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Physiol."},{"key":"10.1016\/j.celrep.2025.116469_bib81","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.cell.2019.02.028","article-title":"Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage","volume":"177","author":"Uderhardt","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116469_bib82","doi-asserted-by":"crossref","DOI":"10.1002\/wsbm.1479","article-title":"Intracellular signaling dynamics and their role in coordinating tissue repair","volume":"12","author":"Ghilardi","year":"2020","journal-title":"Wiley Interdiscip. Rev. Syst. Biol. 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Biol."},{"key":"10.1016\/j.celrep.2025.116469_bib103","doi-asserted-by":"crossref","DOI":"10.1016\/j.biomaterials.2023.122393","article-title":"Regenerative capacity of neural tissue scales with changes in tissue mechanics post injury","volume":"303","author":"Carnicer-Lombarte","year":"2023","journal-title":"Biomaterials"},{"key":"10.1016\/j.celrep.2025.116469_bib104","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1038\/s41467-020-15647-5","article-title":"Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis","volume":"11","author":"Tsukui","year":"2020","journal-title":"Nat. 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Cell Sci."},{"key":"10.1016\/j.celrep.2025.116469_bib116","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007157","article-title":"Neutrophils use superoxide to control bacterial infection at a distance","volume":"14","author":"Phan","year":"2018","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.celrep.2025.116469_bib117","article-title":"Basal keratinocytes contribute to all strata of the adult zebrafish epidermis","volume":"9","author":"Lee","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.celrep.2025.116469_bib118","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1006\/dbio.2000.9898","article-title":"Analysis of upstream elements in the HuC promoter leads to the establishment of transgenic zebrafish with fluorescent neurons","volume":"227","author":"Park","year":"2000","journal-title":"Dev. 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