{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T13:45:30Z","timestamp":1790689530482,"version":"4.1.0"},"reference-count":83,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,8,16]],"date-time":"2024-08-16T00:00:00Z","timestamp":1723766400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,8,16]],"date-time":"2024-08-16T00:00:00Z","timestamp":1723766400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100000156","name":"Fonds de Recherche du Qu\u00e9bec - Sant\u00e9","doi-asserted-by":"publisher","award":["318466"],"award-info":[{"award-number":["318466"]}],"id":[{"id":"10.13039\/501100000156","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Yale-Boehringer Ingelheim"},{"DOI":"10.13039\/100004411","name":"Heart and Stroke Foundation of Canada","doi-asserted-by":"publisher","award":["G-18-0022118"],"award-info":[{"award-number":["G-18-0022118"]}],"id":[{"id":"10.13039\/100004411","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["169062"],"award-info":[{"award-number":["169062"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-024-69426-z","type":"journal-article","created":{"date-parts":[[2024,8,16]],"date-time":"2024-08-16T14:02:02Z","timestamp":1723816922000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Dissecting glial scar formation by spatial point pattern and topological data analysis"],"prefix":"10.1038","volume":"14","author":[{"given":"Daniel","family":"Manrique-Castano","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dhananjay","family":"Bhaskar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayman","family":"ElAli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,8,16]]},"reference":[{"key":"69426_CR1","doi-asserted-by":"publisher","first-page":"3879","DOI":"10.1038\/s41467-019-11707-7","volume":"10","author":"EJ Bradbury","year":"2019","unstructured":"Bradbury, E. J. & Burnside, E. R. Moving beyond the glial scar for spinal cord repair. Nat. Commun. 10, 3879 (2019).","journal-title":"Nat. Commun."},{"key":"69426_CR2","doi-asserted-by":"publisher","first-page":"12870","DOI":"10.1523\/JNEUROSCI.2121-13.2013","volume":"33","author":"IB Wanner","year":"2013","unstructured":"Wanner, I. B. et al. Glial scar borders are formed by newly proliferated elongated astrocytes that interact to corral inflammatory and fibrotic cells via STAT3-dependent mechanisms after spinal cord injury. J. Neurosci. 33, 12870\u201312886 (2013).","journal-title":"J. Neurosci."},{"key":"69426_CR3","doi-asserted-by":"publisher","first-page":"199","DOI":"10.3389\/fneur.2016.00199","volume":"7","author":"AR Hackett","year":"2016","unstructured":"Hackett, A. R. & Lee, J. K. Understanding the NG2 glial scar after spinal cord injury. Front. Neurol. 7, 199 (2016).","journal-title":"Front. Neurol."},{"key":"69426_CR4","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/s41467-019-08446-0","volume":"10","author":"V Bellver-Landete","year":"2019","unstructured":"Bellver-Landete, V. et al. Microglia are an essential component of the neuroprotective scar that forms after spinal cord injury. Nat. Commun. 10, 518 (2019).","journal-title":"Nat. Commun."},{"key":"69426_CR5","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2022.113500","volume":"153","author":"C Zhang","year":"2022","unstructured":"Zhang, C. et al. Spatiotemporal dynamics of the cellular components involved in glial scar formation following spinal cord injury. Biomed. Pharmacother. 153, 113500 (2022).","journal-title":"Biomed. Pharmacother."},{"key":"69426_CR6","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1002\/glia.24166","volume":"70","author":"P Conforti","year":"2022","unstructured":"Conforti, P. et al. Fibrinogen regulates lesion border-forming reactive astrocyte properties after vascular damage. Glia 70, 1251\u20131266 (2022).","journal-title":"Glia"},{"key":"69426_CR7","doi-asserted-by":"publisher","first-page":"11511","DOI":"10.1523\/JNEUROSCI.1514-09.2009","volume":"29","author":"RR Voskuhl","year":"2009","unstructured":"Voskuhl, R. R. et al. Reactive astrocytes form scar-like perivascular barriers to leukocytes during adaptive immune inflammation of the CNS. J. Neurosci. 29, 11511\u201311522 (2009).","journal-title":"J. Neurosci."},{"key":"69426_CR8","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s12974-020-02059-x","volume":"18","author":"S Yoshizaki","year":"2021","unstructured":"Yoshizaki, S. et al. Microglial inflammation after chronic spinal cord injury is enhanced by reactive astrocytes via the fibronectin\/\u03b21 integrin pathway. J. Neuroinflammation 18, 12 (2021).","journal-title":"J. Neuroinflammation"},{"key":"69426_CR9","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/nature17623","volume":"532","author":"MA Anderson","year":"2016","unstructured":"Anderson, M. A. et al. Astrocyte scar formation aids central nervous system axon regeneration. Nature 532, 195\u2013200 (2016).","journal-title":"Nature"},{"key":"69426_CR10","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1038\/s41419-020-2733-4","volume":"11","author":"H Fu","year":"2020","unstructured":"Fu, H. et al. Depletion of microglia exacerbates injury and impairs function recovery after spinal cord injury in mice. Cell Death Dis. 11, 528 (2020).","journal-title":"Cell Death Dis."},{"key":"69426_CR11","doi-asserted-by":"publisher","first-page":"78","DOI":"10.3389\/fncel.2020.00078","volume":"14","author":"T Yang","year":"2020","unstructured":"Yang, T., Dai, Y. J., Chen, G. & Cui, S. S. Dissecting the dual role of the glial scar and scar-forming astrocytes in spinal cord injury. Front. Cell. Neurosci. 14, 78 (2020).","journal-title":"Front. Cell. Neurosci."},{"key":"69426_CR12","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1038\/s41598-018-36598-4","volume":"9","author":"L Buscemi","year":"2019","unstructured":"Buscemi, L., Price, M., Bezzi, P. & Hirt, L. Spatio-temporal overview of neuroinflammation in an experimental mouse stroke model. Sci. Rep. 9, 507 (2019).","journal-title":"Sci. Rep."},{"key":"69426_CR13","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1161\/01.STR.32.5.1208","volume":"32","author":"D Ito","year":"2001","unstructured":"Ito, D., Tanaka, K., Suzuki, S., Dembo, T. & Fukuuchi, Y. Enhanced expression of Iba1, ionized calcium-binding adapter molecule 1, after transient focal cerebral ischemia in rat brain. Stroke 32, 1208\u20131215 (2001).","journal-title":"Stroke"},{"key":"69426_CR14","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1016\/j.bbi.2020.10.016","volume":"91","author":"D Manrique-Castano","year":"2021","unstructured":"Manrique-Castano, D. et al. Tenascin-C preserves microglia surveillance and restricts leukocyte and more specifically, T cell infiltration of the ischemic brain. Brain Behav. Immun. 91, 639\u2013648 (2021).","journal-title":"Brain Behav. Immun."},{"key":"69426_CR15","doi-asserted-by":"publisher","first-page":"1036","DOI":"10.1002\/glia.22800","volume":"63","author":"W Kamphuis","year":"2015","unstructured":"Kamphuis, W. et al. GFAP and vimentin deficiency alters gene expression in astrocytes and microglia in wild-type mice and changes the transcriptional response of reactive glia in mouse model for Alzheimer\u2019s disease. Glia 63, 1036\u20131056 (2015).","journal-title":"Glia"},{"key":"69426_CR16","doi-asserted-by":"publisher","first-page":"2309","DOI":"10.1002\/glia.24253","volume":"70","author":"S Schacke","year":"2022","unstructured":"Schacke, S. et al. Ezrin deficiency triggers glial fibrillary acidic protein upregulation and a distinct reactive astrocyte phenotype. Glia 70, 2309\u20132329 (2022).","journal-title":"Glia"},{"key":"69426_CR17","doi-asserted-by":"publisher","first-page":"7980","DOI":"10.1111\/jcmm.16728","volume":"25","author":"X Lu","year":"2021","unstructured":"Lu, X. et al. Gramine promotes functional recovery after spinal cord injury via ameliorating microglia activation. J. Cell. Mol. Med. 25, 7980\u20137992 (2021).","journal-title":"J. Cell. Mol. Med."},{"key":"69426_CR18","doi-asserted-by":"publisher","first-page":"668340","DOI":"10.3389\/fmolb.2021.668340","volume":"8","author":"ER Parra","year":"2021","unstructured":"Parra, E. R. Methods to determine and analyze the cellular spatial distribution extracted from multiplex immunofluorescence data to understand the tumor microenvironment. Front. Mol. Biosci. 8, 668340 (2021).","journal-title":"Front. Mol. Biosci."},{"key":"69426_CR19","first-page":"9","volume":"4","author":"M Jafari-Mamaghani","year":"2010","unstructured":"Jafari-Mamaghani, M., Andersson, M. & Krieger, P. Spatial point pattern analysis of neurons using Ripley\u2019s K-function in 3D. Front. Neuroinform. 4, 9 (2010).","journal-title":"Front. Neuroinform."},{"key":"69426_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-017-01747-8","volume":"7","author":"BM Davis","year":"2017","unstructured":"Davis, B. M., Salinas-Navarro, M., Cordeiro, M. F., Moons, L. & Groef, L. D. Characterizing microglia activation: a spatial statistics approach to maximize information extraction. Sci. Rep. 7, 1\u201312 (2017).","journal-title":"Sci. Rep."},{"key":"69426_CR21","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.jneumeth.2006.08.017","volume":"160","author":"D Prodanov","year":"2007","unstructured":"Prodanov, D., Nagelkerke, N. & Marani, E. Spatial clustering analysis in neuroanatomy: Applications of different approaches to motor nerve fiber distribution. J. Neurosci. Methods 160, 93\u2013108 (2007).","journal-title":"J. Neurosci. Methods"},{"key":"69426_CR22","doi-asserted-by":"publisher","first-page":"4653","DOI":"10.1039\/D1SM00072A","volume":"17","author":"D Bhaskar","year":"2021","unstructured":"Bhaskar, D., Zhang, W. Y. & Wong, I. Y. Topological data analysis of collective and individual epithelial cells using persistent homology of loops. Soft Matter 17, 4653\u20134664 (2021).","journal-title":"Soft Matter"},{"key":"69426_CR23","doi-asserted-by":"publisher","first-page":"16414","DOI":"10.1038\/s41598-021-94847-5","volume":"11","author":"H Masoomy","year":"2021","unstructured":"Masoomy, H., Askari, B., Tajik, S., Rizi, A. K. & Jafari, G. R. Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach. Sci. Rep. 11, 16414 (2021).","journal-title":"Sci. Rep."},{"key":"69426_CR24","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1008407","volume":"16","author":"LL Bonilla","year":"2020","unstructured":"Bonilla, L. L., Carpio, A. & Trenado, C. Tracking collective cell motion by topological data analysis. PLoS Comput. Biol. 16, e1008407 (2020).","journal-title":"PLoS Comput. Biol."},{"key":"69426_CR25","doi-asserted-by":"publisher","DOI":"10.1002\/pan3.10461","author":"M Malavasi","year":"2023","unstructured":"Malavasi, M. et al. Ecology meets archaeology: Past present and future vegetation-derived ecosystems services from the Nuragic Sardinia. People Nat. https:\/\/doi.org\/10.1002\/pan3.10461 (2023).","journal-title":"People Nat."},{"key":"69426_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12942-020-00225-1","volume":"19","author":"C Scarpone","year":"2020","unstructured":"Scarpone, C. et al. A multimethod approach for county-scale geospatial analysis of emerging infectious diseases: A cross-sectional case study of COVID-19 incidence in Germany. Int. J. Health Geogr. 19, 1\u201317 (2020).","journal-title":"Int. J. Health Geogr."},{"key":"69426_CR27","doi-asserted-by":"publisher","first-page":"308","DOI":"10.3390\/cancers14020308","volume":"14","author":"BA Maisel","year":"2022","unstructured":"Maisel, B. A. et al. Spatial metrics of interaction between CD163-positive macrophages and cancer cells and progression-free survival in chemo-treated breast cancer. Cancers 14, 308 (2022).","journal-title":"Cancers"},{"key":"69426_CR28","doi-asserted-by":"publisher","first-page":"1924","DOI":"10.3390\/cancers13081924","volume":"13","author":"J Kaufmann","year":"2021","unstructured":"Kaufmann, J. et al. Using the R package Spatstat to assess inhibitory effects of microregional hypoxia on the infiltration of cancers of the head and neck region by cytotoxic T lymphocytes. Cancers (Basel) 13, 1924 (2021).","journal-title":"Cancers (Basel)"},{"key":"69426_CR29","doi-asserted-by":"publisher","first-page":"e2102166118","DOI":"10.1073\/pnas.2102166118","volume":"118","author":"O Vipond","year":"2021","unstructured":"Vipond, O. et al. Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors. Proc. Natl. Acad. Sci. 118, e2102166118 (2021).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"69426_CR30","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1038\/s41598-018-36798-y","volume":"9","author":"P Lawson","year":"2019","unstructured":"Lawson, P., Sholl, A. B., Brown, J. Q., Fasy, B. T. & Wenk, C. Persistent homology for the quantitative evaluation of architectural features in prostate cancer histology. Sci. Rep. 9, 1139 (2019).","journal-title":"Sci. Rep."},{"key":"69426_CR31","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1002\/dvdy.175","volume":"249","author":"EJ Am\u00e9zquita","year":"2020","unstructured":"Am\u00e9zquita, E. J., Quigley, M. Y., Ophelders, T., Munch, E. & Chitwood, D. H. The shape of things to come: Topological data analysis and biology from molecules to organisms. Dev. Dyn. 249, 816\u2013833 (2020).","journal-title":"Dev. Dyn."},{"key":"69426_CR32","doi-asserted-by":"publisher","first-page":"3230","DOI":"10.1038\/s41467-020-17035-5","volume":"11","author":"J Townsend","year":"2020","unstructured":"Townsend, J., Micucci, C. P., Hymel, J. H., Maroulas, V. & Vogiatzis, K. D. Representation of molecular structures with persistent homology for machine learning applications in chemistry. Nat. Commun. 11, 3230 (2020).","journal-title":"Nat. Commun."},{"key":"69426_CR33","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s12021-017-9341-1","volume":"16","author":"L Kanari","year":"2017","unstructured":"Kanari, L. et al. A topological representation of branching neuronal morphologies. Neuroinformatics 16, 3\u201313 (2017).","journal-title":"Neuroinformatics"},{"key":"69426_CR34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009094","volume":"17","author":"JT Nardini","year":"2021","unstructured":"Nardini, J. T., Stolz, B. J., Flores, K. B., Harrington, H. A. & Byrne, H. M. Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis. PLOS Comput. Biol. 17, e1009094 (2021).","journal-title":"PLOS Comput. Biol."},{"key":"69426_CR35","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.expneurol.2005.05.013","volume":"195","author":"MS Dittmar","year":"2005","unstructured":"Dittmar, M. S. et al. The role of ECA transection in the development of masticatory lesions in the MCAO filament model. Exp. Neurol. 195, 372\u2013378 (2005).","journal-title":"Exp. Neurol."},{"key":"69426_CR36","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"},{"key":"69426_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-017-17204-5","volume":"7","author":"P Bankhead","year":"2017","unstructured":"Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Sci. Rep. 7, 1\u20137 (2017).","journal-title":"Sci. Rep."},{"key":"69426_CR38","doi-asserted-by":"publisher","DOI":"10.1201\/b19708","volume-title":"Spatial Point Patterns","author":"A Baddeley","year":"2015","unstructured":"Baddeley, A., Rubak, E. & Turner, R. Spatial Point Patterns (Apple Academic Press, 2015)."},{"key":"69426_CR39","unstructured":"Hijmans, R. J. raster: Geographic data analysis and modeling. (2023)."},{"key":"69426_CR40","unstructured":"Zhang, S., Xiao, M. & Wang, H. GPU-Accelerated Computation of Vietoris-Rips Persistence Barcodes. in 36th International Symposium on Computational Geometry (SoCG 2020) (Schloss Dagstuhl-Leibniz-Zentrum f\u00fcr Informatik, 2020)."},{"key":"69426_CR41","doi-asserted-by":"publisher","first-page":"681108","DOI":"10.3389\/frai.2021.681108","volume":"4","author":"F Hensel","year":"2021","unstructured":"Hensel, F., Moor, M. & Rieck, B. A survey of topological machine learning methods. Front. Artif. Intell. 4, 681108 (2021).","journal-title":"Front. Artif. Intell."},{"key":"69426_CR42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000173","volume":"4","author":"A Ben-Hur","year":"2008","unstructured":"Ben-Hur, A., Ong, C. S., Sonnenburg, S., Sch\u00f6lkopf, B. & R\u00e4tsch, G. Support vector machines and kernels for computational biology. PLoS Comput. Biol. 4, e1000173 (2008).","journal-title":"PLoS Comput. Biol."},{"key":"69426_CR43","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/s13321-023-00709-9","volume":"15","author":"TM Dutschmann","year":"2023","unstructured":"Dutschmann, T. M., Kinzel, L., ter Laak, A. & Baumann, K. Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation. J. Cheminformatics 15, 49 (2023).","journal-title":"J. Cheminformatics"},{"key":"69426_CR44","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1080\/10485252.2017.1404598","volume":"30","author":"Y Jung","year":"2017","unstructured":"Jung, Y. Multiple predicting K-fold cross-validation for model selection. J. Nonparametric Stat. 30, 197\u2013215 (2017).","journal-title":"J. Nonparametric Stat."},{"key":"69426_CR45","doi-asserted-by":"publisher","first-page":"395","DOI":"10.32614\/RJ-2018-017","volume":"10","author":"PC B\u00fcrkner","year":"2018","unstructured":"B\u00fcrkner, P. C. Advanced Bayesian multilevel modeling with the R package brms. R J. 10, 395 (2018).","journal-title":"R J."},{"key":"69426_CR46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v012.i06","volume":"12","author":"A Baddeley","year":"2005","unstructured":"Baddeley, A. & Turner, R. Spatstat: An R-package for analyzing spatial point patterns. J. Stat. Softw. 12, 1\u201342 (2005).","journal-title":"J. Stat. Softw."},{"key":"69426_CR47","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1016\/j.bjpt.2018.12.006","volume":"23","author":"L Hespanhol","year":"2019","unstructured":"Hespanhol, L., Vallio, C. S., Costa, L. M. & Saragiotto, B. T. Understanding and interpreting confidence and credible intervals around effect estimates. Braz. J. Phys. Ther. 23, 290\u2013301 (2019).","journal-title":"Braz. J. Phys. Ther."},{"key":"69426_CR48","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1080\/01621459.2012.688463","volume":"107","author":"U Hahn","year":"2012","unstructured":"Hahn, U. A studentized permutation test for the comparison of spatial point patterns. J. Am. Stat. Assoc. 107, 754\u2013764 (2012).","journal-title":"J. Am. Stat. Assoc."},{"key":"69426_CR49","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1007\/s00401-009-0619-8","volume":"119","author":"MV Sofroniew","year":"2009","unstructured":"Sofroniew, M. V. & Vinters, H. V. Astrocytes: Biology and pathology. Acta Neuropathol. 119, 7\u201335 (2009).","journal-title":"Acta Neuropathol."},{"key":"69426_CR50","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1016\/j.brainres.2004.04.032","volume":"1015","author":"I Unal-Cevik","year":"2004","unstructured":"Unal-Cevik, I., Kilin\u00e7, M., G\u00fcrsoy-Ozdemir, Y., Gurer, G. & Dalkara, T. Loss of NeuN immunoreactivity after cerebral ischemia does not indicate neuronal cell loss: A cautionary note. Brain Res. 1015, 169\u2013174 (2004).","journal-title":"Brain Res."},{"key":"69426_CR51","doi-asserted-by":"publisher","unstructured":"Manrique-Castano, D. & ElAli, A. Neurovascular Reactivity in Tissue Scarring Following Cerebral Ischemia. in Cerebral Ischemia, pp 111\u2013130 (Exon Publications, 2021). https:\/\/doi.org\/10.36255\/exonpublications.cerebralischemia.2021.neurovascularreactivity.","DOI":"10.36255\/exonpublications.cerebralischemia.2021.neurovascularreactivity"},{"key":"69426_CR52","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1038\/nm1425","volume":"12","author":"S Okada","year":"2006","unstructured":"Okada, S. et al. Conditional ablation of Stat3 or Socs3 discloses a dual role for reactive astrocytes after spinal cord injury. Nat. Med. 12, 829\u2013834 (2006).","journal-title":"Nat. Med."},{"key":"69426_CR53","unstructured":"Spatial Point Patterns: Methodology and Applications with R. (Chapman and Hall\/CRC Press, 2015)."},{"key":"69426_CR54","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.4103\/1673-5374.357912","volume":"18","author":"H Zhang","year":"2023","unstructured":"Zhang, H. et al. Microglial depletion impairs glial scar formation and aggravates inflammation partly by inhibiting STAT3 phosphorylation in astrocytes after spinal cord injury. Neural Regen. Res. 18, 1325 (2023).","journal-title":"Neural Regen. Res."},{"key":"69426_CR55","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/j.bbi.2019.04.016","volume":"80","author":"Y Gu","year":"2019","unstructured":"Gu, Y. et al. Conditional ablation of reactive astrocytes to dissect their roles in spinal cord injury and repair. Brain Behav. Immun. 80, 394\u2013405 (2019).","journal-title":"Brain Behav. Immun."},{"key":"69426_CR56","doi-asserted-by":"publisher","first-page":"7231","DOI":"10.1523\/JNEUROSCI.1709-08.2008","volume":"28","author":"JE Herrmann","year":"2008","unstructured":"Herrmann, J. E. et al. STAT3 is a regulator of astrogliosis and scar formation after spinal cord injury. J. Neurosci. 28, 7231\u20137243 (2008).","journal-title":"J. Neurosci."},{"key":"69426_CR57","doi-asserted-by":"publisher","first-page":"10285","DOI":"10.1523\/JNEUROSCI.4915-13.2014","volume":"34","author":"JP Rodriguez","year":"2014","unstructured":"Rodriguez, J. P. et al. Abrogation of -catenin signaling in oligodendrocyte precursor cells reduces glial scarring and promotes axon regeneration after CNS injury. J. Neurosci. 34, 10285\u201310297 (2014).","journal-title":"J. Neurosci."},{"key":"69426_CR58","doi-asserted-by":"publisher","first-page":"1366","DOI":"10.1523\/JNEUROSCI.3953-16.2017","volume":"38","author":"ZC Hesp","year":"2017","unstructured":"Hesp, Z. C. et al. Proliferating NG2-cell-dependent angiogenesis and scar formation alter axon growth and functional recovery after spinal cord injury in mice. J. Neurosci. 38, 1366\u20131382 (2017).","journal-title":"J. Neurosci."},{"key":"69426_CR59","doi-asserted-by":"publisher","first-page":"3758","DOI":"10.1038\/s41467-019-11674-z","volume":"10","author":"E Spangenberg","year":"2019","unstructured":"Spangenberg, E. et al. Sustained microglial depletion with CSF1R inhibitor impairs parenchymal plaque development in an Alzheimer\u2019s disease model. Nat. Commun. 10, 3758 (2019).","journal-title":"Nat. Commun."},{"key":"69426_CR60","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1016\/j.bbi.2021.07.016","volume":"99","author":"MA Al-Onaizi","year":"2022","unstructured":"Al-Onaizi, M. A. et al. Early monocyte modulation by the non-erythropoietic peptide ARA 290 decelerates AD-like pathology progression. Brain Behav. Immun. 99, 363\u2013382 (2022).","journal-title":"Brain Behav. Immun."},{"key":"69426_CR61","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1093\/brain\/awz363","volume":"143","author":"JD Crapser","year":"2019","unstructured":"Crapser, J. D. et al. Microglial depletion prevents extracellular matrix changes and striatal volume reduction in a model of Huntingtons disease. Brain 143, 266\u2013288 (2019).","journal-title":"Brain"},{"key":"69426_CR62","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1186\/s40478-022-01440-6","volume":"10","author":"H Sekiya","year":"2022","unstructured":"Sekiya, H. et al. Discrepancy between distribution of alpha-synuclein oligomers and Lewy-related pathology in Parkinson\u2019s disease. Acta Neuropathol. Commun. 10, 133 (2022).","journal-title":"Acta Neuropathol. Commun."},{"key":"69426_CR63","doi-asserted-by":"publisher","first-page":"12870","DOI":"10.1523\/JNEUROSCI.2121-13.2013","volume":"33","author":"IB Wanner","year":"2013","unstructured":"Wanner, I. B. et al. Glial scar borders are formed by newly proliferated, elongated astrocytes that interact to corral inflammatory and fibrotic cells via STAT3-dependent mechanisms after spinal cord injury. J. Neurosci. 33, 12870\u201312886 (2013).","journal-title":"J. Neurosci."},{"key":"69426_CR64","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1111\/bpa.12162","volume":"24","author":"F Fern\u00e1ndez-Klett","year":"2014","unstructured":"Fern\u00e1ndez-Klett, F. & Priller, J. The fibrotic scar in neurological disorders. Brain Pathol. 24, 404\u2013413 (2014).","journal-title":"Brain Pathol."},{"key":"69426_CR65","doi-asserted-by":"publisher","first-page":"175628641881809","DOI":"10.1177\/1756286418818092","volume":"11","author":"E Dzyubenko","year":"2018","unstructured":"Dzyubenko, E., Manrique-Castano, D., Kleinschnitz, C., Faissner, A. & Hermann, D. M. Role of immune responses for extracellular matrix remodeling in the ischemic brain. Ther. Adv. Neurol. Disord. 11, 175628641881809 (2018).","journal-title":"Ther. Adv. Neurol. Disord."},{"key":"69426_CR66","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.matbio.2022.04.003","volume":"110","author":"E Dzyubenko","year":"2022","unstructured":"Dzyubenko, E. et al. Tenascin-C restricts reactive astrogliosis in the ischemic brain. Matrix Biol. 110, 1\u201315 (2022).","journal-title":"Matrix Biol."},{"key":"69426_CR67","doi-asserted-by":"publisher","first-page":"5501","DOI":"10.1038\/s41467-021-25585-5","volume":"12","author":"DO Dias","year":"2021","unstructured":"Dias, D. O. et al. Pericyte-derived fibrotic scarring is conserved across diverse central nervous system lesions. Nat. Commun. 12, 5501 (2021).","journal-title":"Nat. Commun."},{"key":"69426_CR68","doi-asserted-by":"publisher","first-page":"13882","DOI":"10.1523\/JNEUROSCI.2524-13.2013","volume":"33","author":"C Soderblom","year":"2013","unstructured":"Soderblom, C. et al. Perivascular fibroblasts form the fibrotic scar after contusive spinal cord injury. J. Neurosci. 33, 13882\u201313887 (2013).","journal-title":"J. Neurosci."},{"key":"69426_CR69","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1126\/science.1203165","volume":"333","author":"C G\u00f6ritz","year":"2011","unstructured":"G\u00f6ritz, C. et al. A pericyte origin of spinal cord scar tissue. Science 333, 238\u2013242 (2011).","journal-title":"Science"},{"key":"69426_CR70","doi-asserted-by":"publisher","first-page":"659037","DOI":"10.3389\/frai.2021.659037","volume":"4","author":"A Bukkuri","year":"2021","unstructured":"Bukkuri, A., Andor, N. & Darcy, I. K. Applications of topological data analysis in oncology. Front. Artif. Intell. 4, 659037 (2021).","journal-title":"Front. Artif. Intell."},{"key":"69426_CR71","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/s13244-023-01413-w","volume":"14","author":"Y Singh","year":"2023","unstructured":"Singh, Y. et al. Topological data analysis in medical imaging: Current state of the art. Insights Imaging 14, 58 (2023).","journal-title":"Insights Imaging"},{"key":"69426_CR72","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s41540-023-00302-8","volume":"9","author":"D Bhaskar","year":"2023","unstructured":"Bhaskar, D., Zhang, W. Y., Volkening, A., Sandstede, B. & Wong, I. Y. Topological data analysis of spatial patterning in heterogeneous cell populations: Clustering and sorting with varying cell-cell adhesion. npj Syst. Biol. Appl. 9, 43 (2023).","journal-title":"npj Syst. Biol. Appl."},{"key":"69426_CR73","doi-asserted-by":"publisher","first-page":"3023","DOI":"10.3934\/mbe.2023143","volume":"20","author":"M Dawson","year":"2022","unstructured":"Dawson, M., Dudley, C., Omoma, S., Tung, H. R. & Ciocanel, M. V. Characterizing emerging features in cell dynamics using topological data analysis methods. Math. Biosci. Eng. 20, 3023\u20133046 (2022).","journal-title":"Math. Biosci. Eng."},{"key":"69426_CR74","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1038\/s41598-020-79391-y","volume":"11","author":"T Yamanashi","year":"2021","unstructured":"Yamanashi, T. et al. Topological data analysis (TDA) enhances bispectral EEG (BSEEG) algorithm for detection of delirium. Sci. Rep. 11, 304 (2021).","journal-title":"Sci. Rep."},{"key":"69426_CR75","doi-asserted-by":"publisher","first-page":"4791","DOI":"10.1038\/s41467-022-32381-2","volume":"13","author":"M Saggar","year":"2022","unstructured":"Saggar, M., Shine, J. M., Li\u00e9geois, R., Dosenbach, N. U. F. & Fair, D. Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest. Nat. Commun. 13, 4791 (2022).","journal-title":"Nat. Commun."},{"key":"69426_CR76","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0276419","volume":"18","author":"S Das","year":"2023","unstructured":"Das, S., Anand, D. V. & Chung, M. K. Topological data analysis of human brain networks through order statistics. PLOS ONE 18, e0276419 (2023).","journal-title":"PLOS ONE"},{"key":"69426_CR77","doi-asserted-by":"publisher","first-page":"702","DOI":"10.1007\/s13311-016-0463-1","volume":"13","author":"E Kim","year":"2016","unstructured":"Kim, E. & Cho, S. Microglia and monocyte-derived macrophages in stroke. Neurotherapeutics 13, 702\u2013718 (2016).","journal-title":"Neurotherapeutics"},{"key":"69426_CR78","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1002\/glia.20281","volume":"53","author":"T Imura","year":"2005","unstructured":"Imura, T., Nakano, I., Kornblum, H. I. & Sofroniew, M. V. Phenotypic and functional heterogeneity of GFAP-expressing cells in vitro: Differential expression of LeX\/CD15 by GFAP-expressing multipotent neural stem cells and non-neurogenic astrocytes. Glia 53, 277\u2013293 (2005).","journal-title":"Glia"},{"key":"69426_CR79","doi-asserted-by":"publisher","first-page":"102989","DOI":"10.1016\/j.xpro.2024.102989","volume":"5","author":"D Manrique-Castano","year":"2024","unstructured":"Manrique-Castano, D. & ElAli, A. Unbiased quantification of the spatial distribution of murine cells using point pattern analysis. STAR Protoc. 5, 102989 (2024).","journal-title":"STAR Protoc."},{"key":"69426_CR80","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-018-2375-z","volume":"19","author":"Y Al-Kofahi","year":"2018","unstructured":"Al-Kofahi, Y., Zaltsman, A., Graves, R., Marshall, W. & Rusu, M. A deep learning-based algorithm for 2-D cell segmentation in microscopy images. BMC Bioinf. 19, 1\u201311 (2018).","journal-title":"BMC Bioinf."},{"key":"69426_CR81","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/s41587-021-01094-0","volume":"40","author":"NF Greenwald","year":"2021","unstructured":"Greenwald, N. F. et al. Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. Nat. Biotechnol. 40, 555\u2013565 (2021).","journal-title":"Nat. Biotechnol."},{"key":"69426_CR82","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41592-020-01018-x","volume":"18","author":"C Stringer","year":"2020","unstructured":"Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods 18, 100\u2013106 (2020).","journal-title":"Nat. Methods"},{"key":"69426_CR83","doi-asserted-by":"publisher","first-page":"155","DOI":"10.3758\/s13423-017-1272-1","volume":"25","author":"JK Kruschke","year":"2018","unstructured":"Kruschke, J. K. & Liddell, T. M. Bayesian data analysis for newcomers. Psychon. Bull. Rev. 25, 155\u2013177 (2018).","journal-title":"Psychon. Bull. Rev."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-69426-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-69426-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-69426-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,16]],"date-time":"2024-08-16T15:03:16Z","timestamp":1723820596000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-69426-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,16]]},"references-count":83,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["69426"],"URL":"https:\/\/doi.org\/10.1038\/s41598-024-69426-z","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.10.04.560910","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,16]]},"assertion":[{"value":"17 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"19035"}}