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Search results for: anion binding
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Assessment of Adjustment of GNSS Railway Measurements with Parameter-Binding Conditions in a Stationary Scenario
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NK1 receptor binding of a few low molecular weight 3,5-bistrifluoromethylbenzene derivatives
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Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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Assessment of Adjustment of GNSS Railway Measurements with Parameter-Binding Conditions in a Stationary Scenario
PublicationThe study aims to assess the applicability of the ordinary least squares method, robust estimation, and conditions-binded adjustment in processing the six synchronous coordinate pairs of global navigation satellite system (GNSS) receivers. The research is part of the research project InnoSatTrack, focused on the enhancement of the determination of geometrical parameters of railway tracks using GNSS, inertial, and other sensors....
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Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublicationBiałka wiążące się do jednoniciowego DNA (SSB) odgrywają ważną rolę w replikacji, rekombinacji i naprawie DNA u bakterii, archea i eukariota. Ostatnio wzrosło zainteresowanie białkami SSB jako przydatnymi narzędziami w metodach badawczych biologii molekularnej, analitycznych i diagnostycznych. Większość znanych prokariotycznych białek SSB zbudowanych jest z czterech podjednostek (homotetramer) z jedną domeną wiążąca (OB) jednoniciowe...
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Daylight recommendation for building interiors in the selected national building and lighting regulations in the EU
PublicationThe quality of life within building environment is closely linked to the quality of daylight effectively delivered into the living space. The paper describes the results of the normative documents review and a comparative analysis, based on which daylight recommendations present in national regulations have been compiled.
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Comparative analysis of national and regional models of the silver economy in the European Union
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Substance Flow Analysis of Mercury Affecting Water Quality in the European Union
PublicationW pracy zastosowano metodę SFA (Substance Flow Analysis) do oceny źródeł transportu i składowania rtęci w wodzie na terenie UE. W wyniku analizy stopnia zanieczyszczenia środowiska w przeszłości jak i scenariuszy zmian tego zanieczyszczenia w przyszłości stwierdzono, że spalanie paliw zawierających rtęć, takich jak węgiel i olej stanowi główne źródło zanieczyszczenia wody rtęcią.
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Municipal Waste Management in Poland Compared to Other European Union Countries
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Assessment of the Feasibility of Energy Transformation Processes in European Union Member States
PublicationThe energy transition is now treated in most countries as a necessary condition for their long-term development. The process of energy transformation assumes the simultaneous implementation of the Sustainable Development Goals, which are a major challenge for modern economies and introduce significant restrictions in their functioning. Our study aims to group EU member states according to their ability to achieve energy transition...
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Typology of low developed non-metropolitan sub-regions in the European Union
PublicationThis paper shows a typology of 319 NUTS-3 sub-regions in the European Union. The selected sub-regions are non-metropolitan sub-regions, whose gross domestic product per capita in 2011 was below 75% of the EU average. The objective of this typology was to recognize diversity in the examined sub-regions as a starting point for the selection of areas for future comparative research. The typology takes into account 24 variables related...
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EU-Turkey Customs Union and Bilateral Foreign Direct Investment Flows
PublicationMain aim of this text is presentation of the effects of customs union between the European Union and turkey on bilateral FDI flows in light of the theory of linkages between economic integration and FDI flows. First section of the text is a survey of main theoretical links between economic integration and FDI flows. Second section focuses on the history and scope of the customs union. Third and fourth sections are empirical and...
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The Impact of Concentration on Secors' Output Level in the European Union (1997-2005)
PublicationThis paper examines the impact of concentration on growthof selected 43 sectors within ten European countries over the period of time 1997-2005. We apply system GMM estimator to the extendedversion of production function, including as explanatory variablesindustry specific measures of concentration. We found the relationbetween output and concentration measured by the Herfindahl-Hirschman Index (HHI) to be non-monotonic having...
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Repulsive Coulomb Barriers in Compact Stable and Metastable Multiply Charged Anions
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Stable anions formed by organic molecules substituted with superhalogen functional groups
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A metastable [(MgF3)2]2− dianion composed of two superhalogen anions
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Theoretical Search for Alternative Nine-Electron Ligands Suitable for Superhalogen Anions
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EUDEM2: The European Union in humanitarian demining. State of the art on humanitarian demining.
PublicationPrzedstawiono projekt 5 Programu Ramowego. Opisano stan technologii technik wykrywania min lądowych w krajach europejskich.
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A polynomial algorithm for finding T-span of generalized cacti
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Finding deformation of the straight rail track by GNSS measurements
PublicationW 2009 roku na Politechnice Gdańskiej i Akademii Marynarki Wojennej w Gdyni zostały przeprowadzone, po raz pierwszy, ciągłe pomiary satelitarne toru kolejowego z wykorzystaniem względnej metody fazowej na bazie polskiej Aktywnej Sieci Geodezyjnej ASG-EUPOS i serwisu czasu rzeczywistego RTK (GPRS) - NAVGEO. Przeprowadzona analiza wykazała silny związek między lokalizacją odbiornika GNSS i dokładnością wyznaczania pozycji, wpływ...
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Finding the right balance in oxygen delivery after resuscitation
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Fractal dimension for bending–torsion fatigue fracture characterisation
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Fractal dimension for bending–torsion fatigue fracture characterisation
PublicationFracture surfaces after biaxial fatigue tests were compared using fractal dimension for three types of metallic materials in smooth and notched specimens made of S355J2 and 10HNAP steels and 2017-T4 aluminium alloy, considering both proportional and nonproportional cyclic loading. High-resolution optical 3D measurement studies were performed on the entire fracture surface. A direct correlation between fractal dimension and fatigue...
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Complex Root Finding Algorithm Based on Delaunay Triangulation
PublicationA 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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Influence of compaction effectiveness on interlayer bonding of asphalt layers
PublicationThe paper presents the results of research on the interlayer bonding of asphalt layers compacted in the laboratory and in the field. To measure the interlayer bonding at a temperature of 20°C the Leutner test apparatus was used and load was applied at a rate of 50 mm/minute. Three types of interlayer interfaces were tested: no tack coat and tack coats made of two types of the pure bitumen emulsions. Four compaction techniques were...
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Innovative Cold-formed GEB Section under Bending
PublicationThis paper is concerned with the numerical bending capacity study of the innovative cold-formed GEB sections. Both linear buckling analysis and non-linear static analysis incorporating geometric and material nonlinearity were carried out employing a shell structural model. The magnitudes of buckling load and limit load with respect to GEB section depth and thickness were obtained. The opened cold-formed section was tested assuming...
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On root finding algorithms for complex functions with branch cuts
PublicationA simple and versatile method is presented, which enhances the complex root finding process by eliminating branch cuts and branch points in the analyzed domain. For any complex function defined by a finite number of Riemann sheets, a pointwise product of all the surfaces can be obtained. Such single-valued function is free of discontinuity caused by branch cuts and branch points. The roots of the new function are the same as the...
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FEM simulation of laminate failure in the three point bending
PublicationThe paper presents a FEM simulation of failure of laminate subjected to the three point bending. The numeri-cal model is based on the equivalent single layer approach with 6-paramater non-linear shell theory kinematics. It is implemented in the non-commercial FEM code. The failure initiation is detected with the use of Tsai-Wu criterion. After the failure onset the progressive failure process is modelled through the appropriate...
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A polynomial algorithm for finding T-span of generalized cacti.
PublicationW pracy opisano wielomianowy algorytm wyznaczający optymalne T-pokolorowania dla uogólnionych kaktusów.
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Cations of amino acid alkyl esters conjugated with an anion from the group of NSAIDs – As tunable pharmaceutical active ionic liquids
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Investigations of ternary complexes of Co(II) and Ni(II) with thiodiacetate anion and 1,10-phenanthroline or 2,2’-bipyridine in aqueous solutions
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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Combining tight-binding and molecular dynamics methods to model the behaviour of metals in the plastic regime
PublicationOpisujemy zastosowanie metody dwuskalowej (kwantowo-klasycznej) w zastosowaniu do metali. Region energetycznie najważniejszy jest traktowany kwantowo, podczas gdy reszta układu jest traktowana klasycznie. Wprowadzamy własną implementację metody oraz przedstawiamy uzyskane wyniki dla metali.
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Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis
PublicationW celu zbadania właściwości biochemicznych białka wiążącego się do jednoniciowego DNA (SSB) pochodzącego z Deinococcus geothermalis (DgeSSB), sklonowano gen ssb otrzymany w reakcji PCR, a następnie uzyskano wydajną biosyntezę białka DgeSSB. Gen składa się z 900 par zasad, kodujących białko złożone z 300 reszt aminokwasowych, o wyliczonej masie molekularnej równej 32.45 kDa. Sekwencja aminokwasowa wykazuje 43, 44% i 75% identyczności...
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Novel Potential Binding Sites for Selective Inhibitor Design of Human Soluble Epoxide Hydrolase
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Adipocyte Fatty Acid‐Binding Protein as a Novel Marker of Psoriasis and Clinical Response to Acitretin
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The effect of topical treatment and psoriasis severity on serum retinol-binding protein-4 levels
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Inhibition Ability of Natural Compounds on Receptor-Binding Domain of SARS-CoV2: An In Silico Approach
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Studies on Aryl-Substituted Phenylalanines: Synthesis, Activity, and Different Binding Modes at AMPA Receptors
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Naphthyl-vs. anthrylpyridine-2,6-dicarboxamides in cation binding studies. Synthesis and spectroscopic properties
PublicationPyridine-2,6-carboxamides bearing - or -naphthyl- and - or -anthryl- residues were prepared using simple method from pyridine-2,6-carboxylic acid dichloride and the respective aromatic amines. For the obtained receptors selective binding of lead(II), and copper(II) was found. Ion-receptor interactions were studied using UV-vis spectroscopy, spectrofluorimetry, 1H NMR, and FTIR spectroscopy. The reversible lead(II) and copper(II)...
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
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Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative
PublicationThrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain...
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Induced-fit binding of laccase to gold and carbon electrodes for the biological fuel cell applications
PublicationAnalogues of laccase natural substrates (syringic, veratric, ferulic, vanillic, isovanillic, 3,5-dimethoxybenzoic aldehydes) were employed to bind and orient laccase molecules in a way which facilitates adsorption of the catalyst molecules and their electrical connection with the conductive support. Laccase was bound efficiently to these substrates both on gold and carbon electrodes forming, respectively, 2D and 3D films sensitive...
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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublicationIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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The Ellenbogen's "Matter as Software" Concept for Quantum Computer Implementation: II Bonding Between the C60 and X@C60 Molecules as Available Molecular Building Blocks (MBBs) for Tip-Based Nanofabrication (TBN) of Quantum Computing Devices
PublicationThe binding energy, BE of the X@C60-X@C60 homodimer and the X@C60-Y@C60 heterodimer resulting from the bond formation between the occupied X@C60 MBB and the C60 molecule was studied by means of semiempirical PM7 calculations, where X and Y denote atoms from H to Bi, excluding Tc and lanthanides. All possible combinations of N = 68 guest atoms were considered, which resulted in K = 2346 of different calculated dimers of (X@C60-Y@C60)...