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Bayesian estimation for percolation models of disease spread in plant populations

G. J. Gibson, W. Otten, J. A. N. Filipe, A. Cook, G. Marion, C. A. Gilligan
2006 Statistics and computing  
Bayesian methods for fitting the model to observations of disease spread through space and time in replicate populations are developed.  ...  Statistical methods are formulated for fitting and testing percolation-based, spatio-temporal models that are generally applicable to biological or physical processes that evolve in spatially distributed  ...  We thank Darroch Hall for assistance in processing the experimental data.  ... 
doi:10.1007/s11222-006-0019-z fatcat:m5ovs5euczemxa6yfhytzvwir4

時間と空間を考慮する統計モデル(<特集2>始めよう!ベイズ推定によるデータ解析)
An introduction to spatio-temporal models for ecological data(A starting guide for data analyses using Bayesian estimation)

Taku Kadoya
2009 Nihon Seitai Gakkaishi  
Bull Math Biol 69:2005-2025 (2009) . 59:171-186 (2009) . 59:167-170 Gibson GJ, Otten W, Filipe JAN, Cook A, Marion G, Gilligan CA (2006) Bayesian estimation for percolation models of disease spread  ...  in plant populations.  ... 
doi:10.18960/seitai.59.2_219 fatcat:tmmqaqr7yzhppkliqlppiqi6ny

Estimation of multiple transmission rates for epidemics in heterogeneous populations

A. R. Cook, W. Otten, G. Marion, G. J. Gibson, C. A. Gilligan
2007 Proceedings of the National Academy of Sciences of the United States of America  
Word and character counts: abstract: 249 words; number of characters in the paper: 43 660.  ...  Contributions to the paper: All authors were involved in modeling and methodological development and in co-writing the paper.  ...  The experimental data were collected by WO in a previous joint BBSRC project with CAG and GJG.  ... 
doi:10.1073/pnas.0706461104 pmid:18077378 pmcid:PMC2154441 fatcat:t27dnn4r5rezboe72hvnhcymru

Applications of percolation theory to fungal spread with synergy

J. J. Ludlam, G. J. Gibson, W. Otten, C. A. Gilligan
2011 Journal of the Royal Society Interface  
There is increasing interest in the use of the percolation paradigm to analyze and predict the progress of disease spreading in spatially-structured populations of animals and plants.  ...  In the current paper we elicit evidence that such synergistic interactions may underlie transmission dynamics in real-world systems by first formulating a model for the spread of a ubiquitous parasitic  ...  Within animal populations, the percolation paradigm has recently been used to analyse the spread of plague in gerbil populations in Kazakstan [7] .  ... 
doi:10.1098/rsif.2011.0506 pmid:22048947 pmcid:PMC3306640 fatcat:pho72itpfne7xb5wkh3yyjssw4

The Effect of Heterogeneity on Invasion in Spatial Epidemics: From Theory to Experimental Evidence in a Model System

Franco M. Neri, Anne Bates, Winnie S. Füchtbauer, Francisco J. Pérez-Reche, Sergei N. Taraskin, Wilfred Otten, Douglas J. Bailey, Christopher A. Gilligan, Mark M. Tanaka
2011 PLoS Computational Biology  
The experimental data are analysed via Bayesian inference methods, estimating pathogen transmission parameters for each individual population.  ...  In this paper, we test recent theoretical results, which extend the established "percolation paradigm" to the spread of a pathogen in discrete heterogeneous host populations.  ...  Stutt for providing tools for data acquisition. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002174 pmid:21980273 pmcid:PMC3182855 fatcat:jua2beklsnebzcfkubdrxmwbka

Host Growth Can Cause Invasive Spread of Crops by Soilborne Pathogens

Melen Leclerc, Thierry Doré, Christopher A. Gilligan, Philippe Lucas, João A. N. Filipe, Anna-Liisa Laine
2013 PLoS ONE  
To test hypothesis 2 and our prediction, we used the pathozone to parameterise a stochastic model of pathogen spread in a host population, contrasting scenarios of spread with and without host growth.  ...  We extend this paradigm by examining how plant-root growth may alter the conditions for occurrence of soilborne pathogen epidemics in plant populations.  ...  Blavy for his advice in C++ coding and F. Maupas for providing data on plant growth. Author Contributions  ... 
doi:10.1371/journal.pone.0063003 pmid:23667560 pmcid:PMC3648505 fatcat:hbqdsa7cwveldmmuj6cihh4oju

Inference and Optimal Design for Nearest-Neighbour Interaction Models [article]

Andrei Iu. Bejan, Gavin J. Gibson, Stan Zachary
2010 arXiv   pre-print
We consider problems of Bayesian inference for a spatial epidemic on a graph, where the final state of the epidemic corresponds to bond percolation, and where only the set or number of finally infected  ...  In particular, we demonstrate that for lattice-based processes an experiment on a sparsified lattice can yield more information on model parameters than one conducted on a complete lattice.  ...  Acknowledgments We thank Dr Alex Cook for useful discussions at early stages of this work. A. Iu.  ... 
arXiv:1008.2453v1 fatcat:3jyui3aysrg4hjtaclk2xfjaky

Current Knowledge on Pathogenicity and Management of Stemphylium botryosum in Lentils (Lens culinaris ssp. culinaris Medik)

Arpita Das, Subrata Dutta, Subhendu Jash, Ashis Roy Barman, Raju Das, Shiv Kumar, Sanjeev Gupta
2019 Pathogens  
The role of different weather variables as predisposing factors for the rapid spread of the pathogen necessitates devising a disease predictive model for the judicial application of fungicides.  ...  Therefore, a detailed understanding of spatial diversity and population structure of the pathogen is pertinent for producing source material for resistance breeding.  ...  spread of the pathogen to disease-free countries.  ... 
doi:10.3390/pathogens8040225 pmid:31717347 pmcid:PMC6963855 fatcat:nezz3f2m3jah5jgdlwwvwkrbqe

Rivers and Landscape Ecology of a Plant Virus, Rice Yellow Mottle Virus Along the Niger Valley

Souley Issaka, Oumar Traoré, Régis Dimitri Skopé Longué, Agnès Pinel-Galzi, Mandev S Gill, Simon Dellicour, Paul Bastide, Stéphane Guindon, Eugénie Hébrard, Marie-Jo Dugué, Séré Yacouba, Silla Semballa (+3 others)
2021 Virus Evolution  
The spatial resolution along this section of the Niger River was the highest implemented for RYMV and possibly for any plant virus.  ...  The role of the hydrographic network of the Niger Basin in RYMV spread was examined, and the link between virus population dynamics and the extent of irrigated rice was assessed.  ...  ACKNOWLEDGEMENTS We thank Jamel Aribi and Louisiane Bachabi for technical help, Gill Mahé and Nathalie Rouche for the numerical map of the hydrographic basin of the Niger River, and Adrien Rieux for discussions  ... 
doi:10.1093/ve/veab072 fatcat:eblnzvkysrfpvkgnkwakt577h4

Reducing the Use of Pesticides with Site-Specific Application: The Chemical Control of Rhizoctonia solani as a Case of Study for the Management of Soil-Borne Diseases

Ronan Le Cointe, Thomas E. Simon, Patrick Delarue, Maxime Hervé, Melen Leclerc, Sylvain Poggi, Sabrina Sarrocco
2016 PLoS ONE  
Most control strategies currently focus on the temporal aspect of epidemics, e.g. determining the optimal date for spraying, regardless of the spatial mechanics and ecology of disease spread.  ...  Our results showed that Monceren 1 L mainly inhibits the saprotrophic spread of the fungus in soil and may prevent the fungus from reaching its host plant.  ...  ML thanks JAN Filipe and CA Gilligan for their previous contributions to the development of pathozone models that were used in this study.  ... 
doi:10.1371/journal.pone.0163221 pmid:27668731 pmcid:PMC5036793 fatcat:ub4rcsrs2zh43chsbhefeychbm

Percolation on feature-enriched interconnected systems

Oriol Artime, Manlio De Domenico
2021 Nature Communications  
Percolation is an emblematic model to assess the robustness of interconnected systems when some of their components are corrupted.  ...  Our framework not only provides a natural generalization of percolation but, more importantly, offers an accurate way to test the robustness of networks in realistic scenarios.  ...  Code availability The code for the Bayesian Machine Scientist is available at https://bitbucket.org/ rguimera/machine-scientist/.  ... 
doi:10.1038/s41467-021-22721-z pmid:33931643 fatcat:5wjx2mrb6nb7tct5v6jvpuxwma

Epidemics and Rumours: A Survey

Klaus Dietz
1967 Journal of the Royal Statistical Society Series A (General)  
I should like to thank several authors for allowing me to see their papers in draft prior to publication.  ...  ACKNOWLEDGEMENTS I wish to thank the editor for the invitation to write this review, and I am grateful to Professor J. M. Gani who very kindly consented to read and criticize the manuscript.  ...  A Bayesian method for the estimation of the parameters in connection with point-source epidemics is given by Hill (1963) .  ... 
doi:10.2307/2982521 fatcat:hql5m2gj2jcu3mlicmjiylumf4

Machine Learning for High-Throughput Stress Phenotyping in Plants

Arti Singh, Baskar Ganapathysubramanian, Asheesh Kumar Singh, Soumik Sarkar
2016 Trends in Plant Science  
Advances in automated and high-throughput imaging technologies have resulted in a deluge of high-resolution images and sensor data of plants.  ...  A classic example is high-throughput phenotyping (HTP), which has unlocked new prospects for non-destructive field-based phenotyping in plants for a large number of traits including physiological, biotic  ...  Hicks for reviewing this article and Marcus Naik for helping with the development of figures.  ... 
doi:10.1016/j.tplants.2015.10.015 pmid:26651918 fatcat:bkrddy6mxjgrfozkym2qfful3m

The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen

Bart T. L. H. van de Vossenberg, Balázs Brankovics, Hai D. T. Nguyen, Marga P. E. van Gent-Pelzer, Donna Smith, Kasia Dadej, Jarosław Przetakiewicz, Jan F. Kreuze, Margriet Boerma, Gerard C. M. van Leeuwen, C. André Lévesque, Theo A. J. van der Lee
2018 BMC Evolutionary Biology  
Quarantine measures have been implemented globally to control the disease and prevent its spread.  ...  Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease.  ...  Wulff (Danish Veterinary and Food Administration, Denmark), Ian Adams (FERA, United Kingdom), Olga Afanasenko (All Russian Research Institute for Plant Protection, Russian Federation) for kindly providing  ... 
doi:10.1186/s12862-018-1246-6 pmid:30200892 pmcid:PMC6131824 fatcat:js4ibqejlrglljqjkguc2cycii

Risk of COVID-19 hospitalisation rises exponentially with age, inversely proportional to T-cell production [article]

Sam Palmer, Nik Cunniffe, Ruairi Donnelly
2020 medRxiv   pre-print
In addition, incidence of severe disease and mortality due to COVID-19 are both higher in men, consistent with the degree to which thymic involution (and the decrease in T-cell production with age) is  ...  A Bayesian analysis of daily hospitalisations, accounting for contact-based and environmental transmission, indicates that non-adults are the only age group to deviate significantly from the exponential  ...  Bayesian 95% credible intervals for the rate parameter in the exponential dependence of probability of severe disease. Baseline represents the model in Fig. 2 .  ... 
doi:10.1101/2020.08.25.20181487 fatcat:wstrn43xmfey7leryqv5twpwha
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