Modeling and Control of Infectious Diseases in the Host: With MATLAB and R PDF
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Modeling and Control of Infectious Diseases in the Host Modeling and Control of Infectious Diseases in the Host With Matlab and R Esteban A. Hernandez-Vargas FrankfurtamMain,Germany Series Editor Edgar Sánchez AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom Copyright©2019ElsevierInc.Allrightsreserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronicormechanical, includingphotocopying,recording,oranyinformationstorageandretrievalsystem,withoutpermissioninwritingfrom thepublisher.Detailsonhowtoseekpermission,furtherinformationaboutthePublisher’spermissionspoliciesandour arrangementswithorganizationssuchastheCopyrightClearanceCenterandtheCopyrightLicensingAgency,canbe foundatourwebsite:www.elsevier.com/permissions. ThisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythePublisher(otherthanas maybenotedherein). Notices Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchandexperiencebroadenour understanding,changesinresearchmethods,professionalpractices,ormedicaltreatmentmaybecomenecessary. Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluatingandusingany information,methods,compounds,orexperimentsdescribedherein.Inusingsuchinformationormethodstheyshould bemindfuloftheirownsafetyandthesafetyofothers,includingpartiesforwhomtheyhaveaprofessional responsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assumeanyliabilityforany injuryand/ordamagetopersonsorpropertyasamatterofproductsliability,negligenceorotherwise,orfromanyuseor operationofanymethods,products,instructions,orideascontainedinthematerialherein. LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary ISBN:978-0-12-813052-0 ForinformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:MaraConner AcquisitionEditor:ChrisKatsaropoulos EditorialProjectManager:PeterAdamson ProductionProjectManager:PaulPrasadChandramohan Designer:MatthewLimbert TypesetbyVTeX Totheentirelymerciful,God totheconsciousnessofmylife,myfatherandmother andtotheoriginandendofmydeepestthoughts,mywife. EstebanAbelardo About the Author Esteban A. Hernandez-Vargas is a research group leader and principal investigator at the Frankfurt Institute for Advanced Studies, Germany. In 2011, he obtained his PhD in Mathe- matics from the Hamilton Institute at the National University of Ireland. During three years, heholdapostdoctoralscientistpositionattheHelmholtzCentreforInfectionResearch(HZI) in Braunschweig, Germany. In July 2014, he founded the pioneering research group of Sys- temsMedicineofInfectiousDiseasesattheHZI.SinceMarch2017,heandhisresearchgroup movedtotheFrankfurtInstituteforAdvancedStudies.Furthermore,hewasavisitingscholar atLosAlamosNationalLaboratory(USA)andUniversidaddeGuadalajara(Mexico)andad- junctlecturerattheOttovonGuerickeUniversitätMagdeburg,Germany.Hehaswrittenmore than50peer-reviewedpublications.HeisamemberoftheIEEEControlSystemsSociety,the SocietyofMathematicalBiology,theEuropeanSocietyofVirology,andtheMexicanResearch Council(CONACYT).Additionally,heisanEditorialBoardmemberofInfectiousDiseasesof FrontiersinMedicineandPublicHealthJournalaswellasaResearchTopicEditoratFrontiers of Microbiology and Frontiers of Immunology. He is also involved in a number of IEEE and IFACConferenceOrganizingCommittees. ix Preface Modeling infectious diseases have undergone substantial development over the past two decades.Considerableeffortswereinitiallyinvestedtomodelthebasicinteractionsofchronic viralinfectionswiththeirrespectivetargetcells,forexample,HIVinfection.However,morere- cently,acuteinfectiousdiseasessuchasinfluenzaandEbolahavelargelyincreasedtheattention ofthemodelingcommunity. Oncemodelparametersarefittedwithexperimentaldata,mathematicalmodelshavethepoten- tial to serveas virtual clinical trials touncover thesuccessand pitfalls of antiviral treatments aswellasvaccines.Couplingwithin-hostinfectionmodels,PK/PDdynamics,andcontrolthe- oreticalapproachesarehavingapromisingfuturetotailortreatmentsatahostlevelbutalsoto implementpublichealthpoliciestotackleinfectiousdiseasespandemicsandoutbreaks. Thisbookreflectsrecentdevelopmentsininfectiousdiseasesmodelingwhileprovidingacom- prehensiveintroductiontomultidisciplinaryfieldslikevirology,immunesystem,epidemiology, statistics, parameter fitting, and control systems. The first two parts of the book are recom- mended for teaching mathematical biology to undergraduates. Basic knowledge of program- mingandlinearalgebraarehelpfulthoughnotessentialasthebookincludesaself-contained introduction.Thefirstpartofthebook(Chapters1–3)bringstogetherthebasicsnecessaryfor modeling a broad of biological applications. The second part (Chapters 4–5) presents mathe- matical modelsforacute infections suchasinfluenzaand Ebola.Additionally,modeling HIV infectionanditsrespectiveevolutionduringtreatmentisdescribedinChapter6and7.Forgrad- uatestudentsandscientistsworkinginthecontrolfieldofinfectiousdiseases,thethirdpartof thebook(Chapters8–10)isrecommended,wheremorerigorousmathematicalanalysisisintro- duced.ThebookissupportedbyadditionalmaterialincludingMatlabandRcodes.Otherad- vancedapplicationstogetherwithitscodescanbefoundinhttps://github.com/systemsmedicine. EstebanA.Hernandez-Vargas FrankfurtamMain,Germany August2018 xi Acknowledgments A central element to prepare this book is attributed to my students and the members of my research group of Systems Medicine of Infectious Diseases, in particular, Kinh Van Nguyen, AlessandroBoianelli,andGustavoHernandezMejia.Ifeeltrulyfortunatetohavehadtheop- portunitytoworkwithmanypeoplewhosecollaborationsanddiscussionsenrichedthematerial presentedinthisbook,includingRichardMiddleton(NewcastleUniversity,Australia)andPa- trizioColaneri(PolitecnicodiMilano,Italy). Furthermore,Iacknowledgedifferentfundinginstitutionsthatsupportedmyresearchpositions atdifferentstagessuchastheAlfonsundGertrudKassel-Stiftung,theBohringerIngelheimEx- plorationGrant,theHelmholtzInitiativeonPersonalizedMedicineGrant,theDAADGerman AcademicExchangeService,theMexicanNationalCouncilofScienceandTechnologyCONA- CYT,andtheScienceFoundationofIreland.Finally,IthanktheeditorEdgarSánchezandthe ElsevierteamcomposedbyChrisKatsaropoulosandKatieChanforguidancethroughoutthe publishingprocess.Iamalsogratefultoalltheanonymousrefereesforcarefullyreviewingand selectingthefinalchaptersofthisbook. EstebanA.Hernandez-Vargas FrankfurtamMain,Germany December2018 xiii
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