Portail HAL Institut Agro Montpellier
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Adapting BERT and AgriBERT for agroecology: A small-corpus pretraining approach
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/614086/) * Autres projets (id;sigle;titre): 101081973;IntercropValuES;(EU) Developing Intercropping for agrifood Value chains and Ecosystem Services delivery in Europe and Southern countries//International audienceSource variables, or observable properties, used to describe agroecological experiments are often heterogeneous, non-standardized, and multilingual, making them challenging to understand, explain, and utilize in cropping system modeling and multicriteria evaluations of agroecological system performance. A potential solution is data annotation via a controlled vocabulary, known as candidate variables, from the Agroecological Global Information System (AEGIS). However, matching source and candidate variables via their textual descriptions remains a challenging task in agroecology. Domain-general language models, such as BERT, often struggle with domain-specific tasks due to their general-purpose training data. In the literature, these models are adapted to specialized domains through further pretraining, pretraining from scratch, and/or fine-tuning on downstream tasks. However, pretraining a domain-general model on a domain-specific corpus is resource-intensive, requiring substantial time, energy, and computational resources. To the best of our knowledge, no study has further pretrained a domain-general model on a small corpus (less than 100 MB) to adapt it to a domain-specific task and evaluated it on downstream tasks without fine-tuning. To address these shortcomings, this paper proposes further pretraining BERT and AgriBERT on a small agroecology-related corpus. This approach is designed to be both time- and resource-efficient while enhancing domain adaptation. We evaluate the pretrained models on the task of matching source and candidate variable descriptions without fine-tuning. Our results show that our further pretrained AgriBERT (+ Experts + Core) model outperforms all others by more than 8% from P@1 to P@10. These findings showed that small-scale pretraining can significantly improve performance on domain-specific tasks without requiring fine-tuning
The value of GIs for Rwandan coffee: A market perspective
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/613947/)International audienceIn the specialty coffee market, geographical origin serves as a strong selling point, particularly within the single-origin segment, provided that the origin is reputed and sought after. However, for Rwandan coffee, a primary challenge for exporters lies in the relatively underdeveloped brand image compared to that of neighboring countries such as Ethiopia and Kenya. This situation results in a general lack of awareness among buyers and end consumers regarding Rwandan coffee, and the specificities of its ”terroirs”. From a market perspective, interviews conducted with eight buyers of Rwandan coffee indicate that the primary advantage anticipated from implementing a GI scheme lies in the certification process and the associated traceability system. The importance of traceability has grown in light of the recent EU regulation on imported deforestation. In this context, GIs are viewed as a crucial mechanism for reducing information asymmetry between producers, buyers, and ultimately, consumers. This aligns with Ponte and Gibbon's (2005) argument that trust has become institutionalized within the GI label, as quality information is codified in the GI product specifications. However, some buyers, particularly in Asian markets, prioritize establishing long-term, privileged relationships with producers and building interpersonal trust over time, rather than relying solely on certifications. This perspective resonates with the traditional definition of domestic convention. Such buyers may still find value in the enhanced focus that GIs place on the local communities involved in the production process
Using PADI-web to monitor animal and plant diseases in digital media sources
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/613934/)International audienc
A user-friendly software to accurately count and measure cysts from the parasitic nematode Heterodera glycines
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/613923/)International audienceThe soybean-cyst nematode (SCN; Heterodera glycines) is one of the most destructive pests affecting soybean crops. Effective management of SCN is imperative for the sustainability of soybean agriculture. A promising approach to achieving this goal is the development and breeding of new resistant soybean varieties. Researchers and breeders typically employ exploratory methods such as Genome-Wide Association Studies or Quantitative Trait Loci mapping to identify genes linked to resistance. These methods depend on extensive phenotypic screening. The primary phenotypic measure for assessing SCN resistance is often the number of cysts that form on a plant's root system. Manual counting hundreds of cysts on a given root system is not only laborious but also subject to variability due to individual assessor differences. Additionally, while measuring cyst size could provide valuable insights due to its correlation with cyst development, this aspect is frequently overlooked because it demands even more hands-on work. To address these challenges, we have created Nemacounter, an intuitive software designed to detect, count, and measure the size of cysts autonomously. Nemacounter boasts a user-friendly graphical interface, simplifying the process for users to obtain reliable results. It enhances productivity by delivering annotated images and compiling data into csv files for easy analysis and reporting
Cold vs. CO₂: anaesthetic effects on insect antennal functionality
No full textInternational audienceAnaesthesia methods play a crucial role in ensuring the integrity of the animal during experimental studies. This study investigates the impact of two anaesthesia methods, CO₂ and cold treatment, on an insect antennal response to synthetic alarm pheromone compounds. Adult worker hornets were anesthetised, and their antennae excised and tested using an electroantennography set-up with controlled stimulation of alarm pheromone components. Results showed that CO₂-anesthetised hornets exhibited robust antennal responses, while cold-anesthetised individuals displayed none. This result suggests that freezing may impair the functionality of olfactory receptors. In contrast, CO₂ anaesthesia preserves receptor integrity, offering reliable and interpretable results. This study highlights the importance of selecting appropriate anaesthesia techniques to avoid artefacts in insect sensory physiology research and underscores the ecological relevance of studying Vespa velutina nigrithorax alarm signalling
Using a serious game to engage agrifood system actors for unlocking the production of local neglected legume crops: a case study in South Eastern Senegal
No full textInternational audienceFood insecurity in West Africa, particularly in the Sahel, is worsened by reliance on major crops like groundnut and millet. Underutilized indigenous legumes offer a solution for diversifying cropping systems, improving soil fertility, reducing water needs, enhancing nutrition, and promoting gender equity and economic stability. In South Eastern Senegal, diverse legume crops are cultivated, including Bambara groundnut (Vigna subterranea) and cowpea (Vigna ungiculata). Despite their benefits, these crops only represent small production volume and have no dedicated value chains. Such contradiction raises questions about possible lockers that bend down the development of such crops. It also emphasizes the need for an approach that combines multilevel and dynamic processes, engaging diverse stakeholders across scales—from the farm level to national or regional food systems. Fostering such a change requires to create the conditions for an endogenous process in which the different actors share their questions and knowledge to apprehend complex reality into a systemic thinking, to reflect and collaborate to create and achieve scenarios of change. This study investigates the application of a serious game, TerriStories®, to engage multi-stakeholder commitments for increasing the production of underutilized legume crops(Bambara groundnut and cowpea) in South Eastern Senegal. The participatory TerriStories® approach effectively engaged stakeholders, fostering dialogue and promoting innovative solutions. Participants identified challenges, reconsidered practices, and proposed actionable strategies. Sustained engagement with the TerriStories® approach is crucial for building momentum and ensuring lasting change. Establishing strategic collaboration with local actors will support autonomous and durable improvements in legume production
Understanding and supporting a territory's transition towards zero pesticide use: the case of the western plain of Montpellier. Co-designing agrifood systems across scales: methods and tools for multi-actor approaches
No full textInternational audienc
Monitoring satellite-based crop irrigation water requirements for maize, cotton and hay in distinct Mediterranean regions
No full textInternational audienceThe water requirements of plants are crucial for the sustainable water resources management since in the Mediterranean region, agriculture is the major consumer of water. In recent decades, remote sensing (Landsat, Sentinel, etc) has been used with appropriate methodologies that allow the estimation of evapotranspiration. The proposed methodology in this research has been developed in parallel with a similar methodology by the European Space Agency (ESA), based on a double energy balance. The proposed method has received an improvement as compared to the ESA's method, since the Weather Research & Forecasting Model (WRF) is used instead of ERA5, the fifth generation ECMWF, for better estimation of the meteorological conditions. Despite the improvement, the method still presents a systematic overestimation in relation to the field values mainly in the second half of the growing season. To address this problem and to successfully estimate daily actual evapotranspiration (ETa) values, the calibration and validation of the method for two crops (maize, cotton) and hay (mixture of forage crops) is presented. The first two crops were based on experiments carried out in central Greece and the third (hay) in experimental fields in southern France. Soil-water balance models, AquaCrop (for Greece) and PILOTE (for France), are used to monitor the daily crop irrigation water requirements throughout the growing season. The adopted satellite ETa adjustment factor in all crops is close to 0.59-0.63 and R 2 ranges from 0.87 to 0.97. The results show that a reliable estimation of ETa can be obtained using satellite data
Horizontal gene transfer, segregation loss, and the speed of microbial adaptation
No full textInternational audienceMicrobial adaptation is driven by the circulation of mobile genetic elements (MGEs) among bacteria. On the one hand, MGEs can be viewed as selfish genes that spread like infectious diseases in a host population. On the other hand, the horizontal transfer and the loss of these MGEs are often viewed as a form of sexual reproduction that reshuffles genetic diversity in a way that may sometimes be adaptive for bacteria cells. Here, we show how these 2 perspectives can be reconciled using a single unified framework capturing the dynamics of multiple, interacting MGEs. We apply this framework to study how interactions between MGEs affecting rates of horizontal gene transfer and segregation loss shape the short- and long-term evolutionary dynamics of MGEs and the bacteria population. We show that these interactions produce nonrandom MGE associations that can speed up or slow down microbial adaptation depending on the evolutionary conflicts between MGEs as well as between MGEs and their bacterial hosts. Moreover, we show how these interactions affect the evolutionary potential of the bacteria population. We discuss the implications of these predictions for the community response to environmental stressors such as antibiotic treatment or vaccination campaigns as well as the evolution of accessory genomes
Molecular biology 2000-2023
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/615459/)International audienc