{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T00:15:41Z","timestamp":1789776941044,"version":"4.0.1"},"reference-count":138,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T00:00:00Z","timestamp":1749081600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006492","name":"National Institute of Allergy and Infectious Diseases Division of Intramural Research","doi-asserted-by":"publisher","award":["R01 AI50684"],"award-info":[{"award-number":["R01 AI50684"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Theoretical Biology"],"published-print":{"date-parts":[[2025,8]]},"DOI":"10.1016\/j.jtbi.2025.112176","type":"journal-article","created":{"date-parts":[[2025,6,1]],"date-time":"2025-06-01T18:01:16Z","timestamp":1748800876000},"page":"112176","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":4,"special_numbering":"C","title":["Rankings of tuberculosis antibiotic treatment regimens are sensitive to spatial scale, detection limit, and initial host bacterial burden"],"prefix":"10.1016","volume":"611","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3583-6097","authenticated-orcid":false,"given":"Christian T.","family":"Michael","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7934-4230","authenticated-orcid":false,"given":"Maral","family":"Budak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pauline","family":"Maiello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kara","family":"Kracinovsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9800-3362","authenticated-orcid":false,"given":"Mark","family":"Rodgers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaime","family":"Tomko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philana Ling","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"JoAnne","family":"Flynn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1519-5088","authenticated-orcid":false,"given":"Jennifer J.","family":"Linderman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1053-2591","authenticated-orcid":false,"given":"Denise","family":"Kirschner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jtbi.2025.112176_b0005","series-title":"Gloal Tuberculosis Report 2024","author":"WHO","year":"2024"},{"key":"10.1016\/j.jtbi.2025.112176_b0010","series-title":"World Health Organization News Release","author":"Mackenzie","year":"2024"},{"key":"10.1016\/j.jtbi.2025.112176_b0015","doi-asserted-by":"crossref","first-page":"2541","DOI":"10.4049\/jimmunol.1800993","article-title":"The end of the binary era: revisiting the spectrum of tuberculosis","volume":"201","author":"Lin","year":"2018","journal-title":"J. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0020","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1038\/nri.2017.69","article-title":"Heterogeneity in tuberculosis","volume":"17","author":"Cadena","year":"2017","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0025","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1005739","article-title":"PET CT identifies reactivation risk in cynomolgus macaques with latent M. tuberculosis","volume":"12","author":"Lin","year":"2016","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jtbi.2025.112176_b0030","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00159-19","article-title":"Caseum: a Niche for mycobacterium tuberculosis drug-tolerant persisters","volume":"33","author":"Sarathy","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.jtbi.2025.112176_b0035","doi-asserted-by":"crossref","first-page":"e1516","DOI":"10.1128\/mBio.01586-16","article-title":"Origins of combination therapy for tuberculosis: lessons for future antimicrobial development and application","volume":"8","author":"Kerantzas","year":"2017","journal-title":"MBio"},{"key":"10.1016\/j.jtbi.2025.112176_b0040","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1093\/cid\/ciw566","article-title":"Executive summary: official american thoracic society\/centers for disease control and prevention\/infectious diseases society of america clinical practice guidelines: treatment of drug-susceptible tuberculosis","volume":"63","author":"Nahid","year":"2016","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.jtbi.2025.112176_b0045","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1016\/S0140-6736(15)60570-0","article-title":"WHO's new end TB strategy","volume":"385","author":"Uplekar","year":"2015","journal-title":"Lancet"},{"key":"10.1016\/j.jtbi.2025.112176_b0050","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s12195-017-0507-6","article-title":"Applying optimization algorithms to tuberculosis antibiotic treatment regimens","volume":"10","author":"Cicchese","year":"2017","journal-title":"Cell. Mol. Bioeng."},{"key":"10.1016\/j.jtbi.2025.112176_b0055","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.coisb.2017.05.014","article-title":"A review of computational and mathematical modeling contributions to our understanding of Mycobacterium tuberculosis within-host infection and treatment","volume":"3","author":"Kirschner","year":"2017","journal-title":"Curr. Opin. Syst. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0060","doi-asserted-by":"crossref","unstructured":"Nanda, P., Budak, M., Michael, C. T., Krupinsky, K. & Kirschner, D. E. in Predicting Pandemics in a Globally Connected World, Volume 2 Modeling and Simulation in Science, Engineering and Technology Ch. Chapter 2, 11-43 (Cold Spring Harbor Laboratory, 2024).","DOI":"10.1007\/978-3-031-56794-0_2"},{"key":"10.1016\/j.jtbi.2025.112176_b0065","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-based model","volume":"231","author":"Segovia-Juarez","year":"2004","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0070","doi-asserted-by":"crossref","first-page":"3706","DOI":"10.4049\/jimmunol.0802297","article-title":"Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection","volume":"182","author":"Ray","year":"2009","journal-title":"J. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0075","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000778","article-title":"Identification of key processes that control tumor necrosis factor availability in a tuberculosis granuloma","volume":"6","author":"Fallahi-Sichani","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0080","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.712457","article-title":"Neutrophil dynamics affect mycobacterium tuberculosis granuloma outcomes and dissemination","volume":"12","author":"Hult","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0085","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1128\/IAI.02494-14","article-title":"Macrophage polarization drives granuloma outcome during \u201cMycobacterium tuberculosis\u201d infection","volume":"83","author":"Marino","year":"2015","journal-title":"Infect. Immun."},{"key":"10.1016\/j.jtbi.2025.112176_b0090","first-page":"644","article-title":"IL-10 impairs local immune response in lung granulomas and lymph nodes during early Mycobacterium tuberculosis","volume":"204","author":"Wong","year":"2020","journal-title":"Infection"},{"key":"10.1016\/j.jtbi.2025.112176_b0095","article-title":"Spatial organization and recruitment of non-specific t cells may limit t cell-macrophage interactions within Mycobacterium tuberculosis granulomas","volume":"11","author":"Millar","year":"2020","journal-title":"Front. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0100","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0068680","article-title":"Multi-scale modeling predicts a balance of tumor necrosis factor-alpha and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection","volume":"8","author":"Cilfone","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jtbi.2025.112176_b0105","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1111\/imr.12258","article-title":"Immunology studies in non-human primate models of tuberculosis","volume":"264","author":"Flynn","year":"2015","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.jtbi.2025.112176_b0110","unstructured":"Flynn, J. L., Tsenova, L., Izzo, A. & Kaplan, G. in Handbook of Tuberculosis (eds S. H. E. Kaufmann, E. Rubin, W. J. Britton, & P. Helden) Ch. 15, 389-426 (2017)."},{"key":"10.1016\/j.jtbi.2025.112176_b0115","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005650","article-title":"Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach","volume":"13","author":"Pienaar","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0120","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.jtbi.2014.11.021","article-title":"A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment","volume":"367","author":"Pienaar","year":"2015","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0125","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s12918-015-0221-8","article-title":"In silico evaluation and exploration of antibiotic tuberculosis treatment regimens","volume":"9","author":"Pienaar","year":"2015","journal-title":"BMC Syst. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0130","doi-asserted-by":"crossref","unstructured":"Cicchese, J., Sambarey, A., Kirschner, D., Linderman, J. & Chandrasekaran, S. A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs. (2020). https:\/\/doi.org\/10.1101\/2020.09.03.281550.","DOI":"10.1101\/2020.09.03.281550"},{"key":"10.1016\/j.jtbi.2025.112176_b0135","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1010823","article-title":"Optimizing tuberculosis treatment efficacy: Comparing the standard regimen with Moxifloxacin-containing regimens","volume":"19","author":"Budak","year":"2023","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0140","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.tube.2005.08.008","article-title":"Animal models of tuberculosis","volume":"85","author":"Gupta","year":"2005","journal-title":"Tuberculosis (Edinb.)"},{"key":"10.1016\/j.jtbi.2025.112176_b0145","doi-asserted-by":"crossref","DOI":"10.3389\/fsysb.2023.1283341","article-title":"A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons","volume":"3","author":"Michael","year":"2024","journal-title":"Front. Syst. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0150","doi-asserted-by":"crossref","DOI":"10.1016\/j.jtbi.2022.111042","article-title":"A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes","volume":"539","author":"Joslyn","year":"2022","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0155","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1164\/rccm.202011-4239PP","article-title":"Latent tuberculosis: two centuries of confusion","volume":"204","author":"Behr","year":"2021","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0160","article-title":"Intracellular growth of Mycobacterium tuberculosis after macrophage cell death leads to serial killing of host cells","volume":"6","author":"Mahamed","year":"2017","journal-title":"Elife"},{"key":"10.1016\/j.jtbi.2025.112176_b0165","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0196322","article-title":"Emergence and selection of isoniazid and rifampin resistance in tuberculosis granulomas","volume":"13","author":"Pienaar","year":"2018","journal-title":"PLoS One"},{"key":"10.1016\/j.jtbi.2025.112176_b0170","doi-asserted-by":"crossref","DOI":"10.1128\/aac.00671-23","article-title":"A preclinical model of TB meningitis to determine drug penetration and activity at the sites of disease","volume":"67","author":"Lanni","year":"2023","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0175","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00924-17","article-title":"Ethambutol Partitioning in Tuberculous Pulmonary Lesions Explains Its Clinical Efficacy","volume":"61","author":"Zimmerman","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0180","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2321336121","article-title":"Normalizing granuloma vasculature and matrix improves drug delivery and reduces bacterial burden in tuberculosis-infected rabbits","volume":"121","author":"Datta","year":"2024","journal-title":"PNAS"},{"key":"10.1016\/j.jtbi.2025.112176_b0185","doi-asserted-by":"crossref","first-page":"14188","DOI":"10.1073\/pnas.1121497109","article-title":"Metronidazole prevents reactivation of latent Mycobacterium tuberculosis infection in macaques","volume":"109","author":"Lin","year":"2012","journal-title":"PNAS"},{"key":"10.1016\/j.jtbi.2025.112176_b0190","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1038\/nm.3937","article-title":"The association between sterilizing activity and drug distribution into tuberculosis lesions","volume":"21","author":"Prideaux","year":"2015","journal-title":"Nat. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0195","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1002\/psp4.13117","article-title":"A systematic efficacy analysis of tuberculosis treatment with BPaL-containing regimens using a multiscale modeling approach","volume":"13","author":"Budak","year":"2024","journal-title":"CPT Pharmacometrics Syst. Pharmacol."},{"key":"10.1016\/j.jtbi.2025.112176_b0200","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1056\/NEJMoa1407426","article-title":"Four-month moxifloxacin-based regimens for drug-sensitive tuberculosis","volume":"371","author":"Gillespie","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0205","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1164\/rccm.200310-1380OC","article-title":"Moxifloxacin-containing regimen greatly reduces time to culture conversion in murine tuberculosis","volume":"169","author":"Nuermberger","year":"2004","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0210","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1164\/rccm.200407-885OC","article-title":"Moxifloxacin-containing regimens of reduced duration produce a stable cure in murine tuberculosis","volume":"170","author":"Nuermberger","year":"2004","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0215","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01178-20","article-title":"Preserved efficacy and reduced toxicity with intermittent linezolid dosing in combination with bedaquiline and pretomanid in a murine tuberculosis model","volume":"64","author":"Bigelow","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0220","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1128\/AAC.01691-15","article-title":"Contribution of oxazolidinones to the efficacy of novel regimens containing bedaquiline and pretomanid in a mouse model of tuberculosis","volume":"60","author":"Tasneen","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0225","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1056\/NEJMoa1901814","article-title":"Treatment of highly drug-resistant pulmonary tuberculosis","volume":"382","author":"Conradie","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0230","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1056\/NEJMoa2119430","article-title":"Bedaquiline-pretomanid-linezolid regimens for drug-resistant tuberculosis","volume":"387","author":"Conradie","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0235","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1164\/rccm.200901-0078OC","article-title":"Substitution of moxifloxacin for isoniazid during intensive phase treatment of pulmonary tuberculosis","volume":"180","author":"Dorman","year":"2009","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0240","doi-asserted-by":"crossref","first-page":"4026","DOI":"10.1128\/AAC.00105-15","article-title":"Evaluation of moxifloxacin-containing regimens in pathologically distinct murine tuberculosis models","volume":"59","author":"Li","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0245","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1093\/cid\/cix247","article-title":"Comparing the efficacy of drug regimens for pulmonary tuberculosis: meta-analysis of endpoints in early-phase clinical trials","volume":"65","author":"Bonnett","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.jtbi.2025.112176_b0250","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00913-17","article-title":"Bactericidal and sterilizing activity of a novel regimen with bedaquiline, pretomanid, moxifloxacin, and pyrazinamide in a murine model of tuberculosis","volume":"61","author":"Li","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0255","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a018564","article-title":"Modeling tuberculosis in nonhuman primates","volume":"4","author":"Scanga","year":"2014","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0260","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.74690","article-title":"Macrophage innate training induced by IL-4 and IL-13 activation enhances OXPHOS driven anti-mycobacterial responses","volume":"11","author":"Lundahl","year":"2022","journal-title":"Elife"},{"key":"10.1016\/j.jtbi.2025.112176_b0265","doi-asserted-by":"crossref","first-page":"664","DOI":"10.4049\/jimmunol.1400734","article-title":"Computational modeling predicts IL-10 control of lesion sterilization by balancing early host immunity-mediated antimicrobial responses with caseation during mycobacterium tuberculosis infection","volume":"194","author":"Cilfone","year":"2015","journal-title":"J. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0270","doi-asserted-by":"crossref","DOI":"10.3791\/55559","article-title":"An in vitro caseum binding assay that predicts drug penetration in tuberculosis lesions","author":"Sarathy","year":"2017","journal-title":"J. Vis. Exp."},{"key":"10.1016\/j.jtbi.2025.112176_b0275","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1182\/blood-2005-03-1281","article-title":"Neutrophils rapidly migrate via lymphatics after Mycobacterium bovis BCG intradermal vaccination and shuttle live bacilli to the draining lymph nodes","volume":"106","author":"Abadie","year":"2005","journal-title":"Blood"},{"key":"10.1016\/j.jtbi.2025.112176_b0280","doi-asserted-by":"crossref","DOI":"10.1155\/2017\/8619307","article-title":"Neutrophils in tuberculosis: heterogeneity shapes the way?","volume":"2017","author":"Lyadova","year":"2017","journal-title":"Mediators Inflamm."},{"key":"10.1016\/j.jtbi.2025.112176_b0285","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.it.2011.10.003","article-title":"Neutrophils in tuberculosis: friend or foe?","volume":"33","author":"Lowe","year":"2012","journal-title":"Trends Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0290","doi-asserted-by":"crossref","first-page":"5643","DOI":"10.1038\/s41598-021-84827-0","article-title":"A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs","volume":"11","author":"Cicchese","year":"2021","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jtbi.2025.112176_b0295","doi-asserted-by":"crossref","first-page":"2909","DOI":"10.1128\/IAI.00632-13","article-title":"Differential virulence and disease progression following Mycobacterium tuberculosis complex infection of the common marmoset (Callithrix jacchus)","volume":"81","author":"Via","year":"2013","journal-title":"Infect. Immun."},{"key":"10.1016\/j.jtbi.2025.112176_b0300","article-title":"The immunometabolic topography of tuberculosis granulomas governs cellular organization and bacterial control","author":"McCaffrey","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.jtbi.2025.112176_b0305","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1038\/s41591-018-0224-2","article-title":"A patient-level pooled analysis of treatment-shortening regimens for drug-susceptible pulmonary tuberculosis","volume":"24","author":"Imperial","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0310","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1016\/S1473-3099(24)00223-8","article-title":"Bedaquiline-pretomanid-moxifloxacin-pyrazinamide for drug-sensitive and drug-resistant pulmonary tuberculosis treatment: a phase 2c, open-label, multicentre, partially randomised controlled trial","volume":"24","author":"Cevik","year":"2024","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.jtbi.2025.112176_b0315","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1056\/NEJMra1413919","article-title":"Treatment of tuberculosis","volume":"373","author":"Horsburgh","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0320","doi-asserted-by":"crossref","first-page":"9966","DOI":"10.1038\/s41467-024-54116-1","article-title":"Rapid biphasic decay of intact and defective HIV DNA reservoir during acute treated HIV disease","volume":"15","author":"Barbehenn","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jtbi.2025.112176_b0325","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1164\/rccm.200603-360OC","article-title":"Moxifloxacin versus ethambutol in the first 2 months of treatment for pulmonary tuberculosis","volume":"174","author":"Burman","year":"2006","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0330","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1016\/S0140-6736(09)60333-0","article-title":"Moxifloxacin versus ethambutol in the initial treatment of tuberculosis: a double-blind, randomised, controlled phase II trial","volume":"373","author":"Conde","year":"2009","journal-title":"Lancet"},{"key":"10.1016\/j.jtbi.2025.112176_b0335","doi-asserted-by":"crossref","first-page":"177","DOI":"10.7326\/0003-4819-149-3-200808050-00241","article-title":"Systematic review: T-cell-based assays for the diagnosis of latent tuberculosis infection: an update","volume":"149","author":"Pai","year":"2008","journal-title":"Ann. Intern. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0340","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/0022-1759(93)90389-O","article-title":"A competitive inhibition ELISA for the quantification of human interferon-gamma","volume":"162","author":"Wilson","year":"1993","journal-title":"J. Immunol. Methods"},{"key":"10.1016\/j.jtbi.2025.112176_b0345","doi-asserted-by":"crossref","first-page":"129","DOI":"10.4049\/jimmunol.109.1.129","article-title":"Enzyme-linked immunosorbent Assay, Elisa","volume":"109","author":"Engvall","year":"1972","journal-title":"J. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0350","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1008632","article-title":"Lymph nodes-the neglected battlefield in tuberculosis","volume":"16","author":"Ganchua","year":"2020","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jtbi.2025.112176_b0355","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02627-19","article-title":"Transcriptomic signatures predict regulators of drug synergy and clinical regimen efficacy against tuberculosis","volume":"10","author":"Ma","year":"2019","journal-title":"MBio"},{"key":"10.1016\/j.jtbi.2025.112176_b0360","first-page":"601","article-title":"Pharmacokinetic drug-drug interaction and their implication in clinical management","volume":"18","author":"Palleria","year":"2013","journal-title":"J. Res. Med. Sci."},{"key":"10.1016\/j.jtbi.2025.112176_b0365","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1016\/j.immuni.2024.08.002","article-title":"CD4(+) T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection","volume":"57","author":"Bromley","year":"2024","journal-title":"Immunity"},{"key":"10.1016\/j.jtbi.2025.112176_b0370","article-title":"A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination","volume":"16","author":"Wessler","year":"2020","journal-title":"J. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0375","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.4049\/jimmunol.166.3.1951","article-title":"A model to predict cell-mediated immune regulatory mechanisms during human infection with Mycobacterium tuberculosis","volume":"166","author":"Wigginton","year":"2001","journal-title":"J. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0380","doi-asserted-by":"crossref","first-page":"4296","DOI":"10.4049\/jimmunol.176.7.4296","article-title":"Contribution of CD8+ T cells to control of Mycobacterium tuberculosis infection","volume":"176","author":"Sud","year":"2006","journal-title":"J. Immunol."},{"key":"10.1016\/j.jtbi.2025.112176_b0385","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.jtbi.2011.03.022","article-title":"A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis","volume":"280","author":"Marino","year":"2011","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0390","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":"Marino","year":"2008","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0395","doi-asserted-by":"crossref","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":"Martin","year":"2017","journal-title":"MBio"},{"key":"10.1016\/j.jtbi.2025.112176_b0400","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nm.3412","article-title":"Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing","volume":"20","author":"Lin","year":"2014","journal-title":"Nat. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0405","doi-asserted-by":"crossref","first-page":"4631","DOI":"10.1128\/IAI.00592-09","article-title":"Quantitative comparison of active and latent tuberculosis in the cynomolgus macaque model","volume":"77","author":"Lin","year":"2009","journal-title":"Infect. Immun."},{"key":"10.1016\/j.jtbi.2025.112176_b0410","doi-asserted-by":"crossref","unstructured":"Laubenbacher, R. et al. Building digital twins of the human immune system: toward a roadmap. npj Digital Medicine 5 (2022). https:\/\/doi.org\/10.1038\/s41746-022-00610-z.","DOI":"10.1038\/s41746-022-00610-z"},{"key":"10.1016\/j.jtbi.2025.112176_b0415","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/s43588-024-00607-6","article-title":"Digital twins in medicine","volume":"4","author":"Laubenbacher","year":"2024","journal-title":"Nat. Comput. Sci."},{"key":"10.1016\/j.jtbi.2025.112176_b0420","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004603","article-title":"Variability in tuberculosis granuloma T cell responses exists, but a balance of pro- and anti-inflammatory cytokines is associated with sterilization","volume":"11","author":"Gideon","year":"2015","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jtbi.2025.112176_b0425","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004804","article-title":"Computational and empirical studies predict Mycobacterium tuberculosis-specific t cells as a biomarker for infection outcome","volume":"12","author":"Marino","year":"2016","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0430","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007305","article-title":"Concurrent infection with Mycobacterium tuberculosis confers robust protection against secondary infection in macaques","volume":"14","author":"Cadena","year":"2018","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jtbi.2025.112176_b0435","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41541-019-0113-9","article-title":"Boosting BCG with proteins or rAd5 does not enhance protection against tuberculosis in rhesus macaques","volume":"4","author":"Darrah","year":"2019","journal-title":"NPJ Vaccines"},{"key":"10.1016\/j.jtbi.2025.112176_b0440","doi-asserted-by":"crossref","unstructured":"Joslyn, L., Kirschner, D. & Linderman, J. CaliPro: A calibration protocol that utilizes parameter density estimation to explore parameter space and calibrate complex biological models. Cel. Mol. Bioeng., 31-47 https:\/\/doi.org\/10.1007\/s12195-020-00650-z.","DOI":"10.1007\/s12195-020-00650-z"},{"key":"10.1016\/j.jtbi.2025.112176_b0445","doi-asserted-by":"crossref","DOI":"10.3389\/fams.2023.1256443","article-title":"Calibration methods to fit parameters within complex biological models","volume":"9","author":"Nanda","year":"2023","journal-title":"Front. Appl. Math. Stat."},{"key":"10.1016\/j.jtbi.2025.112176_b0450","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pmed.1002773","article-title":"Tuberculosis drugs' distribution and emergence of resistance in patient's lung lesions: a mechanistic model and tool for regimen and dose optimization","volume":"16","author":"Strydom","year":"2019","journal-title":"PLoS Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0455","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aai7786","article-title":"Pharmacokinetics of rifapentine and rifampin in a rabbit model of tuberculosis and correlation with clinical trial data","volume":"10","author":"Rifat","year":"2018","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0460","doi-asserted-by":"crossref","first-page":"2951","DOI":"10.1128\/AAC.48.8.2951-2957.2004","article-title":"Isoniazid pharmacokinetics-pharmacodynamics in an aerosol infection model of tuberculosis","volume":"48","author":"Jayaram","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0465","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.02266-17","article-title":"Extreme drug tolerance of Mycobacterium tuberculosis in caseum","volume":"62","author":"Sarathy","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0470","doi-asserted-by":"crossref","first-page":"2118","DOI":"10.1128\/AAC.47.7.2118-2124.2003","article-title":"Pharmacokinetics-pharmacodynamics of rifampin in an aerosol infection model of tuberculosis","volume":"47","author":"Jayaram","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0475","first-page":"6","article-title":"The curious characteristics of pyrazinamide: a review","volume":"7","author":"Zhang","year":"2003","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"10.1016\/j.jtbi.2025.112176_b0480","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.tube.2006.12.001","article-title":"Differential drug susceptibility of intracellular and extracellular tuberculosis, and the impact of P-glycoprotein","volume":"87","author":"Hartkoorn","year":"2007","journal-title":"Tuberculosis (Edinb.)"},{"key":"10.1016\/j.jtbi.2025.112176_b0485","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1093\/jac\/dku457","article-title":"Comprehensive physicochemical, pharmacokinetic and activity profiling of anti-TB agents","volume":"70","author":"Lakshminarayana","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0490","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1128\/AAC.00414-06","article-title":"Moxifloxacin, ofloxacin, sparfloxacin, and ciprofloxacin against Mycobacterium tuberculosis: evaluation of in vitro and pharmacodynamic indices that best predict in vivo efficacy","volume":"51","author":"Shandil","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0495","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.tube.2010.07.004","article-title":"Bactericidal activity of the diarylquinoline TMC207 against Mycobacterium tuberculosis outside and within cells","volume":"90","author":"Dhillon","year":"2010","journal-title":"Tuberculosis"},{"key":"10.1016\/j.jtbi.2025.112176_b0500","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1016\/j.cels.2021.08.004","article-title":"Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis","volume":"12","author":"Larkins-Ford","year":"2021","journal-title":"Cell Syst."},{"key":"10.1016\/j.jtbi.2025.112176_b0505","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01695-18","article-title":"Effect of moxifloxacin plus pretomanid against Mycobacterium tuberculosis in log phase, acid phase, and nonreplicating-persister phase in an in vitro assay","volume":"63","author":"de Miranda Silva","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0510","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.00598-23","article-title":"A novel tool to identify bactericidal compounds against vulnerable targets in drug-tolerant m. tuberculosis found in caseum","volume":"14","author":"Sarathy","year":"2023","journal-title":"mBio"},{"key":"10.1016\/j.jtbi.2025.112176_b0515","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.ijantimicag.2016.11.027","article-title":"Activity of moxifloxacin and linezolid against Mycobacterium tuberculosis in combination with potentiator drugs verapamil, timcodar, colistin and SQ109","volume":"49","author":"de Knegt","year":"2017","journal-title":"Int. J. Antimicrob. Agents"},{"key":"10.1016\/j.jtbi.2025.112176_b0520","doi-asserted-by":"crossref","first-page":"872","DOI":"10.15252\/msb.20156777","article-title":"Chemogenomics and orthology-based design of antibiotic combination therapies","volume":"12","author":"Chandrasekaran","year":"2016","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.jtbi.2025.112176_b0525","first-page":"933","article-title":"Uptake of antibiotics by human alveolar macrophages","volume":"129","author":"Hand","year":"1984","journal-title":"Am. Rev. Respir. Dis."},{"key":"10.1016\/j.jtbi.2025.112176_b0530","first-page":"429","article-title":"Antibiotic uptake by alveolar macrophages","volume":"95","author":"Johnson","year":"1980","journal-title":"J. Lab. Clin. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0535","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1128\/AAC.27.1.42","article-title":"Antibiotic uptake by alveolar macrophages of smokers","volume":"27","author":"Hand","year":"1985","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0540","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00506-21","article-title":"Lesion penetration and activity limit the utility of second-line injectable agents in pulmonary tuberculosis","volume":"65","author":"Ernest","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0545","doi-asserted-by":"crossref","first-page":"2540","DOI":"10.1128\/AAC.01723-09","article-title":"Cellular pharmacokinetics of the novel biaryloxazolidinone radezolid in phagocytic cells: studies with macrophages and polymorphonuclear neutrophils","volume":"54","author":"Lemaire","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0550","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1128\/AAC.49.6.2429-2437.2005","article-title":"Influence of efflux transporters on the accumulation and efflux of four quinolones (ciprofloxacin, levofloxacin, garenoxacin, and moxifloxacin) in J774 macrophages","volume":"49","author":"Michot","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0555","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.41115","article-title":"High-resolution mapping of fluoroquinolones in TB rabbit lesions reveals specific distribution in immune cell types","volume":"7","author":"Blanc","year":"2018","journal-title":"Elife"},{"key":"10.1016\/j.jtbi.2025.112176_b0560","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1186\/s13063-022-06331-8","volume":"23","author":"Berry","year":"2022","journal-title":"Trials"},{"key":"10.1016\/j.jtbi.2025.112176_b0565","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1016\/S0140-6736(14)62002-X","volume":"385","author":"Dawson","year":"2015","journal-title":"Lancet"},{"key":"10.1016\/j.jtbi.2025.112176_b0570","doi-asserted-by":"crossref","first-page":"305","DOI":"10.5588\/ijtld.20.0513","article-title":"A partially randomised trial of pretomanid, moxifloxacin and pyrazinamide for pulmonary TB","volume":"25","author":"Tweed","year":"2021","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"10.1016\/j.jtbi.2025.112176_b0575","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1016\/S2213-2600(19)30366-2","article-title":"Bedaquiline, moxifloxacin, pretomanid, and pyrazinamide during the first 8 weeks of treatment of patients with drug-susceptible or drug-resistant pulmonary tuberculosis: a multicentre, open-label, partially randomised, phase 2b trial","volume":"7","author":"Tweed","year":"2019","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0580","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1016\/S0140-6736(12)61080-0","article-title":"14-day bactericidal activity of PA-824, bedaquiline, pyrazinamide, and moxifloxacin combinations: a randomised trial","volume":"380","author":"Diacon","year":"2012","journal-title":"Lancet"},{"key":"10.1016\/j.jtbi.2025.112176_b0585","doi-asserted-by":"crossref","DOI":"10.1164\/rccm.201410-1801OC","article-title":"Bactericidal activity of pyrazinamide and clofazimine alone and in combinations with pretomanid and bedaquiline","author":"Diacon","year":"2015","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0590","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0017556","article-title":"Sterilizing activity of second-line regimens containing TMC207 in a murine model of tuberculosis","volume":"6","author":"Veziris","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.jtbi.2025.112176_b0595","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1164\/rccm.200807-1152OC","article-title":"Sterilizing activity of R207910 (TMC207)-containing regimens in the murine model of tuberculosis","volume":"180","author":"Ibrahim","year":"2009","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.jtbi.2025.112176_b0600","doi-asserted-by":"crossref","first-page":"5485","DOI":"10.1128\/AAC.05293-11","article-title":"Sterilizing activity of novel TMC207- and PA-824-containing regimens in a murine model of tuberculosis","volume":"55","author":"Tasneen","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jtbi.2025.112176_b0605","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.tube.2010.03.007","article-title":"Early clinical development of anti-tuberculosis drugs: science, statistics and sterilizing activity","volume":"90","author":"Davies","year":"2010","journal-title":"Tuberculosis (Edinb)"},{"key":"10.1016\/j.jtbi.2025.112176_b0610","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1186\/s13063-015-1050-1","article-title":"Quality of outcome reporting in phase II studies in pulmonary tuberculosis","volume":"16","author":"Bonnett","year":"2015","journal-title":"Trials"},{"key":"10.1016\/j.jtbi.2025.112176_b0615","first-page":"1024","article-title":"Liquid vs. solid culture for tuberculosis: performance and cost in a resource-constrained setting","volume":"14","author":"Chihota","year":"2010","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"10.1016\/j.jtbi.2025.112176_b0620","first-page":"471","article-title":"Reliability of mycobacterial growth indicator tube (MGIT) 960 for the detection of isoniazid resistance in a tuberculosis endemic setting","volume":"139","author":"Gomathi","year":"2014","journal-title":"Ind. J. Med. Res."},{"key":"10.1016\/j.jtbi.2025.112176_b0625","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1111\/j.1539-6924.1988.tb01155.x","article-title":"An investigation of uncertainty and sensitivity analysis techniques for computer models","volume":"8","author":"Iman","year":"1988","journal-title":"Risk Anal."},{"key":"10.1016\/j.jtbi.2025.112176_b0630","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/0951-8320(90)90065-U","article-title":"Nonparametric statistics in sensitivity analysis for model output - a comparison of selected techniques","volume":"28","author":"Saltelli","year":"1990","journal-title":"Reliab. Eng. Syst. Safe"},{"key":"10.1016\/j.jtbi.2025.112176_b0635","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/S0167-9473(97)00043-1","article-title":"An alternative way to compute Fourier amplitude sensitivity test (FAST)","volume":"26","author":"Saltelli","year":"1998","journal-title":"Comput. Stat Data an"},{"key":"10.1016\/j.jtbi.2025.112176_b0640","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1016\/j.ress.2005.11.014","article-title":"Sensitivity analysis practices: Strategies for model-based inference","volume":"91","author":"Saltelli","year":"2006","journal-title":"Reliab. Eng. Syst. Safe"},{"key":"10.1016\/j.jtbi.2025.112176_b0645","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/j.ress.2005.06.003","article-title":"Random balance designs for the estimation of first order global sensitivity indices","volume":"91","author":"Tarantola","year":"2006","journal-title":"Reliab. Eng. Syst. Safe"},{"key":"10.1016\/j.jtbi.2025.112176_b0650","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1016\/j.cpc.2007.07.011","article-title":"State dependent parameter metamodelling and sensitivity analysis","volume":"177","author":"Ratto","year":"2007","journal-title":"Comput. Phys. Commun."},{"key":"10.1016\/j.jtbi.2025.112176_b0655","doi-asserted-by":"crossref","unstructured":"Renardy, M. Global sensitivity analysis of biological multi-scale models. Current Opinion in Biomedical Engineering In press (2019).","DOI":"10.1016\/j.cobme.2019.09.012"},{"key":"10.1016\/j.jtbi.2025.112176_b0660","series-title":"Sensitivity analysis","author":"Saltelli","year":"2000"},{"key":"10.1016\/j.jtbi.2025.112176_b0665","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/S0378-4754(00)00270-6","article-title":"Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates","volume":"55","author":"Sobol\u2032","year":"2001","journal-title":"Math. Comput. Simul"},{"key":"10.1016\/j.jtbi.2025.112176_b0670","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0200917","article-title":"A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow","volume":"13","author":"Link","year":"2018","journal-title":"PLoS One"},{"key":"10.1016\/j.jtbi.2025.112176_b0675","article-title":"Illustration of sampling-based methods for uncertainty and sensitivity analysis","volume":"591\u2013622","author":"Helton","year":"2002","journal-title":"Risk Anal."},{"key":"10.1016\/j.jtbi.2025.112176_b0680","doi-asserted-by":"crossref","first-page":"309","DOI":"10.3389\/fcimb.2017.00309","article-title":"Modeling immune response to leishmania species indicates adenosine as an important inhibitor of th-cell activation","volume":"7","author":"Ribeiro","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.jtbi.2025.112176_b0685","doi-asserted-by":"crossref","DOI":"10.1016\/j.mbs.2021.108593","article-title":"To Sobol or not to Sobol? The effects of sampling schemes in systems biology applications","volume":"337","author":"Renardy","year":"2021","journal-title":"Math. Biosci."},{"key":"10.1016\/j.jtbi.2025.112176_b0690","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20230707","article-title":"CD8+ lymphocytes are critical for early control of tuberculosis in macaques","volume":"220","author":"Winchell","year":"2023","journal-title":"J. Exp. Med."}],"container-title":["Journal of Theoretical Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022519325001420?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022519325001420?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T22:52:30Z","timestamp":1762210350000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022519325001420"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":138,"alternative-id":["S0022519325001420"],"URL":"https:\/\/doi.org\/10.1016\/j.jtbi.2025.112176","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.04.10.648004","asserted-by":"object"}]},"ISSN":["0022-5193"],"issn-type":[{"value":"0022-5193","type":"print"}],"subject":[],"published":{"date-parts":[[2025,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Rankings of tuberculosis antibiotic treatment regimens are sensitive to spatial scale, detection limit, and initial host bacterial burden","name":"articletitle","label":"Article Title"},{"value":"Journal of Theoretical Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jtbi.2025.112176","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"112176"}}