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Mora T, Walczak AM. Towards a quantitative theory of tolerance. Trends Immunol 2023; 44:512-518. [PMID: 37263823 DOI: 10.1016/j.it.2023.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
A cornerstone of the classical view of tolerance is the elimination of self-reactive T cells via negative selection in the thymus. However, high-throughput T cell receptor (TCR) sequencing data have so far failed to detect substantial signatures of negative selection in the observed repertoires. In addition, quantitative estimates as well as recent experiments suggest that the elimination of self-reactive T cells is at best incomplete. We discuss several recent theoretical ideas that might explain tolerance while being consistent with these observations, including collective decision-making through quorum sensing, and sensitivity to change through dynamic tuning and adaptation. We propose that a unified quantitative theory of tolerance should combine these elements to help to explain the plasticity of the immune system and its robustness to autoimmunity.
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Affiliation(s)
- Thierry Mora
- Laboratoire de Physique de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Université Paris Sciences et Lettres (PSL University), Sorbonne Université, and Université Paris-Cité, 75005 Paris, France.
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Université Paris Sciences et Lettres (PSL University), Sorbonne Université, and Université Paris-Cité, 75005 Paris, France.
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2
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Kerepesi C, Bakács T, Szabados T. MiStImm: an agent-based simulation tool to study the self-nonself discrimination of the adaptive immune response. Theor Biol Med Model 2019; 16:9. [PMID: 31046789 PMCID: PMC6498635 DOI: 10.1186/s12976-019-0105-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is an increasing need for complex computational models to perform in silico experiments as an adjunct to in vitro and in vivo experiments in immunology. We introduce Microscopic Stochastic Immune System Simulator (MiStImm), an agent-based simulation tool, that is designed to study the self-nonself discrimination of the adaptive immune system. MiStImm can simulate some components of the humoral adaptive immune response, including T cells, B cells, antibodies, danger signals, interleukins, self cells, foreign antigens, and the interactions among them. The simulation starts after conception and progresses step by step (in time) driven by random simulation events. We also have provided tools to visualize and analyze the output of the simulation program. RESULTS As the first application of MiStImm, we simulated two different immune models, and then we compared performances of them in the mean of self-nonself discrimination. The first model is a so-called conventional immune model, and the second model is based on our earlier T-cell model, called "one-signal model", which is developed to resolve three important paradoxes of immunology. Our new T-cell model postulates that a dynamic steady state coupled system is formed through low-affinity complementary TCR-MHC interactions between T cells and host cells. The new model implies that a significant fraction of the naive polyclonal T cells is recruited into the first line of defense against an infection. Simulation experiments using MiStImm have shown that the computational realization of the new model shows real patterns. For example, the new model develops immune memory and it does not develop autoimmune reaction despite the hypothesized, enhanced TCR-MHC interaction between T cells and self cells. Simulations also demonstrated that our new model gives better results to overcome a critical primary infection answering the paradox "how can a tiny fraction of human genome effectively compete with a vastly larger pool of mutating pathogen DNA?" CONCLUSION The outcomes of our in silico experiments, presented here, are supported by numerous clinical trial observations from the field of immunotherapy. We hope that our results will encourage investigations to make in vitro and in vivo experiments clarifying questions about self-nonself discrimination of the adaptive immune system. We also hope that MiStImm or some concept in it will be useful to other researchers who want to implement or compare other immune models.
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Affiliation(s)
- Csaba Kerepesi
- Institute for Computer Science and Control, Hungarian Academy of Sciences, Kende u 13-17, Budapest, 1111 Hungary
| | - Tibor Bakács
- Alfréd Rényi Institute of Mathematics, Hungarian Academy of Sciences, Reáltanoda u 13-15, Budapest, 1053 Hungary
| | - Tamás Szabados
- Department of Stochastics, Budapest University of Technology and Economics, Müegyetem rkp 3, Budapest, 1521 Hungary
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Spottiswoode CN, Busch R. Vive la difference! Self/non-self recognition and the evolution of signatures of identity in arms races with parasites. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180206. [PMID: 30967089 PMCID: PMC6388040 DOI: 10.1098/rstb.2018.0206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/24/2022] Open
Abstract
In arms races with parasites, hosts can evolve defences exhibiting extensive variability within populations, which signals individual identity ('signatures'). However, few such systems have evolved, suggesting that the conditions for their evolution are uncommon. We review (a) polymorphic egg markings that allow hosts of brood-parasitic birds to recognize and reject parasitic eggs, and (b) polymorphic tissue antigens encoded in the major histocompatibility complex (MHC), which present self- and pathogen-derived peptides to T cells of the immune system. Despite the profound differences between these systems, they share analogous features: (i) self/non-self discrimination by a highly specific recognition system (bird eyes and T-cell antigen receptor, respectively), which antagonists may escape by evolving evasion or mimicry; (ii) a self substrate upon which diversifying selection can act (eggs, and MHC molecules); (iii) acquired knowledge of self (resulting in acceptance of own eggs, and immune tolerance); and (iv) fitness costs associated with attack on self or lack of parasite detection. We suggest that these features comprise a set of requirements for parasites to drive the evolution of identity signatures in hosts, which diminish the likelihood of recognition errors. This may help to explain the variety of trajectories arising from arms races in different antagonistic contexts. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
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Affiliation(s)
- Claire N. Spottiswoode
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Robert Busch
- Department of Life Sciences, Whitelands College, University of Roehampton, Holybourne Avenue, London SW15 4JD, UK
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Akiyama T, Tateishi R, Akiyama N, Yoshinaga R, Kobayashi TJ. Positive and Negative Regulatory Mechanisms for Fine-Tuning Cellularity and Functions of Medullary Thymic Epithelial Cells. Front Immunol 2015; 6:461. [PMID: 26441966 PMCID: PMC4568481 DOI: 10.3389/fimmu.2015.00461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023] Open
Abstract
Self-tolerant T cells and regulatory T cells develop in the thymus. A wide variety of cell-cell interactions in the thymus is required for the differentiation, proliferation, and repertoire selection of T cells. Various secreted and cell surface molecules expressed in thymic epithelial cells (TECs) mediate these processes. Moreover, cytokines expressed by cells of hematopoietic origin regulate the cellularity of TECs. Tumor necrosis factor (TNF) family RANK ligand, lymphotoxin, and CD40 ligand, expressed in T cells and innate lymphoid cells (ILCs), promote the differentiation and proliferation of medullary TECs (mTECs) that play critical roles in the induction of immune tolerance. A recent study suggests that interleukin-22 (IL-22) produced by ILCs promotes regeneration of TECs after irradiation. Intriguingly, tumor growth factor-β and osteoprotegerin limit cellularity of mTECs, thereby attenuating regulatory T cell generation. We will review recent insights into the molecular basis for cell-cell interactions regulating differentiation and proliferation of mTECs and also discuss about a perspective on use of mathematical models for understanding this complicated system.
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Affiliation(s)
- Taishin Akiyama
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
| | - Ryosuke Tateishi
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
| | - Nobuko Akiyama
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
| | - Riko Yoshinaga
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo , Tokyo , Japan
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Sawicka M, Stritesky GL, Reynolds J, Abourashchi N, Lythe G, Molina-París C, Hogquist KA. From pre-DP, post-DP, SP4, and SP8 Thymocyte Cell Counts to a Dynamical Model of Cortical and Medullary Selection. Front Immunol 2014; 5:19. [PMID: 24592261 PMCID: PMC3924582 DOI: 10.3389/fimmu.2014.00019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/15/2014] [Indexed: 01/15/2023] Open
Abstract
Cells of the mature αβ T cell repertoire arise from the development in the thymus of bone marrow precursors (thymocytes). αβ T cell maturation is characterized by the expression of thousands of copies of identical αβ T cell receptors and the CD4 and/or CD8 co-receptors on the surface of thymocytes. The maturation stages of a thymocyte are: (1) double negative (DN) (TCR−, CD4− and CD8−), (2) double positive (DP) (TCR+, CD4+ and CD8+), and (3) single positive (SP) (TCR+, CD4+ or CD8+). Thymic antigen presenting cells provide the appropriate micro-architecture for the maturation of thymocytes, which “sense” the signaling environment via their randomly generated TCRs. Thymic development is characterized by (i) an extremely low success rate, and (ii) the selection of a functional and self-tolerant T cell repertoire. In this paper, we combine recent experimental data and mathematical modeling to study the selection events that take place in the thymus after the DN stage. The stable steady state of the model for the pre-DP, post-DP, and SP populations is identified with the experimentally measured cell counts from 5.5- to 17-week-old mice. We make use of residence times in the cortex and the medulla for the different populations, as well as recently reported asymmetric death rates for CD4 and CD8 SP thymocytes. We estimate that 65.8% of pre-DP thymocytes undergo death by neglect. In the post-DP compartment, 91.7% undergo death by negative selection, 4.7% become CD4 SP, and 3.6% become CD8 SP. Death by negative selection in the medulla removes 8.6% of CD4 SP and 32.1% of CD8 SP thymocytes. Approximately 46.3% of CD4 SP and 27% of CD8 SP thymocytes divide before dying or exiting the thymus.
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Affiliation(s)
- Maria Sawicka
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Gretta L Stritesky
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota , Minneapolis, MN , USA
| | - Joseph Reynolds
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Niloufar Abourashchi
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Kristin A Hogquist
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota , Minneapolis, MN , USA
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Abstract
The peripheral T cell repertoire is sculpted from prototypic T cells in the thymus bearing randomly generated T cell receptors (TCR) and by a series of developmental and selection steps that remove cells that are unresponsive or overly reactive to self-peptide–MHC complexes. The challenge of understanding how the kinetics of T cell development and the statistics of the selection processes combine to provide a diverse but self-tolerant T cell repertoire has invited quantitative modeling approaches, which are reviewed here.
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Affiliation(s)
- Andrew J Yates
- Departments of Systems and Computational Biology, Microbiology and Immunology, Albert Einstein College of Medicine , New York, NY , USA
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Caridade M, Graca L, Ribeiro RM. Mechanisms Underlying CD4+ Treg Immune Regulation in the Adult: From Experiments to Models. Front Immunol 2013; 4:378. [PMID: 24302924 PMCID: PMC3831161 DOI: 10.3389/fimmu.2013.00378] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/03/2013] [Indexed: 12/29/2022] Open
Abstract
To maintain immunological balance the organism has to be tolerant to self while remaining competent to mount an effective immune response against third-party antigens. An important mechanism of this immune regulation involves the action of regulatory T-cell (Tregs). In this mini-review, we discuss some of the known and proposed mechanisms by which Tregs exert their influence in the context of immune regulation, and the contribution of mathematical modeling for these mechanistic studies. These models explore the mechanisms of action of regulatory T cells, and include hypotheses of multiple signals, delivered through simultaneous antigen-presenting cell (APC) conjugation; interaction of feedback loops between APC, Tregs, and effector cells; or production of specific cytokines that act on effector cells. As the field matures, and competing models are winnowed out, it is likely that we will be able to quantify how tolerance-inducing strategies, such as CD4-blockade, affect T-cell dynamics and what mechanisms explain the observed behavior of T-cell based tolerance.
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Affiliation(s)
- Marta Caridade
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa , Lisbon , Portugal ; Instituto Gulbenkian de Ciência , Oeiras , Portugal
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Bains I, van Santen HM, Seddon B, Yates AJ. Models of self-peptide sampling by developing T cells identify candidate mechanisms of thymic selection. PLoS Comput Biol 2013; 9:e1003102. [PMID: 23935465 PMCID: PMC3723501 DOI: 10.1371/journal.pcbi.1003102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 05/01/2013] [Indexed: 11/18/2022] Open
Abstract
Conventional and regulatory T cells develop in the thymus where they are exposed to samples of self-peptide MHC (pMHC) ligands. This probabilistic process selects for cells within a range of responsiveness that allows the detection of foreign antigen without excessive responses to self. Regulatory T cells are thought to lie at the higher end of the spectrum of acceptable self-reactivity and play a crucial role in the control of autoimmunity and tolerance to innocuous antigens. While many studies have elucidated key elements influencing lineage commitment, we still lack a full understanding of how thymocytes integrate signals obtained by sampling self-peptides to make fate decisions. To address this problem, we apply stochastic models of signal integration by T cells to data from a study quantifying the development of the two lineages using controllable levels of agonist peptide in the thymus. We find two models are able to explain the observations; one in which T cells continually re-assess fate decisions on the basis of multiple summed proximal signals from TCR-pMHC interactions; and another in which TCR sensitivity is modulated over time, such that contact with the same pMHC ligand may lead to divergent outcomes at different stages of development. Neither model requires that T(conv) and T(reg) are differentially susceptible to deletion or that the two lineages need qualitatively different signals for development, as have been proposed. We find additional support for the variable-sensitivity model, which is able to explain apparently paradoxical observations regarding the effect of partial and strong agonists on T(conv) and T(reg) development.
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Affiliation(s)
- Iren Bains
- Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Hisse M. van Santen
- Centro Biologia Molecular Severo Ochoa, CSIC/Universidad Autonoma de Madrid, Madrid, Spain
| | - Benedict Seddon
- Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Andrew J. Yates
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, United States of America
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Tuulasvaara A, Baussand J, Laine P, Paulin L, Salminen J, Auvinen P, Gorochov G, Arstila TP. High-sequence diversity and structural conservation in the human T-cell receptor β junctional region during thymic development. Eur J Immunol 2013; 43:2185-93. [DOI: 10.1002/eji.201343360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 03/28/2013] [Accepted: 05/08/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Anni Tuulasvaara
- Department of Bacteriology and Immunology; Haartman Institute; University of Helsinki; Helsinki; Finland
| | | | - Pia Laine
- Institute of Biotechnology; University of Helsinki; Helsinki; Finland
| | - Lars Paulin
- Institute of Biotechnology; University of Helsinki; Helsinki; Finland
| | - Jukka Salminen
- Department of Surgery; Hospital for Children and Adolescents; Helsinki University Hospital; Helsinki; Finland
| | - Petri Auvinen
- Institute of Biotechnology; University of Helsinki; Helsinki; Finland
| | | | - T. Petteri Arstila
- Department of Bacteriology and Immunology; Haartman Institute; University of Helsinki; Helsinki; Finland
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10
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Saeki K, Iwasa Y. Advantage of having regulatory T cells requires localized suppression of immune reactions. J Theor Biol 2009; 260:392-401. [DOI: 10.1016/j.jtbi.2009.06.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 06/20/2009] [Accepted: 06/22/2009] [Indexed: 11/26/2022]
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Carneiro J, Leon K, Caramalho I, van den Dool C, Gardner R, Oliveira V, Bergman ML, Sepúlveda N, Paixão T, Faro J, Demengeot J. When three is not a crowd: a Crossregulation model of the dynamics and repertoire selection of regulatory CD4+ T cells. Immunol Rev 2007; 216:48-68. [PMID: 17367334 DOI: 10.1111/j.1600-065x.2007.00487.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regulatory CD4(+) T cells, enriched in the CD25 pool of healthy individuals, mediate natural tolerance and prevent autoimmune diseases. Despite their fundamental and potential clinical significance, regulatory T (T(R)) cells have not yet been incorporated in a coherent theory of the immune system. This article reviews experimental evidence and theoretical arguments supporting a model of T(R) cell dynamics, uncovering some of its most relevant biological implications. According to this model, the persistence and expansion of T(R) cell populations depend strictly on specific interactions they make with antigen-presenting cells (APCs) and conventional effector T (T(E)) cells. This three-partner crossregulation imposes that T(R) cells feed on the specific autoimmune activities they suppress, with implications ranging from their interactions with other cells to their repertoire selection in the periphery and in the thymus, and to the relationship between these cells and the innate immune system. These implications stem from the basic prediction that the peripheral dynamics sort the CD4(+) T-cell repertoire into two subsets: a less diverse set of small clones of autoreactive effector and regulatory cells that regulate each other's growth, and a more diverse set of barely autoreactive T(E) cell clones, whose expansion is limited only by APC availability. It is argued that such partitioning of the repertoire sets the ground for self-non-self discrimination.
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Monteiro MC, Couceiro S, Penha-Gonçalves C. The multigenic structure of the MHC locus contributes to positive selection efficiency: a role for MHC class II gene-specific restriction. Eur J Immunol 2006; 35:3622-30. [PMID: 16259007 DOI: 10.1002/eji.200535190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The study of T cell positive selection in the thymus has long been focused on the specificity of the MHC-TCR interactions, making use of genetically manipulated mice that display TCR specificities or selecting peptides of limited diversity. However, little is known on the role of the MHC molecules irrespective of the peptide specificity and the implications of MHC multigenic structure in thymic positive selection have not been addressed. Here, we investigated the effect of MHC class II genetic configuration on the positive selection efficiency of naturally generated pre-selection repertoires in the mouse thymus. Analysis of positively selected thymocyte populations in MHC-congenic and -transgenic mice revealed that expression of I-E molecule in the thymic cortex increases positive selection efficiency of CD4 cells by approximately 50%. We show that increments in positive selection attributable to either the I-A and I-E genes are not due to increased MHC class II expression in the thymic cortex and are not affected by the number of MHC alleles. Collectively, our findings imply that MHC class II gene-restricted TCR specificities significantly contribute to positive selection efficiency, introducing the notion that multigenic structure of the MHC locus serves to increase selection of non-overlapping TCR repertoires.
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