Predicting plant disease epidemics from functionally represented weather series.

Epidemics are often triggered by specific weather patterns favouring the pathogen on susceptible hosts. For plant diseases, models predicting epidemics have therefore often emphasized the identification of early season weather patterns that are correlated with a disease outcome at some later point. Toward that end, window-pane analysis is an exhaustive search algorithm traditionally used in plant pathology for mining correlations in a weather series with respect to a disease endpoint. Here we show, with reference to Fusarium head blight (FHB) of wheat, that a functional approach is a more principled analytical method for understanding the relationship between disease epidemics and environmental conditions over an extended time series. We used scalar-on-function regression to model a binary outcome (FHB epidemic or non-epidemic) relative to weather time series spanning 140 days relative to flowering (when FHB infection primarily occurs). The functional models overall fit the data better than previously described standard logistic regression (lr) models. Periods much earlier than heretofore realized were associated with FHB epidemics. The findings were used to create novel weather summary variables which, when incorporated into lr models, yielded a new set of models that performed as well as existing lr models for real-time predictions of disease risk. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.

Functional Data Analysis of Weather Variables Linked to Fusarium Head Blight Epidemics in the United States.

In past efforts, input weather variables for Fusarium head blight (FHB) prediction models in the United States were identified after following some version of the window-pane algorithm, which discretizes a continuous weather time series into fixed-length windows before searching for summary variables associated with FHB risk. Functional data analysis, on the other hand, reconstructs the assumed continuous process (represented by a series of recorded weather data) by using smoothing functions, and is an alternative way of working with time series data with respect to FHB risk. Our objective was to functionally model weather-based time series data linked to 865 observations of FHB (covering 16 states and 31 years in total), classified as epidemics (FHB disease index ≥ 10%) and nonepidemics (FHB disease index < 10%). Altogether, 94 different time series variables were modeled by penalized cubic B-splines for the smoothing function, from 120 days pre-anthesis to 20 days post-anthesis. Functional mean curves, standard deviations, and first derivatives were plotted for FHB epidemics relative to nonepidemics. Function-on-scalar regressions assessed the temporal trends of the magnitude and significance of the mean difference between functionally represented weather time series associated with FHB epidemics and nonepidemics. The mean functional weather-variable curve for epidemics started to deviate, in general, from that for nonepidemics as early as 40 days pre-anthesis for several weather variables. The greatest deviations were often near anthesis, the period of maximum susceptibility of wheat to FHB-causing fungi. The most consistent separations between the mean functional curves were seen with the daily averages of moisture-related variables (such as average relative humidity) and with variables summarizing the daily variation in temperature (as opposed to the daily mean). Functional data analysis was useful for extending our knowledge of relationships between weather variables and FHB epidemics.

Perceptions of Midwestern Crop Advisors and Growers on Foliar Fungicide Adoption and Use in Maize.

Foliar fungicide use in hybrid maize in the United States was rare before 2000. The decade from 2000 to 2010 saw foliar fungicides increasingly applied to maize in the absence of appreciable disease pressure, a practice seemingly at odds with integrated pest management philosophy. Yet, it is commonly believed that growers do not employ management strategies unless there are perceived benefits. Maize (corn) growers (CGs) and certified crop advisors (CCAs) across four Midwestern states (Iowa, Illinois, Ohio, and Wisconsin) were surveyed to better understand their practices, values and perceptions concerning the use of foliar fungicides during 2005 to 2009. The survey results demonstrated the rapid rise in maize foliar fungicide applications from 2000 through 2008, with 84% of CGs who sprayed having used a foliar fungicide in maize production for the very first time during 2005 to 2009. During 2005 to 2009, 73% of CCAs had recommended using a foliar fungicide, but only 35% of CGs sprayed. Perceived yield gains, conditional on having sprayed, were above the break-even point on average. However, negative yield responses were also observed by almost half of CCAs and a quarter of CGs. Hybrid disease resistance was a more important factor to economically successful maize production than foliar fungicides. Diseases as a yield-limiting factor were more important to CGs than CCAs. As a group, CGs were not as embracing of foliar fungicide as were CCAs, and remained more conservative about the perceived benefits to yield.

Ethyl 2-amino-1-(4-fluoro-phen-yl)-5-oxo-4,5-di-hydro-1H-pyrrole-3-carboxyl-ate: crystal structure and Hirshfeld surface analysis.

In the title mol-ecule, C12H13FN2O3, the central pyrrole ring makes a dihedral angle of 9.2 (3)° with the eth-oxy carbonyl moiety whereas the fluoro-phenyl ring is rotated by 67.6 (2)° from the pyrrole ring. Supra-molecular aggregation is due to off-centric π-π stacking inter-actions involving screw-related pairs of mol-ecules, which are further connected by N-H⋯O and C-H⋯O inter-actions, forming a sinusoidal pattern along the [001] direction on the bc plane. Three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint plots confirm the contributions of these inter-actions.

Environmental Conditions Associated with Stripe Rust in Kansas Winter Wheat.

Stripe rust has reemerged as a problematic disease in Kansas wheat. However, there are no stripe rust forecasting models specific to Kansas wheat production. Our objective was to identify environmental variables associated with stripe rust epidemics in Kansas winter wheat as an initial step in the longer-term goal of developing predictive models for stripe rust to be used within the state. Mean yield loss due to stripe rust on susceptible varieties was estimated from 1999 to 2012 for each of the nine Kansas crop reporting districts (CRD). A CRD was classified as having experienced a stripe rust epidemic when yield loss due to the disease equaled or exceeded 1%, and a nonepidemic otherwise. Epidemics were further classified as having been moderate or severe if yield loss was 1 to 14% or greater than 14%, respectively. The binary epidemic categorizations were linked to a matrix of 847 variables representing monthly meteorological and soil moisture conditions. Classification trees were used to select variables associated with stripe rust epidemic occurrence and severity (conditional on an epidemic having occurred). Selected variables were evaluated as predictors of stripe rust epidemics within a general estimation equations framework. The occurrence of epidemics within CRD was linked to soil moisture during the fall and winter months. In the spring, severe epidemics were linked to optimal (7 to 12°C) temperatures. Simple environmentally based stripe rust models at the CRD level may be combined with field-level disease observations and an understanding of varietal reaction to stripe rust as part of an operational disease forecasting system in Kansas.

Does the P Value Have a Future in Plant Pathology?

The P value (significance level) is possibly the mostly widely used, and also misused, quantity in data analysis. P has been heavily criticized on philosophical and theoretical grounds, especially from a Bayesian perspective. In contrast, a properly interpreted P has been strongly defended as a measure of evidence against the null hypothesis, H0. We discuss the meaning of P and null-hypothesis statistical testing, and present some key arguments concerning their use. P is the probability of observing data as extreme as, or more extreme than, the data actually observed, conditional on H0 being true. However, P is often mistakenly equated with the posterior probability that H0 is true conditional on the data, which can lead to exaggerated claims about the effect of a treatment, experimental factor or interaction. Fortunately, a lower bound for the posterior probability of H0 can be approximated using P and the prior probability that H0 is true. When one is completely uncertain about the truth of H0 before an experiment (i.e., when the prior probability of H0 is 0.5), the posterior probability of H0 is much higher than P, which means that one needs P values lower than typically accepted for statistical significance (e.g., P = 0.05) for strong evidence against H0. When properly interpreted, we support the continued use of P as one component of a data analysis that emphasizes data visualization and estimation of effect sizes (treatment effects).

Predicting Fusarium head blight epidemics with boosted regression trees.

Predicting major Fusarium head blight (FHB) epidemics allows for the judicious use of fungicides in suppressing disease development. Our objectives were to investigate the utility of boosted regression trees (BRTs) for predictive modeling of FHB epidemics in the United States, and to compare the predictive performances of the BRT models with those of logistic regression models we had developed previously. The data included 527 FHB observations from 15 states over 26 years. BRTs were fit to a training data set of 369 FHB observations, in which FHB epidemics were classified as either major (severity ≥ 10%) or non-major (severity < 10%), linked to a predictor matrix consisting of 350 weather-based variables and categorical variables for wheat type (spring or winter), presence or absence of corn residue, and cultivar resistance. Predictive performance was estimated on a test (holdout) data set consisting of the remaining 158 observations. BRTs had a misclassification rate of 0.23 on the test data, which was 31% lower than the average misclassification rate over 15 logistic regression models we had presented earlier. The strongest predictors were generally one of mean daily relative humidity, mean daily temperature, and the number of hours in which the temperature was between 9 and 30°C and relative humidity ≥ 90% simultaneously. Moreover, the predicted risk of major epidemics increased substantially when mean daily relative humidity rose above 70%, which is a lower threshold than previously modeled for most plant pathosystems. BRTs led to novel insights into the weather-epidemic relationship.

Development and validation of a liquid chromatographic method for estimation of dicyclomine hydrochloride, mefenamic Acid and paracetamol in tablets.

Liquid chromatographic method was developed for simultaneous quantitative determination of dicyclomine hydrochloride, mefenamic acid and paracetamol in their combined dosage form. The separation was achieved using a C18 column (250×4.6 mm id, 5 µm) using acetonitrile:20 mM potassium dihydrogen phosphate 70:30 (v/v) adjusted to pH 4 using orthophosphoric acid as mobile phase at a flow rate of 1 ml/min and detection at 220 nm. Separation was completed within 12 min. The retention times of dicyclomine hydrochloride, mefenamic acid and paracetamol were 3.8, 9.3 and 2.5 minutes respectively. The proposed method was found to have linearity in concentration range of 10-100 µg/ml for dicyclomine hydrochloride, 0.05-10 µg/ml for mefenamic acid and 0.1-20 µg/ml for paracetamol. The developed method has been statistically validated and was found to be simple, precise, reproducible and accurate. The developed and validated method was successfully used for the quantitative analysis of commercially available dosage form.

Predicting fusarium head blight epidemics with weather-driven pre- and post-anthesis logistic regression models.

Our objective was to identify weather-based variables in pre- and post-anthesis time windows for predicting major Fusarium head blight (FHB) epidemics (defined as FHB severity ≥ 10%) in the United States. A binary indicator of major epidemics for 527 unique observations (31% of which were major epidemics) was linked to 380 predictor variables summarizing temperature, relative humidity, and rainfall in 5-, 7-, 10-, 14-, or 15-day-long windows either pre- or post-anthesis. Logistic regression models were built with a training data set (70% of the 527 observations) using the leaps-and-bounds algorithm, coupled with bootstrap variable and model selection methods. Misclassification rates were estimated on the training and remaining (test) data. The predictive performance of models with indicator variables for cultivar resistance, wheat type (spring or winter), and corn residue presence was improved by adding up to four weather-based predictors. Because weather variables were intercorrelated, no single model or subset of predictor variables was best based on accuracy, model fit, and complexity. Weather-based predictors in the 15 final empirical models selected were all derivatives of relative humidity or temperature, except for one rainfall-based predictor, suggesting that relative humidity was better at characterizing moisture effects on FHB than other variables. The average test misclassification rate of the final models was 19% lower than that of models currently used in a national FHB prediction system.

Managing Foliar Diseases of Processing Sweet Corn in New York with Strobilurin Fungicides.

Processing sweet corn (Zea mays) growers in New York are more concerned about the cost effectiveness of fungicide use against foliar fungal diseases (common rust and Northern corn leaf blight) and less about whether such sprays will reduce disease intensity. To address this concern, field trials were done in 2006 and 2007 with three processing sweet corn hybrids (Jubilee, Bold, and GH 9597) that differed in susceptibility to common rust and Northern corn leaf blight, and two strobilurin fungicides (azoxystrobin and pyraclostrobin). Single strobilurin applications were applied in response to foliar disease severity thresholds of 1, 10, and 20%. Single fungicide applications did reduce foliar disease severities. Applications were most cost effective when made in response to the 1 and 10% foliar severity thresholds, and generally only in the susceptible hybrid Bold. Spraying at the 20% severity threshold did reduce final foliar disease severity but was not cost effective. Azoxystrobin and pyraclostrobin were equally effective in disease management. The results suggest that a single application of a strobilurin fungicide against common rust and Northern corn leaf blight can be cost effective for New York processing sweet corn growers when such an application is made before foliar disease severity exceeds 20%.

Transmission efficiency of Cucumber mosaic virus by aphids associated with virus epidemics in snap bean.

Cucumber mosaic virus (CMV) is a major component of the virus complex that has become more pronounced in snap bean in the midwestern and northeastern United States since 2001. Multiple-vector-transfer tests were done to estimate the CMV transmission efficiencies (p) of the main aphid species identified in commercial snap bean fields in New York and Pennsylvania. The four most efficient vectors (p > 0.05) were Aphis gossypii, A. glycines, Acyrthosiphon pisum, and Therioaphis trifolii, which were all significant species in the migratory aphid populations in snap bean. Moderately efficient vectors (0.01 < p < 0.04) were A. spiraecola, A. craccivora, Macrosiphum euphorbiae, and Rhopalosiphum maidis. Poor vectors (p < 0.01) included A. fabae, Nearctaphis bakeri, and Myzus persicae. Only one species, Sitobion avenae, failed to transmit CMV in replicated tests. Estimates of p were consistent between different clones of the same aphid species and among three different field isolates of CMV tested. Single-vector-transfer test results for a subset of the species supported those obtained via the multiple-vector-transfer approach. Our results are consistent with the notion that A. glycines is a major vector of recent CMV epidemics in snap bean, but that species is only one of several that are involved.

RP-HPLC Estimation of Risperidone in Tablet Dosage Forms.

A simple, specific, accurate, and precise reverse phase liquid chromatographic method was developed and validated for the estimation of risperidone in tablet dosage forms. A Phenomenex Gemini C-18, 5 mum column having 250x4.6 mm i.d. in isocratic mode, with mobile phase containing methanol: acetonitrile: 50 mM potassium dihydrogen orthophosphate (80:10:10 v/v) was used. The flow rate was 1.3 ml/min and effluents were monitored at 234 nm. Clozapine was used as an internal standard. The retention time of risperidone and clozapine were 2.5 min and 3.3 min, respectively. The method was validated for linearity, accuracy, precision, specificity, limit of quantification, limit of detection, robustness and stability. The limit of detection and limit of quantification for estimation of risperidone was found to be 500 ng/ml and 990 ng/ml, respectively. Recovery of risperidone was found to be in the range of 99.02-101.68%. Proposed method was successfully applied for the quantitative determination of risperidone in tablet formulations.

Stability Indicating RP-HPLC Estimation of Atorvastatin Calcium and Amlodipine Besylate in Pharmaceutical Formulations.

A simple, specific, accurate and stability indicating reversed phase high performance liquid chromatographic method was developed for the simultaneous determination of atorvastatin calcium and amlodipine besylate in tablet dosage forms. A phenomenex Gemini C-18, 5 µm column having 250×4.6 mm i.d. in isocratic mode, with mobile phase containing 0.02 M potassium dihydrogen phosphate:acetonitrile:methanol (30:10:60, v/v/v) adjusted to pH 4 using ortho phosphoric acid was used. The flow rate was 1.0 ml/min and effluents were monitored at 240 nm. The retention times of atorvastatin calcium and amlodipine besylate were 11.6 min and 4.5 min, respectively. The calibration curves were linear in the concentration range of 0.08-20 µg/ml for atorvastatin calcium and 0.1-20 µg/ml for amlodipine besylate. Atorvastatin calcium and amlodipine besylate stock solutions were subjected to acid and alkali hydrolysis, chemical oxidation and dry heat degradation. The degraded product peaks were well resolved from the pure drug peak with significant difference in their retention time values. The proposed method was validated and successfully applied to the estimation of atorvastatin calcium and amlodipine besylate in combined tablet dosage forms.

Stability Indicating RP-HPLC Estimation of Nebivolol Hydrochloride in Pharmaceutical Formulations.

A simple, specific, accurate and stability indicating reversed phase liquid chromatographic method was developed for the determination of nebivolol hydrochloride in tablet dosage forms. A phenomenex Gemini C-18, 5 µm column having 250×4.6 mm i.d., with mobile phase containing methanol: acetonitrile: 0.02 M potassium dihydrogen phosphate (60:30:10, v/v/v; pH 4.0) was used. The retention time of nebivolol hydrochloride was 2.6 min. The linearity for nebivolol hydrochloride was in the range of 0.2-10 µg/ml. The recovery was found to be in the range of 98.68-100.86%. The detection limit and quantification limit were found to be 0.06 µg/ml and 0.2 µg/ml, respectively. Nebivolol stock solutions were subjected to acid, alkali and neutral hydrolysis, chemical oxidation and dry heat degradation. The degraded product peaks were well resolved from the pure drug peak with significant difference in their retention time values. The proposed method was validated and successfully applied to the estimation of nebivolol hydrochloride in tablet formulations.

RP-HPLC Estimation of Venlafaxine Hydrochloride in Tablet Dosage Forms.

A simple, specific, accurate, and precise reverse phase high performance liquid chromatographic method was developed and validated for the estimation of venlafaxine hydrochloride in tablet dosage forms. A Phenomenex Gemini C-18, 5 mum column having 250 x 4.6 mm i.d. in isocratic mode, with mobile phase containing methanol: 0.05 M potassium dihydrogen orthophosphate (70:30, v/v; pH 6.2) was used. The flow rate was 1.0 ml/min and effluents were monitored at 226 nm. Carbamazepine was used as an internal standard. The retention time of venlafaxine hydrochloride and carbamazepine were 3.7 min and 5.3 min, respectively. The method was validated for specificity, linearity, accuracy, precision, limit of quantification, limit of detection, robustness and solution stability. Limit of detection and limit of quantification for estimation of venlafaxine hydrochloride were found to be 100 ng/ml and 300 ng/ml, respectively. Recoveries of venlafaxine hydrochloride in tablet formulations were found to be in the range of 99.02-101.68%. Proposed method was successfully applied for the quantitative determination of venlafaxine hydrochloride in tablet dosage forms.

Effect of Fertilization and Biopesticides on the Infection of Catharanthus roseus by Phytophthora nicotianae.

Experiments were carried out in a greenhouse to determine the effect of fertilizer concentration (0, 0.5, 1.0, and 2.0× Hoagland solutions) and various commercial biopesticides on the severity of Phytophthora nicotianae infection of Madagascar periwinkle. Application of biopesticides and fertilizer concentration significantly influenced the severity of infection, but there was no significant effect from the interaction of these two factors. Overall, disease severity showed a tendency to increase with the concentration of applied fertilizer. Compared with the control plants, disease was significantly less severe in plants that were treated with the biopesticides, except for plants treated with metabolites of Myrothecium verrucaria (DiTera). However, only the products containing potassium phosphonates and potassium phosphates (FNX-100 and FNX-2500) provided a satisfactory level of control when compared with either the control plants or those that received any of the other products tested. Additional experiments were carried out in growth chambers to test the effects of increasing fertilizer concentrations in plants that were inoculated with different P. nicotianae inoculum levels. In these trials, there was no consistent indication that disease is most severe in plants that received the highest fertilizer concentration even at the highest inoculum level.

Identification and Characterization of Russet on Snap Beans Caused by Plectosporium tabacinum.

Russet symptoms of unknown etiology are sporadically observed on snap bean (Phaseolus vulgaris) pods in New York and Maryland. Symptoms can render the whole crop unmarketable, and seem to appear when heavy rainfall occurs around harvest time. In 2000 and 2004, a microorganism not previously encountered was isolated from russet lesions on snap bean pods from commercial fields in Maryland and New York. Typical russet symptoms were produced on snap bean pods of cv. Brio after inoculation with spores of the isolates. Koch's postulates were also fulfilled. The organism was identified as Plectosporium tabacinum (Van Beyma) M.E. Palm, W. Gams & Nirenberg. A continuous 48-h leaf wetness duration at 23 to 27°C was essential for rapid symptom development. Large (11 cm long on average) snap bean pods were more susceptible to disease than smaller (pin) pods in cvs. Brio and Gold Mine. Light mechanical damage to the pods did not enhance infection. Four isolates of P. tabacinum (three from snap bean pods, one from zucchini) were inoculated onto large pods of the snap bean cvs. Brio, Gold Mine, and Hercules. All four isolates induced a russet on the pods, but the severity was significantly lower with the zucchini isolate.

Nonparametric analysis of ordinal data in designed factorial experiments.

ABSTRACT Plant disease severity often is assessed using an ordinal rating scale rather than a continuous scale of measurement. Although such data usually should be analyzed with nonparametric methods, and not with the typical parametric techniques (such as analysis of variance), limitations in the statistical methodology available had meant that experimental designs generally could not be more complicated than a one-way layout. Very recent advancements in the theoretical formulation of hypotheses and associated test statistics within a nonparametric framework, together with development of software for implementing the methods, have made it possible for plant pathologists to analyze properly ordinal data from more complicated designs using nonparametric techniques. In this paper, we illustrate the nonparametric analysis of ordinal data obtained from two-way factorial designs, including a repeated measures design, and show how to quantify the effects of experimental factors on ratings through estimated relative marginal effects.

Foci of stagonospora nodorum blotch in winter wheat before canopy development.

ABSTRACT Stagonospora nodorum blotch (SNB) often develops explosively on upper leaves and glumes of wheat. Inoculum for late season infections may arise from early disease foci in the lower canopy or from recent immigration of wind-dispersed ascospores. Research was conducted to determine if foci of SNB are present and secondary spread has occurred in fields before tiller elongation. We determined the incidence of infection by Stagonospora nodorum for plants sampled at the mid-tillering stage in 96 1-m(2) quadrats in each of two fields. Isolates of S. nodorum were recovered from 32 quadrats, one per infected plant where possible. Multilocus restriction fragment length polymorphism haplotypes were determined for each isolate. Of 55 isolates collected from one field, there were 22 distinct haplotypes. Diseased plants were aggregated in both fields; aggregates sometimes extended to adjacent quadrats. Plants within aggregates were often infected by the same haplotype, suggesting that secondary spread had occurred. Foci overlapped because some aggregates were infected by more than one haplotype. Our results show that genetically diverse populations of S. nodorum were already established in fields before canopy development and were comprised of sometimes overlapping foci undergoing clonal expansion.

Velocity measurements within confined turbulent jets: application to cardiovalvular regurgitation.

An expression for centerline mean velocity distributions for circular and noncircular confined turbulent jets has been obtained by assuming self-preservation of flow downstream of the jet potential core. It was assumed that the velocity decay was not only dependent on the streamwise distance x in terms of x/d, as in the case of free jets, but also on the ratio of the orifice diameter d to the confining pipe diameter D. To validate the expression and to determine the empirical constants, measurements of the centerline velocities within the confined jets issuing from different size circular orifices and various noncircular orifices of different shapes were conducted. The results indicate that the validity of the expression is restricted to d/D < or =0.25 and is weakly dependent on the particular orifice shape. It is suggested that, as for the case of free turbulent jets reported earlier, that this expression may be used potentially to predict the valvular lesion size or to estimate the volume of valvular regurgitation for confined jets provided the value of D, which corresponds to the "atrial diameter," is known or statistically available.