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Search results for: molecular biology and genetics
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Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties
PublicationAminotransferases catalyze reversibly the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5′-phosphate (PLP) as a cofactor. Various aminotransferases acting on a range of substrates have been reported. Aromatic transaminases are able to catalyze the transamination reaction with both aromatic and acidic substrates. Two aminotransferases from C. albicans, Aro8p and Aro9p, have been identified recently, exhibiting...
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Anticancer imidazoacridinone C-1311 inhibits hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) and angiogenesis
PublicationAntitumor imidazoacridinone C-1311 is a DNA-reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor. Here, we demonstrate the mechanism of C-1311 inhibitory action on novel targets: hypoxia-inducible factor-1α (HIF-1α), vascular-endothelial growth factor (VEGF), and angiogenesis. In a cell-free system, C-1311 prevented HIF-1α binding to an oligonucleotide encompassing a canonical hypoxia-responsive element (HRE),...
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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Multiscale model for blood flow after a bileaflet artificial aortic valve implantation
PublicationCardiovascular diseases are the leading cause of mortality in the world, mainly due to atherosclerosis and its consequences. The article presents the numerical model of the blood flow through artificial aortic valve. The overset mesh approach was applied to simulate the valve leaflets motion and to realize the moving mesh, in the aortic arch and the main branches of cardiovascular system. To capture the cardiac system’s response...
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Evaluating the risk of endometriosis based on patients’ self-assessment questionnaires
PublicationBackground Endometriosis is a condition that significantly affects the quality of life of about 10 % of reproductive-aged women. It is characterized by the presence of tissue similar to the uterine lining (endometrium) outside the uterus, which can lead lead scarring, adhesions, pain, and fertility issues. While numerous factors associated with endometriosis are documented, a wide range of symptoms may still be undiscovered. Methods In...
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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
PublicationControlled ovarian stimulation is tailored to the patient based on clinical parameters but estimating the number of retrieved metaphase II (MII) oocytes is a challenge. Here, we have developed a model that takes advantage of the patient’s genetic and clinical characteristics simultaneously for predicting the stimulation outcome. Sequence variants in reproduction-related genes identified by next-generation sequencing were matched...
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Ensembling noisy segmentation masks of blurred sperm images
PublicationBackground: Sperm tail morphology and motility have been demonstrated to be important factors in determining sperm quality for in vitro fertilization. However, many existing computer-aided sperm analysis systems leave the sperm tail out of the analysis, as detecting a few tail pixels is challenging. Moreover, some publicly available datasets for classifying morphological defects contain images limited only to the sperm head. This...
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Synthesis and Cholinesterase Inhibitory Activity of N-Phosphorylated /N-Tiophosphorylated Tacrine
PublicationNovel phosphorus and thiophosphorus tacrine derivatives were designed, synthesized and their biological activity and molecular modeling was investigated as a new potential anti-Alzheimer's disease (AD) agents. All new synthesized compound exhibited lower toxicity against neuroblastoma cell line (SH-SY5Y) in comparison with tacrine. Two analogues in the series, 7 and 9, demonstrated lack of cytotoxicity against hepatocellular cells...
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Dissociation of 2-oxopropanoic acid by low energy electrons
PublicationElectron attachment to molecular target can lead to a variety of negative fragment ions. We experimentally probe the main dissociative electron attachment (DEA) channels in 2-oxopropanoic acid (CH3 - CO - COOH) - an important trace component in the Earth's atmosphere. In our studies we utilise nearly mono-energetic electrons at electron energies from 0 eV up to 15 eV.
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Proton affinities of simple organic compounds
PublicationThe Restricted Hatree-Fock method with 6-311G** split-valence molecular orbitals basis sets has been applied to geometrical optimizations and calculations of total electronic, zero point vibrational energies and proton affinities at 298 K for small neutral and protonated alkanes, alcohols, acetic acid, methyl and ethyl acetate, acetone, and acetaldehyde. Calculated values of proton affinities are compared with experimental data.
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Unlocking the Secrets of River Pollution: Analyzing Organic Pollutants in Sediments—Experimental Study
PublicationUntreated wastewater released into rivers can result in water pollution, the spread of waterborne diseases, harm to ecosystems, contamination of soil and groundwater, as well as air pollution and respiratory problems for nearby humans and animals due to the release of greenhouse gases. The current study aims to investigate the recent input of anthropogenic loads into the rivers using linear alkylbenzene (LAB), which is one of the...
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On various modelling approaches to real-time visualisation of blood flow
PublicationThis paper reviews various modelling approaches to real-time visualisation of blood flow. These include classic, macroscale approach based on the momentum conservation equation together with a proper constitutive equation. Moreover, modern micro- and mesoscale approaches, such as molecular dynamics and dissipative particle dynamics, are discussed. Advantages and disadvantages of the discussed methods are highlighted with particular...
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Metabolomics analysis of the effect of time and oxygen on the fibrosarcoma cell line (HT1080) - model studies
PublicationOxygen molecular effect on cancer cells metabolism has been a concern for decades,at the beginning with Louis Pasteur’s and his understanding of glucose fermentation.In the 1930s, Otto Warburg came with his new understanding of cancer biology by introducingthe alteration of cancer cells' metabolism in the presence or absence of oxygen moleculesby increasing glucose uptake and producing lactate through...
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KNOWING WHEN TO SAY NO / SAPERE QUANDO DIRE NO
PublicationEver since we began illuminating the exterior of the slender skyscrapers built during the of 20s and 30s in XX century, urban lighting has been considered a way to beautify cities, and make them more visually prominent and safe. At that time, we knew so little about the impact of lighting on humans, flora and fauna, so it never occurred to lighting designers then, that their actions would have harmful consequences. In those days,...
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Enzyme Conjugation - A Promising Tool for Bio-catalytic and Biotransformation Applications – A Review
PublicationEnzymes have revolutionized conventional industrial catalysts as more efficient, eco-friendly, and sustainable substitutes that can be used in different biotechnological processes, food, and pharmaceutical industries. Yet, the enzymes from nature are engineered to make them adapt and enhance their durability in the industrial environment. One promising approach involves the combined use of multiple enzymes that catalyze highly...
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Topical delivery of pharmaceutical and cosmetic macromolecules using microemulsion systems
PublicationMicroemulsions are transparent, thermodynamically stable colloidal systems. Over the recent years, they have been increasingly investigated due to their potential as skin delivery vehicles for a wide range of drug molecules. The nanoscale particle size and the specificity of microemulsion components are the main features determining the skin permeation process. However, in order to effectively cross the skin barrier, the active...
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Structural, functional, and stability change predictions in human telomerase upon specific point mutations,
PublicationOverexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation,...
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Ipertrofan Revisited—The Proposal of the Complete Stereochemistry of Mepartricin A and B
PublicationBeing a methyl ester of partricin, the mepartricin complex is the active substance of a drug called Ipertrofan (Tricandil), which was proven to be useful in treatment of benign prostatic hyperplasia and chronic nonbacterial prostatitis/chronic pelvic pain syndrome. Nevertheless, no direct structural evidence on the stereochemistry of its components has been presented to date. In this contribution, we have conducted detailed, NMR-driven...
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Synthesis and characterization of novel renewable polyesters based on 2,5-furandicarboxylic acid and 2,3-butanediol
PublicationNovel polyesters from 2,5-furandicarboxylic acid or 2,5-dimethyl-furandicarboxylate and 2,3-butanediol have been synthesized via bulk polycondensation catalyzed by titanium (IV) n-butoxide, tin (IV) ethylhexanoate, or zirconium (IV) butoxide. The polymers were analyzed by size exclusion chromatography, nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy (FTIR), matrix-assisted laser ionization-desorption...
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Determination of polycyclic aromatic hydrocarbons (PAHs) and other organic pollutants in freshwaters on the western shore of Admiralty Bay (King George Island, Maritime Antarctica).
PublicationOrganic contamination in freshwater samples has never been investigated at the western shore of Admiralty Bay. Therefore, the presence of polycyclic aromatic hydrocarbons (PAHs) in five different sites distributed along a shore running from the Arctowski Station to the Baranowski Glacier was studied. Moreover, organic compounds such as n-alkanes, toluene and ethylbenzene were also noted. Increased ΣPAHs in late Austral summer 2016...
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Enhanced trap-assisted recombination in organic semiconductors
PublicationAn analytical model to describe the interaction of excitons and charge transfer states with deep traps is formulated for the case of molecular materials. Here, we have considered the influence of a trap-assisted recombination on this phenomenon. The final expression for the effective recombination rate has been derived from the Shockley–Read–Hall theory and kinetic equations which characterize different photophysical processes....
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Modeling the Influence of Salts on the Critical Micelle Concentration of Ionic Surfactants
PublicationWe show for the first time that a phenomenological, augmented volume-based thermodynamics (aVBT) model is capable to predict the critical micelle concentrations of ionic surfactants, including ionic liquids, with added salts. The model also adjusts for the type of salt added by including its molecular volume, which might form a connection to the Hofmeister effect. The other physico-chemically relevant quantities included in the...
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Future of medicine: personalized oncology
PublicationUnderstanding genetic and epigenetic mechanisms of tumorigenesis allows identifying many vital mutations affected the formation of various malignancies. This led to the discovery of a new therapeutic approach, based on molecular mechanisms in the world of medicine, which is called personalized medicine (PM). This review aims to outline the state of the art of the personalized medicine in treatment, taking into account anti-cancer...
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L1 Cell Adhesion Molecule Overexpression Down Regulates Phosphacan and Up Regulates Structural Plasticity-Related Genes Rostral and Caudal to the Complete Spinal Cord Transection
PublicationL1 cell adhesion molecule (L1CAM) supports spinal cord cellular milieu after contusion and compression lesions, contributing to neuroprotection, promoting axonal outgrowth, and reducing outgrowth-inhibitory molecules in lesion proximity. We extended investigations into L1CAM molecular targets and explored long-distance effects of L1CAM rostral and caudal to complete spinal cord transection (SCT) in...
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Fuzzy Divisive Hierarchical Clustering of Solvents According to Their Experimentally and Theoretically Predicted Descriptors
PublicationThe present study describes a simple procedure to separate into patterns of similarity a large group of solvents, 259 in total, presented by 15 specific descriptors (experimentally found and theoretically predicted physicochemical parameters). Solvent data is usually characterized by its high variability, dierent molecular symmetry, and spatial orientation. Methods of chemometrics can usefully be used to extract and explore accurately...
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Application of the neural networks for developing new parametrization of the Tersoff potential for carbon
PublicationPenta-graphene (PG) is a 2D carbon allotrope composed of a layer of pentagons having sp2- and sp3-bonded carbon atoms. A study carried out in 2018 has shown that the parameterization of the Tersoff potential proposed in 2005 by Ehrhart and Able (T05 potential) performs better than other potentials available for carbon, being able to reproduce structural and mechanical properties of the PG. In this work, we tried to improve the...
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Selection of effective cocrystals former for dissolution rate improvement of active pharmaceutical ingredients based on lipoaffinity index
PublicationNew theoretical screening procedure was proposed for appropriate selection of potential cocrystal formers possessing the ability of enhancing dissolution rates of drugs. The procedure relies on the training set comprising 102 positive and 17 negative cases of cocrystals found in the literature. Despite the fact that the only available data were of qualitative character, performed statistical analysis using binary classification...
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Influence of addition of carbon nanotubes on rheological properties of selected liquid lubricants - a computer simulation study
PublicationThis work is motivated by the improvement of anti-friction properties of lubricants by addition of CNTs proved experimentally in literature. In particular, a methodology is developed to compute the shear viscosity of liquid lubricants (Propylene Glycol) based on Molecular Dynamics simulation. Non-Equilibrium molecular dynamics (NEMD) approach is used with a reactive force field ReaxFF implemented in LAMMPS. The simulations are...
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Investigation of Thermoplastic Polyurethanes Synthesized via Two Different Prepolymers
PublicationThe man aim of this work was to investigate the effect of the molecular weight of polyols, mixture of prepolymers, and [NCO]/[OH] molar ratio used during the prepolymer chain extending step on the chemical structure, thermomechanical and mechanical properties, and thermal stability of thermoplastic poly(ether-urethane)s In this work thermoplastic poly(ether-urethane)s were synthesized by using polyols with a various molecular weight,...
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Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide – volumetric and compressibility studies
PublicationThe density and sound velocity of the solutions of ionic liquids based on N-alkyl-N-methyl-morpholinium cations, N-ethyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-butyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-methyl-N-octyl-morpholinium bis(trifluoromethanesulfonyl)imide and N-decyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide in dimethylsulfoxide were measured at T = (298.15 to 318.15)...
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Novel, Fully Biobased Semicrystalline Polyamides
PublicationNovel, semicrystalline polyamides and co(polyamides) were synthesized from biobased sebacic acid (SA), 2,5-diamino-2,5-dideoxy-1,4;3,6-dianhydroiditol (diaminoisoidide, DAII) as well as from 1,4-diaminobutane (DAB), also known as putrescine in nature. Low molecular weight polyamides were obtained by melt polycondensation of the salts based on these monomers or by interfacial polycondensation. In order to increase their molecular...
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Weldability of pipe grade polyethylenes as realized from thermal and mechanical properties assessments
PublicationSince polyethylene (PE) has been widely accepted for the production of high-pressure fluid conveying pipelines, studies devoted to weldability of PE connections were always of major importance. In this study, two industrial PE grades designed for pipe production, namely PE80 and PE100, were injection molded, cut, and then welded as PE100-PE100, PE100-PE80, and PE80-PE80. The heat-welded joints were assessed by differential scanning...
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Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes
PublicationUntil recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North–East Atlantic, no such reduction...
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MoS2-containing composite membranes for separation of environmental energy-relevant liquid and gas mixtures: A comprehensive review
PublicationMolybdenum sulfide (MoS2) materials adapted into membranes have demonstrated potential for different areas dealing with molecular separations. For instance, MoS2-based membranes have been proposed for distinct environmental applications, such as water treatment, seawater desalination, gas separation, and solvent separation. Emergently, such membranes have been ultimately investigated for energy-relevant gas separation mixtures,...
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Interactions of positrons with atoms and molecules
PublicationThe positron is the antiparticle of the electron. It has the same mass as the electron, but opposite charge. The understanding of the interactions of positrons with normal matter, like atoms and molecules, is of interest in various scientific fields, like nuclear medicine, plasma physics and astronomy. In this talk we will give a short introduction to some theoretical methods to describe the interactions of positrons with atoms...
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Low energy elastic electron scattering from benzonitrile (C6H5CN)
PublicationWe present experimental differential elastic scattering cross sections (DCSs) for low energy electron scattering from benzonitrile along with integral and momentum-transfer cross sections that are determined from these DCSs. The measurements of DCSs are obtained using the relative flow method with helium as the standard gas, in a crossed electron-molecular gas beam arrangement. Our measurements are made at incident electron energies...
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Correlated Particle Motion and THz Spectral Response of Supercritical Water
PublicationMolecular dynamics simulations of supercritical water reveal distinctly different distance-dependent modulations of dipolar response and correlations in particle motion compared to ambient conditions. The strongly perturbed H-bond network of water at supercritical conditions allows for considerable translationaland rotational freedom of individual molecules. These changes give rise to substantially different infrared spectra and...
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Toward Polyethylene–Polyester Block and Graft Copolymers with Tunable Polarity
PublicationThe synthesis and characterization of polyethylene–polyester block and graft copolymers and their potential as compatibilizers in polyethylene-based polymer blends are being described. The various routes to functionalized polyethylenes and the corresponding block/graft copolymers have been compared and evaluated for their scalability to industrial scale production. Hydroxyl chain-end and randomly OH-functionalized HDPE as well...
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Acid–Base Equilibrium and Self-Association in Relation to High Antitumor Activity of Selected Unsymmetrical Bisacridines Established by Extensive Chemometric Analysis
PublicationUnsymmetrical bisacridines (UAs) represent a novel class of anticancer agents previously synthesized by our group. Our recent studies have demonstrated their high antitumor potential against multiple cancer cell lines and human tumor xenografts in nude mice. At the cellular level, these compounds affected 3D cancer spheroid growth and their cellular uptake was selectively modulated by quantum dots. UAs were shown to undergo metabolic...
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A comparative study on the decolorization of Tartrazine, Ponceau 4R, and Coomassie Brilliant Blue using persulfate and hydrogen peroxide based Advanced Oxidation Processes combined with Hydrodynamic Cavitation
PublicationDecolorization of Ponceau 4R, Tartrazine, and Coomassie Brilliant Blue (CBB) was studied using hybrid processes of hydrodynamic cavitation (HC) with potassium persulfate (KPS) and hydrogen peroxide (H2O2). The different properties of these dyes such as hydrophobicity, molecular structures, and molecular weights provided this opportunity to investigate the effects of these factors by comparing the decolorization values of the dyes....
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Novel Biomass-Based Polymers: Synthesis, Characterization, and Application
PublicationA wide range of polymers were prepared from biomass-derivatives, using different polymerization mechanisms. Well-defined, fully hydroxy-functional polyesters based on aliphatic diols were synthesized, using either conventional metal-based catalysts or the organic superbase 1,5,7-triazabicyclododecene (TBD). Unsaturated polyesters were also made, offering additional functionality to these biobased resins. Metal-catalyzed or enzymatic...
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublicationA significant number of DNA-based techniques has been introduced into the field of microorganisms’ characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before...
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Multicomponent ionic liquid CMC prediction
PublicationWe created a model to predict CMC of ILs based on 704 experimental values published in 43 publications since 2000. Our model was able to predict CMC of variety of ILs in binary or ternary system in a presence of salt or alcohol. The molecular volume of IL (Vm), solvent-accessible surface (Sˆ), solvation enthalpy (DsolvGN), concentration of salt (Cs) or alcohol (Ca) and their molecular volumes (Vms and Vma, respectively) were chosen...
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Modelling charge transfer processes in C2+ -tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks
PublicationInvestigations of collision-induced processes involving carbon ions and molecules of biological interest in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest...
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Thermosensitive composite based on agarose and chitosan saturated with carbon dioxide. Preliminary study of requirements for production of new CSAG bioink.
PublicationThis study introduces a method for producing printable, thermosensitive bioink formulated from agarose (AG) and carbon dioxide-saturated chitosan (CS) hydrogels. The research identified medium molecular weight chitosan as optimal for bioink production, with a preferred chitosan hydrogel content of 40–60 %. Rheological analysis reveals the bioink's pseudoplastic behavior and a sol-gel phase transition between 27.0 and 31.5 °C. The...
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Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents
PublicationSolubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and...
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The use of chain extenders as processing aids in the valorization of single-use polylactide (PLA) products by rotomolding
PublicationBiodegradable plastics in single-use products have increased in popularity as a way to reduce the negative environmental impact of conventional plastics and meet the tightening law regulations. However, their recyclability needs to be assessed, as the environmental behavior of single-use plastics, even if compostable, is not negligible. Polylactide (PLA) is susceptible to thermal, oxidative, hydrolytic, and mechanical degradation...
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Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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Electron impact fragmentation of pyrrole molecules studied by fluorescence emission spectroscopy
PublicationThe fluorescence emission spectroscopy using electron impact excitation technique was employed to study fragmentation processes of the gas phase pyrrole molecules. The following excited fragmentation species were observed by detection of their fluorescence decay: the atomic hydrogen H(n), n = 4-7 and the diatomic CH(A2Δ), CN(B2Σ+), NH(A3Π) and C2(d3Πg) fragments. These atomic and molecular products differ from those previously...