Performance of outbreak management plans for emerging plant diseases: the case of almond leaf scorch caused by Xylella fastidiosa in mainland Spain.

Outbreak response to quarantine pathogens and pests in the European Union (EU) is regulated by the EU Plant Health Law, but the performance of outbreak management plans in terms of their effectiveness and efficiency has been quantified only to a limited extent. As a case study, the disease dynamics of almond leaf scorch, caused by Xylella fastidiosa (Xf), in the affected area of Alicante, Spain, were approximated using an individual-based spatial epidemiological model. The emergence of this outbreak was dated based on phylogenetic studies, and official surveys were used to delimit the current extent of the disease. Different survey strategies and disease control measures were compared to determine their effectiveness and efficiency for outbreak management in relation to a baseline scenario without interventions. One-step and two-step survey approaches were compared with different confidence levels, buffer zone sizes and eradication radii, including those set by the EU legislation for Xf. The effect of disease control interventions was also considered by decreasing the transmission rate in the buffer zone. All outbreak management plans reduced the number of infected trees (effectiveness) but large differences were observed in the number of susceptible trees not eradicated (efficiency). The two-step survey approach and high confidence level increased the efficiency, while also reducing the transmission rate. Only the outbreak management plans with the two-step survey approach removed infected trees completely, but they required greater survey efforts. Although control measures reduced disease spread, surveillance was the key factor in the effectiveness and efficiency of the outbreak management plans.

Modeling the Airborne Inoculum of Polystigma amygdalinum to Optimize Fungicide Programs Against Almond Red Leaf Blotch.

Red leaf blotch (RLB) of almond, caused by the ascomycete Polystigma amygdalinum, is a severe foliar disease endemic in the Mediterranean Basin and Middle East. Airborne ascospores of P. amygdalinum were monitored from 2019 to 2021 in two almond orchards in Lleida, Spain, and a Bayesian beta regression was used to model its seasonal dynamics. The selected model incorporated accumulated degree-days (ADD), ADD considering both vapor pressure deficit and rainfall as fixed effects, and a random effect for the year and location. The performance of the model was evaluated in 2022 to optimize RLB fungicide programs by comparing the use of model predictions and action thresholds with the standard program. Two variants were additionally considered in each program to set the frequency between applications, based on (i) a fixed frequency of 21 days or (ii) specific meteorological criteria (spraying within 7 days after rainfalls greater than 10 mm, with daily mean temperatures between 10 and 20°C, and with a minimum frequency of 21 days between applications). Programs were evaluated in terms of RLB incidence and number of applications. The program based on the model with periodic fungicide applications was similarly effective as the standard program, resulting only in a 2.6% higher RLB incidence but with fewer applications (three to four, compared with seven in the standard program). When setting the frequency between applications by using the meteorological criteria, a higher reduction in the number of applications (two to three) was observed, while RLB incidence increased by roughly 16% in both programs. Therefore, the model developed in this study may represent a valuable tool toward a more sustainable fungicide schedule for the control of almond RLB in northeast Spain.

Bayesian survival analysis with BUGS.

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.

Bayesian regularization for flexible baseline hazard functions in Cox survival models.

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.

Arsenic adsorption and plant availability in an agricultural soil irrigated with As-rich water: Effects of Fe-rich amendments and organic and inorganic fertilisers.

The use of As-rich water for irrigation in agricultural soils may result in As accumulation in soil and crops, with the consequent risk of its entry into the food chain. The effectiveness of three different Fe-based materials (a commercial iron oxide (Bayoxide®), lamination slag (a by-product of the hot rolling of steel) and a commercial red mud derivative (ViroBind™)) used as soil amendments to minimise the impact of irrigation with As-rich water in an agricultural soil-plant system was evaluated in a pot experiment. Simultaneously, the influence of organic and inorganic fertilisation (olive oil mill waste compost versus NPK fertiliser) on the effectiveness of iron oxide in As adsorption processes was also assessed. The As adsorption capacity of the amendments was determined in a preliminary batch experiment using sorption isotherms. Then, a pot experiment was carried out in a growth chamber using an agricultural soil (arenosol) from Segovia province (central Spain), amended with the different materials, in which Lactuca sativa (lettuce) was grown for two months. The As adsorption capacity was higher in the commercial iron oxide and in the red mud derivative, which fitted the Freundlich model (no saturation), than in the lamination slag, which fitted the Langmuir model (limited adsorption). All the materials decreased the pore water As concentration compared to the control (by 29-80%), but only iron oxide reduced As availability in the soil, and none of the amendments decreased the As concentration in plant leaves. The combination of iron oxide and compost did not significantly improve plant growth, but increased nutrients (N, K, Ca, Na and Mg) concentrations and availability in the soil and their concentration in the plants, relative to the other treatments and the control. Therefore, this seems to be a viable option to prevent As leaching and improve the plant nutritional status.

Multiple perforation of small-intestine diverticula in a patient with Ehlers-Danlos syndrome.

Ehlers-Danlos syndrome represents a group of hereditary connective tissue disorders characterized by ligamentous hyperlaxity, fragile skin and joint hypermobility. Gastrointestinal complications in this syndrome are less well known.

Risk-based regionalization approach for area-wide management of HLB vectors in the Mediterranean Basin.

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.

Pyrolysis temperature influences the capacity of biochar to immobilize copper and arsenic in mining soil remediation.

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.

Climate suitability of the Mediterranean Basin for citrus black spot disease (Phyllosticta citricarpa) based on a generic infection model.

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.

Economic evaluation of a novel community-based diabetes care model in rural Mexico: a cost and cost-effectiveness study.

OBJECTIVES: Diabetes is the leading cause of disability-adjusted life years in Mexico, and cost-effective care models are needed to address the epidemic. We sought to evaluate the cost and cost-effectiveness of a novel community-based model of diabetes care in rural Mexico, compared with usual care. DESIGN: We performed time-driven activity-based costing to estimate annualised costs associated with typical diabetes care in Chiapas, Mexico, as well as a novel diabetes care model known as Compañeros En Salud Programa de Enfermedades Crónicas (CESPEC). We conducted Markov chain analysis to estimate the cost-effectiveness of CESPEC compared with usual care from a societal perspective. We used patient outcomes from CESPEC in 2016, as well as secondary data from existing literature. SETTING: Rural primary care clinics in Chiapas, Mexico. PARTICIPANTS: Adults with diabetes. INTERVENTIONS: CESPEC is a novel, comprehensive, diabetes care model that integrates community health workers, provider education, supply chain management and active case finding. OUTCOME MEASURE: The primary outcome was the incremental cost-effectiveness of CESPEC compared with care as usual, per quality-adjusted life year (QALY) gained, expressed in 2016 US dollars. RESULTS: The economic cost of the CESPEC diabetes model was US$144 per patient per year, compared with US$125 for diabetes care as usual. However, CESPEC care was associated with 0.13 additional years of health-adjusted life expectancy compared with usual care and 0.02 additional years in the first 5 years of treatment. This translated to an incremental cost-effectiveness ratio (ICER) of US$2981 per QALY gained over a patient's lifetime and an ICER of US$10 444 over the first 5 years. Findings were robust to multiple sensitivity analyses. CONCLUSIONS: CESPEC is a cost-effective, community-based model of diabetes care for patients in rural Mexico. Given the high prevalence and significant morbidity associated with diabetes in Mexico and other countries in Central America, this model should be considered for broader scale up and evaluation.

FNA cytology of postoperative pseudotumoral lesions induced by oxidized cellulose hemostatic agents.

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.

Implementation and clinical effectiveness of a community-based non-communicable disease treatment programme in rural Mexico: a difference-in-differences analysis.

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.

S. Typhimurium virulence changes caused by exposure to different non-thermal preservation treatments using C. elegans.

The aims of this research study were: (i) to postulate Caenorhabditis elegans (C. elegans) as a useful organism to describe infection by Salmonella enterica serovar Typhimurium (S. Typhimurium), and (ii) to evaluate changes in virulence of S. Typhimurium when subjected repetitively to different antimicrobial treatments. Specifically, cauliflower by-product infusion, High Hydrostatic Pressure (HHP), and Pulsed Electric Fields (PEF). This study was carried out by feeding C. elegans with different microbial populations: E. coli OP50 (optimal conditions), untreated S. Typhimurium, S. Typhimurium treated once and three times with cauliflower by-product infusion, S. Typhimurium treated once and four times with HHP and S. Typhimurium treated once and four times with PEF. Bayesian survival analysis was applied to estimate C. elegans lifespan when fed with the different microbial populations considered. Results showed that C. elegans is a useful organism to describe infection by S. Typhimurium because its lifespan was reduced when it was infected. In addition, the application of antimicrobial treatments repetitively generated different responses: when cauliflower by-product infusion and PEF treatment were applied repetitively the virulence of S. Typhimurium was lower than when the treatment was applied once. In contrast, when HHP treatment was applied repetitively, the virulence of S. Typhimurium was higher than when it was applied once. Nevertheless, in all the populations analyzed treated S. Typhimurium had lower virulence than untreated S. Typhimurium.

Arsenic(V) adsorption-desorption in agricultural and mine soils: Effects of organic matter addition and phosphate competition.

High total and bioavailable concentrations of As in soils represent a potential risk for groundwater contamination and entry in the food chain. The use of organic amendments in the remediation of As-contaminated soils has been found to produce distinct effects on the solubility of As in the soil. Therefore, knowledge about As adsorption-desorption processes that govern its solubility in soil is of relevance in order to predict the behaviour of this element during these processes. In this paper, the objective was to determine As adsorption and desorption in four different soils, with and without compost addition, and also in competition with phosphate, through the determination of sorption isotherms. Batch experiments were carried out using three soils affected differently by previous mining activity of the Sierra Minera of La Unión-Cartagena (SE Spain) and an agricultural soil from Segovia province (central Spain). Adsorption was higher in the mining soils (and highest in the acidic one) than in the agricultural soils, although the latter were not affected negatively by organic matter or phosphate competition for sorption sites. The results show that As adsorption in most soils, both with and without compost, fitted better a multimolecular layer model (Freundlich), whereas As adsorption in competition with P fitted a monolayer model (Langmuir). Moreover, the use of compost and phosphate reduced the adsorption of As in the mining soils, while in the agricultural soils compost increased their low adsorption capacity. Therefore, the use of compost can be a good option to favour As immobilisation in soils of low adsorption, but knowledge of the soil composition will be crucial to predict the effects of organic amendments on As solubility in soils and its associated environmental risk.

Efecto terapéutico del extracto etanólico de Erythroxylum coca spp. en anemia ferropénica inducida en ratas Holtzman macho / Therapeutic effect of Erythroxylum coca spp. ethanol extract in experimental iron-deficiency anemia in male Holtzman rats

Introducción: La hoja de coca ha sido usada tradicionalmente con fines medicinales y contiene altos niveles de hierro. Objetivos: Determinar el efecto del extracto etanólico de Erythroxylum coca spp. frente a anemia ferropénica inducida por dieta deficiente en hierro, en ratas Holtzman macho. Diseño: Experimental. Lugar: Laboratorio del Instituto de Patología, Facultad de Medicina, Universidad Nacional Mayor de San Marcos. Material biológico: Dieciocho ratas Holtzman macho de 16 días de edad recién destetadas. Intervenciones: Se formó tres grupos de seis ratas cada uno: a) grupo hierro suficiente (HS), recibió 25 g/d de alimento balanceado durante 7 semanas; b) grupo hierro deficiente (HD), recibió 25 g/d de dieta ferropénica durante 7 semanas; y, c) el grupo hierro deficiente - extracto E. coca (HD-EC), recibió 25 g/d de dieta ferropénica durante 7 semanas y a partir de la semana 5 se agregó 18 g/d de extracto de E. coca. Principales medidas de resultados: Nivel sérico de hemoglobina, peso y talla. Resultados: Al finalizar el tratamiento, se observó aumento significativo de la hemoglobina en el grupo HD-EC (p=0,04). Se encontró diferencia significativa en los niveles séricos de hemoglobina entre los grupos HD-EC y HD (p=0,0062). No se encontró diferencia significativa en los valores de hemoglobina entre los grupos HD-EC y HS (p= 0,06). No se evidenció diferencia en el peso y la talla entre los grupos HD y HD-EC (p=0,20 y p=0,23, respectivamente). Conclusiones: E. coca presenta efecto antianémico experimental, sustentado en los resultados de los niveles de hemoglobina.

Introduction: Coca leaf has been traditionally used for medical purposes and contains high iron levels. Objective: To determine the effect of Erythroxylum coca spp. ethanol extract in iron-deficiency anemia induced by iron-deficient diet in male Holtzman rats. Design: Experimental. Setting: Institute of Pathology Laboratory, Universidad Nacional Mayor de San Marcos. Biologic material: Eighteen weaned male Holtzman rats 16 days old. Interventions: Rats were allocated to three groups of six rats each: a) iron-sufficient group (IS) received 25 g/d of balanced diet for 7 weeks; b) iron-deficient group (ID) received 25 g/d of iron-deficient diet for 7 weeks; and, c) iron deficient/E. coca extract group (ID-CE) received 25 g/d of iron-deficient diet for 7 weeks, and in the fifth week 18 g/d of E. coca extract were added. Main outcome measures: Serum hemoglobin level, weight and height. Results: At the end of the treatment, there was significant difference of hemoglobin in the ID-CE group (p=0.04). There was significant difference in serum hemoglobin levels between ID-CE and ID groups (p=0.0062). No significant difference was found in serum hemoglobin levels between ID-CE and IS groups (p=0.06). No significant difference was found in weight and height between ID and ID-CE groups (p=0.20 and p=0.23, respectively). Conclusions: E. coca had experimental antianemic effect supported by findings in the serum hemoglobin levels.