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1. How to combine soil and plant indicators to manage nitrogen fertilisation in vineyards?

Author

Sylvain Vrignon-Brenas, Bénédicte Fontez, Denis Caboulet, Gabriel Ruetsch, Olivier Demarle, Aurélie Metay, and Anne Pellegrino

Subjects
Grapevine, Chlorophyll meter, Yeast assimilable nitrogen, Nitrogen management, Minerals, Organic, Science (General), Q1-390, Social sciences (General), H1-99
Abstract

Context: Although grapevine nitrogen (N) needs are moderate, N fertilisation in vineyards requires carefully management because berry development, aromatic composition and hence winemaking are largely influenced by N nutrition. Our objective was to develop a method for reasoned N fertilisation between and during the seasons. Methods: Specific sensitivities of soil and plant indicators to N supply and availability were estimated and indicator robustness was quantified using contrasted environmental conditions, crop management and N fertilisation in an experimental network comprising five vineyards in southern France over four successive years. The effects of four N fertilisation treatments combining contrasted amounts, forms and timing on the indicators were tested using linear models. Multiple factorial multiple analysis was used to study the effect of environmental and management factors on indicator sensitivity to mineral N fertilisation at budburst. Results: Yield, soil mineral nitrogen at budburst, chlorophyll concentration (SPAD) at veraison, leaf nitrogen content and yeast assimilable nitrogen (YAN) at harvest, were all sensitive to N fertilisation after four years. Different effects of the N treatments were observed from year three for SPAD and from year one for YAN. Additionally, SPAD and YAN indicators distinguished contrasted strategies based on different timings of N supply or the form of N fertiliser. Lastly, the response of the SPAD and YAN indicators was only slightly influenced by pedoclimatic conditions or cultural practices, at least for the variables tested here. Conclusion: Two N indicators measured from veraison (SPAD) to harvest (YAN), can provide valuable information for tactical and long-term fertilisation decisions. Notably, early SPAD information may improve technical vineyard management of interactions between fertilisation and other practices (e.g. weed control or tillage) that interfere with plant N nutrition and enable later correction of YAN values. Combining these indicators with non-destructive imaging techniques should improve N and mineral monitoring in general.

Published
2024
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2. Exploring Corbières red wine typicity: evaluation of the impact of winemaking processes on the chemical composition and organoleptic properties of wines from different terroirs

Author

Alice Argentero, Soline Caillé, Floriano Joaquim Engenheiro, Bénédicte Fontez, Peggy Rigou, and Laetitia Mouls

Subjects
aroma compounds, polyphenols, sensorial analysis, multifactorial analysis, terroir, wine, Agriculture, Botany, QK1-989
Abstract

Aromatic and polyphenolic compounds play an important role in the quality of red wines, contributing not only to flavour, but also to colour, astringency and bitterness. To explore the influence of climate and oenological practices on the chemical and sensory profile of wines, red blends from five terroirs of the Corbières appellation were analysed, taking into account two production years (2018 and 2019). The wines were a blend of at least two of four main grape varieties: Syrah, Grenache, Carignan and Mourvèdre. Volatile compounds were evaluated by HS-SPME-GC-MS, while wine pigments and derived pigments were evaluated by spectrophotometric measurements. In addition, the wines were compared using a quantitative descriptive analysis sensory profile method. The percentage of the blend significantly influenced the polyphenolic and aromatic characteristics of the wines, showing distinct 'typicity' characteristics between sub-regions. Maceration techniques, on the other hand, did not did not allow us to discriminate between sub-regions, but enabled a better understanding of chemical and sensory differences between samples.

Published
2024
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3. Short and long-term acclimation to water status at leaf and plant level of fungus-tolerant genotypes

Author

Luciana Wilhelm de Almeida, Anne Pellegrino, Bénédicte Fontez, Laurent Torregrosa, and Hernán Ojeda

Subjects
water deficit, grapevine, water use efficiency, yield, quantitative analysis, GiESCO, Agriculture, Botany, QK1-989
Abstract

Today’s viticulture faces the double challenge of reducing chemical input while adapting plant material to future climate conditions. Adopting fungus disease-tolerant varieties appears to be a long-term solution as long as they are performant under abiotic constraints, such as drought. This study aimed to study the effects of water deficit (WD) and characterise the different strategies adopted to cope with drought in six new fungus disease-tolerant varieties selected by INRAE compared to Syrah. During five consecutive seasons (2018 to 2022), a gradient of WD was applied in field conditions and monitored through vine predawn water potential measurements. Grape development was non-destructively tracked by imaging to determine the arrest of berry phloem unloading. All variables were collected at the single plant level. The impacts of WD on leaf gas exchange and intrinsic water use efficiency (WUEi), vegetative development and yield components were assessed, as well as the genotypic sensitivity to WD at the leaf, vegetative and reproductive levels. All variables were negatively impacted by WD, except for intrinsic water use efficiency and total non-structural carbohydrate concentrations. Genotypes were differently impacted by WD at the physiological and vegetative levels, while no genotype-dependent response was observed for most reproductive variables. Generally, genotypes with the highest potential (highest intercept) in a certain variable were also the most sensitive to water deficit (higher slope). The most sensitive genotype regarding physiological and reproductive variables was G5, which showed higher reductions in berry weight, photosynthesis and WUEi, contrasting with Syrah, 3159B and Floreal. In this study, we observed a diversity of strategies to cope with WD in the long term, where some genotypes opted to reduce most variables (G5 and Artaban) or to maintain functioning at higher levels (Syrah and 3176N). Others displayed mixed responses: either reducing vegetative growth more than yield (3159B) or vice-versa (G14).

Published
2023
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4. Link between Flavor Perception and Volatile Compound Composition of Dark Chocolates Derived from Trinitario Cocoa Beans from Dominican Republic

Author

Santiago Guzmán Penella, Renaud Boulanger, Isabelle Maraval, Gabi Kopp, Marcello Corno, Bénédicte Fontez, and Angélique Fontana

Subjects
cocoa, chocolate, flavor perception, volatile compounds, flavor predictive models, PLS, Organic chemistry, QD241-441
Abstract

The chemical composition of dark chocolate has a significant impact on its complex flavor profile. This study aims to investigate the relationship between the volatile chemical composition and perceived flavor of 54 dark chocolate samples made from Trinitario cocoa beans from the Dominican Republic. The samples were evaluated by a trained panel and analyzed using gas chromatography-mass spectrometry (GC-MS) to identify and quantify the volatile compounds. Predictive models based on a partial least squares regression (PLS) allowed the identification of key compounds for predicting individual sensory attributes. The models were most successful in classifying samples based on the intensity of bitterness and astringency, even though these attributes are mostly linked to non-volatile compounds. Acetaldehyde, dimethyl sulfide, and 2,3-butanediol were found to be key predictors for various sensory attributes, while propylene glycol diacetate was identified as a possible marker for red fruit aroma. The study highlights the potential of using volatile compounds to accurately predict chocolate flavor potential.

Published
2023
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5. Kalman Filter With Impulse Noised Outliers : a Robustsequential Algorithm to Filter Data With a Large Number Of outliers

Author

Bertrand Cloez, Bénédicte Fontez, Eliel GONZÀLEZ-GARCÌA, and Isabelle Sanchez

Abstract

Impulse noised outliers are data points that differs significantly from other observations. They are generally removed from the data set through local regression or Kalman filter algorithm. However, these methods, or their generalizations, are not well suited when the number of outliers is of the same order as the number of low-noise data. In this article, we propose a new model for impulse noised outliers based on simple latent linear Gaussian processes as in the Kalman Filter. We present a fast forward-backward algorithm to filter and smooth sequential data and which also detect these outliers. We compare the robustness and efficiency of this algorithm with classical methods. Finally, we apply this method on a real data set from a Walk Over Weighing system admitting around $60\%$ of outliers. For this application, we further develop an (explicit) EM algorithm to calibrate some algorithm parameters.

Published
2022
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6. Massively Distributed Clustering via Dirichlet Process Mixture

Author

Isabelle Sanchez, Nadine Hilgert, Bénédicte Fontez, Khadidja Meguelati, Florent Masseglia, Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
Clustering high-dimensional data, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Series (mathematics), Computer science, Process (computing), Hyperspectral imaging, Parallelism, 020207 software engineering, Gaussian random process, Hardware_PERFORMANCEANDRELIABILITY, 02 engineering and technology, computer.software_genre, Clustering, Data point, ComputingMethodologies_PATTERNRECOGNITION, Dirichlet process mixture, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, ComputerSystemsOrganization_SPECIAL-PURPOSEANDAPPLICATION-BASEDSYSTEMS, Data mining, Reproducing Kernel Hilbert Space, Cluster analysis, computer, Dirichlet Process Mixture Model, Curse of dimensionality
Abstract

International audience; Dirichlet Process Mixture (DPM) is a model used for multivariate clustering with the advantage of discovering the number of clusters automatically and offering favorable characteristics, but with prohibitive response times, which makes centralized DPM approaches inefficient. We propose a demonstration of two parallel clustering solutions : i) DC-DPM that gracefully scales to millions of data points while remaining DPM compliant, which is the challenge of distributing this process, ii) HD4C that addresses the curse of dimensionality by performing a distributed DPM clustering of high dimensional data such as time series or hyperspectral data.

Published
2020
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7. Assessment of acoustic-mechanical measurements for texture of French fries: Comparison of deep-fat frying and air frying

Author

Philippe Bohuon, Christian Mestres, Céline Hofleitner, Bénédicte Fontez, Têko Gouyo, Isabelle Maraval, SEB France, Ecully, Démarche intégrée pour l'obtention d'aliments de qualité (UMR Qualisud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de La Réunion (UR)-Université de Montpellier (UM)-Avignon Université (AU)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SEB Group, and CIRADMontpellier

Subjects
[SPI.OTHER]Engineering Sciences [physics]/Other, Hot Temperature, Friture, 030309 nutrition & dietetics, Microphone, French fries, Mineralogy, Sensory analysis, Linear distance, 03 medical and health sciences, 0404 agricultural biotechnology, Plant Oils, Cooking, Texture (crystalline), Texture, Sound pressure, Solanum tuberosum, Propriété physicochimique, Mathematics, Hot air frying, 0303 health sciences, Acoustic properties, Taste Perception, Q01 - Sciences et technologies alimentaires - Considérations générales, 04 agricultural and veterinary sciences, Propriété acoustique, cooking methods [EN], 040401 food science, Crispness, Aliment préparé, French fries [EN], Analyse organoleptique, Cone penetration test, Food Science
Abstract

International audience; The aim of this study was to develop an instrumental method for measuring the texture of French fries and correlated it with sensory measurements. For seven samples of French fries with different crispness levels, a cone penetrometer test was conducted simultaneously with microphone recording of sound emissions. A descriptive sensory analysis was also performed on these samples. The results showed that the number of sound peaks, the linear distance of sound peaks, the area under the sound-displacement curve and the mean sound pressure were strongly positively correlated (r ≥ 0.80; P-value

Published
2020
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8. High Dimensional Data Clustering by means of Distributed Dirichlet Process Mixture Models

Author

Khadidja Meguelati, Bénédicte Fontez, Nadine Hilgert, Florent Masseglia, Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ‘Programme d'Investissements d'Avenir’ (PIA)., ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), European Project: 732051,H2020-ICT-2016-1,CloudDBAppliance(2016), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), The research leading to these results has received funds from the European Union's Horizon 2020 Framework Programme for Research and Innovation, under grant agreement No. 732051., This work was supported by the ‘Infrastructure Biologie Santé’ PHENOME‐EMPHASIS project (ANR‐11‐INBS‐0012) funded by the National Research Agency and the ‘Programme d'Investissements d'Avenir’ (PIA)., and ANR-11-INBS-0012/11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011)

Subjects
Clustering high-dimensional data, Computer science, Gaussian random process, 02 engineering and technology, computer.software_genre, Dirichlet distribution, Clustering, symbols.namesake, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, [INFO]Computer Science [cs], Cluster analysis, Dirichlet Process Mixture Model, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Hyperspectral imaging, Parallelism, Function (mathematics), ComputingMethodologies_PATTERNRECOGNITION, Data analysis, symbols, 020201 artificial intelligence & image processing, Data mining, Reproducing Kernel Hilbert Space, computer, Curse of dimensionality, Reproducing kernel Hilbert space
Abstract

International audience; Clustering is a data mining technique intensively used for data analytics, with applications to marketing, security, text/document analysis, or sciences like biology, astronomy, and many more. Dirichlet Process Mixture (DPM) is a model used for multivariate clustering with the advantage of discovering the number of clusters automatically and offering favorable characteristics. However, in the case of high dimensional data, it becomes an important challenge with numerical and theoretical pitfalls. The advantages of DPM come at the price of prohibitive running times, which impair its adoption and makes centralized DPM approaches inefficient, especially with high dimensional data. We propose HD4C (High Dimensional Data Distributed Dirichlet Clustering), a parallel clustering solution that addresses the curse of dimensionality by two means. First it gracefully scales to massive datasets by distributed computing, while remaining DPM-compliant. Second, it performs clustering of high dimensional data such as time series (as a function of time), hyperspectral data (as a function of wavelength) etc. Our experiments, on both synthetic and real world data, illustrate the high performance of our approach.

Published
2019

9. GALTON-WATSON PROCESS AND BAYESIAN INFERENCE: A TURNKEY METHOD FOR THE VIABILITY STUDY OF SMALL POPULATIONS

Author

C. Bertrand, Bénédicte Fontez, M. Kerioui, T. Daufresne, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), MethodS in Patients-centered outcomes and HEalth ResEarch (SPHERE), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Cloez, Bertrand, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
FOS: Computer and information sciences, 0106 biological sciences, Extinction probability, Stochastic modelling, Offspring, Computer science, Population, Bayesian inference, 010603 evolutionary biology, 01 natural sciences, Statistics - Applications, 010104 statistics & probability, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [STAT.AP] Statistics [stat]/Applications [stat.AP], [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, Applied mathematics, Turnkey, Quantitative Biology::Populations and Evolution, Applications (stat.AP), 0101 mathematics, education, education.field_of_study, [STAT.AP]Statistics [stat]/Applications [stat.AP], Extinction, Small population size, Galton–Watson process, Population model, Deterministic system
Abstract

Sharp prediction of extinction times is needed in biodiversity monitoring and conservation management.The Galton-Watson process is a classical stochastic model for describing population dynamics. Its evolution is like the matrix population model where offspring numbers are random. Extinction probability, extinction time, abundance are well known and given by explicit formulas. In contrast with the deterministic model, it can be applied to small populations.Parameters of this model can be estimated through the Bayesian inference framework. This enables to consider nonarbitrary scenarios.We show how coupling Bayesian inference with the Galton-Watson model provides several features: i) a flexible modelling approach with easily understandable parameters ii) compatibility with the classical matrix population model (Leslie type model) iii) A non-computational approach which then leads to more information with less computing iv) a non-arbitrary choice for scenarios, parameters… It can be seen to go one step further than the classical matrix population model for the viability problem.To illustrate these features, we provide analysis details for two examples whose one of which is a real life example.

Published
2019

10. Coviability of social and ecological systems : reconnecting mankind to the biosphere in an era of global change. Vol. 2 : Coviability questioned by a diversity of situations

Author

Eric Delaître, Deiane Jorge Macedo, Izildinha Souza Miranda, Laurent Demagistri, Bénédicte Fontez, Nikolay Sirakov, Hélène Rey-Valette, Maria Regina Teixeira da Rocha, Patrice Loisel, Danielle Mitja, Thérèse Libourel, Sol González-Pérez, Alessio Moreira dos Santos, Institut de Recherche pour le Développement (IRD), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universidade Federal do Sul e Sudeste do Para (UNIFESSPA), Universidade Federal Rural da Amazônia (UFRA), Universidade Federal do Pará (UFPA), Centre d'Economie de l'Environnement - Montpellier - FRE2010 (CEE-M), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM), the Foundation Agropolis Open Science program (project sustainable management of the babassu palm, 2014-2017) and the CNES TOSCA program (project CIC-TOOB 2013-2014), Barrière, Olivier (ed.), Behnassi, M. (ed.), David, Gilbert (ed.), Douzal, V. (ed.), Fargette, Mireille (ed.), Libourel, T. (ed.), Loireau, Maud (ed.), Pascal, L. (ed.), Prost, C. (ed.), Ravena Canete, V. (ed.), Seyler, Frédérique (ed.), Morand, S. (ed.), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, eco-socio-system, écosociosystème, télédétection, Population, 010501 environmental sciences, 010603 evolutionary biology, 01 natural sciences, Amazonian rainforest, remote sensing, Attalea speciosa, education, uses, 0105 earth and related environmental sciences, education.field_of_study, babaçu, [SHS.SOCIO]Humanities and Social Sciences/Sociology, [SHS.STAT]Humanities and Social Sciences/Methods and statistics, biology, Land use, babassu, Agroforestry, 15. Life on land, biology.organism_classification, Tree (data structure), Geography, dynamique de population, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, Sustainability, extractivism, dynamics of the population, extractivisme, usages, Palm, Forage crop
Abstract

Vol. 2: Coviability Questioned by a Diversity of Situations Chapitre 40 La version en français sera publiée ultérieurement aux éditions Matériologiques en co-édition avec les éditions IRD; International audience; The babassu palm tree (Attalea speciosa Mart. ex Spreng.) is a species native to the Amazonian rainforest. The invasive nature of this palm tree results in a high density of babassu palm trees with a subsequent decrease in forage crop production. This is a serious problem for local farmers who have tried to resolve it by removing mature palms, seedlings and young individuals. Within these conditions, is coviability between the babassu palm tree and society possible? Our work consisted in developing tools and methods with the aim of producing knowledge and providing answers to this issue within a given territory. To understand the eco-socio-system, we have explored the available knowledge in the literature, produced specific field data, tools and methods such as mathematical modeling (dynamics of the palm tree population) and remote sensing (land use analysis thanks to Landsat high-resolution images and automatic detection of mature palm trees using Pleiades and GeoEye very high-resolution images). This multidisciplinary research in progress has already given us a good overview of the current situation of this eco-socio-system, enabling us to consider the best way to ensure its sustainability.

Published
2019
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11. A stage-structured hierarchical Bayes model for the babassu palm tree population dynamics – Estimated from anthropogenic open area data sets

Author

Patrice Loisel, Danielle Mitja, Bénédicte Fontez, Alessio Moreira dos Santos, Thérèse Libourel, Nikolay Sirakov, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UMR 228 Espace-Dev, Espace pour le développement, Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), Université de Montpellier (UM), SARH – Instituto Ambiental e de Recursos Hídricos, Universidade Federal Rural da Amazônia (UFRA), This research work has been accomplished as a part of the Open Science research project (under the reference ID 1403-026) financed by the Agropolis Foundation and by the French National Institute of Agronomical Research (INRA) and Montpellier SupAgro., Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and Université des Antilles (UA)-Université de Guyane (UG)-Université de Montpellier (UM)-Université de La Réunion (UR)-Avignon Université (AU)-Université de Perpignan Via Domitia (UPVD)-Institut de Recherche pour le Développement (IRD)

Subjects
0106 biological sciences, Population dynamics, Population, Bayesian statistics, palmier, 010603 evolutionary biology, 01 natural sciences, Bottleneck, Bayes' theorem, modèle mathématique, Deforestation, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Attalea speciosa, population dynamics, mathematical modelling, education, estimation statistique, education.field_of_study, Mathematical modelling, biology, Amazon rainforest, Agroforestry, 010604 marine biology & hydrobiology, Ecological Modeling, 15. Life on land, biology.organism_classification, modèle bayésien, Tree (data structure), statistical estimation, dynamique des populations, Geography, palm tree, Babassu palm tree, mathematical model
Abstract

The babassu palm tree (Attalea speciosa Mart. ex Spreng.) is an endemic species of Amazon forests, and has social and economical impact/utility. Deforestation highlights this palm tree in anthropogenic open areas (pastures and cultivated fields). Simultaneously, knowledge concerning the sustainable functioning of the species within these manmade environments is sorely lacking: its life cycle is not well known, and its population dynamics remains unstudied. In this study, our objective was to generate a model of the population dynamics of the babassu palm tree, validated by in situ analysis, to understand how babassu, a forest species, adapts to pastureland and, under certain conditions, becomes invasive. We propose a random matrix model with aggregated variables based on the biological stages of the species as the input. The probabilities of the between-stage transition matrix were modelled using a Dirichlet-multinomial model with a hierarchy taking geographical organization, i.e. transect level, into account. The integration of prior information was formulated through a Bayesian approach. This Bayesian hierarchical matrix model enabled us to demonstrate a bottleneck in the population dynamics and a high year-dependent mortality rate at an early stage.

Published
2019
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12. Bayesian hierarchical modeling: application to the babassu palm tree population dynamics in Brazil

Author

Nikolay Sirakov, Patrice Loisel, Bénédicte Fontez Nguyen The, Danielle Mitja, Thérèse Libourel Rouge, Alessio dos Santos Moreira, Izildinha Miranda, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD), Universidade Federal Rural da Amazônia (UFRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)

Subjects
population dynamics, babassu palm tree, bayesian modeling, [INFO]Computer Science [cs], [MATH]Mathematics [math]
Abstract

International audience; The babassu palm tree (Attalea speciosa Mart. ex Spreng.) is an endemic species of the amazonian forests. For decades, the progress of the pioneer front highlights this palm tree in the anthropogenic open areas: pastures and cultivated fields. The babassu is one of the "extractive" resources in Brazil: gathering activity followed by marketing of non-timber products. This activity involves people among the most disadvantaged in the country. Despite this fact, the knowledge of long term functioning of the palm tree is sorely lacking. Our goal is to understand its population dynamics in the pastures and to guide local populations towards a sustainable management of the species. Our modelization process is based on field data series collected between 2013 and 2015. This field research work was conducted in situ in the community of Benefica, state of Para, Brazil. First we selected transects inside pastures randomly, then we counted systematically all the individuals inside those transects. We had analyzed the babassu life cycle and we decided to modelize each one of the three major biological processes: mortality, growth and recruitment. We actually develop a multinomial hierarchical model approach which relies on aggregated data: sum of the individuals per stage and per transect. In this talk we present a Bayesian modeling framework analysis with MCMC algorithms for estimate mortality, growth and recruitment rates. Mortality and growth rates are estimated for all six biological stages. We detect and highlight a critical transition between stages 3 and 4. Biologicaly this transition corresponds to the transfer of the bud from the soil to the surface. The vulnerability of babassu thus increases enormously. Our results also underline differences between transects - important location variability.

Published
2016

13. Reciprocal sign epistasis and truncation selection: When is recombination favorable in a pre-breeding program with a selfing species?

Author

Bénédicte Fontez, Muriel Tavaud, Constance Vagne, Jacques David, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
Statistics and Probability, Linkage disequilibrium, bistability, reciprocal sign epistasis, Population, Biology, truncation selection, Haploidy, General Biochemistry, Genetics and Molecular Biology, Gene Frequency, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, education, Selection (genetic algorithm), Recombination, Genetic, education.field_of_study, Truncation selection, General Immunology and Microbiology, Models, Genetic, Applied Mathematics, Epistasis, Genetic, General Medicine, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Genetic architecture, recombination, Plant Breeding, Evolutionary biology, Modeling and Simulation, Epistasis, General Agricultural and Biological Sciences, Reciprocal, Sign (mathematics)
Abstract

Since the dawn of agriculture, humans have applied artificial selection on traits of interest, regardless of their genetic architecture. Yet, still today, most models used to study and streamline this process overlook genetic interactions. In this study, we determined the conditions in which a target genotype can be fixed when truncation selection is applied on an epistatic trait. Previous studies have shown that reciprocal sign epistasis with two fitness peaks of unequal height involves multiple equilibrium states, i.e. below one critical parameter value, such as a critical recombination rate, one genotype may be fixed, and above it, another one may be fixed. Using a haploid bi-locus model, we identified which genotype would be fixed, and how quickly, in an infinite population selected for a phenotypic trait subject to reciprocal sign epistasis with unequal peak heights, depending on two criteria: the recombination rate and percentage of selected individuals. The critical parameter values at which bistability sets in, were also calculated. These results were complemented by stochastic simulations in finite populations. Our results confirmed that, in the case of fitness under reciprocal sign epistasis, high recombination rates induce blockage at the local optimum or attainment of an equilibrium state between the two peaks. However, if linkage disequilibrium is negative in the initial population, recombination is necessary to create the most favorable genotype. Therefore, in this case, reciprocal sign epistasis favors non-null recombination rates, particularly if selection is intense.

Published
2015
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14. Prevalence of multidrug resistant (MDR) Salmonella in bovine dairy herds in western France

Author

Joël Chadoeuf, Renaud Lailler, Anne Brisabois, Moez Sanaa, Yves Millemann, Bénédicte Fontez, Catherine Colmin, Biostatistique et Processus Spatiaux (BioSP), and Institut National de la Recherche Agronomique (INRA)

Subjects
Salmonella, Veterinary medicine, Epidemiologic study, 040301 veterinary sciences, animal diseases, Cattle Diseases, Microbial Sensitivity Tests, Drug resistance, Biology, medicine.disease_cause, 0403 veterinary science, Feces, 03 medical and health sciences, Food Animals, Risk Factors, Drug Resistance, Multiple, Bacterial, Odds Ratio, Prevalence, medicine, Animals, Cluster Analysis, [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Salmonella Infections, Animal, 0303 health sciences, 030306 microbiology, Dairy herds, REPARTITION SPATIALE, 04 agricultural and veterinary sciences, Multiple drug resistance, Herd, Population study, Cattle, Female, Animal Science and Zoology, France, Herd prevalence
Abstract

As a part of our effort in quantitative risk analysis of food-borne diseases, we carried out an epidemiologic study to estimate the prevalence of multidrug resistant (MDR) Salmonella in dairy herds situated in western France. The study population consisted of 489 farms in the region and manure or slurry was sampled from these operations and tested for the Salmonella spp. All strains isolated during the study were serotyped and tested for their antimicrobial susceptibility. Salmonella spp. was isolated from 8.1% (95% confidence interval (CI 95%): 4.5–13.3%) of the sampled herds. The herd prevalence of MDR Salmonella among the sampled herds was 1.9% (CI 95%: 0.5–5.4%). Spatial statistics were used to check for sampling representativeness and to determine if infected herds were clustered spatially.

Published
2005
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15. Test d'adéquation en régression non-linéaire, cas des fonctions monotones

Author

Bénédicte Fontez, Gilles R. Ducharme, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
Combinatorics, 010104 statistics & probability, Goodness of fit, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Model selection, 010102 general mathematics, Test statistic, General Medicine, 0101 mathematics, 01 natural sciences, Nonlinear regression, ComputingMilieux_MISCELLANEOUS, Mathematics
Abstract

Resume Nous proposons un test d'adequation pour des modeles de regression non-lineaire monotone. Ce test s'appuie sur le paradigme des tests lisses de Neyman (1937) pour tester l'adequation des densites. Il s'applique tout particulierement aux fonctions de croissance. Nous completons cette approche en incorporant une methode de selection automatique des parametres du test par les donnees. Pour citer cet article : B. Fontez, G.R. Ducharme, C. R. Acad. Sci. Paris, Ser. I 338 (2004).

Published
2004
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16. Bayesian hierarchical model used to analyze regression between fish body size and scale size: application to rare fish species Zingel asper

Author

Bénédicte Fontez, L. Cavalli, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
Fish farming, Bayesian probability, hierarchical Bayes model, scales, Management, Monitoring, Policy and Law, Aquatic Science, lcsh:Aquaculture. Fisheries. Angling, mathematical method, Bayes' theorem, poisson, Frequentist inference, Statistics, Biologie animale, statistique appliquée, Bayesian hierarchical modeling, 14. Life underwater, zingel asper, méthode mathématique, Nature and Landscape Conservation, Water Science and Technology, Mathematics, lcsh:SH1-691, Animal biology, fish, Ecology, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Sampling (statistics), approche bayésienne, biology.organism_classification, Regression, back-calculation, Zingel asper, pisciculture, fish farming
Abstract

Key-words: hierarchical Bayes model, backcalculation, fish, scales, Zingel asper Back-calculation allows to increase available data on fish growth. The accuracy of back-calculation models is of paramount importance for growth analysis. Frequentist and Bayesian hierarchical approaches were used for regression between fish body size and scale size for the rare fish species Zingel asper. The Bayesian approach permits more reliable estimation of back-calculated size, taking into account biological information and cohort variability. This method greatly improves estimation of backcalculated length when sampling is uneven and/or small.

Published
2014
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17. Établissement d’équations entre le diamètre et le volume total de bois des arbres, adaptées au Cameroun

Author

Adeline Giraud, B. Riera, Samba Dorisca, Luc Durrieu De Madron, Bénédicte Fontez, Office National des Forêts International (ONFI), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Mécanismes adaptatifs : des organismes aux communautés (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Mécanismes adaptatifs : des organismes aux communautés, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, stock de carbone, 010504 meteorology & atmospheric sciences, REDD, Biomass, 01 natural sciences, resource preservation, biomasse, équation allométrique, redd, biomass, allometric equations, carbon stocks, Cameroon, méthode, forest, physiologie végétale, cameroun, conservation de la nature, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, forêt, conservation des ressources, applied mathematics, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Mathematics, Ecology, afrique, sahel, Forestry, statistique, 15. Life on land, nature preservation, mathématiques appliquées, foresterie, tree cultivation, 010606 plant biology & botany
Abstract

Le mécanisme financier de la Réduction des émissions dues à la déforestation et à la dégradation des forêts (Redd) intéresse les pays du bassin du Congo, qui disposent de peu de données précises sur les stocks de carbone en forêt. Les principales équations allométriques pantropicales disponibles ont pour paramètres : le diamètre, la hauteur et la densité spécifique du bois ; mais aucun des arbres mesurés ne provient de forêts africaines. Les rares équations établies en Afrique s'avèrent insuffisantes, notamment par déficit d'échantillon en arbres de grande taille. Ainsi, pour pallier cette carence, 55 arbres de 10 à 120 cm de diamètre, appartenant à 23 espèces, ont été mesurés en forêt dense semidécidue du Sud-Est du Cameroun. Après abattage, les arbres tronçonnés ont été mesurés jusqu'à la découpe d'un centimètre de diamètre. Cet échantillon a permis de relier le diamètre et le volume total de bois des arbres via des modèles polynomiaux et non linéaires (additif et multiplicatif). La biomasse des arbres pourra être alors déduite par l'utilisation de la densité spécifique et un facteur correctif pour le feuillage. Dans la perspective de cette étude, afin d'affiner les mesures, l'échantillon sera augmenté lors d'une prochaine campagne de mesures, pour mieux estimer le volume total des gros arbres., The REDD mechanism (Reducing Emissions from Deforestation and forest Degradation) is of interest to the Congo Basin countries, but they have few precise data on their forest carbon stocks. The parameters for the main pan-tropical allometric equations are tree height and diameter and specific timber density, but none of the trees measured are from African forests. The few equations established for Africa turn out to be insufficient, in particular because large trees are not sufficiently represented in the samples measured. To address this data deficit, we measured 55 trees with a diameter of 10 to 120 cm, from 23 different species in a dense semi-deciduous forest in south-eastern Cameroon. After felling, the logs were cross-cut and measured until the one centimetre in diameter cutting. The sample was used to link the diameter and total timber volume of the trees via polynomial non-linear models (addition and multiplication). Then tree biomass should be deduced by applying the specific density and a correction factor for foliage. In order to refine these measurements, the sample will be enlarged during a further measurement campaign to produce a closer estimation of the total volume of huge trees., El impacto de una explotación forestal en términos de emisión de carbono ha sido raramente contemplado en trabajos de investigación reales en África Central. Sin embargo, en el marco de los mecanismos REDD (Reducción de Emisiones por la Defo- restación y la Degradación), este problema plantea importantes desafíos con el incre- mento del número de concesiones sujetas a ordenación y la creciente importancia de las técnicas de aprovechamiento de bajo impacto. Este estudio constituye un ensayo de metanálisis que incluye las distintas experiencias procedentes de la literatura existente. Los datos así obtenidos se apli- caron a una hipotética explotación para elaborar un balance teórico del impacto en las reservas de carbono. Los resultados ponen de manifiesto que, con las hipótesis adoptadas, la ordenación de un bosque permitiría una reducción de la décima parte de las pérdidas de carbono, para una extracción por hectárea de 10 a 20 m 3 de madera de construcción; todo ello compa- rado con una concesión forestal convencio- nal sin manejo planificado. La parte funda- mental en el ahorro del carbono procedería sobre todo del aumento de los diámetros mínimos de aprovechamiento. Por otra parte, los beneficios que podrían impulsar la práctica de un aprovechamiento de bajo impacto serían los derivados de la mejora del trazado de pistas y carreteras, esto es: del 5 al 8% de las pérdidas de carbono debidas al aprovechamiento convencional. Estos beneficios son superiores al error constatado en la medición de biomasa por tala total, la más cerca de la realidad, hecho en Guayana francesa. Sin embargo, dichos beneficios son muy inferiores a los errores calculados en la estimación de la biomasa en varios estudios disponibles en la literatura científica. En cualquier caso, la implementación de la ordenación en una concesión forestal y el uso de técnicas de aprovechamiento de bajo impacto son capaces de generar una diferencia favora- ble de las reservas de carbono en el bos- que denso.

Published
2011

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