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Locally-weighted-RoBoost-PLS: A multivariate calibration approach to simultaneously cope with non-linearities and outliers
Get PDFBackground: Partial Least Squares regression (PLS) is a widely used tool for predictive modelling, particularly when dealing with multivariate datasets with dependent variables exhibiting strong collinearities. However, when relationships between variables are non-linear or atypical data points have to be coped with, PLS calibration models may face challenges. In recent years, different variants of the original PLS algorithm have been proposed to overcome these limitations. On the one hand, several robust regression methods that down-weigh outlying observations during the model training phase like RoBoost-PLS have been developed to reduce the detrimental effect of outliers on the performance of PLS. On the other hand, local modelling approaches, like K-Nearest-Neighbours-Locally-Weighted-PLS (KNN-LW-PLS), have been designed to handle non-linearities by fitting for each new incoming sample a separate linear calibration model considering only its nearest-neighbours. Unfortunately, none of these strategies can address the two aforementioned problems simultaneously. This paper introduces a novel approach named Locally-Weighted-RoBoost-PLS (LW-RoBoost-PLS), that combines the strengths of both local and robust modelling methodologies in order to deal with non-linearities while mitigating at the same time the influence of outliers. Results: The performance of LW-RoBoost-PLS was evaluated on simulated and real industrial data (with this latter resulting from a continuous Acrylonitrile-Butadiene-Styrene ABS production process conducted at Versalis S.p.A.), both characterised by the simultaneous presence of outliers and non-linear relationships among measured variables. In the two case-studies investigated here, LW-RoBoost-PLS outperformed RoBoost-PLS and KNN-LW-PLS, achieving considerable reductions in the prediction error and prediction bias, which demonstrates that this technique permits to effectively overcome the limitations of the other approaches. Significance: This paper describes a novel multivariate calibration approach named LW-RoBoost-PLS, which provides a solution for predictive modelling in scenarios where outliers and non-linearities co-exist. LW-RoBoost-PLS simultaneously handles non-linearities and outliers by combining local and robust modelling strategies, leading to improved prediction accuracy and reduced bias
Acción colectiva y políticas públicas: Cambios recientes en la ganadería familiar de Uruguay
Get PDFUruguay históricamente ha brindado la imagen de una ganadería basada en productores independientes, aislados en explotaciones dispersas. Sin embargo, en los ganaderos familiares la acción colectiva es una práctica frecuente que constituye una de las estrategias económicas para la persistencia y la reproducción. Las políticas públicas implementadas entre 2005 y 2019 promovieron diversas formas de acción colectiva para la producción familiar desde una visión de desarrollo rural territorial. El artículo proviene de un estudio que procuró caracterizar la acción colectiva de los ganaderos familiares de la región Litoral norte del país, mediante la revisión de fuentes documentales y la realización de entrevistas semiestructuradas a informantes calificados (30) y referentes de colectivos (50). En la región existe una diversidad de colectivos que, según objetivos y trayectorias, se clasifican en cuatro tipos, integrales, económicos, tradicionales y productivos. En los cuatro tipos se observan procesos de coordinación de acción colectiva, que se diferencian en el grado de madurez logrado de acuerdo con las trayectorias recorridas. En todos los casos se evidencia que la formalización o institucionalización de los colectivos otorga legitimidad a prácticas desarrolladas desde siempre por los ganaderos familiares, como la ayuda mutua o la gestión compartida de bienes
Quantifying canopy structural traits in agroforestry systems through Terrestrial Laser Scanning: A case study in cocoa-based agroforestry systems
No full textAgroforestry systems might contribute to balance some of the production, environmental and social challenges associated with agricultural intensification in tropical regions. However, the intricate functional dynamics within agroecosystems, combined with their diverse objectives, make it difficult to maximise productivity and identifying factors that constrain crop yields. Canopy structural traits strongly influence light distribution in agroforestry systems, affecting crop variability in light-use efficiency and productivity. Yet, information on 3D vegetation structure in agroforestry systems remains scarce, despite its potential to provide valuable information to better understand the functional complexity of these systems. Our workflow overcome this limitation by incorporating Terrestrial Laser Scanning (TLS) technology and a voxelization approach for light ray tracing (AMAPVox). In this context, this study aims to determine how TLS data, processed using a voxelization approach, can be applied in multi-strata agroforestry systems to quantify the three-dimensional (3D) distribution of Plant Area Density (PAD) across vegetation strata and the total Plant Area Index (PAI). We used detailed multi-scan voxelized data from 28 experimental plots established in Côte d'Ivoire with different species compositions and planting arrangements to quantify the 3D distribution of PAD and key structural traits (PAI, light attenuation and transmittance) at multiple spatial resolutions. Validation with estimates of light measurements based on hemispherical photographs at tree level showed a high level of concordance (R2 > 0.42; p-value < 0.05) in estimating plant area index (PAI). Species composition, rather than planting arrangement, notably influenced the vertical distribution of PAD and canopy structural traits. PAI in the plots ranged from 4.94 m2 m−2 to 22.31 m2 m−2. The proposed approach, using TLS data and a voxel-based methodology, enables high-resolution modelling of canopy structural traits in multi-strata agroforestry systems. These results provide highly detailed measurements of key crop yield indicators, allowing decision support to develop management activities that increase crop production while minimising inputs and maintaining ecosystem services
Characterization and control of emerging viral diseases in Cambodia: insights from bat coronaviruses and chikungunya virus
Get PDFAsia, including Cambodia, is a recognized hotspot for emerging infectious diseases (EIDs), particularly zoonotic and vector-borne infections. Recent emergences of coronaviruses (CoVs), such as sarbecoviruses (SARS-CoV-1 and the SARS-CoV-2), underscore the ongoing zoonotic transmission risk, but their prevalence and evolution in Rhinolophid bats remain poorly understood due to limited sampling. The discovery of SARS-CoV-2 related viruses in archived bat samples collected in Cambodia as early as 2010 reinforces the urgent need for enhanced surveillance and characterization of these viruses to better assess their emergence potential and public health risks. The re-emergence of chikungunya virus (CHIKV) in Cambodia in 2011 and 2020 highlights the virus evolution and the risk of re-emergence worldwide. It exemplifies the need for effective response strategies to EIDs. Insights from viral kinetics and immune response studies of CHIKV infections can improve treatment and prevention. Building on studies of bat CoVs and CHIKV, our work aims to enhance general prevention and control strategies for EIDs in Cambodia and beyond. A major aim of this work was to assess the diversity of CoVs in multiple bat species in Cambodia through longitudinal surveillance, and to characterize viruses of interest. Over three years, 1,462 bats were sampled and analyzed, revealing extensive and diverse CoVs co-circulation. Metatranscriptomic and amplicon sequencing generated 33 complete sarbecovirus genomes, revealing four novel lineages associated with different Rhinolophus species. Our study highlights the rapid migration and recombination of sarbecovirus lineages over short distances and timescales and identifies two novel viral groups with receptor-binding domains similar to those of SARS-CoV-2, capable of mediating entry into cells expressing human ACE2, suggesting potential zoonotic risk. In parallel, our study explored the viral kinetics, immune responses, and the potential of monoclonal antibody (mAb) therapies to mitigate viremia and transmission during acute CHIKV infection, providing new insights into early intervention strategies. Using data from 29 patients in Cambodia, viral load quantification on serial samples revealed that the population-average peak viral load occurred approximately 1.87 days before symptom onset. Children showed higher peak viral loads and faster replication rates compared to adults. IgM antibodies appeared earlier in adults than in children. C-reactive protein (CRP) levels were transiently elevated in about 50% of patients but showed no correlation with disease severity. Mathematical modeling highlighted that prophylactic mAb therapies, when administered three days before symptom onset, could substantially reduce viral load and potentially prevent detectable viremia. In conclusion, this project revealed a large diversity of bat CoVs in a small area in northern Cambodia, including novel lineages capable of infecting cells expressing human ACE2. Although concerns remain, the absence of a furin cleavage site and immunity induced by SARS-CoV-2 exposure or vaccination may offer cross-protection against these lineages, limiting the immediate public health risk. However, the observed genetic diversity and frequent recombination events underscore the urgent need for enhanced surveillance to mitigate future zoonotic threats. We also determined the optimal timing for mAb administration to reduce Chikungunya disease duration and transmission. Further research will be required to cross-validate these findings and assess their practical implications for controlling CHIKV outbreaks. By integrating insights from bat CoVs and CHIKV, we can bridge advanced scientific research with real world public health strategies, strengthening preparedness and response to EID threats
Pollen performance under controlled temperatures and chromosome stability of diploid and tetraploid citrus
Get PDFBackground Polyploidization plays a major role in citrus breeding, particularly in generating triploid hybrids through controlled crosses between diploid female and tetraploid male parents. However, limited information is available on how polyploidy affects pollen performance in citrus, and in particular, how temperature influences these processes. In this study, we compared pollen viability under field conditions and pollen tube growth at different temperatures in diploid and tetraploid genotypes, and assessed whether the observed differences were related to genomic instability caused by the tetraploidization treatment. Results Tetraploid `Clemenules´ and `Fortune´, both colchicine-derived, showed a higher proportion of collapsed pollen grains and reduced viability compared with their diploid counterparts, whereas the spontaneous tetraploid `Pineapple´ displayed values similar to those of the diploid. Pollen tube growth assays revealed slightly faster tube elongation in tetraploids, and notably, self-incompatible diploid pistils of `Fortune´ were successfully fertilized by pollen from its tetraploid form. Genotyping-by-sequencing (GBS) analyses of diploid and tetraploid plants revealed no chromosomal rearrangements or dosage alterations, suggesting that colchicine treatment did not induce large-scale genomic instability. Conclusions Our findings demonstrate that tetraploidy influences several aspects of citrus pollen performance, while genomic stability remains largely preserved in colchicine-induced genotypes. These results provide new insights into the reproductive biology of citrus polyploids under different temperature scenarios and reinforce the potential use of tetraploid parents in triploid breeding programs
A Glaring deficit: Decent work in the agricultural and food sectors
Get PDFWhether wages, security or social protection are at issue: the work environment can be as diverse as methods of production. Findings from Ghana demonstrate where improvements can be implemented
Local species-specific effect of trees and shrubs on the incidence of the millet head miner, Heliocheilus albipunctella (Lepidoptera, Noctuidae)
Get PDFUnderstanding the interactions between crop pests, natural enemies and semi-natural habitats in agricultural landscapes is crucial for developing ecology-based pest management in agroecosystems. In the present study, we investigated the local-scale species-specific effect of tree and shrub cover and diversity on the incidence and natural pest regulation of the millet head miner (MHM), Heliocheilus albipunctella (Lepidoptera: Noctuidae) de Joannis and subsequent grain losses in a tree-crop agroforestry system in Senegal. To this purpose, we monitored a network of 60 millet fields with variable tree and shrub species composition within a 50-m radius buffer around the centre of millet fields. The proportion of egg-infested panicles increased with the area covered by baobabs (Adansonia digitata) but decreased with that of soapberry trees (Balanites aegyptiaca). Baobabs and apple-ring acacias (Faidherbia albida) locally increased pest incidence and associated grain loss, likely by providing favourable microhabitats for MHM and limiting the impact of larval parasitoids, respectively. In contrast, bushwillow shrubs (Combretum micranthum) increased egg parasitism, but not enough to disrupt the relationships between crop colonization, pest incidence and yield loss. Furthermore, Shannon's diversity index had no measurable influence on pest dynamics, suggesting that species identity and functional traits are more important than diversity per se. These findings underline the importance of careful selection of tree and shrub species in agroforestry design strategies for optimizing the delivery of multiple ecosystem services. Integrating tree functional traits, seasonal canopy dynamics and spatial scale considerations is key to enhancing ecosystem services such as biological control in tree-crop agroforestry systems
Distribution of agroforestry and cropping systems across smallholder farm types in clove-dominated landscapes of Madagascar
No full textAtlas cidadão: consolidando a agricultura familiar do Planalto Santareno. Diagnóstico realizado nos municípios de Santarém, Mojuí dos Campos e Belterra, Pará, Amazônia brasileira
Get PDFConsolidando a agricultura familiar do Planalto Santareno, PA: diagnóstico realizado nos municípios de Santarém, Mojuí dos Campos e Belterra, Pará, Amazônia brasileira. Organizadores: Mariana Piva da Silva, Emilie Coudel, Beatriz Abreu dos Santos, Stéphanie Nasuti, Danielle Wagner Vincent Bonnal, Denise Lima, Ricardo Folhes Resumo Este atlas expõe resultados da campanha de coleta de dados “Consolidando a agricultura familiar”, realizada em 2019 como atividade de pesquisa dos projetos Odyssea e INCT – Odisseia. A pesquisa que deu origem a este Atlas Cidadão está registrada no comitê de ética da Universidade de Brasília (certificado de apreciação ética nº 95385318.7.0000.5540). Nele, se apresentam os caminhos percorridos e os resultados de um processo de coconstrução de conhecimento baseado em princípios da ciência cidadã, que ocorreu no âmbito dos projetos INCT Odisseia e Odyssea, realizados na região de Santarém, Pará, no Baixo Amazonas. Esse processo foi se desenhando para a coconstrução de um observatório-piloto na região. As principais mudanças socioambientais que emergiram a partir do diálogo e das interações entre pesquisadores e atores locais no trabalho em torno do observatório estiveram relacionadas, principalmente, a transformações envolvendo sistemas de produção de alimentos, que vêm afetando a agricultura familiar