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  1. Article ; Online: Practical Identifiability of Plant Growth Models: A Unifying Framework and Its Specification for Three Local Indices.

    Velluet, Jean / Noce, Antonin Della / Letort, Véronique

    Plant phenomics (Washington, D.C.)

    2024  Volume 6, Page(s) 133

    Abstract: ... identifiability analysis addresses this issue under the assumption of perfect observations of system dynamics ... whereas practical identifiability considers limited measurements and the accompanying noise. In the literature ... definitions for structural identifiability vary only slightly among authors, whereas the concept and ...

    Abstract Amid the rise of machine learning models, a substantial portion of plant growth models remains mechanistic, seeking to capture an in-depth understanding of the underlying phenomena governing the system's dynamics. The development of these models typically involves parameter estimation from experimental data. Ensuring that the estimated parameters align closely with their respective "true" values is crucial since they hold biological interpretation, leading to the challenge of uniqueness in the solutions. Structural identifiability analysis addresses this issue under the assumption of perfect observations of system dynamics, whereas practical identifiability considers limited measurements and the accompanying noise. In the literature, definitions for structural identifiability vary only slightly among authors, whereas the concept and quantification of practical identifiability lack consensus, with several indices coexisting. In this work, we provide a unified framework for studying identifiability, accommodating different definitions that need to be instantiated depending on each application case. In a more applicative second step, we focus on three widely used methods for quantifying practical identifiability: collinearity indices, profile likelihood, and average relative error. We show the limitations of their local versions, and we propose a new risk index built on the profile likelihood-based confidence intervals. We illustrate the usefulness of these concepts for plant growth modeling using a discrete-time individual plant growth model, LNAS, and a continuous-time plant population epidemics model. Through this work, we aim to underline the significance of identifiability analysis as a complement to any parameter estimation study and offer guidance to the modeler.
    Language English
    Publishing date 2024-02-09
    Publishing country United States
    Document type Journal Article
    ISSN 2643-6515
    ISSN (online) 2643-6515
    DOI 10.34133/plantphenomics.0133
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Predicting tomato water consumption in a hydroponic greenhouse: contribution of light interception models.

    Florakis, Konstantinos / Trevezas, Samis / Letort, Véronique

    Frontiers in plant science

    2023  Volume 14, Page(s) 1264915

    Abstract: ... employing reference parameter values from previously published papers and re-estimating, for identifiability ...

    Abstract In recent years, hydroponic greenhouse cultivation has gained increasing popularity: the combination of hydroponics' highly efficient use of resources with a controlled environment and an extended growing season provided by greenhouses allows for optimized, year-round plant growth. In this direction, precise and effective irrigation management is critical for achieving optimal crop yield while ensuring an economical use of water resources. This study explores techniques for explaining and predicting daily water consumption by utilizing only easily readily available meteorological data and the progressively growing records of the water consumption dataset. In situations where the dataset is limited in size, the conventional purely data-based approaches that rely on statistically benchmarking time series models tend to be too uncertain. Therefore, the objective of this study is to explore the potential contribution of crop models' main concepts in constructing more robust models, even when plant measurements are not available. Two strategies were developed for this purpose. The first strategy utilized the Greenlab model, employing reference parameter values from previously published papers and re-estimating, for identifiability reasons, only a limited number of parameters. The second strategy adopted key principles from crop growth models to propose a novel modeling approach, which involved deriving a Stochastic Segmentation of input Energy (SSiE) potentially absorbed by the elementary photosynthetically active parts of the plant. Several model versions were proposed and adjusted using the maximum likelihood method. We present a proof-of-concept of our methodology applied to the ekstasis Tomato, with one recorded time series of daily water uptake. This method provides an estimate of the plant's dynamic pattern of light interception, which can then be applied for the prediction of water consumption. The results indicate that the SSiE models could become valuable tools for extracting crop information efficiently from routine greenhouse measurements with further development and testing. This, in turn, could aid in achieving more precise irrigation management.
    Language English
    Publishing date 2023-11-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1264915
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Parameter estimation of perfusion models in dynamic contrast-enhanced imaging: a unified framework for model comparison.

    Romain, Blandine / Rouet, Laurence / Ohayon, Daniel / Lucidarme, Olivier / d'Alché-Buc, Florence / Letort, Véronique

    Medical image analysis

    2017  Volume 35, Page(s) 360–374

    Abstract: ... global sensitivity analysis, structural and practical identifiability analysis, parameter estimation and ...

    Abstract Patients follow-up in oncology is generally performed through the acquisition of dynamic sequences of contrast-enhanced images. Estimating parameters of appropriate models of contrast intake diffusion through tissues should help characterizing the tumour physiology. However, several models have been developed and no consensus exists on their clinical use. In this paper, we propose a unified framework to analyse models of perfusion and estimate their parameters in order to obtain reliable and relevant parametric images. After defining the biological context and the general form of perfusion models, we propose a methodological framework for model assessment in the context of parameter estimation from dynamic imaging data: global sensitivity analysis, structural and practical identifiability analysis, parameter estimation and model comparison. Then, we apply our methodology to five of the most widely used compartment models (Tofts model, extended Tofts model, two-compartment model, tissue-homogeneity model and distributed-parameters model) and illustrate the results by analysing the behaviour of these models when applied to data acquired on five patients with abdominal tumours.
    MeSH term(s) Abdominal Neoplasms/diagnostic imaging ; Algorithms ; Humans ; Models, Biological ; Perfusion ; Tomography, X-Ray Computed/methods
    Language English
    Publishing date 2017
    Publishing country Netherlands
    Document type Comparative Study ; Journal Article
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2016.07.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  4. Article ; Online: Microtubule Dynamics Scale with Cell Size to Set Spindle Length and Assembly Timing.

    Lacroix, Benjamin / Letort, Gaëlle / Pitayu, Laras / Sallé, Jérémy / Stefanutti, Marine / Maton, Gilliane / Ladouceur, Anne-Marie / Canman, Julie C / Maddox, Paul S / Maddox, Amy S / Minc, Nicolas / Nédélec, François / Dumont, Julien

    Developmental cell

    2018  Volume 45, Issue 4, Page(s) 496–511.e6

    Abstract: ... Our results suggest that scalability of the microtubule growth rate when cell size varies adapts spindle ...

    Abstract Successive cell divisions during embryonic cleavage create increasingly smaller cells, so intracellular structures must adapt accordingly. Mitotic spindle size correlates with cell size, but the mechanisms for this scaling remain unclear. Using live cell imaging, we analyzed spindle scaling during embryo cleavage in the nematode Caenorhabditis elegans and sea urchin Paracentrotus lividus. We reveal a common scaling mechanism, where the growth rate of spindle microtubules scales with cell volume, which explains spindle shortening. Spindle assembly timing is, however, constant throughout successive divisions. Analyses in silico suggest that controlling the microtubule growth rate is sufficient to scale spindle length and maintain a constant assembly timing. We tested our in silico predictions to demonstrate that modulating cell volume or microtubule growth rate in vivo induces a proportional spindle size change. Our results suggest that scalability of the microtubule growth rate when cell size varies adapts spindle length to cell volume.
    MeSH term(s) Animals ; Caenorhabditis elegans/embryology ; Caenorhabditis elegans/physiology ; Caenorhabditis elegans Proteins/metabolism ; Carrier Proteins/metabolism ; Cell Size ; Embryo, Nonmammalian/cytology ; Embryo, Nonmammalian/physiology ; Microtubules/physiology ; Paracentrotus/embryology ; Paracentrotus/physiology ; Spindle Apparatus/physiology
    Chemical Substances Caenorhabditis elegans Proteins ; Carrier Proteins
    Language English
    Publishing date 2018-05-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2018.04.022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5742: Show issues Location:
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