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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublikacjaMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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Synthesis and biological evaluation of novel analogues of batracylin with synthetic amino acids and adenosine: an unexpected effect on centromere segregation in tumor cells through a dual inhibition of topoisomerase IIa and Aurora B
PublikacjaIn the search for new anticancer agents we designed and synthesized batracylin derivatives with linking synthetic amino acid side chains of different lengths and adenosine. Unexpectedly, we have found that in water and the culture media adenosine–amino acid–BAT conjugates form supramolecular structures and this prevents these compounds from entering cells. Consequently, these compounds exerted no biological activity when tested...
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Folding‐upon‐repair DNA nanoswitches for monitoring DNA repair enzymes activity
PublikacjaWe demonstrate here a new class of DNA‐based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding‐upon‐repair DNA nanoswitches are synthetic DNA sequences containing O6‐methyl‐guanine (O6‐MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation...
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Improving Clairvoyant: reduction algorithm resilient to imbalanced process arrival patterns
PublikacjaThe Clairvoyant algorithm proposed in “A novel MPI reduction algorithm resilient to imbalances in process arrival times” was analyzed, commented and improved. The comments concern handling certain edge cases in the original pseudocode and description, i.e., adding another state of a process, improved cache friendliness more precise complexity estimations and some other issues improving the robustness of the algorithm implementation....
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Comparison of bacterial production in the water column between two Arctic fjords, Hornsund and Kongsfjorden (West Spitsbergen)
PublikacjaBacterial production and the accompanying environmental factors were measured in the water columns of two Arctic fjords during the cruise in July and August 2013. Water samples were collected at six stations located in the central part of Hornsund and Kongsfjorden. In Hornsund, where average water temperatures were 1.25-fold lower than in Kongsfjorden, the bacterial production was twice as high (0.116 ± 0.102 vs 0.05 ± 0.03 mg...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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Experimental and theoretical solubility advantage screening of bi-component solid curcumin formulations
PublikacjaA comprehensive experimental and theoretical screening was performed for identification of curcumin solubilizers. Experimental data led to formulation of a non-linear QSPR model correlating molecular descriptors with measured solubilities. The majority of synthesized binary systems exhibited a moderate enhancement of curcumin solubility, which was found to be the highest in the case of curcumin cocrystallized with pyrogallol. New...
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Improvement of derivatized amino acid detection sensitivity in micellar electrokinetic capillary chromatography by means of acid-induced pH-mediated stacking technique
PublikacjaDerivatization is a frequently used sample prepara-tion procedure applicable to the enhancement of analyte de-tection sensitivity. Amino acids mostly require derivatization prior to electrophoretic or chromatographic analysis, especial-ly if spectrophotometric detection is used. This study presents an on-line preconcentration technique for derivatized amino acids. The sensitivity of the method was improved by the utilization of...
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TIME-AND-SPACE STRUCTURE OF FORCE-DRIVEN RIGID SPHEREWAVEFIELD
PublikacjaThis paper introduces a time-domain, causality-inspired description of a vector-source acoustic wavefield of arbitrary time evolution, where a sphere is a practical realisation of quasi-point contact surface without which a point force would not be able to exert an impact onto non-viscous fluid. At every space location, the resulting acoustic field is described by a pair of physical variables characterising the time evolution of...
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The psychrotrophic yeast Sporobolomyces roseus LOCK 1119 as a source of a highly active aspartic protease for the in vitro production of antioxidant peptides
PublikacjaA psychrotrophic yeast strain producing a cold-adapted protease at low temperature was classified as Sporobolomyces roseus. In standard YPG medium, S. roseus LOCK 1119 synthesized an extracellular protease with an activity of approximately 560 U/L. Optimization of medium composition and process temperature considerably enhanced enzyme biosynthesis; an approximate 70% increase in activity (2060 U/L). The native enzyme was purified...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublikacjaWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Accuracy, Memory and Speed Strategies in GPU-based Finite-Element Matrix-Generation
PublikacjaThis paper presents strategies on how to optimize GPU-based finite-element matrix-generation that occurs in the finite-element method (FEM) using higher order curvilinear elements. The goal of the optimization is to increase the speed of evaluation and assembly of large finite-element matrices on a single GPU (Graphics Processing Unit) while maintaining the accuracy of numerical integration at the desired level. For this reason,...
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Prediction of the Biogenic Amines Index of Poultry Meat Using an Electronic Nose
PublikacjaThe biogenic amines index of fresh chicken meat samples during refrigerated storage was predicted based on the headspace analysis using an electronic nose equipped with an array of electrochemical sensors. The reference biogenic amines index values were obtained using dispersive liquid–liquid microextraction–gas chromatography–mass spectrometry. A prototype electronic nose with modular construction and a dedicated sample chamber...
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Insights into Compatibilization of Poly(ε-caprolactone)-based Biocomposites with Diisocyanates as Modifiers of Cellulose Fillers
PublikacjaThis study aimed to analyze the impact of cellulose fillers’ modification with diisocyanates on the performance of composites based on the poly(ε-caprolactone) (PCL) matrix. Four most commonly used diisocyantes (isophorone, hexamethylene, toluene, and methylene diphenyl) were applied as modifiers of cellulose fillers (5 and 15 wt% per mass of filler). Modified fillers were introduced in the amount of 30 wt% into the PCL matrix....
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Fish gelatin films containing aqueous extracts from phenolic-rich fruit pomace
PublikacjaThe aim of the work was to study the feasibility of using aqueous extracts from rowanberry, blue-berried honeysuckle, and chokeberry pomace for the formulation of fish gelatin films with antioxidant and antimicrobial activity as well as improved mechanical and water barrier properties. The predominant phenolic components in rowanberry and chokeberry extracts were hydroxycinnamates, and in blue-berried honeysuckle extract antho cyanins. Although...
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Caffeine Inhibits Differentiation Of Lung Cancer Stem Cells By Modulating Their Respiratory Metabolism
PublikacjaIt is ell established that many tumor types contain a fraction of cells, with stem cell-like properties, called cancer stem cells (CSCs), that are resistant to apoptosis induced by therapeutic agents. The presence of CSCs may explain why a standard anticancer treatment, that eliminates only differentiated cancer cells, does not lead to cancer cure.We previously showed the existence of caffeine-sensitive mechanism that controls...
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Investigating COVID-19 active pharmaceutical ingredients (APIs) degradation using Peroxydisulfate/FeMnOx binary metal oxide/Ultrasound System
PublikacjaDegradation of Favipiravir using a hybrid system of peroxydisulfate, FeMnOx binary metal oxide, and ultrasound irradiation was studied. A novel catalyst was synthesized with deep eutectic solvent (DES). The effects of DES type on catalytic performance was evaluated and the catalysts were characterized using XRD, SEM, BET, XPS, and EDS. DES-based catalysts exhibited higher efficiency due to structure change, surface area enhancement...
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Pendant Proton-Relays Systematically Tune the Rate and Selectivity of Electrocatalytic Ammonia Generation in a Fe-Porphyrin Based Metal-Organic Framework
PublikacjaElectrocatalytic nitrite reduction (eNO2RR) is a promising alternative route to produce ammonia (NH3). Until now, several molecular catalysts have shown capability to homogeneously reduce nitrite to NH3, while taking advantage of added secondary-sphere functionalities to direct catalytic performance. Yet, realizing such control over heterogeneous electrocatalytic surfaces remains a challenge. Herein, we demonstrate that heterogenization...
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Investigating Noise Interference on Speech Towards Applying the Lombard Effect Automatically
PublikacjaThe aim of this study is two-fold. First, we perform a series of experiments to examine the interference of different noises on speech processing. For that purpose, we concentrate on the Lombard effect, an involuntary tendency to raise speech level in the presence of background noise. Then, we apply this knowledge to detecting speech with the Lombard effect. This is for preparing a dataset for training a machine learning-based...
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A novel hierarchically-porous diamondized polyacrylonitrile sponge-like electrodes for acetaminophen electrochemical detection
PublikacjaA novel composite electrode material consisting of tangled fibrous polyacrylonitrile-based hierarchically-struc- tured nanocomposites has been produced by wet-spinning, carbonized and decorated with a carbon nano- architecture by microwave plasma-enhanced chemical vapor deposition and investigated as a metal-free electrode for the enhanced electrochemical detection of acetaminophen. Surprisingly, the hierarchical fiber ar- chitecture...
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Automated Classifier Development Process for Recognizing Book Pages from Video Frames
PublikacjaOne of the latest developments made by publishing companies is introducing mixed and augmented reality to their printed media (e.g. to produce augmented books). An important computer vision problem that they are facing is classification of book pages from video frames. The problem is non-trivial, especially considering that typical training data is limited to only one digital original per book page, while the trained classifier...
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Development of Sulfamoylated 4‑(1-Phenyl‑1H‑1,2,3-triazol-4-yl)phenol Derivatives as Potent Steroid Sulfatase Inhibitors for Efficient Treatment of Breast Cancer
PublikacjaWe present here the advances achieved in the development of new sulfamoylated 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives as potent steroid sulfatase (STS) inhibitors for the treatment of breast cancer. Prompted by promising biological results and in silico analysis, the initial series of similar compounds were extended, appending a variety of m-substituents at the outer phenyl ring. The inhibition profiles of the newly...
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cDNA fingerprint from the hepatopancreatic glands of pond snails (Lymnaea stagnalis) exposed to benzo[a]pyrene
PublikacjaIdentification of differentially expressed genes that could be potentially used as biomarkers of PAH exposure of common invertebrate animal (like freshwater snail) would be a valuable resource for investigators interested in toxicology and biomonitoring of aquatic environments. Therefore, the aim of this research was to investigate effects of waterborne benzo[a]pyrene (B[a]P) exposure on mRNA expression in the pond snail’s (Lymnaea...
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A highly-efficient technique for evaluating bond-orientational order parameters
PublikacjaWe propose a novel, highly-efficient approach for the evaluation of bond-orientational order parameters (BOPs). Our approach exploits the properties of spherical harmonics and Wigner 3jj-symbols to reduce the number of terms in the expressions for BOPs, and employs simultaneous interpolation of normalised associated Legendre polynomials and trigonometric functions to dramatically reduce the total number of arithmetic operations....
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Implementation of FDTD-compatible Green's function on heterogeneous CPU-GPU parallel processing system
PublikacjaThis paper presents an implementation of the FDTD-compatible Green's function on a heterogeneous parallel processing system. The developed implementation simultaneously utilizes computational power of the central processing unit (CPU) and the graphics processing unit (GPU) to the computational tasks best suited to each architecture. Recently, closed-form expression for this discrete Green's function (DGF) was derived, which facilitates...
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Finger Vein Presentation Attack Detection Method Using a Hybridized Gray-Level Co-Occurrence Matrix Feature with Light-Gradient Boosting Machine Model
PublikacjaPresentation Attack Detection (PAD) is crucial in biometric finger vein recognition. The susceptibility of these systems to forged finger vein images is a significant challenge. Existing approaches to mitigate presentation attacks have computational complexity limitations and limited data availability. This study proposed a novel method for identifying presentation attacks in finger vein biometric systems. We have used optimal...
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A Novel Spatio–Temporal Deep Learning Vehicle Turns Detection Scheme Using GPS-Only Data
PublikacjaWhether the computer is driving your car or you are, advanced driver assistance systems (ADAS) come into play on all levels, from weather monitoring to safety. These modern-day ADASs use various assisting tools for drivers to keep the journey safe; these sophisticated tools provide early signals of numerous events, such as road conditions, emerging traffic scenarios, and weather warnings. Many urban applications, such as car-sharing...
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Broadening the scope of measurement and analysis of vibrations of an organ pipe employing intensity probe, simulations, and highspeed camera
PublikacjaThis paper shows an integrated approach to measure, analyze, and model phenomena occurring in an organ pipe driven by pressurized air. The aim of this paper is two-fold, i.e., to measure the pressure signal and the intensity field around the mouth by means of an intensity probe and to visualize and observe the motion of the air jet, which represents the excitation mechanism of the system. This is realized through two techniques,...
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Social Media and Knowledge Sharing – What Do We Know So Far?
PublikacjaThe aim of this paper is to examine previous studies on topic of social media and how it influences knowledge sharing online and thereafter establish respective body of knowledge. The background investigation has been organized as a theoretical review with qualitative premises. The multi-layered Systematic Literature Review process has been utilized and carried out to fetch the most relevant peer-reviewed researches in the past....
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Silver-modified titania with enhanced photocatalytic and antimicrobial properties under UV and visible light irradiation
PublikacjaCommercial titania photocatalysts were modified with 2 wt% of silver by photodeposition. The properties of the samples were characterized by DRS, XPS, XRD, FE-SEM and STEM. The modified samples exhibited activity under visible light and enhanced activity under UV irradiation for 2-propanol and acetic acid oxidation, respectively. The time-resolved microwave conductivity (TRMC) analysis indicated that enhanced activity (2.5–8-fold...
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Lead-free bismuth-based perovskites coupled with g–C3N4: A machine learning based novel approach for visible light induced degradation of pollutants
PublikacjaThe use of metal halide perovskites in photocatalytic processes has been attempted because of their unique optical properties. In this work, for the first time, Pb-free Bi-based perovskites of the Cs3Bi2X9 type (X = Cl, Br, I, Cl/Br, Cl/I, Br/I) were synthesized and subjected to comprehensive morphological, structural, and surface analyses, and photocatalytic properties in the phenol degradation reaction were examined. Furthermore,...
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Experimental Research on the Energy Efficiency of a Parallel Hybrid Drive for an Inland Ship
PublikacjaThe growing requirements for limiting the negative impact of all modes of transport on the natural environment mean that clean technologies are becoming more and more important. The global trend of e-mobility also applies to sea and inland water transport. This article presents the results of experimental tests carried out on a life-size, parallel diesel-electric hybrid propulsion system. The eciency of the propulsion system was...
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Wear Resistance Enhancement of Al6061 Alloy Surface Layer by Laser Dispersed Carbide Powders
PublikacjaIn this paper, results of the experimental study on improving wear resistance in sliding friction of Al-based alloy are presented. The technique used involves the formation of a metal matrix composite (MMC) in the alloy surface layer by laser dispersion of carbide powders such as WC, TiC and SiC. For WC and TiC MMC surface coatings fabricated under conditions typical for most of the technologically relevant solid-state lasers (wavelength...
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Landscape of Automated Log Analysis: A Systematic Literature Review and Mapping Study
PublikacjaLogging is a common practice in software engineering to provide insights into working systems. The main uses of log files have always been failure identification and root cause analysis. In recent years, novel applications of logging have emerged that benefit from automated analysis of log files, for example, real-time monitoring of system health, understanding users’ behavior, and extracting domain knowledge. Although nearly every...
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Creating a Remote Choir Performance Recording Based on an Ambisonic Approach
PublikacjaThe aim of this paper is three-fold. First, the basics of binaural and ambisonic techniques are briefly presented. Then, details related to audio-visual recordings of a remote performance of the Academic Choir of the Gdańsk University of Technology are shown. Due to the COVID-19 pandemic, artists had a choice, namely, to stay at home and not perform or stay at home and perform. In fact, staying at home brought in the possibility...
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BP-EVD: Forward Block-Output Propagation for Efficient Video Denoising
PublikacjaDenoising videos in real-time is critical in many applications, including robotics and medicine, where varying light conditions, miniaturized sensors, and optics can substantially compromise image quality. This work proposes the first video denoising method based on a deep neural network that achieves state-of-the-art performance on dynamic scenes while running in real-time on VGA video resolution with no frame latency. The backbone...
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Application of Multivariate Adaptive Regression Splines (MARSplines) Methodology for Screening of Dicarboxylic Acids Cocrystal Using 1D and 2D Molecular Descriptors
PublikacjaDicarboxylic acids (DiAs) are probably one of the most popular cocrystals formers. Due to the high hydrophilicity and non-toxicity, they are promising solubilizes of active pharmaceutical ingredients (APIs). Although DiAs appear to be highly capable of forming multicomponent crystals with various compounds, some systems reported in the literature are physical mixtures the solid state without forming stable intermolecular complex....
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Band Gap Engineering toward Semimetallic Character of Quinone-Rich Polydopamine
PublikacjaSemiconductor|melanin interfaces have received increasingly more attention in the fields of photocatalysis and applied electrochemistry because of their facile synthesis, unique electrical properties, and strong capability toward photosensitization. In this work, we describe the electropolymerization of quinone-rich polydopamine (PDA) on the surface of hydrogenated TiO2 nanotubes with enhanced photoactivity in the visible spectrum....
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublikacjaThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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The influence of plant protection by effective microorganisms on the content of bioactive phytochemicals in apples
PublikacjaThe phytochemicals of two apple cultivars (Yellow Transparent and Early Geneva) protected in two ways, conventionally with chemical pesticides or by effective microorganisms (EM), were compared. Two types of components were determined: lipids synthesised constitutively and generated via inducible pathways polyphenols along with antioxidant activity and profiles. The antioxidant activities assessed with ABTS, DPPH and Folin–Ciocalteu...
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Local dynamics of fluids and dielectrics as the foundation of signal-carrying wave properties
PublikacjaThis paper develops an original approach to fundamental problems of classical linear acoustics and electromagnetics, proving a crucial role of doubly-dynamic local properties of a propagation medium in supporting wave-like fields able to carry information signals. The proof is composed of two steps concerning, subsequently, fluid acoustics and dielectric electromagnetics. The first step consists in complementing a common, practically...
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Modulation of CYP1A1, CYP1A2 and CYP1B1 expression by cabbage juices and indoles in human breast cell lines
PublikacjaEpidemiological studies have shown that consumption of cab- bage and sauerkraut is connected with significant reduction of breast cancer incidences. Estrogens are considered a major breast cancer risk factor and their metabolism by P450 enzymes substan- tially contributes to carcinogenic activity. The aim of this study was to investigate the effect of cabbage and sauerkraut juices of differ- ent origin on the expression profile...
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Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublikacjaThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublikacjaTo 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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Late cultivars of cabbage can better cope with cadmium- involved stress than early one
PublikacjaThe usefulness of white cabbage (Brassica oleracea ssp. capitata L. f. alba) for phytoremediation of heavy metals (cadmium and zine) due to the rapid growth and a large biomass of its heads has been already described (Bączek-Kwinta et al., 2011. Kusznierewicz et al., 2012). As the photosynthetic apparatus supplies the whole plant with sugars necessary for various physiological processes and, in consequence, results in the yield,...
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Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
PublikacjaGraphical Processor Units (GPUs) are nowadays widely used in all-atom molecular simulations because of the advantage of efficient partitioning of atom pairs between the kernels to compute the contributions to energy and forces, thus enabling the treatment of very large systems. Extension of time- and size-scale of computations is also sought through the development of coarse-grained (CG) models, in which atoms are merged into extended...
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Water uptake kinetics and electrical transport in BaCe0.6Zr0.2Y0.1M0.1O3−δ (M = Tb, Pr, Fe) protonic conductors
PublikacjaBaCe0.6Zr0.2Y0.1M0.1O3−d (M = Fe, Pr, Tb) is a mixed conducting oxide in which three mobile charge carriers – oxygen ion, electron/hole, and protonic defects – are present. These types of materials have gained much interest as electrode materials for protonic ceramic fuel cells (PCFCs) and protonic ceramic electrolysis cells (PCECs). In this study, the water uptake and oxygen transport properties of different BaCe0.6Zr0.2Y0.1M0.1O3−d...
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Laboratory fatigue assessment of large geocomposite-reinforced double-layered asphalt concrete beams
PublikacjaGeosynthetic reinforcement of asphalt layers has been used for several decades. Evaluation of the influence of these materials on pavement fatigue life is still ongoing, especially for new types of geocomposites. This paper presents the evaluation of fatigue performance of large asphalt concrete beams reinforced with a new type of composite in which square or hexagonal polypropylene stiff monolithic paving grid with integral junctions...
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Laboratory fatigue assessment of large geocomposite-reinforced double-layered asphalt concrete beams
PublikacjaGeosynthetic reinforcement of asphalt layers has been used for several decades. Evaluation of the influence of these materials on pavement fatigue life is still ongoing, especially for new types of geocomposites. This paper presents the evaluation of fatigue performance of large asphalt concrete beams reinforced with a new type of composite in which square or hexagonal polypropylene stiff monolithic paving grid with integral junctions...
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Linear and Nonlinear Optical Properties of Azobenzene Derivatives Modified with an (Amino)naphthalene Moiety
PublikacjaThe design of two-photon absorbing azobenzene (AB) derivatives has received much attention; however, the two-photon absorption (2PA) properties of bis-conjugated azobenzene systems are relatively less explored. Here, we present the synthesis of six azobenzene derivatives and three bisazobenzenes substituted (or not) at para position(s) with one or two amino group(s). Their linear and nonlinear absorption properties are studied...