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Open Access Publications from the University of California

Scholarly Works (13 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2020)
In a previous study, air sampling using vortex air samplers combined with species-specific amplification of pathogen DNA was carried out over two years in four or five locations in the Salinas Valley of California. The resulting time series data for the abundance of pathogen DNA trapped per day displayed complex dynamics with features of both deterministic (chaotic) and stochastic uncertainty. Methods of nonlinear time series analysis developed for the reconstruction of low dimensional attractors provided new insights into the complexity of pathogen abundance data. In particular, the analyses suggested that the length of time series data that it is practical or cost-effective to collect may limit the ability to definitively classify the uncertainty in the data. Over the two years of the study, five location/year combinations were classified as having stochastic linear dynamics and four were not. Calculation of entropy values for either the number of pathogen DNA copies or for a binary string indicating whether the pathogen abundance data were increasing revealed (1) some robust differences in the dynamics between seasons that were not obvious in the time series data themselves and (2) that the series were almost all at their theoretical maximum entropy value when considered from the simple perspective of whether instantaneous change along the sequence was positive.
    Cover page: Characterization of Pathogen Airborne Inoculum Density by Information Theoretic Analysis of Spore Trap Time Series Data
    • Article
    • Peer Reviewed
    California Agriculture, Volume 72, Issue 4 (2018)
    As the information revolution sweeps through the agricultural sector, extension professionals may be lagging behind their clients in the use of information and communication technology (ICT) such as social media, which could be a valuable tool for outreach and education. We surveyed sustainable agriculture stakeholders in California — extension professionals, county agricultural commissioners, and members of farm bureaus and producer groups — to measure their ICT behavior and attitudes. Drawing on diffusion of innovation theory, we characterized the innovation attributes of ICT that may influence the adoption and use of new technology among extension professionals. We also studied their demographic characteristics to establish whether there was a connection with ICT use. The main perceived benefit of ICT was that it can quickly reach larger, more diverse and more distant audiences. The perceived challenges included lack of professional support, the potential for misinformation on social media platforms, and the time requirements and technical complexity of technology use. Extension professionals experienced these challenges more than other sustainable agriculture stakeholders, creating a technology gap between extension professionals and their clientele. An ICT community of practice and clear organizational guidelines for measuring and reporting performance relating to ICT might help extension professionals close the gap.
      Cover page: Closing the extension gap: Information and communication technology in sustainable agriculture
      • Thesis
      • Peer Reviewed
      UC Davis Electronic Theses and Dissertations (2021)

      Huanglongbing (HLB) is an invasive disease of citrus trees associated with the bacterium “Candidatus Liberibacter asiaticus” and transmitted by the Asian citrus psyllid (ACP), Diaphorina citri, that is threatening citrus production in California and other citrus-producing areas of the world. Current strategies to prevent citrus trees from being infected with HLB are based on the application of coordinated insecticide treatments for the insect vector, detection and removal of HLB-positive trees and use of certified plant material. These measures are most effective if applied on an area-wide scale by all citrus growers in a region, yet little is known about the California citrus growers’ willingness to coordinate measures across property boundaries. When individuals need to make contributions to achieve a collective effort but may benefit from the efforts of others without bearing the costs, they may be tempted to free-ride on others’ efforts, giving rise to a collective action problem. This type of problem has been extensively studied by the social-ecological systems literature, but it has rarely been addressed in the context of plant diseases. In this dissertation, a social-ecological systems perspective was used to integrate the social and ecological dimensions of HLB management in order to explore what strategies may be more effective to achieve collective action for this disease. The first chapter introduces the idea of plant health provision as a public good collective action problem. Ostrom’s design principles for long-enduring common-pool resource institutions are used as a reference to compare the institutional approaches that have been developed to achieve collective action for HLB in California and other citrus-producing areas, illustrating how these principles could be applied to other plant diseases that are threatening food security, and suggesting a link between institutional approaches that follow the design principles and successful collective outcomes. The second chapter explores the California citrus industry’s propensity to adopt voluntary measures to manage HLB. A multivariate ordinal logistic regression model is used to analyze a survey distributed to 300 participants, showing that the propensity to adopt management measures may depend on the citrus stakeholder’s perceived vulnerability to HLB, as well as their intention to stay informed and communicate with the regional coordinators of the HLB control program and their neighbors. In addition, the analysis sheds light into what combinations of management measures may be adopted together as an integrated pest management approach to HLB. The third chapter focuses on the area-wide management (AWM) program for ACP in Southern California, examining the individual perceptions and group-level determinants of collective action for AWM. It shows that citrus stakeholders are aware of the benefits of coordinating insecticide treatments for ACP, but they identify the lack of participation as the main obstacle for collective action, and some do not believe that their neighbors will coordinate. To face this collective action problem, two distinct institutional approaches have been developed to coordinate insecticide treatments for ACP, one in which treatments are voluntary, and one in which they are mandatory. An analysis of participation in AWM in Southern California over nine seasons shows that these two institutional approaches have followed a different trajectory over time. In addition, group-level variables from collective action theory, such as the size of the group or the heterogeneity in grove size, have had a negative impact on participation and may be relevant for the design of future AWM programs. This dissertation contributes to answering the question of what institutional approaches and strategies might be more effective to deal with the spatial and temporal dynamics of plant diseases while staying aligned with the preferences, values and needs of the societies affected, setting the basis for further interdisciplinary research that will likely benefit the management of HLB and other plant diseases that give rise to collective action problems.

        Cover page: A social-ecological systems perspective of huanglongbing management in California
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2020)
        Diagrammatic formats are useful for summarizing the processes of evaluation and comparison of forecasts in plant pathology and other disciplines where decisions about interventions for the purpose of disease management are often based on a proxy risk variable. We describe a new diagrammatic format for disease forecasts with two categories of actual status and two categories of forecast. The format displays relative entropies, functions of the predictive values that characterize expected information provided by disease forecasts. The new format arises from a consideration of earlier formats with underlying information properties that were previously unexploited. The new diagrammatic format requires no additional data for calculation beyond those used for the calculation of a receiver operating characteristic (ROC) curve. While an ROC curve characterizes a forecast in terms of sensitivity and specificity, the new format described here characterizes a forecast in terms of relative entropies based on predictive values. Thus it is complementary to ROC methodology in its application to the evaluation and comparison of forecasts.
          Cover page: Information Graphs Incorporating Predictive Values of Disease Forecasts
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2020)
          The predictive receiver operating characteristic (PROC) curve differs from the more well-known receiver operating characteristic (ROC) curve in that it provides a basis for the evaluation of binary diagnostic tests using metrics defined conditionally on the outcome of the test rather than metrics defined conditionally on the actual disease status. Application of PROC curve analysis may be hindered by the complex graphical patterns that are sometimes generated. Here we present an information theoretic analysis that allows concurrent evaluation of PROC curves and ROC curves together in a simple graphical format. The analysis is based on the observation that mutual information may be viewed both as a function of ROC curve summary statistics (sensitivity and specificity) and prevalence, and as a function of predictive values and prevalence. Mutual information calculated from a 2 × 2 prediction-realization table for a specified risk score threshold on an ROC curve is the same as the mutual information calculated at the same risk score threshold on a corresponding PROC curve. Thus, for a given value of prevalence, the risk score threshold that maximizes mutual information is the same on both the ROC curve and the corresponding PROC curve. Phytopathologists and clinicians who have previously relied solely on ROC curve summary statistics when formulating risk thresholds for application in practical agricultural or clinical decision-making contexts are thus presented with a methodology that brings predictive values within the scope of that formulation.
            Cover page: Mutual Information as a Performance Measure for Binary Predictors Characterized by Both ROC Curve and PROC Curve Analysis
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2023)
            Early detection and prompt response are key factors in the eradication of huanglongbing (HLB) in California. Currently, qPCR testing of leaf tissue guides the removal of infected trees. However, because of the uneven distribution of Candidatus Liberibacter asiaticus (CLas) in an infected tree and asymptomatic infection, selecting the best leaves to sample, from a mature tree with more than 200,000 estimated leaves, is a major hurdle for timely detection. The goal of this study was to address this issue by testing alternative tissues that might improve the CLas detection rate. Using two years of field data, old and young leaves, peduncle bark of fruit, and feeder roots were evaluated for the presence of CLas. Quadrant-peduncle (Q-P) tissue sampling consistently resulted in better CLas detection than any other tissue type. Q-P samples had a 30% higher qPCR positivity rate than quadrant-leaf (Q-L) samples. No significant seasonal patterns were observed. Roots and single peduncles had similar detection rates; both were higher than single leaves or Q-L samples. If symptoms were used to guide sampling, 30% of infected trees would have been missed. Taken together, these results suggest that Q-P tissue sampling is the optimal choice for improved CLas detection under California growing conditions.
              Cover page: Alternative Tissue Sampling for Improved Detection of Candidatus Liberibacter asiaticus.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2019)
              Systemic acquired resistance (SAR) is a mechanism through which plants may respond to initial challenge by a pathogen through activation of inducible defense responses, thereby increasing resistance to subsequent infection attempts. Fitness costs are assumed to be incurred by plants induced for SAR, and several studies have attempted to quantify these costs. We developed a mathematical model, motivated by game-theoretic concepts, to simulate competition between hypothetical plant populations with and without SAR to examine conditions under which the phenomenon of SAR may have evolved. Data were gathered from various studies on fitness costs of induced resistance on life history traits in different plant hosts and scaled as a proportion of the values in control cohorts in each study (i.e., healthy plants unprimed for SAR). With unprimed healthy control plants set to a fitness value of 1, primed healthy plants incurred a fitness cost of about 10.4% (0.896, n = 157), primed diseased plants incurred a fitness cost of about 15.5% (0.845, n = 54), and unprimed diseased plants incurred a fitness cost of about 28.9% (0.711, n = 69). Starting from a small proportion of the population (0.5%) and competing against a population with constitutive defenses alone in stochastic simulations, the SAR phenotype almost always dominated the population after 1000 generations when the probability of disease was greater than or equal to 0.5 regardless of the probability for priming errors.
                Cover page: Using Game Theory to Understand Systemic Acquired Resistance as a Bet-Hedging Option for Increasing Fitness When Disease Is Uncertain
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2019)
                We describe a series of operational questions posed during the state-wide response in California to the arrival of the invasive citrus disease Huanglongbing. The response is coordinated by an elected committee from the citrus industry and operates in collaboration with the California Department of Food and Agriculture, which gives it regulatory authority to enforce the removal of infected trees. The paper reviews how surveillance for disease and resource allocation between detection and delimitation have been addressed, based on epidemiological principles. In addition, we describe how epidemiological analyses have been used to support rule-making to enact costly but beneficial regulations and we highlight two recurring themes in the programme support work: (i) data are often insufficient for quantitative analyses of questions and (ii) modellers and decision-makers alike may be forced to accept the need to make decisions on the basis of simple or incomplete analyses that are subject to considerable uncertainty. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.
                  Cover page: Using models to provide rapid programme support for California's efforts to suppress Huanglongbing disease of citrus
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2020)
                  For millennia humans have benefitted from application of the acute canine sense of smell to hunt, track and find targets of importance. In this report, canines were evaluated for their ability to detect the severe exotic phytobacterial arboreal pathogen Xanthomonas citri pv. citri (Xcc), which is the causal agent of Asiatic citrus canker (Acc). Since Xcc causes only local lesions, infections are non-systemic, limiting the use of serological and molecular diagnostic tools for field-level detection. This necessitates reliance on human visual surveys for Acc symptoms, which is highly inefficient at low disease incidence, and thus for early detection. In simulated orchards the overall combined performance metrics for a pair of canines were 0.9856, 0.9974, 0.9257 and 0.9970, for sensitivity, specificity, precision, and accuracy, respectively, with 1-2 s/tree detection time. Detection of trace Xcc infections on commercial packinghouse fruit resulted in 0.7313, 0.9947, 0.8750, and 0.9821 for the same performance metrics across a range of cartons with 0-10% Xcc-infected fruit despite the noisy, hot and potentially distracting environment. In orchards, the sensitivity of canines increased with lesion incidence, whereas the specificity and overall accuracy was >0.99 across all incidence levels; i.e., false positive rates were uniformly low. Canines also alerted to a range of 1-12-week-old infections with equal accuracy. When trained to either Xcc-infected trees or Xcc axenic cultures, canines inherently detected the homologous and heterologous targets, suggesting they can detect Xcc directly rather than only volatiles produced by the host following infection. Canines were able to detect the Xcc scent signature at very low concentrations (10,000× less than 1 bacterial cell per sample), which implies that the scent signature is composed of bacterial cell volatile organic compound constituents or exudates that occur at concentrations many fold that of the bacterial cells. The results imply that canines can be trained as viable early detectors of Xcc and deployed across citrus orchards, packinghouses, and nurseries.
                    Cover page: Canine Olfactory Detection of a Non-Systemic Phytobacterial Citrus Pathogen of International Quarantine Significance
                    • Article
                    • Peer Reviewed
                    California Agriculture, Volume 73, Issue 2 (2019)

                    Viruses are of great concern in vineyards. They cost the California wine grape industry as much as $91,661 per acre over the life of a vineyard, according to a 2015 economic study of the North Coast wine-growing region. As a first step toward managing viruses, growers are encouraged to plant certified material regulated by the California Grapevine Registration and Certification program. There are risks in sourcing plant material from stocks that are not subject to the same level of regulation. We surveyed vineyards of varying ages for eight common viruses to demonstrate the value of selecting certified material for new plantings.

                      Cover page: Virus surveys of commercial vineyards show value of planting certified vines
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