Computational simulation and model of a generalized prototype of an ornamental root
ilustraciones, fotografías, graficas
- Autores:
-
Moreno Chaparro, Daniela
- Tipo de recurso:
- Fecha de publicación:
- 2022
- Institución:
- Universidad Nacional de Colombia
- Repositorio:
- Universidad Nacional de Colombia
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.unal.edu.co:unal/81727
- Palabra clave:
- 620 - Ingeniería y operaciones afines::629 - Otras ramas de la ingeniería
Biological models
Plant physiology
Modelos biológicos
Fisiología vegetal
Growth algorithm
Root architecture
Growth plant model
Algoritmo de crecimiento
Arquitectura de raíz
Modelo de crecimiento de plantas
- Rights
- openAccess
- License
- Atribución-NoComercial-CompartirIgual 4.0 Internacional
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Universidad Nacional de Colombia |
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|
dc.title.eng.fl_str_mv |
Computational simulation and model of a generalized prototype of an ornamental root |
dc.title.translated.spa.fl_str_mv |
Simulación y modelo computacional de un prototipo de raíz ornamental generalizada |
title |
Computational simulation and model of a generalized prototype of an ornamental root |
spellingShingle |
Computational simulation and model of a generalized prototype of an ornamental root 620 - Ingeniería y operaciones afines::629 - Otras ramas de la ingeniería Biological models Plant physiology Modelos biológicos Fisiología vegetal Growth algorithm Root architecture Growth plant model Algoritmo de crecimiento Arquitectura de raíz Modelo de crecimiento de plantas |
title_short |
Computational simulation and model of a generalized prototype of an ornamental root |
title_full |
Computational simulation and model of a generalized prototype of an ornamental root |
title_fullStr |
Computational simulation and model of a generalized prototype of an ornamental root |
title_full_unstemmed |
Computational simulation and model of a generalized prototype of an ornamental root |
title_sort |
Computational simulation and model of a generalized prototype of an ornamental root |
dc.creator.fl_str_mv |
Moreno Chaparro, Daniela |
dc.contributor.advisor.none.fl_str_mv |
Garzón Alvarado, Diego Alexander Vargas Silva, Gustavo |
dc.contributor.author.none.fl_str_mv |
Moreno Chaparro, Daniela |
dc.contributor.researchgroup.spa.fl_str_mv |
Gnum Grupo de Modelado y Métodos Numericos en Ingeniería |
dc.subject.ddc.spa.fl_str_mv |
620 - Ingeniería y operaciones afines::629 - Otras ramas de la ingeniería |
topic |
620 - Ingeniería y operaciones afines::629 - Otras ramas de la ingeniería Biological models Plant physiology Modelos biológicos Fisiología vegetal Growth algorithm Root architecture Growth plant model Algoritmo de crecimiento Arquitectura de raíz Modelo de crecimiento de plantas |
dc.subject.lemb.eng.fl_str_mv |
Biological models Plant physiology |
dc.subject.lemb.spa.fl_str_mv |
Modelos biológicos Fisiología vegetal |
dc.subject.proposal.eng.fl_str_mv |
Growth algorithm Root architecture Growth plant model |
dc.subject.proposal.spa.fl_str_mv |
Algoritmo de crecimiento Arquitectura de raíz Modelo de crecimiento de plantas |
description |
ilustraciones, fotografías, graficas |
publishDate |
2022 |
dc.date.accessioned.none.fl_str_mv |
2022-07-22T14:09:28Z |
dc.date.available.none.fl_str_mv |
2022-07-22T14:09:28Z |
dc.date.issued.none.fl_str_mv |
2022-07 |
dc.type.spa.fl_str_mv |
Trabajo de grado - Maestría |
dc.type.driver.spa.fl_str_mv |
info:eu-repo/semantics/masterThesis |
dc.type.version.spa.fl_str_mv |
info:eu-repo/semantics/acceptedVersion |
dc.type.content.spa.fl_str_mv |
Text |
dc.type.redcol.spa.fl_str_mv |
http://purl.org/redcol/resource_type/TM |
status_str |
acceptedVersion |
dc.identifier.uri.none.fl_str_mv |
https://repositorio.unal.edu.co/handle/unal/81727 |
dc.identifier.instname.spa.fl_str_mv |
Universidad Nacional de Colombia |
dc.identifier.reponame.spa.fl_str_mv |
Repositorio Institucional Universidad Nacional de Colombia |
dc.identifier.repourl.spa.fl_str_mv |
https://repositorio.unal.edu.co/ |
url |
https://repositorio.unal.edu.co/handle/unal/81727 https://repositorio.unal.edu.co/ |
identifier_str_mv |
Universidad Nacional de Colombia Repositorio Institucional Universidad Nacional de Colombia |
dc.language.iso.spa.fl_str_mv |
eng |
language |
eng |
dc.relation.references.spa.fl_str_mv |
Adu, M. O., Yawson, D. O., Bennett, M. J., Broadley, M. R., Dupuy, L. X., and White, P. J. (2017). A scanner-based rhizobox system enabling the quantification of root system development and response of brassica rapa seedlings to external p availability. Plant Root, 11, 16–32. https://doi.org/10.3117/plantroot.11.16. Aziz, A. A., Lim, K. B., Rahman, E. K. A., Nurmawati, M. H., & Zuruzi, A. S. (2020). Agar with embedded channels to study root growth. Scientific Reports, 10(1), 1-12 Bentley, L. P., Stegen, J. C., Savage, V. M., Smith, D. D., von Allmen, E. I., Sperry, J. S., and Enquist, B. J. (2013). An empirical assessment of tree branching networks and implications for plant allometric scaling models. Ecology letters, 16(8), 1069-1078. https://doi.org/10.1111/ele.12127. Bodner, G., Alsalem, M., Nakhforoosh, A., Arnold, T., and Leitner, D. (2017). RGB and spectral root imaging for plant phenotyping and physiological research: Experimental setup and imaging protocols. Journal of Visualized Experiments, 2017(126). https://doi.org/10.3791/56251. Bodner, G., Leitner, D., Nakhforoosh, A., Sobotik, M., Moder, K., and Kaul, H. P. (2013). A statistical approach to root system classification. Frontiers in Plant Science, 4(AUG). https://doi.org/10.3389/fpls.2013.00292. Boudon, F., Chopard, J., Ali, O., Gilles, B., Hamant, O., Boudaoud, A., .and Godin, C. (2015). A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution. PLoS Comput Biol, 11(1), e1003950. https://doi.org/10.1371/journal.pcbi.1003950. Boyer, J. S., Silk, W. K., & Watt, M. (2010). Path of water for root growth. Functional Plant Biology, 37(12), 1105-1116. Bouma, T. J., Nielsen, K. L., & Koutstaal, B. A. S. (2000). Sample preparation and scanning protocol for computerised analysis of root length and diameter. Plant and soil, 218(1), 185-196. Cannon, W. A. (1949). A tentative classification of root systems. Ecology, 542-548. https://doi.org/10.2307/1932458 Clark, L. J., Whalley, W. R., and Barraclough, P. B. (2003). How do roots penetrate strong soil? Plant and Soil (Vol. 255). https://doi.org/10.1007/978-94-017-2923-9 10. Courne`de, P. H., Kang, M. Z., Mathieu, A., Barczi, J. F., Yan, H. P., Hu, B. G., and De Reffye, P. (2006). Structural factorization of plants to compute their functional and architectural growth. Simulation, 82(7), 427-438. https://doi.org/10.1177/0037549706069341 de Moraes, M. T., Bengough, A. G., Debiasi, H., Franchini, J. C., Levien, R., Schnepf, A., and Leitner, D. (2018). Mechanistic framework to link root growth models with weather and soil physical properties, including example applications to soybean growth in Brazil. Plant and Soil, 428(1–2), 67–92. https://doi.org/10.1007/s11104-018-3656-z Doussan, C., Page`s, L., and Pierret, A. (2009). Soil exploration and resource acquisition by plant roots: An architectural and modelling point of view. In Sustainable Agriculture (pp. 583–600). Springer Netherlands. https://doi.org/10.1007/978-90-481-2666-8-36. Esau, K. (1965). Plant anatomy. Plant Anatomy., (2nd Edition). Dowdy, R. H., Smucker, A. J. M., Dolan, M. S., & Ferguson, J. C. (1998). Automated Image Analysis for Separating Plant Roots from Soil Debris Elutriated from Soil Cores. In Root Demographics and Their Efficiencies in Sustainable Agriculture, Grasslands and Forest Ecosystems (pp. 737-744). Springer, Dordrecht. Eshel, A., and Beeckman, T. (Eds.). (2013). Plant roots: the hidden half. CRC press. Esmon, C. A., Pedmale, U. V., and Liscum, E. (2005). Plant tropisms: Providing the power of movement to a sessile organism. International Journal of Developmental Biology. https://doi.org/10.1387/ijdb.052028ce Fang, S., Clark, R. T., Zheng, Y., Iyer-Pascuzzi, A. S., Weitz, J. S., Kochian, L. V., . . Benfey, P. N. (2013). Genotypic recognition and spatial responses by rice roots. Proceedings of the National Academy of Sciences of the United States of America, 110(7), 2670–2675. https://doi.org/10.1073/pnas.1222821110. Fitter, A. H. (1987). An architectural approach to the comparative ecology of plant root systems. New phytologist, 106, 61-77. https://doi.org/10.1111/j.1469-8137.1987.tb04683.x French, A., Ubeda-Toma´s, S., Holman, T. J., Bennett, M. J., and Pridmore, T. (2009). High-throughput quantification of root growth using a novel image-analysis tool. Plant physiol- ogy, 150(4), 1784-1795. https://doi.org/10.1104/pp.109.140558 Glin´ski, J., and Lipiec, J. (2018). Soil physical conditions and plant roots. CRC press. Godin, C., Costes, E., and Sinoquet, H. (1999). A method for describing plant architec- ture which integrates topology and geometry. Annals of botany, 84(3), 343-357 Gregory, P. J. (2008). Plant roots: growth, activity and interactions with the soil. John Wiley & Sons. Hochholdinger, F., Yu, P., and Marcon, C. (2018). Genetic control of root system development in maize. Trends in plant science, 23(1), 79-88. Hodge, A., Berta, G., Doussan, C., Merchan, F., and Crespi, M. (2009). Plant root growth, architecture and function. Plant and soil, 321(1), 153-187. https://doi.org/10.1007/s11104-009- 9929-9. Leitner, D., Klepsch, S., Knieß, A., and Schnepf, A. (2010). The algorithmic beauty of plant roots–an L-System model for dynamic root growth simulation. Mathematical and Computer Modelling of Dynamical Systems, 16(6), 575-587. https://doi.org/10.1080/13873954.2010.491360 Lobet G, Koevoets IT, Noll M, Tocquin P, Meyer PE, Pagès L, et al. Using a structural root system model to evaluate and improve the accuracy of root image analysis pipelines. Front Plant Sci. Frontiers; 2017;8. doi:10.3389/fpls.2017.00447 Lynch, J. (1995). Root architecture and plant productivity. Plant physiology, 109(1), 7. https://doi.org/10.1104/pp.109.1.7 Miyazawa, Y., Yamazaki, T., Moriwaki, T., and Takahashi, H. (2011). Root Tropism. Its Mechanism and Possible Functions in Drought Avoidance. Advances in Botanical Research (Vol. 57). https://doi.org/10.1016/B978-0-12-387692- 8.00010-2. Narisetti, N., Henke, M., Seiler, C., Shi, R., Junker, A., Altmann, T., & Gladilin, E. (2019). Semi-automated root image analysis (saRIA). Scientific reports, 9(1), 1-10. Orman-Ligeza, B., Civava, R., de Dorlodot, S., and Draye, X. (2014). Root system architecture. In Root engineering (pp. 39-56). Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3- 642-54276-3 3 Popova, L., Russino, A., Ascrizzi, A., and Mazzolai, B. (2012). Analysis of movement in primary maize roots. Biologia, 67(3), 517–524. https://doi.org/10.2478/s11756-012-0023-z. Pornaro, Cristina & Macolino, Stefano & Menegon, Alessandro & Richardson, Mike. (2017). WinRHIZO Technology for Measuring Morphological Traits of Bermudagrass Stolons. Agronomy Journal. 109. 10.2134/agronj2017.03.0187. Schleicher, S., Lienhard, J., Poppinga, S., Speck, T., and Knippers, J. (2015). A method- ology for transferring principles of plant movements to elastic systems in architecture. Computer-Aided Design, 60, 105-117. https://doi.org/10.1016/j.cad.2014.01.005. Seethepalli, A., Dhakal, K., Griffiths, M., Guo, H., Freschet, G. T., & York, L. M. (2021). RhizoVision Explorer: Open-source software for root image analysis and measurement standardization. bioRxiv. Taiz, L. and Zeiger, E. (2003). Plant physiology. 3rd edn. Annals of Botany, 91(6), 750–751. Walter, A., Silk, W. K., and Schurr, U. (2009). Environmental Effects on Spatial and Temporal Patterns of Leaf and Root Growth. Annual Review of Plant Biology, 60(1), 279–304. https://doi.org/10.1146/annurev.arplant.59.032607.092819 Yang, M., Defossez, P., Danjon, F., and Fourcaud, T. (2014). Tree stability under wind: simulating uprooting with root breakage using a finite element method. Annals of botany, 114(4), 695-709. https://doi.org/10.1093/aob/mcu122. Youssef, R. A., and Chino, M. (1988). Development of a new rhizobox system to study the nutrient status in the rhizosphere. Soil Science and Plant Nutrition, 34(3), 461–465. https://doi.org/10.1080/00380768.1988.10415701. |
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xiii, 59 páginas |
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Universidad Nacional de Colombia |
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Bogotá - Ingeniería - Maestría en Ingeniería - Ingeniería Mecánica |
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Departamento de Ingeniería Mecánica y Mecatrónica |
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Facultad de Ingeniería |
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Bogotá, Colombia |
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Universidad Nacional de Colombia - Sede Bogotá |
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Universidad Nacional de Colombia |
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Atribución-NoComercial-CompartirIgual 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Garzón Alvarado, Diego Alexandera780fc0a2dd14ac611c37bca9998c94bVargas Silva, Gustavoa356f7c4a307c20815c9d734d9c231a1Moreno Chaparro, Daniela55308a44a47c6fd63d0e6fa00c205653600Gnum Grupo de Modelado y Métodos Numericos en Ingeniería2022-07-22T14:09:28Z2022-07-22T14:09:28Z2022-07https://repositorio.unal.edu.co/handle/unal/81727Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustraciones, fotografías, graficasThe growth of a healthy and productive plant depends on the correct development of its roots and the surrounding environment. In this context, root growth is crucial because it provides support, anchoring, and feeding characteristics. Multiple reported studies have focused on interpreting and understanding the root behavior, providing different morphological and topological classifications of root archetypes. This document proposes and evaluates two computational models to simulate the root growth. The first model corresponds to the geometrical representation of root growth in 2D and 3D space. In this scheme, four common root archetypes were addressed and considered their tropisms: adventitious, primary root, napiform, and fasciculate. The visual inspection of different root plants such as beans, carrots, and orchids was considered to develop the algorithm. Then, computational simulations were carried out to obtain the desired root archetypes or morphologies. This model has a stochastic factor providing greater versatility in the simulations, similarly to actual roots. The second computational scheme used is Reaction-diffusion Root Branching (RDRB), which models the dynamic root growth using the finite element method (FEM) in 1D for the roots and 2D for the growing media. This model provides a more detailed and more complex description than the first one, considering the reaction-diffusion of the species, representing the biochemical search for nutrients. Additionally, it accounts for an elastic contribution to account for the mechanical effects of root growing and the media interaction. This model involves biochemical, biophysical, and tropism stimuli. The two proposed mathematical/computational models can correctly represent the plant root growth, incorporating geometrical aspects and biophysical and biochemical features. Furthermore, these models have the potential to be adopted to investigate other natural branching phenomena such as slime mold, fractures, circulatory systems, respiratory systems, and thunders.El crecimiento de una planta sana y productiva depende del correcto desarrollo de sus raíces y del entorno que la rodea. En este contexto, el crecimiento de las raíces es crucial porque proporciona características de soporte, anclaje y alimentación. Múltiples estudios se han centrado en interpretar y comprender el comportamiento de la raíz, proporcionando diferentes clasificaciones morfológicas y topológicas de los arquetipos de raíz. Este documento propone y evalúa dos modelos computacionales para simular el crecimiento de las raíces. El primer modelo corresponde a la representación geométrica del crecimiento de raíces en el espacio 2D y 3D. En este esquema, se abordaron cuatro arquetipos de raíces comunes como lo son: adventicia, raíz primaria, napiforme y fasciculada, adicionalmente se consideraron sus tropismos. Para desarrollar el algoritmo se consideró la inspección visual de diferentes plantas de raíz como frijoles, zanahorias y orquídeas. Seguido de esto, se realizaron simulaciones computacionales para obtener los arquetipos o morfologías de raíces deseadas. Este modelo tiene un factor estocástico que proporciona una mayor versatilidad en las simulaciones, de forma similar a las raíces reales. El segundo modelo computacional utilizado es Reaction-diffusion Root Branching (RDRB), que modela el crecimiento dinámico de raíces usando el método de elementos finitos (FEM) en 1D para las raíces y 2D para los medios de cultivo. Este modelo proporciona una descripción más detallada y compleja que el primero, considerando la reacción-difusión de las especies, representando la búsqueda bioquímica de nutrientes. Además, explica los efectos mecánicos del crecimiento de las raíces y la interacción con el medio de crecimiento. Este modelo involucra estímulos bioquímicos, biofísicos y de tropismo. Los dos modelos matemáticos/computacionales propuestos pueden representar correctamente el crecimiento de las raíces de las plantas, incorporando aspectos geométricos y características biofísicas y bioquímicas. Además, estos modelos tienen el potencial de ser adaptados para investigar otros fenómenos naturales de ramificación, como moho mucilaginoso, fracturas, sistema circulatorio, sistema respiratorio y relámpagos. (Texto tomado de la fuente)MaestríaMagíster en Ingeniería MecánicaMecánica computacionalxiii, 59 páginasapplication/pdfengUniversidad Nacional de ColombiaBogotá - Ingeniería - Maestría en Ingeniería - Ingeniería MecánicaDepartamento de Ingeniería Mecánica y MecatrónicaFacultad de IngenieríaBogotá, ColombiaUniversidad Nacional de Colombia - Sede Bogotá620 - Ingeniería y operaciones afines::629 - Otras ramas de la ingenieríaBiological modelsPlant physiologyModelos biológicosFisiología vegetalGrowth algorithmRoot architectureGrowth plant modelAlgoritmo de crecimientoArquitectura de raízModelo de crecimiento de plantasComputational simulation and model of a generalized prototype of an ornamental rootSimulación y modelo computacional de un prototipo de raíz ornamental generalizadaTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionTexthttp://purl.org/redcol/resource_type/TMAdu, M. O., Yawson, D. O., Bennett, M. J., Broadley, M. R., Dupuy, L. X., and White, P. J. (2017). A scanner-based rhizobox system enabling the quantification of root system development and response of brassica rapa seedlings to external p availability. Plant Root, 11, 16–32. https://doi.org/10.3117/plantroot.11.16.Aziz, A. A., Lim, K. B., Rahman, E. K. A., Nurmawati, M. H., & Zuruzi, A. S. (2020). Agar with embedded channels to study root growth. Scientific Reports, 10(1), 1-12Bentley, L. P., Stegen, J. C., Savage, V. M., Smith, D. D., von Allmen, E. I., Sperry, J. S., and Enquist, B. J. (2013). An empirical assessment of tree branching networks and implications for plant allometric scaling models. Ecology letters, 16(8), 1069-1078. https://doi.org/10.1111/ele.12127.Bodner, G., Alsalem, M., Nakhforoosh, A., Arnold, T., and Leitner, D. (2017). RGB and spectral root imaging for plant phenotyping and physiological research: Experimental setup and imaging protocols. Journal of Visualized Experiments, 2017(126). https://doi.org/10.3791/56251.Bodner, G., Leitner, D., Nakhforoosh, A., Sobotik, M., Moder, K., and Kaul, H. P. (2013). A statistical approach to root system classification. Frontiers in Plant Science, 4(AUG). https://doi.org/10.3389/fpls.2013.00292.Boudon, F., Chopard, J., Ali, O., Gilles, B., Hamant, O., Boudaoud, A., .and Godin, C. (2015). A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution. PLoS Comput Biol, 11(1), e1003950. https://doi.org/10.1371/journal.pcbi.1003950.Boyer, J. S., Silk, W. K., & Watt, M. (2010). Path of water for root growth. Functional Plant Biology, 37(12), 1105-1116. Bouma, T. J., Nielsen, K. L., & Koutstaal, B. A. S. (2000). Sample preparation and scanning protocol for computerised analysis of root length and diameter. Plant and soil, 218(1), 185-196.Cannon, W. A. (1949). A tentative classification of root systems. Ecology, 542-548. https://doi.org/10.2307/1932458Clark, L. J., Whalley, W. R., and Barraclough, P. B. (2003). How do roots penetrate strong soil? Plant and Soil (Vol. 255). https://doi.org/10.1007/978-94-017-2923-9 10.Courne`de, P. H., Kang, M. Z., Mathieu, A., Barczi, J. F., Yan, H. P., Hu, B. G., and De Reffye, P. (2006). Structural factorization of plants to compute their functional and architectural growth. Simulation, 82(7), 427-438. https://doi.org/10.1177/0037549706069341de Moraes, M. T., Bengough, A. G., Debiasi, H., Franchini, J. C., Levien, R., Schnepf, A., and Leitner, D. (2018). Mechanistic framework to link root growth models with weather and soil physical properties, including example applications to soybean growth in Brazil. Plant and Soil, 428(1–2), 67–92. https://doi.org/10.1007/s11104-018-3656-zDoussan, C., Page`s, L., and Pierret, A. (2009). Soil exploration and resource acquisition by plant roots: An architectural and modelling point of view. In Sustainable Agriculture (pp. 583–600). Springer Netherlands. https://doi.org/10.1007/978-90-481-2666-8-36. Esau, K. (1965). Plant anatomy. Plant Anatomy., (2nd Edition).Dowdy, R. H., Smucker, A. J. M., Dolan, M. S., & Ferguson, J. C. (1998). Automated Image Analysis for Separating Plant Roots from Soil Debris Elutriated from Soil Cores. In Root Demographics and Their Efficiencies in Sustainable Agriculture, Grasslands and Forest Ecosystems (pp. 737-744). Springer, Dordrecht.Eshel, A., and Beeckman, T. (Eds.). (2013). Plant roots: the hidden half. CRC press.Esmon, C. A., Pedmale, U. V., and Liscum, E. (2005). Plant tropisms: Providing the power of movement to a sessile organism. International Journal of Developmental Biology. https://doi.org/10.1387/ijdb.052028ceFang, S., Clark, R. T., Zheng, Y., Iyer-Pascuzzi, A. S., Weitz, J. S., Kochian, L. V., . . Benfey, P. N. (2013). Genotypic recognition and spatial responses by rice roots. 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