Публикации
| 53 | O. Mikhailovskii, Y. Xue, N.R. Skrynnikov: Modeling a unit cell: Crystallographic refinement procedure using the biomolecular MD simulation platform Amber, IUCrJ. 9 (2022). |
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| 52 | Majhi D., Kharkov B.B. et al.: Sign determination of dipolar couplings in liquid crystals by off-magic-angle sample spinning // CHEMICAL PHYSICS LETTERS. 2021. Vol. 781. |
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| 51 | Sheedlo M.J. c: Insights into Ubiquitin Product Release in Hydrolysis Catalyzed by the Bacterial Deubiquitinase SdeA // BIOCHEMISTRY. 2021. Vol. 60, № 8. P. 584–596. |
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| 50 | Rabdano S.O. et al.: Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA // ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2021. Vol. 60, № 12. P. 6480–6487. |
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| 49 | Kharkov B.B. et al.: The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils // ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2021. Vol. 60, № 28. P. 15445–15451. |
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| 48 | Skrynnikov N.R.: Toward a proper interpretation of hydrogen exchange data in disordered proteins // BIOPHYSICAL JOURNAL. 2021. Vol. 120, № 18. P. 3855–3856. |
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| 47 | Case D.A. et al.: AMBER 2021. San Francisco: University of California, 2021. 959 p. |
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| 46 | Bolgov A. et al. : Crystal structure of the SH3 domain of growth factor receptor-bound protein 2 // Acta Crystallographica Section F — Structural Biology Communications. 2020. Vol. 76, № 6. P. 263–270. |
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| 45 | Rabdano S.O. et al.: NMR Relaxation of Nuclei of Buffer as a Probe for Monitoring Protein Solutions Including Aggregation Processes // Applied Magnetic Resonance. 2020. |
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| 44 | Cabal C. et al.: Assessment of Contribution of Curie-Spin Mechanism in Proton Relaxation During Aggregation Process of Hemoglobin S // Applied Magnetic Resonance. 2020. |
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| 43 | Case D.A. et al.: AMBER 2020. San Francisco:University of California, 2020. 918 p. |
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| 42 | Izmailov, S. A., Rabdano, S. O., Hasanbasri, Z., Podkorytov, I. S., Saxena, S. & Skrynnikov, N. R.: Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories. Sci Rep 10, 957 (2020). |
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| 41 | D.A. Luzik, O.N. Rogacheva, S.A. Izmailov, M.I. Indeykina, A.S. Kononikhin, N.R. Skrynnikov: Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2, SCIENTIFIC REPORTS. 9 (2019) Article number: 20219. |
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| 40 | Titov, A. A., Filippov, O. A., Smol’yakov, A. F., Godovikov, I. A., Shakirova, J. R., Tunik, S. P., Podkorytov, I. S. & Shubina, E. S.: Luminescent Complexes of the Trinuclear Silver(I) and Copper(I) Pyrazolates Supported with Bis(diphenylphosphino)methane. Inorg. Chem. 58, 8645–8656 (2019). |
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| 39 | Podkorytov, I. S., Cherkasova, T. G., Kayfadzhyan, E. A. & Varshavsky, Yu. S.: Multiplet-Matched Filtering of 103Rh Signal Using Information Contained in 31P Spectrum of AA′XX′ 31P–103Rh Spin System. Appl Magn Reson 50, 563–568 (2019). |
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| 38 | Kharkov, B., Duan, X., Tovar, E. S., Canary, J. W. & Jerschow, A.: Singlet excitation in the intermediate magnetic equivalence regime and field-dependent study of singlet–triplet leakage. Physical Chemistry Chemical Physics 21, 2595–2600 (2019). |
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| 37 | Varshavsky, Yu. S., Cherkasova, T. G., Galding, M. R., Korlyukov, A. A., Podkorytov, I. S., Gindin, V. A., Smirnov, S. N., Mazur, A. S. & Rubaylo, A. I.: 13C NMR spectrum of crystalline [Rh(Acac) (CO)2]: A contribution to the discussion on [Rh(Acac) (CO)2] molecular structure in the solid state. Journal of Organometallic Chemistry 874, 70–73 (2018). |
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| 36 | Kharkov, B., Strouk, L., Skinner, T. E. & Jerschow, A.: Optimal control RF pulses for excitation and suppression of NMR signals in a conductive medium. The Journal of Chemical Physics 149, 034201 (2018). |
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| 35 | Kaempf, K., Izmailov, S. A., Rabdano, S. O., Groves, A. T., Podkorytov, I. S. & Skrynnikov, N. R.: What Drives N-15 Spin Relaxation in Disordered Proteins? Combined NMR/MD Study of the H4 Histone Tail. Biophysical Journal 115, 2348–2367 (2018). |
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| 34 | Jackalin, L., Kharkov, B. B., Komolkin, A. V. et al.: Experimental strategies for 13 C– 15 N dipolar NMR spectroscopy in liquid crystals at the natural isotopic abundance. Physical Chemistry Chemical Physics 20, 22187–22196 (2018). |
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| 33 | Dai, J., Kharkov, B. et al.: Molecular and Segmental Orientational Order in a Smectic Mesophase of a Thermotropic Ionic Liquid Crystal. Crystals 9, 18 (2018). |
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| 32 | Rogacheva, O. N., Izmailov, S. A., Slipchenko, L. V. & Skrynnikov, N. R.: Non-native disulfide bridges in protein-peptide complex and in protein homodimers trigger unfolding and aggregation. The FEBS Journal 284 (Suppl. 1), 311 (2017). |
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| 31 | Rogacheva, O. N., Izmailov, S. A., Slipchenko, L. V. & Skrynnikov, N. R.: A new structural arrangement in proteins involving lysine NH3 + group and carbonyl. Scientific Reports 7, 16402 (2017). |
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| 30 | Rabdano, S., Podkorytov, I., Luzik, D. & Skrynnikov, N.: Characterizing the size of protein aggregate particles using a combination of NMR diffusion measurements and dynamic light scattering: case study of RRM2 domain from protein TDP-43. The FEBS Journal 284 (Suppl. 1), 212 (2017). |
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| 29 | Rabdano, S. O., Izmailov, S. A., Luzik, D. A., Groves, A., Podkorytov, I. S. & Skrynnikov, N. R.: Onset of disorder and protein aggregation due to oxidation-induced intermolecular disulfide bonds: case study of RRM2 domain from TDP-43. Scientific Reports 7, 11161 (2017). |
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| 28 | Podkorytov, I. S., Belousov, M., Bondarev, S., Kaempf, K., Zhouravleva, G., Skrynnikov, N. R et al.: Detection of flexible portion of protein chain in Sup35NM amyloid fibrils by means of diffusion-filtered NMR experiment. The FEBS Journal 284 (Suppl. 1), 215 (2017). |
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| 27 | Luzik, D. A., Rabdano, S. O. & Skrynnikov, N. R.: Non-native disulfide bridges in protein-peptide complex and in protein homodimers trigger unfolding and aggregation. The FEBS Journal 284 (Suppl. 1), 212 (2017). |
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| 26 | Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse, J., Shilova, A., Xue, Y., Yuwen, T., Coquelle, N., Colletier, J.-P., Skrynnikov, N. R. & Schanda, P.: Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications 8, (2017). |
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| 25 | Tyuryaeva, I. I., Lyublinskaya, O. G., Podkorytov, I. S. & Skrynnikov, N. R.: Origin of anti-tumor activity of the cysteine-containing GO peptides and further optimization of their cytotoxic properties. Scientific Reports 7, 40217 (2017). |
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| 24 | Solomatina, A. I., Chelushkin, P. S., Krupenya, D. V., Podkorytov, I. S., Artamonova, T. O., Sizov, V. V., Melnikov, A. S., Gurzhiy, V. V., Koshel, E. I., Shcheslavskiy, V. I., Tunik, S. P.: Coordination to Imidazole Ring Switches on Phosphorescence of Platinum Cyclometalated Complexes: The Route to Selective Labeling of Peptides and Proteins via Histidine Residues. Bioconjugate Chem. (2016). |
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| 23 | Rogacheva, O. N., Izmailov, S. A., Kurauskas, V., Shilova, A., Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., Hessel, A., Woodhouse, J., Mikhailovskii, O., Willbold, D., Colletier, J., Skrynnikov, N. R., Schanda, P.: Dynamics in Protein Crystals: Insights from MD Simulations Complement New Solid-State NMR and X-Ray Data. FEBS Journal 283, 237 (2016). |
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| 22 | Yuwen, T., Xue, Y., Skrynnikov, N. R.: Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos. Biochemistry 55 (12), 1784–1800 (2016). |
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| 21 | Rabdano, S. O., Podkorytov, I. S., Izmailov, S. A., Pivovarova, Y. V., Yakimov, A. P., Yuwen, T., Groves, A., Skrynnikov, N. R.: Loss of Protein Stability due to Formation of Intermolecular Disulfide Bonds under the Effect of Oxidative Stress: Case Study of the RRM2 Domain from Neuropathological Protein TDP-43. Biophysical Journal 110 (3), 210a (2016). |
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| 20 | Izmailov, S. A., Podkorytov, I. S., Skrynnikov, N. R.: MD Modeling of Oxidative Folding in Peptides and Proteins. Biophysical Journal 110 (3), 644a–645a (2016). |
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| 19 | Ledovskaya, M. S., Molchanov, A. P., Kostikov, R. R., Panikorovsky, T. L., Gurzhiy, V. V., Ryazantsev, M. N., Boitsov, V. M., Stepakov, A. V.: Anthracene-Fused isoxazolopyrrolo[2,1-A]isoquinolines via an Endocyclic N-Acyliminium Ion Cyclization: A Joint Experimental and Theoretical Study. Tetrahedron 72 (32), 4827–4834 (2016). |
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| 18 | Struts, A. V., Barmasov, A. V., Brown, M. F.: Spectral Methods for Study of the G-Protein-Coupled Receptor Rhodopsin. II. Magnetic Resonance Methods. Opt. Spectrosc. 120 (2), 286–293 (2016). |
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| 17 | Xu, X., Struts, A. V., Kumar Giri, A., Molugu, T. R., Guruge, C., Faylough, S., Nascimento, C. L., Nesnas, N., Hruby, V. J., Brown, M. F.: Dynamics of Methyl Groups in Membrane Proteins Studied by Deterium Solid State NMR Relaxation. Biophysical Journal 110 (3), 73a (2016). |
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| 16 | Struts, A. V., Xu, X., Molugu, T. R., Pitman, M. C., Faylough, S., Guruge, C., Nascimento, C., Nesnas, N., Brown, M. F.: Retinal Chromophore Structure in Meta-II Rhodopsin Revealed by Solid-State 2H NMR and Molecular Modeling. Biophysical Journal 110 (3), 229a–230a (2016). |
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| 15 | Perera, S. M. D. C., Shrestha, U., Bhowmik, D., Chawla, U., Struts, A. V., Chu, X., Brown, M. F.: Neutron Scattering Reveals Protein Fluctuations in GPCR Activation. Biophysical Journal 110 (3), 228a–229a (2016). |
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| 14 | Chawla, U., Perera, S. M. D. C., Struts, A. V., Pitman, M. C., Brown, M. F.: Hydration Mediated G-Protein-Coupled Receptor Activation. Biophysical Journal 110 (3), 83a (2016). |
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| 13 | Smekalova, T. N., Yatsishina, E. B., Garipov, A. S., Pasumanskii, A. E., Ketsko, R. S., Chudin, A. V.: Natural Science Methods in Field Archaeology, with the Case Study of Crimea. Crystallogr. Rep. 61 (4), 533–542 (2016). |
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| 12 | Shmyreva, A. A., Safdari, M., Furó, I. et al.: NMR Longitudinal Relaxation Enhancement in Metal Halides by Heteronuclear Polarization Exchange during Magic-Angle Spinning. The Journal of Chemical Physics 144 (22), 224201 (2016). |
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| 11 | Kharkov, B. B., Chizhik, V. I. et al.: Broadband Cross-Polarization-Based Heteronuclear Dipolar Recoupling for Structural and Dynamic NMR Studies of Rigid and Soft Solids. The Journal of Chemical Physics 144 (3), 34201 (2016). |
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| 10 | Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., Mikhailovskii, O., Willbold, D., Colletier, J.-P., Skrynnikov, N. R., Schanda, P.: Observing the Overall Rocking Motion of a Protein in a Crystal. Nature Communications 6, 8361 (2015). |
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| 9 | Abrahamsson, C., Nordstierna, L., Nordin, M., et al.: Magnetic orientation of nontronite clay in aqueous dispersions and its effect on water diffusion. Journal of Colloid and Interface Science 437, 205–210 (2015). |
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| 8 | Gerts, E. D., Komolkin, A. V., Burmistrov, V. A., Alexandriysky, V. V. et al.: Comparative study of local structure of two cyanobiphenyl liquid crystals by molecular dynamics method. The Journal of Chemical Physics 141, 074503 (2014). |
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| 7 | Kharkov, B. B., Corkery, R. W. et al.: Phase Transitions and Chain Dynamics of Surfactants Intercalated into the Galleries of Naturally Occurring Clay Mineral Magadiite. Langmuir 30, 7859–7866 (2014). |
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| 6 | Xue, Y. & Skrynnikov, N. R.: Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics: Ensemble MD Simulations. Protein Science 23, 488–507 (2014). |
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| 5 | Yuwen, T. & Skrynnikov, N. R.: CP-HISQC: a better version of HSQC experiment for intrinsically disordered proteins under physiological conditions. Journal of Biomolecular NMR 58, 175–192 (2014). |
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| 4 | Xu, X., Struts, A. V. & Brown, M. F.: Generalized Model-Free Analysis of Nuclear Spin Relaxation Experiments. eMagRes, 2014, Vol 3: 275–286. |
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| 3 | Brown, M. F. & Struts, A. V.: Retinal in Rhodopsin Activation Viewed by Solid-State 2H NMR Spectroscopy. In New Developments in NMR, F. Separovic, and A. Naito, eds. (Cambridge: Royal Society of Chemistry), 320–352 (2014). |
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| 2 | Kharkov, B. B., Chizhik, V. I. et al.: Probing Molecular Mobility in Nanostructured Composites by Heteronuclear Dipolar NMR Spectroscopy. The Journal of Physical Chemistry C 118, 28308–28313 (2014). |
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| 1 | Xue, Y., Yuwen, T., Zhu, F. & Skrynnikov, N. R.: Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets. 1. NMR and MD Characterization of the Complex between the c-Crk N-SH3 Domain and the Peptide Sos. Biochemistry 53, 6473–6495 (2014). |
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Тезисы
| Debashis Majhi, Jing Dai, Boris B. Kharkov, Andrei V. Komolkin et al.: Ionic liquid crystals studied by solid‑state NMR spectroscopy // Magnetic resonance and its applications. Spinus-2021. Proceedings. Saint-Petersburg State University, 2021. P. 142. |
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| Salikov V.A., Skrynnikov N.R., Podkorytov I.S.: Improved Processing Scheme for Diffusion NMR Data Implemented in Web Server DDfit // Modern development of magnetic resonance 2021. Kazan, 2021. P. 26. |
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| O. O. Lebedenko, S. A. Izmailov, V. A. Salikov, N. R. Skrynnikov: Validating MD Models of Disordered Proteins Using NMR Data on Translational Diffusion // Modern development of magnetic resonance 2021. Kazan, 2021. P. 25. |
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| Kharkov B.B. et al.: The Role of Rotation in Diffusion NMR Experiments on Supramolecular Assemblies // Modern development of magnetic resonance 2021. Kazan, 2021. P. 21. |
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| Izmailov S.A. et al. : Structural and Dynamic Origins of ESR Lineshapes in Spin-Labeled GB1 Domain: the Insights from Experiments and Spin Dynamics Simulations Based on MD Trajectories // Modern development of magnetic resonance 2021. Kazan, 2021. P. 21. |
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| Lebedenko O. et al. : How Accurate are Pre-Derived Distances? Combined MD and Experimental Study of Spin-Labeled GB1 Domain // BIOPHYSICAL JOURNAL. 2021. Vol. 120, № 3, 1. P. 76A-77A. |
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| Lebedenko O.O. et al.: Benchmarking MD Models of Disordered Proteins using NMR Data on Translational Diffusion // BIOPHYSICAL JOURNAL. 2021. Vol. 120, № 3, 1. P. 310A. |
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| Luzik D., Rogacheva O., Skrynnikov N.: How Effective are Retro-Inverso Peptides? Insights from MD Supported by Paramagnetic NMR Data // BIOPHYSICAL JOURNAL. 2021. Vol. 120, № 3, 1. P. 81A. |
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| Salikov V. A. , Podkorytov I. S. , Kharkov B. B. , Luzik D. A. , Matiiv A. B. , Bondarev S. A. ; Skrynnikov N. R.: Diffusion NMR Measurements: What can we Learn about the Compactness of Disordered Proteins? // BIOPHYSICAL JOURNAL. 2021. Vol. 120, № 3, 1. P. 311A. |
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| Rabdano S.O. et al.: The NMR Relaxation of Solvent Nuclei for Monitoring Protein Aggregation // Magnetic resonance and its applications. Spinus-2020. Proceedings. Saint-Petersburg State University, 2020. P. 130. |
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| Rogacheva O. et al.: Parallel bias metadynamics and sketch-map dimensionality reduction as powerful tools to explore free energy landscapes of intrinsically disordered peptides // Bioinformatics of genome regulation and structure/systems biology (BGRS/SB-2020). Abstracts. Novosibirsk, Russia, 2020. P. 188. |
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