systems, for example, in motor vehicle suspensions, was used for the study. A metal-rubber bushing component was selected for analysis, and numerical analysis was carried out along with a fatigue model proposal based on a modification of the...
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Structure of the US investment company industry over the period 2000 to 2017: substitution analysis
PublicationOver the last years the investment company industry has undergone deep transformation in the majority of the most advanced economies, including the United States. Traditional investment companies, such as mutual funds, have lost their market share to innovative exchange-traded funds (ETFs). The main distinctive features of ETFs are listing and trading in their units on the stock exchanges as well as lower costs for investors. The...
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The lemniscate knowledge flow model
PublicationKnowledge is seen as one of the main resources for organizations providing knowledge-intensive services. Therefore, sharing and reusing are the main goals of modern knowledge management (KM) approach, driven by information and communication technologies (ICT). However, one can ask for the details in order to provide means and tools to design and deploy environment able to fulfil these two goals. We observed that occurred interactions...
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A Stand for Measurement and Prediction of Scattering Properties of Diffusers
PublicationIn this paper we present a set of solutions which may be used for prototyping and simulation of acoustic scattering devices. A system proposed is capable of measuring sound field. Also a way to use an open source solution for simulation of scattering phenomena occurring in proximity of acoustic diffusers is shown. The result of our work are measurement procedure and a prototype of the simulation script based on FEniCS - an open source...
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Creep failure prediction of pipelines in elevated temperature
PublicationW pracy omówiono zastoswanie modelu konstytutytwnego pełzania pozwalającego na analizę trwałości metalowych ruruciągów pracujących w wysokich temperaturach. Zaprezentowano wyniki obliczeń opartych na metodzie elementów skończonych (MES) wykonanych z wykorzystaniem procedur użytkownika w komercyjnym programie MES. Porównano wyniki dla dwóch typów 4-węzłowych elementów powłokowych.
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Prediction of Deflagrative Explosions in Variety of Closed Vessels
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Prediction of Weld Deformations by Numerical Methods - Review
PublicationThe welding process is the basic technique of joining in the shipbuilding industry. This method generates welding distortions that cause a lot of problems during the manufacturing process due to both the time and cost of straightening as well as their influence on later stages of production. Proper preparation of welding processes plays a growing role in the shipbuilding industry and the development of calculating tools is being...
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Pitch etection enhancement employing music prediction.
PublicationW artykule przedstawiono przegląd metod detekcji częstotliwości podstawowej we frazach muzycznych. Wskazano też główne problemy występujące w procesie estymacji dźwięków muzycznych. W celu zmniejszenia błędów oktawowych zaproponowano uwzględnienie w systemie predyktora neuronalnego. Opracowana przez Autorów metoda predykcji zdarzeń muzycznych wykorzystywana jest jako moduł wspomagający pracę systemu. Proponowane podejście pozwala...
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Prediction of ship resistance with the use of Full-scale CFD simulations
PublicationIn recent years, the IMO has introduced new regulations to reduce the negative impact of ships on the natural environment. A particularly important step forcing technological innovations is the increasing requirement of ship energy efficiency. It is expressed by the Energy Efficiency Design Index (EEDI). Another important step towards green shipping is rising the required quality of fuel used for propulsion, so called Tier limits....
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Syntheses and structures of the first terminal phosphanylphosphido complex of hafnium [cp2hf(cl){η1-(me3si)p-p(net2)2}] and the firstzirconocene-phosphanylphosphinidene dimer [cp2zr{μ2-p-p(net2)2}2zrcp2]
PublicationReactions of (Et2N)2P-P(SiMe3)Li with [Cp2MCl2] (M= Zr, Hf) in toluene or pentane yield the related terminal phosphanylphosphido complexes [Cp2M(Cl){η1-(Me3Si)P-P(NEt2)2}]. The solid statestructure of [Cp2Hf(Cl){η1-(Me3Si)P-P(NEt2)2}] was established by single crystal X-ray diffraction. The reaction of (Et2N)2P-P(SiMe3)Li with [Cp2ZrCl2] in THF or DME solutions leads to the formationof deep red crystals of the first neutral diamagnetic...
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Highly selective impedimetric determination of Haemophilus influenzae protein D using maze-like boron-doped carbon nanowall electrodes
PublicationThis study reports a novel impedimetric immunosensor for protein D detection in purified and bacterial (Haemophilus influenzae, Hi) samples. The detection was based on antigen recognition by anti-protein D antibodies (apD) immobilised at the maze-like boron-doped carbon nanowall electrodes (B:CNW). The B:CNW electrodes were synthesised, and their surface was characterised by scanning electron microscopy (SEM) and X-ray photoelectron...
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Posttraumatic Orbital Emphysema: A Numerical Model
PublicationOrbital emphysema is a common symptom accompanying orbital fracture. The pathomechanism is still not recognized and the usually assumed cause, elevated pressure in the upper airways connected with sneezing or coughing, does not always contribute to the occurrence of this type of fracture. Observations based on the finite model (simulating blowout type fracture) of the deformations of the inferior orbital wall after a strike in...
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Cobalt(II) tri-tert-butoxysialanethiolates.Synthesis, properties, crystal and molecular structures of [Co{SSi(OtBu)3}2(L)] and[Co{SSi(OtBu)3}2(L)2] type complexes with monodentate nitrogen ligands.
PublicationThe title heteroleptic neutral cobalt(II) tri-tert-butoxysilanethiolate complexes with monodentate nitrogen bases (L) as additional ligands have been prepared by the reactions of [Co{μ-SSi(OtBu)3}{SSi(OtBu)3}(NH3)]2 (1) with respective bases. For pyridine both types have been prepared...
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Optimization of Nuclear Power Share in the Structure of Electricity Production in Poland in Time Perspective by 2060
PublicationThe author of this paper presented the results of a system analysis using MARKAL model, aiming at the optimization of nuclear power share in power generation structure in Poland in time perspective by 2060. Optimization criterion is the minimization of the objective function, i.e. the total cost of energy system, taking into account constraints related to CO2, SOx and NOx emissions and obligatory shares of electricity from renewable...
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublicationImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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Effects of the Covid-19 travel restrictions on metropolises mobility: empirical evidence from the Tricity metropolis (Poland)
PublicationThis paper aims to assess changes in mobility and modal shift caused by COVID-19 travel restrictions among the residents of Gdańsk Bay Metropolis (Poland). Measurement’s moments were assumed in periods differing in the level of restric- tions. The computer-assisted telephone interview (CATI) was carried out in November and December 2020. The results did not confirm the expected modal shift. However, significant changes in the number...
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Metal ion directed template synthesis using 2-acetyl-1,3-indandione and ethylenediamine: steric and electronic restrictions
PublicationA template synthesis using 2-acetyl-1,3-indandione and ethylenediamine results in formation of octahedral Ni complex, whose crystal structure has been resolved using single crystal X-ray diffraction. The structure indicates that only exocyclic enolic oxygen atom of the triketone takes part in the condensation with ethylenediamine.
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Structures, physicochemical and cytoprotective properties of new oxidovanadium(IV) complexes -[VO(mIDA)(dmbipy)]·1.5H 2 O and [VO(IDA)(dmbipy)]·2H 2 O
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Evaluation of Medical Staff Satisfaction for Workplace Architecture in Temporary COVID-19 Hospital: A Case Study in Gdańsk, Poland
PublicationThis article analyses the architecture that was used in the temporary AmberExpo hospital in Gdańsk, Poland which was installed during the COVID-19 pandemic. The construction of this type of facility is often based on experimental approaches, aimed at caring for patients suffering from an infectious disease in emergency conditions. In order to assess the level of employee satisfaction with the architectural and technical elements...
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The spectral finite element model for analysis of flexural-shear coupled wave propagation. Part 2, Delaminated multilayer composite beam
PublicationW pracy przedstawiono, wykorzystując metodę elementów spektralnych, analizę wpływu delaminacji na propagację fali giętno-ścinającej w belce kompozytowej.
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The spectral finite element model for analysis of flexural-shear coupled wave propagation. Part 2: Delaminated multilayer composite beam
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Prediction of Overall In Vitro Microsomal Stability of Drug Candidates Based on Molecular Modeling and Support Vector Machines. Case Study of Novel Arylpiperazines Derivatives
PublicationOther than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach its therapeutic site of action. Despite many recent excellent achievements in the field of computational methods supporting drug metabolism studies, a well-recognized procedure to model...
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Wyznaczanie współczynnika przejmowania ciepła podczas wrzenia w przepływie dwutlenku węgla (Prediction of flow boling heat transfer coefficient for carbon dioxide in minichannels)
PublicationW pracy przedstawiono wyniki obliczeń uzyskane za pomocą własnego modelu półemirycznego dla wybranych danych eksperymentalnych dla wrzenia w przepływie dwutlenku węgla. Metoda obliczeniowa została zweryfikowana z danymi eksperymentalnymi Docoulombiera i innych (2011) oraz Mastrullo i innych (2009). Badania eksperymentalne dotyczą pełnego zakresu zmienności stopnia suchości oraz zakresu prędkości masowej G=200-1200 kg/m2s. rozwijany...
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Bio and slide biobearings, their lubrication by non-newtonian fluids and application in non-conventional systems. Vol. 2, The theory of human joint unsteady lubrication.
PublicationW monografii przedstawiono zasady niestacjonarnego smarowania stawów człowieka o odkształcalnych chrząstkach i powierzchniach kostnych w polach indukcji magnetycznej. W opisie stochastycznym uwzględnione zostały nienewtonowskie, lepkosprężyste właściwości cieczy synowialnych jako czynnika smarującego. Monografia prezentuje rozkłady wartości ciśnienia i nośności stawów człowieka w warunkach niestacjonarnego smarowania dla drgań...
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Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode
PublicationThis work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10−18 to 10−8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10−14 M for PD-L1 (S/N = 3.3) and at a concentration of 10−14...
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Ekspertyza(2)
PublicationEkspertyza dotycząca odrzucenia odwołania złożonego przez firmę MLU Sp. z o.o. z siedzibą w Katowicach, ul. Połomińska 16 40-585 Katowice w Krajowej Izbie Odwoławczej przy Prezesie Urzędu Zamówień Publicznych, ul. Postępu 17a 02-676 Warszawa, wobec treści ogłoszenia o zamówieniu opublikowanym dnia 8 maja 2013r. w Dzienniku Urzędowym Unii Europejskiej pod numerem 151218-2013, dotyczącym postępowania o udzielenie zamówienia publicznego...
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Lattice filter based autoregressive spectrum estimation with joint model order and estimation bandwidth adaptation
PublicationThe problem of parametric, autoregressive model based estimation of a time-varying spectral density function of a nonstationary process is considered. It is shown that estimation results can be considerably improved if identification of the autoregressive model is carried out using the two-sided doubly exponentially weighted lattice algorithm which combines results yielded by two one-sided lattice algorithms running forward in...
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An Alternative Proof of a Lower Bound on the 2-Domination Number of a Tree
PublicationA 2-dominating set of a graph G is a set D of vertices of G such that every vertex not in D has a at least two neighbors in D. The 2-domination number of a graph G, denoted by gamma_2(G), is the minimum cardinality of a 2-dominating set of G. Fink and Jacobson [n-domination in graphs, Graph theory with applications to algorithms and computer science, Wiley, New York, 1985, 283-300] established the following lower bound on the 2-domination...
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Prediction of flow boiling heat transfer coefficient for carbon dioxide in minichannels and conventional channels
PublicationIn the paper presented are the results of calculations using authors own model to predict heat transfer coefficient during flow boiling of carbon dioxide. The experimental data from various resea rches were collected. Calculations were conducted for a full range of quality variation and a wide range of mass velocity. The aim of the study was to test the sensitivity of the in-house model. The results show the importance of taking into...
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A DFT/TD DFT study of the structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion
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Heterogeneity of quaternary structure of glucosamine-6-phosphate deaminase from Giardia lamblia
PublicationThe oligoHis-tagged versions of glucosamine-6- phosphate deaminase from Giardia lamblia (GlmNagB-HisN, GlmNagB-HisC) were constructed and purified to hear homogeneity, and their kinetic and structural properties were compared to those of the wild-type enzyme (GlmNagB). Introduction of the oligoHis tag at the GlmNagB C-terminus resulted in almost complete loss of the catalytic activity, while the catalytic properties of GlmNagB-HisN...
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Apple pectin complexes with whey protein isolate
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Some applications of thermophiles and their enzymes for protein processing
PublicationPrzedstawiono charakterystykę, właściwości oraz możliwości zastosowań enzymów proteolitycznych wytwarzanych przez termofile. Zaletą tych biokatalizatorów jest między innymi duża odporność na działanie rozpuszczalników organicznych, detergentów i innych czynników denaturujących białka oraz mała wrażliwość na zmiany pH. Dokonano też przeglądu czynników powodujących dużą stabilność proteaz z termofili.
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Pea Protein for Hempseed Oil Nanoemulsion Stabilization
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Construction and development of IT Competence Centers - organizational structure
PublicationThe author presents the situation of the current units working between academic environment and business. the paper presents the possibility of using a dynamic structure to develop UCC.
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...