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Towards understanding the triggering of the malignant cell death in high-efficiency magneto-mechanical anticancer therapy / P. N. Semina, I. L. Isaev, S. K. Komogortsev [et al.] // J. Phys. D. - 2023. - Vol. 56, Is. 6. - Ст. 065401, DOI 10.1088/1361-6463/acb0dd. - Cited References: 146. - P N S, A S K, D E K, S P P, S V K acknowledge the support by the Ministry of Science and High Education of Russian Federation (Project No. FSRZ-2020-0008). Experimental analyses were funded by the Ministry of Science and Higher Education of the Russian Federation (Project FWES-2022-0005) – A S K, T N Z. The authors thank Dr S V Saikova for providing the TEM image in figure (b) . - ISSN 0022-3727. - ISSN 1361-6463
Кл.слова (ненормированные):
magnetic nanoparticle -- malignant cell membrane -- apoptosis -- anticancer therapy -- aptamer
Аннотация: The paper discusses schemes for the implementation of magneto-mechanical anticancer therapy and the most probable scenarios of damaging mechanical eﬀects on the membranes of malignant cells by targeted magnetic nanoparticles selectively bound to membrane mechanoreceptors employing aptamers. The conditions for selective triggering of the malignant cell apoptosis in a low-frequency non-heating alternating magnetic ﬁeld, corresponding to the exceeding threshold value of the force acting on the membrane and its mechanoreceptors, are established using a nanoparticle dynamic simulation. The requirements for the functionality of magnetic nanoparticles and their suitability for biomedical applications are analysed. Attention is paid to the possibility of the formation of magnetite nanoparticle aggregates in an external magnetic ﬁeld and their localization near tumor cell membranes. It is shown that the scenario involving the process of aggregation of magnetite nanoparticles provides a suﬃcient magneto-mechanical impact to achieve a therapeutic eﬀect. A possible explanation for the experimentally established fact of successful application of magneto-mechanical therapy using magnetite nanoparticles is presented, in which complete suppression of the Ehrlich carcinoma in an alternating magnetic ﬁeld as a response to a magnetome-chanical stimulus was demonstrated. This result conﬁrmed the possibility of using the method for high eﬃciency treatment of malignant neoplasms. The paper is provided with an extensive review of key publications and the state of art in this area.

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Держатели документа:
International Research Center of Spectroscopy and Quantum Chemistry—IRC SQC, Siberian Federal University, Krasnoyarsk 660041, Russia
Institute of Computational Modelling of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
L. V. Kirensky Institute of Physics, Federal Research Center KSC the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Siberian Federal University, Krasnoyarsk 660041, Russia
Tomsk State University, Tomsk 634050, Russia
Federal Siberian Research Clinical Center, Federal Medical Biological Agency of Russian Federation, Krasnoyarsk 660037, Russia

Доп.точки доступа:
Semina, P. N.; Семина, Полина Николаевна; Isaev, I. L.; Исаев, Иван Леонидович; Komogortsev, S. V.; Комогорцев, Сергей Викторович; Klyuchantsev, A. B.; Ключанцев, А. Б.; Kostyukov, A. S.; Blagodatova, A. V.; Khrennikov, D. E.; Kichkailo, A. S.; Кичкайло, Анна Сергеевна; Zamay, T. N.; Замай, Т. Н.; Lapin, I. N.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Polyutov, S. P.; Полютов, Сергей Петрович; Karpov, S. V.; Карпов, Сергей Васильевич
}
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The role of small-angle X-ray scattering and molecular simulations in 3D structure elucidation of a DNA aptamer-cancer cells magnetic separation agent / R. V. Moryachkov, D. Morozov, V. Mironov [et al.] // 4th International Baltic Conference on Magnetism (IBCM 2021) : Book of abstracts. - 2021. - P. 168. - Cited References: 2. - The reported study was funded by RFBR, project number 19-32-90266

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS

Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Morozov, D.; Mironov, V.; Shchugoreva, I.; Artyushenko, P. V.; Артюшенко, Полина Владимировна; Zamay, G. S.; Замай Г. С.; Molodenskiy, D. S.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Kichkailo, A.S.; Кичкайло, Анна Сергеевна; Sokolov, A. Е.; Соколов, Алексей Эдуардович; International Baltic Conference on Magnetism: focus on nanobiomedicine and smart materials(4 ; 2021 ; Aug. 29-Sept. 2 ; Svetlogorsk, Russia); Балтийский федеральный университет им. И. Канта
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    The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer / D. Morozov, V. Mironov, R. V. Moryachkov [et al.] // Mol. Ther. Nucl. Acids. - 2021. - Vol. 25. - P. 316-327, DOI 10.1016/j.omtn.2021.07.015. - Cited References: 84. - The research was performed using equipment of the Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University. The synchrotron SAXS data were collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany). A.S.K. is grateful to Aptamerlab LLC for the assistance in aptamer design and 3D structure analyses. We thank Ivan Lapin for his help with microscopic analyses. Microscopic analyses using Carl Zeiss LSM 800 were carried out at the Center for Bioassay, Nanotechnology and Nanomaterials Safety (“Biotest-Nano”) (Multiple-Access Center, Tomsk State University, Tomsk, Russia). D.M. also thanks the CSC-IT Center in Espoo, Finland, for providing computational resources. The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. R.V.M aknowledges Russian Foundation for Basic Research (project number 19-32-90266) for funding. D.G.F. acknowledges financial support by JSPS KAKENHI, grant number 19H02682. D.S.M. acknowledges financial support by BMBF grant number 16QK10A (SAS-BSOFT). Y.A.’s work at Argonne National Laboratory was supported by the US Department of Energy, Office of Science, under contract DE-AC02-06CH11357. D.M. received funding as a part of BioExcel CoE (https://bioexcel.eu/), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043) for funding . - ISSN 2162-2531
   Перевод заглавия: Роль малоуглового рентгеновского рассеяния и молекулярного моделирования в выснении трёхмерной структуры ДНК аптамера против рака лёгкого
Кл.слова (ненормированные):
aptamer -- oligonucleotide -- tertiary structure -- spatial structure -- lung adenocarcinoma -- small-angle X-ray scattering -- SAXS -- molecular dynamics -- fragment molecular orbital -- molecular simulations
Аннотация: Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

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Держатели документа:
Nanoscience Center and Department of Chemistry, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, 40014, Finland
Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk, 660022, Russian Federation
Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, 660041, Russian Federation
European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan
Computational Science Division, Argonne National Laboratory, Lemont, IL, United States

Доп.точки доступа:
Morozov, D.; Mironov, V.; Moryachkov, R. V.; Морячков, Роман Владимирович; Shchugoreva, I. A.; Artyushenko, P. V.; Zamay, G. S.; Kolovskaya, O. S.; Zamay, T. N.; Krat, A. V.; Molodenskiy, D. S.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Veprintsev, D. V.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zukov, R. A.; Berezovski, M. V.; Tomilin, F. N.; Томилин, Феликс Николаевич; Fedorov, D. G.; Alexeev, Y.; Kichkailo, A. S.
}
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The Ca2+-regulated photoprotein obelin as a tool for SELEX monitoring and DNA aptamer affinity evaluation / V. V. Krasitskaya, N. S. Goncharova, V. V. Biriukov [et al.] // Photochem. Photobiol. - 2020. - Vol. 96, Is. 5. - P. 1041-1046, DOI 10.1111/php.13274. - Cited References: 25. - This work has been supported by the Russian Foundation for Basic Research (RFBR) under the grant no 18-38-00531. . - ISSN 0031-8655. - ISSN 1751-1097

РУБ Biochemistry & Molecular Biology + Biophysics
Рубрики:
CARDIAC TROPONIN-I
   BIOLUMINESCENCE
   IMMUNOASSAY
   APTASENSOR
   DIAGNOSIS
Аннотация: Bioluminescent solid-phase analysis was proposed to monitor the selection process and to determine binding characteristics of the aptamer-target complexes during design and development of the specific aptamers. The assay involves Ca2+-regulated photoprotein obelin as a simple, sensitive and fast reporter. Applicability and the prospects of the approach were exemplified by identification of DNA aptamers to cardiac troponin I, a highly specific early biomarker for acute myocardial infarction. Two structurally different aptamers specific to various epitopes of troponin I were obtained and then tested in a model bioluminescent assay.

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Держатели документа:
Fed Res Ctr KSC SB RAS, Inst Biophys SB RAS, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Inst Chem Biol & Fundamental Med SB RAS, Novosibirsk, Russia.
Fed Res Ctr KSC SB RAS, Kirensky Inst Phys, Krasnoyarsk, Russia.

Доп.точки доступа:
Krasitskaya, V. V.; Goncharova, N. S.; Biriukov, V. V.; Bashmakova, E. E.; Kabilov, M. R.; Baykov, I. K.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Frank, L. A.; Russian Foundation for Basic Research (RFBR)Russian Foundation for Basic Research (RFBR) [18-38-00531]
}
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The antitumor effect of magnetic nanodisks and DNA aptamer conjugates / P. D. Kim [et al.] // Dokl. Biochem. Biophys. - 2016. - Vol. 466, Is. 1. - P. 66-69, DOI 10.1134/S1607672916010154. - Cited References:7. - This work was supported by the Russian Science Foundation (project no. 14-15-00805). . - ISSN 1607-6729. - ISSN 1608-3091

РУБ Biochemistry & Molecular Biology + Biophysics
Рубрики:
Nanoparticles
Cells
Аннотация: Here we describe a method of forming large arrays (up to 109 pieces) of free magnetic Ni-nanodisks 50 nm thick coated on both sides with layers of 5 nm thick Au. The antitumor effect of the magnetic nickel gold-coated nanodisks and DNA aptamer conjugates was evaluated in vivo and in vitro. Under the influence of rotating magnetic field, the studied nanodisks can cause the death of Ehrlich ascites carcinoma cells.

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Публикация на русском языке Противоопухолевый эффект конъюгатов магнитных нанодисков с ДНК-аптамерами [Текст] / П. Д. Ким [и др.] // Докл. Акад. наук : Наука, 2016. - Т. 466 № 5. - С. 616-619

Держатели документа:
Russian Acad Sci, Siberian Branch, Krasnoyarsk Res Ctr, Krasnoyarsk 660036, Russia.
Voinoyasenetskii State Med Univ, Minist Hlth Russian Federat, Ul Partizana Zheleznyaka 1, Krasnoyarsk 660022, Krasnoyarsk Kra, Russia.
Siberian Fed Univ, Svobodnyi Pr 79, Krasnoyarsk 660041, Russia.
Russian Acad Sci, Siberian Branch, Inst Chem & Chem Technol, Krasnoyarsk, Russia.
Russian Acad Sci, Siberian Branch, Inst Semicond Phys, Pr Akad Lavrenteva 13, Novosibirsk 630090, Russia.
Russian Acad Sci, Siberian Branch, Kirenskii Inst Phys, Krasnoyarsk 660036, Russia.
Astafev Krasnoyarsk State Pedag Univ, Ul A Lebedevoi 89, Krasnoyarsk 660049, Russia.

Доп.точки доступа:
Kim, P. D.; Ким, Пётр Дементьевич; Zamay, S. S.; Замай С. С.; Zamay, T. N.; Prokopenko, V. S.; Kolovskaya, O. S.; Zamay, G. S.; Princ, V. Ya.; Seleznev, V. A.; Komonov, A. I.; Spivak, E. A.; Rudenko, R. Y.; Руденко, Роман Юрьевич; Dubinina, A. V.; Komarov, A. V.; Denisenko, V. V.; Komarova, M. A.; Sokolov, A. E.; Соколов, Алексей Эдуардович; Narodov, A. A.; Zjivaev, V. P.; Zamay, A. S.; Russian Science Foundation [14-15-00805]
}
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    Small-angle scattering applications to the analysis of aptamer structure and conformational changes / R. V. Moryachkov, V. N. Zabluda, A. N. Berlina [et al.] // AIP Conference Proceedings : book of abstracts. - 2020. - Vol. 2299. - Ст. 040002 ; Synchrotron and free electron laser radiation: generation and application (SFR-2020). - Novosibirsk. - P. 45-46, DOI 10.1063/5.0030394. - Cited References: 40. - The reported study was funded by RFBR, project number 19-32-90266 (investigation of the structure changes). This work was financially supported by Russian Science Foundation (project # 19-44-02020, obtaining of the complexes of aptamer and lead ions). We acknowledge the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities (experiment #MX-2039) and we would like to thank Bart Van Laer for assistance in using beamline BM29
   Перевод заглавия: Использование малоуглового рассеяния для анализа структуры и конформационных изменений аптамеров
Аннотация: Aptamers, structured single-chain oligonucleotides, are promising tools for detection of a wide variety of compounds, from high to low molecular weight, and affecting on them. The aptamers that are most affine for a detectable compound are selected from the libraries of random sequences by the SELEX method (Systematic evolution of ligands by exponential enrichment). The reason why aptamers deserve a special consideration lies in the specific features of their structure and the mechanism of binding to their target. Aptamers can be exploited for metal-ion sensing, biosensing, drug delivery and other functions. To apply the oligonucleotides in the medicine, ecology, food production, agriculture, etc., we need to know how the aptamers bind to their targets, how they change their conformation upon specific binding and how the environment influences on the affinity of aptamers. Small-Angle X-ray scattering showed that the interaction of aptamers with heavy metal and other divalent ions proceeds according to different mechanisms, and the aptamers used undergo different conformational changes.

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Держатели документа:
Kirensky Institute of Physics, Akademgorodok 50, bld. 38, Krasnoyarsk, 660012, Russian Federation
Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50, Krasnoyarsk, 660012, Russian Federation
A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation
National Research Center “Kurchatov Institute”, Akademika Kurchatova pl. 1, Moscow, 123182, Russian Federation

Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Berlina, A. N.; Peters, G. S.; Kichkailo, A. S.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Internetional Conference on Synchrotron and Free Electron Laser Radiation: Generation and Application(2020 ; 13-16 July ; Novosibirsk)

}
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Small-Angle scattering applications to the analysis of aptamer structure and conformational changes / R. V. Moryachkov, V. N. Zabluda, A. Е. Sokolov [et al.] // Molecular Therapy - Nucleic Acids : book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P. 4

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Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Shchugoreva, I. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Peters, G.; Петерс Георгий; Spiridonova, V. A.; Спиридонова В. А.; Aptamers in Russia, international conference(1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk)
}
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Small angle X-ray scattering on RE31 aptamer / R. Moryachkov [et al.] // VI Euro-Asian Symposium "Trends in MAGnetism" (EASTMAG-2016) : abstracts / ed.: O. A. Maksimova, R. D. Ivantsov. - Krasnoyarsk : KIP RAS SB, 2016. - Ст. P12.3. - P. 559-560. - References: 3. - The work was supported by Ministry of education and science of Russia (Agreement No.14.607.21.0104 (RFMEFI60714X0104)) . - ISBN 978-5-904603-06-9
Кл.слова (ненормированные):
SAXS -- aptamer -- biomolecules structure -- ATSAS -- DAMMIN

Доп.точки доступа:
Moryachkov, R.; Spiridonova, V. A.; Спиридонова В. А.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G.; Петерс Георгий; Sokolov, A. E.; Соколов, Алексей Эдуардович; Euro-Asian Symposium "Trends in MAGnetism"(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); "Trends in MAGnetism", Euro-Asian Symposium(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); Институт физики им. Л.В. Киренского Сибирского отделения РАН

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Small angle X-ray scattering and atomic structure of aptamer biomolecules / R. Moryachkov [et al.] // Int. workshop on actual probl. of cond. matt. phys. : Program. Book of abstracts / Fed. Res. Center KSC SB RAS, Kirensky Inst. of phys., Sib. Fed. Univ. - Krasnoyarsk, 2017. - P. 14-15

Материалы совещания

Доп.точки доступа:
Ovchinnikov, S. G. \предс. прогр. ком.\; Овчинников, Сергей Геннадьевич; Moryachkov, R.; Tomilin, F. N.; Томилин, Феликс Николаевич; Shchugoreva, I.; Spiridonova, V.; Peters, G.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Federal Research Center KSC SB RAS; Kirensky Institute of Physics; Siberian Federal Univercity; International workshop on actual problems of condensed matter physics(27 March - 1 Apr. 2017 ; Krasnoyarsk / Cheremushki)
}
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10.

Preparation and properties of magnetic composites γ-Fe2O3/SiO2/aptamer(FAS9) for magnetic resonance hyperthermia / S. V. Stolyar, O. A. Li, E. D. Nikolaeva [et al.] // Phys. Met. Metallogr. - 2023. - Vol. 124, Is. 14. - P. 1689-1696, DOI 10.1134/S0031918X23601439. - Cited References: 27 . - ISSN 0031-918X. - ISSN 1555-6190
Кл.слова (ненормированные):
ferromagnetic resonance -- magnetic hyperthermia -- maghemite
Аннотация: Powders of maghemite γ-Fe2O3 with an average diameter of 8 nm, γ-Fe2O3/SiO2 composites with an agglomerate diameter of about 50 nm and a size of interspersed γ-Fe2O3 particles of 6 nm, and γ‑Fe2O3/SiO2/aptamer(FAS9) composites were synthesized by chemical deposition. Mössbauer spectra were measured, the static and dynamic magnetic properties of the powders were studied, and the coercive force was determined, which decreases from 14 Oe for γ-Fe2O3 powders to 3 Oe for the γ-Fe2O3/SiO2 composite. It is shown that the particle blocking temperature is close to room temperature. The increment of temperature of the powders was measured in the ferromagnetic resonance mode; the temperature of the Fe2O3/SiO2 composite (ΔT ≈ 16°C) turned out to be higher than that of the pure γ-Fe2O3 powder (ΔT ≈ 10°C). It has been experimentally shown that temperature increment ΔT is proportional to the square of the microwave field amplitude. It has been shown that the composition γ-Fe2O3/SiO2/aptamer FAS9 is able to effectively bind to tumor cells, and FMR hyperthermia leads to a decrease in the viability of tumor cells.

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Federal Research Center, Krasnoyarsk Science Center, Siberian Branch of the Russian Academy of Sciences, 660036, Krasnoyarsk, Russia
Siberian Federal University, 660041, Krasnoyarsk, Russia
Kirensky Institute of Physics, Federal Research Center KSC, Siberian Branch Russian Academy of Sciences, 660036, Krasnoyarsk, Russia

Доп.точки доступа:
Stolyar, S. V.; Столяр, Сергей Викторович; Li, O. A.; Nikolaeva, E. D.; Vorotynov, A. M.; Воротынов, Александр Михайлович; Velikanov, D. A.; Великанов, Дмитрий Анатольевич; Knyazev, Yu. V.; Князев, Юрий Владимирович; Bayukov, O. A.; Баюков, Олег Артемьевич; Iskhakov, R. S.; Исхаков, Рауф Садыкович; Kryukova, O. V.; Pyankov, V. F.; Volochaev, M. N.; Волочаев, Михаил Николаевич; Mokhov, A. A.
}
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