Toward high-content/high-throughput imaging and analysis of embryonic morphogenesis

In vivo study of embryonic morphogenesis tremendously benefits from recent advances in live microscopy and computational analyses. Quantitative and automated investigation of morphogenetic processes opens the field to high-content and high-throughput strategies. Following experimental workflow currently developed in cell biology, we identify the key challenges for applying such strategies in developmental biology. We review the recent progress in embryo preparation and manipulation, live imaging, data registration, image segmentation, feature computation, and data mining dedicated to the study of embryonic morphogenesis. We discuss a selection of pioneering studies that tackled the current methodological bottlenecks and illustrated the investigation of morphogenetic processes in vivo using quantitative and automated imaging and analysis of hundreds or thousands of cells simultaneously, paving the way for high-content/high-throughput strategies and systems analysis of embryonic morphogenesis

To Develop a Database Management Tool for Multi-Agent Simulation Platform

Depuis peu, la Modélisation et Simulation par Agents (ABMs) est passée d'une approche dirigée par les modèles à une approche dirigée par les données (Data Driven Approach, DDA). Cette tendance vers l’utilisation des données dans la simulation vise à appliquer les données collectées par les systèmes d’observation à la simulation (Edmonds and Moss, 2005; Hassan, 2009). Dans la DDA, les données empiriques collectées sur les systèmes cibles sont utilisées non seulement pour la simulation des modèles mais aussi pour l’initialisation, la calibration et l’évaluation des résultats issus des modèles de simulation, par exemple, le système d’estimation et de gestion des ressources hydrauliques du bassin Adour-Garonne Français (Gaudou et al., 2013) et l’invasion des rizières du delta du Mékong au Vietnam par les cicadelles brunes (Nguyen et al., 2012d). Cette évolution pose la question du « comment gérer les données empiriques et celles simulées dans de tels systèmes ». Le constat que l’on peut faire est que, si la conception et la simulation actuelles des modèles ont bénéficié des avancées informatiques à travers l’utilisation des plateformes populaires telles que Netlogo (Wilensky, 1999) ou GAMA (Taillandier et al., 2012), ce n'est pas encore le cas de la gestion des données, qui sont encore très souvent gérées de manière ad-hoc. Cette gestion des données dans des Modèles Basés Agents (ABM) est une des limitations actuelles des plateformes de simulation multiagents (SMA). Autrement dit, un tel outil de gestion des données est actuellement requis dans la construction des systèmes de simulation par agents et la gestion des bases de données correspondantes est aussi un problème important de ces systèmes. Dans cette thèse, je propose tout d’abord une structure logique pour la gestion des données dans des plateformes de SMA. La structure proposée qui intègre des solutions de l’Informatique Décisionnelle et des plateformes multi-agents s’appelle CFBM (Combination Framework of Business intelligence and Multi-agent based platform), elle a plusieurs objectifs : (1) modéliser et exécuter des SMAs, (2) gérer les données en entrée et en sortie des simulations, (3) intégrer les données de différentes sources, et (4) analyser les données à grande échelle. Ensuite, le besoin de la gestion des données dans les simulations agents est satisfait par une implémentation de CFBM dans la plateforme GAMA. Cette implémentation présente aussi une architecture logicielle pour combiner entrepôts deIv données et technologies du traitement analytique en ligne (OLAP) dans les systèmes SMAs. Enfin, CFBM est évaluée pour la gestion de données dans la plateforme GAMA à travers le développement de modèles de surveillance des cicadelles brunes (BSMs), où CFBM est utilisé non seulement pour gérer et intégrer les données empiriques collectées depuis le système cible et les résultats de simulation du modèle simulé, mais aussi calibrer et valider ce modèle. L'intérêt de CFBM réside non seulement dans l'amélioration des faiblesses des plateformes de simulation et de modélisation par agents concernant la gestion des données mais permet également de développer des systèmes de simulation complexes portant sur de nombreuses données en entrée et en sortie en utilisant l’approche dirigée par les données.Recently, there has been a shift from modeling driven approach to data driven approach inAgent Based Modeling and Simulation (ABMS). This trend towards the use of data-driven approaches in simulation aims at using more and more data available from the observation systems into simulation models (Edmonds and Moss, 2005; Hassan, 2009). In a data driven approach, the empirical data collected from the target system are used not only for the design of the simulation models but also in initialization, calibration and evaluation of the output of the simulation platform such as e.g., the water resource management and assessment system of the French Adour-Garonne Basin (Gaudou et al., 2013) and the invasion of Brown Plant Hopper on the rice fields of Mekong River Delta region in Vietnam (Nguyen et al., 2012d). That raises the question how to manage empirical data and simulation data in such agentbased simulation platform. The basic observation we can make is that currently, if the design and simulation of models have benefited from advances in computer science through the popularized use of simulation platforms like Netlogo (Wilensky, 1999) or GAMA (Taillandier et al., 2012), this is not yet the case for the management of data, which are still often managed in an ad hoc manner. Data management in ABM is one of limitations of agent-based simulation platforms. Put it other words, such a database management is also an important issue in agent-based simulation systems. In this thesis, I first propose a logical framework for data management in multi-agent based simulation platforms. The proposed framework is based on the combination of Business Intelligence solution and a multi-agent based platform called CFBM (Combination Framework of Business intelligence and Multi-agent based platform), and it serves several purposes: (1) model and execute multi-agent simulations, (2) manage input and output data of simulations, (3) integrate data from different sources; and (4) analyze high volume of data. Secondly, I fulfill the need for data management in ABM by the implementation of CFBM in the GAMA platform. This implementation of CFBM in GAMA also demonstrates a software architecture to combine Data Warehouse (DWH) and Online Analytical Processing (OLAP) technologies into a multi-agent based simulation system. Finally, I evaluate the CFBM for data management in the GAMA platform via the development of a Brown Plant Hopper Surveillance Models (BSMs), where CFBM is used ii not only to manage and integrate the whole empirical data collected from the target system and the data produced by the simulation model, but also to calibrate and validate the models.The successful development of the CFBM consists not only in remedying the limitation of agent-based modeling and simulation with regard to data management but also in dealing with the development of complex simulation systems with large amount of input and output data supporting a data driven approach

To Develop a Database Management Tool for Multi-Agent Simulation Platform

Depuis peu, la Modélisation et Simulation par Agents (ABMs) est passée d'une approche dirigée par les modèles à une approche dirigée par les données (Data Driven Approach, DDA). Cette tendance vers l’utilisation des données dans la simulation vise à appliquer les données collectées par les systèmes d’observation à la simulation (Edmonds and Moss, 2005; Hassan, 2009). Dans la DDA, les données empiriques collectées sur les systèmes cibles sont utilisées non seulement pour la simulation des modèles mais aussi pour l’initialisation, la calibration et l’évaluation des résultats issus des modèles de simulation, par exemple, le système d’estimation et de gestion des ressources hydrauliques du bassin Adour-Garonne Français (Gaudou et al., 2013) et l’invasion des rizières du delta du Mékong au Vietnam par les cicadelles brunes (Nguyen et al., 2012d). Cette évolution pose la question du « comment gérer les données empiriques et celles simulées dans de tels systèmes ». Le constat que l’on peut faire est que, si la conception et la simulation actuelles des modèles ont bénéficié des avancées informatiques à travers l’utilisation des plateformes populaires telles que Netlogo (Wilensky, 1999) ou GAMA (Taillandier et al., 2012), ce n'est pas encore le cas de la gestion des données, qui sont encore très souvent gérées de manière ad-hoc. Cette gestion des données dans des Modèles Basés Agents (ABM) est une des limitations actuelles des plateformes de simulation multiagents (SMA). Autrement dit, un tel outil de gestion des données est actuellement requis dans la construction des systèmes de simulation par agents et la gestion des bases de données correspondantes est aussi un problème important de ces systèmes. Dans cette thèse, je propose tout d’abord une structure logique pour la gestion des données dans des plateformes de SMA. La structure proposée qui intègre des solutions de l’Informatique Décisionnelle et des plateformes multi-agents s’appelle CFBM (Combination Framework of Business intelligence and Multi-agent based platform), elle a plusieurs objectifs : (1) modéliser et exécuter des SMAs, (2) gérer les données en entrée et en sortie des simulations, (3) intégrer les données de différentes sources, et (4) analyser les données à grande échelle. Ensuite, le besoin de la gestion des données dans les simulations agents est satisfait par une implémentation de CFBM dans la plateforme GAMA. Cette implémentation présente aussi une architecture logicielle pour combiner entrepôts deIv données et technologies du traitement analytique en ligne (OLAP) dans les systèmes SMAs. Enfin, CFBM est évaluée pour la gestion de données dans la plateforme GAMA à travers le développement de modèles de surveillance des cicadelles brunes (BSMs), où CFBM est utilisé non seulement pour gérer et intégrer les données empiriques collectées depuis le système cible et les résultats de simulation du modèle simulé, mais aussi calibrer et valider ce modèle. L'intérêt de CFBM réside non seulement dans l'amélioration des faiblesses des plateformes de simulation et de modélisation par agents concernant la gestion des données mais permet également de développer des systèmes de simulation complexes portant sur de nombreuses données en entrée et en sortie en utilisant l’approche dirigée par les données.Recently, there has been a shift from modeling driven approach to data driven approach inAgent Based Modeling and Simulation (ABMS). This trend towards the use of data-driven approaches in simulation aims at using more and more data available from the observation systems into simulation models (Edmonds and Moss, 2005; Hassan, 2009). In a data driven approach, the empirical data collected from the target system are used not only for the design of the simulation models but also in initialization, calibration and evaluation of the output of the simulation platform such as e.g., the water resource management and assessment system of the French Adour-Garonne Basin (Gaudou et al., 2013) and the invasion of Brown Plant Hopper on the rice fields of Mekong River Delta region in Vietnam (Nguyen et al., 2012d). That raises the question how to manage empirical data and simulation data in such agentbased simulation platform. The basic observation we can make is that currently, if the design and simulation of models have benefited from advances in computer science through the popularized use of simulation platforms like Netlogo (Wilensky, 1999) or GAMA (Taillandier et al., 2012), this is not yet the case for the management of data, which are still often managed in an ad hoc manner. Data management in ABM is one of limitations of agent-based simulation platforms. Put it other words, such a database management is also an important issue in agent-based simulation systems. In this thesis, I first propose a logical framework for data management in multi-agent based simulation platforms. The proposed framework is based on the combination of Business Intelligence solution and a multi-agent based platform called CFBM (Combination Framework of Business intelligence and Multi-agent based platform), and it serves several purposes: (1) model and execute multi-agent simulations, (2) manage input and output data of simulations, (3) integrate data from different sources; and (4) analyze high volume of data. Secondly, I fulfill the need for data management in ABM by the implementation of CFBM in the GAMA platform. This implementation of CFBM in GAMA also demonstrates a software architecture to combine Data Warehouse (DWH) and Online Analytical Processing (OLAP) technologies into a multi-agent based simulation system. Finally, I evaluate the CFBM for data management in the GAMA platform via the development of a Brown Plant Hopper Surveillance Models (BSMs), where CFBM is used ii not only to manage and integrate the whole empirical data collected from the target system and the data produced by the simulation model, but also to calibrate and validate the models.The successful development of the CFBM consists not only in remedying the limitation of agent-based modeling and simulation with regard to data management but also in dealing with the development of complex simulation systems with large amount of input and output data supporting a data driven approach

Application of poly-β-hydroxybutyrate accumulating bacteria in crustacean larviculture

This PhD research was first illustrated that the use of amorphous PHB contained in whole cells of the bacterium Alcaligenes eutrophus in lyophilized and freshly grown cell forms induced similar and even better beneficial effects on the growth performance or disease resistance of Artemia nauplii or M. rosenbergii larvae than crystalline PHB particles. In the second part, the change in carbonaceous compounds (trehalose, glycerol, glycogen and total organic carbon) and total nitrogen in the axenic hatching medium of decapsulated Artemia fransicana cysts was determined throughout the hatching process. Three different salinities (5, 12 and 35 g/L) of the incubation medium were applied. Trehalose appeared in the medium in small quantities (maximally 2.6 mg C/g incubated dry cysts) as compared to glycerol and glycogen (maximally 28.5 ± 1.2 and 13.8 ± 1.0 mg C/g incubated dry cysts, respectively). Overall, the C/N ratio in Artemia hatching medium at a salinity of 12 g/L (which is most relevant for practice) was about 10 throughout incubation. In the final part of this work, the reuse of the hatching medium of Artemia was investigated as a cost-efficient strategy to culture the PHB accumulating bacterium Bacillus sp. LT12 and supply it to Artemia nauplii or M. rosenbergii laviculture as an antimicrobial agent. The PHB level in Bacillus sp. LT12 was increased about 2-fold when this bacterium was cultured in the axenic hatching medium of Artemia (AHMA) harvested at the different times points during the incubation process (16, 20 & 24 h). Adding the bacterium which was cultured in AHMA harvested at 16 or 20 h, into the culture water of Artemia nauplii challenged with Vibrio campbellii LMG21363 showed to completely protect the nauplii when they were added at a density of 5 x 107 CFU/mL. Moreover, the disease resistance of M. rosenbergii larvae in the challenge test with Vibrio harveyi BB120 was significantly increased when feeding Artemia nauplii enriched with 109 CFU/mL of Bacillus sp. LT12 grown as well in the hatching medium of Artemia harvested at 16, 20 or 24 h. When Bacillus sp. LT12 was co-cultured with Artemia during cyst incubation and supplementary glycerol was added at 0.17 and 0.51 g/L, the results showed that the PHB content in the bacteria and the disease resistance of M. rosenbergii larvae were significantly increased as compared to control treatment (without adding extra glycerol). The results in this PhD work illustrate that whole bacterial cells containing amorphous PHB are more promising to use as a disease control strategy in crustacean larviculture than crystalline PHB. The reuse of Artemia hatching medium in crustacean hatcheries as the nutrient medium to culture PHB accumulating bacteria to be fed to the cultured animals does not only result in an increased culture efficiency of the larvae but also reduces the load on the environment by reducing the volume of waste water originating from crustacean hatcheries

Combination Framework of BI solution & Multi-agent platform (CFBM) for multi-agent based simulations

International audienceIntegrated environmental modeling in general and specifically Multi-agent-based modeling and simulation approach are increasingly used in decision-support systems with, as a major consequence, to manipulate and generate a huge amount of data for their functioning (parametrization, use of real data in the simulation, ...). Therefore there is a need to manage efficiently these data being either used or generated by the simulation. Practically, existing general-ist simulation platforms lack database access and analysis tools and simulation outputs are usually stored as text files or spreadsheets to be manipulated later by dedicated tools. In this paper, we propose a solution to handle simulation models data, i.e. their outputs as well as corresponding real data. We designed a conceptual framework based on a combination of two components, a Business Intelligence (BI) solution and a multi-agent platform. Such a framework aims at managing simulation models data throughout the lifespan of the simulation, from its execution and its coupling with real data to the generation of simulation results order to use the simulation model as an effective decision-support sys-tem with what-if scenarios

MANAGING DEVELOPMENT OF TEACHING STAFF IN HIGH SCHOOLS IN NINH KIEU DISTRICT, CAN THO CITY, VIETNAM

In the context of the ongoing implementation of the general education program, especially in primary education, effectively managing the development of high school teaching staff is crucial for achieving comprehensive educational reforms. This study focuses on the current state of development of teaching staff in high schools in Ninh Kieu District, Can Tho City, Vietnam and aims to identify the challenges, advantages, and influencing factors. The study was conducted using a survey from a questionnaire of 216 respondents, including school managers and teachers of 03 high schools in Can Tho City, including An Khanh, Chau Van Liem, and Nguyen Viet Hong. Various obstacles hinder the effective development of teaching staff, namely resource limitations, inadequate training programs, and insufficient support mechanisms. Some suggested solutions might be implemented synchronously, considering specific conditions and timeframes. The prioritization of measures based on feasibility and impact is essential to maximize effectiveness. And the proposed measures aim to address various aspects of management and teaching staff, fostering an environment conducive to the development of high school teachers. By doing so, these measures will contribute to meeting the requirements of the 2018 General Education Program by the Vietnamese Education and Training, thereby enhancing the overall quality of education in Ninh Kieu District, Can Tho City as well.  Article visualizations

Dynamical Study of Guest-Host Orientational Interaction in LiquidCrystalline Materials

Guest-host interaction has long been a subject of interest in many disciplines. Emphasis is often on how a small amount of guest substance could significantly affect the properties of a host material. This thesis describe our work in studying a guest-host effect where dye-doping of liquid crystalline materials greatly enhances the optical Kerr nonlinearity of the material. The dye molecules, upon excitation and via intermolecular interaction, provides an extra torque to reorient the host molecules, leading to the enhanced optical Kerr nonlinearity. We carried out a comprehensive study on the dynamics of the photoexcited dye-doped liquid crystalline medium. Using various experimental techniques, we separately characterized the dynamical responses of the relevant molecular species present in the medium following photo-excitation, and thus were able to follow the transient process in which photo-excitation of the dye molecules exert through guest-host interaction a net torque on the host LC material, leading to the observed enhanced molecular reorientation. We also observed for the first time the enhanced reorientation in a pure liquid crystal system, where the guest population is created through photoexcitation of the host molecules themselves. Experimental results agree quantitatively with the time-dependent theory based on a mean-field model of the guest-host interaction

Vietnamese American women’s beliefs and perceptions on cervical cancer, cervical cancer screening, and cancer prevention vaccines: A community-based participatory study

Cervical cancer remains commonly diagnosed in Vietnamese American women. Despite efforts to increase cervical cancer screening among Vietnamese American women, participation rates are persistently lower than the national goal. The objective of this study is to explore beliefs of Vietnamese American women about cervical cancer, cervical cancer screening, and cancer prevention vaccines. A qualitative descriptive investigation captured group perceptions about meaning and beliefs of cervical cancer, screening, and cancer prevention vaccines, and participants’ stories using a community-based participatory research approach. Forty Vietnamese American women were recruited from the Portland, Oregon metropolitan area into four focus groups. Using a process of directed content analysis, focus group transcripts were coded for themes. We found that cervical cancer continues to be a difficult topic to discuss, and Vietnamese American women may not bring the topic up themselves to their health care providers. Some women experienced intense emotions of fear or shame of having their cervix examined. Women delayed seeking cervical cancer screening and needed to have early warning signs, which guided them as to when to seek health care. Women focused on cleanliness through vaginal and/or perineal washing as primary prevention for cervical cancer. There were limited awareness and knowledge about cancer prevention vaccines, specifically the human papillomavirus. Some women relied heavily on their informal social networks of family, friends, or community for health knowledge. Fear and misunderstanding dominated the beliefs of Vietnamese American women about cervical cancer screening and prevention. These findings underscored the importance of having culturally-specific findings, which will inform a multicomponent intervention to promote cervical cancer screening and cancer prevention vaccine uptake within this population

To Calibrate & Validate an Agent-Based Simulation Model - An Application of the Combination Framework of BI solution & Multi-agent platform

National audienceIntegrated environmental modeling approaches, especially the agent-based modeling one, are increasingly used in large-scale decision support systems. A major consequence of this trend is the manipulation and generation of huge amount of data in simulations, which must be efficiently managed. Furthermore, calibration and validation are also challenges for Agent-Based Modelling and Simulation (ABMS) approaches when the model has to work with integrated systems involving high volumes of input/output data. In this paper, we propose a calibration and validation approach for an agent-based model, using a Combination Framework of Business intelligence solution and Multi-agent platform (CFBM). The CFBM is a logical framework dedicated to the management of the input and output data in simulations, as well as the corresponding empirical datasets in an integrated way. The calibration and validation of Brown Plant Hopper Prediction model are presented and used throughout the paper as a case study to illustrate the way CFBM manages the data used and generated during the life-cycle of simulation and validation