Monitoring MBE substrate deoxidation via RHEED image-sequence analysis by deep learning

Reflection high-energy electron diffraction (RHEED) is a powerful tool in molecular beam epitaxy (MBE), but RHEED images are often difficult to interpret, requiring experienced operators. We present an approach for automated surveillance of GaAs substrate deoxidation in MBE using deep learning based RHEED image-sequence classification. Our approach consists of an non-supervised auto-encoder (AE) for feature extraction, combined with a supervised convolutional classifier network. We demonstrate that our lightweight network model can accurately identify the exact deoxidation moment. Furthermore we show that the approach is very robust and allows accurate deoxidation detection during months without requiring re-training. The main advantage of the approach is that it can be applied to raw RHEED images without requiring further information such as the rotation angle, temperature, etc.Comment: 6 pages, 6 figure

PyMoosh : a comprehensive numerical toolkit for computing the optical properties of multilayered structures

We present PyMoosh, a Python-based simulation library designed to provide a comprehensive set of numerical tools allowing to compute essentially all optical characteristics of multilayered structures, ranging from reflectance and transmittance to guided modes and photovoltaic efficiency. Optimization tools are also included. PyMoosh is designed not just for research purposes, but also for use-cases in education. To this end, we have invested significant effort in ensuring user-friendliness and simplicity of the interface. PyMoosh has been developed in line with the principles of Open Science and taking into account the fact that multilayered structures are increasingly being used as a testing ground for optimization and deep learning approaches. We provide in this paper the theoretical basis at the core of PyMoosh, an overview of its capabilities, as well as a comparison between the different numerical methods implemented in terms of speed and stability. We are convinced such a versatile tool will be useful for the community in many ways

Illustrated tutorial on global optimization in nanophotonics

Numerical optimization for the inverse design of photonic structures is a tool which is providing increasingly convincing results -- even though the wave nature of problems in photonics makes them particularly complex. In the meantime, the field of global optimization is rapidly evolving but is prone to reproducibility problems, making it harder to identify the right algorithms to use. This paper is thought as a tutorial on global optimization for photonic problems. We provide a general background on global optimization algorithms and a rigorous methodology for a physicist interested in using these tools -- especially in the context of inverse design. We suggest algorithms and provide explanations for their efficiency. We provide codes and examples as an illustration than can be run online, integrating quick simulation code and Nevergrad, a state-of-the-art benchmarking library. Finally, we show how physical intuition can be used to discuss optimization results and to determine whether the solutions are satisfactory or not

The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The external audit of the djiboutian public institutions : descriptive analysis of the request of external audit within the framework of the public governance

Cette thèse porte sur analyser la place de l'audit, plus particulièrement l'audit externe, dans l'évolution de gouvernance des organisations publiques à Djibouti qui a débuté depuis plus de quinze (15) ans. Il s'agit aussi d'apporter des éléments de réponse sur les formes d'audit qui sont associés à cette évolution de la gouvernance. Il s'agit ici d'une l'analyse des pratiques de contrôle externe relatives au secteur public djiboutien et plus particulièrement celles concernant les établissements publics, en s’appuyant sur un cadre théorique privilégiant les relations entre parties prenantes de la gouvernance de ces organisations.Pour ce faire, cette recherche se propose, après avoir proposer un cadre d'analyse de la gouvernance et des systèmes de contrôle externe dans lequel évoluent les établissements public djiboutien, de montrer la place essentiel de l’audit externe dans la gouvernance de ces établissements publics en tant que mécanisme de règlement des conflits d’intérêts entre les principaux acteurs de la vie publique.This thesis analyzes the place of the audit, more particularly the external audit, in the evolution of governance of the public organizations in Djibouti which began for more than fifteen years. This study is also bringing answers on the forms of audit which are associated to this evolution of the governance.To do it, this search proposes, having proposed a frame of analysis of the governance and the systems of external control in which evolve the Djiboutian public institutions, to show the essential place of the external audit in the governance of these public institutions as mechanism of regulation of conflicts between the main actors of the public administration

Diffusion of dissolved carbon dioxide in Champagne wines by molecular dynamics

Les travaux présentés dans cette thèse sont consacrés à l’étude par dynamique moléculaire des propriétés detransport (ie, diffusion et viscosité) et des propriétés thermodynamiques (ie, compressibilité isotherme, capacité calorifique, et dilatation thermique) de solutions hydroalcooliques carbonatées pauvres en sucres, telles que les vins de Champagne bruts, en fonction de la température à une pression de 1 bar. Dans un premier temps je me suis attaché à évaluer les modèles moléculaires optimaux pour étudier la diffusion du CO2. Une combinaison du modèle d’eau OPC (ou éventuellement TIP4P/2005) et du modèle de CO2 EPM2 a été identifiée comme un excellent choix pour reproduire les coefficients de diffusion tirés de mesures de RMN 13C. Ce modèle a par la suite été utilisé pour analyser l’influence du degré alcoolique sur la diffusion du CO2 et de l’éthanol. Les coefficients de diffusion théoriques ont été comparés à des estimations expérimentales obtenues en appliquant la relation de Stokes-Einstein, qui relie le coefficient de diffusion d’une espèce à son rayon hydrodynamique et à la viscosité du liquide. Un accord satisfaisant a été obtenu pour le CO2, l’éthanol conduisant cependant à une légère surestimation des valeurs expérimentales. Enfin, la qualité des solutions hydroalcooliques carbonatées modèles considérée dans ma thèse a aussi été évaluée en analysant leur aptitude à prédire les viscosités et les propriétés thermodynamiques de ces mélanges. La plupart de ces propriétés sont bien reproduites ce qui démontre la robustesse de notre approche théorique. Tous ces travaux centrés autour des boissons carbonatées, et notamment des vins de Champagne, devraient permettre d’ouvrir de nouvelles voies vers des modélisations numériques encore plus sophistiquées des boissons effervescentes.Mots-clés : Boissons effervescentes, champagne, eau, dioxyde de carbone, éthanol, dynamique moléculaire, champs de force, diffusion, viscosité, rayon hydrodynamique, compressibilité isotherme, capacité calorifique, dilatation thermique.The works presented in this thesis were devoted to the study by molecular dynamics of transport properties (eg, diffusion and viscosity) and thermodynamic properties (ie, isothermal compressibility, heat capacity, and thermal expansivity) of carbonated hydroalcoholic solutions poor in sugars, such as brut-labeled champagnes, as a function of temperature at a pressure of 1 bar. Firstly, I evaluated the optimal molecular models to study the diffusion of CO2. A combination of the OPC water model (or possibly TIP4P/2005 model) with the EPM2 CO2 model was found to be an excellent choice to reproduce the diffusion coefficients derived from 13C NMR measurements. Then, this model was used to analyze the influence of the alcoholic degree on the diffusion of CO2 and ethanol. The theoretical diffusion coefficients have been compared with experimental estimates obtained by applying the Stokes-Einstein relation, which relates the diffusion coefficient of a species to its hydrodynamic radius and the viscosity of the liquid. A suitable agreement is obtained for CO2 but ethanol yields a slight overestimation of experimental values. Eventually, the quality of model carbonated hydroalcoholic solutions considered in my thesis has also been assessed by analyzing their ability to predict the viscosities and thermodynamic properties of these mixtures. Most of these properties are well reproduced which demonstrates the robustness of our theoretical approach. All these works focused on carbonated beverages, and in particular on Champagne wines, should enable the opening of new paths toward even more sophisticated numerical modelings of fizzy drinks.Keywords : Sparkling beverages, champagne, water, carbon dioxide, ethanol, molecular dynamics, force fields, diffusion, viscosity, hydrodynamic radius, isothermal compressibility, heat capacity, thermal expansivity

data_for_ox_deox_paper_reviewers.tar.gz

data, models and scripts aimed to ox/deox classification paper reviewers.</p

Etude du paludisme dans les zones de faible transmission : vers la pre-élimination du paludisme à Djibouti

A eux seuls, le Nigeria, la République Démocratique du Congo, l'Ouganda, l'Ethiopie et la Tanzanie représentent 50% de la mortalité liée au paludisme et 47% du total des cas de paludisme. Cependant, la diminution du nombre de cas et l'augmentation des activités de lutte à l'échelle mondiale sont autant de bonnes nouvelles encourageantes qui font déclarer à l'OMS que le paludisme peut être contrôlé et plus tard éliminé. Les recommandations des experts de la lutte contre le paludisme à l'échelle mondiale recommandent de cibler les zones où l'élimination est possible, les zones de faible transmission, et de là progresser vers les zones plus impaludées. Cela impose une connaissance précise de la situation du paludisme dans la région concernée. Les ensembles géographiques régionaux où la transmission du paludisme connait une diminution sensible, comme la Corne d'Afrique, et ayant des frontières extrêmement poreuses aux mouvements de populations humaines donc aux pathogènes, sont donc à cibler en priorité. Cela nécessite une évaluation du niveau de transmission et du risque de résurgence potentiel, posé par l'importation de nouvelles souches, afin d'aboutir à une élimination durable. Dans ce contexte, la République de Djibouti, ayant montré une prévalence extrêmement faible au cours de ces dernières années, s'est lancée dans une tentative de pré-élimination du paludisme. L'objectif de notre étude a été d'observer l'évolution, sur une durée de onze années (1998-2009), du taux d'incidence de l'infection palustre, du niveau de transmission du paludisme, de la possibilité d'importation depuis les pays voisins et enfin, de la distribution des vecteurs de la maladie.Nigeria, the Democratic Republic of Congo, Uganda, Ethiopia and Tanzania represent 50% of malaria deaths and 47% of total malaria cases. However, the decrease in the number of cases and worldwide increased control activities were encouraging news which lead the WHO to declare that malaria can be controlled and eliminated later. The recommendations of experts in the worldwide fight against malaria recommend targeting areas where elimination is possible, areas of low transmission, and hence moving towards areas more affected by malaria. This requires a precise knowledge of the malaria situation in the region. Geographical regional assemblies where malaria transmission is experiencing a significant decrease, as the Horn of Africa, and having extremely porous frontiers to the movement of human populations, therefore pathogens, must be the priority target. Thus an assessment of the level of transmission and the risk of potential recurrence, posed by the importation of new strains, was indispensable in order to achieve sustainable elimination. In this context, the Republic of Djibouti, who showed extremely low prevalence in recent years, is embarked on an attempt to pre-eliminate malaria. The aim of our study was to observe changes, over a period of 11 years (1998-2009), in the level of malaria occurrence, malaria transmission, but also the level of its potential importation from neighboring countries and finally the vectors population dynamics. These results could serve as a basis of reflection, for the health authorities of the country or international partners, to a possible adjustment of the current policy of fight against malaria