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@Article{ArinoBajeuxKirkland2019,
author="Arino, J. and Bajeux, N. and Kirkland, S.",
title="Number of Source Patches Required for Population Persistence in a Source--Sink Metapopulation with Explicit Movement",
journal="Bulletin of Mathematical Biology",
year="2019",
month="Jun",
day="01",
volume="81",
number="6",
pages="1916--1942",
abstract="We consider a simple metapopulation model with explicit movement of individuals between patches, in which each patch is either a source or a sink. We prove that similarly to the case of patch occupancy metapopulations with implicit movement, there exists a threshold number of source patches such that the population potentially becomes extinct below the threshold and established above the threshold. In the case where the matrix describing the movement of populations between spatial locations is irreducible, the result is global; further, assuming a complete mobility graph with equal movement rates, we use the principle of equitable partitions to obtain an explicit expression for the threshold. Brief numerical considerations follow.",
issn="1522-9602",
}


@Article{Arino2017,
  Title                    = {Spatio-temporal spread of infectious pathogens of humans},
  Author                   = {Arino, J.},
  Journal                  = {Infectious Disease Modelling},
  Year                     = {2017},
  Number                   = {2},
  Pages                    = {218--228},
  Volume                   = {2},
  Owner                    = {jarino},
  Timestamp                = {2017.07.09}
}

@InBook{Arino2009,
  Title                    = {Modeling and Dynamics of Infectious Diseases},
  Author                   = {Arino, J.},
  Chapter                  = {Diseases in {M}etapopulations},
  Editor                   = {Ma, Z. and Zhou, Y. and Wu, J.},
  Pages                    = {65-123},
  Publisher                = {World Scientific Publishing},
  Year                     = {2009},
  Series                   = {Series in Contemporary Applied Mathematics},
  Volume                   = {11},
  Abstract                 = {Metapopulation models consist of graphs, with systems of differential equations at each vertex. This modeling paradigm is appropriate for the description of the spatio-temporal spread of infectious diseases. In this document, I present the setting of these models, and some of the mathematical techniques that can be used to study them. I conclude with a brief review of some models using this approach.},
  Booktitle                = {Modeling and Dynamics of Infectious Diseases},
  Owner                    = {jarino},
  Timestamp                = {22.05.2008}
}

@Article{ArinoBauchBrauerDriedgerEtAl2011,
  Title                    = {Pandemic influenza: modelling and public health perspectives},
  Author                   = {Arino, J. and Bauch, C. and Brauer, F. and Driedger, S.M. and Greer, A.L. and Moghadas, S.M. and Pizzi, N.J. and Sander, B. and Tuite, A. and van den Driessche, P. and Watmough, J. and Wu, J. and Yan, P.},
  Journal                  = {Mathematical Biosciences and Engineering},
  Year                     = {2011},
  Number                   = {1},
  Pages                    = {1-20},
  Volume                   = {8},
  Abstract                 = {We describe the application of mathematical models in the study of disease epidemics with particular focus on pandemic influenza. We outline the general mathematical approach and the complications arising from attempts to apply it for disease outbreak management in a real public health context.},
  Doi                      = {10.3934/mbe.2011.8.1},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/Arino_etal-2011-MBE8.pdf}
}

@Article{ArinoBowmanGumelPortet2007,
  Title                    = {Effect of pathogen-resistant vectors on the transmission dynamics of a vector-borne disease},
  Author                   = {Arino, J. and Bowman, C.S. and Gumel, A. and Portet, S.},
  Journal                  = {Journal of Biological Dynamics},
  Year                     = {2007},
  Number                   = {4},
  Pages                    = {320-346},
  Volume                   = {1},
  Abstract                 = {A model is introduced for the transmission dynamics of a vector-borne disease with two vector strains, one wild and one pathogen-resistant; resistance comes at the cost of reduced reproductive fitness. The model, which assumes that vector reproduction can lead to the transmission or loss of resistance (reversion), is analyzed in a particular case with specified forms for the birth and force of infection functions. The vector component can have, in the absence of disease, a coexistence equilibrium where both strains survive. In the case where reversion is possible, this coexistence equilibrium is globally asymptotically stable when it exists. This equilibrium is still present in the full vector-host system, leading to a reduction of the associated reproduction number, thereby making elimination of the disease more feasible. When reversion is not possible, there can exist an additional equilibrium with only resistant vectors.},
  Doi                      = {10.1080/17513750701605614},
  Keywords                 = {Vector-host disease; Pair formation; Multiple disease-free equilibria},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://www.informaworld.com/smpp/ftinterface~content=a783945018~fulltext=713240930}
}

@Article{ArinoBowmanMoghadas2009,
  Title                    = {Antiviral resistance during pandemic influenza: implications for stockpiling and drug use},
  Author                   = {Arino, J. and Bowman, C.S. and Moghadas, S.M.},
  Journal                  = {BMC Infectious Diseases},
  Year                     = {2009},
  Number                   = {8},
  Volume                   = {9},

  Abstract                 = {Background
The anticipated extent of antiviral use during an influenza pandemic can have adverse consequences for the development of drug resistance and rationing of limited stockpiles. The strategic use of drugs is therefore a major public health concern in planning for effective pandemic responses.

Methods
We employed a mathematical model that includes both sensitive and resistant strains of a virus with pandemic potential, and applies antiviral drugs for treatment of clinical infections. Using estimated parameters in the published literature, the model was simulated for various sizes of stockpiles to evaluate the outcome of different antiviral strategies.

Results
We demonstrated that the emergence of highly transmissible resistant strains has no significant impact on the use of available stockpiles if treatment is maintained at low levels or the reproduction number of the sensitive strain is sufficiently high. However, moderate to high treatment levels can result in a more rapid depletion of stockpiles, leading to run-out, by promoting wide-spread drug resistance. We applied an antiviral strategy that delays the onset of aggressive treatment for a certain amount of time after the onset of the outbreak. Our results show that if high treatment levels are enforced too early during the outbreak, a second wave of infections can potentially occur with a substantially larger magnitude. However, a timely implementation of wide-scale treatment can prevent resistance spread in the population, and minimize the final size of the pandemic.

Conclusion
Our results reveal that conservative treatment levels during the early stages of the outbreak, followed by a timely increase in the scale of drug-use, will offer an effective strategy to manage drug resistance in the population and avoid run-out. For a 1918-like strain, the findings suggest that pandemic plans should consider stockpiling antiviral drugs to cover at least 20% of the population.},
  Doi                      = {10.1186/1471-2334-9-8},
  Owner                    = {jarino},
  Timestamp                = {03.11.2008},
  Url                      = {http://www.biomedcentral.com/content/pdf/1471-2334-9-8.pdf}
}

@Article{ArinoBrauerVdDWatmoughWu2008,
  Title                    = {A model for influenza with vaccination and antiviral treatment},
  Author                   = {Arino, J. and Brauer, F. and van den Driessche, P. and Watmough, J. and Wu, J.},
  Journal                  = {Journal of Theoretical Biology},
  Year                     = {2008},
  Number                   = {1},
  Pages                    = {118-130},
  Volume                   = {253},

  Abstract                 = {Compartmental models for influenza that include control by vaccination and antiviral treatment are formulated. Analytic expressions for the basic reproduction number, control reproduction number and the final size of the epidemic are derived for this general class of disease transmission models. Sensitivity and uncertainty analyses of the dependence of the control reproduction number on the parameters of the model give a comparison of the various intervention strategies. Numerical computations of the deterministic models are compared with those of recent stochastic simulation influenza models. Predictions of the deterministic compartmental models are in general agreement with those of the stochastic simulation models.},
  Doi                      = {10.1016/j.jtbi.2008.02.026},
  Owner                    = {jarino},
  Timestamp                = {22.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ABVdDWW-2008-JTB253.pdf}
}

@Article{ArinoBrauerVdDWatmoughWu2007,
  Title                    = {A final size relation for epidemic models},
  Author                   = {Arino, J. and Brauer, F. and van den Driessche, P. and Watmough, J. and Wu, J.},
  Journal                  = {Mathematical Biosciences and Engineering},
  Year                     = {2007},
  Number                   = {2},
  Pages                    = {159-175},
  Volume                   = {4}
}

@Article{ArinoBrauerVdDWatmoughWu2006,
  Title                    = {Simple models for containment of a pandemic},
  Author                   = {Arino, J. and Brauer, F. and van den Driessche, P. and Watmough, J. and Wu, J.},
  Journal                  = {Journal of the Royal Society Interface},
  Year                     = {2006},
  Number                   = {8},
  Pages                    = {453-457},
  Volume                   = {3}
}

@Article{ArinoCookeVdDVelascohernandez2004,
  Title                    = {An epidemiology model that includes a leaky vaccine with a general waning function},
  Author                   = {Arino, J. and Cooke, K.L. and van den Driessche, P. and Velasco-Hern\'andez, J.},
  Journal                  = {DCDS-B},
  Year                     = {2004},
  Number                   = {2},
  Pages                    = {479-495},
  Volume                   = {4},

  Abstract                 = {Vaccination that gives partial protection for both newborns and susceptibles is included in a transmission model for a disease that confers no immunity. A general form of the vaccine waning function is assumed, and the interplay of this together with the vaccine efficacy and vaccination rates is discussed. The integro-differential system describing the model is studied for a constant vaccine waning rate, in which case it reduces to an ODE system, and for a constant waning period, in which case it reduces to a system of delay differential equations. For some parameter values, the model is shown to exhibit a backward bifurcation, leading to the existence of subthreshold endemic equilibria. Numerical examples are presented that demonstrate the consequence of this bifurcation in terms of epidemic control. The model can alternatively be interpreted as one consisting of two social groups, with education playing the role of vaccination.},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoCookeVelascoVdD-2004-DCDSB4.pdf}
}

@Article{ArinoDavisHartleyJordanEtAl2005,
  Title                    = {A multi-species epidemic model with spatial migration},
  Author                   = {Arino, J. and Davis, J.R. and Hartley, D. and Jordan, R. and Miller, J. and van den Driessche, P.},
  Journal                  = {Mathematical Medicine and Biology},
  Year                     = {2005},
  Number                   = {2},
  Pages                    = {129-142},
  Volume                   = {22},

  Abstract                 = {A model is formulated that describes the spatial propagation of a disease that can be transmitted between multiple species. The spatial component consists, for each species, of a certain number of patches that make up the vertices of a digraph, the arcs of which represent the movement of the various species between the patches. In each of the patches and for each species, a susceptible-exposed-infectious-recovered (SEIR) epidemic model describes the evolution of the disease status of individuals. Also in each patch, there is transmission of the disease from species to species. An analysis of the system is given, beginning with results on the mobility component. A formula is derived for the computation of the basic reproduction number R0 for sspecies and npatches, which then determines the global stability properties of the disease free equilibrium. Simulations for the spread of a disease in one species and two patches are presented.},
  Doi                      = {10.1093/imammb/dqi003},
  Keywords                 = {spatial epidemic, multiple species, basic reproduction number, global stability},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://imammb.oxfordjournals.org/cgi/reprint/dqi003?ijkey=v4tq7KbJe5YyVbM&keytype=ref}
}

@InBook{ArinoVdD2006,
  Title                    = {Delay Differential Equations and Applications},
  Author                   = {Arino, J. and van den Driessche, P.},
  Chapter                  = {Time delays in epidemic models: modeling and numerical considerations},
  Editor                   = {Arino, O. and Hbid, M.L. and Ait Dads, E.},
  Pages                    = {539-578},
  Publisher                = {Springer},
  Year                     = {2006},

  Owner                    = {jarino},
  Timestamp                = {2013.07.22}
}

@Article{ArinoVdD2006a,
  Title                    = {Metapopulations epidemic models. {A} survey},
  Author                   = {Arino, J. and van den Driessche, P.},
  Journal                  = {Fields Institute Communications},
  Year                     = {2006},
  Pages                    = {1-12},
  Volume                   = {48},

  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoVdD_FIC.pdf}
}

@InProceedings{ArinoVdD2006b,
  Title                    = {Time delays in epidemic models: modeling and numerical considerations},
  Author                   = {Arino, J. and van den Driessche, P.},
  Booktitle                = {Delay Differential Equations and Applications},
  Year                     = {2006},
  Pages                    = {539-578},
  Publisher                = {Springer Verlag},

  Abstract                 = {Continuous time deterministic epidemic models are traditionally formulated as systems of ordinary differential equations for the numbers of individuals in various disease states, with the sojourn time in a state being exponentially distributed. Time delays are introduced to model constant sojourn times in a state, for example, the infective or immune state. Models then become delay-differential and/or integral equations. For a review of some epidemic models with delay see van den Driessche [228]. More generally, an arbitrarily distributed sojourn time in a state, for example, the infective or immune state, is used by some authors (see [69] and the references therein).},
  Doi                      = {10.1007/1-4020-3647-7_13},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoVdD-2006-DelayBook.pdf}
}

@Article{ArinoVdD2003a,
  Title                    = {A multi-city epidemic model},
  Author                   = {Arino, J. and van den Driessche, P.},
  Journal                  = {Mathematical Population Studies},
  Year                     = {2003},
  Number                   = {3},
  Pages                    = {175-193},
  Volume                   = {10},

  Abstract                 = {Some analytical results are given for a model that describes the propagation of a disease in a population of individuals who travel between n cities. The model is formulated as a system of 2n 2 ordinary differential equations, with terms accounting for disease transmission, recovery, birth, death, and travel between cities. The mobility component is represented as a directed graph with cities as vertices and arcs determined by outgoing (or return) travel. An explicit formula that can be used to compute the basic reproduction number, lcub\cal Rrcub_0 , is obtained, and explicit bounds on lcub\cal Rrcub_0 are determined in the case of homogeneous contacts between individuals within each city. Numerical simulations indicate that lcub\cal Rrcub_0 is a sharp threshold, with the disease dying out if lcub\cal Rrcub_0 1 .},
}

@Article{ArinoVdD2003b,
  Title                    = {The basic reproduction number in a multi-city compartmental epidemic model},
  Author                   = {Arino, J. and van den Driessche, P.},
  Journal                  = {Lecture Notes in Control and Information Science},
  Year                     = {2003},
  Pages                    = {135-142},
  Volume                   = {294},

  Abstract                 = {A directed graph with cities as vertices and arcs determined by outgoing (or return) travel represents the mobility component in a population of individuals who travel between $n$ cities. A model with 4 epidemiological compartments in each city that describes the propagation of a disease in this population is formulated as a system of $4n^2$ ordinary differential equations. Terms in the system account for disease transmission, latency, recovery, temporary immunity, birth, death, and travel between cities. The basic reproduction number R0 is determined as the spectral radius of a nonnegative matrix product, and easily computable bounds on R0 are obtained.},
  Doi                      = {10.1007/978-3-540-44928-7_19},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoVdD-2003-LNCIS294.pdf}
}

@Article{ArinoDucrotZongo2012,
  Title                    = {A metapopulation model for malaria with transmission-blocking partial immunity in hosts},
  Author                   = {Arino, J. and Ducrot, A. and Zongo, P.},
  Journal                  = {Journal of Mathematical Biology},
  Year                     = {2012},
  Number                   = {3},
  Pages                    = {423--448},
  Volume                   = {64},
  Abstract                 = {A metapopulation malaria model is proposed using SI and SIRS models for the vectors and hosts, respectively. Recovered hosts are partially immune to the disease and while they cannot directly become infectious again, they can still transmit the parasite to vectors. The basic reproduction number R0 is shown to govern the local stability of the disease free equilibrium but not the global behavior of the system because of the potential occurrence of a backward bifurcation. Using type reproduction numbers, we identify the reservoirs of infection and evaluate the effect of control measures. Applications to the spread to non-endemic areas and the interaction between rural and urban areas are given.},
  Doi                      = {10.1007/s00285-011-0418-4},
  Owner                    = {jarino},
  Timestamp                = {2011.03.06},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoDucrotZongo-2011-JMB.pdf}
}

@Article{ArinoHuKhanKossowskySanz2011,
  Title                    = {Some methodological aspects involved in the study by the {Bio.Diaspora Project} of the spread of infectious diseases along the global air transportation network},
  Author                   = {Arino, J. and Hu, W. and Khan, K. and Kossowsky, D. and Sanz, L.},
  Journal                  = {Canadian Applied Mathematics Quarterly},
  Year                     = {2011},
  Number                   = {2},
  Pages                    = {125-137},
  Volume                   = {19},

  Owner                    = {jarino},
  Timestamp                = {2012.02.27},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoHuKhanKossowskySanz-2012-CAMQ19.pdf}
}

@Article{ArinoJordanVdD2007,
  Title                    = {Quarantine in a multi-species epidemic model with spatial dynamics},
  Author                   = {Arino, J. and Jordan, R. and van den Driessche, P.},
  Journal                  = {Mathematical Biosciences},
  Year                     = {2007},
  Number                   = {1},
  Pages                    = {46-60},
  Volume                   = {206},

  Abstract                 = {Motivation is provided for the development of infectious disease models that incorporate the movement of individuals over a range of spatial scales. A general model is formulated for a disease that can be transmitted between different species and multiple patches, and the behavior of the system is investigated in the case in which the spatial component consists of a ring of patches. The influence of various parameters on the spatial and temporal spread of the disease is studied numerically, with particular focus on the role of quarantine in the form of travel restriction.},
  Doi                      = {10.1016/j.mbs.2005.09.002},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoJordanVdD-2007-MBS206.pdf}
}

@InBook{ArinoKhan2014,
  Title                    = {Analyzing and Modeling Spatial and Temporal Dynamics of Infectious Diseases},
  Author                   = {Arino, J. and Khan, K.},
  Chapter                  = {Using mathematical modelling to integrate disease surveillance and global air transportation data},
  Editor                   = {Chen, D. and Moulin, B. and Wu, J.},
  Publisher                = {Wiley},
  Year                     = {2014},
  Note                     = {To appear},

  Booktitle                = {Analyzing and Modeling Spatial and Temporal Dynamics of Infectious Diseases},
  Owner                    = {jarino},
  Timestamp                = {10.04.2014},
}

@Unpublished{ArinoKhanSoliman2013,
  Title                    = {Population mobility and the spread of tuberculosis},
  Author                   = {Arino, J. and Khan, K. and Soliman, I.},
  Year                     = {2013},

  Owner                    = {jarino},
  Timestamp                = {2013.05.13}
}

@Article{ArinoMccluskey2010,
  Title                    = {Effect of a sharp change of the incidence function on the dynamics of a simple disease},
  Author                   = {Arino, J. and McCluskey, C.C.},
  Journal                  = {Journal of Biological Dynamics},
  Year                     = {2010},
  Number                   = {5},
  Pages                    = {490-505},
  Volume                   = {4},

  Abstract                 = {We investigate two cases of a sharp change of incidencec functions on the dynamics of a susceptible-infective-susceptible epidemic model. In the first case, low population levels have mass action incidence, while high population levels have proportional incidence, the switch occurring when the total population reaches a certain threshold. Using a modified Dulac theorem, we prove that this system has a single equilibrium which attracts all solutions for which the disease is present and the population remains bounded. In the second case, an increase of the number of infectives leads to a mass action term being added to a standard incidence term. We show that this allows a Hopf bifurcation to occur, with periodic orbits being generated when a locally asymptotically stable equilibrium loses stability.},
  Doi                      = {10.1080/17513751003793017},
  Keywords                 = {epidemiology, incidence function},
  Owner                    = {jarino},
  Timestamp                = {22.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoMccluskey-2010-JBD4.pdf}
}

@Article{ArinoMccluskeyVdD2003,
  Title                    = {Global results for an epidemic model with vaccination that exhibits backward bifurcation},
  Author                   = {Arino, J. and McCluskey, C.C. and van den Driessche, P.},
  Journal                  = {SIAM J. Appl. Math.},
  Year                     = {2003},
  Number                   = {1},
  Pages                    = {260-276},
  Volume                   = {64},

  Abstract                 = {Vaccination of both newborns and susceptibles is included in a transmission model for a disease that confers immunity. The interplay of the vaccination strategy together with the vaccine efficacy and waning is studied. In particular, it is shown that a backward bifurcation leading to bistability can occur. Under mild parameter constraints, compound matrices are used to show that each orbit limits to an equilibrium. In the case of bistability, this global result requires a novel approach since there is no compact absorbing set.},
  Doi                      = {10.1137/S0036139902413829},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/ArinoMccluskeyVdD-2003-SIAP64_1.pdf}
}

@Article{ArinoPortet2015,
  Title                    = {Epidemiological implications of mobility between a large urban centre and smaller satellite cities},
  Author                   = {Arino, J. and Portet, S.},
  Journal                  = {Journal of Mathematical Biology},
  Year                     = {2015},
  Number                   = {5},
  Pages                    = {1243--1265},
  Volume                   = {71},

  Owner                    = {jarino},
  Timestamp                = {2014.07.31}
}

@Article{BowmanArinoMoghadas2011,
  Title                    = {Evaluation of vaccination strategies during pandemic outbreaks},
  Author                   = {Bowman, C. and Arino, J. and Moghadas, S.M.},
  Journal                  = {Mathematical Biosciences and Engineering},
  Year                     = {2011},
  Note                     = {To appear},
  Number                   = {1},
  Volume                   = {8},

  Doi                      = {10.3934/mbe.2011.8.113},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/BowmanArinoMoghadas-2011-MBE8.pdf}
}

@Article{HansenDayArinoWuMoghadas2010,
  Title                    = {Strategies for use of Oseltamivir and Zanamivir during pandemic outbreaks},
  Author                   = {Hansen, E. and Day, T. and Arino, J. and Wu, J. and Moghadas, S.M.},
  Journal                  = {Canadian Journal of Infectious Diseases \& Medical Microbiology},
  Year                     = {2010},
  Number                   = {1},
  Pages                    = {e28-e63},
  Volume                   = {21},

  Abstract                 = {BACKGROUND: The use of neuraminidase inhibitors (oseltamivir and zanamivir) for the treatment of ill individuals has been an important intervention during the 2009 H1N1 pandemic. However, the emergence and spread of drug resistance remains a major concern and, therefore, optimizing antiviral strategies is crucial to retain the longterm effectiveness of these pharmaceutical interventions.
METHODS: A dynamic model of disease transmission was developed to investigate optimal scenarios for the use of a secondary drug (eg, zanamivir). Considering both small and large stockpiles, attack rates were projected by simulating the model to identify �tipping points� for switching to zanamivir as resistance to oseltamivir develops.
RESULTS: The use of a limited stockpile of zanamivir can substantially reduce the overall attack rate during pandemic outbreaks. For a reasonably large stockpile of zanamivir, it is optimal to delay the use of this drug for a certain amount of time during which oseltamivir is used as the primary drug. For smaller stockpiles, however, earlier use of zanamivir will be most effective in reducing the overall attack rate. Given a limited stockpile of zanamivir (1.8% in the Canadian plan) without replenishment, and assuming that the fraction of ill individuals being treated is maintained below 60%, the results suggest that zanamivir should be dispensed as the primary drug for thresholds of the cumulative number of oseltamivir resistance below 20%.
INTERPRETATION: Strategic use of a secondary drug becomes crucial for pandemic mitigation if vaccination and other interventions fail to sufficiently reduce disease transmission in the community. These findings highlight the importance of enhanced surveillance and clinical monitoring for rapid identification of resistance emergence and its population incidence, so that optimal timing for adaptation to the use of drugs can be achieved.},
  Owner                    = {jarino},
  Timestamp                = {2010.01.29},
  Url                      = {http://www.pulsus.com/journals/abstract.jsp?sCurrPg=abstract&jnlKy=3&atlKy=9384&isuKy=904&isArt=t&fromfold=Current%20Issue}
}

@TechReport{KhanArinoCalderonEtAl2009,
  Title                    = {An analysis of {C}anada's vulnerability to emerging infectious disease threats via the global airline transportation network},
  Author                   = {Khan, K. and Arino, J. and Calderon, F. and Chan, A. and Gardam, M. and Heidebrecht, C. and Hu, W. and Janes, D.A. and Macdonald, M. and Sears, J. and Raposo, P. and Wang, J.},
  Institution              = {The Bio.Diaspora Project (St Michael's Hospital, Toronto, Ontario, Canada)},
  Year                     = {2009},

  Owner                    = {jarino},
  Timestamp                = {2010.01.31},
  Url                      = {http://www2.biodiaspora.com/low\_res.pdf}
}

@TechReport{KhanArinoEckhardtGardamEtAl2010,
  Title                    = {Global Air Traffic Patterns During the {H1N1} Influenza Pandemic and their Public Health Implications},
  Author                   = {Khan, K. and Arino, J. and Eckhardt, R. and Gardam, M. and Hu, W. and Kossowsky, D. and Macdonald, M. and Sears, J. and Wang, J.},
  Institution              = {The Bio.Diaspora Project (St Michael's Hospital, Toronto, Ontario, Canada)},
  Year                     = {2010},

  Owner                    = {jarino},
  Timestamp                = {2011.10.04}
}

@Article{KhanArinoHuRaposoEtAl2009,
  Title                    = {Spread of a novel influenza {A} ({H1N1}) virus via global airline transportation.},
  Author                   = {Khan, K. and Arino, J. and Hu, W. and Raposo, P. and Sears, J. and Calderon, F. and Heidebrecht, C. and Macdonald, M. and Liauw, J. and Chan, A. and Gardam, M.},
  Journal                  = {N Engl J Med},
  Year                     = {2009},

  Month                    = {Jul},
  Number                   = {2},
  Pages                    = {212--214},
  Volume                   = {361},

  Doi                      = {10.1056/NEJMc0904559},
  Keywords                 = {Aerospace Medicine; Aircraft; Humans; Influenza A Virus, H1N1 Subtype; Influenza, Human, transmission/virology; Mexico; ROC Curve; Travel},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {jarino},
  Pii                      = {NEJMc0904559},
  Pmid                     = {19564630},
  Timestamp                = {2012.05.30},
  Url                      = {http://dx.doi.org/10.1056/NEJMc0904559}
}

@Article{KhanEckhardtBrownsteinNaqviEtAl2013,
  Title                    = {Entry and exit screening of airline travellers during the {A(H1N1)} 2009 pandemic: a retrospective evaluation},
  Author                   = {Khan, K. and Eckhardt, R. and Brownstein, J.S. and Naqvi, R. and Hu, W. and Kossowsky, D. and Scales, D. and Arino, J. and Macdonald, M. and Wang, J. and Sears, J. and Cetron, M.S.},
  Journal                  = {Bulletin of the World Health Organization},
  Year                     = {2013},
  Pages                    = {368-376},
  Volume                   = {91},

  Abstract                 = {Objective

To evaluate the screening measures that would have been required to assess all travellers at risk of transporting A(H1N1)pdm09 out of Mexico by air at the start of the 2009 pandemic.

Methods

Data from flight itineraries for travellers who flew from Mexico were used to estimate the number of international airports where health screening measures would have been needed, and the number of travellers who would have had to be screened, to assess all air travellers who could have transported the H1N1 influenza virus out of Mexico during the initial stages of the 2009 A(H1N1) pandemic.

Findings

Exit screening at 36 airports in Mexico, or entry screening of travellers arriving on direct flights from Mexico at 82 airports in 26 other countries, would have resulted in the assessment of all air travellers at risk of transporting A(H1N1)pdm09 out of Mexico at the start of the pandemic. Entry screening of 116 travellers arriving from Mexico by direct or connecting flights would have been necessary for every one traveller at risk of transporting A(H1N1)pdm09. Screening at just eight airports would have resulted in the assessment of 90% of all air travellers at risk of transporting A(H1N1)pdm09 out of Mexico in the early stages of the pandemic.

Conclusion

During the earliest stages of the A(H1N1) pandemic, most public health benefits potentially attainable through the screening of air travellers could have been achieved by screening travellers at only eight airports.},
  Owner                    = {jarino},
  Timestamp                = {2013.03.27},
  Url                      = {http://www.who.int/bulletin/volumes/91/5/12-114777.pdf}
}

@Article{McCallumBarlowHone2001,
  Title                    = {How should pathogen transmission be modelled?},
  Author                   = {McCallum, H. and Barlow, N. and Hone, J.},
  Journal                  = {Trends Ecol. Evol.},
  Year                     = {2001},
  Number                   = {6},
  Pages                    = {295--300},
  Volume                   = {16}
}


@Article{KhanMcNabbMemishEckhardtEtAl2012,
  Title                    = {Infectious disease surveillance and modelling across geographic frontiers and scientific specialties.},
  Author                   = {Khan, K. and McNabb, S.J.N. and Memish, Z.A. and Eckhardt, R. and Hu, W. and Kossowsky, D. and Sears, J. and Arino, J. and Johansson, A. and Barbeschi, M. and McCloskey, B. and Henry, B. and Cetron, M. and Brownstein, J.S.},
  Journal                  = {Lancet Infect Dis},
  Year                     = {2012},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {222--230},
  Volume                   = {12},

  Abstract                 = {Infectious disease surveillance for mass gatherings (MGs) can be directed locally and globally; however, epidemic intelligence from these two levels is not well integrated. Modelling activities related to MGs have historically focused on crowd behaviours around MG focal points and their relation to the safety of attendees. The integration of developments in internet-based global infectious disease surveillance, transportation modelling of populations travelling to and from MGs, mobile phone technology for surveillance during MGs, metapopulation epidemic modelling, and crowd behaviour modelling is important for progress in MG health. Integration of surveillance across geographic frontiers and modelling across scientific specialties could produce the first real-time risk monitoring and assessment platform that could strengthen awareness of global infectious disease threats before, during, and immediately after MGs. An integrated platform of this kind could help identify infectious disease threats of international concern at the earliest stages possible; provide insights into which diseases are most likely to spread into the MG; help with anticipatory surveillance at the MG; enable mathematical modelling to predict the spread of infectious diseases to and from MGs; simulate the effect of public health interventions aimed at different local and global levels; serve as a foundation for scientific research and innovation in MG health; and strengthen engagement between the scientific community and stakeholders at local, national, and global levels.},
  Doi                      = {10.1016/S1473-3099(11)70313-9},
  Institution              = {Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada. khank@smh.ca},
  Keywords                 = {Communicable Diseases, epidemiology; Crowding; Disease Outbreaks, prevention /&/ control; Disease Transmission, Infectious, prevention /&/ control; Humans; Influenza A Virus, H1N1 Subtype; Influenza, Human, prevention /&/ control; Models, Theoretical; Population Surveillance; Travel; World Health},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {jarino},
  Pii                      = {S1473-3099(11)70313-9},
  Pmid                     = {22252149},
  Timestamp                = {2012.05.30},
  Url                      = {http://dx.doi.org/10.1016/S1473-3099(11)70313-9}
}

@Article{KhanMemishChabbraLiauwEtAl2010,
  Title                    = {Global public health implications of a mass gathering in {M}ecca, {S}audi {A}rabia during the midst of an influenza pandemic},
  Author                   = {Khan, K. and Memish, Z.A. and Chabbra, A. and Liauw, J. and Hu, W. and Janes, D.A. and Sears, J. and Arino, J. and Macdonald, M. and Calderon, F. and Raposo, P. and Heidebrecht, C. and Wang, J. and Chan, A. and Brownstein, J. and Gardam, M.},
  Journal                  = {Journal of Travel Medicine},
  Year                     = {2010},
  Number                   = {2},
  Pages                    = {75-81},
  Volume                   = {17},

  Abstract                 = {Background. Every year millions of pilgrims from around the world gather under extremely crowded conditions in Mecca, Saudi Arabia to perform the Hajj. In 2009, the Hajj coincided with influenza season during the midst of an influenza A (H1N1) pandemic. After the Hajj, resource-limited countries with large numbers of traveling pilgrims could be vulnerable, given their limited ability to purchase H1N1 vaccine and capacity to respond to a possible wave of H1N1 introduced via returning pilgrims.
Methods. We studied the worldwide migration of pilgrims traveling to Mecca to perform the Hajj in 2008 using data from the Saudi Ministry of Health and international air traffic departing Saudi Arabia after the 2008 Hajj using worldwide airline ticket sales data. We used gross national income (GNI) per capita as a surrogate marker of a country's ability to mobilize an effective response to H1N1.
Results. In 2008, 2.5 million pilgrims from 140 countries performed the Hajj. Pilgrims (1.7 million) were of international (non-Saudi) origin, of which 91.0% traveled to Saudi Arabia via commercial flights. International pilgrims (11.3%) originated from low-income countries, with the greatest numbers traveling from Bangladesh (50,419), Afghanistan (32,621), and Yemen (28,018).
Conclusions. Nearly 200,000 pilgrims that performed the Hajj in 2008 originated from the world's most resource-limited countries, where access to H1N1 vaccine and capacity to detect and respond to H1N1 in returning pilgrims are extremely limited. International efforts may be needed to assist resource-limited countries that are vulnerable to the impact of H1N1 during the 2009 to 2010 influenza season.},
  Doi                      = {10.1111/j.1708-8305.2010.00397.x},
  Owner                    = {jarino},
  Timestamp                = {2010.01.21},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/Khan_etal-2010-JTM17.pdf}
}

@Article{MoghadasBowmanArino2011,
  Title                    = {Competitive interference between influenza viral strains},
  Author                   = {Moghadas, S.M. and Bowman, C.S. and Arino, J.},
  Journal                  = {Canadian Applied Mathematics Quarterly},
  Year                     = {2011},
  Note                     = {Published in 2011 with 2009 date [publisher delay]. So actual reference is Vol. 17, 2009.},
  Number                   = {2},
  Pages                    = {309-316},
  Volume                   = {17},

  Owner                    = {jarino},
  Timestamp                = {2011.01.17},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/MoghadasBowmanArino-2009-CAMQ17.pdf}
}

@Article{PortetArino2009,
  Title                    = {An \emph{in vivo} intermediate filament assembly model},
  Author                   = {Portet, S. and Arino, J.},
  Journal                  = {Mathematical Biosciences and Engineering},
  Year                     = {2009},
  Number                   = {1},
  Volume                   = {6},

  Abstract                 = {A model is developed to study the in vivo intermediate filament organization in terms of repartition between four different structural states: soluble proteins, particles, short, and long filaments. An analysis is conducted, showing that the system has a unique, globally asymptotically stable equilibrium. By means of sensitivity analysis, the influence of parameters on the system is studied. It is shown that, in agreement with biological observations, posttranslational modifications of intermediate filament proteins resulting in filament solubilization are the main regulators of the intermediate filament organization. A high signalling-dependent solubilization of filaments favours the intermediate filament aggregation in particles.},
  Doi                      = {10.3934/mbe.2009.6.117},
  Keywords                 = {cytoskeleton assembly dynamics, intermediate filaments},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/PortetArino-2009-MBE6.pdf}
}

@Article{PortetVassyHogueArinoEtAl2004,
  Title                    = {Intermediate filament network organization: in vitro and in vivo kinetic models},
  Author                   = {Portet, S. and Vassy, J. and Hogue, C. and Arino, J. and Arino, O.},
  Journal                  = {Comptes Rendus: Biologies},
  Year                     = {2004},
  Number                   = {11},
  Pages                    = {970-976},
  Volume                   = {327},

  Abstract                 = {We propose two systems of ordinary differential equations modeling the assembly of intermediate filament networks. The first one describes the in vitro intermediate filament assembly dynamics. The second one deals with the in vivo evolution of cytokeratin, which is the intermediate filament protein expressed by epithelial cells. The in vitro model is then briefly analyzed in a simplified case},
  Doi                      = {10.1016/j.crvi.2004.06.005},
  Keywords                 = {intermediate filaments, assembly dynamics},
  Owner                    = {jarino},
  Timestamp                = {21.10.2007},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/PVHAA-2004-CRB327.pdf}
}

@Article{SunYangArinoKhan2011,
  Title                    = {Effect of media-induced social distancing on disease transmission in a two patch setting},
  Author                   = {Sun, C. and Yang, W. and Arino, J. and Khan, K.},
  Journal                  = {Mathematical Biosciences},
  Year                     = {2011},
  Number                   = {2},
  Pages                    = {87-95},
  Volume                   = {230},

  Doi                      = {10.1016/j.mbs.2011.01.005},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/SunYangArinoKhan-2011-MBS.pdf}
}

@Article{YangSunArino2010,
  Title                    = {Global analysis for a general epidemiological model with vaccination and varying population},
  Author                   = {Yang, W. and Sun, C. and Arino, J.},
  Journal                  = {Journal of Mathematical Analysis and Applications},
  Year                     = {2010},
  Number                   = {1},
  Pages                    = {208-223},
  Volume                   = {372},

  Abstract                 = {An SIR model with vaccination and varying population is formulated. The global dynamics of this model and its corresponding proportionate system are investigated. The correlations between the two systems in terms of disease eradication and persistence are presented. Three critical vaccination rates phi1c, phi2c and phi3c are obtained. It is found that when phi>phi1c the disease can be eradicated by increasing the vaccination rate until it exceeds phi3c. When phi<phi1c, the disease can be controlled to an endemic level by taking the appropriate vaccination rate phi2c.},
  Doi                      = {10.1016/j.jmaa.2010.07.017},
  Owner                    = {jarino},
  Timestamp                = {2010.08.10},
  Url                      = {http://server.math.umanitoba.ca/~jarino/papers/YangSunArino-2010-JMAA372.pdf}
}

@Proceedings{ArinoPortet2009b,
  Title                    = {Proceedings of the Second International Conference of the French-speaking Society for Theoretical Biology (Winnipeg, Manitoba, Canada, 4-6 June, 2007)},
  Year                     = {2009},
  Editor                   = {Arino, J. and Portet, S.},
  Number                   = {4},
  Volume                   = {57},

  Owner                    = {jarino},
  Timestamp                = {2010.01.31},
  Url                      = {http://www.springerlink.com/content/0001-5342/57/4/}
}

@Article{ArinoSunYang2016,
  author    = {Arino, J. and Sun, C. and Yang, W.},
  title     = {Revisiting a two-patch SIS model with infection during transport},
  journal   = {Mathematical Medicine and Biology},
  year      = {2016},
  volume    = {33},
  number    = {1},
  pages     = {29--55},
  abstract  = {We incorporate parameter heterogeneity in a two-patch SIS epidemic model with infection during transport and prove that the disease free and endemic equilibria are globally asymptotically stable when the basic reproduction number $\R_0<1$ and $\R_0>1$, respectively. We find that infection during transport increases the possibility that the disease persists in both patches and amplifies prevalence when disease is present. We then study the effect of a perfect unilateral exit screening program. Finally, we compare numerically the effects of using different incidence functions for infection within and while travelling between patches, and find that using mass action incidence to model infection during transport has the effect of maintaining disease prevalence at a higher level compared to when standard incidence is used.},
  doi       = {10.1093/imammb/dqv001},
  owner     = {jarino},
  timestamp = {2014.11.04},
  url       = {http://server.math.umanitoba.ca/~jarino/papers/ArinoSunYang-2016-MMB33.pdf},
}

@Book{Thieme2003,
  Title                    = {Mathematics in Population Biology},
  Author                   = {Thieme, H.R.},
  Publisher                = {Princeton University Press},
  Year                     = {2003},
  Series                   = {Princeton Series in Theoretical and Computational Biology},
  Owner                    = {jarino},
  Timestamp                = {2013.05.08}
}

@article{WHORespTeam2015,
  title={West {A}frican {E}bola epidemic after one year-slowing but not yet under control},
  author={{WHO Ebola Response Team}},
  journal={New England Journal of Medicine},
  volume={372},
  number={6},
  pages={584--587},
  year={2015},
  publisher={Mass Medical Soc}
}

@article{ValleronBouvetGarnerinMenares_etal1986,
  title={A computer network for the surveillance of communicable diseases: the French experiment.},
  author={Valleron, A.-J. and Bouvet, E. and Garnerin, P. and M{\'e}nares, J. and Heard, I. and Letrait, S. and Lefaucheux, J.},
  journal={American journal of public health},
  volume={76},
  number={11},
  pages={1289--1292},
  year={1986},
  publisher={American Public Health Association}
}

@Comment{jabref-meta: databaseType:bibtex;}