Structural characteristics in network control of molecular multiplex networks.

Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood....
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Cheng Yuan [verfasserIn] Zu-Yu Qian [verfasserIn] Jie Zhou [verfasserIn] Shi-Ming Chen [verfasserIn] Sen Nie [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Übergeordnetes Werk:	In: PLoS ONE - Public Library of Science (PLoS), 2007, 18(2023), 3, p e0283768
Übergeordnetes Werk:	volume:18 ; year:2023 ; number:3, p e0283768

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1371/journal.pone.0283768

Katalog-ID:	DOAJ089544110

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allfields	10.1371/journal.pone.0283768 doi (DE-627)DOAJ089544110 (DE-599)DOAJ0260d36498b14594b75440aa52d15e6c DE-627 ger DE-627 rakwb eng Cheng Yuan verfasserin aut Structural characteristics in network control of molecular multiplex networks. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species. Medicine R Science Q Zu-Yu Qian verfasserin aut Jie Zhou verfasserin aut Shi-Ming Chen verfasserin aut Sen Nie verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 3, p e0283768 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:3, p e0283768 https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/article/0260d36498b14594b75440aa52d15e6c kostenfrei https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 3, p e0283768
spelling	10.1371/journal.pone.0283768 doi (DE-627)DOAJ089544110 (DE-599)DOAJ0260d36498b14594b75440aa52d15e6c DE-627 ger DE-627 rakwb eng Cheng Yuan verfasserin aut Structural characteristics in network control of molecular multiplex networks. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species. Medicine R Science Q Zu-Yu Qian verfasserin aut Jie Zhou verfasserin aut Shi-Ming Chen verfasserin aut Sen Nie verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 3, p e0283768 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:3, p e0283768 https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/article/0260d36498b14594b75440aa52d15e6c kostenfrei https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 3, p e0283768
allfields_unstemmed	10.1371/journal.pone.0283768 doi (DE-627)DOAJ089544110 (DE-599)DOAJ0260d36498b14594b75440aa52d15e6c DE-627 ger DE-627 rakwb eng Cheng Yuan verfasserin aut Structural characteristics in network control of molecular multiplex networks. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species. Medicine R Science Q Zu-Yu Qian verfasserin aut Jie Zhou verfasserin aut Shi-Ming Chen verfasserin aut Sen Nie verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 3, p e0283768 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:3, p e0283768 https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/article/0260d36498b14594b75440aa52d15e6c kostenfrei https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 3, p e0283768
allfieldsGer	10.1371/journal.pone.0283768 doi (DE-627)DOAJ089544110 (DE-599)DOAJ0260d36498b14594b75440aa52d15e6c DE-627 ger DE-627 rakwb eng Cheng Yuan verfasserin aut Structural characteristics in network control of molecular multiplex networks. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species. Medicine R Science Q Zu-Yu Qian verfasserin aut Jie Zhou verfasserin aut Shi-Ming Chen verfasserin aut Sen Nie verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 3, p e0283768 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:3, p e0283768 https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/article/0260d36498b14594b75440aa52d15e6c kostenfrei https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 3, p e0283768
allfieldsSound	10.1371/journal.pone.0283768 doi (DE-627)DOAJ089544110 (DE-599)DOAJ0260d36498b14594b75440aa52d15e6c DE-627 ger DE-627 rakwb eng Cheng Yuan verfasserin aut Structural characteristics in network control of molecular multiplex networks. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species. Medicine R Science Q Zu-Yu Qian verfasserin aut Jie Zhou verfasserin aut Shi-Ming Chen verfasserin aut Sen Nie verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 3, p e0283768 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:3, p e0283768 https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/article/0260d36498b14594b75440aa52d15e6c kostenfrei https://doi.org/10.1371/journal.pone.0283768 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 3, p e0283768
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author	Cheng Yuan
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title	Structural characteristics in network control of molecular multiplex networks.
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title_auth	Structural characteristics in network control of molecular multiplex networks.
abstract	Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species.
abstractGer	Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species.
abstract_unstemmed	Numerous real-world systems can be naturally modeled as multilayer networks, providing an efficient tool to characterize these complex systems. Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. Our results provide a comprehensive understanding of the roles of genes in biology and network control across several species.
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title_short	Structural characteristics in network control of molecular multiplex networks.
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up_date	2024-07-03T23:36:43.475Z
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Although recent progress in understanding the controlling of synthetic multiplex networks, how to control real multilayer systems remains poorly understood. Here, we explore the controllability and energy requirement of molecular multiplex networks coupled by transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network from the perspective of network structural characteristics. Our findings reveal that the driver nodes tend to avoid essential or pathogen-related genes. However, imposing external inputs on these essential or pathogen-related genes can remarkably reduce the energy cost, implying their crucial role in network control. Moreover, we find that the minimal driver nodes, as well as the energy required, are associated with disassortative coupling between TRN and PPI networks. 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Structural characteristics in network control of molecular multiplex networks.

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