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HPLC-coupled post-column derivatization aims at characterization and monitoring of plant phytocomplexes, not at assessing their biological properties
PublicationTwo recent decades of research identified a number of environmental factors as well as mechanisms leading to pathogenic processes in the human organism. A common factor in pathogenesis of many diseases is oxidative stress, a condition in which the production of damaging reactive oxygen species (ROS), present in the body as an inevitable consequence of respiration and exacerbated by the inflammatory response and by exogenous factors...
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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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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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KernelHive: a new workflow-based framework for multilevel high performance computing using clusters and workstations with CPUs and GPUs
PublicationThe paper presents a new open-source framework called KernelHive for multilevel parallelization of computations among various clusters, cluster nodes, and finally, among both CPUs and GPUs for a particular application. An application is modeled as an acyclic directed graph with a possibility to run nodes in parallel and automatic expansion of nodes (called node unrolling) depending on the number of computation units available....
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Elemental characteristics of mushroom species cultivated in China and Poland
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
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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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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Magnetic hydrophobic deep eutectic solvents for orbital shaker-assisted dispersive liquid-liquid microextraction (MAGDES-OS-DLLME) - determination of nickel and copper in food and water samples by FAAS
PublicationIn this work, a cheap and widely applicable dispersive liquid-liquid microextraction (DLLME) method was developed for the extraction of Ni(II) and Cu(II) from water and food samples and analysis using flame atomic absorption spectrometry. DLLME was assisted by orbital shaker, while ferrofluid as an extractant was based on deep eutectic solvent (DES). This ferrofluid was made of hydrophobic DES (hDES), composed of lauric acid and...
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Quality control of cheese samples for the presence of natamycin preservative – A natural deep eutectic solvent (NADES) based extraction coupled with HPLC
PublicationA new protocol for the determination of natamycin – an antifungal agent used as a food preservative - in cheese samples – is described. This new method is based on a natural deep eutectic solvent (NADES) green extraction procedure. High-performance liquid chromatography (HPLC) was used for detection and quantification. NADESs with different molar ratios were evaluated for efficient and selective extraction. NADES made of thymol...
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Optimization of vortex-assisted supramolecular solvent-based liquid liquid microextraction for the determination of mercury in real water and food samples
PublicationA novel method was developed for sample preparation for spectrophotometric determination of Hg(II) in water and food samples. The method was based on vortex-assisted supramolecular solvent-assisted liquid-liquid microextraction (VA-SUPRASs-LLME). Analytical parameters such as pH, chelating agent, solvent type and volume, vortex time and salting out effect were optimized. Surface and normal probability plots were drawn for the variables...
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Combination of homogeneous liquid–liquid extraction and vortex assisted dispersive liquid–liquid microextraction for the extraction and analysis of ochratoxin A in dried fruit samples: Central composite design optimization
PublicationThis paper presents a new analytical procedure based on combination of homogeneous liquid–liquid extraction (HLLE) and vortex-assisted dispersive liquid–liquid microextraction (VA-DLLME) for the accurate and reliable determination of ochratoxin A (OTA) in dried fruit samples. To enable selective extraction of the OTA, six hydrophobic deep eutectic solvents (hDESs) were prepared and tested as extraction solvents. Optimization of...
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Application of chemometric modeling for ionic liquid-based ultrasonic-assisted dispersive liquid-liquid microextraction: Analysis of fosetyl-aluminum in fruit and vegetable samples
PublicationThis manuscript presents a new method for selective extraction and determination of fosetyl-aluminum in fruits and vegetable samples based on ultrasonic-assisted dispersive liquid-liquid microextraction method using ionic liquids (IL-UA-DLLME). A UV-Visible spectrophotometer was used for detection and quantification. Plants used for sample collection were grown under controlled conditions in a greenhouse. Central composite design...
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A multithreaded CUDA and OpenMP based power‐aware programming framework for multi‐node GPU systems
PublicationIn the paper, we have proposed a framework that allows programming a parallel application for a multi-node system, with one or more GPUs per node, using an OpenMP+extended CUDA API. OpenMP is used for launching threads responsible for management of particular GPUs and extended CUDA calls allow to manage CUDA objects, data and launch kernels. The framework hides inter-node MPI communication from the programmer who can benefit from...
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Comparison of the contents of bioactive compounds and the level of antioxidant activity in different kiwifruit cultivars
PublicationGłównym celem prowadzonych badań było stwierdzenie która z odmian owoców kiwi (''Hayward'', ''Daeheuhg'', ''Haenam'' oraz ''Bidan'') jest najbardziej odpowiednią z punktu widzenia konsumpcji przez człowieka. Z tego powodu w odpowiednio przygotowanych próbkach ekstraktów z owoców kiwi oznaczono:- profile związków bioaktywnych;- poziomy aktywności przeciwutleniającej. Wyniki pomiarów zawartości polifenoli (flawonoidy oraz kwasy fenolowe)...
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Application of a commercially available derivatization instrument and commonly used reagents to HPLC on-line determination of antioxidants
PublicationThis study demonstrates the potential of a commercially available derivatization instrument coupled with HPLC for separation and on-line determination of antioxidants detected with widely used screening reagents - DPPH (2,2-diphenyl-1-picrylhydrazyl), ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) or FCR (Folin-Ciocalteu's phenol reagent ). As the result of optimization, key parameters of the analytical procedure,...
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Thermal and spectroscopic profiles variation of cold-pressed raspberry seed oil studied by DSC, UV/VIS, and FTIR techniques
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High quality speech coding using combined parametric and perceptual modules. [Kodowanie sygnału mowy z zachowaniem wysokiej jakości przy wykorzystaniu modułu parametrycznego i perceptualnego]
PublicationW komunikacie zaprezentowano nową metodę hybrydowego kodowania sygnału mowy. Techniki kodowania parametrycznego oraz perceptualnego zostały wykorzystane w celu zapewnienia wysokiej jakości kodowania sygnału mowy. Przedstawiono wyniki badań dla dwóch architektur kodeka. Jedna z nich bazuje na algorytmie pozwalajacym wyodrębnić składowe dźwięczne, bezdźwięczne oraz transjenty. Składowe dźwięczne kodowane są metodą perceptualną, bezdźwięczne...
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Workflow applications in GridLab and PROGRESS projects
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Flexibility and user‐friendliness of Grid portals: the PROGRESS approach
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Plugging grids into computing portals: the PROGRESS grid resource broker plug‐in mechanism
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Determination of biogenic amines in processed and unprocessed mushrooms from the Polish market
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Particle swarm optimization–artificial neural network modeling and optimization of leachable zinc from flour samples by miniaturized homogenous liquid–liquid microextraction
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An Assessment of RASSCF and TDDFT Energies and Gradients on an Organic Donor−Acceptor Dye Assisted by Resonance Raman Spectroscopy
PublicationThe excitation energies and gradients in the ground and the first excited state of a novel donor−(π- bridge)−acceptor 4-methoxy-1,3-thiazole-based chromophore were investigated by means of MS-RASPT2/RASSCF and TDDFT in solution. Within both methods, the excitation energies strongly depend on the employed equilibrium structures, whose differences can be rationalized in terms of bond length alternation indexes. It is shown that functionals with...
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Extraction and Analysis of Bisphenols and Their Derivatives in Infant and Toddler Ready-to-feed Meals by Ultrasound-assisted Membrane Extraction Followed by LC MS/MS
PublicationThis research developed an ultrasound-assisted membrane extraction coupled with liquid chromatography-tandem mass spectrometry method for the determination of nineteen bisphenols and their derivatives in infant and toddler ready-to-feed meals. The calibration curves for all analytes were linear in the tested range, and the limit of detection and limit of quantitation were in the range 0.27 to 0.79 ng/g and 0.80 to 2.4 ng/g, respectively....
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A comprehensive lipidomic analysis of oilseeds using LC-Q-TOF-MS and dispersive micro-solid phase (D-μ-SPE) extraction techniques
PublicationGrowing public health awareness increased the demand for natural products with positive health benefits. Vegetable oils containing omega-3 fatty acids (FA) such as alpha-linolenic acid (ALA) has been proposed as a possible source of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). In this work, a comprehensive lipidome analysis and comparison of seven oilseeds, including flaxseed, chia, hemp, black cumin, white sesame,...
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Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule
PublicationThe ground state geometries and vibrational frequencies as well as the excitation energies and excited state gradients of the S 1(nπ*) and S 2(ππ * ) states of trans - and cis -azobenzene are investigated by several DFT methods, namely B3LYP, PBE, M06-2X, CAM-B3LYP, and ω B97X. Excited state properties and in particular gradients are also assessed using the wave function based methods EOM-CCSD and RASPT2/RASSCF. Comparison with...
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Ionogel sorbent coatings for determining organophosphorus and pyrethroid insecticides in water and fresh juice samples by headspace-solid phase microextraction
PublicationThe sol–gel method yielded three different ionogel sorbent coatings that were obtained based on a silica material containing ionic liquids (ILs) immobilized in its pores. Two ILs, triethylsulfonium bis(trifluoromethylsulfonyl) imide [Set3][TFSI] and 1-butyl-1-methylpiperidinium bis(trifluoromethylsulfonyl)imide [C4C1Pip][TFSI], as well as their equimolar mixture [Set3/C4C1Pip], were used to obtain ionogel fibers. The developed...
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Mercury content in beetroot and beetroot-based dietary supplements
PublicationTotal mercury (THg) concentrations in fifty-four beetroot-based DSs and seven lots of conventional and organic beetroots (divided into unpeeled, peeled, and skins) were determined by direct thermal decomposition-gold amalgamation cold vapour atomic absorption spectrometry. The analytical procedure was optimised and validated. The recovery (%) for Hg was 101.9 and 92.73 in BCR-463 and DOLT 4, respectively. The intermediate precision...
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Analysis of bisphenols and their derivatives in infant and toddler ready-to-feed milk and powdered milk by LC MS/MS
PublicationReady-to-feed milk and powdered milk packed in different types of packaging lined with resin are chosen as the primary or complementary diet for infants and toddlers. An HPLC–MS/MS method was established and validated for the determination of nineteen bisphenols and their derivatives in such samples. The recoveries were from 31% to 120%, while the values of limit of detection and quantification were in the range of 0.24–0.40 and...
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Solvent dependency of carbon dioxide Henry's constant in aqueous solutions of choline chloride-ethylene glycol based deep eutectic solvent
PublicationThe Henry's constants of carbon dioxide absorbed in aqueous solutions of ethaline (choline chloride-ethylene glycol) were determined for temperatures ranging from 303.15 to 323.15 K based on solubility measurement at CO2 pressure ranging from 0 to 6 bar (0.6 MPa). These studies revealed that the Henry's constant increased with the increase of temperature. Data indicated the highest capacity of CO2 absorption is obtained for ethaline...
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Uniform expansion estimates in the quadratic map as a function of the parameter, with a large range of parameters
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Uniform expansion estimates in the quadratic map as a function of the parameter, with a very small critical neighborhood
Open Research DataThis dataset contains selected results of numerical computations described in the paper "Quantitative hyperbolicity estimates in one-dimensional dynamics" by S. Day, H. Kokubu, S. Luzzatto, K. Mischaikow, H. Oka, P. Pilarczyk, published in Nonlinearity, Vol. 21, No. 9 (2008), 1967-1987, doi: 10.1088/0951-7715/21/9/002.
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Wykorzystanie wiązań niekowalencyjnych do otrzymywania jedno- i dwuskładnikowych struktur supramolekularnych
PublicationPrzedstawiona rozprawa doktorska dotyczy badań nad wykorzystaniem oddziaływań międzycząsteczkowych do projektowania i syntezy uporządkowanych struktur krystalicznych, ze szczególnym uwzględnieniem wiązań halogenowych i chalkogenowych jako stosunkowo nowych i bardzo atrakcyjnych z punktu widzenia inżynierii kryształu. Praca podzielona jest na kilka części. Pierwsza z nich stanowi wstęp teoretyczny obejmujący opis, założenia oraz...
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The consideration to the dynamic systems parameter identification
PublicationIn this paper, a concept for continuous-time dynamic systems parameter identification using modulating function approach is presented. It refers to linear as well as selected non-linear systems. It shows the possibility of direct application without converting differential equation. In particular cases direct application can decrease the amount of computation in non-linear system identification, which generally requires Fourier...
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Mineral and Organic Matter Constituents in Weak Interfaces in Shales
PublicationThis paper identifies formation interfaces that would appear to be "weak interfaces", in the Jurassic, Early- Cretaceous Vaca Muerta formation, in the Neuquén Basin, Argentina. Significant distribution of the weak interfaces was observed including contacts between volcanic ash layers of varying thicknesses, calcite-filled veins, and contacts between lithology changes, such as between argillaceous mudstone and mottled carbonates....
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Efficient signal processing in spectroscopic optical coherence tomography
PublicationSpectroscopic optical coherence tomography (SOCT) is an extension of a standard OCT technique, which allows to obtain depth-resolved, spectroscopic information on the examined sample. It can be used as a source of additional contrast in OCT images e.g. by encoding certain features of the light spectrum into the hue of the image pixels. However, SOCT require computation of time-frequency distributions of each OCT A-scan, what is...
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Microemulsion Delivery Systems with Low Surfactant Concentrations: Optimization of Structure and Properties by Glycol Cosurfactants
PublicationExtensive use of microemulsions as delivery systems raises interest in the safe ingredients that can form such systems. Here, we assessed the use of two glycols, i.e., propylene glycol and pentylene glycol, and their mixtures to manipulate the properties and structure of microemulsions. Obtained systems with glycols were extensively characterized in terms of capacity to incorporate water phase, droplet size, polydispersity, structure...
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CONCRETE MIX DESIGN USING ABRAMS AND BOLOMEY METHODS
PublicationOne way to reduce the consumption of cement is to optimize its use. Many known methods of concrete design, based on the Abrams law and the Bolomey method. Therefore, the authors chose those methods for analysis. The concrete composition with the assumed strength class, calculated by any method differs significantly. This applies especially to the cement content, as its content in the composition of concrete varies from 20 to 50%....
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Investigation of buckling resistance of columns using non-linear static and dynamic analysis
PublicationThe aim of this paper is to investigate the stability process in an axially compressed column using a static and dynamic finite element analysis by taking both the geometric and material non-linearity into account. The perfect column and column with geometric imperfections were analysed. The linear buckling analyses were used to obtain the lowest buckling load and shapes of buckled forms that were taken into account as initial...
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Human Centric Lighting. The New X Factor?
PublicationWe live in challenging times, and one could even claim we’re experiencing a revolution in lighting with LED technology taking over the world. Part of this rapid change involves a concept called Human Centric Lighting (HCL). In Frankfurt this year, during Light+Building, it was the buzzword, with nearly every second manufacturer’s stand claiming they had figured out the special formula necessary to create perfect HCL illumination....
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Continuum models for pantographic blocks with second gradient energies which are incomplete
PublicationWe postulate a deformation energy for describing the mechanical behavior of so called pantographic blocks, that is bodies constituted by stacking of layers of pantographic sheets. We remark that the pantographic effect is limited in the plane of pantographic sheets and therefore only the second derivatives of transverse displacements along the pantographic fibers appear in the chosen deformation energy. We use this novel energy...