Minimum complexity drives regulatory logic in Boolean models of living systems
The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningf...
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| Vydáno v: | PNAS nexus Ročník 1; číslo 1; s. pgac017 |
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Oxford University Press
01.03.2022
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| Abstract | The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningful types of BFs, and perform a systematic study of their preponderance in a compilation of 2,687 functions extracted from published models. A surprising feature is that most of these BFs have odd “bias”, that is they produce “on” outputs for a total number of input combinations that is odd. Upon further analysis, we are able to explain this observation, along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of 2 complexity measures: Boolean complexity based on string lengths in formal logic, which is yet unexplored in biological contexts, and the so-called average sensitivity. RoFs minimize Boolean complexity and all such functions have odd bias. Furthermore, NCFs minimize not only the Boolean complexity but also the average sensitivity. These results reveal the importance of minimum complexity in the regulatory logic of biological networks. |
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| AbstractList | The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningful types of BFs, and perform a systematic study of their preponderance in a compilation of 2,687 functions extracted from published models. A surprising feature is that most of these BFs have odd "bias", that is they produce "on" outputs for a total number of input combinations that is odd. Upon further analysis, we are able to explain this observation, along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of 2 complexity measures: Boolean complexity based on string lengths in formal logic, which is yet unexplored in biological contexts, and the so- called average sensitivity. RoFs minimize Boolean complexity and all such functions have odd bias. Furthermore, NCFs minimize not only the Boolean complexity but also the average sensitivity. These results reveal the importance of minimum complexity in the regulatory logic of biological networks. The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on types of BFs, and perform a systematic study of their preponderance in a compilation of 2,687 functions extracted from published models. A surprising feature is that most of these BFs have odd "bias", that is they produce "on" outputs for a total number of input combinations that is odd. Upon further analysis, we are able to explain this observation, along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of 2 complexity measures: based on string lengths in formal logic, which is yet unexplored in biological contexts, and the so-called . RoFs minimize Boolean complexity and all such functions have odd bias. Furthermore, NCFs minimize not only the Boolean complexity but also the average sensitivity. These results reveal the importance of minimum complexity in the regulatory logic of biological networks. The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningful types of BFs, and perform a systematic study of their preponderance in a compilation of 2,687 functions extracted from published models. A surprising feature is that most of these BFs have odd "bias", that is they produce "on" outputs for a total number of input combinations that is odd. Upon further analysis, we are able to explain this observation, along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of 2 complexity measures: Boolean complexity based on string lengths in formal logic, which is yet unexplored in biological contexts, and the so- called average sensitivity. RoFs minimize Boolean complexity and all such functions have odd bias. Furthermore, NCFs minimize not only the Boolean complexity but also the average sensitivity. These results reveal the importance of minimum complexity in the regulatory logic of biological networks. Keywords: gene regulatory networks, Boolean networks, update rules, Boolean complexity, average sensitivity The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningful types of BFs, and perform a systematic study of their preponderance in a compilation of 2,687 functions extracted from published models. A surprising feature is that most of these BFs have odd "bias", that is they produce "on" outputs for a total number of input combinations that is odd. Upon further analysis, we are able to explain this observation, along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of 2 complexity measures: Boolean complexity based on string lengths in formal logic, which is yet unexplored in biological contexts, and the so-called average sensitivity. RoFs minimize Boolean complexity and all such functions have odd bias. Furthermore, NCFs minimize not only the Boolean complexity but also the average sensitivity. These results reveal the importance of minimum complexity in the regulatory logic of biological networks.The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningful types of BFs, and perform a systematic study of their preponderance in a compilation of 2,687 functions extracted from published models. A surprising feature is that most of these BFs have odd "bias", that is they produce "on" outputs for a total number of input combinations that is odd. Upon further analysis, we are able to explain this observation, along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of 2 complexity measures: Boolean complexity based on string lengths in formal logic, which is yet unexplored in biological contexts, and the so-called average sensitivity. RoFs minimize Boolean complexity and all such functions have odd bias. Furthermore, NCFs minimize not only the Boolean complexity but also the average sensitivity. These results reveal the importance of minimum complexity in the regulatory logic of biological networks. |
| Audience | Academic |
| Author | Subbaroyan, Ajay Martin, Olivier C Samal, Areejit |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36712790$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1007/s11538-008-9304-7 10.1103/PhysRevLett.93.048701 10.1002/cplx.21819 10.1016/j.jmp.2006.05.007 10.1103/PhysRevE.72.055101 10.1016/0012-365X(76)90058-3 10.1016/S0022-2496(02)00025-1 10.1137/0112012 10.1093/bioinformatics/15.7.593 10.1186/1752-0509-6-96 10.1007/978-3-642-14295-6_5 10.1016/0022-5193(69)90015-0 10.1016/j.biosystems.2006.06.007 10.1126/science.7624793 10.1038/224177a0 10.1038/nrg1272 10.1201/9781420011432 10.1016/j.biosystems.2005.10.003 10.1016/j.biosystems.2016.03.002 10.1186/1752-0509-4-1 10.1016/0022-5193(73)90247-6 10.1016/S0022-5193(03)00035-3 10.1039/c3mb25562j 10.1093/oso/9780195079517.001.0001 10.1006/jtbi.2002.3081 10.1073/pnas.0930314100 10.1137/1.9780898718539 10.1126/science.1065103 10.1088/1751-8113/40/16/006 10.1016/j.physd.2007.06.022 10.1242/jcs.02714 10.1017/CBO9780511790515 10.1016/j.tcs.2013.02.020 10.1038/35036586 10.1002/cplx.10022 10.1007/978-3-540-32667-0 10.1089/10665270252833208 10.5402/2012/613174 10.1016/j.jtbi.2011.08.015 10.1137/0115129 10.1371/journal.pone.0064371 10.1002/j.1538-7305.1956.tb03835.x 10.1080/00029890.1955.11988710 10.1098/rspb.2000.1280 10.1103/PhysRevLett.94.088701 10.1073/pnas.2036429100 10.1137/0215006 10.1103/PhysRevLett.121.138102 |
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| Keywords | Boolean complexity gene regulatory networks update rules average sensitivity Boolean networks |
| Language | English |
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| References | McCluskey (2022111622073206500_bib37) 1956; 35 Harper (2022111622073206500_bib45) 1964; 12 Hinkelmann (2022111622073206500_bib57) 2012; 2012 Cook (2022111622073206500_bib25) 1986; 15 Henry (2022111622073206500_bib56) 2013; 9 Wagner (2022111622073206500_bib6) 2005 Buchler (2022111622073206500_bib54) 2003; 100 Kauffman (2022111622073206500_bib19) 2003; 100 Kauffman (2022111622073206500_bib2) 1993 de Jong (2022111622073206500_bib16) 2002; 9 Albert (2022111622073206500_bib18) 2003; 223 Bornholdt (2022111622073206500_bib3) 2000; 267 Helikar (2022111622073206500_bib21) 2012; 6 Kauffman (2022111622073206500_bib12) 1969; 22 Murrugarra (2022111622073206500_bib51) 2011; 288 Alon (2022111622073206500_bib9) 2006 Nikolajewa (2022111622073206500_bib43) 2007; 90 Palsson (2022111622073206500_bib15) 2006 Brayton (2022111622073206500_bib35) 2010 Daniels (2022111622073206500_bib47) 2018; 121 Harris (2022111622073206500_bib50) 2002; 7 Bernstein (2022111622073206500_bib46) 1967; 15 Samal (2022111622073206500_bib20) 2008; 2 Raeymaekers (2022111622073206500_bib38) 2002; 218 Berkeley Logic Synthesis, Verification Group (2022111622073206500_bib34) 2010 Li (2022111622073206500_bib49) 2010; 4 Kaneko (2022111622073206500_bib8) 2006 Golumbic (2022111622073206500_bib26) 2011 Albert (2022111622073206500_bib7) 2005; 118 Anthony (2022111622073206500_bib40) 2001 Thomas (2022111622073206500_bib27) 1979 Klotz (2022111622073206500_bib52) 2013; 8 Kauffman (2022111622073206500_bib10) 1969; 224 Vigo (2022111622073206500_bib33) 2006; 50 Jarrah (2022111622073206500_bib41) 2007; 233 Çoban (2022111622073206500_bib53) 2021 Givone (2022111622073206500_bib30) 1970 Thomas (2022111622073206500_bib11) 1973; 42 Aracena (2022111622073206500_bib39) 2008; 70 Barabási (2022111622073206500_bib5) 2004; 5 Mendoza (2022111622073206500_bib17) 1999; 15 Zhou (2022111622073206500_bib55) 2016; 142-143 Garey (2022111622073206500_bib32) 1990 Li (2022111622073206500_bib42) 2013; 481 Feldman (2022111622073206500_bib24) 2000; 407 Reichhardt (2022111622073206500_bib29) 2007; 40 Gherardi (2022111622073206500_bib23) 2016; 21 Maslov (2022111622073206500_bib4) 2002; 296 Klemm (2022111622073206500_bib14) 2005; 72 McAdams (2022111622073206500_bib1) 1995; 269 Quine (2022111622073206500_bib36) 1955; 62 Hart (2022111622073206500_bib44) 1976; 14 Shmulevich (2022111622073206500_bib22) 2004; 93 Gonzalez (2022111622073206500_bib48) 2006; 84 Drossel (2022111622073206500_bib13) 2005; 94 Feldman (2022111622073206500_bib28) 2003; 47 Wegener (2022111622073206500_bib31) 1987 |
| References_xml | – start-page: 448 volume-title: Encyclopedia of Mathematics and its Applications year: 2011 ident: 2022111622073206500_bib26 article-title: Read-once functions – volume: 70 start-page: 1398 issue: 5 year: 2008 ident: 2022111622073206500_bib39 article-title: Maximum number of fixed points in regulatory Boolean networks publication-title: Bull Math Biol doi: 10.1007/s11538-008-9304-7 – volume: 93 start-page: 48701 issue: 4 year: 2004 ident: 2022111622073206500_bib22 article-title: Activities and sensitivities in Boolean network models publication-title: Phys Rev Lett doi: 10.1103/PhysRevLett.93.048701 – volume: 21 start-page: 397 issue: S2 year: 2016 ident: 2022111622073206500_bib23 article-title: Measuring logic complexity can guide pattern discovery in empirical systems publication-title: Complexity doi: 10.1002/cplx.21819 – volume: 50 start-page: 501 issue: 5 year: 2006 ident: 2022111622073206500_bib33 article-title: A note on the complexity of Boolean concepts publication-title: J Math Psychol doi: 10.1016/j.jmp.2006.05.007 – volume: 72 start-page: 055101 issue: 5 year: 2005 ident: 2022111622073206500_bib14 article-title: Stable and unstable attractors in Boolean networks publication-title: Phys Rev E doi: 10.1103/PhysRevE.72.055101 – volume: 14 start-page: 157 issue: 2 year: 1976 ident: 2022111622073206500_bib44 article-title: A note on the edges of the n-cube publication-title: Discr Math doi: 10.1016/0012-365X(76)90058-3 – volume: 47 start-page: 75 issue: 1 year: 2003 ident: 2022111622073206500_bib28 article-title: A catalog of Boolean concepts publication-title: J Math Psychol doi: 10.1016/S0022-2496(02)00025-1 – volume: 12 start-page: 131 issue: 1 year: 1964 ident: 2022111622073206500_bib45 article-title: Optimal assignments of numbers to vertices publication-title: J Soc Indus Appl Math doi: 10.1137/0112012 – year: 2021 ident: 2022111622073206500_bib53 article-title: Nested canalizing functions minimize sensitivity and simultaneously promote criticality – volume: 15 start-page: 593 issue: 7 year: 1999 ident: 2022111622073206500_bib17 article-title: Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis publication-title: Bioinformatics doi: 10.1093/bioinformatics/15.7.593 – volume: 6 start-page: 1 issue: 1 year: 2012 ident: 2022111622073206500_bib21 article-title: The cell collective: toward an open and collaborative approach to systems biology publication-title: BMC Syst Biol doi: 10.1186/1752-0509-6-96 – start-page: 24 volume-title: Computer aided verification year: 2010 ident: 2022111622073206500_bib35 article-title: ABC: an academic industrial-strength verification tool doi: 10.1007/978-3-642-14295-6_5 – volume: 22 start-page: 437 issue: 3 year: 1969 ident: 2022111622073206500_bib12 article-title: Metabolic stability and epigenesis in randomly constructed genetic nets publication-title: J Theor Biol doi: 10.1016/0022-5193(69)90015-0 – volume: 90 start-page: 40 issue: 1 year: 2007 ident: 2022111622073206500_bib43 article-title: Boolean networks with biologically relevant rules show ordered behavior publication-title: BioSystems doi: 10.1016/j.biosystems.2006.06.007 – volume: 269 start-page: 650 issue: 5224 year: 1995 ident: 2022111622073206500_bib1 article-title: Circuit simulation of genetic networks publication-title: Science doi: 10.1126/science.7624793 – volume: 224 start-page: 177 issue: 5215 year: 1969 ident: 2022111622073206500_bib10 article-title: Homeostasis and differentiation in random genetic control networks publication-title: Nature doi: 10.1038/224177a0 – volume: 5 start-page: 101 issue: 2 year: 2004 ident: 2022111622073206500_bib5 article-title: Network biology: understanding the cell’s functional organization publication-title: Nat Rev Genet doi: 10.1038/nrg1272 – volume-title: An introduction to systems biology: design principles of biological circuits year: 2006 ident: 2022111622073206500_bib9 doi: 10.1201/9781420011432 – volume: 84 start-page: 91 issue: 2 year: 2006 ident: 2022111622073206500_bib48 article-title: GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks publication-title: BioSystems doi: 10.1016/j.biosystems.2005.10.003 – volume: 2 start-page: 1 issue: 21 year: 2008 ident: 2022111622073206500_bib20 article-title: The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response publication-title: BMC Syst Biol – volume: 142-143 start-page: 15 year: 2016 ident: 2022111622073206500_bib55 article-title: Relative stability of network states in Boolean network models of gene regulation in development publication-title: BioSystems doi: 10.1016/j.biosystems.2016.03.002 – volume: 4 start-page: 1 issue: 1 year: 2010 ident: 2022111622073206500_bib49 article-title: BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models publication-title: BMC Syst Biol doi: 10.1186/1752-0509-4-1 – volume-title: Robustness and evolvability in living systems year: 2005 ident: 2022111622073206500_bib6 – volume: 42 start-page: 563 issue: 3 year: 1973 ident: 2022111622073206500_bib11 article-title: Boolean formalization of genetic control circuits publication-title: J Theor Biol doi: 10.1016/0022-5193(73)90247-6 – volume: 223 start-page: 1 issue: 1 year: 2003 ident: 2022111622073206500_bib18 article-title: The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster publication-title: J Theor Biol doi: 10.1016/S0022-5193(03)00035-3 – volume: 9 start-page: 1726 issue: 7 year: 2013 ident: 2022111622073206500_bib56 article-title: Network function shapes network structure: the case of the Arabidopsis flower organ specification genetic network publication-title: Mol BioSyst doi: 10.1039/c3mb25562j – volume-title: The origins of order: self-organization and selection in evolution year: 1993 ident: 2022111622073206500_bib2 doi: 10.1093/oso/9780195079517.001.0001 – volume-title: Introduction to switching circuit theory. McGraw-Hill computer science series year: 1970 ident: 2022111622073206500_bib30 – volume: 218 start-page: 331 issue: 3 year: 2002 ident: 2022111622073206500_bib38 article-title: Dynamics of Boolean networks controlled by biologically meaningful functions publication-title: J Theor Biol doi: 10.1006/jtbi.2002.3081 – year: 2010 ident: 2022111622073206500_bib34 article-title: ABC: a system for sequential synthesis and verification – volume: 100 start-page: 5136 issue: 9 year: 2003 ident: 2022111622073206500_bib54 article-title: On schemes of combinatorial transcription logic publication-title: Proc Nat Acad Sci doi: 10.1073/pnas.0930314100 – volume-title: Discrete mathematics of neural networks year: 2001 ident: 2022111622073206500_bib40 doi: 10.1137/1.9780898718539 – volume: 296 start-page: 910 issue: 5569 year: 2002 ident: 2022111622073206500_bib4 article-title: Specificity and stability in topology of protein networks publication-title: Science doi: 10.1126/science.1065103 – volume: 40 start-page: 4339 issue: 16 year: 2007 ident: 2022111622073206500_bib29 article-title: Canalization and symmetry in Boolean models for genetic regulatory networks publication-title: J Phys A Math Theo doi: 10.1088/1751-8113/40/16/006 – volume: 233 start-page: 167 issue: 2 year: 2007 ident: 2022111622073206500_bib41 article-title: Nested canalyzing, unate cascade, and polynomial functions publication-title: Phys D doi: 10.1016/j.physd.2007.06.022 – volume: 118 start-page: 4947 issue: 21 year: 2005 ident: 2022111622073206500_bib7 article-title: Scale-free networks in cell biology publication-title: J Cell Sci doi: 10.1242/jcs.02714 – volume-title: Systems biology: properties of reconstructed networks year: 2006 ident: 2022111622073206500_bib15 doi: 10.1017/CBO9780511790515 – volume: 481 start-page: 24 year: 2013 ident: 2022111622073206500_bib42 article-title: Boolean nested canalizing functions: a comprehensive analysis publication-title: Theor Comp Sci doi: 10.1016/j.tcs.2013.02.020 – volume-title: The complexity of Boolean functions year: 1987 ident: 2022111622073206500_bib31 – volume: 407 start-page: 630 issue: 6804 year: 2000 ident: 2022111622073206500_bib24 article-title: Minimization of Boolean complexity in human concept learning publication-title: Nature doi: 10.1038/35036586 – volume: 7 start-page: 23 issue: 4 year: 2002 ident: 2022111622073206500_bib50 article-title: A model of transcriptional regulatory networks based on biases in the observed regulation rules publication-title: Complexity doi: 10.1002/cplx.10022 – volume-title: Life: an introduction to complex systems biology year: 2006 ident: 2022111622073206500_bib8 doi: 10.1007/978-3-540-32667-0 – volume: 9 start-page: 67 issue: 1 year: 2002 ident: 2022111622073206500_bib16 article-title: Modeling and simulation of genetic regulatory systems: a literature review publication-title: J Comp Biol doi: 10.1089/10665270252833208 – volume: 2012 start-page: 613174 year: 2012 ident: 2022111622073206500_bib57 article-title: Inferring biologically relevant models: nested canalyzing functions publication-title: ISRN Biomathematics doi: 10.5402/2012/613174 – volume: 288 start-page: 66 year: 2011 ident: 2022111622073206500_bib51 article-title: Regulatory patterns in molecular interaction networks publication-title: J Theor Biol doi: 10.1016/j.jtbi.2011.08.015 – volume: 15 start-page: 1485 issue: 6 year: 1967 ident: 2022111622073206500_bib46 article-title: Maximally connected arrays on the n-cube publication-title: SIAM J Appl Math doi: 10.1137/0115129 – volume: 8 start-page: e64371 issue: 5 year: 2013 ident: 2022111622073206500_bib52 article-title: Bounds on the average sensitivity of nested canalizing functions publication-title: PLOS ONE doi: 10.1371/journal.pone.0064371 – volume: 35 start-page: 1417 issue: 6 year: 1956 ident: 2022111622073206500_bib37 article-title: Minimization of Boolean functions publication-title: Bell Syst Tech J doi: 10.1002/j.1538-7305.1956.tb03835.x – volume: 62 start-page: 627 issue: 9 year: 1955 ident: 2022111622073206500_bib36 article-title: A way to simplify truth functions publication-title: Am Math Mont doi: 10.1080/00029890.1955.11988710 – volume-title: Computers and intractability; a guide to the theory of NP-completeness year: 1990 ident: 2022111622073206500_bib32 – volume: 267 start-page: 2281 issue: 1459 year: 2000 ident: 2022111622073206500_bib3 article-title: Robustness as an evolutionary principle publication-title: Proc R Soc Lond Ser B Biol Sci doi: 10.1098/rspb.2000.1280 – volume: 94 start-page: 088701 issue: 8 year: 2005 ident: 2022111622073206500_bib13 article-title: Number and length of attractors in a critical Kauffman model with connectivity one publication-title: Phys Rev Lett doi: 10.1103/PhysRevLett.94.088701 – volume: 100 start-page: 14796 issue: 25 year: 2003 ident: 2022111622073206500_bib19 article-title: Random Boolean network models and the yeast transcriptional network publication-title: Proc Nat Acad Sci doi: 10.1073/pnas.2036429100 – volume: 15 start-page: 87 issue: 1 year: 1986 ident: 2022111622073206500_bib25 article-title: Upper and lower time bounds for parallel random access machines without simultaneous writes publication-title: SIAM J Comput doi: 10.1137/0215006 – volume-title: Kinetic logic: a Boolean approach to the analysis of complex regulatory systems, proceedings of the EMBO course “Formal analysis of genetic regulation”, held in Brussels, September 6–16, 1977, Lecture notes in Biomathematics year: 1979 ident: 2022111622073206500_bib27 – volume: 121 start-page: 138102 issue: 13 year: 2018 ident: 2022111622073206500_bib47 article-title: Criticality distinguishes the ensemble of biological regulatory networks publication-title: Phys Rev Lett doi: 10.1103/PhysRevLett.121.138102 |
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| SubjectTerms | Algebra, Boolean Bias Biological complexity Boolean Boolean functions Complexity Logic Mathematical logic Physical Sciences and Engineering Sensitivity |
| Title | Minimum complexity drives regulatory logic in Boolean models of living systems |
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