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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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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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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp.,recognizes novel asymmetric sequence 5´-ACGGA(N11/9)-3
PublicationA novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have been established: TspGWI recognizes the non-palindromic 5-bp sequence 5′-ACGGA-3′ and cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In addition, an accompanying endonuclease, TspGWII, an isoschizomer of Pst I, was found...
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A new Thermus sp. class-IIS enzyme subfamily: isolation of a ''twin'' endo nuclease TspDTI with a novel specificity 5´-ATGAA(N11/9)-3´, related to TspGWI, Taqll and Tth111II. 5´-ATGAA(N11/9)-3´, spokrewnionej z TspGWI, TaqII i Tth111II.
PublicationOdkryto i scharakteryzowano nową subrodzinę enzymów klasy IIS z Thermus sp.
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Application of Artificial Intelligence by Poland’s Public Administration
PublicationThis chapter presents an overview and analysis of artificial intelligence-driven solutions created and implemented by or with the support of Poland’s central public administration (PA). After discussing governance of AI-related issues, we analyze a set of examples of AI innovation to map the actors and their relations within the ecosystem, describe the field where innovation in AI for PA occurs, and highlight the potentialities...
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Conceptualizing Digital Government for Social Solidarity
PublicationThis paper motivates the study of the impact of digital government on social solidarity; builds a conceptual foundation with four types of solidarity – group-based, compassionate, instrumental and emphatic; relates digital government to the type and moment – pre-technological, technological and post-technological of solidarity; and puts forward the type-moment frame to study how digital government is supporting social solidarity...
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Trust and Distrust in e-Democracy
PublicationIn the digital government research literature, the concept of trust is typically used as a precondition for the adoption of digital technology in the public sector or an outcome of a roadmap leading up to such adoption. The concept plays a central role in many decisions linked to the planning, adoption and management of the public sector technology. In contrast, the concept of...
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Technology and democracy: the who and how in decision-making. The cases of Estonia and Catalonia
PublicationThis paper focuses on the use of technology to improve democracy, comparing the cases of Estonia and Catalonia. Both examples are closely related in their use of technology to further democratize the decision-making processes but have opposite starting points. Estonia’s internet voting system is an offshoot of the comprehensive e-governance system developed by the Estonian government. It is meant to make it more convenient for...
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Trust and Distrust in e-Democracy
PublicationIn the digital government research literature, the concept of trust is typically used as a precondition for the adoption of digital technology in the public sector or an outcome of a roadmap leading up to such adoption. The concept plays a central role in many decisions linked to the planning, adoption and management of the public sector technology. In contrast, the concept of distrust is almost neglected in such literature but,...
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Safeguarding democracy during pandemics. Social distancing, postal, or internet voting—the good, the bad, or the ugly?
PublicationDuring a pandemic, many countries and organizations must decide whether to postpone upcoming elections or to hold them (Krimmer et al., 2020a). If the decision is made to hold the election, three main scenarios come to mind: continue using the existing system but include measures to ensure the health of participants; or look for alternatives among remote voting channels which could ensure social distancing is guaranteed either...
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New methodology for calculating cost-efficiency of different ways of voting: is internet voting cheaper?
PublicationNew ways of voting in elections are being sought by electoral administrations worldwide who want to reverse declining voter turnouts without increasing electoral budgets. This paper presents a novel approach to cost accounting for multi-channel elections based on local elections in Estonia. By doing so, it addresses an important gap in the academic literature in this field. The authors confirm that internet voting was most cost-efficient...
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Feminidad online:¿ ni feminista ni auténtica?
PublicationMucho se ha escrito sobre internet y sus múltiples y diversos impactos sobre la vida de las personas, la economía, la política o cualquier otro ámbito de la sociedad. Evidentemente, lo relacionado con los modos de expresar las relaciones de género en entornos digitales no ha quedado al margen de esta espiral analítica. De hecho, ha generado una abundante literatura que cubre múltiples subtemas, incluyendo aspectos tan diversos...
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Analyzing Preconditions to Introduce Internet Voting in Portugal: Insights from the Estonian Model
PublicationInternet voting has been trialed or introduced for several countries, including Norway, Portugal, United States, United Kingdom and Switzerland as an additional voting channel to increase voter turnout and, also to modernize the electoral process. However, only Estonia has successful introduced internet voting, deploying e-enabled elections in general governmental levels. This paper aims to provide an exploratory study on the Estonian...
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E-Voting System Evaluation Based on the Council of Europe Recommendations: nVotes
PublicationE-voting implantation has been facing important challenges in recent years. Several incidents, together with a lack of evaluation methodologies social and cultural customs hinder a broader application. In this work, the authors aim to contribute to a safer introduction of e-voting tools by applying a practical evaluation framework strongly based on the security requirements issued by the Council of Europe (CoE) in 2017 to nvotes,...
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Tailoring the electrochemical degradation of iron protected with polypyrrole films for biodegradable cardiovascular stents
PublicationThe degradation of polypyrrole (PPy) coated iron is studied in phosphate buffer saline solution at 37 °C by odd random phase multisine electrochemical impedance spectroscopy (ORP-EIS). PPy is electropolymerized with anti-inflammatory salicylates incorporated in the film, as a drug release system. The modelling of EIS over time provides the quantitative description of the corrosion behaviour of the material. Thus, the reliable...
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Evaluating the mobile robot positions using accelerometer data
PublicationThis paper analyzes the problem of determining the position of a robot using an accelerometer, which is an essential part of inertial measurement units (IMU). The information gained from such a gauge, however, requires double integration of sensor data. To assure an expected effect, a mathematical model of a low-cost accelerometer of the MEMS type is derived. Moreover, in order to improve the performance of positioning based on...
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Developing Novel Solutions to Realise the European Energy - Information Sharing & Analysis Centre
PublicationFor more effective decision making in preparation for and response to cyberevents in the energy sector, multilevel situation awareness, from technical to strategic is essential. With an uncertain picture of evolving threats, sharing of the latest cybersecurity knowledge among all sector stakeholders can inform and improve decisions and responses. This paper describes two novel solutions proposed during the formation of the European...
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ZASTOSOWANIE APLIKACJI INTERNETOWEJ W OCENIE JAKOŚCI DOPASOWANIA APARATÓW SŁUCHOWYCH
PublicationW pracy opisano zastosowanie aplikacji internetowej do oceny jakości dopasowania aparatów słuchowych. Metoda oceny polega na badaniu ankietowym, uzupełnionym testem rozumienia słów jednosylabowych w polu swobodnym. Opisywana aplikacja internetowa pozwala na przeprowadzenie badania z dowolnego komputera z dostępem do sieci. Dzięki implementacji metody w postaci aplikacji internetowej, można w systematyczny i uporządkowany sposób...
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublicationFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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Chemical, Aroma and Pro-Health Characteristics of Kaffir Lime Juice—The Approach Using Optimized HS-SPME-GC-TOFMS, MP-OES, 3D-FL and Physiochemical Analysis
PublicationThe study aimed to provide the chemical, aroma and prohealth characteristics of the kaffir lime juice. A procedure using solid-phase microextraction with gas chromatography (SPME-GC-TOFMS) was optimized and validated for the determination of terpenes of kaffir lime. Main physicochemical parameters: pH, vitamin C, citric acid and °Brix were evaluated. Micro- and macro elements were determined using microwave plasma optic emission...
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Applications of Alkanethiols in Organic Synthesis
PublicationThis manuscript is an update to the earlier Science of Synthesis contribution describing methods for the synthesis of alkanethiols. Thiols can be converted into sulfonic, sulfinic, sulfenic acid and their derivatives, sulfides, disulfides, polysulfides, sulfonium salts, and thiiranes, etc. These transformations are accomplished by nucleophilic displacement or addition, oxidation, condensation, or coupling reactions involving thiol...
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Interactions of fish gelatin and chitosan in uncrosslinked and crosslinked with EDC films: FT-IR study
PublicationFilms based on fish gelatin, chitosan and blend of fish gelatin and chitosan before and after cross-linking with EDC have been characterized by FT-IR spectroscopy. The FT-IR spectrum of fish gelatin film showed the characteristic amide I, amide II and amide III bands, and the FT-IR spectrum of chitosan film confirmed that the polymer was only a partially deacetylated product, and included CH3-C=O and NH2 groups, the latter both...
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Experimental and Machine-Learning-Assisted Design of Pharmaceutically Acceptable Deep Eutectic Solvents for the Solubility Improvement of Non-Selective COX Inhibitors Ibuprofen and Ketoprofen
PublicationDeep eutectic solvents (DESs) are commonly used in pharmaceutical applications as excellent solubilizers of active substances. This study investigated the tuning of ibuprofen and ketoprofen solubility utilizing DESs containing choline chloride or betaine as hydrogen bond acceptors and various polyols (ethylene glycol, diethylene glycol, triethylene glycol, glycerol, 1,2-propanediol, 1,3-butanediol) as hydrogen bond donors. Experimental...
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Experimental and Machine-Learning-Assisted Design of Pharmaceutically Acceptable Deep Eutectic Solvents for the Solubility Improvement of Non-Selective COX Inhibitors Ibuprofen and Ketoprofen
PublicationDeep eutectic solvents (DESs) are commonly used in pharmaceutical applications as excellent solubilizers of active substances. This study investigated the tuning of ibuprofen and ketoprofen solubility utilizing DESs containing choline chloride or betaine as hydrogen bond acceptors and various polyols (ethylene glycol, diethylene glycol, triethylene glycol, glycerol, 1,2-propanediol, 1,3-butanediol) as hydrogen bond donors. Experimental...
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Influence of Two-Stage Anodization on Properties of the Oxide Coatings on the Ti–13Nb–13Zr Alloy
PublicationThe increasing demand for titanium and its alloys used for implants results in need of such innovative surface treatment that may jointly increase corrosion resistance and biocompatibility, and demonstrate antibacterial protection at no cytotoxicity. The purpose of this research was to characterize the effect of two-stage anodization, performed for 30 min in phosphoric acid, at the presence of hydrofluoric acid in the second stage....
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NASBA – IZOTERMICZNA AMPLIFIKACJA RNA
PublicationNASBA (ang. Nucleic Acid Sequence-Based Amplification) jest skuteczną i czułą techniką izotermicznej amplifikacji opartej na transkrypcji, służąca głównie do detekcji cząsteczek RNA. Znalazła ona zastosowanie do wykrywania RNA wirusowego, bakteryjnego i grzybiczego w próbkach klinicznych oraz żywości.
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Zastosowanie niedrogich modułów bezprzewodowych do sterowania oświetleniem
PublicationW artykule zaprezentowano niedrogi system zdalnego sterowania oświetleniem w budynku. Dokonano krótkiego przeglądu dostępnych na rynku, gotowych rozwiązań. Zaproponowano własną strukturę sterowania wykorzystując tanie moduły bezprzewodowe. Przedstawiono projekt najistotniejszych elementów systemu. Omówiono sposób oprogramowania modułów oraz nadrzędną aplikację sterującą. Artykuł zawiera ocenę systemu, z uwzględnieniem możliwości...
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Comparison of thresholding algorithms for automatic overhead line detection procedure
PublicationThe article presents an overview of the thresholding algorithms. It compares the algorithms proposed by Pun, Kittler, Niblack, Huang, Rosenfeld, Remesh, Lloyd, Riddler, Otsu, Yanni, Kapur and Jawahar. Additionally, it was tested how the tuning of the Pun, Jawahar and Niblack methods affects the thresholding efficiency and proposed a combination of the Pun algorithm with a priori algorithm. All presented algorithms have been implemented...
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Cztero-gałęziowy estymator dyskretnej pulsacji chwilowej sygnałów zespolonych
PublicationW pracy zaproponowano nowy pomysł na estymator dyskretnej pulsacji chwilowej sygnału zespolonego wyposażony w skuteczny rozwijacz fazy wspomagany 4-filtrowym estymatorem bieżącego widma mocy. To tanie numerycznie, pracujące potokowo, rozwiązanie pozwala zdecydowanie poprawić dokładność uzyskiwanej estymaty pulsacji chwilowej. Skuteczność działania zaproponowanego rozwiązania przedstawiono na przykładzie specjalnie skonstruowanego...
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Results of nanoindentation, XRD and microscopic studies of bacterial cellulose
Open Research DataThe archive contains the results of research on BNC bacterial biocellulose, which was modified in two ways. When BNC was synthesized, it was subjected to in situ modification involving the addition of hyuloronic acid to the bacterial medium. The second way of ex situ modification consisted of soaking the BNC in water and then convectionally drying it...
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Influence of the internal electrolyte composition on amperometric sulphur dioxide sensor properties
PublicationIn this work amperometric sulphur dioxide sensor with a liquid electrolyte, a mercury sulphate reference electrode and solid polymer electrolyte (Nafion) covered with gold as a working electrode will be presented. The main goal of this research is to determine the influence of internal electrolyte composition on the sensor properties. Sensor filled with 1M and 5M sulphuric acid has been investigated.
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Investigation of solid polymer electrolyte gas sensor with different electrochemical techniques
PublicationIn this work solid polymer electrolyte (SPE) amperometric sulphur dioxide sensor is investigated. Nafion was used as a membrane electrode and 1M sulphuric acid as an internal electrolyte. Sensor response to sulphur dioxide was measured. Besides traditional constant voltage amperometry also different electrochemical techniques were used. Results obtained by these methods are compared.
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Determination of phenylbutazone, sulfamethazine, carbendazim and linuron using a novel pine bark biosorbent for solid-phase extraction (SPE) with high-performance liquid chromatography (HPLC)
PublicationThe paper presents a novel pine bark based biosorbent for solid-phase extraction (SPE). The morphology and composition of the pine bark were characterized using Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The biosorbent was used for the preparation of wastewater for the determination of phenylbutazone, sulfamethazine, carbendazim, and linuron by high performance liquid chromatography with...
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Elemental and tight monogamy relations in nonsignaling theories
PublicationPhysical principles constrain the way nonlocal correlations can be distributed among distant parties. These constraints are usually expressed by monogamy relations that bound the amount of Bell inequality violation observed among a set of parties by the violation observed by a different set of parties. We prove here that much stronger monogamy relations are possible for nonsignaling correlations by showing how nonlocal correlations...
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Application of Potentiometric Taste Sensor with All Solid State Electrodes for Distinguishing of Red Dry Wines from Polish and French Vineyards
PublicationOpracowano nowy potencjometryczny czujnik smaku z sześcioma różnymi elektrodami typu All Solid State Electrode (ASSE). Każda z elektrod zawiera dwie warstwy: polimer przewodzący i membranę lipidowo-polimerową, w której rozpuszczone są poszczególne związki lipidowe. Potencjometryczny sensor smaku charakteryzuje się globalną selektywnością. Zastosowano go w celu odróżnienia próbek wytrawnych czerwonych win pochodzących z różnych...
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Czujniki tlenu pracujące bez układu odniesienia
PublicationW celu wyznaczenia stężenia lub ciśnienia parcjalnego tlenu w danym środowisku zastosować można potencjometryczne, amperometryczne lub rezystancyjne czujniki tlenu. W niniejszej pracy scharakteryzowane zostaną wszystkie trzy typy urządzeń. Szczególnie interesujące są czujniki amperometryczne i rezystancyjne, gdyż nie wymagają stosowania układu odniesienia i dzięki temu są to rozwiązania stosunkowo proste, tanie i trwałe.
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Influence of the internal electrolyte composition on amperometric sulphur dioxide sensor properties
PublicationIn this work investigation of an amperometric sulphur dioxide sensor with a liquid electrolyte, a mercury sulphate reference electrode and solid polymer electrolyte (Nafion) covered with gold as a working electrode properties is presented. The main goal of this research is to determine the influence of internal electrolyte composition on the sensor properties. Sensor filled with 1M and 5M sulphuric acid has been studied.
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Design of new cholinesterase inhibitors based on phosphorus analogs of tacrine as potential anti-Alzheimer’s disease agents
PublicationBased on the analysis of the determined free binding energy (using the AutoDock Vina 1.1.2 docking program), the most potent cholinesterase inhibitors were selected. Moreover, studies of 3D visualization of the results of molecular modeling led to the identification of potential sites for the interaction of new potential inhibitors with amino acid residues building active sites of investigated cholinesterases.
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The reactions of dialkyl phosphites and phosphine oxides with iodosylbenzene
PublicationThe reaction of iodosylbenzene with >P(O)H type of acids (dialkyl phosphites, secondary phosphine oxides) was studied. The acids of >P(O)H type add to iodosylbenzene to yield intermediate 6 which in the aprotic solvents yields oxidation products, it means >P(O)OH acids and/or anhydride of >P(O)OP(O)< type. On the other hand if the reaction is performed in alcohol as a solvent in the presence of sodium alcoholate >P(O)OR ester is...
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Hydrogen-bonded one-dimensional networks in 1:1 complexes of N,N`-bis(2-pi-rydyl)aryldiamines with anilic acid. Acta Cryst. Sect. C Crystal Struct.Commun.**2002 vol. 58 s. o735-o738, 4 rys. 4 tab. bibliogr. 15 poz. Jednowymiarowe sieci krystaliczne tworzone w wyniku oddziaływań wodorowych pomiędzy N,N`-bis(2-pirydylo)aryloaminami a kwasem anilowym.
PublicationOtrzymano związki kompleksowe kwasu anilowego z N,N`-bis(2-pirydylo)-1,4-diaminobenzenem oraz N,N`-bis(2-pirydylo)-4,4`-diaminobifenylem o stechiometrii1:1, a następnie przeprowadzono analizę rentgenograficzną monokryształów. Wobu przypadkach cząsteczki, wchodzące w skład kompleksu są powiązane ze sobąkonwencjonalnymi oddziaływaniami wodorowymi. Tym samym tworzy się jednowy-miarowa sieć krystaliczna z dziewięcioczłonowym pierścieniowym...
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The influence of humic substances in treated sewage on the quality of surface waters
PublicationAt present the evaluation of WWTP effectiveness is based upon organic matter and nutrients removal. Recently it was found out that sewage treatment leads to formation of resistant to biochemical degradation organic compounds, similar to humic acids. The humic acids formed during sewage treatment process play diversified functions when discharged to surface waters - for instance they can act as carriers of hydrophobic organic pollutants...
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Treated wasetewater as a source of humic substances in surface waters
PublicationHumic substances impose substantial effect on the aquatic environment as well as the water organisms and human health. Among other features, the humic acids determine organoleptic properties of surface waters. Therefore explanation of the origin and properties of humic acids in surface waters is one of the priorities of water technology.Recently it was pointed out that in the wastewater treatment process organic compounds characterized...
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Impact of Cultivation Conditions, Ethylene Treatment, and Postharvest Storage on Selected Quality and Bioactivity Parameters of Kiwifruit “Hayward” Evaluated by Analytical and Chemometric Methods
PublicationOrganic, semiorganic, and conventional “Hayward” kiwifruits, treated with ethylene for 24 h and stored during 10 days, were assessed by UV spectrometry, fluorometry, and chemometrical analysis for changes in selected characteristics of quality (firmness, dry matter and soluble solid contents, pH, and acidity) and bioactivity (concentration of polyphenols via Folin-Ciocalteu and p-hydroxybenzoic acid assays). All of the monitored...
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Comprehensive study on graphene hydrogels and aerogels synthesis and their ability of gold nanoparticles adsorption
PublicationGraphene hydrogels were prepared by ascorbic acid-assisted gelation of graphene oxide (GO) aqueous suspensions both in acidic and basic conditions. Different mass ratio of ascorbic acid (AA) to GO was used (namely 20:1 and 10:1). In order to eliminate the influence of AA on the final structure of hydrogels, samples without AA were prepared by a hydrothermal gelation of GO in an autoclave. An in-depth structural characterization...
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Hydrazinolysis Products of Selected Sugar Lactones—Crystal Structure and Microbiological Activity
PublicationCommercially available lactones, as well as those synthesized by us, turned out to be good substrates for the synthesis of sugar hydrazides. The exception was L-ascorbic acid, whose hydrazinolysis led to the formation of a hydrazinium salt, not the hydrazide as expected. The structure of all compounds was confirmed by NMR and X-ray analyses. The lower durability of hydrazinium L-ascorbate was additionally confirmed by thermogravimetric...
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Bile conjugation and its effect on in vitro lipolysis of emulsions
PublicationBile Salts (BS) are responsible for stimulating lipid digestion in our organism. Gut microbiota are responsible for the deconjugation process of primary conjugated to secondary unconjugated BS. We use two structurally distinct BS and characterize the rate of lipolysis as a compound parameter. A static in-vitro digestion model as well as meta-analysis of literature data has been performed to determine the most influential factors...
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Comparison of the Efficiency of Hetero- and Homogeneous Catalysts in Cellulose Liquefaction
PublicationBiomass liquefaction is a well-known and extensively described process. Hydrothermal processes are well understood and can be used in the fuel industry. The use of organic solvents can result in full-fledged products for use in the synthesis of polyurethanes. The plastics industry, including polyurethanes, is targeting new, more environmentally friendly solutions. One of these is the replacement of petrochemical polyols with compounds...