Translating surveillance data into incidence estimates.

Monitoring a population for a disease requires the hosts to be sampled and tested for the pathogen. This results in sampling series from which we may estimate the disease incidence, i.e. the proportion of hosts infected. Existing estimation methods assume that disease incidence does not change between monitoring rounds, resulting in an underestimation of the disease incidence. In this paper, we develop an incidence estimation model accounting for epidemic growth with monitoring rounds that sample varying incidence. We also show how to accommodate the asymptomatic period that is the characteristic of most diseases. For practical use, we produce an approximation of the model, which is subsequently shown to be accurate for relevant epidemic and sampling parameters. Both the approximation and the full model are applied to stochastic spatial simulations of epidemics. The results prove their consistency for a very wide range of situations. The estimation model is made available as an online application. 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'.

Early detection surveillance for an emerging plant pathogen: a rule of thumb to predict prevalence at first discovery.

Emerging plant pathogens are a significant problem for conservation and food security. Surveillance is often instigated in an attempt to detect an invading epidemic before it gets out of control. Yet in practice many epidemics are not discovered until already at a high prevalence, partly due to a lack of quantitative understanding of how surveillance effort and the dynamics of an invading epidemic relate. We test a simple rule of thumb to determine, for a surveillance programme taking a fixed number of samples at regular intervals, the distribution of the prevalence an epidemic will have reached on first discovery (discovery-prevalence) and its expectation E(q*). We show that E(q*) = r/(N/Δ), i.e. simply the rate of epidemic growth divided by the rate of sampling; where r is the epidemic growth rate, N is the sample size and Δ is the time between sampling rounds. We demonstrate the robustness of this rule of thumb using spatio-temporal epidemic models as well as data from real epidemics. Our work supports the view that, for the purposes of early detection surveillance, simple models can provide useful insights in apparently complex systems. The insight can inform decisions on surveillance resource allocation in plant health and has potential applicability to invasive species generally.

Postharvest Quarantine Treatments for Diaphorina citri on Infested Curry Leaves.

Studies were conducted to evaluate treatments that reduce survival and attachment of Diaphorina citri nymphs on infested curry leaves (Bergera koenigii). Decontamination of curry leaves infested with D. citri in relation to disinfectant (none or Pro-San), temperature (0, 40, and 50°C), and treatment duration (0, 5, 10, and 20 min) was examined using a split-split plot design. Experiments were performed three times. Treatment duration did not significantly affect D. citri nymph survival or removal (P > 0.2). Temperature and disinfectant each significantly affected D. citri nymph survival and removal (P < 0.031). The interaction of temperature and disinfectant was significant with respect to nymph survival (P < 0.0001) but did not significantly affect removal (P = 0.4589). Tissue damage was significantly affected by temperature (P = 0.0056), duration (P = 0.0023), the interaction of temperature and duration (P = 0.0320), and the interaction of disinfectant, temperature, and duration (P = 0.0410). Of the treatments resulting in 100% D. citri nymph mortality on infested curry leaves, 40°C for 5 min with Pro-San was accompanied with the least proportion of curry leaf tissue damage (0.14 greater than untreated control, P = 0.25). Results from these studies may be useful in formulation of future regulatory policies regarding trade of citrus foliage, especially those used as condiments.

DC current pulses for OTSC clip fragmentation: technology and experimental study.

BACKGROUND: The OTSC clip is used in endoscopic management of gastrointestinal lesions. In rare cases, the removal of the OTSC clip might be desirable. The objective of the study is to investigate feasibility, efficacy, and safety of a novel endoscopic instrument system for removal of the OTSC clip. METHODS: The study series has been conducted in a porcine model. Clip removal is performed with a prototype instrumentation that is designed to locally melt the clip by applying an electrical current pulse onto the clip structure. This system has been evaluated in an animal study (n = 10) in a pig model. A cap prototype with an elongated sleeve has been used for extraction of the OTSC clip fragments. RESULTS: 23 of 24 implanted OTSC clips were successfully opened by applying in a total of 74 current pulses. Superficial mucosal coagulation marks were observed in 14 of the 24 application sites. No other findings such as hemorrhage, deep thermal wall lesions, or perforation were observed. CONCLUSIONS: The study confirms the effectiveness and safety of the proposed endoscopic removal technique. Safe extraction of the clip fragments was feasible with an elongated sleeve at the distal cap. Limitations of the methods are the animal model and the experimental nature of the prototype instrumentation.

A generic risk-based surveying method for invading plant pathogens.

Invasive plant pathogens are increasing with international trade and travel, with damaging environmental and economic consequences. Recent examples include tree diseases such as sudden oak death in the Western United States and ash dieback in Europe. To control an invading pathogen it is crucial that newly infected sites are quickly detected so that measures can be implemented to control the epidemic. However, since sampling resources are often limited, not all locations can be inspected and locations must be prioritized for surveying. Existing approaches to achieve this are often species specific and rely on detailed data collection and parameterization, which is difficult, especially when new arrivals are unanticipated. Consequently regulatory sampling responses are often ad hoc and developed without due consideration of epidemiology, leading to the suboptimal deployment of expensive sampling resources. We introduce a flexible risk-based sampling method that is pathogen generic and enables available information to be utilized to develop epidemiologically informed sampling programs for virtually any biologically relevant plant pathogen. By targeting risk we aim to inform sampling schemes that identify high-impact locations that can be subsequently treated in order to reduce inoculum in the landscape. This "damage limitation" is often the initial management objective following the first discovery of a new invader. Risk at each location is determined by the product of the basic reproductive number (R0), as a measure of local epidemic size, and the probability of infection. We illustrate how the risk estimates can be used to prioritize a survey by weighting a random sample so that the highest-risk locations have the highest probability of selection. We demonstrate and test the method using a high-quality spatially and temporally resolved data set on Huanglongbing disease (HLB) in Florida, USA. We show that even when available epidemiological information is relatively minimal, the method has strong predictive value and can result in highly effective targeted surveying plans.

Presymptomatic Fibrous Root Decline in Citrus Trees Caused by Huanglongbing and Potential Interaction with Phytophthora spp.

Huanglongbing (HLB), associated with 'Candidatus Liberibacter asiaticus', was first detected in Florida in late 2005 and is now widely distributed throughout the commercial citrus-growing regions. In recent seasons, concurrent with freeze and drought episodes, symptomatic HLB-infected trees were much more affected by the extremes of temperature and moisture than trees without HLB. Symptoms exhibited by the stressed trees were excessive leaf loss and premature fruit drop even when HLB-infected trees were managed with good nutritional and irrigation practices recommended to support health of HLB-affected trees. This stress intolerance may be due to a loss of fibrous roots. To assess root status of HLB-infected trees on 'Swingle' citrumelo rootstock (Citrus paradisi × Poncirus trifoliata), blocks of 2,307 3-year-old 'Hamlin' orange trees and 2,693 4-year-old 'Valencia' orange trees were surveyed visually and with a real-time polymerase chain reaction (PCR) assay to determine 'Ca. L. asiaticus' infection status. The incidence of 'Ca. L. asiaticus'-infected trees (presymptomatic: 'Ca. L. asiaticus'+, visually negative; and symptomatic: 'Ca. L. asiaticus'+, visually positive) trees was 89% for the Hamlin block and 88% for the Valencia block. 'Ca. L. asiaticus'+ trees had 30 and 37% lower fibrous root mass density for presymptomatic and symptomatic trees, respectively, compared with 'Ca. L. asiaticus'- trees. In a second survey, 10- to 25-year-old Valencia trees on Swingle citrumelo or 'Carrizo' citrange (C. sinensis (L.) × P. trifoliata) rootstock were sampled within 3 to 6 months after identification of visual HLB status as symptomatic ('Ca. L. asiaticus'+, visually positive) or nonsymptomatic ('Ca. L. asiaticus'-, visually negative) in orchards located in the central ridge, south-central, and southwest flatwoods. Pairs of HLB symptomatic and nonsymptomatic trees were evaluated for PCR status, fibrous root mass density, and Phytophthora nicotianae propagules in the rhizosphere soil. 'Ca. L. asiaticus'+ trees had 27 to 40% lower fibrous root mass density and, in one location, higher P. nicotianae per root but Phytophthora populations per cubic centimeter of soil were high on both 'Ca. L. asiaticus'+ and 'Ca. L. asiaticus'- trees. Fibrous root loss from HLB damage interacted with P. nicotianae depending on orchard location and time of year.

An improved regulatory sampling method for mapping and representing plant disease from a limited number of samples.

A key challenge for plant pathologists is to develop efficient methods to describe spatial patterns of disease spread accurately from a limited number of samples. Knowledge of disease spread is essential for informing and justifying plant disease management measures. A mechanistic modelling approach is adopted for disease mapping which is based on disease dispersal gradients and consideration of host pattern. The method is extended to provide measures of uncertainty for the estimates of disease at each host location. In addition, improvements have been made to increase computational efficiency by better initialising the disease status of unsampled hosts and speeding up the optimisation process of the model parameters. These improvements facilitate the practical use of the method by providing information on: (a) mechanisms of pathogen dispersal, (b) distance and pattern of disease spread, and (c) prediction of infection probabilities for unsampled hosts. Two data sets of disease observations, Huanglongbing (HLB) of citrus and strawberry powdery mildew, were used to evaluate the performance of the new method for disease mapping. The result showed that our method gave better estimates of precision for unsampled hosts, compared to both the original method and spatial interpolation. This enables decision makers to understand the spatial aspects of disease processes, and thus formulate regulatory actions accordingly to enhance disease control.

Estimating the incidence of an epidemic when it is first discovered and the design of early detection monitoring.

The early detection of an invading epidemic is crucial for successful disease control. Although models have been used extensively to test control strategies following the first detection of an epidemic, few studies have addressed the issue of how to achieve early detection in the first place. Moreover, sampling theory has made great progress in understanding how to estimate the incidence or spatial distribution of an epidemic but how to sample for early detection has been largely ignored. Using a simple epidemic model we demonstrate a method to calculate the incidence of an epidemic when it is discovered for the first time (given a monitoring programme taking samples at regular intervals). We use the method to explore how the intensity and frequency of sampling influences early detection. In particular, we find that for epidemics characterised by high population growth rates it is most effective to spread sampling resources evenly in time. In addition we derive a useful approximation to our method which results in a simple equation capturing the relation between monitoring and epidemic dynamics. Not only does this provide valuable new insight but it provides a simple rule of thumb for the design of monitoring programmes in practice.

Beam purification by photodetachment (invited).

Ion beam purity is of crucial importance to many basic and applied studies in nuclear science. Selective photodetachment has been proposed to suppress unwanted species in negative ion beams while preserving the intensity of the species of interest. A highly efficient technique based on photodetachment in a gas-filled radio frequency quadrupole ion cooler has been demonstrated. In off-line experiments with stable ions, up to 10(4) times suppression of the isobar contaminants in a number of interesting radioactive negative ion beams has been demonstrated. For selected species, this technique promises new experimental possibilities in studies on exotic nuclei, accelerator mass spectrometry, and fundamental properties of negative atomic and molecular ions.

Laser ion source development at Holifield Radioactive Ion Beam Facility.

This report describes the efforts made to develop a resonant-ionization laser ion source based on tunable Ti:sapphire lasers for nuclear physics and astrophysics research at Holifield Radioactive Ion Beam Facility. Three Ti:sapphire lasers have been upgraded with individual pump lasers to eliminate laser power losses due to synchronization delays. Ionization schemes for 14 elements have been obtained. Off-line studies show that the overall efficiency of the laser ion source can be as high as 40%. TaC surface coatings have been investigated for minimizing surface and bulk trapping of the atoms of interest.

Transmission of Citrus leprosis virus C by Brevipalpus phoenicis (Geijskes) to Alternative Host Plants Found in Citrus Orchards.

The equivalent of US$75 million is spent each year in Brazil to control Brevipalpus phoenicis, a mite vector of Citrus leprosis virus C (CiLV-C). In this study, we investigated the possibility that hedgerows and windbreaks normally found in citrus orchards could host CiLV-C. Mites confined by an adhesive barrier were reared on sweet orange fruit with leprosis symptoms then were transferred to leaves of Hibiscus rosa-sinensis, Malvaviscus arboreus, Grevilea robusta, Bixa orellana, and Citrus sinensis. Ninety days post infestation, the descendant mites were transferred to Pera sweet orange plants to verify the transmissibility of the virus back to citrus. Nonviruliferous mites which had no feeding access to diseased tissue were used as controls. Local chlorotic or necrotic spots and ringspots, symptoms of leprosis disease, appeared in most plants tested. Results generated by reversetranscription polymerase chain reaction with primers specific for CiLV-C and by electron microscope analyses confirmed the susceptibility of these plants to CiLV-C.

The anal fistula claw: the OTSC clip for anal fistula closure.

AIM: Surgical closure of high or complex anal fistulae is often a difficult challenge. A special Nitinol clip, the OTSC clip (Ovesco AG), was evaluated for fistula closure in a porcine model. METHOD: A total of 20 fistulae were created in 10 animals by seton insertion. Four weeks after fistula induction the setons were removed: one internal fistula opening per animal was left untreated as control whereas the other opening was closed by the OTSC clip using a specially developed transanal clip applicator. The safety and technical feasibility of the clip application were tested. Another 4 weeks later, fistulae were macroscopically assessed for closure. For histological examination, the anorectum including the fistula tract was excised en bloc. RESULTS: Four weeks after clip placement, all external and internal fistula openings were macroscopically closed. The clip application site presented with an increased scarring. Microscopically, 40% of residual tracts and a more intense chronic inflammation were seen in the untreated control fistulae. After clip placement, 10% of the fistulae persisted associated with a higher density of collagen fibres indicating a better fistula scarring and healing. No unexpected side-effects or complications caused by the clip were observed. CONCLUSION: Fistula closure using the OTSC clip represents a promising sphincter-preserving minimally invasive procedure. This study demonstrated the safety and feasibility of the 'anal fistula claw' for fistula closure. In spite of limitations of the porcine model the results justify clinical applications and further investigations.

A stochastic optimization method to estimate the spatial distribution of a pathogen from a sample.

Information on the spatial distribution of plant disease can be utilized to implement efficient and spatially targeted disease management interventions. We present a pathogen-generic method to estimate the spatial distribution of a plant pathogen using a stochastic optimization process which is epidemiologically motivated. Based on an initial sample, the method simulates the individual spread processes of a pathogen between patches of host to generate optimized spatial distribution maps. The method was tested on data sets of Huanglongbing of citrus and was compared with a kriging method from the field of geostatistics using the well-established kappa statistic to quantify map accuracy. Our method produced accurate maps of disease distribution with kappa values as high as 0.46 and was able to outperform the kriging method across a range of sample sizes based on the kappa statistic. As expected, map accuracy improved with sample size but there was a high amount of variation between different random sample placements (i.e., the spatial distribution of samples). This highlights the importance of sample placement on the ability to estimate the spatial distribution of a plant pathogen and we thus conclude that further research into sampling design and its effect on the ability to estimate disease distribution is necessary.

Some consequences of using the Horsfall-Barratt scale for hypothesis testing.

Comparing treatment effects by hypothesis testing is a common practice in plant pathology. Nearest percent estimates (NPEs) of disease severity were compared with Horsfall-Barratt (H-B) scale data to explore whether there was an effect of assessment method on hypothesis testing. A simulation model based on field-collected data using leaves with disease severity of 0 to 60% was used; the relationship between NPEs and actual severity was linear, a hyperbolic function described the relationship between the standard deviation of the rater mean NPE and actual disease, and a lognormal distribution was assumed to describe the frequency of NPEs of specific actual disease severities by raters. Results of the simulation showed standard deviations of mean NPEs were consistently similar to the original rater standard deviation from the field-collected data; however, the standard deviations of the H-B scale data deviated from that of the original rater standard deviation, particularly at 20 to 50% severity, over which H-B scale grade intervals are widest; thus, it is over this range that differences in hypothesis testing are most likely to occur. To explore this, two normally distributed, hypothetical severity populations were compared using a t test with NPEs and H-B midpoint data. NPE data had a higher probability to reject the null hypothesis (H0) when H0 was false but greater sample size increased the probability to reject H0 for both methods, with the H-B scale data requiring up to a 50% greater sample size to attain the same probability to reject the H0 as NPEs when H0 was false. The increase in sample size resolves the increased sample variance caused by inaccurate individual estimates due to H-B scale midpoint scaling. As expected, various population characteristics influenced the probability to reject H0, including the difference between the two severity distribution means, their variability, and the ability of the raters. Inaccurate raters showed a similar probability to reject H0 when H0 was false using either assessment method but average and accurate raters had a greater probability to reject H0 when H0 was false using NPEs compared with H-B scale data. Accurate raters had, on average, better resolving power for estimating disease compared with that offered by the H-B scale and, therefore, the resulting sample variability was more representative of the population when sample size was limiting. Thus, there are various circumstances under which H-B scale data has a greater risk of failing to reject H0 when H0 is false (a type II error) compared with NPEs.

The effect of landscape pattern on the optimal eradication zone of an invading epidemic.

A number of high profile eradication attempts on plant pathogens have recently been attempted in response to the increasing number of introductions of economically significant nonnative pathogen species. Eradication programs involve the removal of a large proportion of a host population and can thus lead to significant social and economic costs. In this paper we use a spatially explicit stochastic model to simulate an invading pathogen and show that it is possible to identify an optimal control radius, i.e., one that minimizes the total number of hosts removed during an eradication campaign that is effective in eradicating the pathogen. However, by simulating the epidemic and eradication processes in multiple landscapes, we demonstrate that the optimal radius depends critically on landscape pattern (i.e., the spatial configuration of hosts within the landscape). In particular, we find that the optimal radius, and also the number of host removals associated with it, increases with both the level of aggregation and the density of hosts in the landscape. The result is of practical significance and demonstrates that the location of an invading epidemic should be a key consideration in the design of future eradication strategies.

Time profile of ion pulses produced in a hot-cavity laser ion source.

The time spreads of Mn ions produced by three-photon resonant ionization in a hot-cavity laser ion source are measured. A one-dimensional ion-transport model is developed to simulate the observed ion time structures. Assuming ions are generated with a Maxwellian velocity distribution and are guided by an axial electric field, the predictions of the model agree reasonably well with the experimental data and suggest that the ions are radially confined in the ion source and a substantial fraction of the ions in the transport tube are extracted.

The laser ion source trap for highest isobaric selectivity in online exotic isotope production.

The improvement in the performance of a conventional laser ion source in the laser ion source and trap (LIST) project is presented, which envisages installation of a repeller electrode and a linear Paul trap/ion guide structure. This approach promises highest isobaric purity and optimum temporal and spatial control of the radioactive ion beam produced at an online isotope separator facility. The functionality of the LIST was explored at the offline test separators of University of Mainz (UMz) and ISOLDE/CERN, using the UMz solid state laser system. Ionization efficiency and selectivity as well as time structure and transversal emittance of the produced ion beam was determined. Next step after complete characterization is the construction and installation of the radiation-hard final trap structure and its first online application.

Ion production from solid state laser ion sources.

Laser ion sources based on resonant excitation and ionization of atoms are well-established tools for selective and efficient production of radioactive ion beams. Recent developments are focused on the use of the state-of-the-art all solid-state laser systems. To date, 35 elements of the periodic table are available from laser ion sources based on tunable Ti:sapphire lasers. Recent progress in this field regarding the establishment of suitable optical excitation schemes for Ti:sapphire lasers are reported.

GISELE: a resonant ionization laser ion source for the production of radioactive ions at GANIL.

SPIRAL2 is the new project under construction at GANIL to produce radioactive ion beams and in particular neutron rich ion beams. For the past 10 yr SPIRAL1 at GANIL has been delivering accelerated radioactive ion beams of gases. Both facilities now need to extend the range of radioactive ion beams produced to condensable elements. For that purpose, a resonant ionization laser ion source, funded by the French Research National Agency, is under development at GANIL, in collaboration with IPN Orsay, University of Mainz (Germany) and TRIUMF, Vancouver (Canada). A description of this project called GISELE (GANIL Ion Source using Electron Laser Excitation) is presented.

Wind Speed Effects on the Quantity of Xanthomonas citri subsp. citri Dispersed Downwind from Canopies of Grapefruit Trees Infected with Citrus Canker.

The epidemic of citrus canker (Xanthomonas citri subsp. citri) in Florida continues to expand since termination of the eradication program in 2006. Storms are known to be associated with disease spread, but little information exists on the interaction of fundamental physical and biological processes involved in dispersal of this bacterium. To investigate the role of wind speed in dispersal, wind/rain events were simulated using a fan to generate wind up to 19 m·s-1 and spray nozzles to simulate rain. Funnels at ground level and panels at 1.3 m height and distances up to 5 m downwind collected wind-driven splash. Greater wind speeds consistently dispersed more bacteria, measured by concentration (colony forming units [CFU] ml-1) or number sampled (bacteria flux density [BFD] = bacteria cm-2 min-1), from the canopy in the splash. The CFU ml-1 of X. citri subsp. citri collected by panels 1 m downwind at the highest wind speed was up to 41-fold greater than that collected at the lowest wind speed. BFD at the highest wind speed was up to 884-fold higher than that collected at the lowest wind speed. Both panels at distances >1 m and funnels at distances >0 m collected many-fold more X. citri subsp. citri at higher wind speeds compared to no wind (up to 1.4 × 103-fold greater CFU ml-1 and 1.8 × 105-fold the BFD). The resulting relationship between wind speed up to 19 m·s-1 and the mean CFU ml-1 collected by panel collectors downwind was linear and highly significant. Likewise, the mean CFU ml-1 collected from the funnel collectors had a linear relationship with wind speed. The relationship between wind speed and BFD collected by panels was generally similar to that described for CFU ml-1 of X. citri subsp. citri collected. However, BFD collected by funnels was too inconsistent to determine a meaningful relationship with increasing wind speed. The quantity of bacteria collected by panels declined with distance, and the relationship was described by an inverse power model (R2 = 0.94 to 1.00). At higher wind speeds, more bacteria were dispersed to all distances. Windborne inoculum in splash in subtropical wet environments is likely to be epidemiologically significant, as both rain intensity and high wind speed can interact to provide conditions conducive for dispersing large quantities of bacteria from canker-infected citrus trees. Disease and crop management aimed at reducing sources of inoculum and wind speeds in a grove should help minimize disease spread by windborne inoculum.