Portail Hal-l'Institut Agro Rennes-Angers
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Multilingual Textual Data: an Approach though Multiple Factor Analysis
No full textInternational audienceThis paper focuses on the analysis of open-ended questions answered in dif-ferent languages. Closed-ended questions, called contextual variables, are asked to allrespondents in order to understand the relationships between open-ended and closed-ended responses across samples, as the latter are likely to influence word choice. We havedeveloped "Multiple Factor Analysis on Generalised Aggregated Lexical Tables" (MFA-GALT) to examine together open-ended responses in different languages through the re-lationships between word choice and the variables that drive that choice. MFA-GALT investigates whether the variability between words is structured in the same way as thevariability between variables, and vice versa, from one sample to another. An applicationto an international satisfaction survey shows the easy-to-interpret results proposed
In vitro protein digestibility of gluten-free pasta made from climate-smart raw matters
No full textInternational audienceTraditionally made from durum wheat semolina (DWS), pasta composition has evolved in recent years, incorporating diverse raw materials such as legumes, wholegrain and/or other nutritious flours. The objective of our study is to go deeper in the development of nutritionally optimized pasta by using climate-smart (CS) crops and assess protein bioacessibility in these new food matrices. It is part of the H2020 Innofood Africa project, bringing together European and African partners to explore CS crops and develop new products for at-risk populations (children and women) suffering from malnutrition or obesity. We have developed optimized pasta made from wholegrain, gluten-free, CS African cereals and legumes. Special attention has been paid on their in vitro protein digestibility and the nature of the released peptides in relation with protein network structure. Four cowpea-based pasta formulations were obtained by linear programming and met the FAO’s nutritional recommendations for one meal for adult women, ensuring adequate levels of protein, fiber, zinc, iron and B9 vitamin. As all optimized formulations combine cowpea with teff and/or amaranth leaf flours, the impact of adding these two flours individually or in combination on the protein network structure, digestibility and peptides released was studied. The comparison with DWS pasta controls, varying in fiber contents from 3.5 to 16 g/100g d.b allowed to highlight the impact of the high fiber content on the protein structure and digestibility.In vitro protein digestibility was assessed using the enzymatic Megazyme kit and the COST Infogest digestion model with control of the degree of proteolysis by monitoring free NH2. At the end of the intestinal phase, the protein digestibility of DWS pasta controls whatever their fiber contents was higher than that of the four cowpea-based pasta with the Megazyme kit, while the results were reversed with the Infogest model. These difference can be explained by distinct gastric and intestinal proteolysis conditions that will be highlighted during the presentation. Despite the lower protein digestibility assessed for cowpea-based pasta, the Megazyme kit revealed PDCAAS two times higher for these matrices compared to DWS controls due to their higher content of essential amino acids. The peptidomic study shows that all cowpea-based pasta have same size of peptides released at the end of intestinal phase (1150 vs 1120 kDa in DWS controls) and highlights that most peptides were derived from cowpea storage proteins such as vicilin (50%) and legumin (15%) differing thus strongly with gliadin and glutenin derived peptides in DWS controls. With the comparison of two reference methods for digestion, this work has pointed out that pasta associating cowpea with amaranth leaf flour provide superior nutritional benefits combined along with high protein digestibility
Workshop on the Bay of Biscay and Iberian Coast ecoregion Aquaculture Overview (WKBoBICAO)
No full textInternational audienceThe Workshop on Bay of Biscay and Iberian Coast Aquaculture Overview (WKBoBICAO) was established to assemble and synthesize aquaculture related data and information and to inform the aquaculture overview for this ecoregion.The geographic extent of the Bay of Biscay and Iberian Coast ecoregion is extensive and ranges from southern Brittany in France through northern and northwestern Spain, it includes the entire coastline of Portugal (mainland) and culminates in the Gulf of Cadiz in southern Spain. It covers a wide range of habitat types and climatic conditions, which has a bearing on the types of aquaculture practiced in the ecoregion.Aquaculture is practised throughout much of the ecoregion. Both intertidal and subtidal waters are utilized in addition to terrestrial pond culture. The aquaculture production within the ecoregion is dominated by shellfish which are largely produced in France (Oysters and Mussels) and Spain (mussels). Portugal production comprises a mix of shellfish, finfish and crustacean culture and while lower in terms of tonnage produced and value than the other countries.In 2021, the aquaculture sector in the ecoregion reached 310,000 Tons produced and €775 million in value. Shellfish are the most produced in the ecoregion and contribute to almost 75% of total value. Crustacean production in Spain and shellfish and finfish production in Portugal show a clear increase since 2010, other species are static in terms of production. Spain produces the greatest tonnage but is second to France in terms of economic value. A number of other species (e.g. finfish, polychaete worms for bait) in addition macroalgae are also grown at smaller scales throughout the ecoregion.In the ecoregion, aquaculture licencing, regulation and policy are the responsibility of the member state. While overarching policy is defined at the EU level, licensing can be different in the various countries. In Portugal a single federal body is responsible for licensing. In Spain and France, regional or local authorities are responsible for issuing licences and national approvals from relevant Ministries must be sought if public waters are to be used. It is however, acknowledged that EU legislation provides an overarching framework for important regulatory aspects including assessment and monitoring, among others, of environmental (e.g. EIA), food safety and fish health considerations. However, during licencing consultation submissions from other authorities are often required in addition to challenges presented under other legislation (e.g. Natura), which can add to the complexity of the process and lead to delays in the decision-making. Marine Spatial planning, whereby specific areas are designated for aquaculture practices, has been identified as mechanism to reduce delay of licensing decisions. Yet, conflicts with other newly developing sectors (e.g. offshore renewables) is inevitable.Monitoring of shellfish culture practices are primarily focused upon food safety considerations, e.g. biotoxin and faecal coliform analysis. In addition, all species are subject to extensive animal health regulations that are wide ranging and derives primarily from EU legislation. Some persistent issues relate to ongoing bacterial (Vibrio) infections in shellfish hatcheries and mortalities associated with pathogens (e.g. OsHV-1) during grow-out. These represent a major challenge to the industry. Poor mussel recruitment in the wild is also leading to shortages of stock for on-growing.Given the dominance of shellfish culture in the ecoregion, the primary environmental effects relate to interactions with habitats and species which might be measured via assessing ecological carrying capacity. In addition to some emerging contaminants that might affect aquaculture species, aquaculture as a source of microplastics is an increasing cause of concern. The ability of shellfish to bioaccumulate nano-plastics is also considered a risk.Small production units predominate the aquaculture sector within the ecoregion. As identified elsewhere, employment in the sector in all countries is considered modest, however, the importance of these (even part-time) roles in more isolated rural areas is acknowledged.In terms of social interactions given the historical and cultural importance of shellfish farming in the ecoregion the sector has greater social licence and as such there is more a tolerance and less challenge to this sector from the wider public. It is apparent that finfish enterprises face considerably more scrutiny during licensing and subsequently. All aquaculture sectors are challenged by decreasing water quality as a result of terrestrial activities.A number of issues are identified which may affect aquaculture development and are considered common across the ecoregion. Of particular concern are the potential effects or emerging pollutants (associated with industrial development). The impact of climate change on shellfish recruitment and disease proliferation in culture stock is also a concern
Prey Switching and Natural Pest Control Potential of Carabid Communities over the Winter Wheat Cropping Season
No full textInternational audienceCarabids are abundant and diverse arthropods in agroecosystems and are well known for their generalist diet and therefore biocontrol potential. Most studies on carabids' diet have focused on periods of peak pest infestations but their feeding habits through the cropping season are poorly known. In this study, we explored how carabids' trophic interactions with pests (aphids and slugs) and alternative prey (spiders, earthworms and springtails) varied from the wheat seedling emergence to wheat ripening by analysing the prey DNA in their gut. Carabids seemed to switch between prey depending on their availability at the time, reaffirming carabids' opportunistic diet. Regarding biocontrol, carabid taxa contributed complementarily to pest predation over the season and per pest taxon, highlighting the importance of favouring diversity in agroecosystem
L’œuf : un aliment aux qualités nutritionnelles avérées
No full textInternational audienceAn inexpensive foodstuff, eggs are a source of high-quality proteins, lipids (two-thirds of which are unsaturated), minerals and vitamins, as well as carotenoids of interest in the fight against certain eye diseases. Today, the consensus is that there is no link, in healthy subjects, between moderate egg consumption, blood cholesterol levels and the risk of cardiovascular disease. But eggs are also a major allergen inyoung children.Aliment peu coûteux, l’œuf est une source de protéines de très bonne qualité, de lipides pour les deux tiers insaturés, de minéraux et vitamines, ainsi que de caroténoïdes d’intérêt pour lutter contre certaines pathologies de l’œil. L’absence de lien, chez les sujets en bonne santé, entre une consommation modérée d’œuf, le niveau de cholestérol sanguin et le risque de maladies cardiovasculaires fait aujourd’hui consensus. Mais l’œuf est aussi un allergène majeur chez le jeune enfant
Adaptation de Domaines pour des Séries Temporelles par Transport Optimal et Alignement Temporel
No full textInternational audienceLarge amounts of unlabeled data are often available, and the annotation step is usually a tedious and/or costly task. Unsupervised domain adaptation can address this issue by leveraging labels from a source domain to classify data from a related, yet different, target domain. When dealing with time series data, additional challenges arise due to potential temporal shifts alongside the feature distribution shift. We introduce the Match-And-Deform (MAD) approach to address these challenges. MAD aims at identifying matching between source and target time series while taking into accounttemporal distortions. To achieve this, the associated optimization problem simultaneously (1) aligns the series using an optimal transport loss and (2) adjusts the timestamps using dynamic time warping. When integrated into a deep neural network, MAD facilitates the learning of new representations of time series that align the domains and enhance the network’s discriminative power. Empirical evaluations conducted on benchmark datasets and real remote sensing data demonstrate MAD’s effectiveness. These numerical experiments show meaningful sample-to-sample matching and accurately estimates time shifts. Comparable or superior classification performance compared to state-of-the-art deep time series domain adaptation strategies are also achieved.This paper is adapted from Painblanc et al. [2023]. Code and data are publicly available: https://github.com/rtavenar/MatchAndDeformDe grandes quantités de données non étiquetées sont souvent disponibles, mais l'étape d’annotation est généralement une tâche fastidieuse et/ou coûteuse. En apprentissage non supervisé, l’adaptation de domaine peut résoudre ce problème en exploitant les étiquettes d’un domaine source pour classifier des données d’un domaine cible, similaire mais différent. Dans le cas de séries temporelles, des défis supplémentaires surviennent, notamment en raison des décalages temporels potentiels qui s’ajoutent aux décalages de distribution entre les domaines.Nous présentons une méthode dénommée Match-And-Deform (MAD) qui vise à relever ces défis en identifiant les correspondances entre les séries temporelles des domaines source et cible tout en tenant compte des distorsions temporelles. Le problème d’optimisation associé aligne simultanément (1) les séries en optimisant un coût de transport optimal et (2) les temps à l’aide de dynamic time warping. Intégré dans un réseau de neurones profond, MAD permet l’apprentissage de nouvelles représentations des séries temporelles, alignant les domaines et améliorant le pouvoir discriminant du réseau. La méthode est évaluée empiriquement sur des données de référence et des données réelles de télédétection, démontrant l’efficacité de MAD: les séries sont appariées de fa¸con pertinentes et les décalages temporels sont estimés avec précision. Des performances de classification comparables ou supérieures aux stratégies d’adaptation de domaine de séries temporelles profondes de l'état de l’art sont également obtenues.Cet article est issu de Painblanc et al. [2023]. Le code et le jeu de données sont disponibles publiquement: https://github.com/rtavenar/MatchAndDefor
Accurately predicting rare and poorly detectable species habitat for spatial protection
No full textInternational audienceWith the loss of biodiversity worldwide, understanding species distribution is essential for species management, but modelling the distribution of rare and poorly detectable species can be challenging because of data gaps and observer biases. Over‐ or under‐predictions are frequent, leading to uncertainty in spatial management measures, particularly for highly mobile and data‐poor species. Here we developed a ‘Combined Model for Accurate Prediction’ to accurately predict the distribution of data‐poor and rare species. This modelling framework aims to improve the accuracy of both predicted ‘core’ and ‘unsuitable’ habitats, to help support managers with spatial protection measures. We tested the combined modelling approach on 11 data‐poor and rare diadromous fish during their at‐sea life history phase and used the combined model to analyse the adequacy of existing marine protected areas (MPAs) for these fish. The combined modelling approach modelled both ‘core’ and ‘unsuitable’ habitats with high accuracy. Of the seven diadromous species modelled, most MPAs designated to protect diadromous fish are outside their core habitats. Furthermore, when their core habitat was within an MPA, only 50% of this area was designated to protect them. These results highlight inadequate protection of the existing networks of MPAs for protected and threatened species. Synthesis and applications . Being able to accurately model species distribution is critical to reliable and transparent biodiversity and conservation assessments. By modelling accurate ‘core’ and ‘unsuitable’ habitats with models that minimise omission and commission rates respectively, conservation measures could be targeted in specific spatial areas that maximise the protection of rare and poorly detected species. This method therefore helps minimise impacts on stakeholders, while providing managers with increased confidence in the model predictions.Avec la perte de biodiversité mondiale, la compréhension de la distribution des espèces est essentielle pour leur gestion. Néanmoins modéliser la distribution des espèces rares et peu détectables peut s'avérer difficile en raison d'un manque de de données et des biais entre observateurs. Les sur‐prédictions ou sous‐prédictions sont fréquentes. Cela entraîne une incertitude dans les mesures de gestion spatiale, en particulier pour les espèces très mobiles et pour lesquelles les données sont insuffisantes. Nous avons développé ici un ‘modèle combiné pour une prédiction précise’ afin de prédire avec précision la distribution des espèces rares et pauvres en données. Ce cadre de modélisation vise à améliorer la précision des prédictions à la fois sur les habitats ‘cœur’ et des habitats ‘inappropriés’, afin d'aider les gestionnaires à mettre en place des mesures de protection spatiale. Nous avons testé cette approche de modélisation combinée sur 11 poissons migrateurs amphihalins rares et pauvres en données pendant leur phase de vie en mer afin d'analyser la pertinence des aires marines protégées (AMP) existantes pour ces poissons. L'approche de modélisation combinée a permis de modéliser les habitats ‘cœur’ et ‘inappropriés’ avec une grande précision. Sur les sept espèces migratrices amphihalines modélisées, la plupart des AMP désignées pour protéger ces espèces se trouvent en dehors de leurs habitats ‘cœur’. En outre, lorsque ce dernier se trouvait dans une AMP, seuls 50% de cette zone étaient désignés pour les protéger. Ces résultats mettent en évidence la protection insuffisante des réseaux d'AMP existants pour les espèces protégées et menacées. Synthèse et applications . Il est essentiel de pouvoir modéliser avec précision la distribution des espèces pour obtenir des évaluations fiables et transparentes de la biodiversité et mieux guider les mesures de conservation. En modélisant les habitats ‘cœur’ et ‘inappropriés’ avec des modèles qui minimisent à la fois les faux positifs et négatifs, les mesures de conservation pourraient être ciblées dans des zones spatiales spécifiques qui maximisent la protection des espèces rares et mal détectées. Cette méthode permet donc de minimiser l'impact sur les activités socio‐économiques, tout en donnant aux gestionnaires une plus grande confiance dans les prédictions du modèle
PAC 2023-2027 : Levier de transformation de l'agriculture française ?
No full textLa revue Innovations agronomiques s'adresse à l'ensemble des acteurs de la chaîne de valeur agronomique, aux services institutionnels, aux chercheurs, enseignants et apprenants et à la société civile intéressés par les sujets de l’agriculture, de l’alimentation et de l’environnement. Elle reprend et complète les thèmes abordés lors des CIAg ainsi que des synthèses de résultats de programmes de recherche sur ces champs thématiques.National audienceConclusions and perspectives of the Carrefour de l'innovation agronomique sur la PAC, 2023, Rennes. The 2023 reform of the Common Agricultural Policy (CAP) has introduced greater subsidiarity for Member States, who are now responsible for drawing up their own National Strategic Plans (NSP), in line with their national priorities, but with a commitment to contributing to European objectives. At French level, there is a tension between two objectives that are difficult to reconcile in the implementation of the CAP: maintaining income support for farmers on the one hand, and supporting the agro-ecological transition of farms on the other. The compromise reached clearly prioritizes securing incomes for existing farmers, but casts doubt on the ability to achieve the objectives of the Green Pact. To be more effective in achieving the sustainability objectives of European agriculture, the post-2027 CAP will have to consider not only how to secure installations and transitions to production systems consistent with the objectives, but also give clear signals to encourage the transition of European diets.Conclusions et perspectives du Carrefour de l'innovation agronomique sur la PAC, 2023, Rennes. La réforme de la Politique agricole commune (PAC) 2023 a apporté une plus grande subsidiarité des Etats Membres , en charge de construire eux-mêmes leur Plan Stratégique National (PSN), en lien avec leurs priorités nationales, mais en engageant leur Etat dans la contribution aux objectifs européens. Au niveau français, on a bien une tension entre deux objectifs difficiles à concilierdans la mise en œuvre de la PAC : le maintien du soutien au revenu des agriculteurs d’une part, et le soutien de la transition agro-écologique des exploitations d’autre part. Le compromis auquel on aboutit est clairement priorisé sur la sécurisation du revenu des agriculteurs en place, mais amène à douter de la capacité à atteindre les objectifs du pacte vert. Pour gagner en efficacité pour l'atteinte des objectifs de durabilité de l'agriculture européenne, la PAC post-2027 devra envisager non seulement la sécurisation des installations et des transitions vers des systèmes de production cohérents avec les objectifs, mais aussi donner des signaux clairs pour favoriser la transition des régimes alimentaires européens
Multi‐scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy‐transducing organelles
No full textInternational audienceMuch progress has been made in understanding the molecular mechanisms of plant adaptation to heatstress. However, the great diversity of models and stress conditions, and the fact that analyses are oftenlimited to a small number of approaches, complicate the picture. We took advantage of a liquid culture sys-tem in which Arabidopsis seedlings are arrested in their development, thus avoiding interference withdevelopment and drought stress responses, to investigate through an integrative approach seedlings’global response to heat stress and acclimation. Seedlings perfectly tolerate a noxious heat shock (43°C)when subjected to a heat priming treatment at a lower temperature (38°C) the day before, displaying a ther-motolerance comparable to that previously observed for Arabidopsis. A major effect of the pre-treatmentwas to partially protect energy metabolism under heat shock and favor its subsequent rapid recovery, whichwas correlated with the survival of seedlings. Rapid recovery of actin cytoskeleton and mitochondrialdynamics were another landmark of heat shock tolerance. The omics confirmed the role of the ubiquitousheat shock response actors but also revealed specific or overlapping responses to priming, heat shock, andtheir combination. Since only a few components or functions of chloroplast and mitochondria werehighlighted in these analyses, the preservation and rapid recovery of their bioenergetic roles upon acuteheat stress do not require extensive remodeling of the organelles. Protection of these organelles is ratherintegrated into the overall heat shock response, thus allowing them to provide the energy required to elabo-rate other cellular responses toward acclimation
