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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Application of gas chromatography–tandem mass spectrometry for the determination of amphetamine-type stimulants in blood and urine
PublicationAmphetamine, methamphetamine, phentermine, 3,4-methylenedioxyamphetamine (MDA), 3,4-methylenedioxymethamphetamine (MDMA), and 3,4-methylenedioxy-N-ethylamphetamine (MDEA) are the most popular amphetamine-type stimulants. The use of these substances is a serious societal problem worldwide. In this study, a method based on gas chromatography-tandem mass spectrometry (GC-MS/MS) with simple and rapid liquid-liquid extraction (LLE)...
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Noise in biological Raman spectroscopy
PublicationRaman spectroscopy is a widely used method to investigate chemical molecules by analyzing their vibrational transitions. It utilizes inelastic scattering of the laser light irradiating the investigated object. The scattered light requires appropriate filtering to reduce dominant laser light and expose much weaker components having shifted wavelengths of a characteristic spectral pattern. These components are measured by dispersing...
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Up-conversion white emission and other luminescence properties of a YAG:Yb2O3·Tm2O3·Ho2O3@SiO2 glass-nanocomposite
PublicationWe report on a glass-nanocomposite material consisting of yttrium aluminum garnet (Y3Al5O12, YAG) nanocrystals co-doped with Yb3+, Tm3+ and Ho3+ ions as well as entrapped into a SiO2 xerogel. This 94YAG·5Yb2O3·0.8Tm2O3·0.2Ho2O3@SiO2 (abbr. YAG:YbTmHo@SiO2) nanocomposite material has been prepared by sol–gel procedure. Its structure and morphology has been characterized by means of X-ray diffraction (XRD) and scanning electron microscope...
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Eu2Mg3Bi4: Competing Magnetic Orders on a Buckled Honeycomb Lattice
PublicationThe honeycomb lattice and its derived variants provide information on modeling and designing quantum magnets. A novel magnetic material, Eu2Mg3Bi4, which stabilizes in a previously unknown buckled honeycomb lattice, was discovered by high-pressure and high-temperature methods. We report here on the synthesis exploration of pure single crystals, structural determination of the buckled honeycomb lattice of europium moments, and experimental observation...
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A Method for Determination and Compensation of a Cant Influence in a Track Centerline Identification Using GNSS Methods and Inertial Measurement
PublicationAt present, the problem of rail routes reconstruction in a global reference system is increasingly important. This issue is called Absolute Track Geometry, and its essence is the determination of the axis of railway tracks in the form of Cartesian coordinates of a global or local coordinate system. To obtain such a representation of the track centerline, the measurement methods are developed in many countries mostly by the using...
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Brain circuit imprints of developmental 17α-Ethinylestradiol exposure in guppies (Poecilia reticulata): Persistent effects on anxiety but not on reproductive behaviour
PublicationThe effects of endocrine disruptors may vary with the timing of exposure. The physiological implications of adult exposure are present during and shortly after exposure while embryonic exposure can imprint changes manifested in adulthood. In this study, guppy (Poecilia reticulata) embryos were exposed to 2 and 20 ng/L of 17α-ethinylestradiol during development via the mother and reared in clean water from gestation until 6 months...
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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublicationWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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The electronic excited states of dichloromethane in the 5.8-10.8 eV energy range investigated by experimental and theoretical methods
PublicationWe present a comprehensive experimental high-resolution vacuum ultraviolet (VUV) photoabsorption spectrum of dichloromethane, CH 2 Cl 2 , with absolute cross sections determined for the full 5.8–10.8 eV energy-range. The calculations on the vertical excitation energies and oscillator strengths were performed using the equation-of-motion coupled cluster method, restricted to the single and double excitations level (EOM-CCSD), and...
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Synthesis, crystal structure and cytotoxic activity of ruthenium(II) piano-stool complex with N,N-chelating ligand
PublicationA mononuclear compound of the general formula [(η6-p-cymene)RuIICl(2,2′-PyBIm)]PF6 has been synthesized from a bidentate N,N-donor ligand, viz. 2,-(2′-pyridyl)benzimidazole (2,2′-PyBIm) and the corresponding chloro-complex [(η6-p-cymene)Ru(μ-Cl)Cl]2 (precursor). The isolated coordination compound was characterized by IR, UV–vis and 1H, 13C NMR spectroscopies. The single crystal X-ray analysis of the complex reveals that the asymmetric...
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Interactions in aqueous solutions of K-peptide and DMSO – spectroscopic and calorimetric studies
PublicationIntroduction K-peptide (GILQINSRW) – short 9 amino acid fragment of the hen egg white lysozyme has the ability to form amyloid structures. Dimethyl sulfoxide (DMSO) is an osmolyte which can alter this ability. Our goal was to get an insight into the mechanism of Kpeptide-DMSO interactions in aqueous solutions. Such a knowledge can be helpful to understand processes leading to various neurodegenerative diseases. Methods ATR-FTIR...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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Evaluation of Pavement Temperatures in Poland During Winter Conditions
PublicationThe paper presents the analysis of pavement temperatures from meteorological stations located at the Polish national roads during the impact of low winter temperatures. Presented issue is particularly important in view of the problem of low-temperature cracks that occur in the asphalt pavement under the influence of low temperatures. For each location of meteorological station there were analysed measurements of the temperature...
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Modelling Signalised Intersections Reliability of Functioning
PublicationThe article addresses a fundamental aspect of traffic, i.e. the operation of traffic signals at intersections, in reference to the reliability theory. In many cases, when intersections carry substantial amounts of traffic, selecting control parameters to produce satisfactory traffic conditions is quite difficult. Design methods do not cover all possible situations which are the result of intersection geometry and location...
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The carbohydrate glycosylphosphatidylinositol anchor chain under mechanical stress
PublicationCarbohydrates have quite complicated micro heterogenic structure which may undergo different structural transitions. Due to their extreme flexibility it is very difficult to investigate such structural changes experimentally. In these studies we want to predict what structural and conformational changes are possible in the carbohydrate
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A perfect hashing incremental scheme for unranked trees using pseudo-minimal automata
PublicationWe describe a technique that maps unranked trees to arbitrary hash codes using a bottom-up deterministic tree automaton (DTA). In contrast to other hashing techniques based on automata, our procedure builds a pseudo-minimal DTA for this purpose. A pseudo-minimal automaton may be larger than the minimal one accepting the same language but, in turn, it contains proper elements (states or transitions that are unique) for every input...
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Vibrational Properties of LaNb0.8M0.2O4-δ (M=As, Sb, V, and Ta)
PublicationLaNb0.8M0.2O4-δ (where M=As, Sb, V, and Ta) oxides with pentavalent elements of different ionic sizes were synthesized by a solid-state reaction method. The vibrational properties of these oxides have been investigated. These studies revealed that the substituent element influences both Debye temperature value as well as the Raman active vibrational modes. Additionally, the low-temperature vibrational properties of LaNb0.8Sb0.2O4-δ...
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Tunable Dielectric Switching of (Quinuclidinium)[MnCl4] Hybrid Compounds
PublicationInorganic−organic hybrid QMnCl (Q = quinuclidinium) crystals were synthesized and characterized. The X-ray and variable-temperature IR/Raman analysis demonstrate that the crystals undergo a reversible structural phase transition, which originates from an order−disorder process and is related to the dynamics of the organic Q cation. Dielectric function measurements disclose a switchability between low (“OFF”) and high (“ON”) dielectric...
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The Influence of Loop Heat Pipe Evaporator Porous Structure Parameters and Charge on Its Effectiveness for Ethanol and Water as Working Fluids
PublicationAbstract: This paper presents the results of experiments carried out on a specially designed experimental rig designed for the study of capillary pressure generated in the Loop Heat Pipe (LHP) evaporator. The commercially available porous structure made of sintered stainless steel constitutes the wick. Three different geometries of the porous wicks were tested, featuring the pore radius of 1, 3 and 7 um. Ethanol and water as two...