Green approach for fabrication of bacterial cellulose-chitosan composites in the solutions of carbonic acid under high pressure CO<inf>2</inf>
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15.04.2021 |
Novikov I.V.
Pigaleva M.A.
Naumkin A.V.
Badun G.A.
Levin E.E.
Kharitonova E.P.
Gromovykh T.I.
Gallyamov M.O.
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Carbohydrate Polymers |
10.1016/j.carbpol.2021.117614 |
0 |
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© 2021 Elsevier Ltd The functionalization of the bacterial cellulose (BC) surface with a chitosan biopolymer to expand the areas of possible applications of the modified BC is an important scientific task. The creation of such composites in the carbonic acid solutions that were performed in this work has several advantages in terms of being biocompatible and eco-friendly. Quantitative analysis of chitosan content in the composite was conducted by tritium-labeled chitosan radioactivity detection method and this showed three times increased chitosan loading. Different physicochemical methods showed successful incorporation of chitosan into the BC matrix and interaction with it through hydrogen bonds. Microscopy results showed that the chitosan coating with a thickness of around 10 nm was formed in the bulk of BC, covering each microfibril. It was found that the inner specific surface area increased 1.5 times on deposition of chitosan from the solutions in carbonic acid.
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Ultrathin Langmuir–Schaefer films of slipped-cofacial J-type phthalocyanine dimer: Supramolecular organization, UV/Vis/NIR study and nonlinear absorbance of femtosecond laser radiation
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15.04.2021 |
Kazak A.V.
Marchenkova M.A.
Khorkov K.S.
Kochuev D.A.
Rogachev A.V.
Kholodkov I.V.
Usol'tseva N.V.
Savelyev M.S.
Tolbin A.Y.
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Applied Surface Science |
10.1016/j.apsusc.2021.148993 |
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© 2021 Elsevier B.V. Based on a comprehensive theoretical and experimental approach, a low-defect thin film of stable dimeric phthalocyanine zinc complex (bis-[2-hydroxy-9(10),16(17), 23(24)-tri-tert-butylphthalocyanine]zinc – J-[OHPctZn]2) was prepared. It is shown that the dye forms stable amorphous edge-on monolayers at the air/water interface with an insignificant content of cylindrical 3D aggregates. These floating layers keep their structure when transferred by the Langmuir-Schaefer method onto a solid substrate, demonstrating a tendency towards ordered H-aggregation with preserving their linear molecular properties. Mixed two- and three-photon absorption of femtosecond laser pulses (280 fs) was firstly detected on this sample, as well as the ability of a material to the nonlinear attenuation of the intense irradiation, which is important for optical limiting.
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Laser fabrication of composite layers from biopolymers with branched 3D networks of single-walled carbon nanotubes for cardiovascular implants
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15.03.2021 |
Gerasimenko A.Y.
Kurilova U.E.
Savelyev M.S.
Murashko D.T.
Glukhova O.E.
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Composite Structures |
10.1016/j.compstruct.2020.113517 |
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© 2020 Elsevier Ltd A laser technology has been developed for fabricating structures from composite layers based on biopolymers: albumin, collagen, and chitosan with single-walled carbon nanotubes (SWCNT). The structures are intended for cardiovascular devices and tissue-engineered implants. This is evidenced by the results of studies. The composite layers were fabricated due to the phase transition of biopolymers and SWCNT aqueous dispersion under the influence of laser pulses. At the same time branched 3D networks of SWCNT were formed in the biopolymer matrix. The threshold energy fluence of laser pulses was determined (0.032–0.083 J/cm2) at which a bimodal distribution of pores was observed. The calculation of contact resistances between nanotubes at percolation units of 3D networks (20–100 kOhm) was carried out. Composite layers fabricated by laser demonstrated conductivity values that were higher (12.4 S/m) than those for layers by thermostat (4.7 S/m). The maximum hardness of the composite layers with SWCNT (0.01 wt%) by laser was 482 ± 10, 425 ± 10, and 407 ± 15 MPa for albumin, collagen and chitosan, respectively. The hardness of the thermostat layers was less than 100 MPa. The viability of endothelial cells in composite layers was improved. The composite layers ensured a normal level of hemolysis during interaction with erythrocytes.
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Spectrally encoded microspheres for immunofluorescence analysis
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20.02.2021 |
Sankova N.
Shalaev P.
Semeykina V.
Dolgushin S.
Odintsova E.
Parkhomchuk E.
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Journal of Applied Polymer Science |
10.1002/app.49890 |
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© 2020 Wiley Periodicals LLC A modern immunofluorescence analysis based on spectrally encoded microspheres has found numerous and constantly growing applications in disease diagnosis, environmental supervision, and fundamental science. Here we present an overview of microsphere-based methods of multiplex immunofluorescence analysis and consider such important parameters of beads, that are crucial in most microsphere-based immunoassays, as size distribution, fluorescence stability, magnetic properties, and particle material. The preparation methods of the microspheres with tunable diameter, the introduction of various types of fluorochromes, and magnetic particles into the microspheres are discussed in details. This review also addresses the advantages and disadvantages of different approaches to implement technically bead-based immunofluorescence analysis.
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Potential immuno-nanomedicine strategies to fight COVID-19 like pulmonary infections
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01.02.2021 |
Bonam S.R.
Kotla N.G.
Bohara R.A.
Rochev Y.
Webster T.J.
Bayry J.
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Nano Today |
10.1016/j.nantod.2020.101051 |
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© 2020 Elsevier Ltd COVID-19, coronavirus disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic. At the time of writing this (October 14, 2020), more than 38.4 million people have become affected, and 1.0 million people have died across the world. The death rate is undoubtedly correlated with the cytokine storm and other pathological pulmonary characteristics, as a result of which the lungs cannot provide sufficient oxygen to the body's vital organs. While diversified drugs have been tested as a first line therapy, the complexity of fatal cases has not been reduced so far, and the world is looking for a treatment to combat the virus. However, to date, and despite such promise, we have received very limited information about the potential of nanomedicine to fight against COVID-19 or as an adjunct therapy in the treatment regimen. Over the past two decades, various therapeutic strategies, including direct-acting antiviral drugs, immunomodulators, a few non-specific drugs (simple to complex), have been explored to treat Acute Respiratory Distress Syndrome (ARDS), Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), influenza, and sometimes the common flu, thus, correlating and developing specific drugs centric to COVID-19 is possible. This review article focuses on the pulmonary pathology caused by SARS-CoV-2 and other viral pathogens, highlighting possible nanomedicine therapeutic strategies that should be further tested immediately.
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Potential immuno-nanomedicine strategies to fight COVID-19 like pulmonary infections
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01.02.2021 |
Bonam S.R.
Kotla N.G.
Bohara R.A.
Rochev Y.
Webster T.J.
Bayry J.
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Nano Today |
10.1016/j.nantod.2020.101051 |
0 |
Ссылка
© 2020 Elsevier Ltd COVID-19, coronavirus disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic. At the time of writing this (October 14, 2020), more than 38.4 million people have become affected, and 1.0 million people have died across the world. The death rate is undoubtedly correlated with the cytokine storm and other pathological pulmonary characteristics, as a result of which the lungs cannot provide sufficient oxygen to the body's vital organs. While diversified drugs have been tested as a first line therapy, the complexity of fatal cases has not been reduced so far, and the world is looking for a treatment to combat the virus. However, to date, and despite such promise, we have received very limited information about the potential of nanomedicine to fight against COVID-19 or as an adjunct therapy in the treatment regimen. Over the past two decades, various therapeutic strategies, including direct-acting antiviral drugs, immunomodulators, a few non-specific drugs (simple to complex), have been explored to treat Acute Respiratory Distress Syndrome (ARDS), Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), influenza, and sometimes the common flu, thus, correlating and developing specific drugs centric to COVID-19 is possible. This review article focuses on the pulmonary pathology caused by SARS-CoV-2 and other viral pathogens, highlighting possible nanomedicine therapeutic strategies that should be further tested immediately.
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The earthworm species Eisenia fetida accelerates the decomposition rate of cigarette butts on the soil surface
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01.12.2020 |
Korobushkin D.I.
Garibian P.G.
Pelgunova L.A.
Zaitsev A.S.
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Soil Biology and Biochemistry |
10.1016/j.soilbio.2020.108022 |
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© 2020 Cigarette butts (CBs) represent the most common, though poorly biodegradable, type of waste on Earth. Thrown on the soil surface, they can remain unchanged for years, poisoning surrounding ecosystems with toxins accumulated during the smoking process. However, there is practically no data on the effect of smoked CBs on soil biota or soil animals in particular, nor on the potential of edaphic fauna to facilitate their decomposition. One of the most promising agents among soil animals are earthworms, which are known to be beneficial in the processes of recalcitrant organic matter degradation and stimulation of microbial activity in detrital food webs. In a microcosm experiment with the sod podzolic soil, we aimed at testing the effect of the commonly cultured epigeic earthworm Eisenia fetida (Savigny 1826) on the biodegradation rate of CBs and the possible adverse effects of this waste on the species. The experiment had a full-factorial design with three categorical predictors: CB number (0, 1 and 3 per microcosm); smoking condition (smoked and unsmoked CBs) and two levels of earthworm amendment (0 and 4 per microcosm). During 70 days of the experiment, we did not observe any smoked CB-induced mortality of earthworms. The addition of E. fetida significantly increased the CB mass loss across all treatment combinations. Specifically, earthworms improved the decomposition rate from 30 to 36% (p < 0.05), on average. However, this improvement was mainly associated with CB paper wrapping consumption. The inhibition of CO2 emission in microcosms with CBs and earthworms suggested the direct consumption of this waste by E. fetida, rather than modulation of the degradation potential of a microbial community. E. fetida appears to thus be a moderately promising agent for CB biodegradation with the simultaneous reduction in carbon loss from soil through the microbial channel in the studied soil type. These results open perspectives for the further evaluation of the role of soil macroinvertebrates in recalcitrant organic waste management in general and CBs in particular. We demonstrated that earthworms can efficiently decompose smoked and unsmoked cigarette butts regardless of their toxic potential and simultaneously reduce associated microbial activity.
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Tailoring the collagen film structural properties via direct laser crosslinking of star-shaped polylactide for robust scaffold formation
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01.02.2020 |
Bardakova K.
Grebenik E.
Minaev N.
Churbanov S.
Moldagazyeva Z.
Krupinov G.
Kostjuk S.
Timashev P.
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Materials Science and Engineering C |
10.1016/j.msec.2019.110300 |
1 |
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© 2019 Elsevier B.V. Application of restructured collagen-based biomaterials is generally restricted by their poor mechanical properties, which ideally must be close to those of a tissue being repaired. Here, we present an approach to the formation of a robust biomaterial using laser-induced curing of a photosensitive star-shaped polylactide. The created collagen-based structures demonstrated an increase in the Young's modulus by more than an order of magnitude with introduction of reinforcing patterns (from 0.15 ± 0.02 MPa for the untreated collagen to 51.2 ± 5.6 MPa for the reinforced collagen). It was shown that the geometrical configuration of the created reinforcing pattern affected the scaffold's mechanical properties only in the case of a relatively high laser radiation power density, when the effect of accumulated thermomechanical stresses in the photocured regions was significant. Photo-crosslinking of polylactide did not compromise the scaffold's cytotoxicity and provided fluorescent regions in the collagen matrix, that create a potential for noninvasive monitoring of such materials' biodegradation kinetics in vivo.
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Nano-liquid chromatography for enantiomers separation of baclofen by using vancomycin silica stationary phase
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08.11.2019 |
D'Orazio G.
Fanali C.
Gentili A.
Tagliaro F.
Fanali S.
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Journal of Chromatography A |
10.1016/j.chroma.2019.07.012 |
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© 2019 Elsevier B.V. The chiral separation of baclofen (Bac) was obtained by nano-liquid chromatography tandem mass spectrometry (nano-LC–MS/MS) using a 100 μm I.D. fused silica capillary column packed with silica particles chemically modified with vancomycin. Various experimental parameters, such as composition (buffer concentration, water content, organic modifier) and pH of the mobile phase and sample solvent were investigated for method optimization. In order to increase the sensitivity an on-column focusing procedure was applied. Acceptable separation of Bac enantiomers was obtained in less than 11 min eluting in isocratic mode, with 90:10 MeOH/water (v/v) containing 10 mM ammonium acetate at pH 4.5. These optimized experimental conditions were applied to the analysis of human plasma samples spiked with racemic mixture of Bac. The use of a Buckypaper disc as sorbent membrane allows one to recover both enantiomers with yields ≥ 65%. The method was fully validated, following the identification criteria of the European Commission Decision 2002/657/EC.
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Polyisobutylene-based thermoplastic elastomers for manufacturing polymeric heart valve leaflets: In vitro and in vivo results
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01.11.2019 |
Ovcharenko E.
Rezvova M.
Nikishau P.
Kostjuk S.
Glushkova T.
Antonova L.
Trebushat D.
Akentieva T.
Shishkova D.
Krivikina E.
Klyshnikov K.
Kudryavtseva Y.
Barbarash L.
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Applied Sciences (Switzerland) |
10.3390/app9224773 |
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© 2019 by the authors. Superior polymers represent a promising alternative to mechanical and biological materials commonly used for manufacturing artificial heart valves. The study is aimed at assessing poly(styrene-block-isobutylene-block-styrene) (SIBS) properties and comparing them with polytetrafluoroethylene (Gore-texTM, a reference sample). Surface topography of both materials was evaluated with scanning electron microscopy and atomic force microscopy. The mechanical properties were measured under uniaxial tension. The water contact angle was estimated to evaluate hydrophilicity/hydrophobicity of the study samples. Materials' hemocompatibility was evaluated using cell lines (Ea.hy 926), donor blood, and in vivo. SIBS possess a regular surface relief. It is hydrophobic and has lower strength as compared to Gore-texTM (3.51 MPa vs. 13.2/23.8 MPa). SIBS and Gore-texTM have similar hemocompatibility (hemolysis, adhesion, and platelet aggregation). The subcutaneous rat implantation reports that SIBS has a lower tendency towards calcification (0.39 mg/g) compared with Gore-texTM (1.29 mg/g). SIBS is a highly hemocompatible material with a promising potential for manufacturing heart valve leaflets, but its mechanical properties require further improvements. The possible options include the reinforcement with nanofillers and introductions of new chains in its structure.
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Chitosan-g-Polyester Microspheres: Effect of Length and Composition of Grafted Chains
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01.10.2019 |
Demina T.
Sevrin C.
Kapchiekue C.
Akopova T.
Grandfils C.
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Macromolecular Materials and Engineering |
10.1002/mame.201900203 |
1 |
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© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Hydrophobic segments made of oligo(l,l- or d,l-lactides) or poly(l,l-lactide) are grafted onto chitosan backbone in order to use their amphiphilic behavior to prepare degradable microcarriers intended to be used for tissue engineering. Hydrophilic–lipophilic balance of these copolymers is adjusted playing on the respective length of their hydrophilic and hydrophobic moieties. Thanks to their self-emulsifying properties, these graft copolymers are processed into microspheres in the absence of hydrophilic emulsifier commonly added in the aqueous phase of the oil/water emulsion. The copolymers containing amorphous oligolactide segments of medium length are demonstrated to be the most effective ones for microparticle fabrication. The microparticles are characterized using SEM, EDX, and FTIR. The reactivity of amine group is demonstrated using fluorescein isothiocyanate staining. The resulting microspheres disclose a porous core and a shell enriched by the hydrophilic polysaccharide moieties. Stabilization of the oil/water interface during the microsphere fabrication, total yield, size distribution, and microparticle surface morphology are mainly affected by the macromolecular features of the copolymers.
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Conjugates of thermally stable phthalocyanine J-type dimers with single-walled carbon nanotubes for enhanced optical limiting applications
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01.09.2019 |
Savelyev M.
Gerasimenko A.
Podgaetskii V.
Tereshchenko S.
Selishchev S.
Tolbin A.
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Optics and Laser Technology |
10.1016/j.optlastec.2019.04.036 |
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© 2019 Elsevier Ltd The widespread application of laser devices requires development of new protections against light pulses of high intensity. This problem is relevant because of the danger of hitting the civil aviation pilots with bright and powerful radiation originating from the laser sources which are widely used in the everyday life. Therefore, this work is devoted to continuing our research on a new class of macroheterocyclic compounds – thermally and chemically stable J-type phthalocyanine dimers as potential nonlinear absorbers for optical limiting technology. The dimeric complexes of magnesium (1a) and zinc (1b) were covalently bonded to single-walled carbon nanotubes (SWCNTs) to improve the overall characteristics of the potential optical limiters 2a,b as compared to the previously studied corresponding dyes in solutions. The conjugates obtained were investigated using atomic force microscopy (AFM), as well as Raman and IR spectroscopy to confirm formation of the covalent binding of phthalocyanine macrocycles with the carbon surface. Open-aperture Z-scan and a fixed limiter location experiments have demonstrated low values of the limiting threshold and high degree of attenuation of the input laser radiation with the pulses duration located in the nanosecond range.
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Organocatalytic controlled anionic ring-opening polymerization of carbazole-containing thiiranes
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01.08.2019 |
Vaitusionak A.
Vasilenko I.
Jatautiene E.
Simokaitiene J.
Tomkeviciene A.
Ostrauskaite J.
Grazulevicius J.
Kostjuk S.
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European Polymer Journal |
10.1016/j.eurpolymj.2019.05.009 |
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© 2019 Elsevier Ltd The anionic ring-opening polymerization of carbazole-containing monomers, (9-carbazolylmethyl)thiirane (M1)and (3,6-di-tert-butyl-9-carbazolylmethyl)thiirane (M2), with hexanethiol or pentaerythritol tetrakis(3-mercaptopropionate)(PETMP)as initiators and 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD)as catalyst at 20 °C in tetrahydrofuran or N,N-dimethylformamide as solvents has been studied. The polymerization of these monomers proceeds in a living fashion affording linear and star-shaped polymers with controlled molecular weight (Mn = 4000–15,000 g mol−1)and relatively low polydispersity (Đ < 1.3). It was demonstrated that end-capping of polymers by trifluoroacetic anhydride allowed to protect thiol end groups from oxidative coupling, which typically leads to the broadening of molecular weight distribution of the synthesized polymers. The thermal, photophysical and electrochemical properties of the synthesized linear and star-shaped polymers were estimated.
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Method for Selection of New Primers for Identification of the Especially Dangerous Bacterium Acidovorax citrulli
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01.10.2018 |
Shneider Y.
Karimova E.
Smirnova I.
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Bulletin of Experimental Biology and Medicine |
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0 |
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© 2018, Springer Science+Business Media, LLC, part of Springer Nature. We propose a method for selection of new primers for identification of especially dangerous bacterium Acidovorax citrulli. A specific pair of new primers AC-1 F/R that can be used for detection and identification of A. citrulli was successfully tested. This opens up new possibilities for investigation of the role of this bacterium in the ecosystems.
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Advances in the Application of Modified Nucleotides in SELEX Technology
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01.10.2018 |
Antipova O.
Zavyalova E.
Golovin A.
Pavlova G.
Kopylov A.
Reshetnikov R.
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Biochemistry (Moscow) |
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2 |
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© 2018, Pleiades Publishing, Ltd. Aptamers are widely used as molecular recognition elements for detecting and blocking functional biological molecules. Since the common “alphabet” of DNA and RNA consists of only four letters, the chemical diversity of aptamers is less than the diversity of protein recognition elements built of 20 amino acids. Chemical modification of nucleotides enlarges the potential of DNA/RNA aptamers. This review describes the latest achievements in a variety of approaches to aptamers selection with an extended genetic alphabet.
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Large-scale production of stem cells utilizing microcarriers: A biomaterials engineering perspective from academic research to commercialized products
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01.10.2018 |
Tavassoli H.
Alhosseini S.
Tay A.
Chan P.
Weng Oh S.
Warkiani M.
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Biomaterials |
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9 |
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© 2018 Elsevier Ltd Human stem cells, including pluripotent, embryonic and mesenchymal, stem cells play pivotal roles in cell-based therapies. Over the past decades, various methods for expansion and differentiation of stem cells have been developed to satisfy the burgeoning clinical demands. One of the most widely endorsed technologies for producing large cell quantities is using microcarriers (MCs) in bioreactor culture systems. In this review, we focus on microcarriers properties that can manipulate the expansion and fate of stem cells. Here, we provide an overview of commercially available MCs and focus on novel stimulus responsive MCs controlled by temperature, pH and field changes. Different features of MCs including composition, surface coating, morphology, geometry/size, surface functionalization, charge and mechanical properties, and their cellular effects are also highlighted. We then conclude with current challenges and outlook on this promising technology.
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Heat-driven size reduction of biodegradable polyelectrolyte multilayer hollow capsules assembled on CaCO<inf>3</inf> template
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01.10.2018 |
Trushina D.
Bukreeva T.
Borodina T.
Belova D.
Belyakov S.
Antipina M.
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Colloids and Surfaces B: Biointerfaces |
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6 |
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© 2018 Elsevier B.V. Aiming to explore elevated temperatures as a tool for miniaturization of biodegradable polymer multilayer capsules, assembled on spherical vaterite micron- and submicron-sized particles, we subject the shells composed of dextran sulfate (DS) and poly-L-arginine (Parg) to a heat treatment. Changes of the capsule size are studied at various temperatures and ionic strengths of the continuous phase. Unlike some synthetic polymer multilayer shells (their response to heat treatment depends on the number of layers and their arrangement), the biodegradable Parg/DS capsules exhibit size reduction and profound compaction regardless of their initial size, number of polymer layers and polymer layer sequence. The capsule response to heat is stable at ionic strengths of the continuous phase not exceeding 0.1 M NaCl.
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Terahertz continuous-wave solid immersion imaging with spatial resolution beyond the Abbe limit
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13.08.2018 |
Chernomyrdin N.
Kucheryavenko A.
Kolontaeva G.
Komandin G.
Shchedrina M.
Spektor I.
Reshetov I.
Zaytsev K.
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Proceedings - International Conference Laser Optics 2018, ICLO 2018 |
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0 |
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© 2018 IEEE. We have proposed an approach to improve the resolution of terahertz (THz) imaging using the effect of solid immersion - i.e. a reduction in the dimensions of the electromagnetic beam caustic by its formation in a free space, behind the medium possessing high refractive index. We have designed a THz solid immersion lens (SIL) comprised of a polymer wide-aperture aspherical singlet and a crystalline truncated sphere mounted in front of the image plane. We have proposed an approach for the object handling at the focal plane of the THz SIL. We have combined numerical simulations and experimental studies to demonstrate the advanced 0.2λ spatial resolution of the proposed THz SIL - it is beyond the 0.5λ Abbe limit. Finally, we have assembled the continuous-wave THz SIL imaging system and applied it for studying various objects with sub-wavelength variations of structure and dielectric properties.
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Sub-wavelength-resolution imaging of biological tissues using THz solid immersion microscopy
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13.08.2018 |
Chernomyrdin N.
Kucheryavenko A.
Kolontaeva G.
Schadko A.
Beshplav S.
Malakhov K.
Komandin G.
Karasik V.
Spector I.
Tuchin V.
Zaytsev K.
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Proceedings - International Conference Laser Optics 2018, ICLO 2018 |
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0 |
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© 2018 IEEE. We have proposed a method of THz solid immersion microscopy, which yields imaging soft biological tissues with the sub-wavelength resolution up to 0.2-wavelengths. To achieve this advanced resolution, it employs a solid immersion phenomenon - i.e. a reduction in the dimensions of the THz beam caustic by its formation on a small distance behind the medium featuring high refractive index. We have assembled an experimental setup, which realizes the principles of the THz solid immersion microscopy, and proposed an approach for handling the soft tissue at the object plane. This setup uses a backward-wave oscillator, as a source of continuous-wave THz radiation, and a Golay cell, as a detector of the THz field intensity. We have examined the resolution of the THz solid immersion microscopy using both numerical simulations and experimental studies. Finally, in order to highlight the prospective of the proposed THz imaging modality, we have applied the experimental setup for imaging of representative examples of biological tissues.
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Atomic Structural Models of Fibrin Oligomers
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05.06.2018 |
Zhmurov A.
Protopopova A.
Litvinov R.
Zhukov P.
Weisel J.
Barsegov V.
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Structure |
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2 |
Ссылка
© 2018 Elsevier Ltd The space-filling fibrin network is a major part of clots and thrombi formed in blood. Fibrin polymerization starts when fibrinogen, a plasma protein, is proteolytically converted to fibrin, which self-assembles to form double-stranded protofibrils. When reaching a critical length, these intermediate species aggregate laterally to transform into fibers arranged into branched fibrin network. We combined multiscale modeling in silico with atomic force microscopy (AFM) imaging to reconstruct complete atomic models of double-stranded fibrin protofibrils with γ-γ crosslinking, A:a and B:b knob-hole bonds, and αC regions—all important structural determinants not resolved crystallographically. Structures of fibrin oligomers and protofibrils containing up to 19 monomers were successfully validated by quantitative comparison with high-resolution AFM images. We characterized the protofibril twisting, bending, kinking, and reversibility of A:a knob-hole bonds, and calculated hydrodynamic parameters of fibrin oligomers. Atomic structures of protofibrils provide a basis to understand mechanisms of early stages of fibrin polymerization. Zhmurov et al. used 27 relevant crystal structures to computationally reconstruct the full-atomic models of fibrin oligomers and protofibrils, which correlate with high-resolution atomic force microscopy images. The structures contain much valuable information for understanding the early stages of fibrin polymerization.
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