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  1. Article ; Online: Adaptation in a heterogeneous environment II: to be three or not to be.

    Alfaro, Matthieu / Hamel, François / Patout, Florian / Roques, Lionel

    Journal of mathematical biology

    2023  Volume 87, Issue 5, Page(s) 68

    Abstract: We propose a model to describe the adaptation of a phenotypically structured population in a H-patch environment connected by migration, with each patch associated with a different phenotypic optimum, and we perform a rigorous mathematical analysis of ... ...

    Abstract We propose a model to describe the adaptation of a phenotypically structured population in a H-patch environment connected by migration, with each patch associated with a different phenotypic optimum, and we perform a rigorous mathematical analysis of this model. We show that the large-time behaviour of the solution (persistence or extinction) depends on the sign of a principal eigenvalue, [Formula: see text], and we study the dependency of [Formula: see text] with respect to H. This analysis sheds new light on the effect of increasing the number of patches on the persistence of a population, which has implications in agroecology and for understanding zoonoses; in such cases we consider a pathogenic population and the patches correspond to different host species. The occurrence of a springboard effect, where the addition of a patch contributes to persistence, or on the contrary the emergence of a detrimental effect by increasing the number of patches on the persistence, depends in a rather complex way on the respective positions in the phenotypic space of the optimal phenotypes associated with each patch. From a mathematical point of view, an important part of the difficulty in dealing with [Formula: see text], compared to [Formula: see text] or [Formula: see text], comes from the lack of symmetry. Our results, which are based on a fixed point theorem, comparison principles, integral estimates, variational arguments, rearrangement techniques, and numerical simulations, provide a better understanding of these dependencies. In particular, we propose a precise characterisation of the situations where the addition of a third patch increases or decreases the chances of persistence, compared to a situation with only two patches.
    MeSH term(s) Animals ; Models, Biological ; Population Dynamics
    Language English
    Publishing date 2023-10-09
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 187101-8
    ISSN 1432-1416 ; 0303-6812
    ISSN (online) 1432-1416
    ISSN 0303-6812
    DOI 10.1007/s00285-023-01996-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Seed predation-induced Allee effects, seed dispersal and masting jointly drive the diversity of seed sources during population expansion.

    Doublet, Violette / Roques, Lionel / Klein, Etienne K / Lefèvre, François / Boivin, Thomas

    Journal of mathematical biology

    2023  Volume 87, Issue 3, Page(s) 47

    Abstract: The environmental factors affecting plant reproduction and effective dispersal, in particular biotic interactions, have a strong influence on plant expansion dynamics, but their demographic and genetic consequences remain an understudied body of theory. ... ...

    Abstract The environmental factors affecting plant reproduction and effective dispersal, in particular biotic interactions, have a strong influence on plant expansion dynamics, but their demographic and genetic consequences remain an understudied body of theory. Here, we use a mathematical model in a one-dimensional space and on a single reproductive period to describe the joint effects of predispersal seed insect predators foraging strategy and plant reproduction strategy (masting) on the spatio-temporal dynamics of seed sources diversity in the colonisation front of expanding plant populations. We show that certain foraging strategies can result in a higher seed predation rate at the colonisation front compared to the core of the population, leading to an Allee effect. This effect promotes the contribution of seed sources from the core to the colonisation front, with long-distance dispersal further increasing this contribution. As a consequence, our study reveals a novel impact of the predispersal seed predation-induced Allee effect, which mitigates the erosion of diversity in expanding populations. We use rearrangement inequalities to show that masting has a buffering role: it mitigates this seed predation-induced Allee effect. This study shows that predispersal seed predation, plant reproductive strategies and seed dispersal patterns can be intermingled drivers of the diversity of seed sources in expanding plant populations, and opens new perspectives concerning the analysis of more complex models such as integro-difference or reaction-diffusion equations.
    MeSH term(s) Animals ; Predatory Behavior ; Seed Dispersal ; Seeds ; Diffusion
    Language English
    Publishing date 2023-08-26
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 187101-8
    ISSN 1432-1416 ; 0303-6812
    ISSN (online) 1432-1416
    ISSN 0303-6812
    DOI 10.1007/s00285-023-01981-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Adaptation in a heterogeneous environment I: persistence versus extinction.

    Hamel, François / Lavigne, Florian / Roques, Lionel

    Journal of mathematical biology

    2021  Volume 83, Issue 2, Page(s) 14

    Abstract: Understanding how a diversity of plants in agroecosystems affects the adaptation of pathogens is a key issue in agroecology. We analyze PDE systems describing the dynamics of adaptation of two phenotypically structured populations, under the effects of ... ...

    Abstract Understanding how a diversity of plants in agroecosystems affects the adaptation of pathogens is a key issue in agroecology. We analyze PDE systems describing the dynamics of adaptation of two phenotypically structured populations, under the effects of mutation, selection and migration in a two-patch environment, each patch being associated with a different phenotypic optimum. We consider two types of growth functions that depend on the n-dimensional phenotypic trait: either local and linear or nonlocal nonlinear. In both cases, we obtain existence and uniqueness results as well as a characterization of the large-time behaviour of the solution (persistence or extinction) based on the sign of a principal eigenvalue. We show that migration between the two environments decreases the chances of persistence, with in some cases a 'lethal migration threshold' above which persistence is not possible. Comparison with stochastic individual-based simulations shows that the PDE approach accurately captures this threshold. Our results illustrate the importance of cultivar mixtures for disease prevention and control.
    MeSH term(s) Adaptation, Physiological ; Extinction, Biological ; Models, Biological ; Phenotype ; Plants ; Population Dynamics ; Probability
    Language English
    Publishing date 2021-07-06
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 187101-8
    ISSN 1432-1416 ; 0303-6812
    ISSN (online) 1432-1416
    ISSN 0303-6812
    DOI 10.1007/s00285-021-01637-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Towards unified and real-time analyses of outbreaks at country-level during pandemics.

    Soubeyrand, Samuel / Demongeot, Jacques / Roques, Lionel

    One health (Amsterdam, Netherlands)

    2020  Volume 11, Page(s) 100187

    Abstract: The management of public health and the preparedness for health emergencies partly rely on the collection and analysis of surveillance data, which become crucial in the context of an emergency such as the pandemic caused by COVID-19. For COVID-19, ... ...

    Abstract The management of public health and the preparedness for health emergencies partly rely on the collection and analysis of surveillance data, which become crucial in the context of an emergency such as the pandemic caused by COVID-19. For COVID-19, typically, numerous national and global initiatives have been set up from this perspective. Here, we propose to develop a shared vision of the country-level outbreaks during a pandemic, by enhancing, at the international scale, the foundations of the analysis of surveillance data and by adopting a unified and real-time approach to monitor and forecast the outbreak across time and across the world. This proposal, rolled out as a web platform, should contribute to strengthen epidemiological understanding, sanitary democracy as well as global and local responses to pandemics.
    Keywords covid19
    Language English
    Publishing date 2020-10-24
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2834831-X
    ISSN 2352-7714
    ISSN 2352-7714
    DOI 10.1016/j.onehlt.2020.100187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Computer codes for real-time analyses of outbreaks - Application to COVID-19

    Soubeyrand, Samuel / Roques, Lionel

    2020  

    Abstract: ... of outbreaks at country-level during pandemics" co-authored by Samuel Soubeyrand, Jacques Demongeot & Lionel ... Roques. Computer codes for the calculation of transmission indicators (R0 and Rt) and total infected ...

    Abstract Computer codes accompanying the article entitled "Towards unified and real-time analyses of outbreaks at country-level during pandemics" co-authored by Samuel Soubeyrand, Jacques Demongeot & Lionel Roques. Computer codes for the calculation of transmission indicators (R0 and Rt) and total infected population have been developed with Matlab and are available in the present repository. Computer codes for mortality indicators have been developed with the R statistical software and are available at https://gitlab.paca.inrae.fr/biosp/shinyMapCovid19.
    Keywords COVID-19 ; epidemiology ; outbreak indicator ; pandemic ; statistical inference ; SIRD compartmental model ; basic reproduction number ; effective reproduction number ; covid19
    Publishing date 2020-10-07
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Mechanistic-statistical SIR modelling for early estimation of the actual number of cases and mortality rate from COVID-19

    Roques, Lionel / Klein, Etienne / Papaix, Julien / Soubeyrand, Samuel

    medRxiv

    Keywords covid19
    Language English
    Publishing date 2020-03-24
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.03.22.20040915
    Database COVID19

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  7. Article ; Online: Mechanistic-statistical SIR modelling for early estimation of the actual number of cases and mortality rate from COVID-19

    Lionel Roques / Etienne Klein / Julien Papaix / Samuel Soubeyrand

    Abstract: The first cases of COVID-19 in France were detected on January 24, 2020. The number of screening tests carried out and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the ... ...

    Abstract The first cases of COVID-19 in France were detected on January 24, 2020. The number of screening tests carried out and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the mortality rate. In this note, we develop a 'mechanistic-statistical' approach coupling a SIR ODE model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The objective of this model is not to make forecasts but to estimate the actual number of people infected with COVID-19 during the observation window in France and to deduce the mortality rate associated with the epidemic. Main results. The actual number of infected cases in France is probably much higher than the observations: we find here a factor x15 (95%-CI: 4-33), which leads to a 5.2/1000 mortality rate (95%-CI: 1.5/1000-11.7/1000) at the end of the observation period. We find a R0 of 4.8, a high value which may be linked to the long viral shedding period of 20 days.
    Keywords covid19
    Publisher medrxiv
    Document type Article ; Online
    DOI 10.1101/2020.03.22.20040915
    Database COVID19

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  8. Article ; Online: Towards unified and real-time analyses of outbreaks at country-level during pandemics

    Samuel Soubeyrand / Jacques Demongeot / Lionel Roques

    One Health, Vol 11, Iss , Pp 100187- (2020)

    2020  

    Abstract: The management of public health and the preparedness for health emergencies partly rely on the collection and analysis of surveillance data, which become crucial in the context of an emergency such as the pandemic caused by COVID-19. For COVID-19, ... ...

    Abstract The management of public health and the preparedness for health emergencies partly rely on the collection and analysis of surveillance data, which become crucial in the context of an emergency such as the pandemic caused by COVID-19. For COVID-19, typically, numerous national and global initiatives have been set up from this perspective. Here, we propose to develop a shared vision of the country-level outbreaks during a pandemic, by enhancing, at the international scale, the foundations of the analysis of surveillance data and by adopting a unified and real-time approach to monitor and forecast the outbreak across time and across the world. This proposal, rolled out as a web platform, should contribute to strengthen epidemiological understanding, sanitary democracy as well as global and local responses to pandemics.
    Keywords COVID-19 ; Data analysis ; Epidemiological indicators ; Health emergency ; Model ; Public health ; Medicine (General) ; R5-920
    Subject code 306
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Impact of Lockdown on the Epidemic Dynamics of COVID-19 in France.

    Roques, Lionel / Klein, Etienne K / Papaïx, Julien / Sar, Antoine / Soubeyrand, Samuel

    Frontiers in medicine

    2020  Volume 7, Page(s) 274

    Abstract: The COVID-19 epidemic was reported in the Hubei province in China in December 2019 and then spread around the world reaching the pandemic stage at the beginning of March 2020. Since then, several countries went into lockdown. Using a mechanistic- ... ...

    Abstract The COVID-19 epidemic was reported in the Hubei province in China in December 2019 and then spread around the world reaching the pandemic stage at the beginning of March 2020. Since then, several countries went into lockdown. Using a mechanistic-statistical formalism, we estimate the effect of the lockdown in France on the contact rate and the effective reproduction number
    Keywords covid19
    Language English
    Publishing date 2020-06-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2775999-4
    ISSN 2296-858X
    ISSN 2296-858X
    DOI 10.3389/fmed.2020.00274
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Towards unified and real-time analyses of outbreaks at country-level during pandemics

    Soubeyrand, Samuel / Demongeot, Jacques / Roques, Lionel

    One health. 2020 Dec. 20, v. 11

    2020  

    Abstract: The management of public health and the preparedness for health emergencies partly rely on the collection and analysis of surveillance data, which become crucial in the context of an emergency such as the pandemic caused by COVID-19. For COVID-19, ... ...

    Abstract The management of public health and the preparedness for health emergencies partly rely on the collection and analysis of surveillance data, which become crucial in the context of an emergency such as the pandemic caused by COVID-19. For COVID-19, typically, numerous national and global initiatives have been set up from this perspective. Here, we propose to develop a shared vision of the country-level outbreaks during a pandemic, by enhancing, at the international scale, the foundations of the analysis of surveillance data and by adopting a unified and real-time approach to monitor and forecast the outbreak across time and across the world. This proposal, rolled out as a web platform, should contribute to strengthen epidemiological understanding, sanitary democracy as well as global and local responses to pandemics.
    Keywords COVID-19 infection ; monitoring ; pandemic ; public health
    Language English
    Dates of publication 2020-1220
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2834831-X
    ISSN 2352-7714
    ISSN 2352-7714
    DOI 10.1016/j.onehlt.2020.100187
    Database NAL-Catalogue (AGRICOLA)

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