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@book{sethiOptimalControlTheory2021,
address = {Cham},
edition = {4th ed. 2021},
series = {Springer {Texts} in {Business} and {Economics}},
title = {Optimal {Control} {Theory}: {Applications} to {Management} {Science} and {Economics}},
isbn = {978-3-030-91745-6},
shorttitle = {Optimal {Control} {Theory}},
language = {eng},
publisher = {Springer International Publishing},
author = {Sethi, Suresh P.},
year = {2021},
doi = {10.1007/978-3-030-91745-6},
}
@incollection{butlerOptimalControlChemotherapy1997,
address = {Singapore},
series = {Series in mathematical biology and medicine},
title = {Optimal {Control} of {Chemotherapy} {Affecting} the {Infectivity} of {HIV}},
isbn = {978-981-4529-59-4},
abstract = {Pt. I. DNA, viruses and cells -- pt. II. Population dynamics in diseases in man -- pt. III. Further mathematical aspects},
language = {eng},
number = {vol. 6},
booktitle = {Advances in mathematical population dynamics--molecules, cells, and man: proceedings of the 4th {International} {Conference} on {Mathematical} {Population} {Dynamics}, 23-27 {May} 1995},
publisher = {World Scientific Publishing Co. Pte Ltd},
author = {Butler, Shelly and Kirschner, Denise E. and Lenhart, Suzanne},
editor = {Axelrod, David E. and Kimmel, Marek and Arino, Ovide and Capasso, Vincenzo},
year = {1997},
doi = {10.1142/3511},
}
@article{kirschnerOptimalControlChemotherapy1997,
title = {Optimal control of the chemotherapy of {HIV}},
volume = {35},
issn = {0303-6812},
doi = {10.1007/s002850050076},
language = {eng},
number = {7},
journal = {Journal of Mathematical Biology},
author = {Kirschner, Denise E. and Lenhart, Suzanne and Serbin, Steve},
month = aug,
year = {1997},
pmid = {9269736},
pages = {775--792},
}
@article{perelsonDynamicsHIVInfection1993,
title = {Dynamics of {HIV} infection of {CD4}+ {T} cells},
volume = {114},
issn = {0025-5564},
doi = {10.1016/0025-5564(93)90043-a},
language = {eng},
number = {1},
journal = {Mathematical Biosciences},
author = {Perelson, Alan S. and Kirschner, Denise E. and De Boer, Rob J.},
month = mar,
year = {1993},
pmid = {8096155},
pages = {81--125},
}
@incollection{kirschnerModelImmuneSystem1995,
address = {Winnipeg, Canada},
title = {A {Model} for the immune system response to {HIV}: {AZT} treatment studies},
isbn = {978-0-920063-58-3},
language = {eng},
booktitle = {Mathematical population dynamics: analysis of heterogeneity},
publisher = {Wuerz Pub.},
author = {Kirschner, Denise E. and Perelson, Alan S.},
collaborator = {Arino, Ovide},
year = {1995},
note = {OCLC: 34713698},
}
@article{segovia-juarezIdentifyingControlMechanisms2004,
title = {Identifying control mechanisms of granuloma formation during {M}. tuberculosis infection using an agent-based model},
volume = {231},
issn = {0022-5193},
doi = {10.1016/j.jtbi.2004.06.031},
language = {eng},
number = {3},
journal = {Journal of Theoretical Biology},
author = {Segovia-Juarez, Jose L. and Ganguli, Suman and Kirschner, Denise},
month = dec,
year = {2004},
pmid = {15501468},
pages = {357--376},
}
@article{raySynergyIndividualTNFdependent2009,
title = {Synergy between individual {TNF}-dependent functions determines granuloma performance for controlling {Mycobacterium} tuberculosis infection},
volume = {182},
issn = {1550-6606},
doi = {10.4049/jimmunol.0802297},
language = {eng},
number = {6},
journal = {Journal of Immunology (Baltimore, Md.: 1950)},
author = {Ray, J. Christian J. and Flynn, JoAnne L. and Kirschner, Denise E.},
month = mar,
year = {2009},
pmid = {19265149},
pmcid = {PMC3182770},
pages = {3706--3717},
}
@article{fallahi-sichaniMultiscaleComputationalModeling2011,
title = {Multiscale computational modeling reveals a critical role for {TNF}-\textalpha{} receptor 1 dynamics in tuberculosis granuloma formation},
volume = {186},
issn = {1550-6606},
doi = {10.4049/jimmunol.1003299},
language = {eng},
number = {6},
journal = {Journal of Immunology (Baltimore, Md.: 1950)},
author = {Fallahi-Sichani, Mohammad and El-Kebir, Mohammed and Marino, Simeone and Kirschner, Denise E. and Linderman, Jennifer J.},
month = mar,
year = {2011},
pmid = {21321109},
pmcid = {PMC3127549},
pages = {3472--3483},
}
@article{cilfoneMultiscaleModelingPredicts2013,
title = {Multi-scale modeling predicts a balance of tumor necrosis factor-\textalpha{} and interleukin-10 controls the granuloma environment during {Mycobacterium} tuberculosis infection},
volume = {8},
issn = {1932-6203},
doi = {10.1371/journal.pone.0068680},
language = {eng},
number = {7},
journal = {PloS One},
author = {Cilfone, Nicholas A. and Perry, Cory R. and Kirschner, Denise E. and Linderman, Jennifer J.},
year = {2013},
pmid = {23869227},
pmcid = {PMC3711807},
pages = {e68680},
}
@article{pienaarComputationalToolIntegrating2015,
title = {A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment},
volume = {367},
issn = {1095-8541},
doi = {10.1016/j.jtbi.2014.11.021},
language = {eng},
journal = {Journal of Theoretical Biology},
author = {Pienaar, Elsje and Cilfone, Nicholas A. and Lin, Philana Ling and Dartois, Véronique and Mattila, Joshua T. and Butler, J. Russell and Flynn, JoAnne L. and Kirschner, Denise E. and Linderman, Jennifer J.},
month = feb,
year = {2015},
pmid = {25497475},
pmcid = {PMC4332617},
pages = {166--179},
}
@article{pienaarSilicoEvaluationExploration2015,
title = {In silico evaluation and exploration of antibiotic tuberculosis treatment regimens},
volume = {9},
issn = {1752-0509},
doi = {10.1186/s12918-015-0221-8},
language = {eng},
journal = {BMC systems biology},
author = {Pienaar, Elsje and Dartois, Véronique and Linderman, Jennifer J. and Kirschner, Denise E.},
month = nov,
year = {2015},
pmid = {26578235},
pmcid = {PMC4650854},
pages = {79},
}
@article{ciccheseApplyingOptimizationAlgorithms2017,
title = {Applying optimization algorithms to tuberculosis antibiotic treatment regimens},
volume = {10},
issn = {1865-5025},
doi = {10.1007/s12195-017-0507-6},
language = {eng},
number = {6},
journal = {Cellular and Molecular Bioengineering},
author = {Cicchese, Joseph M. and Pienaar, Elsje and Kirschner, Denise E. and Linderman, Jennifer J.},
month = dec,
year = {2017},
pmid = {29276546},
pmcid = {PMC5737793},
pages = {523--535},
}
@article{budakOptimizingTuberculosisTreatment2023,
title = {Optimizing tuberculosis treatment efficacy: {Comparing} the standard regimen with {Moxifloxacin}-containing regimens},
volume = {19},
issn = {1553-7358},
shorttitle = {Optimizing tuberculosis treatment efficacy},
doi = {10.1371/journal.pcbi.1010823},
language = {eng},
number = {6},
journal = {PLoS computational biology},
author = {Budak, Maral and Cicchese, Joseph M. and Maiello, Pauline and Borish, H. Jacob and White, Alexander G. and Chishti, Harris B. and Tomko, Jaime and Frye, L. James and Fillmore, Daniel and Kracinovsky, Kara and Sakal, Jennifer and Scanga, Charles A. and Lin, Philana Ling and Dartois, Véronique and Linderman, Jennifer J. and Flynn, JoAnne L. and Kirschner, Denise E.},
month = jun,
year = {2023},
pmid = {37319311},
pmcid = {PMC10306236},
pages = {e1010823},
}
@article{nahidExecutiveSummaryOfficial2016,
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},
issn = {1537-6591},
shorttitle = {Executive {Summary}},
doi = {10.1093/cid/ciw566},
language = {eng},
number = {7},
journal = {Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America},
author = {Nahid, Payam and Dorman, Susan E. and Alipanah, Narges and Barry, Pennan M. and Brozek, Jan L. and Cattamanchi, Adithya and Chaisson, Lelia H. and Chaisson, Richard E. and Daley, Charles L. and Grzemska, Malgosia and Higashi, Julie M. and Ho, Christine S. and Hopewell, Philip C. and Keshavjee, Salmaan A. and Lienhardt, Christian and Menzies, Richard and Merrifield, Cynthia and Narita, Masahiro and O'Brien, Rick and Peloquin, Charles A. and Raftery, Ann and Saukkonen, Jussi and Schaaf, H. Simon and Sotgiu, Giovanni and Starke, Jeffrey R. and Migliori, Giovanni Battista and Vernon, Andrew},
month = oct,
year = {2016},
pmid = {27621353},
pmcid = {PMC6366011},
pages = {853--867},
}
@book{GlobalTuberculosisReport2024,
address = {Geneva},
title = {Global tuberculosis report 2024},
copyright = {World Health Organization 2024},
isbn = {978-92-4-010153-1},
url = {https://iris.who.int/handle/10665/379339},
publisher = {World Health Organization},
year = {2024},
}
@article{ormerodMultidrugresistantTuberculosisMDRTB2005,
title = {Multidrug-resistant tuberculosis ({MDR}-{TB}): epidemiology, prevention and treatment},
volume = {73-74},
issn = {0007-1420},
shorttitle = {Multidrug-resistant tuberculosis ({MDR}-{TB})},
doi = {10.1093/bmb/ldh047},
language = {eng},
journal = {British Medical Bulletin},
author = {Ormerod, L. P.},
year = {2005},
pmid = {15956357},
pages = {17--24},
}
@article{sarathyCaseumNicheMycobacterium2020,
title = {Caseum: a {Niche} for {Mycobacterium} tuberculosis {Drug}-{Tolerant} {Persisters}},
volume = {33},
issn = {1098-6618},
shorttitle = {Caseum},
doi = {10.1128/CMR.00159-19},
language = {eng},
number = {3},
journal = {Clinical Microbiology Reviews},
author = {Sarathy, Jansy P. and Dartois, Véronique},
month = jun,
year = {2020},
pmid = {32238365},
pmcid = {PMC7117546},
pages = {e00159--19},
}
@article{gideonNeutrophilsExpressPro2019,
title = {Neutrophils express pro- and anti-inflammatory cytokines in granulomas from {Mycobacterium} tuberculosis-infected cynomolgus macaques},
volume = {12},
issn = {1935-3456},
doi = {10.1038/s41385-019-0195-8},
language = {eng},
number = {6},
journal = {Mucosal Immunology},
author = {Gideon, Hannah P. and Phuah, Jiayao and Junecko, Beth A. and Mattila, Joshua T.},
month = nov,
year = {2019},
pmid = {31434990},
pmcid = {PMC6824993},
pages = {1370--1381},
}
@article{martinDigitallyBarcodingMycobacterium2017,
title = {Digitally {Barcoding} {Mycobacterium} tuberculosis {Reveals} {In} {Vivo} {Infection} {Dynamics} in the {Macaque} {Model} of {Tuberculosis}},
volume = {8},
issn = {2150-7511},
doi = {10.1128/mBio.00312-17},
language = {eng},
number = {3},
journal = {mBio},
author = {Martin, Constance J. and Cadena, Anthony M. and Leung, Vivian W. and Lin, Philana Ling and Maiello, Pauline and Hicks, Nathan and Chase, Michael R. and Flynn, JoAnne L. and Fortune, Sarah M.},
month = may,
year = {2017},
pmid = {28487426},
pmcid = {PMC5424202},
pages = {e00312--17},
}
@article{kerantzasOriginsCombinationTherapy2017,
title = {Origins of {Combination} {Therapy} for {Tuberculosis}: {Lessons} for {Future} {Antimicrobial} {Development} and {Application}},
volume = {8},
issn = {2150-7511},
shorttitle = {Origins of {Combination} {Therapy} for {Tuberculosis}},
doi = {10.1128/mBio.01586-16},
language = {eng},
number = {2},
journal = {mBio},
author = {Kerantzas, Christopher A. and Jacobs, William R.},
month = mar,
year = {2017},
pmid = {28292983},
pmcid = {PMC5350467},
pages = {e01586--16},
}
@techreport{sertkayaExaminationClinicalTrial2014,
title = {Examination of {Clinical} {Trial} {Costs} and {Barriers} for {Drug} {Development}},
url = {https://aspe.hhs.gov/reports/examination-clinical-trial-costs-barriers-drug-development-0},
number = {HHSP23337007T},
institution = {U.S. Department of Health and Human Services},
author = {Sertkaya, Aylin and Birkenbach, Anna and Berlind, Ayesha and Eyraud, John},
month = jul,
year = {2014},
}
@article{gillespieFourmonthMoxifloxacinbasedRegimens2014,
title = {Four-month moxifloxacin-based regimens for drug-sensitive tuberculosis},
volume = {371},
issn = {1533-4406},
doi = {10.1056/NEJMoa1407426},
language = {eng},
number = {17},
journal = {The New England Journal of Medicine},
author = {Gillespie, Stephen H. and Crook, Angela M. and McHugh, Timothy D. and Mendel, Carl M. and Meredith, Sarah K. and Murray, Stephen R. and Pappas, Frances and Phillips, Patrick P. J. and Nunn, Andrew J. and {REMoxTB Consortium}},
month = oct,
year = {2014},
pmid = {25196020},
pmcid = {PMC4277680},
pages = {1577--1587},
}
@article{nuermbergerMoxifloxacincontainingRegimenGreatly2004,
title = {Moxifloxacin-containing regimen greatly reduces time to culture conversion in murine tuberculosis},
volume = {169},
issn = {1073-449X},
doi = {10.1164/rccm.200310-1380OC},
language = {eng},
number = {3},
journal = {American Journal of Respiratory and Critical Care Medicine},
author = {Nuermberger, Eric L. and Yoshimatsu, Tetsuyuki and Tyagi, Sandeep and O'Brien, Richard J. and Vernon, Andrew N. and Chaisson, Richard E. and Bishai, William R. and Grosset, Jacques H.},
month = feb,
year = {2004},
pmid = {14578218},
pages = {421--426},
}
@article{conradieBedaquilinePretomanidLinezolidRegimensDrugResistant2022,
title = {Bedaquiline-{Pretomanid}-{Linezolid} {Regimens} for {Drug}-{Resistant} {Tuberculosis}},
volume = {387},
issn = {1533-4406},
doi = {10.1056/NEJMoa2119430},
language = {eng},
number = {9},
journal = {The New England Journal of Medicine},
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