@book{Abbas, title = {Basic immunology: Function and disorders of the immune system}, publisher = {Elsevier}, pages = {888-896}, year = {2001}, author = {A.Abbas and A.Lichtman and S.Pillai}, } @article{abel2018natural, title={Natural killer cells: development, maturation, and clinical utilization}, author={A.Abel and C.Yang and M.S.Thakar and S.Malarkannan}, journal={Frontiers in immunology}, volume={9}, pages={1869}, year={2018}, publisher={Frontiers} } @article{al2022examining, title={Examining Type 1 Diabetes Mathematical Models Using Experimental Data}, author={H.Al Ali and A.Daneshkhah and A.Boutayeb and Z.Mukandavire}, journal={International Journal of Environmental Research and Public Health}, volume={19}, number={2}, pages={737}, year={2022}, publisher={MDPI} } @article{Alfarouk2015_ResistanceChemotherapy, author = {K.O.Alfarouk and C.-M.Stock and S.Taylor and M. Walsh and A.K.Muddathir and D.Verduzco and A.H.H.Bashir and O.Y.Mohammed and G.O.Elhassan and S.Harguindey and S.J.Reshkin and M.E.Ibrahim and C.Rauch}, title = {Resistance to cancer chemotherapy: failure in drug response from {ADME to P-gp}}, journal = {Cancer Cell International}, year = {2015}, volume ={15}, pages = {71}, } @article{anderson1998continuous, title={Continuous and discrete mathematical models of tumor-induced angiogenesis}, author={A.Anderson and M.Chaplain}, journal={Bulletin of mathematical biology}, volume={60}, number={5}, pages={857-899}, year={1998}, publisher={Springer} } @article{afsharian2007effect, title={The effect of repeated administration of cyclophosphamide on cytochrome {P450 2B} in rats}, author={P.Afsharian and Y.Terelius and Z.Hassan and C.Nilsson and S.Lundgren and M.Hassan}, journal={Clinical cancer research}, volume={13}, number={14}, pages={4218-4224}, year={2007}, publisher={AACR} } @article{Apple, title = {Self-Assembled Hydrogels Utilising Polymer-Nanoparticle Interactions}, Journal = {Nature communications}, pages = {1038}, volume = {10}, number = {6295}, year = {2015}, author = {E.Appel and M.W.Tibbitt and M.J.Webber and B.A.Mattix and O.Veiseh and R.Langer }, } @article{Arciero2004, title = {Mathematical model of tumor-immune evasion and {siRNA }treatment}, Journal = {Discrete Contin. Dyn. Syst. Ser. B}, pages = {39-58}, volume = {4}, year = {2004}, author = {J.C.Arciero and T.L.Jackson and D.E.Kirschner} } @article{alsabti1978tumour, title={Tumour dormant state}, author={A.Alsabti}, journal={Tumour Res}, volume={13}, number={1}, pages={1-13}, year={1978} } @misc{alberts2002helper, title={Helper $T$ Cells and lymphocyte activation}, author={B.Alberts and A.Johnson and J.Lewis and M.Raff and K.Roberts and P.Walter}, year={2002}, publisher={Garland Science} } @article{AllavenaMantovani2012, author = {P.Allavena and A.Mantovani}, title = {Immunology in the clinic review series; focus on cancer: tumour-associated macrophages: undisputed stars of the inflammatory tumour microenvironment}, journal = {Clinical and Experimental Immunology}, year = {2012}, volume = {167}, pages = {195-205}, } } @article{Almatroodi2016_M1M2-Th1Th2, author= {S.A.Almatroodi and C.F.McDonald and I.A.Darby and D.S.Pouniotis}, title = {{Characterisation of M1/M2 tumour-associated macrophages (TAMs) and the Th1/Th2 cytokine profiles in patients with NSCLC}}, journal = {Cancer Microenviron.}, year = {2016}, volume = {9}, number = {1}, pages = {1-11}, } @article{Alonso2011_CD4instructMacroph, author = {M.N.Alonso and M.T.Wong and A.L.Zhang and D.Winer and M.M.Suhoski and L.L.Tolentino and J.Gaitan and M.G.Davidson and T.H.Kung and D.M.Galel and K.C.Nadeau and J.Kim P.J.Utz and K.S\"{o}derstr\"{o}m and E.G.Engleman}, title = {{T_{H}1, T_{H}2, and T_{H}17} cells instruct monocytes to differentiate into specialize dendritic cell subsets}, journal = {Blood}, year = {2011}, volume = {118}, number = {12}, pages = {3311-3320}, } @article{alvarezapplied, author={A.{\'A}lvarez-Arenas and J.Belmonte-Beitia and G.F.Calvo}, title = {Nonlinear waves in a simple model of high-grade glioma}, journal = {Applied Mathematics and Nonlinear Sciences}, year = {2016}, volume = {118}, pages = {405-422} } @article{assimakopoulos1991general, title={A general multiple-compartment model for the transport of trace elements through animals.}, author={P.A.Assimakopoulos and K.G.Ioannides and A.A.Pakou}, journal={Health physics}, volume={61}, number={2}, pages={245-253}, year={1991}, publisher={LWW} } @article{Asquith2009_LymphocyteKinetics, author = {B.Asquith and J.A.M.Borghans and V.V.Ganusov and D.C.Macallan}, title = {Lymphocyte kinetics in health and disease}, journal = {Trends in Immunology}, year = {2009}, volume = {30}, number = {4}, pages = {182-189} } @article{atkinson2014type, title={Type 1 diabetes}, author={M.Atkinson and G.Eisenbarth and A.Michels}, journal={The lancet}, volume={383}, number={9911}, pages={69--82}, year={2014}, publisher={Elsevier} } @article{Baloni2013_MathTumDrugImmun, author = {J.Baloni and U.S.Rana}, title = {Mathematical modelling of strategic treatments of tumour growth}, journal = {J. Appl. Computat. Math.}, year = {2013}, volume = {2}, pages = {140} } @Book{Bacaer, Author = {N.Bacaer}, publisher = {Springer-Verlag London Limited}, Title = { A Short History of Mathematical Population Dynamics}, Year = {2011} } @article{Bajzer1996_ModelsTumGrowth, author = {\u{Z}.Bajzer and M.Maru\u{s}i\'{c} and S.Vuk-Pavlovi\'{c}}, title ={Conceptual frameworks for mathematical modelling of tumour growth dynamics}, journal = {Math. Comput. Modelling}, year = {1996}, volume = {23}, number = {6}, pages = {31-46}, } @article{barreto2006bcg, title={BCG vaccine: efficacy and indications for vaccination and revaccination}, author={M.Barreto and S.Pereira and A.Ferreira}, journal={Jornal de pediatria}, volume={82}, pages={s45-s54}, year={2006}, publisher={SciELO Brasil} } @article{Barros_M1M2polarisationDiseases, author = {M.H.M.Barros and F.Hauck and J.H.Dreyer and B.Kemkes and G.Niedobitek}, title = {{Macrophage polarisation: an immunohistochemical approach for identifying M1 and M2 macrophages}}, journal = {PLoS One}, year = {2013}, volume = {8}, number = {11}, pages = {e80908}, } @Article{Basse, author = {B.Basse and B.C. Baguley and E.S.Marshall and W.R.Joseph and B.V.Brunt and G.Wake and D.J.N.Wall}, title = {A mathematical model for analysis of the cell cycle in cell lines derived from human tumors}, journal = { J Math Biol}, year = {2003}, pages = {295--312} } @Article{Behrens, title = {{Helper T cells, dendritic cells and CTL immunity}}, journal = { Immunology and Cell Biology }, volume = {82}, pages = {84-90}, year = {2004}, author = {G.Behrens and M.Li and C.Smith and G.Belz and J.Mintern and F.Carbone and W.Heath} } @article{berd1988effect, title={Effect of low dose cyclophosphamide on the immune system of cancer patients: depletion of CD4+, 2H4+ suppressor-inducer T-cells}, author={D.Berd and M.Mastrangelo}, journal={Cancer research}, volume={48}, number={6}, pages={1671-1675}, year={1988}, publisher={AACR} } @article{Bergmann2001_Th1Th2model, author = {C.Bergmann and J.Leo van Hemmen and L.A.Segel}, title = {{Th1 or Th2: how an appropriate T helper response can be made}}, journal = {Bull. Math. Biol.}, year = {2001}, volume = {63}, pages = {405-430}, } @article{Benzekry2014_ModelTumGrowth, author = {S.Benzekry and C.Lamont and A.Behest and A.Tracz and J.M.L.Ebos and L.Hlatky and P.Hahnfeldt}, title = {Classical mathematical models for description and prediction of experimental tumour growth}, journal = {PLoS Comput. Biol.}, year = {2014}, volume = {10}, number = {8}, pages = {e1003800}, } @article{bellora2010interaction, title={The interaction of human natural killer cells with either unpolarized or polarized macrophages results in different functional outcomes}, author={F.Bellora and R.Castriconi and A.Dondero and G.Reggiardo and L.Moretta and A.Mantovani and A.Moretta and C.Bottino}, journal={Proceedings of the National Academy of Sciences}, volume={107}, number={50}, pages={21659-21664}, year={2010}, publisher={National Acad Sciences} } @article{Bingisser1996_ApoptosisMacrophagesTGFbIl10, author = {R.Bingisser and C.Stey and M.Weller and P.Groscurth and E.Russi and K.Frei}, title = {Apoptosis in human alveolar macrophages is induced by endotoxin and is modulated by cytokines}, journal = {Am. J. Respire. Cell. Mol. Biol.}, year = {1996}, volume = {15}, number = {1}, pages = {64-70} } @book{bill2016clinical, title={Clinical pharmacology and therapeutics for veterinary technicians}, author={R.L.Bill}, year={2016}, publisher={Elsevier Health Sciences} } @article{begg1984bioassay, title={A bioassay for cyclophosphamide in blood, lung and tumour.}, author={A.C.Begg and K.A.Smith}, journal={British journal of cancer}, volume={49}, number={1}, pages={49}, year={1984}, publisher={Nature Publishing Group} } @article{blandino2008anti, title={Anti-proliferative effect of pro-inflammatory cytokines in cultured b cells is associated with extracellular signal-regulated kinase 1/2 pathway inhibition: protective role of glucagon-like peptide-1}, author={M.Blandino-Rosano and G.Perez-Arana and J.Mellado-Gil and C.Segundo and M.Aguilar-Diosdado}, journal={Journal of molecular endocrinology}, volume={41}, number={1}, pages={35}, year={2008}, publisher={Citeseer} } @article{Boondriek2010_CAmodelsReview, author = {A.Boondriek}, journal = {International Mathematical Forum}, year = {2010}, volume = {5}, number = {61}, pages = {3023--3029}, title = {A review of cellular automata models of tumour growth}, } @article{burnet1957cancer, title={Cancer a biological approach: I. The processes of control. II. The significance of somatic mutation}, author={M.Burnet}, journal={British medical journal}, volume={1}, number={5022}, pages={779}, year={1957}, publisher={BMJ Group} } @article{Bracci_2014, Author = {L.Bracci and G.Schiavoni and A.Sistigu and F.Belardelli}, Journal = {Cell Death and Differentiation}, pages = {15-25}, Title = {Immune-based mechanisms of cytotoxic chemotherapy: implications for the design of novel and rationale-based combined treatments against cancer}, volume={21}, Year = {2014} } @article{Bradshaw_2007, Author = {E.Bradshaw-Pierce and S.Eckhardt and D.Gustafson}, Journal = {Clin Cancer Res}, Month = {May}, pages = {2768-76}, Title = {A Physiologically Based Pharmacokinetic Model of docetaxel Disposition: from Mouse to Man}, volume={9}, number={13}, Year = {2007} } @article{bradshaw2008pharmacokinetic, title={Pharmacokinetic-directed dosing of vandetanib and docetaxel in a mouse model of human squamous cell carcinoma}, author={E.Bradshaw-Pierce and C.Steinhauer and D.Raben and D.Gustafson}, journal={Molecular cancer therapeutics}, volume={7}, number={9}, pages={3006-3017}, year={2008}, publisher={AACR} } @article{Brown2005_RoleApoptosisCancer, author = {J.M.Brown and L.D.Attardi}, title = {The role of apoptosis in cancer development and treatment response}, journal = {Nat. Rev. Cancer}, year = {2005}, volume = {5}, pages = {231-237} } @InBook{Byrne2012_MathModelsTumGrowth, author = {H.M.Byrne}, title = {Mathematical biomedicine and modelling avascular tumour growth}, booktitle = {Mathematics and Life Sciences}, year={2012}, publisher={De Gruyter}, } @article{byrne2009individual, title={Individual-based and continuum models of growing cell populations: a comparison}, author={H.Byrne and D.Drasdo}, journal={Journal of mathematical biology}, volume={58}, number={4-5}, pages={657-687}, year={2009}, publisher={Springer} } @article{byrned1996biological, title={Biological inferences from a mathematical model for malignant invasion}, author={A.Perumpanani and J.Sherratt and J.Norbury and H.Byrned}, journal={Invasion Metastasis}, volume={16}, pages={209-22l}, year={1996} } @article{cabral2016apoptotic, title={Apoptotic CD8 T-lymphocytes disable macrophage-mediated immunity to Trypanosoma cruzi infection}, author={M.P.Cabral-Piccin and L.V.C.Guillermo and N.S.Vellozo and A.A.Filardy and S.T.Pereira-Marques and T.S.Rigoni and W.F.Pereira-Manfro and G.A.DosReis and M.F.Lopes}, journal={Cell death \& disease}, volume={7}, number={5}, pages={e2232-e2232}, year={2016}, publisher={Nature Publishing Group} } @article{cassady2016infection, title={To Infection and Beyond: The Multi-Pronged Anti-Cancer Mechanisms of Oncolytic Viruses}, author={K.Cassady and K.Haworth and J.Jackson and J.Markert, and T.Cripe}, journal={Viruses}, volume={8}, number={2}, pages={43}, year={2016}, publisher={Multidisciplinary Digital Publishing Institute} } @Book{cesario, author = {A.cesario and F.B.Marcus}, title = {Cancer systems biology, bioinformatics and medicine}, publisher = {Springer}, year = {2011} } @article{chang2020therapeutic, title={Therapeutic effects of BCG vaccination on type 1 diabetes mellitus: a systematic review and meta-analysis of randomized controlled trials}, author={Y.Chang and C.Lin and Y.Hsiao and Y.Chang and S.Liu and Y.Hsu}, journal={Journal of Diabetes Research}, volume={2020}, number={1}, pages={8954125}, year={2020}, publisher={Wiley Online Library} } @article{chaplain2006mathematical, title={Mathematical modeling of tumor-induced angiogenesis}, author={M.Chaplain and S.McDougall and A.Anderson}, journal={Annu. Rev. Biomed. Eng.}, volume={8}, pages={233-257}, year={2006}, publisher={Annual Reviews} } @article{chaplain2006mathematical2, title={Mathematical modelling of cancer invasion of tissue: dynamic heterogeneity.}, author={M.Chaplain and G.Lolas}, journal={NHM}, volume={1}, number={3}, pages={399--439}, year={2006} } @article{chaplain1995mathematical, title={A mathematical analysis of a model for tumour angiogenesis}, author={M.Chaplain and S.Giles and B.D.Sleeman and R.Jarvis}, journal={Journal of Mathematical Biology}, volume={33}, number={7}, pages={744-770}, year={1995}, publisher={Springer} } @article{chaplain1995mathematical2, title={The mathematical modelling of tumour angiogenesis and invasion}, author={M.Chaplain}, journal={Acta biotheoretica}, volume={43}, number={4}, pages={387-402}, year={1995}, publisher={Springer} } @article{chaplain1993model, title={A model mechanism for the chemotactic response of endothelial cells to tumour angiogenesis factor}, author={M.Chaplain and A.Stuart}, journal={Mathematical Medicine and Biology}, volume={10}, number={3}, pages={149-168}, year={1993}, publisher={IMA} } @article{chaplain1991mathematical, title={A mathematical model for the diffusion of tumour angiogenesis factor into the surrounding host tissue}, author={M.Chaplain and A.Stuart}, journal={Mathematical Medicine and Biology}, volume={8}, number={3}, pages={191-220}, year={1991}, publisher={IMA} } @article{chang2003analyzing, title={Analyzing immunotherapy and chemotherapy of tumors through mathematical modeling}, author={W.Chang and L.Crowl and E.Malm and K.Todd-Brown and L.Thomas and M.Vrable}, journal={Department of Mathematics, Harvey-Mudd University}, year={2003} } @article{chauhan2013strategies, title={Strategies for advancing cancer nanomedicine}, author={V.Chauhan and R.Jain}, journal={Nature materials}, volume={12}, number={11}, pages={958-962}, year={2013}, publisher={Nature Publishing Group} } @Article{Chen, author = {J.Chen and L.Yuan and Q.Fan and F.Su and Y.Chen and S.Hu}, title = {{Adjuvant effect of docetaxel on the immune responses to influenza A H1N1 vaccine in mice}}, journal = {BMC Immunology}, volum = {13}, pages = {16}, year = {2014} } @Article{Chen_MathMod_2014, author = {D.Chen and A.A.Bobko and A.C.Gross and R.Evans and C.B.Marsh and V.V.Khramtsov and T.D.Eubank and A.Friedman}, title = {Involvement of Tumor Macrophage {HIFs} in Chemotherapy Effectiveness: Mathematical Modeling of Oxygen, {pH}, and Glutathione}, journal = {PLOS ONE}, volum = {9}, pages = {10}, year = {2014} } @article{Chen2011_TAMmelanomaGrowth, author = {P.Chen and Y.Huang and R.Bong and Y.Ding and N.Song and X.Wang and X.Song and Y.Lou}, title = {Tumor-associated macrophages promote angiogenesis and melanoma growth via adrenomedullin in a paracrine and autocrine manner}, journal = {Clin. Cancer Res.}, year = {2011}, volume = {17}, number = {23}, pages = {7230-7239}, } @article{chen1997nonlinear, title={Nonlinear pharmacokinetics of cyclophosphamide and 4-hydroxycyclophosphamide/aldophosphamide in patients with metastatic breast cancer receiving high-dose chemotherapy followed by autologous bone marrow transplantation}, author = {T.Chen and M.J.Kennedy and L.W.Anderson and S.B.Kiraly and K.C.Black and O.M.Colvin and L.B.Grochow}, journal={Drug metabolism and disposition}, volume={25}, number={5}, pages={544-551}, year={1997}, publisher={ASPET} } @article{cho2021review, title={A review of the BCG vaccine and other approaches toward tuberculosis eradication}, author={C.Thomas and C.Khatchadourian and H.Nguyen and Y.Dara and S.Jung and V.Venketaraman}, journal={Human vaccines \& immunotherapeutics}, volume={17}, number={8}, pages={2454-2470}, year={2021}, publisher={Taylor \& Francis} } @article{chu2006efficacy, author = {Y. Chu and Li-X. Wang and G. Yang and H. J. Ross and W. J. Urba and R. Prell and K. Jooss and S. Xiong and Hong-M. Hu}, title = {Efficacy of {GM-CSF-producing} Tumor Vaccine after Docetaxel Chemotherapy in Mice Bearing Established Lewis Lung Carcinoma}, journal = {J Immunother.}, year = {2006}, volume = {29}, number = {4}, pages = {367-380}, } @article{chiocca2014oncolytic, title={Oncolytic viruses and their application to cancer immunotherapy}, author={E.A.Chiocca and S.D.Rabkin}, journal={Cancer immunology research}, volume={2}, number={4}, pages={295-300}, year={2014}, publisher={AACR} } @article{Coussens2002_InflammationCancer, author = {L.M.Cousins and Z.Werb}, title = {Inflammation and cancer}, journal = {Nature}, year = {2002}, volume = {420}, pages = {860-867} } @article{collier2011pancreatic, title={Pancreatic $\beta$-cell death in response to pro-inflammatory cytokines is distinct from genuine apoptosis}, author={J.J.Collier and S.J.Burke and M.E.Eisenhauer and D.Lu and R.C.Sapp and C.J.Frydman and S.R.Campagna}, journal={PLoS One}, volume={6}, number={7}, pages={e22485}, year={2011}, publisher={Public Library of Science San Francisco, USA} } @article{Condeelis2006, author = {J.Condeelis and J.W.Pollard}, title = {Macrophages: Obligate Partners for Tumor Cell Migration, Invasion, and Metastasis}, journal = {Cell}, year = {2006}, volume = {124}, pages = {263-6}, } @inproceedings{connelly1996ifosfamide, title={Ifosfamide in the treatment of soft tissue sarcomas.}, author={E. F. Connelly and T. G. Budd}, booktitle={Seminars in oncology}, volume={23}, number={3 Suppl 6}, pages={16-21}, year={1996} } @article{d2008metamodeling, title={Metamodeling tumor-immune system interaction tumor evasion and immunotherapy}, author={A.d\text{'}Onofrio}, journal = {Mathematical and Computer Modelling}, volume={47}, number={5}, pages={614-637}, year={2008}, publisher={Elsevier} } @article{d2005general, title={A general framework for modeling tumor-immune system competition and immunotherapy: Mathematical analysis and biomedical inferences}, author={A.d\text{'}Onofrio}, journal={Physica D: Nonlinear Phenomena}, volume={208}, number={3}, pages={220-235}, year={2005}, publisher={Elsevier} } @Article{Danciu, author = {C.Danciu and A.Falamas and C.Dehelean and C.Soica and H.Radeke and L.Tudoran and F.Bojin and S.P{\^\i}nzaru and M.Munteanu}, title = {A characterization of four {B16} murine melanoma cell sublines molecular fingerprint and proliferation behavior}, doi={10.1186/1475-2867-13-75}, journal = {Cancer Cell International}, year = {2013}, volume = {13}, pages = {75} } @article{de2005validated, title={A validated mathematical model of cell-mediated immune response to tumor growth}, author={L.G.de Pillis and A.E.Radunskaya and C.L.Wiseman}, journal={Cancer research}, volume={65}, number={17}, pages={7950-7958}, year={2005}, publisher={AACR} } @article{demine2020pro, title={Pro-inflammatory cytokines induce cell death, inflammatory responses, and endoplasmic reticulum stress in human iPSC-derived beta cells}, author={S.Demine and A.A.Schiavo and S.Mar{\'\i}n-Ca{\~n}as and P.Marchetti and M.Cnop and D.L.Eizirik}, journal={Stem cell research $\&$ therapy}, volume={11}, number={1}, pages={1-15}, year={2020}, publisher={Springer} } @article{DenBreemsEftimie2015, author = {N.Y.den Breems and R.Eftimie}, title = {{The re-polarization of M2 and M1 macrophages and its role on cancer outcomes}}, journal={Journal of Theoretical Biology}, volume={390}, pages={23-39}, year={2016}, publisher={Elsevier} } @article{derbel2004analysis, title={Analysis of a new model for tumor-immune system competition including long-time scale effects}, author={L.Derbel}, journal={Mathematical Models and Methods in Applied Sciences}, volume={14}, number={11}, pages={1657-1681}, year={2004}, publisher={World Scientific} } @article{dePillis, author = {L.G.de Pillis and A.E.Radunskaya and C.L.Wiseman}, title = {A Validated Mathematical Model of Cell-Mediated Immune Response to Tumor Growth}, journal = {Cancer Res}, year = {2005}, volume = {65}, number={17}, pages = {1916-1940} } @book{dasgupta2009advances, title={Advances in Chromatographic Techniques for Therapeutic Drug Monitoring}, author={A.Dasgupta}, year={2009}, publisher={CRC Press} } @InProceedings{de2003mathematical, title={A mathematical model of immune response to tumor invasion}, author={L.de Pillis and A.Radunskaya}, booktitle = {Second {MIT} Conference on Computational Fluid and Solid Mechanics}, year={2003} } @article{Desmedt1998_MacrophInduceTh1, author = {M.Desmet and P.Rottiers and H.Dooms and W.Fiers and J.Grooten}, title = {{Macrophages induce cellular immunity by activating Th1 cell responses and suppressing Th2 cell responses}}, journal = {J. Immunol.}, year = {1998}, volume = {160}, pages = {5300-5308} } @article{devakiapplied, author={P.Devaki and S.Sreenadh and K.Vajravelu and KV.Prasad and H.Vaidya}, title = {Wall Properties and Slip Consequences on Peristaltic Transport of a Casson Liquid in a Flexible Channel with Heat Transfer}, journal = {Applied Mathematics and Nonlinear Sciences}, year = {2018}, volume = {160}, pages = {277–290} } @article{dibrov1985mathematical, title={Mathematical model of cancer chemotherapy. periodic schedules of phase-specific cytotoxic-agent administration increasing the selectivty of therapy}, author={B.Dibrov and A.Zhabotinsky and Y.Neyfakh and M.Orlova and L.Churikova}, journal={Mathematical biosciences}, volume={73}, number={1}, pages={1-31}, year={1985}, publisher={Elsevier} } @article{Dimitriu_2014, author = {G.Dimitriu and T.Lorenzi234 and R.Stefanescu}, title = {Evolutionary Dynamics of Cancer Cell Populations under Immune Selection Pressure and Optimal Control of Chemotherapy}, journal = {Math. Model. Nat. Phenom.}, year = {2014}, volume = {9}, number={4}, pages = {88-04} } @article{dor2004adult, title={Adult pancreatic $\beta$-cells are formed by self-duplication rather than stem-cell differentiation}, author={Y.Dor and J.Brown and O.I.Martinez and D.A.Melton}, journal={Nature}, volume={429}, number={6987}, pages={41-46}, year={2004}, publisher={Nature Publishing Group} } @article{Eftime, Author = {R.Eftimie and J.L.Bramson and D.J.D.Earn}, title={Interactions between the immune system and cancer: a brief review of non-spatial mathematical models}, journal={Bulletin of mathematical biology}, volume={73}, number={1}, pages={2-32}, year={2011}, publisher={Springer} } @article{Eftimie_Th, title = {Modelling anti-tumour {Th1} and {Th2} immunity in the rejection of melanoma}, journal = {Journal of Theoretical Biology}, volume = {265}, number = {3}, pages = {467-480}, year = {2010}, author = {R.Eftimie and J.L.Bramson and D.J D.Earn.} } @article{eftimie2016mathematical, title={Mathematical Models for Immunology: Current State of the Art and Future Research Directions}, author={R.Eftimie and J.J.Gillard and D.A.Cantrell}, journal={Bulletin of Mathematical Biology}, volume={78}, number={10}, pages={2091-2134}, year={2016}, publisher={Springer} } @article{eftimie2017modelling, title={Modelling and investigation of the{ $CD4^{+}$ T} cells-macrophages paradox in melanoma immunotherapies}, author={R.Eftimie and H.Hamam}, journal={Journal of Theoretical Biology}, volume={420}, pages={82-104}, year={2017}, publisher={Elsevier} } @article{Ehrlich1909_CancerImmuneSurveillance, author = {P.Ehrich}, title = {Ueber den jetzigen stand der karzinomforschung}, journal = {Ned Tijdschr Geneeskd.}, year = {1909}, volume = {5}, pages = {73-290}, } @article{eizirik2023does, title={Why does the immune system destroy pancreatic $\beta$-cells but not $\alpha$-cells in type 1 diabetes?}, author={D.Eizirik and F.Szymczak and R.Mallone}, journal={Nature Reviews Endocrinology}, volume={19}, number={7}, pages={425-434}, year={2023}, publisher={Nature Publishing Group UK London} } @Article{Ekkens, author = {M.Ekkens and D.Shedlock and E.Jung and A.Troy and E.Pearce and H.Shen and E.Pearce}, title = {{Th1} and {Th2} Cells Help {CD8 T}-Cell Responses}, journal={Infection and immunity}, volume={75}, number={5}, pages={2291-2296}, year={2007}, publisher={Am Soc Microbiol} } @article{emens2015interplay, title={The interplay of immunotherapy and chemotherapy: harnessing potential synergies}, author={L.Emens and G.Middleton}, journal={Cancer immunology research}, volume={3}, number={5}, pages={436-443}, year={2015}, publisher={AACR} } @article{enderling2014mathematical, title={Mathematical modeling of tumor growth and treatment}, author={H.Enderling and M.Chaplain}, journal={Current pharmaceutical design}, volume={20}, number={30}, pages={4934-4940}, year={2014}, publisher={Bentham Science Publishers} } @article{Engelhart2011_OptimalControlChemoImmunoTherapy, author = {M.Engelhart and D.Lebiedz and S.Sager}, title = {Optimal control for selected cancer chemotherapy {ODE} models: a view on the potential of optimal schedules and choice of objective function}, journal = {Mathematical Biosciences}, year = {2011}, volume = {229}, number = {1}, pages = {123-134}, } @article{faustman2012proof, title={Proof-of-concept, randomized, controlled clinical trial of Bacillus-Calmette-Guerin for treatment of long-term type 1 diabetes}, author={D.Faustman and L.Wang and Y.Okubo and D.Burger and L.Ban and G.Man and H.Zheng and D.Schoenfeld and R.Pompei and J.Avruch and other}, journal = {PLoS ONE}, year={2012}, publisher={Public Library of Science San Francisco, USA} } @article{feizabadi2015modeling, title={Modeling drug resistance in a conjoint normal-tumor setting}, author={M.Feizabadi and T.Witten}, journal={Theoretical Biology and Medical Modelling}, volume={12}, number={1}, pages={1-11}, year={2015}, publisher={BioMed Central} } @article{fletcher2010t, title={T cells in multiple sclerosis and experimental autoimmune encephalomyelitis}, author={J.M.Fletcher and S.J.Lalor and C.M.Sweeney and N.Tubridy and K.H.G.Mills}, journal={Clinical \& Experimental Immunology}, volume={162}, number={1}, pages={1-11}, year={2010}, publisher={Wiley Online Library} } @article{flores2013novel, title={Novel oral taxane therapies: recent Phase {I results}}, author={J.P.Flores and W.M.Saif}, journal={Clinical investigation}, volume={3}, number={4}, pages={333}, year={2013}, publisher={NIH Public Access} } @article{fremd2013b, title={B cell-regulated immune responses in tumor models and cancer patients}, author={C.Fremd and F.Schuetz and C.Sohn and P.Beckhove and C.Domschke}, journal={Oncoimmunology}, volume={2}, number={7}, pages={e25443}, year={2013}, publisher={Taylor \& Francis} } @article{Friberg1997_DetectionTumSize, author = {S.Friberg and S.Mattson}, title = {On the growth rates of human malignant tumours: implications for medical decision making}, year = {1997}, journal = {J. Surgical Oncology}, volume = {65}, pages = {284-297} } @article{FishmanPerelson1999_Th1Th2, title={{Th1/Th2} differentiation and cross-regulation}, author={M.A.Fishman and A.S.Perelson}, journal={Bulletin of mathematical biology}, volume={61}, number={3}, pages={403-436}, year={1999}, publisher={Springer} } @article{fine2010chemotherapy, title={Chemotherapy-induced genotoxic stress promotes sensitivity to natural killer cell cytotoxicity by enabling missing-self recognition}, author={J.Fine and P.Chen and A.Mesci and D.Allan and S.Gasser and D.Raulet and J.Carlyle}, journal={Cancer research}, volume={70}, number={18}, pages={7102-7113}, year={2010}, publisher={AACR} } @article{fine1995variation, title={Variation in protection by BCG: implications of and for heterologous immunity}, author={P.Fine}, journal={The Lancet}, volume={346}, number={8986}, pages={1339--1345}, year={1995}, publisher={Elsevier} } @article{finegood1995dynamics, title={Dynamics of $\beta$-cell mass in the growing rat pancreas: estimation with a simple mathematical model}, author={D.T.Finegood and L.Scaglia and S.Bonner-Weir}, journal={Diabetes}, volume={44}, number={3}, pages={249-256}, year={1995}, publisher={Am Diabetes Assoc} } @article{folkman1971tumor, title={Tumor angiogenesis: therapeutic implications}, author={J.Folkman}, journal={New england journal of medicine}, volume={285}, number={21}, pages={1182-1186}, year={1971}, publisher={Mass Medical Soc} } @book{gabrielsson2001pharmacokinetic, title={Pharmacokinetic and pharmacodynamic data analysis: concepts and applications}, author={J.Gabrielsson and D.Weiner}, volume={1}, year={2001}, publisher={CRC Press} } @Book{Gahrton, author = {G.Gahrton and B.Durie and D.Samson}, title = {Multiple Myeloma and Related Disorders}, year={2004}, publisher={CRC Press} } @article{gaisford1951bcg, title={BCG Vaccination in the Newborn}, author={W.Gaisford and M.Griffiths}, journal={British Medical Journal}, volume={2}, number={4733}, pages={702}, year={1951} } @article{gajewski2013innate, title={Innate and adaptive immune cells in the tumor microenvironment}, author={T.F.Gajewski and H.Schreiber and Y.Fu}, journal={Nature immunology}, volume={14}, number={10}, pages={1014-1022}, year={2013}, publisher={Nature Publishing Group} } @article{Gautier2013_MacrophagesApoptosis, title={Local apoptosis mediates clearance of macrophages from resolving inflammation in mice}, author = {E.L.Gauthier and S.Ivanov and P.Lesnik and G.J.Randolph}, journal={Blood, The Journal of the American Society of Hematology}, volume={122}, number={15}, pages={2714-2722}, year={2013}, publisher={American Society of Hematology Washington, DC} } @article{gatenby1996reaction, title={A reaction-diffusion model of cancer invasion}, author={R.Gatenby and E.Gawlinski}, journal={Cancer research}, volume={56}, number={24}, pages={5745-5753}, year={1996}, publisher={AACR} } @article{gerlee2013model, title={The model muddle: in search of tumor growth laws}, author={P.Gerlee}, journal={Cancer research}, volume={73}, number={8}, pages={2407-2411}, year={2013}, publisher={AACR} } @article{gershwin1974cyclophosphamide, title={Cyclophosphamide: use in practice}, author={E.M.Gershwin and E.J.Goetzl and A.D.Steinberg}, journal={Annals of internal medicine}, volume={80}, number={4}, pages={531-540}, year={1974}, publisher={Am Coll Physicians} } @article{getz2005bridging, title={Bridging the innate and adaptive immune systems}, author={G.Getz}, journal={Journal of lipid research}, volume={46}, number={4}, pages={619-622}, year={2005}, publisher={Elsevier} } @article{ghazarian2013prevention, title={Prevention or acceleration of type 1 diabetes by viruses}, author={L.Ghazarian and J.Diana and Y.Simoni and L.Beaudoin and A.Lehuen}, journal={Cellular and Molecular Life Sciences}, volume={70}, number={2}, pages={239-255}, year={2013}, publisher={Springer} } @book{gibaldi2007gibaldi, title={Gibaldi's drug delivery systems in pharmaceutical care}, author={M.Gibaldi and M.Lee and A.Desai}, year={2007}, publisher={ASHP} } @article{gianni1990recombinant, title={Recombinant human granulocyte-macrophage colony-stimulating factor reduces hematologic toxicity and widens clinical applicability of high-dose cyclophosphamide treatment in breast cancer and non-Hodgkin's lymphoma.}, author={A.M.Gianni and M.Bregni and S.Sien and A.Orazi and A.C.Stern and L.Gandola and G.Bonadonna}, journal={Journal of Clinical Oncology}, volume={8}, number={5}, pages={768-778}, year={1990} } @article{Goswami2005, author = {S.Goswami and E.Sahai and J.B.Wyckoff and M.Cammer and D.Cox and F.J.Pixley and E.R.Stanley and J.E.Segall, and J.S.Condeelis}, title = {Macrophages Promote the Invasion of Breast Carcinoma Cells via a Colony-Stimulating Factor-1/Epidermal Growth Factor Paracrine Loop}, journal = {Cancer Res}, year = {2005}, volume = {65}, number = {12}, pages = {5278-5283}, } @article{Groh2014_TumDrugTransport, author = {C.M.Groh and M.E.Hubbard and P.F.Jones and P.M.Loadman and N.Periasamy and B.D.Sleeman and S.W.Smye and C.J.Twelves and R.M.Phillips}, title = {Mathematical and computational models of drug transport in tumours}, journal = {J. R. Soc. Interface}, year = {2014}, volume = {11}, pages = {20131173}, } @article{Gross2011_Th1Th2ModelAlergens, author = {F.Gross and G.Metzler and U.Behn}, title = {{Mathematical modeling of allergy and specific immunotherapy: Th1-Th2-Treg interactions}}, journal = {J. Theor. Biol.}, year = {2011}, volume= {269}, number = {1}, pages = {70-78}, } @article{gottesman2002mechanisms, title={Mechanisms of cancer drug resistance}, author={M.M.Gottesman}, journal={Annual review of medicine}, volume={53}, number={1}, pages={615-627}, year={2002}, publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA} } @article{Gyllenberg, Author = {M.Gyllenberg and G.F.Webb}, Journal = {Mathematical Biology}, Month = {January}, Pages = {671-694}, volume={28}, number={6}, Title = {A nonlinear strutted population model of tumor growth with quiescence}, Year = {1990} } @article{hadrup2013effector, title={Effector{ CD4} and {CD8 T} cells and their role in the tumor microenvironment}, author={S.Hadrup and M.Donia and P.Thor Straten}, journal={Cancer Microenvironment}, volume={6}, number={2}, pages={123-133}, year={2013}, publisher={Springer} } @article{Hamam2023, author = {H.Hamam}, title = {A Mathematical Model of Type 1 Diabetes: Interaction Between M1 and M2 Macrophages and $\beta$-Cells}, journal = {Applied Mathematics and Nonlinear Sciences}, volume = {8}, number = {1}, pages = {297-313}, year = {2023}, doi = {10.2478/amns-2021-0032}, url = {https://sciendo.com/article/10.2478/amns-2021-0032} } @article{hashmi2014modeling, title={Modeling the Tumor-Immune Interaction Cultured with Chemotherapy and Cytokine Interleukin {IL-2 }Under the Influence of Immunodeficiency Viruses}, author={M.U.Hashmi and M.Suleman and S.M.J.Zaidi and M.Habib}, year={2014}, journal = {American-Eurasian Journal of Toxicological Sciences}, volume = {6}, number = {4}, pages = {74-82}, } @article{Hind2016, Author = {L.Hind and E.Lurier and M.Dembo and K.L.Spiller and D.A.Hammer}, Journal = { Cellular and Molecular Bioengineering}, Pages = {455-465}, volume={9}, number={3}, Title = {Effect of{ M1-M2} Polarization on the Motility and Traction Stresses of Primary Human Macrophages}, Year = {2016}, } @article{Hsieh1993_IL12_Th1Development, author = {C.S.His and S.E.Macedonia and C.S.Tripp and S.F.Wolf and A.O'Garra and K.M.Murphy}, title = {{Development of Th1 CD4$^{+}$ T cells through IL-12 produced by \textit{Listeria}-induced macrophages}}, journal = {Science}, Year = {1993}, volume = {260}, pages = {547-549}, } @article{huang2001importance, title={On the importance and mechanisms of burst release in matrix-controlled drug delivery systems}, author={X.Huang and C.Brazel}, journal={Journal of controlled release}, volume={73}, number={2-3}, pages={121-136}, year={2001}, publisher={Elsevier} } @Article{Hung, author = {K.Hung and R.Hayashi and A.Walker and C.Lowenstein and D.Pardoll and H.Levitsky}, title = {{The central role of $CD4^{+}T$ cells in the antitumor Immune Response}}, journal = { J. Exp. Med}, year = {1998}, pages = {2357--2368}, } @article{jackson2002vascular, title={Vascular tumor growth and treatment: consequences of polyclonality, competition and dynamic vascular support}, author={T.Jackson}, journal={Journal of mathematical biology}, volume={44}, number={3}, pages={201-226}, year={2002}, publisher={Springer} } @article{jackson2000mathematical, title={A mathematical model to study the effects of drug resistance and vasculature on the response of solid tumors to chemotherapy}, author={T.L.Jackson and H.M.Byrne}, journal={Mathematical biosciences}, volume={164}, number={1}, pages={17-38}, year={2000}, publisher={Elsevier} } @article{jamshidi2023bcg, title={BCG Vaccination and the Risk of Type 1 Diabetes Mellitus: A Systematic Review and Meta-Analysis}, author={P.Jamshidi and B.Danaei and B.Mohammadzadeh and M.Arbabi and A.Nayebzade and L.Sechi and M.Nasiri}, journal={Pathogens}, volume={12}, number={4}, pages={581}, year={2023}, publisher={MDPI} } @article{Jenkins2011_IL4MacrophProlif, author = {S.Jenkins and D.Ruckerl and P.Cook and L.Jones and F.Winkelman and N.van Rooijen and A.MacDonald and J.Allen}, title = {{Local macrophage proliferation, rather than recruitment from the blood, is a signature of Th2 inflammation}}, journal = {Science}, year = {2011}, volume = {332}, number = {6035}, pages = {1284-1288}, } @article{kadota2018mathematical, title={A mathematical model of type 1 diabetes involving leptin effects on glucose metabolism}, author={R.Kadota and K.Sugita, and K.Uchida and H.Yamada and M.Yamashita and H.Kimura}, journal={Journal of Theoretical Biology}, volume={456}, pages={213-223}, year={2018}, publisher={Elsevier} } @article{Kant2013_AgeSpaceStructuredTum, author = {S.Kant}, title = {Age and space structured tumour invasion: a theoretical mathematical formulation}, journal = {African Journal of Mathematics and Computer Science Research}, year = {2013}, volume = {6}, number = {8}, pages= {161-165}, } @article{kaufmann2018bcg, title={BCG educates hematopoietic stem cells to generate protective innate immunity against tuberculosis}, author={E.Kaufmann and J.Sanz and J.Dunnand N.Khan and L.Mendon{\c{c}}a and A.Pacis and F.Tzelepis and E.Pernet and A.Dumaine and J.Grenier and others}, journal={Cell}, volume={172}, number={1}, pages={176-190}, year={2018}, publisher={Elsevier} } @article{kirschner1998modeling, title={Modeling immunotherapy of the tumor--immune interaction}, author={D.Kirschner and J.Panetta}, journal={Journal of mathematical biology}, volume={37}, number={3}, pages={235-252}, year={1998}, publisher={Springer} } @article{kleinnijenhuis2012bacille, title={Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes}, author={J.Kleinnijenhuis and J.Quintin and F.Preijers and L.Joosten and D.Ifrim and S.Saeed and C.Jacobs and J.van Loenhout and D.de Jong and H.Stunnenberg and others}, journal={Proceedings of the National Academy of Sciences}, volume={109}, number={43}, pages={17537-17542}, year={2012}, publisher={National Academy of Sciences} } @article{kleinnijenhuis2015trained, title={Trained immunity: consequences for the heterologous effects of BCG vaccination}, author={J.Kleinnijenhuis and R.Van Crevel and M.Netea}, journal={Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume={109}, number={1}, pages={29-35}, year={2015}, publisher={Oxford University Press} } @article{knutsdottir2014mathematical, title={Mathematical model of macrophage-facilitated breast cancer cells invasion}, author={H.Kn{\'u}tsd{\'o}ttir and E.P{\'a}lsson and L.Edelstein-Keshet}, journal={Journal of theoretical biology}, volume={357}, pages={184-199}, year={2014}, publisher={Elsevier} } @article{kuhtreiber2018long, title={Long-term reduction in hyperglycemia in advanced type 1 diabetes: the value of induced aerobic glycolysis with BCG vaccinations}, author={W.K{\"u}htreiber and L.Tran and T.Kim and M.Dybala and B.Nguyen and S.Plager and D.Huang and S.Janes and A.Defusco and D.Baum and others}, journal={npj Vaccines}, volume={3}, number={1}, pages={23}, year={2018}, publisher={Nature Publishing Group UK London} } @article{kuhtreiber2019bcg, title={BCG therapy for type 1 diabetes: restoration of balanced immunity and metabolism}, author={W.K{\"u}htreiber and D.Faustman}, journal={Trends in Endocrinology \& Metabolism}, volume={30}, number={2}, pages={80-92}, year={2019}, publisher={Elsevier} } @article{lazebnik2023mathematical, title={Mathematical model for BCG-based treatment of type 1 diabetes}, author={T.Lazebnik and S.Bunimovich-Mendrazitsky and A.Kiselyov}, journal={Physica A: Statistical Mechanics and its Applications}, volume={622}, pages={128891}, year={2023}, publisher={Elsevier} } @article{lazebnik2021clinically, title={Clinically Relevant Mathematical Model for the BCG-based Treatment of Type 1 Diabetes}, author={T.Lazebnik and S.Bunimovich-Mendrazitsky and A.Kiselyov}, journal={bioRxiv}, pages={2021-09}, year={2021}, publisher={Cold Spring Harbor Laboratory} } @article{lombarte2018vivo, title={In vivo measurement of the rate constant of liver handling of glucose and glucose uptake by insulin-dependent tissues, using a mathematical model for glucose homeostasis in diabetic rats}, author={M.Lombarte and M.Lupo and L.F.Brenda and G.Campetelli and A.B.Marilia and M.Basualdo and A.Rigalli}, journal={Journal of Theoretical Biology}, volume={439}, pages={205-215}, year={2018}, publisher={Elsevier} } @Article{Looney, author = {W. B. Looney and E. R. Ritenour and H. A. Hopkines}, title = {Changes in growth rate of an experimental solid tumor following increasing doses of cyclophosphamide}, journal={Cancer research}, volume={40}, number={7}, pages={2179-2183}, year={1980}, publisher={AACR} } @Article{Lopez_2014, author = {A.G.Lopez and J.M.Seoane and M.A.F.Sanjuan}, title = {A validated mathematical model of tumor growth including tumor-host interaction, cell-mediated immune response and chemotherapy}, journal = { Bull Math Biol}, volume={76}, number={11}, year = {2014}, pages = {2884--2906}, } @article{Louzoun2014_MathModelPancreaticCancer, author = {Y.Louzoun and C.Xue and G.B.Lesinski and A.Friedman}, title = {A mathematical model for pancreatic cancer growth and treatments}, journal = {J. Theor. Biol.}, year = {2014}, volume = {351}, pages = {74-82}, } @article{Lucey1996_Type1Type2Cytokines, author = {D.R.Lucey and M.Clerici and G.M.Shearer}, title = {Type 1 and type 2 cytokine dysregulation in human infectious, neoplastic, and inflammatory diseases}, journal = {Clinical Microbiology Reviews}, year = {1996}, volume = {9}, number = {4}, pages = {532-562}, } @article{ludden1991nonlinear, title={Nonlinear pharmacokinetics}, author={T.M.Ludden}, journal={Clinical pharmacokinetics}, volume={20}, number={6}, pages={429-446}, year={1991}, publisher={Springer} } @article{maree2006modelling, title={Modelling the onset of Type 1 diabetes: can impaired macrophage phagocytosis make the difference between health and disease?}, author={A.Mar{\'e}e and R.Kublik and D.Finegood and L.Edelstein-Keshet}, journal={Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, volume={364}, number={1842}, pages={1267-1282}, year={2006}, publisher={The Royal Society London} } @article{matzavinos2004mathematical, title={Mathematical modelling of the spatio-temporal response of cytotoxic T-lymphocytes to a solid tumour}, author={A. Matzavinos and M. Chaplain and V. Kuznetsov}, journal={Mathematical Medicine and Biology}, volume={21}, number={1}, pages={1-34}, year={2004}, publisher={IMA} } @article{Martinez2014_M1M2paradigm, author = {F.O.Martinez and S.Gordon}, title = {The {M1} and {M2} paradigm of macrophage activation: time for reassessment}, journal = {F1000 Prime Reports}, year = {2014}, volume={6}, } @book{martin2010fanaroff, title={Fanaroff and Martin's neonatal-perinatal medicine: diseases of the fetus and infant}, author={R.J.Martin and A.A.Fanaroff and M.C.Walsh}, year={2010}, publisher={Elsevier Health Sciences} } @article{maruvsic1996mathematical, title={Mathematical models of tumor growth}, author={M.Maru{\v{s}}i{\'c}}, journal={Mathematical Communications}, volume={1}, number={2}, pages={175-188}, year={1996}, publisher={Odjel za matematiku, Sveu{\v{c}}ili{\v{s}}te JJ Strossmayera u Osijeku} } @article{matzavinos2004travelling, title={Travelling-wave analysis of a model of the immune response to cancer}, author={A.Matzavinos and M.Chaplain}, journal={Comptes rendus biologies}, volume={327}, number={11}, pages={995--1008}, year={2004}, publisher={Elsevier} } @article{mantovani2008tumour, title={Tumour immunity: effector response to tumour and role of the microenvironment}, author={A.Mantovani and P.Romero and A.K.Palucka and F.M.Marincola}, journal={The Lancet}, volume={371}, number={9614}, pages={771-783}, year={2008}, publisher={Elsevier} } @article{mcleod1998evaluation, title={Evaluation of the linearity of docetaxel pharmacokinetics}, author={H.L.McLeod and C.M.Kearns and J.G.Kuhn and R.Bruno}, journal={Cancer chemotherapy and pharmacology}, volume={42}, number={2}, pages={155-159}, year={1998}, publisher={Springer} } @article{mehvar2001principles, title={Principles of nonlinear pharmacokinetics}, author={R.Mehvar}, journal={American Journal of Pharmaceutical Education}, volume={65}, number={2}, pages={178}, year={2001}, publisher={American Association of Colleges of Pharmacy} } @article{messaoudi2011nonhuman, title={Nonhuman primate models of human immunology}, author={I.Messaoudi and R.Estep and B.Robinson and S.W.Wong}, journal={Antioxidants \& redox signaling}, volume={14}, number={2}, pages={261-273}, year={2011}, publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA} } @article{Michelson1997_2TumEq, author = {S.Michelson and J.T.Leith}, title = {Positive feedback and angiogenesis in tumour growth control}, journal = {Bull. Math Biol.}, year = {1997}, volume = {59}, number = {2}, pages = {233-254}, } @article{MillsLey2014_M1M2ChickenEgg, author = {C.D.Mills and K.Ley}, title = {{M1 and M2 macrophages: the chicken and the egg of immunity}}, journal = {J. Innate Immun.}, year = {2014}, volume = {6}, number = {6}, pages = {716-726}, } @book{missailidis2008anticancer, title={Anticancer therapeutics}, author={S.Missailidis}, year={2008}, publisher={John Wiley \& Sons} } @book{monie2017innate, author = {A.Monie}, title = {The innate immune system: a compositional and functional perspective}, publisher = {Academic Press / Elsevier}, address = {London, UK}, year = {2017}, edition = {1st}, isbn = {978-0-12-804464-3} } @article{Moore2004_LeukemiaMathModel, author = {H. Moore and N. K. Li}, title = {A mathematical model for chronic myelogenous leukaemia {(CML) and T} cell interactions}, journal = {J. Theor. Biol.}, year = {2004}, volume = {227}, pages = {513-523} } @article{molina2005infection, title={Infection, vaccines and other environmental triggers of autoimmunity}, author={V.Molina and Y.Shoenfeld}, journal={Autoimmunity}, volume={38}, number={3}, pages={235-245}, year={2005}, publisher={Taylor \& Francis} } @article{Moreira2002_CAmodelsReview, author = {J.Moreira and A.Deutsch}, title = {Cellular automaton models of tumour development: a critical review}, journal = {Advances in Complex Systems}, year = {2002}, volume = {5}, pages= {247-267}, } @incollection{Morel1992_MathModel_Th1Th2, year={1992}, isbn={978-3-642-76979-5}, booktitle={Theoretical and Experimental Insights into Immunology}, volume={66}, series={NATO ASI Series}, editor={A.Perelson and G.Weisbuch}, doi={10.1007/978-3-642-76977-1_11}, title={{Mathematical Modeling of Th1-Th2 Dynamics}}, url={http://dx.doi.org/10.1007/978-3-642-76977-1_11}, publisher={Springer Berlin Heidelberg}, author={B. Morel and J. Kalagnanam and P. Morel}, pages={171-190}, language={English} } @article{murphy2016differences, title={Differences in predictions of {ODE} models of tumor growth: a cautionary example}, author={H.Murphy and H.Jaafari and H.M.Dobrovolny}, journal={BMC cancer}, volume={16}, number={1}, pages={1}, year={2016}, publisher={BioMed Central} } @article{murray1990optimal, title={Optimal control for a cancer chemotheraphy problem with general growth and loss functions}, author={J.Murray}, journal={Mathematical Biosciences}, volume={98}, number={2}, pages={273-287}, year={1990}, publisher={Elsevier} } @article{netea2016trained, title={Trained immunity: a program of innate immune memory in health and disease}, author={M.Netea and L.Joosten and E.Latz and K.Mills and G.Natoli and H.Stunnenberg and L.O’Neill and R.Xavier}, journal={Science}, volume={352}, number={6284}, pages={aaf1098}, year={2016}, publisher={American Association for the Advancement of Science} } @manual{NIH_MouseTumSizeKill, author = {N.I.H. and O.A.C.U}, title = {Guidelines for endpoints in animal study proposals}, year = {1996}, note = {http://oacu.od.nih.gov/ARAC/documents/ASP Endpoints.pdf}, } @article{ochoa2013population, title={Population-based optimization of cytostatic/cytotoxic combination cancer chemotherapy}, author={G.Ochoa and M.Villasana}, journal={Soft Computing}, volume={17}, number={6}, pages={913-924}, year={2013}, publisher={Springer} } @Article{Owen2004, author = {M.R.Owen and H.M.Byrne and C.E.Lewis}, title = {Mathematical modelling of the use of macrophages as vehicles for drug delivery to hypoxic tumour sites}, journal = {J. Theor. Biol}, year = {2004}, pages = {377-391}, volume={226}, } @article{owen1998modelling, title={Modelling the macrophage invasion of tumours: effects on growth and composition}, author={M.Owen and J.Sherratt}, journal={Mathematical Medicine and Biology}, volume={15}, number={2}, pages={165-185}, year={1998} } @article{orme1996, author = {M.E.Orme and M.A.J.Chaplain}, title = { A Mathematical Model of Vascular Tumour Growth and Invasion}, journal = {Mathl. Comput.}, year = {1996}, volume = {23}, number = {10}, pages = {43-60}, } @article{orme1996mathematical, title={A mathematical model of the first steps of tumour-related angiogenesis: capillary sprout formation and secondary branching}, author={M.E.Orme and M.A.J.Chaplain}, journal={Mathematical Medicine and Biology}, volume={13}, number={2}, pages={73-98}, year={1996}, publisher={IMA} } @article{palmer1953variation, title={Variation in technique of intracutaneous BCG vaccination}, author={C.Palmer and P.Edwards}, journal={British Medical Journal}, volume={1}, number={4806}, pages={363}, year={1953} } @article{Panzer2011, title = {Rapid In Vivo Conversion of Effector {T} Cells into {Th2} Cells during Helminth Infection}, journal = {The Journal of Immunology}, pages = {615-623}, volume = {118}, number = {2}, year = {2011}, author = {M.Panzer and S.Sitte and S.Wirth and I.Drexler and T.Sparwasser and D.Voehringer}, } @article{parkin2001overview, title={An overview of the immune system}, author={J.Parkin and B.Cohen}, journal={The Lancet}, volume={357}, number={9270}, pages={1777-1789}, year={2001}, publisher={Elsevier} } @book{ramlaul2013patient, title={Patient Centered Care in Medical Imaging and Radiotherapy}, author={A.Ramlaul and M.Vosper}, year={2013}, publisher={Elsevier Health Sciences} } @book{Rosenfeld2007, title={Pharmacology}, author={G.C.Rosenfeld and D.S.Loose}, year={2007}, publisher={Lippincott Williams and Wilkins} } @article{Rhee_DrugDelivery, author = {Y.-S.Rhee and C.-W.Park and P.P.DeLuca and H.M.Mansour}, title = {Sustained-release injectable drug delivery}, journal = {Pharmaceutical Technology}, year = {2010}, volume = {2010}, number = {6}, } @Book{Roboz, author = {J. Roboz}, title = {Mass spectrometry in cancer research}, publisher = {CRC Press LLC}, year = {2002}, } @book{robinson1985comprehensive, title={Comprehensive biotechnology: The practice of biotechnology: speciality products and service activities/vol. ed. Campbell W. Robinson and John A. Howell}, author={C.W.Robinson}, year={1985}, publisher={Pergamon Press} } @article{roep2021type, title={Type 1 diabetes mellitus as a disease of the $\beta$-cell (do not blame the immune system?)}, author={B.Roep and S.Thomaidou and R.Van Tienhoven and A.Zaldumbide}, journal={Nature Reviews Endocrinology}, volume={17}, number={3}, pages={150-161}, year={2021}, publisher={Nature Publishing Group UK London} } @book{rogge2009preclinical, title={Preclinical drug development}, author={M.C.Rogge and D.R.Taft}, year={2009}, publisher={CRC Press} } @article{russell2014impact, title={The impact of anti-inflammatory cytokines on the pancreatic $\beta$-cell}, author={M.A.Russell and N.G.Morgan}, journal={Islets}, volume={6}, number={3}, pages={e950547}, year={2014}, publisher={Taylor \& Francis} } @article{Sachs, Author = {R.K.Sachs and L.R.Hlatky and P.Hannfeldt}, Journal = {Mathematical and computer modeling}, volume = {33}, pages = {1297-1305}, Title = {Simple {ODE} models of tumor growth and anti-angiogenic or radiation treatment}, Year = {2001}, } @article{santoro1995doxorubicin, title={Doxorubicin versus {CYVADIC} versus doxorubicin plus ifosfamide in first-line treatment of advanced soft tissue sarcomas: a randomized study of the European Organization for Research and Treatment of Cancer Soft Tissue and Bone Sarcoma Group.}, author={A. Santoro and T. Tursz and H. Mouridsen and J. Verweij and W. Steward and R. Somers and J. Buesa and P. Casali and D. Spooner and E. Rankin}, journal={Journal of Clinical Oncology}, volume={13}, number={7}, pages={1537-1545}, year={1995} } @article{shymko1976cellular, title={Cellular and geometric control of tissue growth and mitotic instability}, author={R.Shymko and L.Glass}, journal={Journal of Theoretical Biology}, volume={63}, number={2}, pages={355-374}, year={1976}, publisher={Elsevier} } @article{shpilsky2021bacillus, title={Bacillus Calmette-Guerin's beneficial impact on glucose metabolism: evidence for broad based applications}, author={G.Shpilsky and H.Takahashi and A.Aristarkhova and M.Weil and N.Ng and K.Nelson and A.Lee and H.Zheng and W. K{\"u}htreiber and D.Faustman}, journal={Iscience}, volume={24}, number={10}, year={2021}, publisher={Elsevier} } @Article{Sica_macrophages, author = {A.Sica and A.Mantovani}, title = {Macrophage plasticity and polarization in vivo veritas}, journal={The Journal of clinical investigation}, volume={122}, number={3}, pages={787-795}, year={2012}, publisher={Am Soc Clin Investig} } @article{siepmann2008mathematical, title={Mathematical modeling of drug delivery}, author={J.Siepmann and F.Siepmann}, journal={International journal of pharmaceutics}, volume={364}, number={2}, pages={328-343}, year={2008}, publisher={Elsevier} } @article{singha2024role, title={The role of alternative splicing and splicing factors in diabetes: Current status and future perspectives}, author={D.Singha and M.Mondal and D.Ghosh and D.Choudhury and B.Chakravarti and R.Kar and P.Malakar}, journal={Wiley Interdisciplinary Reviews: RNA}, volume={15}, number={1}, pages={e1831}, year={2024}, publisher={Wiley Online Library} } @article{smith2013metastasis, title={The metastasis-promoting roles of tumor-associated immune cells}, author={H. A. Smith and Y. Kang}, journal={Journal of molecular medicine}, volume={91}, number={4}, pages={411-429}, year={2013}, publisher={Springer} } @Article{Sladek, author = {N.E.Sladek}, title = {Therapeutic Efficacy of Cyclophosphamide as a Function of Its Metabolism}, journal={Cancer research}, volume={32}, number={3}, pages={535-542}, year={1972}, publisher={AACR} } @article{Su2009_ImmuneResponseTissue, author = {B.Su and W.Zhou and K.S.Norman and D.E.Jones}, title = {Mathematical modelling of immune response in tissue}, journal = {Computational and mathematical methods in medicine}, year = {2009}, volume = {10}, number = {1}, pages = {9-38}, } @article{sugimoto2016resolution, title={Resolution of inflammation: what controls its onset?}, author={M.Sugimoto and L.Sousa and V.Pinho and M.Perretti and M.Teixeira}, journal={Frontiers in immunology}, volume={7}, pages={160}, year={2016}, publisher={Frontiers Media SA} } @article{suresh2013pattern, title={Pattern recognition receptors in innate immunity, host defense, and immunopathology}, author={R.Suresh and D.Mosser}, journal={Advances in physiology education}, volume={37}, number={4}, pages={284-291}, year={2013}, publisher={American Physiological Society Bethesda, MD} } @article{tanner2019humoral, title={The humoral immune response to BCG vaccination}, author={R.Tanner and B.Villarreal-Ramos and H.Vordermeier and H.McShane}, journal={Frontiers in immunology}, volume={10}, pages={1317}, year={2019}, publisher={Frontiers Media SA} } @book{teicher1996cancer, title={Cancer therapeutics: experimental and clinical agents}, author={B.A.Teicher}, year={1996}, publisher={Springer Science \& Business Media} } @article{turvey2010innate, title={Innate immunity}, author={S.Turvey and D.Broide}, journal={Journal of Allergy and Clinical Immunology}, volume={125}, number={2}, pages={S24-S32}, year={2010}, publisher={Elsevier} } @article{unni2019mathematical, title={Mathematical modeling, analysis, and simulation of tumor dynamics with drug interventions}, author={P.Unni and P.Seshaiyer}, journal={Computational and mathematical methods in medicine}, volume={2019}, year={2019}, publisher={Hindawi}} @article{wang2010cytokines, title={Cytokines in the progression of pancreatic $\beta$-cell dysfunction}, author={C.Wang and Y.Guan and J.Yang}, journal={International journal of endocrinology}, volume={2010}, year={2010}, publisher={Hindawi} } @article{wang2017beyond, title={Beyond genetics: what causes type 1 diabetes}, author={Z.Wang and Z.Xie and Q.Lu and C.Chang and Z.Zhou}, journal={Clinical reviews in allergy \& immunology}, volume={52}, pages={273-286}, year={2017}, publisher={Springer} } @article{WiggingtonKirschner2001_MacrophagesTuberculosisMath, author = {J.E.Wigginton and D.Kirschner}, title = {{A model to predict cell-mediated immune regulatory mechanisms during human infection with \textit{Mycobacterium tuberculosis}}}, journal = {J. Immunology}, year = {2001}, volume = {2001}, pages = {1951-1967}, } @booklet{Weisser, title = {Methods in molecular biology: Generation and characterization of murine alternatively activated macrophages}, publisher = {Methods Mol Biol}, volume = {946}, OPTpages = {225-239}, year = {2013}, author = {S.B.Weisser and K.W.McLarren and E.Kuroda and L.M.Sly.}, } @Article{Willmann, author = {S. Willmann and W. Schmitt and J. Keldenich and J. B. Dressman}, title = {{A physiologic model for simulating gastrointestinal flow and drug absorption in rats}}, journal = {Pharmaceutical Research}, year = {2003}, volume = {20}, number={11}, pages = {1766-1771}, } @article{xiao2014m2, title={M2 macrophages promote beta-cell proliferation by up-regulation of SMAD7}, author={X.Xiao and I.Gaffar and P.Guo and J.Wiersch and S.Fischbach and L.Peirish and Z.Song and Y.El-Gohary and K.Prasadan and C.Shiota and others}, journal={Proceedings of the National Academy of Sciences}, volume={111}, number={13}, pages={E1211-E1220}, year={2014}, publisher={National Acad Sciences} } @article{xiao2015concise, title={Concise review: new insights into the role of macrophages in $\beta$-cell proliferation}, author={X.Xiao and G.K.Gittes}, journal={Stem cells translational medicine}, volume={4}, number={6}, pages={655-658}, year={2015}, publisher={Oxford University Press} } @article{yatim2015brief, title={A brief journey through the immune system}, author={K.Yatim and F.Lakkis}, journal={Clinical Journal of the American Society of Nephrology}, volume={10}, number={7}, pages={1274-1281}, year={2015}, publisher={LWW} } @mastersthesis{Yu2014_M1M2model_WoundHealing, author = {T.Yu}, title = {Design and validation of a mathematical model to describe macrophage dynamics in wound healing}, school = {Drexel University}, year = 2014, address = {The address of the publisher}, note = {An optional note} } @Article{Zhang_2014, author = {M.Zhang and Y.He and X.Sun and Q.Li and W.Wang and A.Zhao and W.Di}, title = {{A high M1/M2 ratio of tumour-associated macrophages is associated with extended survival in ovarian cancer patients}}, journal = {J. Ovarian Research}, year = {2014}, volume = {7}, pages = {19}, } @Incollection{Zhang, author = {X.Zhang and R.Goncalves and D.Mosser}, title = {The isolation and characterization of murine macrophages}, booktitle = {Current Protocols in Immunology}, editors = {J.E. Coligan et al.}, year = {2008}, pages = {1-18}, publisher = {John Wiley \& Sons, Inc.}, } @article{zhou2012macrophages, title={Macrophages help NK cells to attack tumor cells by stimulatory NKG2D ligand but protect themselves from NK killing by inhibitory ligand Qa-1}, author={Z.Zhou and C.Zhang and J.Zhang and Z.Tian}, journal={PloS one}, volume={7}, number={5}, pages={e36928}, year={2012}, publisher={Public Library of Science San Francisco, USA} } @article{Zhu2002_IL4_Th2Proliferation, author = {J.Zhu and L.Guo and B.Min and C.J.Watson and J.Hu-Li and H.A.Young and P.N.Tsichlis and W.E.Paul}, title = {Growth factor independent-1 induced by {IL-4} regulates {Th2} cell proliferation}, journal ={Immunity}, year = {2002}, volume = {16}, number = {5}, pages = {733-744}, } @article{zitvogel2008immunological, title={Immunological aspects of cancer chemotherapy}, author={L.Zitvogel and L.Apetoh and F.Ghiringhelli and G.Kroemer}, journal={Nature reviews immunology}, volume={8}, number={1}, pages={59}, year={2008}, publisher={Nature Publishing Group} } %%%%%%%%%%%%%%%%%%%% @article{quesada2008physiology, title={Physiology of the pancreatic $\alpha$-cell and glucagon secretion: role in glucose homeostasis and diabetes}, author={I.Quesada and E.Tudur{\'\i} and C.Ripoll and A.Nadal}, journal={Journal of endocrinology}, volume={199}, number={1}, pages={5--19}, year={2008}, publisher={BioScientifica} } @article{Magombedze, title = {{Competition for antigen between Th1 and Th2 responses determines the timing of the immune response switch during mycobaterium avium subspecies paratuberulosis infection in ruminants}}, author = {G.Magombedze and S.Eda and V.Ganusovi}, journal={PLoS Comput Biol}, volume={10}, number={1}, pages={e1003414}, year={2014}, publisher={Public Library of Science} } @article{lombarte2013mathematical, title={Mathematical model of glucose--insulin homeostasis in healthy rats}, author={M.Lombarte and M.Lupo and G.Campetelli and M.Basualdo and A.Rigalli}, journal={Mathematical biosciences}, volume={245}, number={2}, pages={269--277}, year={2013}, publisher={Elsevier} } @article{Lee1985_MacrophagesCount, author = {S.-H.Lee and P.M.Starkey and S.Gordon}, title = {Quantitative analysis of total macrophage content in adult mouse tissues}, journal = {J. Exp. Med.}, year = {1985}, volume = {161}, pages = {475-489}, } @article{Helming, title = {Inflammation: Cell recruitment versus local proliferation.}, journal = {Current Biology}, volume = {21}, number = {14}, pages = {R548--R550}, year = {2011}, author = {L.Helming.}, } @article{Wang, author = {Y.Wang and T.Yang and Y.Ma and G.V.halide and J.Zhang and M.L.Lindsey and Y.-F.Jin}, title = {Mathematical modeling and stability analysis of macrophage activation in left ventricular remodeling post-myocardial infarction}, journal = {BMC Genomics}, year = {2012}, volume = {13}, pages = {S21}, }