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Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens
[article]
2018
biorxiv/medrxiv
pre-print
Preserved Fulltext
To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance. ...
This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological ...
Simulations were performed using the Pearcey cluster within the CSIRO supercomputer platform. ...
doi:10.1101/260836
fatcat:hcntj6xl7natnb3wr3alhdsazq
Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens
2018
PLoS Computational Biology
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To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance. ...
This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological ...
Acknowledgments The authors thank Loïc Houde for computing assistance and Jeremy Burdon for stimulating discussions and for reviewing this manuscript. ...
doi:10.1371/journal.pcbi.1006067
pmid:29649208
pmcid:PMC5918245
fatcat:igybalkxeffunpyhtmozbhwhli
Surrogate Assisted Strategies (The Parameterisation of an Infectious Disease Agent-Based Model)
[article]
2021
arXiv
pre-print
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We propose a more comprehensive and adaptive ABMS Framework that can effectively swap out parameterisation strategies and surrogate models to parameterise an infectious disease ABM. ...
An agent-based model's (ABM) complexity grows as the number of parameters required to be calibrated increases. This parameter expansion leads to the ABMS equivalent of the curse of dimensionality. ...
. 2 Background and Related Work
Agent-Based Modelling and Simulation for Infectious Disease Epidemiology Agent-based modelling and simulation (ABMS) is an effective natural fit for modelling infectious ...
arXiv:2108.08809v1
fatcat:wuxahruvgza7zf2aoodimf73zm
Eight challenges in phylodynamic inference
2015
Epidemics
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Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. ...
The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. ...
Kühnert et al. (2014) fitted a stochastic epidemiological model by simulating epidemiological trajectories, which were used to parameterise a stochastic birth-death process with piecewise constant rates ...
doi:10.1016/j.epidem.2014.09.001
pmid:25843391
pmcid:PMC4383806
fatcat:gtrobnfsgrh6pak5r2lrv2qhla
Towards a comprehensive simulation model of malaria epidemiology and control
2008
Parasitology
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Planning of the control of Plasmodium falciparum malaria leads to a need for models of malaria epidemiology that provide realistic quantitative prediction of likely epidemiological outcomes of a wide range ...
We use individual-based stochastic simulations of malaria epidemiology to predict the impacts of interventions on infection, morbidity, mortality, health services use and costs. ...
is included in the simultaneous multi-objective fitting of the model, or whether the data are used to separately parameterise model components. $ Some scenarios are used to predict several outcomes, so ...
doi:10.1017/s0031182008000371
pmid:18694530
fatcat:d6rgps3ce5h2dosq66ihtdi5ay
Advances in the Application of Machine Learning Techniques in Drug Discovery, Design and Development
[chapter]
2006
Advances in Intelligent and Soft Computing
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In silico screening), bioinformatic (i.e. bio-marker studies, using DNA chip data) and other types of drug research studies. ...
They are inherently suitable for use with 'noisy', high dimensional (many variables) data, as is commonly used in cheminformatic (i.e. ...
The authors wish to thank GSK colleagues, past and present, for their efforts in expressing the nature of their research. ...
doi:10.1007/978-3-540-36266-1_10
fatcat:gdq5kxmbfjfbbaccdcjpsopg4e
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
2014
PLoS Computational Biology
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We apply this method to epidemiological data, where the possibility of sampled ancestors enables us to identify individuals that infected other individuals after being sampled and to infer fundamental ...
We use a family of birth-death models where individuals may remain in the tree process after the sampling, in particular we extend the birth-death skyline model [Stadler et al, 2013] to sampled ancestor ...
We also acknowledge the New Zealand eScience Infrastructure (NeSI) for use of their high-performance computing facilities.
Author Contributions Conceived and designed the experiments: AJD AG DW TS. ...
doi:10.1371/journal.pcbi.1003919
pmid:25474353
pmcid:PMC4263412
fatcat:re2tyrzcv5hqjpvvwnnujuvniq
Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates
2020
PLoS ONE
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To improve accessibility the modified model has been implemented as the R package 'BORIS' for use in future outbreaks. ...
The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in ...
Acknowledgments Components of this research were undertaken on The University of Melbourne's High Performance Computing system SPARTAN [55] . ...
doi:10.1371/journal.pone.0235660
pmid:32667952
fatcat:tbn5yo7dvza77jcwsioqjbkeuy
Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages
2021
Molecular biology and evolution
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Here, we map the eco-evolutionary landscape of co-circulating FMDV lineages within an important endemic virus pool encompassing Western, Central and parts of Southern Asia, reconstructing the evolutionary ...
Livestock farming across the world is constantly threatened by evolutionary turnover of foot-and-mouth disease virus (FMDV) strains in endemic systems, the underlying dynamics of which remain to be elucidated ...
Acknowledgements We thank Prof Daniel Haydon for his insightful revision and constructive comments during the preparation of the manuscript. ...
doi:10.1093/molbev/msab172
pmid:34115138
pmcid:PMC8476141
fatcat:an7zj27j3zgizdvh5z3fx3n7z4
Epidemiological Inference From Pathogen Genomes: A Review of Phylodynamic Models and Applications
2022
Virus Evolution
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We discuss the assumptions linking evolutionary models of pathogen population size to epidemiological models of the infected population size. ...
Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and sta- tistical inference. ...
Birth-death models can also include time dependent rates (i.e. not constant/piecewise-constant), though they tend to be applied more in macroevolutionary work than genomic epidemiology. ...
doi:10.1093/ve/veac045
pmid:35775026
pmcid:PMC9241095
fatcat:7g7x7xopvvcqpn42lckibmk37i
Prioritising COVID-19 vaccination in changing social and epidemiological landscapes
[article]
2020
medRxiv
pre-print
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We used evolutionary game theory and mobility data to model individual adherence to NPIs. ...
We developed a coupled social-epidemiological model of SARS-CoV-2 transmission. Schools and workplaces are closed and re-opened based on reported cases. ...
TC Reluga, Game theory of social distancing in response to an epidemic. PLoS Comput. ...
doi:10.1101/2020.09.25.20201889
fatcat:jlhjgt7snneohebuw5pakdeyqu
A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda
2016
eLife
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We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations. ...
Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce. ...
Here we integrated extensive data from a single 59 cohort in Uganda into an epidemiological-evolutionary model describing the transmission cycle 60 of HIV. ...
doi:10.7554/elife.20492
pmid:27815945
pmcid:PMC5115872
fatcat:f7yjevk4zraghj2vog5ayt4vw4
The space of ultrametric phylogenetic trees
2016
Journal of Theoretical Biology
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In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. ...
More generally, statistical consistency is ensured by the tree space used to analyse the sample. ...
Acknowledgements We are grateful to Mike Steel, David Bryant, and Steffen Klaere for useful comments and advice on possible approaches to the problems considered in this paper. ...
doi:10.1016/j.jtbi.2016.05.001
pmid:27188249
fatcat:i77yrdkxnzba5levvh6eqqi5qu
Understanding and Modelling the Impact of Climate Change on Infectious Diseases – Progress and Future Challenges
[chapter]
2011
Climate Change - Socioeconomic Effects
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Other considerations may include computational resources (e.g. IBMs and climate models are very computationally intensive) and known uncertainties (or variability) in disease and climate inputs. ...
The use of multi-model ensembles in climate modelling has already become an established technique (e.g. ...
They are part of an introduction to the researches being done around the globe in connection with this topic. ...
doi:10.5772/23139
fatcat:7fc4kric2vf6nl66dyw5l7zhv4
Agile Development of an Attitude-Behaviour Driven Simulation of Alcohol Consumption Dynamics
2015
Journal of Artificial Societies and Social Simulation
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This paper sets out the methods of Scrum agile software development, and discusses the experience of using Scrum to organise workflow and guide the development of an agent-based model of alcohol consumption ...
Whilst there have been several advocates for the application of software engineering (SE) methodologies in the development of agent-based models and simulations in the social sciences, the uptake of these ...
(CAMH) at the University of Toronto for helpful discussions, as well as the JASSS reviewers for their useful comments. ...
doi:10.18564/jasss.2841
fatcat:262z5uq5dfca7ettjx5zxe4gpy
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