{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:35:25Z","timestamp":1762508125396,"version":"3.37.3"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2020,5,20]],"date-time":"2020-05-20T00:00:00Z","timestamp":1589932800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010434","name":"\u201cla Caixa\u201d Foundation","doi-asserted-by":"publisher","award":["LCF\/PR\/GN17\/50300003"],"award-info":[{"award-number":["LCF\/PR\/GN17\/50300003"]}],"id":[{"id":"10.13039\/100010434","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010434","name":"\u201cla Caixa\u201d Foundation","doi-asserted-by":"publisher","award":["LCF\/PR\/GN17\/50300003"],"award-info":[{"award-number":["LCF\/PR\/GN17\/50300003"]}],"id":[{"id":"10.13039\/100010434","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014440","name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","doi-asserted-by":"publisher","award":["PGC2018-095456-B-I00 (with FEDER)"],"award-info":[{"award-number":["PGC2018-095456-B-I00 (with FEDER)"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014440","name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","doi-asserted-by":"publisher","award":["PGC2018-095456-B-I00 (with FEDER)"],"award-info":[{"award-number":["PGC2018-095456-B-I00 (with FEDER)"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["ISCIII, CPII18\/00031"],"award-info":[{"award-number":["ISCIII, CPII18\/00031"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003030","name":"Ag\u00e8ncia de Gesti\u00f3 d\u2019Ajuts Universitaris i de Recerca","doi-asserted-by":"publisher","award":["2017-SGR-500"],"award-info":[{"award-number":["2017-SGR-500"]}],"id":[{"id":"10.13039\/501100003030","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003030","name":"Ag\u00e8ncia de Gesti\u00f3 d\u2019Ajuts Universitaris i de Recerca","doi-asserted-by":"publisher","award":["2017-SGR-500"],"award-info":[{"award-number":["2017-SGR-500"]}],"id":[{"id":"10.13039\/501100003030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007772","type":"journal-article","created":{"date-parts":[[2020,5,20]],"date-time":"2020-05-20T17:35:29Z","timestamp":1589996129000},"page":"e1007772","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Modelling the dynamics of tuberculosis lesions in a virtual lung: Role of the bronchial tree in endogenous reinfection"],"prefix":"10.1371","volume":"16","author":[{"given":"Mart\u00ed","family":"Catal\u00e0","sequence":"first","affiliation":[]},{"given":"Jordi","family":"Bechini","sequence":"additional","affiliation":[]},{"given":"Montserrat","family":"Tenesa","sequence":"additional","affiliation":[]},{"given":"Ricardo","family":"P\u00e9rez","sequence":"additional","affiliation":[]},{"given":"Mariano","family":"Moya","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2808-7270","authenticated-orcid":true,"given":"Cristina","family":"Vilaplana","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2346-5041","authenticated-orcid":true,"given":"Joaquim","family":"Valls","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3989-8757","authenticated-orcid":true,"given":"Sergio","family":"Alonso","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"L\u00f3pez","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5623-7873","authenticated-orcid":true,"given":"Pere-Joan","family":"Cardona","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1398-7559","authenticated-orcid":true,"given":"Clara","family":"Prats","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,5,20]]},"reference":[{"key":"pcbi.1007772.ref001","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.coisb.2018.10.004","article-title":"Can systems immunology lead tuberculosis eradication?","volume":"12","author":"PJ Cardona","year":"2018","journal-title":"Current opinion in systems biology"},{"unstructured":"World Health Organization. Global Tuberculosis report. Technical report. 2018. Available from: https:\/\/www.who.int\/tb\/publications\/global_report\/en\/","key":"pcbi.1007772.ref002"},{"key":"pcbi.1007772.ref003","doi-asserted-by":"crossref","first-page":"k2738","DOI":"10.1136\/bmj.k2738","article-title":"Revisiting the timetable of tuberculosis","volume":"362","author":"MA Behr","year":"2018","journal-title":"BMJ"},{"issue":"8","key":"pcbi.1007772.ref004","first-page":"372","article-title":"Mycobacteria and macrophage apoptosis: complex struggle for survival","volume":"1","author":"LE Bermudez","year":"2006","journal-title":"Microbe"},{"key":"pcbi.1007772.ref005","doi-asserted-by":"crossref","first-page":"e22028","DOI":"10.7554\/eLife.22028","article-title":"Intracellular growth of Mycobacterium tuberculosis after macrophage cell death leads to serial killing of host cells","volume":"6","author":"D Mahamed","year":"2017","journal-title":"Elife"},{"issue":"1","key":"pcbi.1007772.ref006","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.eimc.2017.10.015","article-title":"Pathogenesis of tuberculosis and other mycobacteriosis","volume":"36","author":"PJ Cardona","year":"2017","journal-title":"Enfermedades Infecciosas y Microbiolog\u00eda Cl\u00ednica"},{"issue":"1","key":"pcbi.1007772.ref007","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1007\/s00005-009-0062-5","article-title":"Revisiting the natural history of tuberculosis. The inclusion of constant reinfection, host tolerance, and damage-response frameworks leads to a better understanding of latent infection and its evolution towards active disease","volume":"58","author":"PJ Cardona","year":"2010","journal-title":"Arch Immunol Ther Exp (Warsz)"},{"issue":"4","key":"pcbi.1007772.ref008","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1111\/imm.12223","article-title":"Early clearance of Mycobacterium tuberculosis: a new frontier in prevention","volume":"141","author":"A Verrall","year":"2014","journal-title":"Immunology"},{"key":"pcbi.1007772.ref009","doi-asserted-by":"crossref","first-page":"354","DOI":"10.3389\/fmicb.2016.00354","article-title":"The small breathing amplitude at the upper lobes favors the attraction of polymorphonuclear neutrophils to Mycobacterium tuberculosis lesions and helps to understand the evolution toward active disease in an individual-based model","volume":"7","author":"PJ Cardona","year":"2016","journal-title":"Front Microbiol"},{"issue":"3","key":"pcbi.1007772.ref010","doi-asserted-by":"crossref","first-page":"e0148738","DOI":"10.1371\/journal.pone.0148738","article-title":"Modeling granulomas in response to infection in the lung","volume":"11","author":"W Hao","year":"2016","journal-title":"PloS One"},{"issue":"2","key":"pcbi.1007772.ref011","first-page":"407","article-title":"Mathematical model for the growth of Mycobacterium tuberculosis in the granuloma","volume":"15","author":"E Ibarg\u00fcen-Mondrag\u00f3n","year":"2018","journal-title":"Math Biosci Eng"},{"issue":"3","key":"pcbi.1007772.ref012","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.jtbi.2004.06.031","article-title":"Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent\u2010based model","volume":"231","author":"JL Segovia\u2010Juarez","year":"2004","journal-title":"J Theor Biol"},{"issue":"4","key":"pcbi.1007772.ref013","doi-asserted-by":"crossref","first-page":"39","DOI":"10.3390\/computation4040039","article-title":"A multi-compartment hybrid computational model predicts key roles for dendritic cells in tuberculosis infection","volume":"4","author":"S Marino","year":"2016","journal-title":"Computation (Basel)"},{"key":"pcbi.1007772.ref014","doi-asserted-by":"crossref","first-page":"33","DOI":"10.3389\/fmicb.2016.00033","article-title":"Local inflammation, dissemination and coalescence of lesions are key for the progression toward active tuberculosis: the Bubble model","volume":"7","author":"C Prats","year":"2016","journal-title":"Front Microbiol"},{"issue":"1","key":"pcbi.1007772.ref015","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.tube.2013.09.004","article-title":"Damaging role of neutrophilic infiltration in a mouse model of progressive tuberculosis","volume":"94","author":"E Marzo","year":"2014","journal-title":"Tuberculosis (Edinb)"},{"issue":"2","key":"pcbi.1007772.ref016","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1093\/jxb\/10.2.290","article-title":"A flexible growth function for empirical use","volume":"10","author":"F. Richards","year":"1959","journal-title":"Journal of experimental Botany"},{"key":"pcbi.1007772.ref017","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/B978-0-12-404577-4.00003-5","volume-title":"Comparative biology of the normal lung","author":"JL Peake","year":"2015"},{"key":"pcbi.1007772.ref018","doi-asserted-by":"crossref","first-page":"612","DOI":"10.3389\/fmicb.2015.00612","article-title":"The key role of exudative lesions and their encapsulation: lessons learned from the pathology of human pulmonary tuberculosis","volume":"6","author":"PJ Cardona","year":"2015","journal-title":"Front Microbiol"},{"key":"pcbi.1007772.ref019","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1146\/annurev.immunol.22.012703.104635","article-title":"Immunity to tuberculosis","volume":"22","author":"RJ North","year":"2004","journal-title":"Annu. Rev. Immunol"},{"issue":"1\u20132","key":"pcbi.1007772.ref020","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.vetimm.2012.09.022","article-title":"The evolutionary basis for differences between the immune systems of man, mouse, pig and ruminants","volume":"152","author":"M Bailey","year":"2013","journal-title":"Veterinary immunology and immunopathology"},{"key":"pcbi.1007772.ref021","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.tube.2017.07.003","article-title":"The minipig as an animal model to study Mycobacterium tuberculosis infection and natural transmission","volume":"106","author":"L Ramos","year":"2017","journal-title":"Tuberculosis (Edinb)"},{"issue":"4","key":"pcbi.1007772.ref022","doi-asserted-by":"crossref","first-page":"e10030","DOI":"10.1371\/journal.pone.0010030","article-title":"Granuloma encapsulation is a key factor for containing tuberculosis infection in minipigs","volume":"5","author":"O Gil","year":"2010","journal-title":"PLoS One"},{"unstructured":"Bechini J. Estudio de la tuberculosis pulmonar mediante Tomograf\u00eda Computarizada Multidetector en un modelo experimental de minipig. PhD thesis. Universitat Aut\u00f2noma de Barcelona. 2016. Available from: https:\/\/ddd.uab.cat\/pub\/tesis\/2017\/hdl_10803_400765\/jbb1de1.pdf","key":"pcbi.1007772.ref023"},{"unstructured":"Catal\u00e0 M. Modelling and simulation of tuberculosis lesions dynamics in a minipig bronchial tree. Bachelor thesis. Universitat Polit\u00e8cnica de Catalunya. 2015. Available from: https:\/\/upcommons.upc.edu\/handle\/2117\/77133","key":"pcbi.1007772.ref024"},{"unstructured":"Vegu\u00e9 M. Model tridimensional de l\u2019arbre bronquial hum\u00e0 per a l\u2019estudi de la dissemeniaci\u00f3 de Mycobacterium tuberculosis. Master\u2019s thesis. Universitat de Barcelona. 2012.","key":"pcbi.1007772.ref025"},{"key":"pcbi.1007772.ref026","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-87553-3","volume-title":"Morphometry of the human lung","author":"E. Weibel","year":"1963"},{"issue":"12","key":"pcbi.1007772.ref027","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1080\/17460441.2016.1223039","article-title":"Minipigs as models in drug discovery","volume":"11","author":"VK Singh","year":"2016","journal-title":"Expert Opin Drug Discov"},{"issue":"3","key":"pcbi.1007772.ref028","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1073\/pnas.12.3.207","article-title":"The physiological principle of minimum work: I. The vascular system and the cost of blood volume","volume":"12","author":"CD Murray","year":"1926","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"pcbi.1007772.ref029","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1152\/japplphysiol.00984.2010","article-title":"An anatomical and functional model of the human tracheobronchial tree","volume":"110","author":"M Florens","year":"2011","journal-title":"J Appl Physiol (1985)"},{"key":"pcbi.1007772.ref030","first-page":"249","article-title":"Mathematical model of the respiratory system\u2014comparison of the total lung impedance in the adult and neonatal lung","author":"M Rozanek","year":"2007","journal-title":"International Journal of Biomedical Sciences"},{"issue":"6","key":"pcbi.1007772.ref031","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1085\/jgp.9.6.835","article-title":"The physiological principle of minimum work applied to the angle of branching arteries","volume":"9","author":"CD Murray","year":"1926","journal-title":"J Gen Physiol"},{"issue":"6","key":"pcbi.1007772.ref032","doi-asserted-by":"crossref","first-page":"2207","DOI":"10.1152\/jappl.1999.87.6.2207","article-title":"A three-dimensional model of the human airway tree","volume":"87","author":"H Kitaoka","year":"1999","journal-title":"J Appl Physiol (1985)"},{"unstructured":"Ginovart M, Prats C, Portell X. Microbial individual-based models and sensitivity analyses: local and global methods. In: International Conference on Predictive Modeling in Foods (Dublin), 2010; pp. 313\u2013316. Available from: https:\/\/upcommons.upc.edu\/handle\/2117\/13546","key":"pcbi.1007772.ref033"},{"issue":"1","key":"pcbi.1007772.ref034","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.jtbi.2008.04.011","article-title":"A methodology for performing global uncertainty and sensitivity analysis in systems biology","volume":"254","author":"S Marino","year":"2008","journal-title":"Journal of theoretical biology"},{"key":"pcbi.1007772.ref035","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.ejrad.2004.03.009","article-title":"Radiological manifestations of pulmonary tuberculosis","volume":"51","author":"J Andreu","year":"2004","journal-title":"Eur J Radiol"},{"key":"pcbi.1007772.ref036","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-3242-6","volume-title":"Standard book on generalized linear models","author":"P McCullagh","year":"1989","edition":"2"},{"issue":"5147","key":"pcbi.1007772.ref037","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1126\/science.263.5147.641","article-title":"Verification, validation, and confirmation of numerical models in the earth sciences","volume":"263","author":"N Oreskes","year":"1994","journal-title":"Science"},{"issue":"2","key":"pcbi.1007772.ref038","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1007\/s15010-008-8087-y","article-title":"A dynamic reinfection hypothesis of latent tuberculosis infection","volume":"37","author":"PJ Cardona","year":"2009","journal-title":"Infection"},{"issue":"3","key":"pcbi.1007772.ref039","doi-asserted-by":"crossref","first-page":"625","DOI":"10.3934\/mbe.2015.12.625","article-title":"A population model capturing dynamics of tuberculosis granulomas predicts host infection outcomes","volume":"12","author":"C Gong","year":"2015","journal-title":"Mathematical biosciences and engineering: MBE"},{"issue":"3","key":"pcbi.1007772.ref040","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.chom.2018.08.001","article-title":"Alveolar macrophages provide an early Mycobacterium tuberculosis niche and initiate dissemination","volume":"24","author":"SB Cohen","year":"2018","journal-title":"Cell host & microbe"},{"key":"pcbi.1007772.ref041","doi-asserted-by":"crossref","first-page":"6","DOI":"10.3389\/fcimb.2016.00006","article-title":"Oxygen modulates the effectiveness of granuloma mediated host response to Mycobacterium tuberculosis: a multiscale computational biology approach","volume":"6","author":"CL Sershen","year":"2016","journal-title":"Frontiers in cellular and infection microbiology"},{"key":"pcbi.1007772.ref042","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.jtbi.2018.03.006","article-title":"Modelling the effects of bacterial cell state and spatial location on tuberculosis treatment: Insights from a hybrid multiscale cellular automaton model","volume":"446","author":"R Bowness","year":"2018","journal-title":"Journal of theoretical biology"},{"issue":"9","key":"pcbi.1007772.ref043","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1038\/ni.1781","article-title":"Foamy macrophages and the progression of the human tuberculosis granuloma","volume":"10","author":"DG Russell","year":"2009","journal-title":"Nature immunology"},{"issue":"3","key":"pcbi.1007772.ref044","doi-asserted-by":"crossref","first-page":"e00312","DOI":"10.1128\/mBio.00312-17","article-title":"Digitally barcoding Mycobacterium tuberculosis reveals in vivo infection dynamics in the macaque model of tuberculosis","volume":"8","author":"CJ Martin","year":"2017","journal-title":"MBio"},{"key":"pcbi.1007772.ref045","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.tube.2015.10.004","article-title":"Ultra low dose aerosol challenge with Mycobacterium tuberculosis leads to divergent outcomes in rhesus and cynomolgus macaques","volume":"96","author":"S Sharpe","year":"2016","journal-title":"Tuberculosis"},{"key":"pcbi.1007772.ref046","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.3389\/fmicb.2016.01131","article-title":"Strong Inference in Mathematical Modeling: A Method for Robust Science in the Twenty-First Century","volume":"7","author":"VV Ganusov","year":"2016","journal-title":"Front. Microbiol"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007772","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,20]],"date-time":"2020-05-20T17:36:55Z","timestamp":1589996215000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007772"}},"subtitle":[],"editor":[{"given":"Dominik","family":"Wodarz","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,5,20]]},"references-count":46,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,5,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007772","relation":{},"ISSN":["1553-7358"],"issn-type":[{"type":"electronic","value":"1553-7358"}],"subject":[],"published":{"date-parts":[[2020,5,20]]}}}