scholarly journals Estimation of a Time-varying Apparent Infection Rate from Plant Disease Progress Curves: A Particle Filter Approach

2019 ◽  
Author(s):  
Kaique dos S Alves ◽  
Willian B Moraes ◽  
Wellington B da Silva ◽  
Emerson M Del Ponte
Keyword(s):  
Particle Filter ◽  
Infection Rate ◽  
Plant Disease ◽  
Host Susceptibility ◽  
Time Varying ◽  
Factors Affecting ◽  
Initial Inoculum ◽  
Disease Progress ◽  
Progress Curve ◽  
Apparent Infection Rate

AbstractThe parameters of the simplest (two-parameter) epidemiological models that best fit plant disease progress curve (DPC) data are the surrogate for initial inoculum (y0) and the (constant) apparent infection rate (r), both being useful for understanding, predicting and comparing epidemics. The assumption thatris constant is not reasonable and fluctuations are expected due to systematic changes in factors affecting infection (e.g. weather favorability, host susceptibility, etc.), thus leading to a time-varyingr, orr(t). An arrangement of these models (e.g. logistic, monomolecular, etc.) can be used to obtainrbetween two time points, given the disease (y) data are available. We evaluated a data assimilation technique, Particle Filter (PF), as an alternative method for estimatingr(t). Synthetic DPC data for a hypothetical polycyclic epidemics were simulated using the logistic differential equation for scenarios that combined five patterns ofr(t) (constant, increasing, decreasing, random or sinusoidal); five increasing time assessment interval (Δt= 1, 3, 5, 7 or 9 time units - t.u.); and two levels of noise (α = 0.1 or 0.25) assigned toy(t). The analyses of 50 simulated 60-t.u. DPCs showed that the errors of PF-derivedwere lower (RMSE < 0.05) for Δt< 5 t.u. and least affected by the presence of noise in the measure compared with the logit-derivedr(t). The ability to more accurately estimater(t) using the novel method may be useful to increase knowledge of field epidemics and identify within-season drivers that may explainr(t) behaviour.

Effect of nitrogen fertilization on the expression of slow-blasting resistance in rice

2005 ◽  
Vol 143 (5) ◽  
pp. 385-393 ◽  
Author(s):  
A. K. MUKHERJEE ◽  
N. K. MOHAPATRA ◽  
A. V. SURIYA RAO ◽  
P. NAYAK
Keyword(s):  
Infection Rate ◽  
Error Variance ◽  
Blast Disease ◽  
Economic Injury Level ◽  
Disease Progress Curve ◽  
Disease Progress ◽  
Progress Curve ◽  
Rate Of Increase ◽  
Apparent Infection Rate ◽  
Line Intercept

The development of rice blast disease in four slow-blasting (SB) genotypes was compared with that in the fast-blasting (FB) genotype Karuna, under natural field epidemics over a period of 3 years at five levels of nitrogen, in order to determine if the application of high doses of nitrogen influenced the expression of disease progress in the SB types. The treatment effects were compared through estimation of nine parameters viz. (i) lesion number (LN); (ii) area under disease progress curve (AUDPC); (iii) relative area under disease progress curve (RAUDPC); (iv) logistic apparent infection rate (r); (v) Gompertz apparent infection rate (k); (vi) logit line intercept (logit-a); (vii) gompit line intercept (gompit-a); (viii) time required for the disease to reach 0·25 severity in logistic (T25r); and (ix) Gompertz (T25k) models. There was a significant increase in LN, AUDPC, RAUDPC, r and k with increased levels of nitrogen application in all genotypes, but the rate of increase in disease severity was much lower in SB genotypes than the FB one and did not lead to breakdown of resistance in the SB genotypes, since severity level was much below the economic injury level. Among the nine derived parameters for evaluation of resistance LN, AUDPC, RAUDPC, r and k were best. The AUDPC and RAUDPC had lower degrees of error variance compared with the other parameters and hence were considered superior measures for characterization of disease progress curves.

scholarly journals Analysis and simulation of plant disease progress curves in R: introducing the epifitter package

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Kaique S. Alves ◽  
Emerson M. Del Ponte
Keyword(s):  
Plant Disease ◽  
Temporal Analysis ◽  
R Package ◽  
Desktop Computer ◽  
Disease Epidemiology ◽  
Disease Progress Curve ◽  
Disease Progress ◽  
Progress Curve ◽  
Data User ◽  
Population Dynamics Models

AbstractThe analysis of the disease progress curves (DPCs) is central to understanding plant disease epidemiology. The shape of DPCs can vary significantly and epidemics can be better understood and compared with an appropriate depiction and analysis. This paper introduces epifitter, an open-source tool developed in R for aiding in the simulation and analysis of DPC data. User-level functions were developed and their use is demonstrated to the reader using actual disease progress curve data for facilitating the conduction of several tasks, including (a) simulation of synthetic DPCs using four population dynamics models (exponential, monomolecular, logistic, and Gompertz); (b) calculation of the areas under disease progress curve and stairs; (c) fitting and ranking the four above-mentioned models to single or multiple DPCs; and (d) generation and customization of graphs. The package requires the installation of R in any desktop computer and the scripted analysis can be fully documented, reproduced, and shared. The epifitter R package provides a flexible suite for temporal analysis of epidemics that is useful for both research and teaching purposes.

scholarly journals Simulation of Potato Late Blight in the Andes. II: Validation of the LATEBLIGHT Model

2005 ◽  
Vol 95 (10) ◽  
pp. 1200-1208 ◽  
Author(s):  
Jorge L. Andrade-Piedra ◽  
Robert J. Hijmans ◽  
Henry S. Juárez ◽  
Gregory A. Forbes ◽  
Dani Shtienberg ◽  
...  
Keyword(s):  
New York State ◽  
Field Trials ◽  
Potato Cultivars ◽  
Performance Criteria ◽  
Model Parameters ◽  
Acceptance Test ◽  
Initial Inoculum ◽  
Disease Progress ◽  
The Andes ◽  
Progress Curve

LATEBLIGHT, a mathematical model that simulates the effect of weather, host growth and resistance, and fungicide use on asexual development and growth of Phytophthora infestans on potato foliage, was validated for the Andes of Peru. Validation was needed due to recent modifications made to the model, and because the model had not been formally tested outside of New York State. Prior to validation, procedures to estimate the starting time of the epidemic, the amount of initial inoculum, and leaf wetness duration were developed. Observed data for validation were from field trials with three potato cultivars in the Peruvian locations of Comas and Huancayo in the department of Junín, and Oxapampa in the department of Pasco in 1999 and 2000 for a total of 12 epidemics. These data had not been used previously for estimating model parameters. Observed and simulated epidemics were compared graphically using disease progress curves and numerically using the area under the disease progress curve in a confidence interval test, an equivalence test, and an envelope of acceptance test. The level of agreement between observed and simulated epidemics was high, and the model was found to be valid according to subjective and objective performance criteria. The approach of measuring fitness components of potato cultivars infected with isolates of a certain clonal lineage of P. infestans under controlled conditions and then using the experimental results as parameters of LATEBLIGHT proved to be effective. Fungicide treatments were not considered in this study.

scholarly journals Increase in Populations of Rhizoctonia solani and Wirestem of Collard with Velvet Bean Cover Crop Mulch

Plant Disease ◽  
2003 ◽  
Vol 87 (6) ◽  
pp. 719-725 ◽  
Author(s):  
Anthony P. Keinath ◽  
Howard F. Harrison ◽  
Paul C. Marino ◽  
D. Michael Jackson ◽  
Thomas C. Pullaro
Keyword(s):  
United States ◽  
Rhizoctonia Solani ◽  
Infection Rate ◽  
Cover Crop ◽  
Southeastern United States ◽  
Soil Surface ◽  
Velvet Bean ◽  
Organic Mulch ◽  
Progress Curve ◽  
Fallow Soil

Velvet bean has been used traditionally as a summer cover crop in the southeastern United States. We investigated the use of killed velvet bean as a cover crop mulch left on the soil surface before collard was transplanted in the fall. Control treatments were weed-free fallow and velvet bean that was killed and disked into the soil before transplanting. Incidence of wirestem, caused by Rhizoctonia solani, reached a maximum of 25% in 2000 but only 4% in 2001 in cover crop mulch treatments. Nevertheless, in both years, the infection rate, area under the disease progress curve, and final incidence were significantly greater with cover crop mulch than in the fallow or disked treatments. Wirestem incidence did not differ between the disked and fallow treatments in either year. Populations of R. solani in soil were greater after cover crop mulch than in fallow plots in both years and greater in the disked treatment than in fallow soil in 2000 but not 2001. Velvet bean does not appear to be suitable as an organic mulch for fall collard production, but could be used as a summer cover crop if disked into the soil before transplanting collard.

scholarly journals Management of Daylily Rust With Different Fungicides and Fungicide Combinations

2017 ◽  
Vol 18 (3) ◽  
pp. 162-165 ◽  
Author(s):  
Robert S. Emmitt ◽  
James W. Buck
Keyword(s):  
United States ◽  
Disease Management ◽  
Disease Severity ◽  
Low Cost ◽  
Single Application ◽  
Southeast United States ◽  
Disease Progress Curve ◽  
Disease Progress ◽  
Progress Curve ◽  
Disease Pressure

Production nurseries and daylily hybridizers in the southeast United States rely on the use of fungicides to manage daylily rust, caused by the fungus Puccinia hemerocallidis. Foliar sprays of pyraclostrobin, flutolanil, tebuconazole, myclobutanil, chlorothalonil, mancozeb, pyraclostrobin + boscalid, flutolanil + tebuconazole, flutolanil + myclobutanil, flutolanil + chlorothalonil, and flutolanil + mancozeb applied on 14-day intervals, and a nontreated control, were evaluated under high disease pressure at three locations in Griffin, GA, in 2015. Tebuconazole or the tebuconazole + flutolanil treatment consistently had the lowest area under the disease progress curve (AUDPC) of the treatments. The addition of flutolanil to chlorothalonil or mancozeb did not improve rust control and no difference in disease severity was observed in any treatment containing contact fungicides on all assessment dates. Single application costs ranged from $10.21 to $95.96 with tebuconazole providing excellent disease management at a relatively low cost per application ($13.90).

scholarly journals Banana Moko disease management with resistance inducers and chlorine dioxide

2015 ◽  
Vol 33 (2) ◽  
pp. 194-202
Author(s):  
Joaquín Guillermo Ramírez G. ◽  
Melissa Muñoz A. ◽  
Luis Fernando Patiño H. ◽  
Juan Gonzalo Morales O.
Keyword(s):  
Methyl Jasmonate ◽  
Chlorine Dioxide ◽  
Plant Disease ◽  
Sodium Salicylate ◽  
Bacterial Disease ◽  
Disease Development ◽  
Musa Sp ◽  
Progress Curve ◽  
Potassium Phosphite ◽  
Resistance Inducers

The plant disease Moko, caused by Ralstonia solanacearum, is the most important bacterial disease in banana and plantain crops worldwide. In the present study, chlorine dioxide and seven resistance inducers in banana plants (Musa sp.) infected with this bacterium were evaluated under greenhouse conditions. For the evaluation of chlorine dioxide, three doses were used (10, 30 and 50 mg L-1). The evaluation of the resistance inducers included the following: sodium salicylate 0.4 g L-1; hydrogen peroxide 1 mM; potassium phosphite 1.5 mL L-1; 3-aminobutanoic acid 1.0 g L-1; methyl jasmonate 0.2 g L-1; acibenzolar-s-methyl 0.3 mL L-1 and chitosan 3.0 mg mL-1. The results showed a significant reduction of 74% in the area under the disease progress curve (AUDPC) value, which was calculated for the disease development when the injected chlorine dioxide dose was 50 mg L-1. The AUDPC value for the resistance inducers was reduced by 45.4% for chitosan, 75.5% for methyl jasmonate and 65.5% for 3-aminobutanoic acid. Therefore, the results indicated that these molecules have the potential to be used for control of the Moko disease.

scholarly journals Coevolving Dynamics between Epidemic and Information Spreading considering the Dependence between Vigilance and Awareness Prevalence

Complexity ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Yixiao Zhang ◽  
Xing Lu ◽  
Ni Cui ◽  
Jingtai Tang ◽  
Xiyun Zhang
Keyword(s):  
Infection Rate ◽  
Nonlinear Dependence ◽  
Rational Behavior ◽  
Time Varying ◽  
Protective Measures ◽  
Positive Correlation ◽  
Epidemic Dynamics ◽  
Disease Information ◽  
Information Spreading

It has been demonstrated that the propagation of information and awareness regarding a disease can assist in containing the outbreak of epidemics. Previous models for this coevolving usually introduced the dependence between these two processes by setting a lower but time-independent infection rate for individuals with awareness. However, a realistic scenario can be more complicated, as individual vigilance and the adopted protective measures may depend on the extent of the discussion on the disease, whereas individuals may be irrational or lack relevant knowledge, leading to improper measures being taken. These can introduce a time-varying dependence between epidemic dynamics and awareness prevalence and may weaken the effect of spreading awareness in containing a pandemic. To better understand this effect, we introduce a nonlinear dependence of the epidemic infection rate on awareness prevalence, focusing on the effect of different forms of dependence on the coevolving dynamics. We demonstrate that a positive correlation between vigilance and awareness prevalence can enhance the effect of information spreading in suppressing epidemics. However, this enhancement can be weakened if some individuals are irrational. Our results demonstrate the importance of rational behavior in the strategy of containing epidemics by propagation of disease information.

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