1,614 research outputs found

    A Method for Reducing the Severity of Epidemics by Allocating Vaccines According to Centrality

    Full text link
    One long-standing question in epidemiological research is how best to allocate limited amounts of vaccine or similar preventative measures in order to minimize the severity of an epidemic. Much of the literature on the problem of vaccine allocation has focused on influenza epidemics and used mathematical models of epidemic spread to determine the effectiveness of proposed methods. Our work applies computational models of epidemics to the problem of geographically allocating a limited number of vaccines within several Texas counties. We developed a graph-based, stochastic model for epidemics that is based on the SEIR model, and tested vaccine allocation methods based on multiple centrality measures. This approach provides an alternative method for addressing the vaccine allocation problem, which can be combined with more conventional approaches to yield more effective epidemic suppression strategies. We found that allocation methods based on in-degree and inverse betweenness centralities tended to be the most effective at containing epidemics.Comment: 10 pages, accepted to ACM BCB 201

    Identifying spatial invasion of pandemics on metapopulation networks via anatomizing arrival history

    Get PDF
    Spatial spread of infectious diseases among populations via the mobility of humans is highly stochastic and heterogeneous. Accurate forecast/mining of the spread process is often hard to be achieved by using statistical or mechanical models. Here we propose a new reverse problem, which aims to identify the stochastically spatial spread process itself from observable information regarding the arrival history of infectious cases in each subpopulation. We solved the problem by developing an efficient optimization algorithm based on dynamical programming, which comprises three procedures: i, anatomizing the whole spread process among all subpopulations into disjoint componential patches; ii, inferring the most probable invasion pathways underlying each patch via maximum likelihood estimation; iii, recovering the whole process by assembling the invasion pathways in each patch iteratively, without burdens in parameter calibrations and computer simulations. Based on the entropy theory, we introduced an identifiability measure to assess the difficulty level that an invasion pathway can be identified. Results on both artificial and empirical metapopulation networks show the robust performance in identifying actual invasion pathways driving pandemic spread.Comment: 14pages, 8 figures; Accepted by IEEE Transactions on Cybernetic

    Where and how to conserve : Extending the scope of spatial reserve network design

    Get PDF
    Ongoing habitat loss and fragmentation threaten much of the biodiversity that we know today. As such, conservation efforts are required if we want to protect biodiversity. Conservation budgets are typically tight, making the cost-effective selection of protected areas difficult. Therefore, reserve design methods have been developed to identify sets of sites, that together represent the species of conservation interest in a cost-effective manner. To be able to select reserve networks, data on species distributions is needed. Such data is often incomplete, but species habitat distribution models (SHDMs) can be used to link the occurrence of the species at the surveyed sites to the environmental conditions at these locations (e.g. climatic, vegetation and soil conditions). The probability of the species occurring at unvisited location is next predicted by the model, based on the environmental conditions of those sites. The spatial configuration of reserve networks is important, because habitat loss around reserves can influence the persistence of species inside the network. Since species differ in their requirements for network configuration, the spatial cohesion of networks needs to be species-specific. A way to account for species-specific requirements is to use spatial variables in SHDMs. Spatial SHDMs allow the evaluation of the effect of reserve network configuration on the probability of occurrence of the species inside the network. Even though reserves are important for conservation, they are not the only option available to conservation planners. To enhance or maintain habitat quality, restoration or maintenance measures are sometimes required. As a result, the number of conservation options per site increases. Currently available reserve selection tools do however not offer the ability to handle multiple, alternative options per site. This thesis extends the existing methodology for reserve design, by offering methods to identify cost-effective conservation planning solutions when multiple, alternative conservation options are available per site. Although restoration and maintenance measures are beneficial to certain species, they can be harmful to other species with different requirements. This introduces trade-offs between species when identifying which conservation action is best applied to which site. The thesis describes how the strength of such trade-offs can be identified, which is useful for assessing consequences of conservation decisions regarding species priorities and budget. Furthermore, the results of the thesis indicate that spatial SHDMs can be successfully used to account for species-specific requirements for spatial cohesion - in the reserve selection (single-option) context as well as in the multi-option context. Accounting for the spatial requirements of multiple species and allowing for several conservation options is however complicated, due to trade-offs in species requirements. It is also shown that spatial SHDMs can be successfully used for gaining information on factors that drive a species spatial distribution. Such information is valuable to conservation planning, as better knowledge on species requirements facilitates the design of networks for species persistence. This methods and results described in this thesis aim to improve species probabilities of persistence, by taking better account of species habitat and spatial requirements. Many real-world conservation planning problems are characterised by a variety of conservation options related to protection, restoration and maintenance of habitat. Planning tools therefore need to be able to incorporate multiple conservation options per site, in order to continue the search for cost-effective conservation planning solutions. Simultaneously, the spatial requirements of species need to be considered. The methods described in this thesis offer a starting point for combining these two relevant aspects of conservation planning.Monien lajien elinympĂ€ristöt vĂ€henevĂ€t, mikĂ€ uhkaa lajien selviytymistĂ€ pitkĂ€llĂ€ aikavĂ€lillĂ€. Lajien sukupuuttoja voidaan ehkĂ€istĂ€ luonnonsuojelualueita perustamalla. SuojelutyöhĂ€n varatut varat ovat kuitenkin rajalliset, joten luonnonsuojelualueiden sijoittaminen tĂ€ytyy harkita tarkkaan. Suojelualueverkostojen suunnittelu on tieteenala, joka kĂ€sittelee suojelualueiden hankintaan varattujen varojen tehokasta kĂ€yttöÀ. Alueiden suojelu ei ole ainoa tapa auttaa lajien sĂ€ilymistĂ€. Laadultaan heikentyneiden elinympĂ€ristöjen kuntoa voidaan parantaa. Jotkin elinympĂ€ristötyypit vaativat hoitoa pysyĂ€kseen tietynlaisina. Esimerkiksi kedot, joista monet lajit ovat riippuvaisia, metsittyvĂ€t vĂ€hitellen ilman hoitoa. NiinpĂ€ suojelusuunnittelussa tĂ€ytyy pÀÀttÀÀ kĂ€ytetÀÀnkö suojelun tukena hoitotoimia elinympĂ€ristöjen sĂ€ilyttĂ€miseksi. Suojelusuunnittelussa kĂ€ytettĂ€vĂ€t tietokoneohjelmistot eivĂ€t osaa vastata kysymykseen siitĂ€, kuinka suojeltavia alueita tulisi hoitaa niiden avulla saadaan selville vain se, mitkĂ€ alueet kannattaa suojella. Olen kehittĂ€nyt vĂ€itöskirjatyössĂ€ni menetelmiĂ€, joiden avulla voidaan mÀÀrittÀÀ mikĂ€ suojelun taso tai hoitotoimi alueelle kannattaa kohdentaa toimittaessa kustannustehokkaasti. Kun hoitotoimi on suotuisa yhdelle lajille, saattaa se olla haitallinen toiselle lajille. TĂ€stĂ€ syystĂ€ kokonaisuuden kannalta parhaan hoitotoimen mÀÀrittĂ€minen on vaikeaa. KehittĂ€mĂ€ni menetelmĂ€t auttavat vaihtoehtoisten suojelu- ja hoitotoimien suunnittelemisessa sekĂ€ suojelupÀÀtösten seurausten arvioimisessa. Suojelualuesuunnittelussa on tĂ€rkeÀÀ huomioida alueiden sijoittelu toisiinsa nĂ€hden, sillĂ€ yksilöiden liikkuminen eri suojelualueiden vĂ€lillĂ€ on lajiston sĂ€ilymisen kannalta tĂ€rkeÀÀ. Koska eri lajien leviĂ€miskyvyt ovat erilaiset, tulee suojelualueverkoston rakennetta arvioida lajien ominaisuudet huomioiden. Osoitan työssĂ€ni kuinka lajien esiintymisen todennĂ€köisyys kasvaa kun suojeluverkoston rakenteessa huomioidaan lajien leviĂ€miskyvyt. Suojelualueverkoston rakenteen huomioiminen on erityisen vaikeaa silloin, kun kĂ€ytettĂ€vissĂ€ on useita vaihtoehtoisia suojelutoimia, mutta esitĂ€n työssĂ€ni tĂ€lle ongelmalle yhtĂ€ lajia kerrallaan tarkastelevan ratkaisun. Jotta lajien pitkĂ€n aikavĂ€lin sĂ€ilymistĂ€ autetaan parhaalla tavalla, tulee suojeluun varatut resurssit kohdentaa mahdollisimman tehokkaasti. Suojelusuunnittelussa tĂ€ytyy yleensĂ€ valita yksi vaihtoehtoisista suojelu- tai hoitotoimista kullekin kohteelle. NĂ€mĂ€ vaihtoehtoiset toimet tulee siten sisĂ€llyttÀÀ suojelusuunnittelussa kĂ€ytettĂ€viin menetelmiin ja tietokoneohjelmistoihin. VĂ€itöskirjatyöni ottaa ensimmĂ€isen askeleen tĂ€hĂ€n suuntaan, ja nĂ€yttÀÀ kuinka suojelualueverkoston rakenteessa voidaan huomioida lajien erilaiset liikkumiskyvyt ja elintilatarpeet.Steeds meer habitat van veel plant- en diersoorten verdwijnt. Deze soorten worden daardoor in hun voortbestaan bedreigd. Om deze soorten en hun habitat te beschermen, kunnen natuurreservaten worden aangewezen. Het budget voor natuurbescherming is echter beperkt, waardoor er nauwkeurig gekeken moet worden welke gebieden het best aangewezen kunnen worden als natuurgebied. Computerprogramma’s kunnen helpen bij het identificeren van gebieden die samen een kosteneffectief natuurnetwerk vormen. Om habitat en soorten te beschermen, is het aanwijzen van natuurgebieden niet de enige mogelijkheid. Natuurherstel en –beheersmaatregelen kunnen nodig zijn om bijvoorbeeld vegetatie in de gewenste conditie te krijgen en te houden. Zo zouden heide of extensief grasland mettertijd bos kunnen worden, als er niet begraasd, gemaaid of geplagd wordt. Hierdoor zou het habitat voor soorten die leven in extensieve graslanden en heide verdwijnen. In het natuurbeheer moet men daarom niet alleen beslissen welke plekken er beschermd moeten worden, maar ook welke herstel- of beheersmaatregelen nodig zijn. De computerprogramma’s die gebruikt worden voor het selecteren van natuurnetwerken, zijn niet geschikt voor het beantwoorden van de vraag hoe plekken het beste beheerd kunnen worden, wanneer er meerdere beschermings- of beheersopties per plek zijn. In dit proefschrift zijn methoden beschreven die wel hulp kunnen bieden bij het maken van beslissingen over hoe verschillende plekken te beheren op een kosteneffectieve manier. Zulke informatie kan gebruikt worden bij het maken van beslissingen over natuurbeheer. Bij het selecteren van natuurreservaten is het belangrijk om de ruimtelijke samenhang van de verschillende reservaten in ogenschouw te nemen. Dit, om de uitwisseling van individuen van soorten tussen de verschillende gebieden mogelijk te maken, wat belangrijk is voor het voorbestaan van soorten. De behoefte voor de grootte van plekken en de ruimtelijke samenhang van die plekken verschilt per soort, waar bij het ontwerp van netwerken rekening moet worden gehouden. Dit proefschrift beschrijft hoe de kans op voorkomen van soorten in het reservaatnetwerk toeneemt, naarmate meer rekening wordt gehouden met de specifieke behoeften aan samenhang van die soorten in het ontwerp van reservaatnetwerken. Wanneer er meerdere beschermings- en beheersopties per plek mogelijk zijn, dan wordt het moeilijk om tegelijkertijd rekening te houden met soort-specifieke eisen aan ruimtelijke samenhang. Dit komt doordat beheersmaatregelen die gunstig zijn voor bepaalde soorten (zoals begrazing van grasland voor graslandsoorten, bijv. sommige vlinders), tegelijkertijd ongunstig kunnen zijn voor andere soorten (bijv. bosplanten). Het proefschrift beschrijft een methode voor het plannen met meerdere opties Ă©n ruimtelijke samenhang, voor Ă©Ă©n soort tegelijkertijd. Om soorten ook op de lange termijn te behouden, is een kosteneffectieve besteding van budget voor natuurbehoud nodig. Het plannen van natuurbeschermingsmaatregelen omvat vaak een keuze tussen meerdere alternatieve maatregelen per plek. De computerprogramma’s ter ondersteuning van planning voor natuurbeheer moeten daarom geschikt gemaakt worden voor meerdere opties. Dit proefschrift maakt een eerste stap in die richting, en geeft ook suggesties hoe expliciet rekening kan worden gehouden met de specifieke eisen van soorten voor ruimtelijke samenhang van natuurgebieden

    Self-extinction through optimizing selection

    Get PDF
    Evolutionary suicide is a process in which selection drives a viable population to extinction. So far such selection-driven self-extinction has been demonstrated in models with frequency-dependent selection. This is not surprising, since frequency-dependent selection can disconnect individual-level and population-level interests through environmental feedback. Hence it can lead to situations akin to the tragedy of the commons, with adaptations that serve the selfish interests of individuals ultimately ruining a population. For frequency-dependent selection to play such a role, it must not be optimizing. Together, all published studies of evolutionary suicide have created the impression that evolutionary suicide is not possible with optimizing selection. Here we disprove this misconception by presenting and analyzing an example in which optimizing selection causes self-extinction. We then take this line of argument one step further by showing, in a further example, that selection-driven self-extinction can occur even under frequency-independent selection

    Optimizing Metapopulation Sustainability through a Checkerboard Strategy

    Get PDF
    The persistence of a spatially structured population is determined by the rate of dispersal among habitat patches. If the local dynamic at the subpopulation level is extinction-prone, the system viability is maximal at intermediate connectivity where recolonization is allowed, but full synchronization that enables correlated extinction is forbidden. Here we developed and used an algorithm for agent-based simulations in order to study the persistence of a stochastic metapopulation. The effect of noise is shown to be dramatic, and the dynamics of the spatial population differs substantially from the predictions of deterministic models. This has been validated for the stochastic versions of the logistic map, the Ricker map and the Nicholson-Bailey host-parasitoid system. To analyze the possibility of extinction, previous studies were focused on the attractiveness (Lyapunov exponent) of stable solutions and the structure of their basin of attraction (dependence on initial population size). Our results suggest that these features are of secondary importance in the presence of stochasticity. Instead, optimal sustainability is achieved when decoherence is maximal. Individual-based simulations of metapopulations of different sizes, dimensions and noise types, show that the system's lifetime peaks when it displays checkerboard spatial patterns. This conclusion is supported by the results of a recently published Drosophila experiment. The checkerboard strategy provides a technique for the manipulation of migration rates (e.g., by constructing corridors) in order to affect the persistence of a metapopulation. It may be used in order to minimize the risk of extinction of an endangered species, or to maximize the efficiency of an eradication campaign
    • 

    corecore