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Huanglongbing (HLB) is one of the most devastating citrus diseases worldwide. It is associated with the non-culture bacteria Candidatus Liberibacter spp., which can be transmitted by grafting and/or the psyllid vectors Diaphorina citri (ACP) and Trioza erytreae (AfCP). Although HLB has not been reported in the Mediterranean Basin to date, both vectors are present, and thus represent a serious threat to the citrus industry in this region. Resistant citrus cultivars or effective therapeutic treatments are not currently available for HLB. Nevertheless, area-wide pest management via coordinated management efforts over large areas has been implemented in Brazil, China and the USA for HLB control. This study proposes an open access flexible methodology to address area-wide management of both HLB vectors in the Mediterranean Basin. Based on a risk-based approach which considers climatic information and other variables that may influence vector introduction and spread, such as conventional, organic, abandoned and residential citrus areas as well as transportation corridors, an area-wide management division in pest management areas (PMAs) is proposed. The size and location of these PMAs were estimated by means of a hierarchical clustering algorithm with spatial constraints whose performance was assessed under different configuration scenarios. This proposal may assist policymakers and the citrus industry of the citrus-growing areas of the Mediterranean Basin in risk management planning in the case of the spread of HLB vectors or a possible introduction of the disease. Additionally, it may be a valuable resource to inform opinion dynamic models, enabling the identification of pivotal factors for the success of control measures. [ABSTRACT FROM AUTHOR]

The dynamics of airborne ascospores and disease progress of red leaf blotch (RLB) of almond, caused by Polystigma amygdalinum, and their correlations with weather variables were studied from 2019 to 2021 in two almond orchards located in Lleida, NE Spain. Airborne ascospores were detected and quantified by real‐time qPCR using species‐specific primers for P. amygdalinum. Ascospores were detected mainly from April to June, with a high variability between the yearly cumulative concentrations. Positive significant correlations were found between the weekly proportion of airborne ascospores and the number of wet and mild days—either combined or separated— accumulated rainfall, number of rainy days, accumulated low temperatures on wet days, and mean and maximum relative humidity. In contrast, several thermal variables (maximum temperature, VPD, and number of warm days) were negatively correlated with ascospore catches. Positive significant correlations were found between the cumulative proportion of ascospores and RLB incidence and severity. Weekly variations in RLB incidence and severity showed significant positive correlations with the number of warm days while negative with the number of mild days. Severity was also positively correlated with several thermal variables (mean, maximum, and minimum temperature, and VPD), and negatively correlated with the number of cold days and wet and mild days. Stronger correlations were generally found with ascospore catches or disease progress when using concurrent weekly weather data. Gompertz, monomolecular, and logistic growth models were evaluated to describe RLB disease progress. [ABSTRACT FROM AUTHOR]

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for Lopholeucaspis japonica is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/lopholeucaspis-japonica [ABSTRACT FROM AUTHOR]

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for Oemona hirta is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/oemona-hirta [ABSTRACT FROM AUTHOR]

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for Eotetranychus lewisi is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/eotetranychus-lewisi. [ABSTRACT FROM AUTHOR]

Biochar is a promising material used for multiple remediation approaches, mainly in polluted soils. Its properties can differ depending on feedstock and pyrolysis temperature. In this context, we tested the capacity of three biochar products made from corncob, pyrolyzed at different temperatures (350, 500, and 650 °C), to remediate a mining soil affected by high levels of Cu and As. We performed an exhaustive characterization of the biochar. We found that biochar showed a higher surface area with increasing pyrolysis temperature, whereas high molecular weight PAHs were detected in biochar produced at the maximum temperature, thus indicating potential ecotoxicological risks. After the application of biochar to the soil, Cu was partially immobilized, especially when using that obtained at 500 °C. This effect is attributed to the structure of this material and an increase in soil pH and organic matter content. Conversely, As was increased in the soluble fraction for all three types of biochar but in a proportion that lacks relevance. On the whole, given its lower PAH content, higher Cu immobilization ratio, and an almost negligible increase in As availability, biochar obtained at 500 °C outperformed the other two products with respect to soil recovery. Of note, data on Cu and As availability were doubled-checked using two extraction methodologies. We propose that this operational approach for determining the most suitable pyrolysis temperature will find application in other soil remediation actions. [ABSTRACT FROM AUTHOR]

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for citrus leprosis viruses is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/citrus-leprosis-viruses [ABSTRACT FROM AUTHOR]

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Citrus black spot (CBS), caused by the fungus Phyllosticta citricarpa, is associated with serious yield and quality losses. The climate suitability of the Mediterranean Basin for CBS development has been long debated. However, CBS has been described in Tunisia. In this study, a generic model was used to simulate potential infections by ascospores and pycnidiospores together with a degree-day model to predict the onset of ascospore release. High-resolution climatic data were retrieved from the ERA5-Land dataset for the citrus-growing regions in the Mediterranean Basin and other locations where CBS is present. In general, the onset of ascospore release was predicted to occur late in spring, but there is no agreement on the adequacy of this empirical model for extrapolation to the Mediterranean Basin. The generic model indicated that infections by ascospores and pycnidiospores would be concentrated mainly in autumn, as well as in spring for pycnidiospores. In contrast to previous studies, the percentage of hours suitable for infection was higher for pycnidiospores than for ascospores. The values obtained with the generic infection model for Tunisia and several CBS-affected locations worldwide were similar to those for other citrus-growing regions in Europe and Northern Africa. These results support previous work indicating that the climate of the Mediterranean Basin is suitable for CBS development. [ABSTRACT FROM AUTHOR]

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for Elsinoë australis, E. citricola and E. fawcettii is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/elsinoe-australis-citricola-fawcettii [ABSTRACT FROM AUTHOR]

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for Pseudocercospora angolensis is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/pseudocercospora-angolensis [ABSTRACT FROM AUTHOR]

Survival analysis is one of the most important fields of statistics in medicine and biological sciences. In addition, the computational advances in the last decades have favored the use of Bayesian methods in this context, providing a flexible and powerful alternative to the traditional frequentist approach. The objective of this article is to summarize some of the most popular Bayesian survival models, such as accelerated failure time, proportional hazards, mixture cure, competing risks, multi-state, frailty, and joint models of longitudinal and survival data. Moreover, an implementation of each presented model is provided using a BUGS syntax that can be run with JAGS from the R programming language. Reference to other Bayesian R-packages is also discussed. [ABSTRACT FROM AUTHOR]

Fully Bayesian methods for Cox models specify a model for the baseline hazard function. Parametric approaches generally provide monotone estimations. Semi‐parametric choices allow for more flexible patterns but they can suffer from overfitting and instability. Regularization methods through prior distributions with correlated structures usually give reasonable answers to these types of situations. We discuss Bayesian regularization for Cox survival models defined via flexible baseline hazards specified by a mixture of piecewise constant functions and by a cubic B‐spline function. For those "semi‐parametric" proposals, different prior scenarios ranging from prior independence to particular correlated structures are discussed in a real study with microvirulence data and in an extensive simulation scenario that includes different data sample and time axis partition sizes in order to capture risk variations. The posterior distribution of the parameters was approximated using Markov chain Monte Carlo methods. Model selection was performed in accordance with the deviance information criteria and the log pseudo‐marginal likelihood. The results obtained reveal that, in general, Cox models present great robustness in covariate effects and survival estimates independent of the baseline hazard specification. In relation to the "semi‐parametric" baseline hazard specification, the B‐splines hazard function is less dependent on the regularization process than the piecewise specification because it demands a smaller time axis partition to estimate a similar behavior of the risk. [ABSTRACT FROM AUTHOR]

At the request of the European Commission, EFSA has prepared these specific guidelines to guide the surveyor through the design of statistically sound and risk‐based surveys for Agrilus planipennis, integrating the key biological information. Based on examples, three different survey designs are simulated: (i) detection surveys to substantiate pest freedom, (ii) delimiting surveys to determine the boundaries of an infested zone, and (iii) buffer zone surveys to monitor a zone that ensures pest detection at low prevalence. The first step of the survey design consists of defining the objectives of the survey, characterising the host plant population and the methods used to detect the pest.The corresponding survey parameters are set while taking into account the importance of the underlying assumptions. The robustness of the survey conclusions will depend on the quality of the information used in this first step. The second step of the survey design consists of the sample size (i.e. number of traps) estimation using the survey parameters as inputs tothe proposed statistical tool (EFSA RiBESS+). The final step of the survey design is the allocation of the sample size in the survey area which depends on the available information about the target population and risk factors. The proposed methodology allows surveys to be compared across time and space, thus contributing to the harmonisation ofA. planipennissurveillance across the EU. The flexible approach allows surveys to be tailored to the specific situation in a Member State, taking into account the ash tree distribution and available resources. Thesuccess of a good survey design relies on the survey preparation and on the involvement of the risk managers. [ABSTRACT FROM AUTHOR]

At the request of the European Commission, EFSA prepared the general guidelines for surveys of plant pests, describing the legal, international and scientific context in which the surveys are designed, the basic principles implemented for surveillance of quarantine pests and introducing the concepts needed for the design of statistically sound and risk‐based surveys. Three types of specific surveys are addressed: detection surveys for substantiation of pest freedom, delimiting surveys for determining the boundaries of an infested zone, and monitoring surveys for prevalence estimation when measuring the progress of eradication measures or for confirming a low pest prevalence area. For each survey, the survey parameters are introduced and their interactions analysed showing the importance of the assumptions that are taken for each one of them: (i) the aims of the survey are defined as the confidence of detectinga given pest prevalence(design prevalence), this reflects the trade‐off between the acceptable level of the risk and availability of resources that determine the strength of the evidence to support the conclusion of the survey;(ii) the target populationis addressed in terms of its structure and size,including the risk factors;and (iii) the method sensitivityis defined as the combination of the sampling effectiveness and the diagnostic sensitivity. EFSA's RiBESS+ tool is introduced for calculating the sample size using the survey parameters as input values for a statistically sound and risk‐based survey design. The mathematical principles behind the tool are in line with the International Standards for Phytosanitary Measures. The survey design is flexible and can be tailored to each pest and specific situation in the Member States. Once the survey is implemented following this approach, the conclusions allow surveys to be compared across time and space, contributing to the harmonisation of surveillance activities across the EU Member States. [ABSTRACT FROM AUTHOR]

At the request of the European Commission, EFSA prepared these specific guidelines to guide the surveyor through the design of statistically sound and risk‐based surveys for Phyllosticta citricarpa, integrating the key biological information. Based on examples, three different survey designs are simulated:(i) detection surveys to substantiate pest freedom, (ii) delimiting surveys to determine the boundaries of an infested zone, and (iii) buffer zone surveys to monitor a zone ensuring pest detection at low levels of prevalence.The first step of the survey design consists of setting the goals of the survey, characterising the host plant population and the methods used to identify the pest. All survey parameters are quantified taking into accountthe importance of the related assumptions. The more accurateand robust the information used for selecting and estimating the survey parameters, the more robust the conclusions of the survey will be. The second step of the survey design consists of the sample size (i.e. number of trees)calculation using the survey parameters as inputs of the proposed statistical tool (EFSA RiBESS+).The last step of the survey design is the allocation of the samples in the survey area which depends on the information available on the target population and risk factors. The robustness of the conclusions of surveys designed using the proposed approaches strongly depends on the survey preparation. The methodology proposed allows surveys to be compared across time and space, thus contributing to the harmonisation of the P.citricarpasurveys across the EU. The extremely flexible approach allows the surveys to be tailored to each specific situation in the Member States, taking into account the citrus tree distribution and available resources. The success of a good survey design relies on the technical aspects of the survey preparation and on the involvement of the risk managers. [ABSTRACT FROM AUTHOR]

At the request of the European Commission, EFSA prepared specific guidelines for the survey of Xylella fastidiosa to guide the survey or through the design of statistically sound and risk‐based surveys, integrating the key biological information. Based on examples, three different survey designs are simulated: detection surveys to substantiate pest freedom, delimiting surveys to determine the boundaries of an infested zone, and buffer zone surveys to monitor a zone ensuring pest detection at a low level of prevalence. The first step of the survey design consists of setting out the aims of the survey, characterising the host plant population and the methods used to identify the pest. All the survey parameters are quantified considering the importance of the related assumptions. The more accurate the information used to select/estimate the survey parameters, the more robust the conclusions of the survey will be. The second step of the survey design consists of the sample‐size calculation using the survey parameters as inputs forthe statistical tool (RiBESS+). The last step of the survey design is the allocation of the samples in the survey area, the method for which depends on the information available on the target population and risk factors. The robustness of the conclusions of surveys designed using these approaches depends strongly on the survey preparation. The methodology here proposed allows surveys to be compared across time and space, thus contributing to harmonisation of the X. fastidiosa surveys in the EU Member States. The extremely flexible approaches allow surveys to be tailored to each specific situation in the Member States, taking into account the host plants, vectors, climate suitability and resources available. The success of a good survey design relies on technical aspects of the survey preparation and on the involvement of the risk managers. [ABSTRACT FROM AUTHOR]

Background: The use of topically applied hemostatic substances during surgery has become a common practice. In some cases, the material is not absorbed or induces a granulomatous reaction resulting in a pseudotumoral lesion. With imaging studies, it is not possible to differentiate this from a tumor recurrence or abscess. This study describes the authors' cytologic experience with a large series of pseudotumoral lesions induced by oxidized cellulose, one of the most commonly used hemostatic agents. Almost no cytologic descriptions are available in the medical literature. Methods: Sixteen patients were evaluated, and the most common sites of fine‐needle aspiration (FNA) were the mediastinum and thyroid surgical bed. Other locations were the axilla, neck, vulva, liver, and retroperitoneum. All these lesions appeared after surgical procedures in which oxidized cellulose was used as a topical hemostatic agent. The interval time between surgery and FNA varied from 4 to 46 months with a mean of 15 months. Results: Cytology samples showed very similar findings. In all cases, foreign‐body material with a variable granulomatous reaction was present. Oxidized cellulose was seen as laminated inorganic fragments and most often showed an elongated, quadrangular appearance. Amorphous, ill‐defined fragments as well as a dense proteinaceous background with phagocytic cells were also present. Conclusions: The current study demonstrates that FNA cytology is a very useful method for the detection of pseudotumoral lesions induced by hemostatic agents. Pathologists must be familiarized with this finding because cytology permits easy differentiation from tumor recurrence. Complications such as delayed absorption and foreign‐body granulomatous reactions associated with the use of oxidized cellulose hemostatic agents are easily recognized via fine‐needle aspiration cytology. Cytologic findings are characteristic and permit easy differentiation from tumor recurrence. [ABSTRACT FROM AUTHOR]

Non-communicable diseases (NCDs) account for the five largest contributors to burden of disease in Mexico, with diabetes representing the greatest contributor. However, evidence supporting chronic disease programmes in Mexico is limited, especially in rural communities. Compañeros En Salud (CES) partnered with the Secretariat of Health of Chiapas, Mexico to implement a novel community-based NCD treatment programme. We describe the implementation of this programme and conducted a population-based, retrospective analysis, using a difference-in-differences regression approach to estimate the impact of the programme. Specifically, we examined changes in diabetes and hypertension control rates between 2014 and 2016, comparing CES intervention clinics (n = 9) to care-as-usual at non-CES clinics (n = 806), adjusting for differences in facility-level characteristics. In 2014, the percent of diabetes patients with this condition under control was 36.9% at non-CES facilities, compared with 41.3% at CES facilities (P > 0.05). For hypertension patients, these figures were 45.2% at non-CES facilities compared with 56.2% at CES facilities (P = 0.02). From 2014 to 2016, the percent of patients with diabetes under control declined by 9.2% at non-CES facilities, while improving by 11.3% at non-CES facilities where the Compañeros En Salud Programa de Enfermedades Crónicas intervention was implemented (P < 0.001). Among hypertension patients, those with the condition under control increased by 21.5% at non-CES facilities between 2014 and 2016, compared with 16.2% at CES facilities (P > 0.05). Introduction of the CES model of NCD care was associated with significantly greater improvements in diabetes management between 2014 and 2016, compared with care-as-usual. Hypertension control measures were already greater at CES facilities in 2014, a difference that was maintained through 2016. These findings highlight the successful implementation of a framework for providing NCD care in rural Mexico, where a rapidly increasing NCD disease burden exists. [ABSTRACT FROM AUTHOR]

Purpose: The presence of high concentrations of trace elements (TEs) in mine soils like those in the Sierra Minera of La Unión-Cartagena (SE Spain) limits the development of a vegetation cover on such sites, and pollution dispersion by water and wind erosion represents a serious risk for the surrounding ecosystems. The aim of this study was to evaluate different phytostabilisation procedures based on the co-culture of a legume ( Bituminaria bituminosa) and a high-biomass ( Piptatherum miliaceum) species for this type of soils. Materials and methods: A pot experiment was carried out where B. bituminosa was tested as a soil pre-treatment strategy. Five different procedures were followed to study the growth stimulation or competition of both species in a contaminated soil from the Sierra Minera: (i) sowing of P. miliaceum without B. bituminosa (control treatment), (ii) sowing of P. miliaceum for co-cultivation of both species, (iii) sowing of P. miliaceum and co-cultivation of both species in soil with compost, (iv) harvesting and elimination of the aerial part of the plants before sowing of P. miliaceum and (v) harvesting and incorporation to the soil of the aerial part of B. bituminosa before sowing of P. miliaceum. Results and discussion: The results showed that the co-culture of both species favoured the growth of P. miliaceum, whilst incorporating the aerial part of the legume to the soil increased nitrogen concentration in P. miliaceum but reduced its growth. The use of compost improved both the growth and N uptake of P. miliaceum and did not inhibit nodulation in B. bituminosa. TE extractability in the soils and accumulation in the plants were rather low and very little affected by the addition of the amendments or by co-culture of species. Conclusions: Nitrogen availability plays an important role in P. miliaceum growth in TE-contaminated mine soils. The addition of compost together with legume cultivation is proposed as an effective combination for the cultivation of P. miliaceum in these soils, as both plant growth and soil conditions were improved following this procedure. [ABSTRACT FROM AUTHOR]

Diseases of fruit and foliage caused by fungi and oomycetes are generally controlled by the application of fungicides. The use of decision support systems (DSSs) may assist to optimize fungicide programs to enhance application on the basis of risk associated with disease outbreak. Case-by-case evaluations demonstrated the performance of DSSs for disease control, but an overall assessment of the efficacy of DSSs is lacking. A literature review was conducted to synthesize the results of 67 experiments assessing DSSs. Disease incidence data were obtained from published peer-reviewed field trials comparing untreated controls, calendar-based and DSS-based fungicide programs. Two meta-analysis generic models, a "fixed-effects" vs. a "random-effects" model within the framework of generalized linear models were evaluated to assess the efficacy of DSSs in reducing incidence. All models were fit using both frequentist and Bayesian estimation procedures and the results compared. Model including random effects showed better performance in terms of AIC or DIC and goodness of fit. In general, the frequentist and Bayesian approaches produced similar results. Odds ratio and incidence ratio values showed that calendar-based and DSS-based fungicide programs considerably reduced disease incidence compared to the untreated control. Moreover, calendar-based and DSS-based programs provided similar reductions in disease incidence, further supporting the efficacy of DSSs. [ABSTRACT FROM AUTHOR]

This pest survey card was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2017‐0137), at the request of the European Commission. The purpose of the document is to assist the Member States to plan annual survey activities of quarantine organisms using a statistically sound and risk‐based pest survey approach, in line with current international standards. The data requirements for such an activity include the pest distribution, its host range, its biology and risk factors, as well as available detection and identification methods. This document is part of a toolkit that consists of pest‐specific documents, such as the pest survey cards, and generic documents relevant for all pests to be surveyed, including the general survey guidelines and statistical software such as RiBESS+. [ABSTRACT FROM AUTHOR]