Parameter identification of the STICS crop model, using an accelerated formal MCMC approach

This study presents a Bayesian approach for the parameters’ identification of the STICS crop model based on the recently developed Differential Evolution Adaptive Metropolis (DREAM) algorithm. The posterior distributions of nine specific crop parameters of the STICS model were sampled with the aim to improve the growth simulations of a winter wheat (Triticum aestivum L.) culture. The results obtained with the DREAM algorithm were initially compared to those obtained with a Nelder-Mead Simplex algorithm embedded within the OptimiSTICS package. Then, three types of likelihood functions implemented within the DREAM algorithm were compared, namely the standard least square, the weighted least square, and a transformed likelihood function that makes explicit use of the coefficient of variation (CV). The results showed that the proposed CV likelihood function allowed taking into account both noise on measurements and heteroscedasticity which are regularly encountered in crop modellingPeer reviewe

Prediction of crop coefficients from fraction of ground cover and height: Practical application to vegetable, field and fruit crops with focus on parameterization

Research PaperThe A&P approach, developed by Allen and Pereira (2009), estimates single and basal crop coefficients (Kc and Kcb) from the observed fraction of ground cover (fc) and crop height (h). The practical application of the A&P for several crops was reviewed and tested in a companion paper (Pereira et al., 2020). The current study further addresses the derivation of optimal values for A&P parameter values representing canopy transparency (ML) and stomatal adjustment (Fr), and tests the resulting model performance. Values reported in literature of ML and Fr were analysed. Optimal ML and Fr values were derived by a numerical search that minimized the differences between Kcb A&P with standard Kcb for vegetable, field, and fruit crops as tabulated by Pereira et al. (2021a, 2021b) and Rallo et al. (2021). Sources for fc were literature reviews supplemented by a remote sensing survey. Computed Kcb and Kc for mid- and end-season together with associated parameters values were tabulated. To improve the usability of the ML and Fr parameters a cross validation was performed, which consisted of the linear regression between Kcb computed by A&P and observed Kcb relative to independent data sets obtained from field observations. Results show that both series of Kcb match well, with regression coefficients very close to 1.0, coefficients of determination near 1.0, and root mean square errors (RMSE) of 0.06 for the annual crops and RMSE = 0.07 for the trees and vines. These errors represent less than 10% of most of the computed tabulated Kcb. The tabulated Fr and ML of this paper can be regarded as defaults to support A&P field practice when observations of fc and h are performed. Therefore, the A&P approach shows to be appropriate for use in irrigation scheduling and planning when fc and h are observed using ground and/or remote sensing, hence supporting irrigation water savingsinfo:eu-repo/semantics/publishedVersio

Non-invasive measurement of fluids exchanges induced by cardiorespiratory activity on the small animal : toward a "virtual aortic flowprobe"

Il est avéré que les signaux de pléthysmographie par inductance comportent des composantes cardiaques et respiratoires pouvant présenter un intérêt pour un suivi physiologique. Cette technique est largement utilisée chez l’homme et chez les mammifères de taille moyenne, mais n’a jamais été mise en œuvre chez les petits rongeurs de laboratoire comme le rat. Cette thèse vise à apporter la preuve analytique et expérimentale (TRL3) d’une application cardiaque de la pléthysmographie cardiorespiratoire par inductance (PCRI) fondée sur le concept amont de « bague aortique virtuelle » (BAOV). La BAOV permet de mettre en œuvre une mesure externe des débits aortiques « instantanés » à l’aide de la PCRI en lieu et place d’un instrument positionné autour du vaisseau lui-même.La thèse a débuté par une phase de spécification et de conception guidée par l’interdépendance entre la physiologie et les contraintes instrumentales. Les performances métrologiques à atteindre sont dictées par un saut d’échelle entre l’homme et le rat. Le développement d’une chaine de mesure optimisée a permis de repousser les limites des systèmes existants en rendant possible la mesure de variations de volumes de quelques microlitres. En parallèle, l’identification de critères de validation, de méthodes de référence et la mise au point de protocoles expérimentaux ont conduit à la définition d’une stratégie de validation de l’instrument de mesure développé et du concept de BAOV.À l’issue de ces trois années, un système de PCRI à ultra-haute résolution a été mis au point. Après calibration, l’exactitude sur les mesures de variations de section est de 5 % sur un banc de test micrométrique. L’interchangeabilité de la mesure des variations de volume du thorax sur la gamme physiologique a été évaluée par rapport à une mesure pneumotachographique sur 9 animaux anesthésiés. Les limites d’agrément obtenues sont inférieures à 20 %. L’induction d’un challenge hémodynamique sur 11 animaux anesthésiés dont le débit aortique est mesuré en parallèle avec la PCRI et une bague de débit ultrasonique placée au niveau sous-diaphragmatique démontre l’équivalence entre les deux systèmes. Par ailleurs, la grande similitude entre les signaux de débits des deux méthodes valide le concept de bague aortique virtuelle proposéIt is recognized that inductive plethysmographic signals contain cardiac and respiratory components, which can be of interest for physiological monitoring. This technology is widely used in humans and medium mammals, but it has never been implemented in small laboratory rodents. This PhD aims to provide the analytic and experimental proof (TRL3) of a cardiac application of the cardio-respiratory inductive plethysmography (CRIP), based on the upstream concept of an “virtual aortic probe” (VAP). The VAP allows to realize an extern measure of “instantaneous” aortic flows thanks to CRIP instead of an instrument located directly around the vessel.The PhD starts with a phase of specification and conception driven by the interdependency between physiology and instrumental constraints. The expected metrological performances are established by a scale jumping between man and rat. The development of an optimized acquisition line has enabled to stretch the limits of existing systems; it allows to measure volume variations of a few microliters. At the same time, validation criteria and reference methods have been identified and experimental protocols have been specified in order to define the validation strategy of the developed instrument and VAP concept.At the end of these 3 years, an ultra-high resolution CRIP system has been developed. After calibration, the accuracy on the section variation measurements is 5% on a micrometric test-bench. The interchangeability of the thorax volume variation measure on a physiological range has been evaluated by comparison with a pneumotachographic measure on 9 anesthetized animals and the limits of agreement are lower than 20%. A hemodynamic challenge has been induced on 11 anesthetized animals, and the aortic flow has been simultaneously measured by CRIP and with an ultrasonic flow probe at under diaphragm level. This demonstrates the equivalence between both systems. And the high similarity between flow signals from both methods validates the proposed concept of virtual aortic prob

Mesure non invasive de suivi des transferts de fluides liés aux activités cardiorespiratoires chez le rat : vers une «bague aortique virtuelle»

It is recognized that inductive plethysmographic signals contain cardiac and respiratory components, which can be of interest for physiological monitoring. This technology is widely used in humans and medium mammals, but it has never been implemented in small laboratory rodents. This PhD aims to provide the analytic and experimental proof (TRL3) of a cardiac application of the cardio-respiratory inductive plethysmography (CRIP), based on the upstream concept of an “virtual aortic probe” (VAP). The VAP allows to realize an extern measure of “instantaneous” aortic flows thanks to CRIP instead of an instrument located directly around the vessel.The PhD starts with a phase of specification and conception driven by the interdependency between physiology and instrumental constraints. The expected metrological performances are established by a scale jumping between man and rat. The development of an optimized acquisition line has enabled to stretch the limits of existing systems; it allows to measure volume variations of a few microliters. At the same time, validation criteria and reference methods have been identified and experimental protocols have been specified in order to define the validation strategy of the developed instrument and VAP concept.At the end of these 3 years, an ultra-high resolution CRIP system has been developed. After calibration, the accuracy on the section variation measurements is 5% on a micrometric test-bench. The interchangeability of the thorax volume variation measure on a physiological range has been evaluated by comparison with a pneumotachographic measure on 9 anesthetized animals and the limits of agreement are lower than 20%. A hemodynamic challenge has been induced on 11 anesthetized animals, and the aortic flow has been simultaneously measured by CRIP and with an ultrasonic flow probe at under diaphragm level. This demonstrates the equivalence between both systems. And the high similarity between flow signals from both methods validates the proposed concept of virtual aortic probeIl est avéré que les signaux de pléthysmographie par inductance comportent des composantes cardiaques et respiratoires pouvant présenter un intérêt pour un suivi physiologique. Cette technique est largement utilisée chez l’homme et chez les mammifères de taille moyenne, mais n’a jamais été mise en œuvre chez les petits rongeurs de laboratoire comme le rat. Cette thèse vise à apporter la preuve analytique et expérimentale (TRL3) d’une application cardiaque de la pléthysmographie cardiorespiratoire par inductance (PCRI) fondée sur le concept amont de « bague aortique virtuelle » (BAOV). La BAOV permet de mettre en œuvre une mesure externe des débits aortiques « instantanés » à l’aide de la PCRI en lieu et place d’un instrument positionné autour du vaisseau lui-même.La thèse a débuté par une phase de spécification et de conception guidée par l’interdépendance entre la physiologie et les contraintes instrumentales. Les performances métrologiques à atteindre sont dictées par un saut d’échelle entre l’homme et le rat. Le développement d’une chaine de mesure optimisée a permis de repousser les limites des systèmes existants en rendant possible la mesure de variations de volumes de quelques microlitres. En parallèle, l’identification de critères de validation, de méthodes de référence et la mise au point de protocoles expérimentaux ont conduit à la définition d’une stratégie de validation de l’instrument de mesure développé et du concept de BAOV.À l’issue de ces trois années, un système de PCRI à ultra-haute résolution a été mis au point. Après calibration, l’exactitude sur les mesures de variations de section est de 5 % sur un banc de test micrométrique. L’interchangeabilité de la mesure des variations de volume du thorax sur la gamme physiologique a été évaluée par rapport à une mesure pneumotachographique sur 9 animaux anesthésiés. Les limites d’agrément obtenues sont inférieures à 20 %. L’induction d’un challenge hémodynamique sur 11 animaux anesthésiés dont le débit aortique est mesuré en parallèle avec la PCRI et une bague de débit ultrasonique placée au niveau sous-diaphragmatique démontre l’équivalence entre les deux systèmes. Par ailleurs, la grande similitude entre les signaux de débits des deux méthodes valide le concept de bague aortique virtuelle propos

Mesure non invasive de suivi des transferts de fluides liés aux activités cardiorespiratoires chez le rat : vers une «bague aortique virtuelle»

It is recognized that inductive plethysmographic signals contain cardiac and respiratory components, which can be of interest for physiological monitoring. This technology is widely used in humans and medium mammals, but it has never been implemented in small laboratory rodents. This PhD aims to provide the analytic and experimental proof (TRL3) of a cardiac application of the cardio-respiratory inductive plethysmography (CRIP), based on the upstream concept of an “virtual aortic probe” (VAP). The VAP allows to realize an extern measure of “instantaneous” aortic flows thanks to CRIP instead of an instrument located directly around the vessel.The PhD starts with a phase of specification and conception driven by the interdependency between physiology and instrumental constraints. The expected metrological performances are established by a scale jumping between man and rat. The development of an optimized acquisition line has enabled to stretch the limits of existing systems; it allows to measure volume variations of a few microliters. At the same time, validation criteria and reference methods have been identified and experimental protocols have been specified in order to define the validation strategy of the developed instrument and VAP concept.At the end of these 3 years, an ultra-high resolution CRIP system has been developed. After calibration, the accuracy on the section variation measurements is 5% on a micrometric test-bench. The interchangeability of the thorax volume variation measure on a physiological range has been evaluated by comparison with a pneumotachographic measure on 9 anesthetized animals and the limits of agreement are lower than 20%. A hemodynamic challenge has been induced on 11 anesthetized animals, and the aortic flow has been simultaneously measured by CRIP and with an ultrasonic flow probe at under diaphragm level. This demonstrates the equivalence between both systems. And the high similarity between flow signals from both methods validates the proposed concept of virtual aortic probeIl est avéré que les signaux de pléthysmographie par inductance comportent des composantes cardiaques et respiratoires pouvant présenter un intérêt pour un suivi physiologique. Cette technique est largement utilisée chez l’homme et chez les mammifères de taille moyenne, mais n’a jamais été mise en œuvre chez les petits rongeurs de laboratoire comme le rat. Cette thèse vise à apporter la preuve analytique et expérimentale (TRL3) d’une application cardiaque de la pléthysmographie cardiorespiratoire par inductance (PCRI) fondée sur le concept amont de « bague aortique virtuelle » (BAOV). La BAOV permet de mettre en œuvre une mesure externe des débits aortiques « instantanés » à l’aide de la PCRI en lieu et place d’un instrument positionné autour du vaisseau lui-même.La thèse a débuté par une phase de spécification et de conception guidée par l’interdépendance entre la physiologie et les contraintes instrumentales. Les performances métrologiques à atteindre sont dictées par un saut d’échelle entre l’homme et le rat. Le développement d’une chaine de mesure optimisée a permis de repousser les limites des systèmes existants en rendant possible la mesure de variations de volumes de quelques microlitres. En parallèle, l’identification de critères de validation, de méthodes de référence et la mise au point de protocoles expérimentaux ont conduit à la définition d’une stratégie de validation de l’instrument de mesure développé et du concept de BAOV.À l’issue de ces trois années, un système de PCRI à ultra-haute résolution a été mis au point. Après calibration, l’exactitude sur les mesures de variations de section est de 5 % sur un banc de test micrométrique. L’interchangeabilité de la mesure des variations de volume du thorax sur la gamme physiologique a été évaluée par rapport à une mesure pneumotachographique sur 9 animaux anesthésiés. Les limites d’agrément obtenues sont inférieures à 20 %. L’induction d’un challenge hémodynamique sur 11 animaux anesthésiés dont le débit aortique est mesuré en parallèle avec la PCRI et une bague de débit ultrasonique placée au niveau sous-diaphragmatique démontre l’équivalence entre les deux systèmes. Par ailleurs, la grande similitude entre les signaux de débits des deux méthodes valide le concept de bague aortique virtuelle propos

Partitioning of stored and current assimilates in sunflower as influenced by timing of water stress

4 tablesInternational audienc

Rapeseed is an efficient energy crop which can still improve

The ability of biofuels to contribute efficiently to the replacement of fossil energy and to the reduction of greenhouse gas emissions has been a matter of debate. Hence, there is a need to assess accurately the energy balance of biofuels and their ability to reduce greenhouse gas emissions, in order to evaluate and to improve the benefit for society. In rapeseed, the energy ratio (energy produced per unit of non-renewable energy input) is well above 2 whatever the method of calculation. In order to investigate the variability of energy ratios and to identify ways of improvement, a study was conducted in France in 2005 and 2006. The method of mass allocation of input energy was used for calculations, instead of the substitution method, because with this method the results do not depend on the utilization of co-products. Hence, this method is better adapted to follow improvements. A great variability in the energy ratio was observed in 2005 and 2006. Seed yields and energy cost of fertilizer N explained most of this variability. Hence, improvements should focus on increasing yield with little increase in energy cost, and on decreasing wasting of N fertilizer. However the farmer incomes, and the net production of energy per hectare, must also be a matter of concern. The inventories of greenhouse gas emissions of biofuels are still uncertain because of the great variability of soil emissions, due to environmental and management factors. Hence, in order to assess the effect of rapeseed on greenhouse gas emissions, methods based on process-oriented models accounting for these factors must be used. Such models give promising results, but further testing is still needed

Rapeseed is an efficient energy crop which can still improve

The ability of biofuels to contribute efficiently to the replacement of fossil energy and to the reduction of greenhouse gas emissions has been a matter of debate. Hence, there is a need to assess accurately the energy balance of biofuels and their ability to reduce greenhouse gas emissions, in order to evaluate and to improve the benefit for society. In rapeseed, the energy ratio (energy produced per unit of non-renewable energy input) is well above 2 whatever the method of calculation. In order to investigate the variability of energy ratios and to identify ways of improvement, a study was conducted in France in 2005 and 2006. The method of mass allocation of input energy was used for calculations, instead of the substitution method, because with this method the results do not depend on the utilization of co-products. Hence, this method is better adapted to follow improvements. A great variability in the energy ratio was observed in 2005 and 2006. Seed yields and energy cost of fertilizer N explained most of this variability. Hence, improvements should focus on increasing yield with little increase in energy cost, and on decreasing wasting of N fertilizer. However the farmer incomes, and the net production of energy per hectare, must also be a matter of concern. The inventories of greenhouse gas emissions of biofuels are still uncertain because of the great variability of soil emissions, due to environmental and management factors. Hence, in order to assess the effect of rapeseed on greenhouse gas emissions, methods based on process-oriented models accounting for these factors must be used. Such models give promising results, but further testing is still needed