545 research outputs found
Towards an EDSL to enhance good modelling practice for non-linear stochastic discrete dynamical models Application to plant growth models
International audienceA computational formalism is presented that structures a C++ library which aims at the modelling, simulation and statistical analysis of stochastic non-linear discrete dynamical system models. Applications concern the development and analysis of general plant growth models
SystÚme informatique d'aide à la modélisation mathématique basé sur un langage de programmation dédié pour les systÚmes dynamiques discrets stochastiques.Application aux modÚles de croissance de plantes.
In agriculture, in order to predict crop yield or to reduce inputs, mathematical models of plant growth open new perspectives by simulating crop growth in interaction with the environment. In this thesis we will particularly focus on âmechanisticâ models based on the description of ecophysiological and archictectural processes in plants.Since the first attempts, in the seventies, the scientific community has created a large number of models with va- rious objectives : for instance, CERES, STICS, APSIM, LNAS as crop models and LIGNUM, ADEL, GreenLab, MAppleT as functional-structural models.These models have to be designed and evaluated with a rigourous process in several steps, according to what is usually described as âgood modelling practicesâ. The methods involved in the different steps are : sensitivity and uncertainty analysis, parameter estimation, model selection, data assimilation, optimal control ... According to the configuration of the study case, various algorithms can be used at each of these steps. The state-of-the-art software systems generally focus on one aspect of the global workflow, but very few focus on the workflow itself and propose the whole chain of mathematical methodologies adapted to the type of models and configurations faced in plant growth modelling : stochastic and nonlinear dynamical models involving a lot of processes and parameters, heterogeneous and irregular system observations.This thesis considers the formalization of stochastic dynamical models, of statistical methods and algorithms dedicated to their study and of the interface between models and algorithms to generate the analysis workflow. We deduce the conception of a software platform which allows modelers (or more exactly modelling teams, since the activity is quite complex) to create and validate crop/plant models by using a single language and dedicated statistical tools. Our system facilitates model design, sensitivity and uncertainty analysis, parameter estimation and evaluation from experimental data and optimization.Our research is at the heart of âquantitative agronomyâ which combines agronomy, modeling, statistics and computer science. We describe and formalize the type of models faced in agronomy and plant sciences and how we simulate them. We detail the good modelling practices workflow and which algorithms are available at all steps. Thanks to this formalization and tools, model studies can be conducted in an easier and more efficient way. It is illustrated on several test cases, particularly for the LNAS and STICS models. Based on this conception and results, we also discuss the possibility to deduce an ontology and a domain-specific language in order to improve the communication between experts. Finally, we conclude about the perspectives in terms of community platforms, first generally for modellers, and second more specifically in quantitative agronomy.Afin de preÌvoir les rendements ou reÌduire la consommation dâintrants nous pouvons, en exploitant les donneÌes expeÌrimentales, creÌer des modeÌles matheÌmatiques afin de simuler la croissance des cultures en fonction des caracteÌristiques de lâenvironnement. Dans cette optique, cette theÌse sâinteÌresse particulieÌrement aux modeÌles dits âmeÌcanistesâ.Des premieÌres tentatives, dans les anneÌes 70, aÌ nos jours, il y a eu pleÌthore de nouveaux modeÌles creÌeÌs, aÌ diffeÌrentes eÌchelles, afin dâeÌtudier certains pheÌnomeÌnes dans les cultures ou au sein des plantes. On peut par exemple citer : CERES, STICS, APSIM, LNAS pour les modeÌles dits de culture ou LIGNUM, ADEL, GreenLab, MAppleT, pour les modeÌles dits structure-fonction.Ces modeÌles neÌcessitent dâeÌtre creÌeÌs et eÌvalueÌs en conduisant une analyse rigoureuse posseÌdant de nombreuses eÌtapes et dont chacune est composeÌe de plusieurs algorithmes complexes. Cette eÌtude devrait sâinscrire dans une deÌmarche dite de bonnes pratiques de modeÌlisation, âGood Modelling Practicesâ. On peut citer comme fonctionnaliteÌs : lâanalyse de sensibiliteÌ, lâestimation parameÌtrique, lâanalyse dâincertitude, lâassimilation de donneÌes, la seÌlection de modeÌles, le controÌle optimal ... En fonction de la configuration du cas, chacune de ces fonctionnaliteÌs peut faire appel aÌ un grand nombre dâalgorithmes avec chacun des caracteÌristiques propres. On retrouve dans lâeÌtat de lâart des plateformes qui sâoccupent souvent dâune fonctionnaliteÌ mais treÌs rarement qui sâattaquent aÌ lâensemble de la chaiÌne de travail.Cette theÌse propose une formalisation des modeÌles dynamiques stochastiques (cadre adapteÌ aÌ la modeÌlisation des plantes), de meÌthodes et algorithmes statistiques deÌdieÌs aÌ leur eÌtude et de lâinterfaçage entre les modeÌles et les algorithmes dans cette chaiÌne de travail. Nous en deÌduisons la conception dâun systeÌme informatique (ou plateforme logicielle) permettant dâaider les modeÌlisateurs, ou plutoÌt les eÌquipes de modeÌlisation tant lâactiviteÌ est complexe et transverse, afin de creÌer et valider des modeÌles agronomiques par le truchement dâun langage deÌdieÌ et dâoutils statistiques associeÌs. Le systeÌme facilite ainsi lâeÌcriture des modeÌles, leur analyse de sensibiliteÌ, leur identification parameÌtrique et leur eÌvaluation aÌ partir de donneÌes expeÌrimentales, leur optimisation. Notre domaine dâeÌtude est au coeur de âlâagronomie quantitativeâ, qui combine aÌ la fois agronomie, modeÌlisation, statistiques et informatique. Nous deÌcrirons les types de modeÌles matheÌmatiques pris en compte et comment nous les traduisons sur machine afin de permettre des simulations. Puis nous passerons en revue le flux de travail geÌneÌral ainsi que les algorithmes utiliseÌs afin de montrer la conduite geÌneÌrale des eÌtudes qui sont deÌsormais plus facilement et rapidement faisables. Ce flux sera testeÌ sur plusieurs cas dâeÌtude, en particulier pour les modeÌles LNAS et STICS. Finalement, nous ouvrirons sur la possibiliteÌ dâinjecter ces eÌtudes dans une base de connaissance geÌneÌrale, ou ontologie, avec un langage deÌdieÌ avant de conclure sur les perspectives du travail deÌveloppeÌ pour la communauteÌ et notamment celles en termes de plateformes aÌ destination des modeÌlisateurs en geÌneÌral et des utilisateurs des modeÌles agronomiques en particulier
RĂŽle de la mutation Vav1R63W dans la sensibilitĂ© Ă lâasthme allergique
Dans mon Ă©quipe dâaccueil, une dissection gĂ©nĂ©tique Ă l'aide des lignĂ©es de rats congĂ©niques BN.LEW a permis d'identifier un polymorphisme sur le gĂšne Vav1. Ce polymorphisme se caractĂ©rise par la substitution dâune arginine (R) chez le rat LEW en tryptophane (W) chez le rat BN, en position 63 de la protĂ©ine Vav1 et pourrait ĂȘtre impliquĂ© dans la diffĂ©rence de sensibilitĂ© des rats LEW (rĂ©sistants) et BN (sensibles) aux manifestations allergiques. Pour tester cette hypothĂšse, une souris Knock-In (KI) Vav1R63W, sur fond gĂ©nĂ©tique C57BL/6, a Ă©tĂ© gĂ©nĂ©rĂ©e et, dans cette Ă©tude, elle est comparĂ©e Ă une souris sauvage (Wild-Type, WT) portant une R. Ma thĂšse a eu pour premier objectif dâĂ©tudier lâimpact de ce polymorphisme sur le dĂ©veloppement et sur la fonction des lymphocytes T. Jâai dĂ©montrĂ© que les souris KI prĂ©sentent un dĂ©veloppement thymique normal mais possĂšdent plus de lymphocytes T rĂ©gulateurs (Treg) que les souris WT. De plus, les lymphocytes T CD4+ de ces souris KI prĂ©sentent un dĂ©sĂ©quilibre de la balance Th1/Th2, caractĂ©risĂ© par une augmentation de la production dâIL-4 (Th2) et une diminution de la production dâIFNy (Th1). Le deuxiĂšme but de ma thĂšse a Ă©tĂ© dâanalyser la susceptibilitĂ© de ces souris KI Ă un modĂšle dâasthme allergique. LâĂ©tude de cette maladie est importante puisquâelle reprĂ©sente un enjeu de santĂ© publique. Lâasthme rĂ©sulte dâune rĂ©ponse immunitaire aberrante de type Th2 Ă des allergĂšnes inhalĂ©s. Chez les souris KI, un protocole dâinduction de lâasthme a entraĂźnĂ© une rĂ©action inflammatoire plus importante que chez les souris WT. Cette Ă©tude prĂ©liminaire tend Ă montrer que les souris KI sont plus sensibles Ă une maladie de type Th2 et quâelles possĂšdent plus de Treg. Elle confirme le rĂŽle important de Vav1 dans la rĂ©ponse immunitaire, et particuliĂšrement dans la balance Th1/Th2
Alan Ayckbourn's theatricality and use of comedy in Woman in Mind, A Small Family Business and Henceforward: marriage, family, private-public and absence of standards
Ankara : Faculty of Letters and Institute of Economics and Social Sciences, Bilkent Univ., 1994.Thesis (Master's) -- Bilkent University, 1994.Includes bibliographical refences.The aim of this dissertation is to focus on three of Alan
Ayckbourn's recent plays, namely Woman in Mind, A Small Business
and Henceforward in order to analyse how Ayckbourn employs visual
elements and how he creates comedy while he writes about such
themes as the destruction of marriage and its effects on
children,the inseparable nature of private and public and the
absence of standards.Bayol, EbruM.S
Corrosion Inhibition of Copper in Sea Water Using Derivatives of Thiosemicarbazides
Three corrosion inhibitors namely: 4-allyl-3-thiosemicarbazide C4H9N3 S, 4-(1-methyl)-3-thiosemicarbazide,4-tolyl-3-thiosemicarbazide were tested as corrosion inhibitors for copper in sea water environmnt.Copper samples were tested using potentiodynamic polarization technique in the absence and in the presence of corrosion inhibitors.  High inhibition efficiencies (â„95%) were shown by the tested inhibitors. The best performance was shown by 4-tolyl-3-TSC
The relationship between secondary and high school education in reading and the reading strategy use of freshman students at Middle East Technical University (METU) while reading in English
Ankara : Institute of Economics and Social Sciences of Bilkent University, 1998.Thesis (Master's) -- -Bilkent University, 1998.Includes bibliographical references leaves 76-78The importance o f use o f strategies by the learners in the learning process has
been recognized due to the developments in cognitive psychology and the relationship
between cognition and language learning. Learning strategies are actions taken by the
learners to facilitate learning and make it more effective. Among the strategies used
by language learners, reading strategies are o f great significance. Especially in
second/foreign language learning contexts for academic purposes, reading is very
often required as university students have to read exhaustively in their studies. Their
comprehension o f the texts they read depends on their effective approach to them.
Therefore, researchers in the field o f second/foreign language reading have identified
reading strategies used by good readers The acquisition o f certain learning strategies start in pre-university years. In
particular, in secondary and high school education learners are required to read in
many content areas and acquire quite a large amount o f knowledge. It can be argued
that learnersâ educational background plays an important role on their university
education where they are confronted with complex reading and learning.
This study investigated the relationship betweeen education in reading in secondary
and high school and the reading strategy use of freshman students at METU while reading ir
English. Data were collected from the students through a three-part questionnaire and thinkaloud
protocols (TAPs). The first part of the questionnaire consisted o f questions related to
reading practices in secondary and high school. The second part included questions directed
towards reading strategies encouraged in pre-university education and reading strategies use
by the students at university while reading in English. The last part o f the questionnaire was
related to reading practices in English at university. TAPs were used in order to support the
data obtained from the questionnaires.
The findings o f the study revealed that the students in this study were âusually
or alwaysâ encouraged to use reading strategies in secondary and high school. With
this particular group o f students this encouragement proved to have positive impact
on their strategy use at university; they said that they use the same strategies âusually
or alwaysâ at university while reading in English, although they reported that practices
related to reading were not satisfactory in their pre-university education.Ćahin, Ebru BayolM.S
Filtrage par noyaux de convolution itératif
International audienceL'estimation paramĂ©trique des modĂšles dynamiques en biologie est souvent rendue complexe par les fortes interactions entre processus et les non-linĂ©aritĂ©s qui en dĂ©coulent, ainsi que par la difficultĂ© de l'observation du systĂšme par expĂ©rimentation. C'est en particulier le cas des modĂšles de croissance de plantes. Dans cet article nous Ă©tudions l'application de la mĂ©thode de filtrage particulaire par convolution, dĂ©veloppĂ©e pour permettre d'estimer les paramĂštres et les Ă©tats cachĂ©s simultanĂ©ment pour des systĂšmes non-linĂ©aires. Nous proposons une variation de cette mĂ©thode mettant en jeu des itĂ©rations multiples du filtre particulaire par convolution, en tenant compte des informations obtenues lors de l'itĂ©ration prĂ©cĂ©dente afin d'amĂ©liorer l'estimation des paramĂštres. Une version conditionnelle de l'approche est Ă©galement proposĂ©e dans le cas d'un systĂšme dynamique bruitĂ©, en rĂ©alisant l'estimation paramĂštres-Ă©tats en supposant les paramĂštres du modĂšle de bruits connus, puis en estimant ces derniers grĂące aux Ă©tats cachĂ©s estimĂ©s, et en relançant l'algorithme avec ces nouveaux paramĂštres. La mĂ©thode a Ă©tĂ© implĂ©mentĂ©e pour un modĂšle de croissance de betterave avec observations rares, et les rĂ©sultats apparaissent meilleurs que la mĂ©thode de filtrage par convolution sans itĂ©ration, mĂȘme rĂ©alisĂ©e avec un nombre bien plus important de particules. La mĂ©thode est par ailleurs gĂ©nĂ©rique, robuste et facilement adaptable
Development and Evaluation of Plant Growth Models: Methodology and Implementation in the PYGMALION platform
International audienceMathematical models of plant growth are generally characterized by a large number of interacting processes, a large number of model parameters and costly experimental data acquisition. Such complexities make model parameterization a difficult process. Moreover, there is a large variety of models that coexist in the literature with generally an absence of benchmarking between the different approaches and insufficient model evaluation. In this context, this paper aims at enhancing good modelling practices in the plant growth modeling community and at increasing model design efficiency. It gives an overview of the different steps in modelling and specify them in the case of plant growth models specifically regarding their above mentioned characteristics. Different methods allowing to perform these steps are implemented in a dedicated platform PYGMALION (Plant Growth Model Analysis, Identification and Optimization). Some of these methods are original. The C++ platform proposes a framework in which stochastic or deterministic discrete dynamic models can be implemented, and several efficient methods for sensitivity analysis, uncertainty analysis, parameter estimation, model selection or data assimilation can be used for model design, evaluation or application. Finally, a new model, the LNAS model for sugar beet growth, is presented and serves to illustrate how the different methods in PYGMALION can be used for its parameterization, its evaluation and its application to yield prediction. The model is evaluated from real data and is shown to have interesting predictive capacities when coupled with data assimilation techniques
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