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See detailSpace-variant optical phase retarders in liquid crystal polymers and their applications
Piron, Pierre ULg

Doctoral thesis (2014)

During the last decade, extensive investigations were performed to achieve optical phase retarders with a space-variant orientation of their fast axis. These retarders present unique behaviors and they ... [more ▼]

During the last decade, extensive investigations were performed to achieve optical phase retarders with a space-variant orientation of their fast axis. These retarders present unique behaviors and they can be used for several applications such as polarization analysis, beam splitting, phase mask coronagraphy, optical tweezers … The present thesis is dedicated to the development of space-variant retarders made out of liquid crystal polymers recorded by polarization holography. The liquid crystals define the fast axis orientation of the retarder. Polarization holography is based on the superimposition of differently polarized beams to achieve the electric field required to properly align the liquid crystals without mechanical action. In the present work, we start with an introduction about the space-variant retarders, their characteristics and current recording methods, which usually require mechanical action. In the second chapter, polarization holography and several simple examples are presented as well as the liquid crystal polymers, their generic recording process and the first prototypes. In chapter three, the first application that we developed is exposed. It consists in a polarization analysis method based on a retarder characterized by a variation in one dimension of its fast axis orientation. The principle of the method, numerical simulations and the first results are exposed. Chapter four cares about the second application based on a separator of polarization state. The mathematical model and its application to shearography are exposed. In chapter five, another kind of retarders is introduced. These retarders are characterized by a rotation of their fast axis along the center of the retarder. Their properties, the recording systems and the first prototypes are detailed and analyzed. In the last chapter, the application of our retarder to coronagraphy is presented and their performances are computed for different configurations based on experimental constrains. Finally, we conclude with the improvements of our applications and future uses of these retarders. [less ▲]

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See detailContribution à l’amélioration de l’épidémiosurveillance des maladies animales en Afrique francophone de l’Ouest et du Centre
Ouagal, Mahamat ULg

Doctoral thesis (2014)

Livestock is an important source of income in most developing countries. In Africa, it often makes up 10% to 20% of the gross national product at level. One of the major constraints to the development of ... [more ▼]

Livestock is an important source of income in most developing countries. In Africa, it often makes up 10% to 20% of the gross national product at level. One of the major constraints to the development of this sector is animal diseases, which sometimes generate significant economic losses with social consequences that are often very burdensome for farmers. They restrict trade between countries. Reducing the impact of these constraints necessarily involves the prevention and the control of diseases. For this purpose, an adequate knowledge of the epidemiology of the diseases is a prerequisite to define a strategy for their prevention and/or the design of appropriate monitoring measures. One of the essential tools of production remains the epidemiological information network for the surveillance of animal diseases. It is also a tool for decision in international trade involving livestock products. For this purpose, its effectiveness is a guarantee for its credibility. An effective network system must be well organized, meet scientific standards and satisfy the efficiency characteristics which are sensitivity, specificity, acceptability, responsiveness and cost. In west and central Africa, epidemiological surveillance networks of animal diseases are mostly created in the 1990s through the Pan African Program for the Control of Epizootics. A 2004 assessment carried out by this program revealed that these networks are at different stages and found weaknesses in their efficiency. To contribute to the improvement of these systems, an analysis of some performance parameters of these networks has been conducted and suggestions for improvement were made. To achieve this overall objective, the following specific objectives were listed: (i) analyze the technical and functional organization of epidemiological surveillance networks in West and Central Africa; (ii) compare the effectiveness of active surveillance and passive surveillance, the two main monitoring methods used by the networks in West and Central Africa using the case study of the epidemiological surveillance network, in Chad, namely REPIMAT; (iii) assess the sensitivity of an epidemiological surveillance network from an approach based on prevalence of a disease such as Foot and Mouth Disease; (iv) develop performance indicators for regular monitoring of the epidemiological surveillance network for animal diseases in West and Central Africa, again by taking the case of REPIMAT; and finally, (v) estimate the cost incurred by an epidemiological surveillance network in West and Central Africa, for example the REPIMAT. Each of these specific objectives leads to a specific study of which results are presented below: Organization of epidemiological surveillance networks in West and Central Africa The survey on technical and institutional organizations networks in west and central Africa was organised on the basis of a written questionnaire. It involved nine networks of which five were in West Africa (Senegal, Burkina Faso, Ivory Coast, Togo, Guinea) and four in Central Africa (Cameroon, Central African Republic, Democratic Republic of Congo and Chad). The results of this survey showed that the oldest epidemiological surveillance network is that of Chad, REPIMAT. There are more similarities than differences between these networks. In general, network monitoring of animal diseases in west and central Africa are technically and institutionally well formalized. The establishment and operation of the networks surveyed are mainly financed by foreign aid. In general, these are epidemiological surveillance networks that monitor several diseases. All countries surveyed have a central national laboratory for the analysis of samples collected. However, only four countries (Cameroon, Côte d'Ivoire, Guinea and Senegal) can make a diagnosis of all diseases selected for monitoring. The laboratories are considered as partners with surveillance networks in most of the countries surveyed. All networks use the PID/ARIS for data management. In addition to the latter, countries such as Guinea, DRC, Senegal and Chad use a national database developed with Access®. On average, 26% of veterinary stations on the total networks surveyed are involved in the monitoring. This proportion varies from 7% to 91%. However, insufficient diagnostic capacity of laboratories and inadequate operational steering committees are the two main weaknesses of the networks concerned with this survey. Comparison between active and passive surveillance within the network of epidemiological surveillance of animal diseases in Chad The comparison between active and passive surveillance involved 106 REPIMAT surveillance stations randomly divided into 52 active surveillance stations and 54 passive surveillance stations. Vaccination status of nine diseases and their respective prevalence levels are monitored by the network. A work plan was developed for each station. The stations of active surveillance make monthly visits to four herds (villages) to look for monitored diseases and also organise four information meetings with farmers how to react in case of suspicion of the monitored diseases. Passive surveillance stations only organise, monthly, four information meetings with farmers. Suspicions in each station are recorded on a specific form developed for each disease. The agent mentions if the suspicion is performed following a breeder call, a visit from herds or a sensitization meeting. Monitoring lasted 24 months. The results of this study showed that regardless of the type of surveillance, diseases monitored with the exception of rare diseases (Rinderpest, and Rift Valley fever) are reported by the monitoring agents. However, we note that the number of calls recorded following suspicions of farmers (41%) was significantly higher (p <0.05) than suspicions made during visits to herds (30%) or in meetings (29%). For moderately prevalent diseases, the suspicions are mainly calls farmers (77%) and regardless of the type of monitoring (73% for active surveillance and 84% for passive surveillance). On the other hand, for FMD, a disease with high prevalence, 37% of suspicions are recorded by visiting farms. Overall, no significant difference was observed between the types of surveillance because of a low rate of disease onset during sensitization meetings by the active surveillance stations. Passive surveillance stimulated by awareness meetings appears to be a mode for surveillance in the conditions of Chad and cheaper. However, for rare diseases, the specific methods of active surveillance (such as, for example, sentinel flocks) seems preferable. Evaluation of the sensitivity of the animal disease epidemiological surveillance network for Foot and Mouth Disease in Chad Evaluation of the sensitivity of the animal disease epidemiological surveillance network for Foot and Mouth Disease in Chad The study on the network sensitivity was carried out in REPIMAT by taking the surveillance of FMD as an example. FMD is the disease most frequently suspected by REPIMAT. However, the reporting of cases is limited to clinical suspicion. The samples for the purpose of laboratory diagnostic for confirmation of these suspicions are not made. In order to assess the sensitivity of REPIMAT for this disease, a serological survey was conducted in eight of the nine regional delegations with the highest cattle population of the country. The samples were analyzed by the National Reference Laboratory for FMD in Brescia (Italy) with the support of the European Commission action against FMD. The 3ABC and SP-ELISA tests were used for the detection of antibodies and the serotype of the virus. The number of FMD suspicions reported within the network was compared with the seroprevalence. Epidemiological information on the disease, including the circulating serotypes in Chad, was also provided. A total of 796 cattle sera were collected. The seroprevalence rate at individual level was 35.6% (95% CI: 32.2 to 39.0) and that at the herd level was 61.9% (95% CI: 51.9 to 71.2). A strong correlation was observed between the estimated prevalence and number of clinical suspicions reported within REPIMAT. The disease is present in all livestock regional delegations surveyed with a high prevalence in the delegations located in the south, the wettest area, and where cross-border movements are the most important. Serotypes A, O, SAT1and SAT2 were identified. Development of operating performance indicators of Chad epidemiological surveillance network for animal diseases: REPIMAT The maintenance and effectiveness of a disease monitoring system requires regular evaluation to identify timely deficiencies that may occur. For this purpose, the performance indicators are essential tools. One approach for developing performance indicators as well as their application in the operation of 43 monitoring stations REPIMAT was carried out. An analysis of the objectives and operation mechanism of REPIMAT allowed retaining three main components, namely the field workers, the animation cell and the laboratory. The activities of each of these components were listed. The analysis of the outcomes of these activities resulted in the development of the performance indicators that can be used in the operation of REPIMAT. The application of these indicators has highlighted the weaknesses of each component. Estimated cost of a network for animal diseases epidemiological surveillance in Central Africa: the case of Chad network In sub-Saharan Africa, most of the networks for epidemiological surveillance of animal diseases were temporarily financed by external aid. The sustainability of such decision support tools should have been insured by national public funds. The objective of this study was to estimate the costs involved in running an animal disease epidemiological surveillance network by taking the example of such network in Chad (REPIMAT) and its weight in the state budget. These costs were then compared to those of other epidemiological surveillance in West Africa networks. The results of this study showed that the total annual operating and implementing cost of REPIMAT is estimated at € 666 349 (437 096 291 FCFA) for the entire system comprising 106 monitoring stations constituting the local level, 26 livestock sectors, nine regional livestock delegations representing the intermediate level and an animation cell constituting the central level. This cost represents only 3% (2% of fixed costs and 1% of variable costs) of the budget allocated by the Chadian Ministry of Livestock. Fixed costs (72%) weighed more than variable costs (28%) regardless of the levels of intervention. This estimate is similar to the estimated costs of epidemiological surveillance networks in Benin, Ghana, Mauritania and Senegal. Considering only the variable costs (operation), the annual cost of operating a surveillance station, the most important entity in the system was only 932 € or 611 352 FCFA. The surveillance cost is mainly related at the local level (surveillance stations) and intermediate level (livestock sectors and regional livestock delegations) to the cost involved in health surveillance as well as the equipment it requires. This thesis allowed to analyze some parameters of effectiveness of a surveillance network for animal diseases including general organization, type of surveillance, sensitivity, cost and to develop a tool for continuous monitoring of operating a network. It is difficult to meet all the efficiency criteria of an animal disease surveillance network, however, the few parameters studied which are interrelated will help if they are used properly to improve the efficiency of an epidemiological surveillance system of animal diseases in sub-Saharan Africa. [less ▲]

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See detailMathematical modeling od the mitral valve. From local to global hemodynamics
Paeme, Sabine ULg

Doctoral thesis (2014)

Mitral valve dysfunction is a relatively common heart disease which typically requires mechanical valve replacement, with consequent high social and economic costs. More specifically, ischemic mitral ... [more ▼]

Mitral valve dysfunction is a relatively common heart disease which typically requires mechanical valve replacement, with consequent high social and economic costs. More specifically, ischemic mitral insufficiency following myocardial infarction has a dynamic behavior that can lead to failure in its detection in certain patients, creating a situation with increased risk of morbidity and mortality. Improving the tracking and the control of valvular pathologies is therefore crucial, as it offers significant opportunities to improve care, costs and prognosis for patients with this disease. To study heart and cardiac valve dysfunction, cardiologists need information about detailed pressure and flow dynamics around and through the valves, atria and ventricles. However, non-invasive information about pressure is currently limited to indices at specific times and invasive catheterization data, which is more traumatic for the patient, is not usually routinely available. One alternative to this involves mathematical modeling of the cardiovascular system which offers a non-invasive and inexpensive way of studying cardiac and circulatory dynamics. This is particularly beneficial where detailed, continuous measurements may not be practicable. This study consisted of the development of a multi-scale closed-loop model of the cardiovascular system that accounted for progressive mitral valve aperture area over the entire cardiac cycle. This multi-scale model, which included detailed mitral valve and left atrium models, was tested over a range of physiological situations and clinical data. The goal was to validate the model’s ability to reproduce clinically measured physiological and pathophysiological behavior in a manner that would enable a model to be made patient-specific using available data. The resulting model was designed to be made patient-specific, and thus capture and reproduce the patient’s unique hemodynamic state on both global and local scales. In particular, it was shown to provide significant information about the patient’s mitral valve dynamics and the detailed flow dynamics and pressure around it. These data are not currently available without extensive, invasive measurements, and this therefore represents a significant step forward in model-based sensing and diagnosis. It is hoped that the model and methods developed in this study will be a powerful tool in assisting medical teams in investigating, tracking, diagnosing and controlling the cardiovascular system. More specifically, the mitral valve, as well as other similar valves, could be directly monitored to improve the diagnosis, costs and prognosis of valvular dysfunction. Furthermore, the overall results justify detailed in vivo animal experiments to thoroughly validate these models and methods in advance of clinical trials. [less ▲]

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See detailProtein Structural Annotation: Multi-Task Learning and Feature Selection
Becker, Julien ULg

Doctoral thesis (2014)

Experimentally determining the three-dimensional structure of a protein is a slow and expensive process. Nowadays, supervised machine learning techniques are widely used to predict protein structures, and ... [more ▼]

Experimentally determining the three-dimensional structure of a protein is a slow and expensive process. Nowadays, supervised machine learning techniques are widely used to predict protein structures, and in particular to predict surrogate annotations, which are much less complex than 3D structures. This dissertation presents, on the one hand, methodological contributions for learning multiple tasks simultaneously and for selecting relevant feature representations, and on the other hand, biological contributions issued from the application of these techniques on several protein annotation problems. Our first methodological contribution introduces a multi-task formulation for learning various protein structural annotation tasks. Unlike the traditional methods proposed in the bioinformatics literature, which mostly treated these tasks independently, our framework exploits the natural idea that multiple related prediction tasks should be designed simultaneously. Our empirical experiments on a set of five sequence labeling tasks clearly highlight the benefit of our multi-task approach against single-task approaches in terms of correctly predicted labels. Our second methodological contribution focuses on the best way to identify a minimal subset of feature functions, {\em i.e.}, functions that encode properties of complex objects, such as sequences or graphs, into appropriate forms (typically, vectors of features) for learning algorithms. Our empirical experiments on disulfide connectivity pattern prediction and disordered regions prediction show that using carefully selected feature functions combined with ensembles of extremely randomized trees lead to very accurate models. Our biological contributions are mainly issued from the results obtained by the application of our feature function selection algorithm on the problems of predicting disulfide connectivity patterns and of predicting disordered regions. In both cases, our approach identified a relevant representation of the data that should play a role in the prediction of disulfide bonds (respectively, disordered regions) and, consequently, in protein structure-function relationships. For example, the major biological contribution made by our method is the discovery of a novel feature function, which has - to our best knowledge - never been highlighted in the context of predicting disordered regions. These representations were carefully assessed against several baselines such as the 10th Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition. [less ▲]

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See detailNanobodies as tools to investigate the mechanism of aggregation of chimeric proteins made by the insertion of polyglutamine stretches into the beta-lactamase BlaP
Pain, Coralie ULg

Doctoral thesis (2014)

Among the neurodegenerative amyloidoses, ten disorders, referred to as polyglutamine (polyQ) diseases and including Huntington's disease and several spinocerebellar ataxias, are associated with ten ... [more ▼]

Among the neurodegenerative amyloidoses, ten disorders, referred to as polyglutamine (polyQ) diseases and including Huntington's disease and several spinocerebellar ataxias, are associated with ten proteins within which a polyQ tract is expanded above a threshold of typically 35-45 glutamine residues. Such expanded polyQ tracts lead to the aggregation of the host protein into amyloid fibrils that accumulate in the nucleus of some populations of neurons; these aggregates or some of their precursors are thought to contribute to neuronal death. So far, no preventive or curative treatment exists for these devastating pathologies. While the expansion of the polyQ tract above the threshold is the determinant factor for aggregation, recent studies suggest that non-polyQ regions of these proteins can play a significant role, either preventative or facilitative, in the aggregation process. The general principles governing the complex interplay between the role of the expanded polyQ tract and the role of the non-polyQ regions in the aggregation process are not well understood yet. In order to develop therapeutic strategies, it is important to better understand this complex interplay. To contribute to this aim, we have engineered chimeric proteins via the insertion of polyQ repeats of various lengths (23, 30, 55 and 79Q) into two sites (197 and 216) of the BlaP beta-lactamase from Bacillus licheniformis 749/C. The properties of these chimeric proteins recapitulate the characteristic features of the disease-associated polyQ proteins, i.e. (i) there is a minimum number of inserted glutamines (threshold) required to trigger the aggregation of the chimeras into amyloid fibrils, and (ii) above the threshold, the longer the polyQ tract, the faster the aggregation. Interestingly, for the same polyQ length, the chimeras with insertions in position 216 have an increased propensity to form amyloid fibrils compared to their counterparts with insertions in position 197. These findings highlight the strong influence of the overall protein context on aggregation triggered by expanded polyQ tracts. This thesis addresses the use of the variable domains of camelid heavy-chain antibodies, referred to as nanobodies or VHHs, as structural and mechanistic probes to better understand the different aggregating properties of the two sets of BlaP-polyQ chimeras (197 and 216). We have also performed limited proteolysis experiments and transglutaminase-mediated reactions on the monomeric form of the BlaP-polyQ chimeras to further investigate the effects of the polyQ insertions on the structure and dynamics of the BlaP moiety, as well as the structure of the polyQ tract itself. From the blood of a llama immunised with BlaP197(Gln)55, we isolated more than 60 VHHs specific to the BlaP-polyQ chimeras. Twenty eight of them were produced, purified and characterised. These VHHs were found to be all specific to the BlaP moiety and could be classified into four different groups recognising distinct epitopes on the surface of BlaP. One representative VHH of each group (i.e. cAb-A3S, cAb-H7S, cAb-F11N and cAb-G10S) was selected as probe to investigate the mechanism of aggregation of the BlaP-polyQ chimeras. The epitope of three of them was determined by X-ray diffraction and/or by NMR spectroscopy. Although they recognise distinct epitopes and exhibit different affinities for BlaP, the binding of the four VHHs significantly slows down the aggregation of all the BlaP-polyQ chimeras investigated (i.e. BlaP197(Gln)55, BlaP197(Gln)79 and BlaP216(Gln)79). The extent of inhibition depends however on the chimera and on the experimental conditions. We show that the inhibition of the aggregation of BlaP197(Gln)55 and BlaP197(Gln)79 upon binding of the four VHHs is correlated with the stabilisation of their native state. In the case of BlaP216(Gln)79, the extent of inhibition could not be only correlated to the stabilisation of its native state; the location of the epitope of the VHH is instead also determinant. This observation demonstrates that the lower thermodynamic stability of BlaP216(Gln)79 is not the unique factor responsible for its increased aggregation propensity. It also further highlights the complexity of the aggregation mechanism of polyQ proteins and the strong influence of the non-polyQ regions on the amyloid fibril formation triggered by the expanded polyQ tract. All together our results suggest that antibodies or antibody fragments raised against the non-polyQ regions of polyQ proteins associated with diseases could constitute a relevant therapeutic strategy. They also further demonstrate the power of nanobodies as probes to get a deeper knowledge of the underlying mechanisms of amyloid fibril formation. The preliminary limited proteolysis and transglutamination experiments obtained suggest that the polyQ tracts are all flexible, except that of 23 glutamines inserted in position 197 of BlaP, which seems to be more rigid than the others. The results obtained confirm that, globally, the structure of BlaP is not significantly modified by the insertions while the 216 chimeras seem more dynamic than the 197 chimeras. [less ▲]

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See detailContribution à l'étude de la réponse immune au cours d'une infection à Microsporum canis et établissement d'un modèle murin de dermatophytose
Cambier, Ludivine ULg

Doctoral thesis (2014)

Les dermatophytoses (ou « teignes ») sont des mycoses cutanées superficielles provoquées par des champignons filamenteux, appelés dermatophytes, affectant les animaux et l’homme. Microsporum canis est un ... [more ▼]

Les dermatophytoses (ou « teignes ») sont des mycoses cutanées superficielles provoquées par des champignons filamenteux, appelés dermatophytes, affectant les animaux et l’homme. Microsporum canis est un dermatophyte zoophile dont l’hôte naturel est le chat. Il touche principalement les carnivores domestiques et est un agent fréquent de zoonose. Les dermatophytes envahissant les structures kératinisées de l’épiderme, de nombreuses études ont porté sur la caractérisation des protéases sécrétées comme facteurs de virulence potentiels. Cependant, peu de recherches ont été consacrées aux mécanismes impliqués dans la mise en place de la réponse immune anti-dermatophytes. Il est couramment admis que la réponse immune protectrice lors d’une dermatophytose est une réponse à médiation cellulaire impliquant les lymphocytes de type Th1 et caractérisée par une réaction cutanée d’hypersensibilité de type retardé (Delayed Type Hypersentivity, DTH). Un constituant sécrété de M. canis correspondant au surnageant de culture du champignon cultivé sur milieu de Sabouraud liquide, appelé surnageant non induit (SNI), provoque des DTH chez le cobaye immunisé après une primo-infection, ce qui suggère que le SNI contient des antigènes potentiellement intéressants pour le développement d’un vaccin. Le cobaye est le modèle animal le plus utilisé pour étudier l’immunologie des dermatophytoses. Cependant, la quasi absence d’outils génétiques et immunologiques dans cette espèce ne permet pas d’étudier la réponse immune induite lors de dermatophytoses de manière satisfaisante. La mise au point d’un modèle murin de dermatophytose permettrait de pallier tous ces inconvénients. Au cours d’une dermatophytose à M. canis, les premières cellules rencontrées par le champignon lors de l’infection sont les kératinocytes qui, suite à l’activation par des composants fongiques, peuvent attirer les polymorphonucléaires neutrophiles (PMN) sur le site d’infection. Ces leucocytes sont, avec les macrophages, responsables in fine de l’élimination du dermatophyte. Cependant, le rôle des PMN dans les mécanismes liés à l’établissement de l’immunité anti-dermatophytes demeure inconnu. L’objectif général de ce travail était de contribuer à l’étude de la réponse immune au cours d’une dermatophytose à M. canis et de mettre au point un nouveau modèle animal de dermatophytose. Pour l’atteindre, trois études ont été réalisées : (1) l’évaluation du rôle des PMN félins dans la mise en place d’une réponse immune protectrice au cours d’une dermatophytose à M. canis, (2) l’évaluation des propriétés protectrices du SNI de M. canis dans un essai vaccinal en utilisant le cobaye comme modèle expérimental et (3) la mise au point d’un modèle murin de dermatophytose pour l’étude de l’immunité anti-dermatophytes. Résumé 2 Les résultats obtenus dans la première étude montrent que les PMN félins produisent des cytokines pro-inflammatoires telles le tumor necrosis factor (TNF)-α, l’interleukin (IL)-1β et l’IL-8 lorsqu’ils sont stimulés par les arthrospores vivantes du champignon ainsi que par des constituants structuraux, représentés par des arthrospores tuées par la chaleur, et sécrétés comme le SNI. De plus, après stimulation pendant 2 ou 4 heures par les arthrospores vivantes et tuées ainsi que par les protéases sécrétées Sub3 et Sub6, disponibles sous forme recombinante dans notre laboratoire, les taux d’ARNm du toll like receptor (TLR)-2 et du TLR-4 étaient augmentés dans les PMN. Ces résultats suggèrent que les PMN félins jouent un rôle dans l’établissement de la réponse immune anti-M. canis en produisant des cytokines pro-inflammatoires et que les mécanismes responsables de cette activation feraient intervenir les récepteurs TLR-2 et TLR-4. Dans la deuxième étude, les résultats indiquent que l’adjuvant monophosphoryl lipid-A (MPLA), dérivé non toxique du lipopolysaccharide et agoniste du TLR-4 a, à lui seul, un effet protecteur partiel chez les cobayes soumis à une épreuve d’infection par M. canis. En effet, les symptômes cutanés observés chez les cobayes ayant préalablement reçu l’adjuvant, étaient moins importants que ceux développés par les cobayes infectés n’ayant pas reçu l’adjuvant. En revanche, le SNI ne semble pas protéger les cobayes d’une infection expérimentale dans cet essai vaccinal. Les résultats obtenus dans la troisième étude démontrent que notre modèle murin de dermatophytose est valide et reproductible, en utilisant Arthroderma benhamiae et Arthroderma vanbreuseghemii. Ce n’est pas le cas avec M. canis. En effet, 100 % et 80 % des souris infectées respectivement par A. vanbreuseghemii et A. benhamiae ont développé des symptômes cutanés typiques de dermatophytose, à savoir de l’érythème, des squames, des croûtes et de l’alopécie alors que seulement 40 % des souris infectées par M. canis ont développé des signes cliniques, par ailleurs très discrets. Le recrutement important de PMN dans la peau des souris infectées par A. benhamiae et A. vanbreuseghemii et le profil cytokinique (transforming growth factor (TGF)-β, l’IL-1β, l’IL-6 et l’IL-22) généré par l’infection suggèrent l’implication de la voie Th17 dans la mise en place de la réponse immune anti-dermatophytes. En conclusion, l’ensemble de ce travail a contribué à élargir nos connaissances sur la réponse immune au cours d’une dermatophytose à M. canis. De plus, un nouveau modèle murin de dermatophytose à A. benhamiae et A. vanbreuseghemii a été mis au point et est approprié pour l’étude de la réponse immune anti-dermatophytes. [less ▲]

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See detailContribution à la compréhension de l'immunopathogénie de l'aspergillose nasosinusale chez le chien
Vanherberghen, Morgane ULg

Doctoral thesis (2014)

Sinonasal aspergillosis is a sever fungal rhinosinusitis mainly affecting large breed dogs in their mid ages. Its most common causal agent is A. fumigatus, a fungus that is largely spread in the ... [more ▼]

Sinonasal aspergillosis is a sever fungal rhinosinusitis mainly affecting large breed dogs in their mid ages. Its most common causal agent is A. fumigatus, a fungus that is largely spread in the atmosphere. As of today, the diagnostic and treatment for this disease remain a challenge for the practicing veterinary doctor. Very little data is available to explain why such a ubiquitous fungus induces a sever rhinosinusitis in otherwise healthy dogs, while other dogs do not present any sign of fungal infection. The authors of a study analysing the expression of mRNA encoding for certain cytokines and chimiokines in the nasal mucosa of SNA affected dogs, propose the assumption that dogs develop a protective immunity (Th1) against A. fumigatus, but that it could be blocked by an excessively intense regulating immunity (massive production of IL-10). Indeed, it is commonly described that in humans affected by invasive aspergillosis, as well as in mice-based models, the production of immunoregulating cytokines (IL-10) should be considered as a sign of the escalation of the sickness and an absence of its remission. The objective of this thesis was to investigate the adaptive immunity reaction of SNA affected dogs based on the assumption that sick subjects develop a protective immunity that is antagonised by a disproportional regulating immunity. Three axes of analysis have been considered to answer this objective. The first looked into the difference of expression and/or production of cytokines and transcriptor factors prototypics of the different adaptative and regulatory immunological paths: Th1 (IFN-γ and Tbet) – Th2 (IL-4 and GATA3) – Th17 (IL-17A and RORc) and Treg (IL-10 and FoxP3) in PBMC of affected and healthy dogs after A. fumigatus stimulation. Secondly, an analysis of genes by microarray has been carried on nasal mucosa biopsies of affected and healthy dogs. Thirdly, the promotor zone of the gene encoding IL-10 in dogs has been analysed by sequencing. This study has been done within three cohortes of dogs: Rottweiler-Labrador and Golden containing affected and healthy dogs. The objective was to investigate, as it is the case in human medicine, the possibility of a genetic modification as a factor susceptible of leading to SNA development. The results of the first study revealed that: (1) the PBMC of half the controls dogs and every affected dogs expressed a relevant overexpression of IFN-γ. This increase was significantly more important within PBMC of affected dogs. The analysis of IFN-γ production in culture supernatants was in accordance with these last observations. A significant increase in the expression of mRNA coding for Tbet was also observed in half of the PBMC of affected dogs. (2) a significant increase in expression of mRNA encoding IL-4 was observed in the PBMC of most of the affected and healthy dogs. This increase was significantly higher in the PBMC of affected dogs than in the healthy dogs. (3) the PBMC of most control and affected dogs also revealed an increase in expression of mRNA encoding IL-17A. This increase was statistically more important in the PBMC of affected dogs than in the healthy dogs. (4) a relevant decrease in mRNA expression encoding IL-10 was observed in the PBMC of more than half of the affected dogs. The expression of the mRNA encoding IL-10 was significantly smaller in the PBMC of affected dogs than in the healthy dogs. The microarray analysis showed that: (1) amongst the 49 overexpressed biological groups, 13 were associated to the immunological or inflammatory process; (2) the nasal mucosa of affected dogs presented an increase in the expression of genes encoding for molecules involved directly (IFN-γ and STAT4) and indirectly (IL-16, CCL3, CCL4, and CXCL10) in the development of protective Th1 immunity, as well as molecules involved in the regulatory branch of the immune response (IL-16 and Ikaros). The sequencing analysis of the promotor region of the gene encoding IL-10 revealed the presence of polymorphisms. Three polymorphisms were observed more frequently in clones belonging to the three studied cohorts, excepted for the clones belonging to SNA affected Rottweiler. The polymorphisms observed in dogs were not similar to those described in humans. The first study showed an increase in the expression of mRNa encoding IFN-γ - Tbet – IL-4 and IL-17A in most of the PBMC of the affected dogs, and a decrease in the expression of IL-10 in comparison with the PBMC of healthy dogs. Similar results were observed in mice repeatedly affected by A. fumigatus. The suggested hypothesis was that an intense Th17 immunity resulted in a massive inflammatory reaction leading to a favourable environment were A. fumigatus was able to proliferate as hyphae. In return, hyphae would lead to the development of a non-protective Th2 immunity. It is tempting to suggest that the same hypothesis could be made for dogs affected by SNA. In order to reinforce this hypothesis, we should compare the expression of the different molecules involved in the Th17 immunity inside the nasal mucosa of affected and healthy dogs. Additionally, we should be running a kinetic study based on the expression of prototypical cytokines in parallel with the analysis of the production of these cytokines in culture supernatants. Ideally these studies should use DC and lymphocytes isolated from the nasal mucosa of affected and healthy dogs. In conclusion, an new hypothesis could be formulated: the possibility that not the overstimulation of the regulatory branch of the immunity response but an overstimulation of the Th17 branch of the immune response could be the cornerstone of the incapacity of dogs to clear from their SNA. The results of the microarray study were partially in accordance to the starting hypothesis. Indeed, the results showed an overexpression of genes involved in in the development of the protective Th1 (IFN-γ, STAT4, IL-16, CCL3, CCL4, and CXCL10) as well as genes involved in the regulatory path of the adaptive immunity (IL-16 and Ikaros). But the results of this study did not show an increase in IL-10. No conclusion could be drawn from these results; indeed, they were only the reflection of a fixed image at a given moment and we cannot consider qPCR results as the exact replica of the production of cytokines in the microenvironment. Nevertheless this study pointed out new possible areas of research. The results obtained after the sequencing of the promotor zone of the gene encoding IL-10 did not show any clear difference between affected and healthy dogs. However, this study was undertaken with a very limited number of dogs. In order to further assess the possibility of a genetic modification as the cornerstone of the development of SNA, more dogs should be analysed and the sequencing analysis should be run in parallel with an ELISA analysis. [less ▲]

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See detailComplémentation précoce en colostrum de vache Azawak chez la chèvre rousse de Maradi au Niger: effets sur les performances de croissance et de reproduction, et sur la survie au cours de la première année de vie.
Abdou, Harouna ULg

Doctoral thesis (2014)

L’élevage  des  petits  ruminants  représente  au  Niger,  la  ressource  principale  pour  plus  de  6  millions  de   paysans pauvres, vivant avec moins de 1 dollar US par jour. C'est un trésor ... [more ▼]

L’élevage  des  petits  ruminants  représente  au  Niger,  la  ressource  principale  pour  plus  de  6  millions  de   paysans pauvres, vivant avec moins de 1 dollar US par jour. C'est un trésor important qui contribue à la renommée des familles. Selon le recensement général  de  l’agriculture  et  de  l’élevage  (2007),  le   cheptel Nigérien se chiffre à 31 millions toutes espèces confondues dont 11 millions de caprins (36,21 %)  et  9  millions  d’ovins  (30  %). Bien  qu'il  occupe  une  place  de  choix,  l’élevage  des  petits  ruminants  reste confronté à des contraintes dont les principales sont: les sécheresses chroniques et répétitives ayant pour conséquence un déficit alimentaire constant, la pression démographique entrainant une concurrence entre les cultures et les animaux   pour   l’occupation de la terre et enfin les pathologies récurrentes (parasitoses gastro- intestinales, affections digestives) accompagnées le plus souvent par des diarrhées. Par ailleurs, la naissance et le sevrage sont deux périodes critiques pour les jeunes animaux. Si à la naissance, le système immunitaire reste en chantier et par conséquent déficient, au sevrage c'est le changement alimentaire qui peut handicaper la croissance des jeunes. Malheureusement, ils ne reçoivent pas toujours   toute   l’attention   et   la   vigilance nécessaire pour optimaliser leur développement. Dans ce contexte,   il   serait   intéressant   d’étudier   les   solutions   possibles   à   ces   problèmes.   L’utilisation   du   colostrum bovin semble être exploitable dans la mesure où il renferme des éléments nutritifs et antimicrobiens  nécessaires  pour  le  bovin,  mais  également  pour  d’autres  espèces  (caprins,  ovins,  porcs,   homme). Pour cette étude, le choix du colostrum bovin a été guidé aussi par sa disponibilité à la station sahélienne expérimentale de Toukounous au Niger. À priori, l’objectif de cette thèse est de vérifier l'hypothèse d'un effet bénéfique de l'administration du colostrum bovin sur la santé et les performances zootechniques des cabris. Le   premier   chapitre   présente   d’abord   le   milieu   physique   du   Niger,   puis   s’intéresse à quelques caractéristiques  des  animaux  de  l’étude  à  savoir  la  race  bovine  Azawak  et  la  race  caprine  dénommée   chèvre rousse de Maradi. En effet, le zébu Azawak est un animal de taille moyenne (1,3 m au garrot), Dans des très bonnes conditions et en élevage intensif, la vache zébu Azawak peut produire en moyenne  12  litres  par  jour.  Le  rendement  à  l’abattage  va  de  50  à  60%.  Quant  à  la  chèvre  rousse,  elle   est de taille moyenne ou petite (0,55-0,65 m). La durée de lactation est de 3 à 4 mois après la mise bas selon   les   conditions   d’élevage   et   la   production   laitière   annuelle   est   de   150   kg   en   200   jours.   Le   rendement  à  l’abattage  (poids  carcasse)  varie  de  50  à  55%  pour  le  sujet  castré. Le deuxième chapitre est une synthèse bibliographique sur la physiologie de la production et composition chimique du colostrum. Cette revue fait la compilation des informations les plus récentes sur le mécanisme de synthèse du colostrum, son aspect physico-chimique, son importance et enfin les facteurs de variation des composants chimiques de cette première sécrétion mammaire après la mise bas. Le colostrum renferme tous les éléments nécessaires permettant non seulement une protection contre les agressions d ́agents pathogènes, mais également une croissance rapide des jeunes animaux. Le chapitre trois est relatif à la comparaison par méta-analyse de la composition chimique du colostrum de la race bovine Azawak à des données synthétisées de la littérature. Cette étude a guidé le choix  de  l’espèce  dont  le  colostrum  doit  être administré au cours des expériences sur le terrain. Les concentrations  moyennes  d’IgG, IgM, MS, protéines et matières grasses pour la vache Azawak ont présenté des  valeurs  plus  faibles  (P  ˂  0,001) que celles obtenus chez d'autres races, mais il convient de noter des niveaux élevés d'IgA (P > 0,05), de  lactose  et  de  cendre  brute  (P  ˂  0,001). En ce qui concerne les minéraux solubles, les concentrations moyennes de Ca, P, Na et Mg dans le colostrum de bovin Azawak étaient  significativement  plus  élevées  (P  ˂  0,001) que celles de moyennes obtenues à partir des données de synthèse. En conclusion, comparé aux données de littérature, le colostrum de vache Azawak semble être plus pauvre en immunoglobuline, en lipides et en protéines, mais plus riche en lactose et en minéraux.  Il  se  pourrait  qu’il  s’agisse  d’une  adaptation  de  la  race  au  milieu  sahélien. Le  chapitre  quatre  est  intitulé  "l'Effet  de  l’administration  du  colostrum  de  bovin  Azawak  sur  le  profil   plasmatique, la croissance et la survie chez les chevreaux roux". Cette  étude  visait  à  évaluer  l’impact   de  l’administration  de  colostrum  hétérologue  Azawak  sur  le  profil  protéique  plasmatique,  la  croissance   et le taux de survie des chevreaux roux au Niger. Après la naissance et ce, jusqu'à la fin de l'essai, les poids vifs ont augmenté avec le temps dans les deux groupes, mais les valeurs ont été plus élevées dans le groupe colostrum que dans le groupe témoin (+ 1,4 kg à j29, P < 0,001). Dans l'ensemble, le groupe colostrum a présenté un gain moyen quotidien largement supérieur à celui du groupe témoin (P < 0,001). Les concentrations moyennes de fractions plasmatiques obtenues à l'âge de 10 et 30 jours ont atteint des valeurs plus élevées dans le lot colostrum que dans le lot contrôle. A 10 jours, le groupe colostrum a tendu à montrer des teneurs supérieures pour l'ɑ-globuline  et  la  β1-globuline (P < 0,06). A 30   jours,   les   protéines   totales   et   les   β2-globulines ont été supérieures dans le groupe colostrum. L’administration  du  colostrum  hétérologue  chez  le  chevreau  semble donc avoir des effets positifs sur certains paramètres plasmatiques et même les performances pondérales. Le  cinquième  chapitre  traite  de  "Effet  de  l’apport  en  colostrum  de  bovin  Azawak  sur  les  performances,   les paramètres de reproduction et la survie chez les chevreaux roux". Cette étude a permis de comparer les performances de croissance pondérale ainsi que le gain moyen quotidien de deux lots de cabris élevés selon les deux modes c'est-à-dire la supplémentation (n = 20) et son absence non (n = 20). Le poids vif moyen du groupe colostrum a atteint une valeur significativement plus élevée que celle obtenu chez les animaux non supplémenté (P < 0,001) et les effets du traitement sur ADG ont été observés jusqu'à 150 jours après la fin de la supplémentation. Une tendance similaire de longue durée a également été observée en relation avec le taux de mortalité (25% pour ColG vs 55% pour ConG, (P = 0,05). L'âge à la première mise bas tendait à être plus faible dans le groupe traité (13,8 ± 0,7 vs 14,1 ± 0,8 mois, p ˂ 0,1). Dans l'ensemble, l'analyse statistique a révélé des différences très significatives en faveur du groupe de colostrum. Globalement,   l’analyse   statistique   des   données   a   révélé   des   différences hautement significatives en faveur du lot colostrum. Le  sixième  chapitre  porte  sur  l’Effet  de  l’administration  post-partum de colostrum bovin Azawak sur les paramètres zootechniques de cabris roux. Un dispositif quasi-similaire à celui du premier essai (chapitre IV) a été appliqué. La différence se situait au niveau de la dose du colostrum administré. En effet, la quantité de colostrum administrée (15 ml) lors du premier essai a été majorée de 66,7 % au cours de cette expérimentation soit une quantité de 25ml/jour/chevreau. Comme le premier essai a été probant,   l’objectif   de   ce   travail   était   de   voir   si   l’augmentation   de   la   dose   du   colostrum   à   administrer   peut améliorer davantage les paramètres zootechniques et réduire considérablement le taux de mortalité. Les résultats indiquent que la supplémentation avec du colostrum bovin augmente la croissance  des  chevreaux  principalement  jusqu’au  sevrage  (P < 0,001),  améliore  l’état  sanitaire  et   diminue le taux de mortalité (P < 0,05), modifie quelques paramètres zootechniques. Cette étude suggère de prodiguer un allaitement  artificiel  chez  d’autres  espèces  animales  dont  les  mères  peinent  à   couvrir les besoins en colostrum et en lait de leur progéniture. A   notre   connaissance,   dans   l’environnement   étudié,   ce   travail   est   original et semble apporter de nouvelles connaissances qui auront probablement des applications pratiques dans les régions présentant  des  conditions  d’élevage  assez  difficiles. [less ▲]

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See detailÉléments optiques biréfringents pour interféromètre à chemins optiques quasi-communs
Blain, Pascal ULg

Doctoral thesis (2014)

Notre étude porte sur l’utilisation de composants optiques biréfringents en tant qu’élément séparateur dans un interféromètre à chemins optiques communs ou quasi-communs. Pour ce type d’interféromètre, la ... [more ▼]

Notre étude porte sur l’utilisation de composants optiques biréfringents en tant qu’élément séparateur dans un interféromètre à chemins optiques communs ou quasi-communs. Pour ce type d’interféromètre, la seule différence introduite dans les chemins optiques des faisceaux objet et de référence est celle résultant du relief de la surface testée. Utiliser un élément biréfringent permet de n’avoir qu’un seul élément pour créer les faisceaux référence et objet. On parle d’auto-référencement. Cette propriété désensibilise l’interféromètre vis-à-vis de certaines perturbations extérieures car les faisceaux sont identiquement affectés par celles-ci. La biréfringence des cristaux étant bien souvent faible mais l’interféromètre à construire devant être le plus compact possible, le cisaillement entre les deux faisceaux s’en retrouve faible comparé à la taille de l’objet observé. Une séparation totale des faisceaux émergents n’est possible qu’avec un faisceau « ponctuel » collimaté. La configuration des interféromètres que nous étudierons sera donc différentielle. Deux types d’éléments biréfringents sont étudiés. Le premier est un assemblage de deux cristaux uniaxes taillés à 45° et dont l’orientation de l’axe de l’un des cristaux est tournée à 90° par rapport à celle de l’autre. Il s’agit de la lame de Savart. Les propriétés de cette lame sont détaillées pour justifier l’intérêt de son utilisation dans l’interféromètre. Ce dernier a été utilisé en shearographie et en profilométrie par projection de franges interférométriques. Une installation originale permet l’association des deux méthodes dans un unique montage compact. Dans la configuration proposée, seule l’orientation du cisaillement par l’interféromètre est possible. Pour faire varier la taille du cisaillement, nous avons décidé d’évoluer vers un autre type d’élément biréfringent. L’essor des éléments optiques à biréfringence spatialement variable nous a incités à investiguer cette voie. Ces éléments ont la particularité de permettre une variation spatiale de l’orientation de l’axe optique. Les réseaux de polarisation font partie de cette famille. Après avoir décrit et simulé leur comportement, nous proposons notre propre méthode d’enregistrement de tels réseaux par holographie de polarisation à l’aide d’une lame de Savart. Nous prouvons par la suite que deux réseaux de polarisation circulaire de même orientation et disposés l’un à la suite de l’autre créent un élément séparateur à taille et orientation de cisaillement variables pour un interféromètre à chemins optiques quasi-communs. Nous proposons une application en shearographie. [less ▲]

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See detailFers et bois dans les combles médiévaux et modernes du sud de la Belgique. Contribution à l'histoire de la construction en Europe occidentale
Maggi, Christophe ULg

Doctoral thesis (2014)

After four years of doctoral research on the topic of iron in the roof framing, a detailed typologic timeline could be established. It covers the period between the thirteenth and eighteenth century. The ... [more ▼]

After four years of doctoral research on the topic of iron in the roof framing, a detailed typologic timeline could be established. It covers the period between the thirteenth and eighteenth century. The development of such an inventory was possible by the development of an interdisciplinary methodology combining dendrochronology, archaeometallurgy and techniques of building archeology. Reflections and comparisons crossed with nearly 750 armatures from the investigation of 68 roof or attic parts, mainly located in Wallonia, helped to inventory 89 differents frames iron models. [less ▲]

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See detailIntegrated dynamical models of down-the-hole percussive drilling
Depouhon, Alexandre ULg

Doctoral thesis (2014)

Due to the overall process complexity, studies about percussive drilling usually focus on a limited set of the subprocesses underlying it, e.g., the hammer thermodynamics or the interaction between the ... [more ▼]

Due to the overall process complexity, studies about percussive drilling usually focus on a limited set of the subprocesses underlying it, e.g., the hammer thermodynamics or the interaction between the bit and the rock. Following this paradigm, the assessment of the process performance is typically performed by considering a single percussive activation and a single interaction cycle between the bit and the rock, from arbitrary initial conditions. The need for an integrated approach to evaluate drilling performance, based on the dynamical interaction of the subprocesses underlying drilling, is evident. Such an approach requires simplified models, however, as the computational cost associated with full scale models is simply unbearable. In this thesis, three dynamical integrated models are proposed and a preliminary analysis is conducted for a reference configuration and around it. The models couple three modules that represent: (i) the dynamics of the mechanical system, (ii) the interaction between the bit and the rock, and (iii) the activation of the mechanical system. For each module, simple representations are considered; of particular importance is the bit/rock interaction model which is a generalization to repeated interactions of experimental evidence observed for a single interaction. In the first model, the dynamics of a rigid bit is cast into a drifting oscillator and the activation modeled as a periodic impulsive force. The second and third models account for the dynamics of the piston and the activation results from the impact of the piston on the bit. They are respectively based on elastic and rigid representations of the two bodies. In the rigid model, analytical results of wave propagation in thin rods are used to represent the contact interaction between the piston and the bit. In the elastic model, wave propagation is resolved. Their preliminary analysis has revealed the occurrence of complex dynamical responses in the space of parameters. Expected trends are recovered around a reference configuration corresponding to a low-size hammer, with an increase of the rate of penetration with the feed force and the percussive frequency. The latter is seen to have a strong influence on the rate of penetration. Interestingly, our analyses show that when the activation period has the same order of magnitude as the timescale associated with the bit/rock interaction, a lower power consumption is observed, indicating a possible resonance phenomenon in the drilling system. Also, the predictions of the rigid model are shown to be in good agreement with the ones of the elastic model, in the explored range of parameters. Given the piecewise linear nature of the proposed models, dedicated numerical tools have been developed to conduct their analysis. As such, the thesis proposes a high-order time integration scheme for structural dynamics as well as a novel framework to evaluate the accuracy of such schemes, and a root-solving module to perform event-detection for coupling with event-driven integration strategies. Specific to the framework is the account for both structural damping and external forcing in the evaluation of the scheme order of accuracy. Specific to the root-solving module is the forcing of event occurrence in the localization procedure. [less ▲]

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See detailFrom censored to cross-sectional data: non and semiparametric new developments
Laurent, Géraldine ULg

Doctoral thesis (2014)

In many statistical studies, an observation is evident: the available data are regularly right-censored. A censorship arises when, for different reasons, the data time of interest can not be observed. A ... [more ▼]

In many statistical studies, an observation is evident: the available data are regularly right-censored. A censorship arises when, for different reasons, the data time of interest can not be observed. A data is so right-censored if, instead of observing its time of interest, a lower bound of this time is considered for this data. For example, the study duration can be shorter than the time of interest leading then to a correspondence between the observed times and the study end time. Moreover, these data can be obtained from cross-sectional process. Cross-sectional process selects only data in progress at a fixed time to constitute the studied sample, determining the data followed for the study. Therefore, cross-sectional process introduces left truncation. A data is described as left-truncated if its time of interest is larger or equal to a fixed time. It is in this context this thesis has been elaborated. The considered estimation problems for such data will be studied with a nonparametric or semiparametric approach. An approach is nonparametric or semiparametric if none assumption is supposed about the belonging to parametric family for the time of interest distribution function, solely based on qualitative hypotheses. These estimation methods have thus the advantage to be based on weaker assumptions in comparison with the parametric approaches. The aim of the different researches developed in this thesis is to improve the current estimation techniques. This thesis is organised in four parts. The first part (first chapter) determines the context of our researches through practical examples and a significant but not exhaustive literature overview as well as our motivation about the different researches presented in this thesis. To conclude this first part, our contributions in these researches are briefly explained. The second part (second chapter) presents a new estimation procedure for the parameters of the parametric conditional variance in the heteroscedastic regression situation applied to right-censored data. This procedure constructs artificial data to replace censored data exploiting a heteroscedastic regression model and then defines the optimal parameters from the least squares method. The interest of this research is to fill a gap in the current literature. The third part (third and fourth chapters) studies, in a regression context, the cross-sectional data, i.e. left-truncated and right-censored data, where the conditional truncation distribution function is supposed to be known. The innovation of the method proposed here consists in the use of information contained in the conditional truncation distribution function for the nonparametric estimation methods. Finally, the fourth part (fifth chapter) is devoted to the cross-sectional data examination but this time for nonparametric estimation of the time of interest distribution function. In this chapter, the truncation distribution function is supposed to belong to a parametric family and not known anymore. The relevance of this approach is due to this weaker assumption than one in the above part. This information about the truncation distribution function is also introduced in the nonparametric estimation. This thesis concludes with a set of suggestions related to possible future researches in these statistical fields. [less ▲]

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See detailFrontière(s), jeu d'acteurs et espace du contrôle: le cas de Ceuta
Bernes, Laure-Anne ULg

Doctoral thesis (2013)

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See detailMarchés boursiers africains : problématique de l’efficience, dynamique de la volatilité, rendement et volume des transactions
Woroucoubou, Habibou ULg

Doctoral thesis (2013)

With the exception of the Johannesburg Stock Exchange, African stock markets are characterized, in their vast majority, by a marginal number of listed companies, low capitalization, low trading volume and ... [more ▼]

With the exception of the Johannesburg Stock Exchange, African stock markets are characterized, in their vast majority, by a marginal number of listed companies, low capitalization, low trading volume and low liquidity. These characteristics raise questions about the volatility, efficiency, optimal compensation risks to investors and, more generally, to the price adjustment speed to the information conveyed by the volume of transactions. The objective of this doctoral work is to study the behavior of African stock markets through volatility, price, return and volume of transactions in connection with the performance and volatility. Compared to the volatility modeling, the study shows that the EGARCH model is the most suitable process may be applied to the data of African stock markets for estimating and forecasting volatility. For efficiency, the study shows that only the market of South Africa seems to be informationally efficient in the weak form. The analysis of the risk-return relationship reveals that only less developed markets (except Botswana) show a positive and significant premium risk. Such a result means that the least developed African stock markets in the sample reach rewarded accordingly risks for investors. For asymmetry, the study shows that there is presence of leverage for all emerging markets, indicating that in these markets, the bad news has a greater impact on volatility than good news of the same magnitude. In contrast, for less developed markets, there is no leverage. With respect to the relationship between the volume of transactions, performance and volatility, the study shows that emerging African stock markets showed a more or less close to the behavior of other emerging and developed markets of the world in terms of leverage, contemporary positive relationship and causality between trading volume and performance on the one hand, and between trading volume and volatility, on the other hand. In contrast, for other less developed stock markets, the impact of volume on return and volatility is less noticeable. [less ▲]

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See detailInsight into the mechanisms underlying the oncogenic potential of BCL-3 through transcriptomic studies
Zhang, Xin ULg

Doctoral thesis (2013)

The abstract will be available after the corresponding papers are published. For more information, please contact Dr. Alain Chariot.

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See detailMéthodes d'accélération du tir de rayons sonores pour la simulation en acoustique des salles
Lesoinne, Stephane ULg

Doctoral thesis (2013)

This thesis provides methods to speed up the acoustical ray tracing for room acoustics. These methods uses 3 complementary axes that have been implemented, tested and analyzed: CPU vectorization, a ... [more ▼]

This thesis provides methods to speed up the acoustical ray tracing for room acoustics. These methods uses 3 complementary axes that have been implemented, tested and analyzed: CPU vectorization, a geometry preprocessing based on visibility and a decrease in the number of traced rays by using variable size receivers. This results in a overall gain that ranges from 120 to 150 on a 8core CPU. [less ▲]

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See detailStructural and biochemical study of the proteins AmiC, NlpD and FtsW involved in the bacterial cell division
Rocaboy, Mathieu ULg

Doctoral thesis (2013)

Cell division in the Gram negative bacterium Escherichia coli is a highly coordinated mechanism involving various physiological functions such as chromosome segregation, cell envelope invagination ... [more ▼]

Cell division in the Gram negative bacterium Escherichia coli is a highly coordinated mechanism involving various physiological functions such as chromosome segregation, cell envelope invagination, peptidoglycan synthesis at the division site and separation of the daughter cells. All these functions require a high level of spatio-temporal regulation in order to preserve the physical integrity of the cell. At least 20 proteins required for a proper cell division are recruited to the division site to form a supramolecular complex called the divisome. This thesis work focused on three major components of the E. coli division machinery: the N-acetylmuramyl L-alanine amidase AmiC, the LytM factor NlpD and the lipid II flippase FtsW. These proteins are recruited at midcell at a late stage of cell division. FtsW is an integral membrane protein crucial for the translocation of the peptidoglycan precursor from the cytoplasm to the periplasm where it will be processed to produce septal peptidoglycan. AmiC acts as a septal peptidoglycan hydrolase that allow the separation of the daughter cells. This enzyme has been shown to be activated by the LytM factor NlpD. The crystal structure of AmiC from E. coli presented in this work confirms the presence of an inhibitory helix in the active site. The AmiC variant lacking this helix exhibits by itself an activity comparable to that of the wild type AmiC activated by NlpD. Furthermore, the direct interaction between AmiC and NlpD has been detected by microscale thermophoresis with an apparent Kd of about 13 µM. The crystal structure of AmiC also reveals the β-sandwich fold of the AMIN domain, responsible for the septal targeting of AmiC to the division site. The two symmetrical four-stranded β-sheets exhibit highly conserved motifs on the two outer faces. Along with the peptidoglycan binding capacity of the AMIN domain, results obtained so far suggest that the AMIN domain could be involved in the recognition of a specific peptidoglycan architecture or a composition different than the lateral peptidoglycan. Production screenings of FtsW from different strains were realized and FstW from E. coli was purified. This challenging project will require additional efforts to obtain sufficient amount of protein for structural investigation. Information gathered in this work confirms the high level of regulation of the hydrolytic activity at the septum and gives a structural basis for a more precise molecular characterization of the division site targeting. Disruption or over-activation of these regulation mechanisms could represent a new strategy in the development of antibacterial compounds. [less ▲]

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See detailDéfinition de propriétés acido-basiques dans les liquides ioniques de seconde génération
Robert, Thierry ULg

Doctoral thesis (2013)

The ionic liquids are salts having the particularity of being molten at temperatures lower than 100 °C. Consequently, these new solvents mainly made up of ions have original physicochemical properties ... [more ▼]

The ionic liquids are salts having the particularity of being molten at temperatures lower than 100 °C. Consequently, these new solvents mainly made up of ions have original physicochemical properties. Within a few years, the ionic liquids passed from a laboratory curiosity to a true field of research impossible to circumvent, currently in full rise. Indeed, the replacement of usual organic solvents in catalytic and/or separation processes by these neoteric solvents offers many advantages but also new opportunities for the “Green Chemistry”. However, the systematic exploitation of the ionic liquids as reactional media rests in particular on the understanding of their chemical properties, which for some of them are still scarcely known, such as the acidity for example. This thesis thus aims to undertake a study of the acido-basic properties of (and in) these solvents, and more particularly to determine the accessible levels of acidity for acid solutions (with added HOTf or HNTf2) in second generation ionic liquids such as [HNEt3][NTf2], [BMIm][NTf2], [BHIm][NTf2], [BMIm][BF4], [BMIm][OTf], [BMIm][PF6] and [BMIm][SbF6]. In order to evaluate these acidity levels, we propose two different methods, each one resting on an extra-thermodynamic assumption. The first, the Hammett acidity function H0, is based on the protonation equilibrium of indicators whose pKa's are proposed as solvent independent. The second, the Strehlow potentiometric function R0(H+), consists in measuring, in a given solvent, the electrochemical potential of the proton compared to the ferricinium/ferrocene redox couple whose potential is supposed to be independent of the solvent, and then to refer it versus the Normal Hydrogen Electrode (NHE) in water. The two methods lead to the same conclusions. Firstly, the ionic liquids are generally contaminated by residual basic impurities (from solvents needed for the synthesis…) which need to be neutralized before reaching the acidity characteristic of the medium. The levels of acidity then obtained are very high and can reach values as high as R00(H+) = -10 in the case of [BMIm][BF4]. Then, the accessible level of acidity in an ionic liquid depends mainly on the nature of its anion, and not of that of its cation. We thus obtain the following classification, by decreasing acidity: [PF6-] > [BF4-] > [NTf2-] > [OTf-], indicating that the triflate is the more solvating anion It was found however that the Hammett acidity function led, for the same concentration in acid, to different levels of acidity, depending on the indicator used. The ionic liquids would consequently be media less dissociating than estimated in the literature and the Hammett function would then be related to an apparent acidity (H0)app, underestimating the real acidity. Finally, a difference in acidity between HNTf2 and HOTf is observed in [BMIm][NTf2] and [BMIm][OTf], HNTf2 showing an acidic character stronger than HOTf. On the other hand, in [BMIm][OTf] these two acids show the same acidity since that of HNTf2 has been leveled by solvent. [less ▲]

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See detailEntomofaune associée à Jatropha curcas (Euphorbiaceae) au Niger et évaluation de l'activité insecticide de son huile
Abdoul Habou, Zakari ULg

Doctoral thesis (2013)

Résumé Jatropha curcas L. est un arbuste de la famille des Euphorbiacées originaire d’Amérique centrale. Cette plante est cultivée pour son huile, valorisée dans la production de biocarburant. Cette huile ... [more ▼]

Résumé Jatropha curcas L. est un arbuste de la famille des Euphorbiacées originaire d’Amérique centrale. Cette plante est cultivée pour son huile, valorisée dans la production de biocarburant. Cette huile possède également une activité insecticide qui constitue un second volet de valorisation de la plante. Malgré la toxicité de la plante, de nombreux insectes causent des dégâts non négligeables au niveau des inflorescences, fruits et/ou des feuilles, réduisant considérablement le rendement en graine et la qualité de l’huile. La première partie de ce travail a consisté en la réalisation d’inventaires de ces insectes au Niger durant la période de juin à octobre, en 2010 et en 2011. Les principaux insectes ravageurs de J. curcas au Niger incluent les familles des Acrididae (Oedaleus senegalensis, O. nigeriensis, Heteracris leani, Parga cyanoptera, Catantops stramineus et Acanthacris ruficornis citrina), Cetoniidae (Pachnoda interrupta, P. marginata, P. sinuata et Rhabdotis sobrina), Coreidae (Leptoglossus membranaceus et Cletus trigonus), Pentatomidae (Agonoscelis versicoloratus, Nezara viridula et Antestia sp.) et Scutelleridae (Calidea panaethiopica). La seconde partie de ce travail a porté sur les possibilités d’utilisation de l’huile de J. curcas dans la lutte contre les ravageurs du niébé et le puceron noir de la fève. Des essais d’efficacité de terrain et de laboratoire ont été menés avec différentes formulations d’huile de Jatropha. Nous avons pu mettre en évidence un effet biocide croissant avec la concentration en huile. Les concentrations de 5% et 7,5% d’huile de J. curcas permettent de réduire le niveau d’attaque des pucerons (Aphis craccivora) de 10 et 50% respectivement par rapport au témoin. Une diminution du nombre des thrips (Megalurothrips sjöstedti) et de punaises (Anoplocnemis curvipes) respectivement de 50 et 75% est observée dans les mêmes conditions. Ces traitements ont conduit à une augmentation significative du rendement [less ▲]

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See detailContribution de la télémétrie à l'investigation urodynamique de la fonction vésico-urétrale chez la chienne.
Noël, Stéphanie ULg

Doctoral thesis (2013)

Micturition disorders are common in veterinary medicine and can occur already in puppies. The congenital urethral sphincter mechanism incompetence represents the second cause of urinary incontinence in ... [more ▼]

Micturition disorders are common in veterinary medicine and can occur already in puppies. The congenital urethral sphincter mechanism incompetence represents the second cause of urinary incontinence in puppies but data on the development and the evolution of the continence mechanism are lacking in veterinary medicine. This study could be the first step in the understanding of the pathophysiology of congenital urethral sphincter mechanism incompetence which resolves spontaneously in half of the affected dogs after the first of the second oestral cycle. The lower urinary tract has been widely investigated in adult female dogs, particularly by urodynamics. Urodynamics is a useful technique providing informations on the vesico-urethral function but some limitations are described. The major limitation is the need for sedation or anaesthesia as it is not feasable to obtain interpretable data from an awake animal. A second limitation is associated with the technique of retrograde cystometry because the technique of bladder filling and the filling rate are not physiological. Therefore, techniques have been developed such as diuresis cystometry or ambulatory urodynamics to decrease the impact of these limitations. In urological research, telemetry allows the investigation of different urodynamic parameters without the need for physical or chemical restraint and during several micturition cycles. The objectives of this work were to study the development and the evolution of the continence mechanism during the prepubertal period and during the two first oestral cycles and to study the vesico-urethral function with telemetry. This technique will be standardized and afterwards will be used to study different current urological drugs commonly used in veterinary medicine. In the first study, we showed that the values of the urodynamic and morphometric parameters of the lower urogenital tract varied in function of the growth of the bitches and also in function of the different phases of the œstrus cycle. The end of the prepubertal period was characterized by an increase of the urethral pressures (maximal urethral pressure, MUP ; maximal urethral closure pressure, MUCP ; integrated pressure, IP) and functional urethral length (FPL) but also by an increase of the urethral (UL) and vaginal lengths (VL) measured by vagino-urethrography compared with values at earlier times. The bladder function was characterized by a non-linear increase of the bladder capacity, which was reached at 6 months of age and by an increase of the bladder threshold pressure observed from 7 months of age. During the oestrus cycle, the urethral pressures significantly decreased during the oestrus and the early dioestrus which are characterized by a decrease in oestrogen plasmatic concentration and by an increase in progesterone plasmatic concentration. The highest values of FPL were observed during the follicular phase (œstrus, prooestrus). Values of UL could not be determined during œstrus of the first cycle because urethras were not identifiable on vaginourethrograms obtained at that time. During the second œstrus cycle, UL was significantly higher during œstrus and early dioestrus compared to anoestrus. No significant variation in Pth was observed during the first cycle ; however during the second cycle, the lowest Pth values were observed during late anoestrus. Pth values were also lower during œstrus compared to proestrus. The luteal phase was associated with an increase in bladder capacity that reached the highest value during the dioestrus. The VL decreased progressively during the second cycle to reach the lowest value during anoestrus. The MUCP and UL were significantly higher during the anoestrus of both cycles compared to the values obtained when the dogs were 9 months old. The same observation was made for IP at the first anoestrus. The increase in values of these parameters during periods with low hormonal influence could suggest an impact of the growth but also a constant improvement of bladder function all along the study. It was interesting to observe that the position of the bladder was variable during the prepubertal period as she was either in an intrapelvic or in an intra-abdominal position. After the prepubertal period, the bladder was always in an intra-abdominal position. In the second study, we showed that a single administration of ephedrine or phenylpropanolamine (PPA) was able to significantly modify the urodynamic and the morphometric parameters. Using conventional urodynamics, both ephedrine or PPA increased the urethral pressures during 4 hours and the FPL during 2 hours. The integrated pressure was elevated during 6 hours with PPA and its value was higher than the value obtained with ephedrine. On the other hand, the FPL remained elevated during 18 hours with ephedrine. Using telemetry, ephedrine, and to a lesser extent PPA, modified bladder function. The administration of ephedrine was associated with an increase in bladder threshold volume and a decrease of the detrusor threshold pressure. An increase in bladder volume was observed after PPA administration. Both drugs modified significantly the hemodynamic parameters. Arterial pressures were significantly increased during 4 to 6 hours after the administration of both drugs and were associated with a decrease in heart rate during 12 hours. These results were in agreement with previous studies and confirmed the fact that sympathetic drugs must be used with caution in incontinent dogs suspected of cardio-vascular diseases. In the third study, we showed that interpretable values of urodynamic parameters were obtained with telemetry. Physiological data were obtained from telemetric recordings because no sedative or analgesic drugs were used during the recording and bladder filling was natural. The location of the implant inside a subcutaneous cavity in the left flank did not disturb the dogs and the quality of the signals were good when the receiver was placed on the lateral wall of the metabolic cage. Telemetry allows continuous recording of values of urodynamic parameters (abdominal pressure, bladder pressure, detrusor pressure and bladder threshold volume) and values of smooth muscle electrical activity parameters. In the first step of the study, conventional urodynamics was compared to telemetry. The values of bladder threshold volume obtained by telemetry was significantly lower than the values obtained by conventional urodynamics. No difference in values of threshold bladder pressure was observed between the two techniques. In the second step of the study, the repeatability of telemetric recordings was assessed between day and night. A good repeatability was obtained with the night recordings. Comparing day and night recordings, higher bladder threshold volumes and lower detrusor threshold pressures were obtained during the night. No variation of the urodynamic parameters was observed during the bladder filling phase. The smooth muscle urethral electrical activity did not vary during the bladder filling phase. The frequency of micturition was not different between day and night but the frequency of involuntary detrusor contractions was higher during the day. In the third step of the study, the effect of drugs currently used to treat different micturition disorders were studied. Oestriol and duloxetine increased the electrical activity at day 8 compared to days 0, 1 and 15. No significant effect of PPA, oestriol, oxybutynin, bethanechol and duloxetine was observed on the values of urodynamic parameters or on the frequency of involuntary detrusor contractions. The results obtained in this study suggest that circadian variations may influence urodynamic measurements and that long-term telemetric studies of the lower urinary tract should be conducted during the night to obtain repeatable recordings. Further pharmacokinetic and pharmacodynamics studies are needed to confirm the effects of the different drugs on vesico-urethral function. [less ▲]

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See detailLa limite Paléocène-Eocène dans le Bassin de Douala Biostratigraphie et essai de reconstitution des paléoenvironnements
Mbesse, Cecile Olive ULg

Doctoral thesis (2013)

ABSTRACT This work consists of the analysis of the palynoflora (dinoflagellates and sporomorphs) identified from four petroleum exploration wells drilled through the Nkapa Formation (Douala Basin ... [more ▼]

ABSTRACT This work consists of the analysis of the palynoflora (dinoflagellates and sporomorphs) identified from four petroleum exploration wells drilled through the Nkapa Formation (Douala Basin, Cameroon). The vertical distribution of index taxa in the Moulongo, Ngata, Mamiwater and North Matanda wells allowed establishing a biostratigraphic frame of the first half of the Paleogene of the Douala Basin and identifying the Paleocene/Eocene boundary in each well through a comparison with surrounding sedimentary basins. Seventy dinoflagellate species have been identified, among which 30 are stratigraphically informative. Four biozones have been established, three for the Paleocene and one for the Early Eocene. The biozone 1 is characterized by Cretaceous species such as Cerodinium diebelii, Lejeunecysta hyalina, Andalusiella gabonensis, Palaeocystodinium australinum and Palaeocystodinium golzowense. The biozone 2 is defined by the acme of Areoligera coronata, Adnatosphaeridium multispinosum and Glaphyrocysta ordinata. The biozone 3 is defined by the acme of several Apectodinium species (A. hyperacanthum, A. homomorphum, A. paniculatum, A. parvum, A. quinquelatum). The biozone 4 is defined by the occurrence of Eocene taxa such as Deflandrea cf. oebisfeldensis, Hystrichosphaeridium tubiferum and Wetzeliella sp. Based on the position of the Paleocene/Eocene boundary in the Moulongo well, correlations have been established with the others sedimentary sequences analysed. Our study shows that, as previously demonstrated for Nigeria in an other study, the acme of Apectodinium in the Douala Basin can be attributed a Late Paleocene age and hence occurred before the carbon isotope excursion (CIE) of the Paleocene-Eocene boundary and the coeval Paleocene-Eocene thermal maximum (PETM). The acme of Apectodinium in the Douala Basin is thus markedly diachronous with the Apectodinium acme identified in various Nordic Basins, where it is contemporaneous with the PETM (earliest Eocene). Ninety-four sporomorph species have been recognized, among which fifty are stratigraphically informative. Three biozones have been established. The biozone 1 is predominantly characterized by Palmae- and Proteaceae-type pollens, the latter with Cretaceous characteristics. The biozone 2, Late Paleocene in age, is characterized by a transition from original floras towards more « modern » floras. The biozone 3 is earliest Eocene in age and shows the early steps of the extant « Leguminosae flora » of West Africa. Together with the biostratigraphic analysis, a palaeoenvironmental reconstruction is proposed, based on dinoflagellate ecology, on the evolution of the dinoflagellate /sporomorph ratio, as well as on the reconstruction of the plant environments in the studied sedimentary sequences. The evolution of the Douala Basin during the timespan studied occurred according to two geographical axes: a WE (Moulongo-Ngata) axis and a SSW-NNE (Moulongo-Mamiwater-North Matanda) axis. During the Early and Middle Paleocene, the Douala Basin was open towards the sea and showed a coastal-estuarine environment, with marginal mangroves and lowland swamp forests. During the Late Paleocene, the marine character of the sedimentation was less prominent as brackish fluvio-lagoonal intertidal environments developped. They were accompanied by gallery forests and surrounded by dense, periodically flooded, forests northwards and by forests on wet soils eastwards. During the earliest Eocene, a marine regression occurred. The palaeoenvironments included confined coastal lagoon systems with a peripheral impoverished local flora northwards, and moist, dense, evergreen forests eastwards. [less ▲]

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See detailLa limite Paléocène-Eocène dans le Bassin de Douala Biostratigraphie et essai de reconstitution des paléoenvironnements
Mbesse, Cécile ULg

Doctoral thesis (2013)

RESUME Ce travail présente une analyse du phytoplancton et des sporomorphes recensés dans divers puits de prospection pétrolière ayant traversé la Formation de Nkapa dans le Bassin de Douala au Cameroun ... [more ▼]

RESUME Ce travail présente une analyse du phytoplancton et des sporomorphes recensés dans divers puits de prospection pétrolière ayant traversé la Formation de Nkapa dans le Bassin de Douala au Cameroun. La distribution verticale de taxons marqueurs dans les sondages de Moulongo, Ngata, Mamiwater et Nord Matanda a permis d’établir une biostratigraphie du Tertiaire inférieur du Bassin et d’y préciser la position de la limite Paléocène-Eocène sur base d’une comparaison avec les bassins sédimentaires avoisinants. En considérant trente espèces de dinoflagellés à caractère stratigraphique sur les quelque septante inventoriées, quatre biozones ont pu être établies, trois pour le Paléocène, une pour l’Eocène basal. La biozone 1 se caractérise par des espèces héritées du Crétacé, Cerodinium diebelii, Lejeunecysta hyalina, Andalusiella gabonensis, Palaeocystodinium australinum et Palaeocystodinium golzowense; les biozones 2 et 3 par les acmés de certaines espèces, pour la 2, de Areoligera coronata, Adnatosphaeridium multispinosum et Glaphyrocysta ordinata, pour la 3, de diverses espèces du genre Apectodinium (A. hyperacanthum, A. homomorphum, A. paniculatum, A. parvum, A. quinquelatum). La biozone 4 voit apparaître des espèces caractéristiques de l’Eocène: Deflandrea cf. oebisfeldensis, Hystrichosphaeridium tubiferum et Wetzeliella sp. En tenant compte de la limite Paléocène/Eocène établie par les stratigraphes pétroliers à Moulongo, les corrélations ont été précisées avec les autres séquences analysées. L’étude a mis en évidence l’existence d’un diachronisme entre deux acmés d’Apectodinium, celui pré-CIE (Carbon Isotope Excursion) observé au Paléocène supérieur dans le Bassin de Douala comme dans celui du Nigeria voisin et celui contemporain du PETM (Paleocene-Eocene Thermal Maximum) dans l’Eocène basal de divers bassins nordiques passés en revue dans le travail. Sur les nonante-quatre espèces de sporomorphes identifiées, une cinquantaine de taxons a été retenue dans un objectif biostratigraphique. Trois biozones à caractère évolutif se sont dégagées: une biozone inférieure à caractère paléocène soulignée par une dominance de formes de types « Palmae » et « Proteaceae », ces dernières d’aspect archaïque crétacé; une biozone intermédiaire du Paléocène supérieur avec évolution de la flore originelle vers un ensemble qui peut être qualifié de plus « moderne » et enfin, à l’Eocène basal, de l’installation d’associations annonçant les prémices de la mise en place de la flore actuelle à « Légumineuses » d’Afrique de l’Ouest. En parallèle de l’analyse biostratigraphique est proposée une reconstitution paléoenvironnementale basée sur l’écologie des dinoflagellés, sur l’évolution du ratio dinoflagellés/pollen et spores et sur la reconstitution des milieux végétaux dans les différentes séquences étudiées. L’évolution du Bassin selon deux axes géographiques a été mise en évidence: un axe WE (Moulongo-Ngata) et un axe SSW-NNE (Moulongo-Mamiwater-Nord Matanda). Au Paléocène inférieur et moyen, le Bassin, largement ouvert sur la mer, présente un milieu côtier-estuarien frangé de mangroves et de forêts de basse plaine marécageuse. Au Paléocène supérieur, l’influence marine se faisant moins importante, des milieux saumâtres fluvio-lagunaires soumis aux marées se développent, ils sont bordés de galeries forestières et entourés de forêts denses périodiquement inondées vers le Nord et de forêts sur sols humides vers l’Est. Avec la régression marine amorcée à la base de l’Eocène, les paléoenvironnements s’individualisent: vers le Nord s’installent des milieux lagunaires confinés entourés d’une flore locale appauvrie et vers l’Est, autour de milieux d’eau douce d’arrière-delta, une forêt dense sempervirente humide de terre ferme occupe le terrain. [less ▲]

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See detailAmélioration de l’efficience d’utilisation de l’eau chez les principales cultures fourragères au Tadla- Maroc
Bouazzama, Bassou ULg

Doctoral thesis (2013)

Aiming to define irrigation strategies improving the water productivity by folder crops under water scarcity in the irrigated perimeter of Tadla (Morocco), this work combines field experimentation and ... [more ▼]

Aiming to define irrigation strategies improving the water productivity by folder crops under water scarcity in the irrigated perimeter of Tadla (Morocco), this work combines field experimentation and modeling. The field study of crop response to water stress is important to maximize yield and improve agricultural water use efficiency (WUE) in areas where water resources are limited. On the silage maize, the results showed that water deficit affected plant height growth, accelerated the senescence of the leaves and reduced the leaf area index. Dry matter yields varied from 3.9 t.ha-1 under T5 (20% ETc) to 16.4 t.ha-1 under T1 (100% ETc). The establishment of the water budget by growth phase showed that the water use efficiency was higher during the linear phase of growth. WUE calculated at harvest varied between 2.99 kg.m-3 under T1 and 1.84 kg.m-3 under T5. The actual evapotranspiration under T1 (100% ETc) was 478 mm and 463 mm in 2009 and 2010, respectively. The yield response factor (Ky) for the silage maize for both growth seasons was 1.12. The ETc of silage maize was determined using lysimeter drainage at 415 mm. the mean values of crop coefficients Kc were 0.56, 1.22 and 1.05 for beginning phase, mid-season and at harvest (grain milky pasty stage) respectively. Drip irrigation allows obtaining dry matter yields similar to flood irrigation but with less water and saves about 30% of irrigation water applied. Over five cycles, berseem dry biomass yields achieved under T1 are 14.3 and 13.9 t/ha in 2009/10 and 2010/11 respectively. The yield reductions by applying 60% of water requirements are 40 and 42% in 2009/10 and 2010/11 respectively. Berseem daily productivity increases with more water applied with the highest value of 102 kg DM/ ha/ day. The dry matter content increases with water stress. The mean values range between 12.3 and 23.7% under T1 (100% ETc) and T4 (40% ETc) respectively. The contribution of without irrigation cycles (rainy period) on the total annual yield may vary from 35% to 52% under treatments T1 and T4 respectively. Water balance achieved by water regime shows that drainage losses increase with more water applied especially in the first cycle. WUE is low during the first cycle, optimal in 2nd, 3rd and 4th cycle and decreases in the last one with water stress. Global WUE of berseem determined over the entire crop period (slope of the regression line) is 3.37 kg.m-3. The yield response factor (Ky) for the berseem for both growth season was 1.11. Berseem ETc determined by drainage lysimeter was 520 mm. The Kc values were estimated for each cycle for all three phases: initial, development (median) and mid-season. Maximum yield average under drip irrigation was 15.7 t/ha and obtained with 411 mm of water supply allowing to save 57% of water compared to traditional irrigation technique. Comparing the behavior of six alfalfa varieties most commonly practiced in the irrigated perimeter of Tadla shows that the "Super Siriver" cultivars followed by «Trifecta» have higher yield potential and higher tolerance to water deficit. Alfalfa maximum annual yield obtained was 24.2 t.ha-1. The contribution of the spring cycles to the annual yields range from 55% under T1 (100% ETc) to 65% under T4 (40 % ETc). In addition to water quantities, alfalfa yields depend on time application during a growth cycle. WUE varies from cycle to another and from one season to another. The maximum value was 2.57 kg.m-3 and obtained in spring 2011, while the low value was 0.64 kg.m-3 and obtained in winter 2010. WUE decreases with water stress, with mean values of 1.83, 1.67, 1.54 and 1.23 kg.m-3 under T1 (100% ETc), T2 (80% ETc), T3 (60% ETc) and T4 (40% ETc) respectively. The yield response factor (Ky) of alfalfa was 0.92. The determination of the alfalfa water requirements was performed on the basis of cycle’s calendar during two years in 2010 and 2011. The values founded for flood irrigation are 1388 and 1364 mm respectively for the two years. Drip irrigation allows achieving similar dry mater yield to flood irrigation with less water and agronomic efficiency. Water applied under T1 in drip irrigation with 50 cm of spacing between ramps was less than water requirements (of alfalfa) by about 7% and 18% in 2010 and 2011 respectively. Under the same treatment in flood irrigation, the water requirements are exceeded by 16% and 21% in 2010 and 2011 respectively. Two crop models, PILOTE and CropSyst, had been selected to be tested on their ability to simulate the growth and yield of the studied crops under the edaphic-climatic conditions of Tadla. Tested on silage maize, both models correctly simulated the growth and development of the crop under different water regimes. The parameters of both models are validated and shown effective for simulation of biomass, leaf area index and soil water storage. Although PILOTE requires less parameters and data than CropSyst, it often proves to be more successful in simulating the biomass of silage maize and water balance. As to berseem, predictions of biomass by CropSyst seem to be more accurate than PILOTE model. The latter was best at predicting the soil water reserve on the soil depth exploited by the roots (0-80 cm). Given its ease of integrating daily climatic data for several years, CropSyst model was chosen to test its ability to simulate the crop rotation of berseem and maize silage. The results show that this model correctly simulates the evolution of biomass and yields of the two crops considered in rotation during three years. Modeling the growth and production of alfalfa is made by both models outside the crop installation period (seeding year). After calibration and validation achieved, the model CropSyst simulates adequately biomass and soil water reserve under all water regimes considered while PILOTE best simulations were limited to non-stressed treatment T1 (100% ETc). Although CropSyst model takes into account several parameters in the simulation of alfalfa growth, their simplifications (unique values) reduce its performance in more water stress situation. Less parameters considered in the PILOTE model makes it validation difficult for perennial crops such as alfalfa. CropSyst model was used to evaluate irrigation practices of farmers and develop irrigation virtual scenarios for the three crops studied. The assessment shows that virtual scenario developed for alfalfa that applying 1600 mm of irrigation water amount through 14 applications divided into six irrigations during the spring, six in summer, one in the fall and another in early winter maximizes irrigation water efficiency (1.21 kg/m3) and achieve a yield of 23.1 t/ha (95% of the yield potential). In the case of maize, if water is available, application of 648 mm according to the combination [2 irrigations in initial phase (after sowing), 2 irrigations in linear and two in final phases] allows to achieve high biomass yield and better water use. On berseem, the simulation results confirm that the adoption of the scenario that provides 625 mm through 7 irrigations (3 in autumn, 2 in winter and 2 in spring) allows obtaining 14.1 t/ha of dry matter which represents 94% of the yield potential of the 6454 cultivar. This scenario allows greater water efficiency (1.24 kg/m3) and results in low water drainage losses estimated at about 17% of applied water. The comparison of the two cropping systems represented by alfalfa and silage maize-berseem rotation shows that the rotation allows the better water use and mobilizes less water than alfalfa, which is distinguished by its profitability. Finally, the coupling of the results of three years (2008 to 2011) "in situ" experimentations with the simulations of scenarios by CropSyst and PILOTE models has shown to be highly effective in order to improve the folder crops irrigation in the Tadla irrigated area in Morocco. [less ▲]

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See detailFundamental and Applied Studies on Freeze-dried Vinegar Starter
Shafiei, Rasoul ULg

Doctoral thesis (2013)

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See detailDynamique d’une espèce ligneuse héliophile longévive dans un monde changeant : le cas de Pericopsis elata (Harms) Meeuwen (Fabaceae) au sud est du Cameroun
Bourland, Nils ULg

Doctoral thesis (2013)

The Central African forests are characterized by high species richness. While little light generally reaches their litter layer, among the species encountered are major long-lived light-demanding logged ... [more ▼]

The Central African forests are characterized by high species richness. While little light generally reaches their litter layer, among the species encountered are major long-lived light-demanding logged trees. These species may have established in the past because of large disturbances. Indeed, major climate changes have occurred in the past few millennia, in some areas coupled with strong human occupations. Among these light-demanding species we find the assamela / afrormosia (Pericopsis elata (Harms) Meeuwen, Fabaceae), a large high trading value tree of African semi-deciduous moist forests. Nowadays this logged species suffers from significant regeneration problems on its natural range from Ghana to the Democratic Republic of Congo. Therefore, it is included in CITES Appendix II and is recorded as “Endangered A1cd” on the IUCN Red List. No convincing solution can be found in the available scientific literature to overcome the deficiency of its regeneration. In addition, little or no information is available describing ca. its population dynamics, genetics, silviculture or the probable origin of its stands. It is in this context that the present PhD was undertaken. In this study, we have adopted a multidisciplinary approach to understanding the dynamics of this population rich in long-lived light-demanding species logged in the Congo basin. Moreover, we have suggested ways for their management and conservation in a changing world. To do so, we have adopted as a study-model the case of P. elata in southeastern Cameroon. The main results of the study show that, on a local scale, physico-chemical soil parameters have no influence on the presence or absence of this clustered species. However, on the same scale, large quantities of charcoal were found in the soil, mainly inside those clusters. The anthracological analysis has also shown that the vegetation at the time of the burn was similar to that of today. Numerous fragments of pottery were also found in the top soil layers only inside clusters formed by the species. Finally, some 14C datings go back to ca. 200 years BP, which is approximately the average age of concerned clusters. This body of evidence leads us to conclude on an ancient form of shifting cultivation as the most likely origin of the assamela populations currently present in southeastern Cameroon. In addition to its current population structure within the study area, several parameters controlling its population dynamics were estimated. While the annualized natural mortality of the species reaches about 1%, its average diameter growth rate is 0.31 cm.year-1, which is a relatively low value compared to other long-lived light-demanding species. Selective logging seems to have only a light influence on the behavior of the species. On the other hand, the impact of logging on its seed tree populations is only ca. 12%. Each seed tree bears fruit on average only once every five years. The minimum diameter of reproduction and the effective flowering diameter were respectively 32 and 37 cm. The recovery rate, varying greatly from one country to another, is more than 100% in Cameroon, where the conservation status assigned to the species seems excessive. A sufficient regeneration by planting should allow the perpetuation of the assamela populations in the long run, as with other major logged light-demanding trees. [less ▲]

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See detailOn the Verification of Programs on Relaxed Memory Models
Linden, Alexander ULg

Doctoral thesis (2013)

Classical model-checking tools verify concurrent programs under the traditional "Sequential Consistency" (SC) memory model, in which all accesses to the shared memory are immediately visible globally, and ... [more ▼]

Classical model-checking tools verify concurrent programs under the traditional "Sequential Consistency" (SC) memory model, in which all accesses to the shared memory are immediately visible globally, and where model-checking consists in verifying a given property when exploring the state space of a program. However, modern multi-core processor architectures implement relaxed memory models, such as "Total Store Order" (TSO), "Partial Store Order" (PSO), or an extension with locks such as "x86-TSO", which allow stores to be delayed in various ways and thus introduce many more possible executions, and hence errors, than those present in SC. Of course, one can force a program executed in the context of a relaxed memory system to behave exactly as in SC by adding synchronization operations after every memory access. But this totally defeats the performance advantage that is precisely the motivation for implementing relaxed memory models instead of SC. Thus, when moving a program to an architecture implementing a relaxed memory model (which includes most current multi-core processors), it is essential to have tools to help the programmer check if correctness (e.g. a safety property) is preserved and, if not, to minimally introduce the necessary synchronization operations. The proposed verification approach uses an operational store-buffer-based semantics of the chosen relaxed memory models and proceeds by using finite automata for symbolically representing the possible contents of the buffers. Store, load, commit and other synchronization operations then correspond to operations on these finite automata. The advantage of this approach is that it operates on (potentially infinite) sets of buffer contents, rather than on individual buffer configurations, and that it is compatible with partial-order reduction techniques. This provides a way to tame the explosion of the number of possible buffer configurations, while preserving the full generality of the analysis. It is thus possible to even check designs that may contain cycles. This verification approach then serves as a basis to a memory fence insertion algorithm that finds how to preserve the correctness of a program when it is moved from SC to TSO or PSO. Its starting point is a program that is correct for the sequential consistency memory model (with respect to a given safety property), but that might be incorrect under TSO or PSO. This program is then analyzed for the chosen relaxed memory model and when errors are found (a violated safety property), memory fences are inserted in order to avoid these errors. The approach proceeds iteratively and heuristically, inserting memory fences until correctness is obtained, which is guaranteed to happen. [less ▲]

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See detailEnzymatic synthesis of glycosylated compounds in non-conventional media
Galonde, Nadine ULg

Doctoral thesis (2013)

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See detailStudy of the roles of Cyprinid herpesvirus 3 ORF134 in the biology of the infection
Ouyang, Ping ULg

Doctoral thesis (2013)

The common carp is one of the most important freshwater fish species in aquaculture, and its colourful subspecies koi is grown for personal pleasure and competitive exhibitions. Both two subspecies are ... [more ▼]

The common carp is one of the most important freshwater fish species in aquaculture, and its colourful subspecies koi is grown for personal pleasure and competitive exhibitions. Both two subspecies are economically important. In the late 1990s, a highly contagious and lethal pathogen called koi herpesvirus (KHV) or cyprinid herpesvirus 3 (CyHV-3) began to cause severe financial losses in these two carp industries worldwide. In 2005, CyHV-3 has been classified in the Alloherpesviridae family of the order Herpesvirales. Because of its economic importance and its numerous original biological properties, CyHV 3 became rapidly an attractive subject for applied and fundamental research. However, to date, there is a little information on the roles of individual CyHV-3 genes in the biology of CyHV-3 infection or its pathogenesis. Moreover, there is a lack of safe and efficacious vaccine for the control of CyHV-3 disease. The goal of this thesis was to study the roles of CyHV-3 ORF134 encoding an IL-10 homologue in the biology of the infection. CyHV-3 ORF134 has been predicted to contain an 84 bp intron flanked by 2 exons encoding together a 179 amino acid product. Transcriptomic analyses reveal that ORF134 is expressed as a spliced early-late gene. The identification of the CyHV-3 secretome was achieved using 2D-LC MS/MS proteomic approach. This method led to the identification of 5 viral and 46 cellular proteins in concentrated infected cell culture supernatant. CyHV-3 ORF12 and ORF134 were amongst the most abundant proteins detected. To investigate the roles of ORF134 in the biological of the infection, a strain deleted for ORF134 and a derived revertant strain were produced by using BAC cloning and prokaryotic recombination technologies. Comparison of these strains demonstrated that CyHV-3 ORF134 does not contribute significantly to viral growth in vitro or to virulence in vivo in the present laboratory setting. The present study addressed for the first time the in vivo role of a vIL-10 encoded by a member of the family Alloherpesviridae. This study has been published in Veterinary Research. During the course of the first study, we obtained an unexpected recombination event while we were reconstituting infectious virus from mutated BAC plasmids. To generate a revertant ORF134 Del galK strain, CCB cells were co-transfected with the FL BAC ORF134 Del galK plasmid and the pGEMT-TK vector to remove the BAC cassette inserted in the ORF55 locus (encoding thymidine kinase). One of the clones obtained had an unexpected recombination leading to the deletion of ORF56 and ORF57 in addition to the expected deletion of ORF134. Unexpectedly, this triple deleted strain replicated efficiently in vitro, exhibited an attenuated phenotype in vivo and was proved to confer in a dose dependent manner an immune protection against a lethal challenge. The goal of the second experimental chapter was to investigate the role of the ORF56-57 and ORF134 deletions in the observed safety/efficacy profile of the triple deleted recombinant. To reach this goal, a collection of recombinant strains were produced using BAC cloning technologies, characterized and tested in vivo for their safety/efficacy profile. The results obtained demonstrated that the ORF56-57 deletion is responsible for the phenotype observed and that ORF134 deletion does not contribute to this phenotype significantly. Finally, the immune protection conferred by ORF56-57 deleted recombinant was investigated by challenging immunized fish with a wild type strain expressing luciferase as a reporter gene. In vivo imaging system (IVIS) analyses of immunized and challenged fish demonstrated that the immune response induced by the ORF56-57 deleted strain was able to prevent subclinical infection of the challenge strain. In conclusion, the present thesis addressed both fundamental and applied aspects of CyHV-3. For the first time, it investigated in vivo the roles of a viral IL-10 homologue encoded by a member of the family Alloherpesviridae. Importantly, it identified the ORF56-57 loci as target for production of safe and efficacious attenuated recombinant vaccines. [less ▲]

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See detailLe Rhin aux époques romaines. Zone grise, frontière, branchements
Dignef, Anthony ULg

Doctoral thesis (2013)

Dans cette thèse de doctorat, j’ai repris l’étude des processus et des conditions d’émergence et d’existence, de stabilisation et d’évolution de la frontière du Rhin aux époques romaines, c’est-à-dire ... [more ▼]

Dans cette thèse de doctorat, j’ai repris l’étude des processus et des conditions d’émergence et d’existence, de stabilisation et d’évolution de la frontière du Rhin aux époques romaines, c’est-à-dire essentiellement les périodes post-républicaine et impériale, de César à Valentinien Ier. L’idée était de procéder à une nouvelle analyse des dynamiques liées au phénomène frontalier. Ainsi, dans un souci d’élargissement du domaine de l’histoire militaire généralement attendue, j’ai tenté le difficile exercice de l’appréhension du système de limite du Nord-Ouest de l’Empire, par une relecture croisée des problématiques de l’affirmation du pouvoir romain, des transformations socio-politiques des sociétés en marge de l’Empire, et des façons dont celles-ci ont conditionné la frontière du Rhin. Ce travail dépasse donc largement le cadre d’une étude des installations frontalières, lesquelles ont déjà considérablement retenu l’attention des chercheurs. Il tient, en outre, et probablement davantage, de l’histoire politique, de l’histoire des relations internationales et de l’histoire connectée, telle que je l’ai découverte à travers les travaux de Sanjay Subrahmanyam et de Romain Bertrand. [less ▲]

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See detailAdaptation de la procédure de Maquet pour le traitement chirurgical de la rupture du ligament croisé crânial chez le chien
Etchepareborde, Sébastien ULg

Doctoral thesis (2013)

La rupture du ligament croisé crânial est la première cause d’ostéoarthrose chez le chien. Récemment, une étude a évalué à plus d’un milliard de dollars le chiffre d’affaire que générait cette pathologie ... [more ▼]

La rupture du ligament croisé crânial est la première cause d’ostéoarthrose chez le chien. Récemment, une étude a évalué à plus d’un milliard de dollars le chiffre d’affaire que générait cette pathologie annuellement aux Etats-Unis. Bien que la rupture du ligament croisé crânial (RLCC) soit la cause la plus fréquente de boiterie du membre postérieur rencontrée dans les centres de référés, aucune technique chirurgicale ne semble prévaloir sur les autres. La pléthore de publications sur la RLCC, pas moins de 160 articles consacrés à ce sujet au cours des 6 dernières années dans les 5 plus importantes revues de chirurgie vétérinaire, témoigne du manque de consensus dans ce domaine. Si les chirurgies intracapsulaires ou la physiothérapie uniquement sont les méthodes les plus employées en médecine humaine pour traiter la rupture du ligament croisé antérieur (RLCA), elles se sont montrées insatisfaisantes en médecine vétérinaire. Les techniques extracapsulaires utilisées depuis des décennies se sont vues, elles aussi, remplacées par des techniques de stabilisation dite dynamique : principalement l’ostéotomie de nivellement du plateau tibial (Tibial Plateau Levelling Osteotomy : TPLO) et l’avancement de la tubérosité tibiale (Tibial Tuberosity Advancement : TTA). Cette dernière chirurgie est une adaptation d’une technique utilisée chez l’homme et décrite par P. Maquet en 1976. Bien que la technique se réalise sans aucun implant synthétique chez l’homme, la technique décrite chez le chien présente de nombreux implants pour stabiliser la crête tibiale une fois son avancement réalisé. La mise en place de ces implants entraine une approche invasive de la face médiale du tibia. Les objectifs de ce travail sont d’adapter progressivement la TTA originalement décrite, pour la simplifier telle qu’elle est réalisée chez l’homme, c’est à dire avec pour seul implant un bloc placé dans le trait d’ostéotomie. Cette simplification s’inscrit dans le mouvement actuel de chirurgie minimalement invasive avec une préservation optimale des tissus. En référence à son inventeur chez l’homme, nous avons baptisé cette chirurgie la Technique de Maquet Modifiée (Modified Maquet Technique : MMT). Dans la première étude, le trait d’ostéotomie décrit dans la technique de TTA a été modifié pour laisser intact la partie la plus distale de la corticale de la crête tibiale créant ainsi une « charnière » osseuse. Après cette nouvelle ostéotomie, la résistance à la traction de la crête tibiale a été testée dans trois cas de figures : 1) lorsque la charnière est intacte et la crête maintenue par un fil de cerclage, 2) lorsque la charnière est intacte mais non maintenue et 3) lorsque la charnière est accidentellement cassée, la crête étant maintenue uniquement par un fil de cerclage. Cette étude biomécanique a montré que lorsque la charnière est intacte, le fil de cerclage n’augmente pas la résistance du montage et que la crête tibiale résiste à des tensions supérieures à celles rencontrées dans le grasset d’un chien au pas. En revanche, si la charnière est cassée, la tension tolérée par la crête est significativement inférieure à celle des deux autres groupes. Dans une deuxième étude, la technique nouvellement testée a été utilisée sur un panel de 20 chiens présentés pour une RLCC. Malgré l’absence de plateforme de marche pour évaluer objectivement la récupération fonctionnelle, la MMT a montré des résultats prometteurs et subjectivement comparables à ceux des autres techniques de stabilisation dynamique. Le temps moyen de cicatrisation de la crête était inférieur à 7 semaines, ce qui est dans la moyenne publiée pour la TTA. Aucune complication majeure n’a nécessité de réintervention dans cette étude préliminaire. Une étude prospective avec une plateforme de marche permettrait de comparer directement ces résultats à ceux déjà publiés sur la TTA. Grâce à notre expérience tant ex-vivo que clinique, il nous est apparu que le trait d’ostéotomie tel que nous l’avions décrit pour réaliser cette charnière osseuse n’était pas optimal. En effet, le trou foré à l’extrémité distale de l’ostéotomie, censé prévenir la propagation de fissures lors de l’avancée de la tubérosité tibiale, non seulement n’empêchait pas toujours l’apparition de telles fissures mais était, de plus, toujours le site de fracture de la crête tibiale dans les rares cas où nous l’avons observée. Au lieu de concentrer toutes les contraintes de la déformation osseuse au niveau de cette charnière, nous avons donc eu l’idée de prolonger distalement l’ostéotomie parallèlement à la corticale afin de diminuer les contraintes de déformation. Cette troisième étude nous a permis de tester de manière approfondie ce nouveau trait d’ostéotomie. Nous en avons conclu que l’avancement maximal autorisé était proportionnel au poids du chien et à l’avancée angulaire de la crête ; la résistance maximale était proportionnelle à l’épaisseur de la charnière. Grâce à cette nouvelle ostéotomie, pour toutes les catégories de chiens, l’avancement permis était supérieur aux valeurs utilisées cliniquement. Par ailleurs, la résistance de la crête à la traction était encore supérieure à celle décrite dans notre première étude. Notre quatrième étude visait poursuivre le processus de simplification pour atteindre notre objectif d’appliquer directement au chien l’avancement de la tubérosité tibiale tel que réalisé chez l’homme. Après une étude monotonique de plusieurs matériaux (cage en titane Kyon, bloc de mousse de titane et bloc d’os synthétique biphasique de différentes porosités), ceux présentant une résistance compatible avec les forces rencontrées in vivo ont été soumis à une étude cyclique afin d’évaluer leur capacité à rester dans le trait d’ostéotomie sans aucun autre moyen de fixation que la friction avec l’os. Le bloc de mousse de titane et le bloc d’os synthétique de porosité 60% ont ainsi été testés cycliquement. Durant le test, aucun des implants n’a migré, prouvant ainsi que la friction était suffisante pour maintenir l’implant dans l’ostéotomie. De plus, l’os synthétique s’est révélé capable de résister aux 200 000 cycles permettant ainsi d’envisager, enfin, la réalisation d’une MMT aussi simplement que l’avancement de la tubérosité tibiale décrite chez l’homme. Nos travaux intensifs sur la technique d’avancement de la tubérosité tibiale nous ont conduit à observer une sous-estimation de l’avancement nécessaire préconisé jusque-là. Bien que cela n’ait jamais été mentionné dans la littérature, la prise en compte de cette sous-estimation est indispensable à la réalisation correcte de la chirurgie. Après avoir étudié, dans un premier papier, la variabilité intra- et inter-opérateur de la mesure de l’angle entre le tendon patellaire et le plateau tibial (PTA), et donc indirectement de celle de l’avancement, une deuxième étude a porté sur la quantification de cette sous-estimation et la proposition d’abaques destinés à la corriger. [less ▲]

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See detailProbabilistic Models of Visual Appearance For Object Identity, Class, and Pose Inference
Teney, Damien ULg

Doctoral thesis (2013)

The topic of object recognition is a central challenge of computer vision. In addition to being studied as a scientific problem in its own right, it also counts many direct practical applications. We ... [more ▼]

The topic of object recognition is a central challenge of computer vision. In addition to being studied as a scientific problem in its own right, it also counts many direct practical applications. We specifically consider robotic applications involving the manipulation, and grasping of everyday objects, in the typical situations that would be encountered by personal service robots. Visual object recognition, in the large sense, is then paramount to provide a robot the sensing capabilities for scene understanding, the localization of objects of interests and the planning of actions such as the grasping of such objects. This thesis presents a number of methods that tackle the related tasks of object detection, localization, recognition, and pose estimation in 2D images, of both specific objects and of object categories. We aim at providing techniques that are the most generally applicable, by considering those different tasks as different sides of a same problem, and by not focusing on a specific type of image information or image features. We first address the use of 3D models of objects for continuous pose estimation. We represent an object by a constellation of points, corresponding to potentially observable features, which serve to define a continuous probability distribution of such features in 3D. This distribution can be projected onto the image plane, and the task of pose estimation is then to maximize its “match” with the test image. Applied to the use of edge segments as observable features, the method is capable of localizing and estimating the pose of non-textured objects, while the probabilistic formulation offers an elegant way of dealing with uncertainty in the definition of the models, which can be learned from observations — as opposed to being available as hand-made CAD models. We also propose a method, framed in a similar probabilistic formulation, in order to obtain, or reconstruct such 3D models, using multiple calibrated views of the object of interest. A larger part of this thesis is then interested in exemplar-based recognition methods, using directly 2D example images for training, without any explicit 3D information. The appearance of objects is also defined as probability distributions of observable features, defined in a nonparametric manner through kernel density estimation, using image features from multiple training examples as supporting particles. The task of object localization is cast as the cross-correlation of distributions of features of the model and of the test image, which we efficiently solve through a voting-based algorithm. We then propose several techniques to perform continuous pose estimation, yielding a precision well beyond a mere classification among the discrete, trained viewpoints. One of the proposed method in this regard consists in a generative model of appearance, capable of interpolating the appearance of learned objects (or object categories), which then allows optimizing explicitly for the pose of the object in the test image. Our model of appearance, initially defined in general terms, is applied to the use of edge segments and of intensity gradients as image features. We are particularly interested in the use of gradients extracted at a coarse scale, and defined densely across images, as they can effectively represent shape as they capture the shading onto smooth non-textured surfaces. This allows handling some cases, common in robotic applications, of objects of primitive shapes with little texture and few discriminative details, which are challenging to recognize with most existing methods. The proposed contributions, which all integrate seamlessly in a same coherent framework, proved successful on a number of tasks and datasets. Most interestingly, we obtain performance on well-studied tasks of localization in clutter and pose estimation, well above baseline methods, often on par with or superior to state-of-the-art method individually designed for each of those specific tasks, whereas the proposed framework is similarly applied to a wide range of problems. [less ▲]

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See detailEtude ab-initio d’oxydes antiferroélectriques de structure pérovskite
Amisi, Safari ULg

Doctoral thesis (2013)

In this thesis we present an original ab-initio study of the evolution of antiferrodistortive (AFD), anti-polar electric (APE), and ferroelectric (FE) instabilities in various ABO3 oxides of perovskite ... [more ▼]

In this thesis we present an original ab-initio study of the evolution of antiferrodistortive (AFD), anti-polar electric (APE), and ferroelectric (FE) instabilities in various ABO3 oxides of perovskite structure, as well as their structural and dynamic properties. The main goal is to understand better the microscopic origin of the antiferroelectricity exhibited in these compounds. Three prototypical compounds are studied in detail : PbZrO3 , NaNbO3 , and SrZrO3. After a general introduction on ABO3 compounds, and the ab-initio techniques, we review the concept of antiferroelectricity in perovskites, highlighting some ambiguities in the usual definition and the necessity of turning to what we call a modern definition of antiferroelectricity. First, we highlight that it is the rigidity of the oxygen cage that tends to favor the FE distortion compared to the APE instability. Although illustrated on BaTiO3 , this argument is general, and confirmed by the inspection of the phonons dispersion curves of the ABO3 compounds in whom the strongest instability of the FE/APE branch is systematically at Γ. We show that the emergence of a stable or meta-stable APE distortion appear naturally through a coupling with other instabilities. The presence of AFD modes turns out to be a concrete way to create mixed FE/AFD and APE/AFD phases, crucial for the emergence of antiferroelectricity (AFE). This clarifies why the known AFE compounds systematically include AFD distortions. In this context, since the FE, APE and AFD instabilities are usually in competition, the coexistence of FE, APE and AFD instabilities of strong amplitudes seems required to create mixed phases combining them. This establishes the context convenient to the development of FE and AFE metastable phases close in energy. Another important element concerns the need of a first order AFE-FE transition under electric field producing a double hysteresis loop, typical of AFE compounds. Here also the AFD modes could play a key-role by allowing the emergence of FE/AFD and APE/AFD phases close in energy and developing distinct tilt patterns. These various elements give a new perspective on AFE and allow us to have a more precise idea of the origin of the AFE behavior in perovskites. We identify some key intrinsic characteristics allowing the prediction of materials with the propensity of developing an AFE behavior. [less ▲]

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See detailVALORISATION INDUSTRIELLE ET ARTISANALE DES ARGILES DU MAROC
El Ouahabi, Meriam ULg

Doctoral thesis (2013)

Dans une perspective de développement local durable, la présente étude est focalisée sur la caractérisation des matériaux argileux du Nord du Maroc en vue de leur valorisation dans le secteur de la ... [more ▼]

Dans une perspective de développement local durable, la présente étude est focalisée sur la caractérisation des matériaux argileux du Nord du Maroc en vue de leur valorisation dans le secteur de la céramique. Elle a l’avantage de contribuer à la promotion des matériaux locaux de construction tout en améliorant la qualité des céramiques artisanales produites. Les sédiments utilisés dans cette étude proviennent de la région du nord du Maroc (Tétouan, Tanger et Meknès), ainsi que de sites argileux utilisés à l’échelle nationale dans la fabrication de la céramique traditionnelle, à savoir les sites de Fès, Salé et Safi. Dans le cadre de ce travail, nous avons procédé à une caractérisation minéralogique, granulométrique, texturale, physique, chimique, thermique et technologiques de ces argiles afin d’évaluer leurs potentialités en industrie céramique. Les argiles de Tétouan et Tanger sont caractérisées par des assemblages minéralogiques diversifiés (en particulier une proportion variable d'argile, de quartz et de calcite). En particulier, les argiles de Meknès, Fès, Salé et Safi présentent une forte teneur en argile, en quartz et en calcite. La fraction argileuse des échantillons de Tétouan et Tanger est dominée par l'illite et la kaolinite avec des proportions variables de chlorite. Ces trois types de minéraux argileux sont responsables en grande partie des propriétés céramiques favorables des échantillons d’argiles étudiées. Les matériaux argileux étudiés sont généralement constitués de fines particules d'argiles avec une plasticité moyenne à forte et une faible teneur en matière organique. Ces échantillons sont composés essentiellement de SiO2 (35 - 60 %), Al2O3 (7 - 30 %) et Fe2O3 (10 - 22 %). La quantité de CaO dans les argiles de Tanger et Meknès est très variable (0 - 30 %). Le CaO n’est présent que dans certaines argiles de Tétouan. Le taux de Fe2O3 est variable allant de 0 à 22 %. Les autres oxydes représentent de faibles proportions (< 6 %). La capacité d’échange cationique et la surface spécifique de tous les échantillons sont faibles. La masse volumique apparente, le volume poreux et le nombre de micropores sont peu variables pour toutes les argiles. Les argiles de Tétouan et de Meknès montrent globalement un bon comportement au séchage, à l’exception de quelques échantillons qui montrent des fissures superficielles au séchage due à la présence des argiles gonflantes (smectite et vermiculite). Les argiles de Tétouan et de Meknès constituent des ressources minérales industrielles de bonne qualité pour la fabrication des produits variés dont des carreaux de sol, des briques et les tuiles. Afin d’avoir de bon produit fini, ces argiles doivent êtres cuites à des températures supérieur à 1050 °C. Les argiles de Tanger montrent des propriétés conformes avec les critères de production des briques. Néanmoins, la présence de sulfates en faible quantité dans quelques échantillons carbonatés conduit après cuisson à 1000 °C à la formation de nodules blancs de sulfate de calcium (CaSO4) à la surface de la brique, résultant de la réaction de sulfates avec le CaO. Néanmoins, quelques produits cuits ont présenté un retrait à la cuisson supérieur à 10% pour de températures allant de 1100 à 1150°C et une perte en poids à la cuisson supérieur à 10%. Pour une bonne rentabilité industrielle, ces retraits peuvent être minimisés par l’ajout d’une quantité optimale de dégraissant ou en faisant des mélanges et/ ou des formulations avec d’autres argiles proche géographiquement afin d’obtenir un mélange adéquat. [less ▲]

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See detailSmart drug delivery systems based on specifically-designed macromolecules and inorganic colloids
Liu, Ji ULg

Doctoral thesis (2013)

In the past few decades, various hybrid nano-vehicles have been developed as new drug delivery systems (DDS), in which inorganic and organic components are integrated within a nano-object. An ideal DDS ... [more ▼]

In the past few decades, various hybrid nano-vehicles have been developed as new drug delivery systems (DDS), in which inorganic and organic components are integrated within a nano-object. An ideal DDS should satisfy the conflicting requirements for high stability in extracellular fluid, so that it maintains its integrity during the in vivo circulation; however, it becomes labile upon the activation of internal or external stimuli after targeting to the disease sites, allowing the triggered release of therapeutic agents. The aim of this thesis was to build different hybrid nano-vehicles, explore the possibility to manipulate the release behaviors and evaluate their potential biomedical application. The first part presents an original work on reversibly-crosslinked nanogels based on poly(vinyl alcohol)-b-poly (Nvinylcaprolactam) copolymers. The second part is devoted to stimuli-responsive hybrid nanovehicles, composed of inorganic cores, e.g. maghemite nanoparticles or gold nanorods, and a stimuli-responsive polymer corona, e.g. poly(vinyl alcohol)-b-poly(acrylic acid) or poly(ethyl glycol)-b-poly(N-vinylcaprolactam). The third part focuses on core-shell nanoparticles made of a maghemite core and a mesoporous silica shell, while phase-changed molecules, e.g. 1-tetradecanol with melting temperature of 39 °C, were introduced as gatekeepers to regulate the release behaviors. These different nanostructures were developed as DDS to accommodate cargo molecules, and the triggered cargo release upon variation in pH or temperature, activation of reductive agent or presence of glucose was explored. Moreover, remote stimuli, e.g. alternating magnetic field or near infrared light, were also applied to trigger the release. Studies on cytotoxicity, cellular uptake and in vitro triggered release with cell culture are also described. [less ▲]

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See detailEcologie, dynamique des populations et intérêts économiques du noisetier d'Afrique (Coula edulis Baill.) au Gabon
Moupela, Christian ULg

Doctoral thesis (2013)

Le noisetier d’Afrique (Coula edulis Baill. Olacaceae) est une espèce à usages multiples des forêts denses humides africaines. Elle produit des graines d’une grande valeur nutritive qui sont régulièrement ... [more ▼]

Le noisetier d’Afrique (Coula edulis Baill. Olacaceae) est une espèce à usages multiples des forêts denses humides africaines. Elle produit des graines d’une grande valeur nutritive qui sont régulièrement collectées et commercialisées par les populations locales. Cependant, la valorisation et la domestication de ce produit forestier non ligneux (PFNL) est entravée faute de connaissances précises sur ses caractères reproductifs, son potentiel de production, ses mécanismes de régénération, et les perspectives de développement d'un marché commercial local pour ce produit. Une étude dédiée à cette espèce a donc été entreprise. L’objectif visé était d’améliorer les connaissances sur cette espèce afin de promouvoir sa place dans les systèmes agroforestiers et fournir des informations permettant d'assurer la conservation in situ de la ressource. Les résultats de l'étude montrent que C. edulis est utilisé selon une stratégie de subsistance par les populations, avant tout pour leur autoconsommation et éventuellement pour un revenu qui reste marginal. La reproduction de l'espèce est annuelle, garantissant une disponibilité régulière des fruits. Le diamètre minimum de floraison est de 10,6 cm tandis que le diamètre de fructification régulière est de 23 cm. L’accroissement annuel moyen de l’espèce est de 0,22 cm/an, une valeur similaire à celles observées chez d'autres arbres du sous-bois. La production fruitière est fortement liée au diamètre des tiges et varie d’une année à l’autre. En forêt naturelle, la dissémination de l'espèce est potentiellement assurée par sept espèces frugivores, le principal étant le potamochère, Potamochoerus porcus. Des rongeurs fouisseurs pourraient également jouer un rôle non négligeable dans la dispersion de C. edulis. Par contre, l'éléphant qui était soupçonné de contribuer significativement à la dispersion de l'espèce s'avère n'être qu'un disperseur anecdotique, voire nul. En matière de domestication, les stratégies ne devront pas être basées sur le semis, la germination de C. edulis étant très lente et échelonnée sur plusieurs années, avec des taux de levée très faibles. En revanche, le marcottage aérien a été un succès relatif sur cette espèce et présente l'avantage de maintenir le potentiel génétique de l'arbre multiplié. Les implications de ces résultats aussi bien en termes de gestion durable des peuplements naturels que de domestication de l'espèce dans un contexte agroforestier sont détaillés dans le document. Si l’on désire que les PFNL d’intérêt local comme C. edulis participent substantiellement au développement en milieu rural gabonais, il est essentiel d’orienter ces ressources à la fois dans une stratégie de gestion durable par leur domestication et leur intégration dans le cycle agricole et dans une stratégie de revenu supplémentaire où l’exploitation répond à une demande marchande. [less ▲]

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See detailCONTRIBUTION A LA CARTOGRAPHIE, PAR ETUDES DE LIAISON ET D’ASSOCIATION, DE LOCI D’INTERET CHEZ LES ANIMAUX DOMESTIQUES.
Zhang, Zhiyan ULg

Doctoral thesis (2013)

Until recently, breeding values were estimated based on phenotypes measured on the individual and its relatives, and the notion that the covariance between breeding values is proportionate to the kinship ... [more ▼]

Until recently, breeding values were estimated based on phenotypes measured on the individual and its relatives, and the notion that the covariance between breeding values is proportionate to the kinship coefficient. Advances in genomics now allow for direct analysis of the genome and identification of the loci that determine the breeding values of individuals. As a consequence, marker assisted selection and genomic selection have become more effective and are replacing conventional selection. The identification of loci influencing the traits of interest requires the use of advanced statistical methods that are constantly evolving. In the context of this thesis, we have (i) contributed to the development of gene mapping methods, (ii) applied these methods to map loci influencing both metric and meristic traits, and (iii) contributed to the development of methods for the integration of genomic information in livestock breeding and management. The mapping methods that we have helped developing distinguish themselves mainly by the fact that (i) they exploit haplotype information (by means of a hidden markov model) which should increase the linkage disequilibrium with causative variants and hence detection power, (ii) they can simultaneously extract linkage information within families, and linkage disequilibrium information across the population, and (iii) they correct for population stratification by means of a random polygenic effect, and (iv) they can be applied to binary as well as quantitative traits. We have applied these and other methods to map loci influencing (i) quantitative hematological parameters in a porcine line-cross, and (ii) binary traits including diseases in bovine and non-syntenic Copy Number Variants in cattle, horse and human. In fine, we have contributed to the development of methods for the utilization of marker information in animal selection and production. We have extended the haplotype-based mapping method to allow imputation and have evaluated the utility of this approach in scenarios mimicking reality. We have also contributed to the development of a method to quantify somatic cell counts in the milk of individual cows by genotyping a sample of milk from the farm’s tank (hence a mixture of milk from all cows on the farm) Our work has resulted in the development of a software package (“GLASCOW”) that is increasingly used by the community to map genes influencing complex traits, primarily binary. By using this tool, we have contributed to the localization of several trait loci in pig, cattle, horse and human. We have contributed to the development of approaches that reduce the costs of genomic analyses in livestock by, on the one hand, complementing real SNP genotypes with genotypes obtained in silico by means imputation, and, on the other hand, by developing a method to deconvolute genotypes obtained on DNA pools. [less ▲]

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See detailA walk into random forests: adaptation and application to Genome-Wide Association Studies
Botta, Vincent ULg

Doctoral thesis (2013)

Understanding underlying mechanisms of common diseases is one of the major goals of current research in medicine. As most of these disorders are linked to genetic factors, identification of the associated ... [more ▼]

Understanding underlying mechanisms of common diseases is one of the major goals of current research in medicine. As most of these disorders are linked to genetic factors, identification of the associated variants forms an excellent strategy towards the elucidation of molecular and cellular dysfunctions, and in fine could lead to better personalised diagnostics and treatments. Genome-Wide Association Studies (GWAS) aim to discover variants spread over the genome that could lead, in isolation or in combination, to a particular trait or an unfortunate phenotype such as a disease. The basic idea behind these studies is to statistically analyse the genetic differences between groups of healthy (controls) and diseased (cases) individuals. Advances in genetic marker technology indeed allow for dense genotyping of hundreds of thousands of Single Nucleotide Polymorphisms (SNPs) per individual. This allows to characterise representative samples composed of several hundreds to several thousands of cases and controls, each one characterised by up to a million of genetic markers sampling the genomic variations among these individuals. The standard approach to genome wide association studies is based on univariate hypothesis tests. In this approach each genetic marker is analysed in isolation from the others, in order to assess its potential association with the studied phenotype, in practice by the computation of so-called p-values based on some statistical assumptions about the data-generation mechanism. Because of the very high ratio between the large number of SNPs genotyped and the limited number of individuals, multiple-testing corrections need to be applied when carrying out these analyses, leading to reduced statistical power. While this standard approach has been at the basis of many novel loci unravelled in the last years for several complex diseases, it has several intrinsic limitations. A first limitation is that this approach does not directly account for correlations among the explanatory variables. A second intrinsic limitation of GWAS is that they can't account for genetic interactions, i.e. causal effects that are only observed when specific combinations of mutations and/or non-mutations are present at the same time. The third limitation of univariate approaches is that they do not directly allow to assess the genetic risk, since many of the identified markers (with similarly small p-values) actually account for the same underlying causal factor: exploiting their information to predict the genetic risk is hence far from straightforward. Within bioinformatics, machine learning has actually become one of the major potential sources of progress. As a matter of fact, biology has become nowadays one of the main drivers of research in machine learning, and is by itself already a very competitive research field. Among the subfields of machine learning, supervised learning and its extensions such as semi-supervised learning, stand out as the most mature and at the same time most rapidly evolving area of research. Within this context, the purpose of this thesis was to study the application of random forest types of methods to genome wide association studies, with the twofold goal of (i) inferring predictive models able to asses disease risk and (ii) to identify causal mutations explaining the phenotype. The choice of this family of methods was originally motivated by the fact that these methods are a priori well suited for that kind of analysis due to some of their interesting properties. They are indeed able to deal efficiently with very large amounts of data without relying on strong assumptions about the underlying mechanisms linking genetic and environmental factors to phenotypes, and they can also provide interpretable information, in the form of scorings and/or rankings of SNPs so as to help in the identification of causal genetic loci. In the first part of this manuscript, we analyse the state-of-the art in the application field of genome wide association studies and in supervised machine learning, and subsequently describe in details the three tree-based ensemble methods that we have implemented and applied in our research; in Part II, we report our empirical investigations, in three successive steps, namely i.) a preliminary study on simulated datasets yielding controlled conditions with known ground-truth and allowing for a first sanity check of the T-Trees methods, in ideal conditions; ii.) a detailed study on a given real-life dataset concerning Crohn's disease, where we try to understand the main features of the three different algorithms in terms of predictive accuracy and capability of identification of relevant genetic information, and their sensitivity with respect to various kinds of quality control procedures and algorithmic parameters; iii.) a systematic replication study, where we confirm, on 7 different datasets from the Wellcome Trust Case Control Consortium, the main outcomes of our study on the Crohn's disease, while using default parameter settings. 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See detailLarge scale phylogenetic patterns of diversification in Bryophytes
Laenen, Benjamin ULg

Doctoral thesis (2013)

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See detailVers une gestion rationnelle de l'eau dans une situation complexe d'urbanisation anarchique dans un pays en développement : cas du bassin versant de l'Abiergué (Yaoundé-Cameroun)
Kouam Kenmogne, Guy Romain ULg

Doctoral thesis (2013)

This study focuses on an analysis of water resource management in cities of developing countries with very rapid rates of urbanization. The objectives are twofold: firstly, to highlight the factors which ... [more ▼]

This study focuses on an analysis of water resource management in cities of developing countries with very rapid rates of urbanization. The objectives are twofold: firstly, to highlight the factors which caused and which govern poor water resources management these cities and secondly to develop a coherent sustainable urban water resources management strategy. The study was conducted in the Abiergue watershed in Yaoundé-Cameroon. The methodology used is based on holistic and participative approaches resulting from the combination of principles of "Integrated Water Resources Management-IWRM" and "Ecosystem and Human Health-ECOHEALTH". Political, economic, social, environmental, historical and mesological factors have resulted in a water resources management system marked by many inadequacies and constraints. Poor access to drinking water and sanitation, recurrent flooding, endemic waterborne diseases, water pollution etc are all permanent pressures that contribute to the impoverishment of households and hamper the development of the area in particular and that of the town of Yaoundé in general. The poor water resources management in the Abiergué watershed is an indicator of an urban governance crisis. Three scenarios to improve this situation were developed: maintaining the status quo; destruction of buildings and a scenario based on IWRM and ECOHEALTH. The optimal strategy integrates principles from IWRM and ECOHEALTH with the base scenario 3.4 focused on actors. Using a sequential process, it takes into account actions on water resources, health and reforms on the legislative, regulatory and institutional framework. Many constraints like land tenure, corruption, limited financial resources and poor urban governance may undermine the implementation of this strategy despite the potential of the watershed. All indicators suggest that water resources management in the Abiergue watershed is poor. There is therefore an urgency to implement this strategy within the framework of the ongoing IWRM process in Cameroon. "Time for Solutions", the theme of the 6th World Water Forum held in Marseille in 2012 is fully translated into action through this study. [less ▲]

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See detailL’Arganeraie des Haha : droits réels, inégalités d’accès aux ressources naturelles et principales dynamiques (Sud Ouest du Maroc)
Bejbouji, Jihane ULg

Doctoral thesis (2013)

Véritable spécificité du Sud-Ouest marocain, l’arganeraie est l’ensemble des écosystèmes dont l’espèce caractéristique est l’arganier, relique de la végétation subtropicale de l’ère tertiaire. Outre son ... [more ▼]

Véritable spécificité du Sud-Ouest marocain, l’arganeraie est l’ensemble des écosystèmes dont l’espèce caractéristique est l’arganier, relique de la végétation subtropicale de l’ère tertiaire. Outre son originalité historique et géographique, l’arganeraie assure de multiples fonctions écologiques et procure de nombreux biens à une population pauvre et vivant dans des conditions précaires. Toutefois, cet espace intrigue. Alors que dans les autres forêts marocaines, les riverains ne disposent que de deux droits (la récolte de bois mort gisant et le parcours), la population de l’arganeraie bénéficie depuis 1925 d’une législation spéciale lui assurant une large gamme d’utilisations et d’exploitations des ressources forestières. Cette thèse, menée dans l’arganeraie des Haha (province d’Essaouira) se propose de contribuer à la gestion durable d’un territoire partagé dans un contexte caractérisé par de nombreuses mutations. Pour appréhender les évolutions de cet éco-socio-système, nous avons privilégié une entrée par l’étude des droits réels, d’accès et d’usage, en accordant une attention particulière aux inégalités qui les caractérisent. Nous nous sommes fixé trois objectifs : identifier les modes de gestion, analyser les dynamiques actuelles des usages et pratiques dans ces écosystèmes à arganier et proposer des scénarios de gestion. Pour ce faire, nous avons mené une enquête qualitative et quantitative auprès de 100 ménages au niveau de trois communes rurales, Smimou, Ida ou Azza et Imgrade, situées autour du massif du Jbel Amsitten, l’une des zones centrales de la Réserve de Biosphère de l’arganier. Notre travail de recherche a d’abord dressé le portrait actuel de l’espace et de l’ensemble des droits qui le régissent. Il montre que leur appropriation s’est faite progressivement par une population en majorité issue d’un brassage récent d’émigrants provenant du sud. Il en résulte une trame de droits récemment forgée et très diversifiée. Ensuite, en partant des représentations que se font les populations de leur patrimoine, nous avons identifié trois grands types de propriétaires se comportant selon des logiques différentes : d’abord des ménages, qui sont les plus nombreux, dont les ressources sont rares ou limitées et qui cherchent avant tout à survivre. Ensuite des ménages dont les ressources sont modérées et qui développent une logique de gestionnaire et finalement, quelques ménages dont les ressources sont importantes et qui poursuivent une logique d’entrepreneur. Par ailleurs, l’étude du compartiment agdal, son concept, ses configurations sociales et spatiales et ses types de gestion a montré l’évolution d’une pratique de mise en défens à celle d’un terroir se révélant comme un agrégat de droits. Et contrairement à ce qu’on croit, la détention de l’agdal ne concerne pas toute la population, mais elle semble plutôt liée à la disponibilité des ressources aux différentes périodes d’arrivée des ménages immigrants. Quant à sa gestion, deux types ont été identifiés : individuel et commun. En ayant recours à une étude monographique, nous avons alors montré que la gestion de cet espace-ressources est complexe. Elle résulte à la fois de l’histoire de l’appropriation des droits, de la délimitation forestière et des stratégies de gestion intergénérationnelle individuelles et collectives adoptées par la population pour mettre en valeur ces ressources. Enfin, moyennant la systémique, nous avons identifié quatre principales dynamiques qui traversent ce système : une dynamique de déprise, de maintien/résistance, de marché et de projet. Ce travail de recherche a mis en lumière le fait que l’arganeraie n’est pas un tout, approprié par un groupe homogène, mais qu’elle renvoie plutôt à un ensemble d’éléments en osmose : une population diversifiée, des patrimoines inégaux et des rapports au territoire variés. Par ailleurs, les formes de gestion en commun dans cet espace déclinent tandis que la tendance à la gestion privée se renforce. La prise en compte de cette complexité, des inégalités d’accès aux ressources naturelles, des stratégies anticipatives adoptées par la population et de la diversité des compartiments et des pratiques, s’avère nécessaire pour la réussite de tout projet d’aménagement, mais aussi pour la durabilité de l’approvisionnement en fruits. C’est ainsi que nous avons construit trois scénarios de gestion qui sont, à notre avis, les plus plausibles : un scénario tendanciel ou de statu quo, un scénario optimiste ou de gestion partagée entre l’Etat et les communautés et un scénario modéré ou de gestion privée. La gestion patrimoniale et intégrée de l’arganeraie serait en mesure de contribuer à sa gestion durable. Renouer avec le corpus de règles qu’entretenait la population avec cet espace-ressources peut être, à notre avis, une des principales portes d’entrée de sa conservation. [less ▲]

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See detailUse of Bacillus subtilis starter cultures during red sorghum malting
Bwanganga Tawaba, Jean-Claude ULg

Doctoral thesis (2013)

Bacillus subtilis was used to inhibit mould growth during red sorghum malting. Improved conditions for achieving good malt properties were studied and mathematical models are proposed for the induction ... [more ▼]

Bacillus subtilis was used to inhibit mould growth during red sorghum malting. Improved conditions for achieving good malt properties were studied and mathematical models are proposed for the induction and the repression phases of α- and β-amylase synthesis. The problems associated with the hydrolysis of β-glucans and the biocontrol steeping effect on β-glucanase activities are discussed. The effect of the biocontrol treatment and that of phytohormones produced by the bacterial strain used on the synthesis of specific red sorghum enzymes are elucidated. Gibberellic acid and abscisic acid diffusion and cross-talk as factors affecting the synthesis of red sorghum malt α- and β-amylase activities are also discussed. The production of 3-indole acetic acid (IAA) by B. subtilis S499 was also a focus in this study and the determination of the conditions for improving the production of indole-3-acetic acid are determined. [less ▲]

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See detailEffet de l'effort, l'entrainement et l'inflammation sur l'immunité innée des voies respiratoires profondes du Trotteur Français
Waldschmidt, Ingrid ULg

Doctoral thesis (2013)

Ce manuscrit rapporte dans un premier temps, l'élaboration du protocole expérimental de stimulation des TLR des macrophages alvéolaires équins ex vivo. Dans un second temps, l'effet de l'exercice et l ... [more ▼]

Ce manuscrit rapporte dans un premier temps, l'élaboration du protocole expérimental de stimulation des TLR des macrophages alvéolaires équins ex vivo. Dans un second temps, l'effet de l'exercice et l'entrainement sur la réponse des macrophages alvéolaires équins en conditions standardisées d'entrainement. Enfin, dans un troisième temps, l'impact de l'inflammation pulmonaire sur la réponse des macrophages alvéolaires ex vivo de chevaux de course atteints d'IAD, en conditions de terrain. [less ▲]

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See detailAnalyse critique de l'économie politique de l'utilisation des ''enfants-soldats''. Etude de cas des pays du fleuve Mano (Liebria, Sierra Léone, Côte d'Ivoire)
Zina, Seydina Ousmane ULg

Doctoral thesis (2013)

Notre thèse a consisté à construire analytiquement le cadre de pensée de la rationalité économique et à le discuter au regard de la littérature et des cas des pays du fleuve Mano (Libéria, Sierra Léone ... [more ▼]

Notre thèse a consisté à construire analytiquement le cadre de pensée de la rationalité économique et à le discuter au regard de la littérature et des cas des pays du fleuve Mano (Libéria, Sierra Léone, Côte d’Ivoire). Et elle a retenu que les variables de l’approche économique (nombre élevé de jeunes, faible niveau d’éducation, faible revenu et pillage des ressources naturelles) sont contrairement à leur fonction utilitariste, des répertoires d’action mobilisés par les jeunes et les groupes armés dans le cadre du ‘’marché de la violence’’. Cette approche de la violence remet le comportement économique du jeune au cœur des contextes socio-économiques, politiques et culturels du conflit armé, et limite l’hypothèse du choix rationnel. [less ▲]

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See detailDynamics of Agrarian Systems in Hai Duong Province, North Vietnam
Han Quang, Hanh ULg

Doctoral thesis (2013)

In Vietnam, the agrarian systems have evolved considerably during the socio-economic transformation period initiated in the late 1980s with the political reform (Doi Moi). In a region around the capital ... [more ▼]

In Vietnam, the agrarian systems have evolved considerably during the socio-economic transformation period initiated in the late 1980s with the political reform (Doi Moi). In a region around the capital, where the process of industrialization, urbanization, and international integration has been accelerating, a number of questions about the sustainability of agrarian systems are raising. By diagnosing and analysing the dynamics of agrarian systems from 1980 to 2010, this study aims to provide decision-makers with some sectorial and territorial policy options authorizing the sustainable development of agriculture and rural society in the new socio-economic context. Combining the historical, adaptive, and systematic approaches, this study shows that farmers in Hai Duong province adapted effectively to the socio-economic and institutional changes, notably by transforming part of the rice land areas into other agricultural land use purposes such as fish ponds, animal buildings, vegetable fields and fruit orchards. These rapid changes, however, do not go in the direction of improving the sustainability of agrarian systems. Farm holders are now facing with many technical and economic contradictions whereas land issues are not only related to the agricultural purposes. Competition functions in land use, fragmentation of plots, the imperfection of the land market and rising property values are all emerging. The prospects for sustainability of agrarian systems are analysed under different scenarios which highlight the complexity of policy options. The recommendations are made not only for the agricultural sector in general, but also for different agrarian systems in specific regions. [less ▲]

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See detailL'impact des politiques internationales de financement du développement sur les marges de manoeuvre politiques (policy space) des pays en développement. Une étude selon la grille d'analyse centre/périphérie
Zacharie, Arnaud ULg

Doctoral thesis (2013)

La thèse de ce travail est que dans le contexte du processus contemporain de globalisation, le système international du financement du développement a renforcé les contraintes de jure et de facto qui ... [more ▼]

La thèse de ce travail est que dans le contexte du processus contemporain de globalisation, le système international du financement du développement a renforcé les contraintes de jure et de facto qui pèsent sur l’autonomie des politiques économiques des pays en développement, mais qu’il offre également de nouvelles opportunités en transformant la géographie de la production mondiale et des flux économiques et financiers qui en découlent. Notre hypothèse est dès lors que l’impact des politiques internationales de financement du développement sur les marges de manœuvre politiques des pays en développement n’a pas été uniforme et que ce sont précisément les pays qui ont réussi à assurer un équilibre entre les contraintes du système international et leur autonomie politico-économique qui ont réussi à tirer profit de ce système et à entamer un processus de convergence économique avec les pays du centre. [less ▲]

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See detailSimulations numériques de la dynamique d’épidémies sur réseaux aléatoires selon une approche de physique statistique
Ababou, Malika ULg

Doctoral thesis (2013)

Dans le présent manuscrit, notre travail est focalisé dans un premier temps, sur l’étude de la dynamique de propagation des épidémies sur un modèle de réseaux complexes qui est une variante du modèle de ... [more ▼]

Dans le présent manuscrit, notre travail est focalisé dans un premier temps, sur l’étude de la dynamique de propagation des épidémies sur un modèle de réseaux complexes qui est une variante du modèle de Barabási-Albert (BA). Les simulations numériques révèlent une transition d’une loi exponentielle à une loi de puissance de la distribution du nombre de liens par nœud en fonction du paramètre de précision ω. Nous avons prouvé aussi que la synchronisation collective σ induite par le processus épidémiologique Susceptible-Infected-Recovered-Susceptible (SIRS ) dépend de la structure topologique du réseau. Dans un second temps, nous nous intéressons à l’étude numérique de ce modèle épidémique en introduisant une source permanente d’infection I_0, afin d’éviter la disparition de la maladie, sur un réseau exponentiel généré par le modèle (BA) d’attachement préférentiel à précision finie. Les simulations montrent que la valeur moyenne de la fraction des personnes infectées dépend de la période naturelle du cycle d’infection τ_0 et du temps d’infection τ_I . Un maximum de synchronisation des personnes infectées est atteint lorsque le rapport τ_I /τ_0 est légèrement plus petit que 1/2. Un autre résultat important est la dépendance linéaire de la valeur moyenne de la fraction d’éléments infectés ⟨n_inf ⟩ en fonction de τ_I /τ_0 bien que, la synchronisation est une fonction non triviale de τ_I /τ_0. [less ▲]

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See detailConstruction of an interactomic map of Ets factors and identification of new functions in mRNA processing
Rambout, Xavier ULg

Doctoral thesis (2013)

The family of Ets factors is one of the largest families of human transcription factors. This thesis aimed at molecularly and biologically defining these well known though not well-understood ... [more ▼]

The family of Ets factors is one of the largest families of human transcription factors. This thesis aimed at molecularly and biologically defining these well known though not well-understood transcription factors using a system biology approach. Combination of interactomic and bioinformatics tools gave rise to the first interactome of the human Ets factors built on more than 400 interactions with nearly 300 interaction partners. We fragmented our interactome in 24 functional highly intraconnected sub-networks (clusters, or CL) and highlighted a new role for Ets transcription factors in mRNA processing (CL1). Steady-state levels of mRNAs result from the balance between transcription and mRNA decay, two events sitting at both ends of the mRNA life. In the traditional and still prominent view, these events are spatially, functionally and temporally independent. Here, we showed that the Erg subfamily of Ets factors (composed of the three members ERG, FLI1, and FEV) regulate mRNA decay of specific targets via promoter-mediated mRNA imprinting with sequence-specific RNA-binding proteins (CL1) and the CCR4-NOT deadenylation complex. This constitutes the first evidence, regardless of the organism, that DNA-binding transcription factors recruit RNA-binding proteins and mRNA decay components to control the degradation of specific mRNAs. This is also the most detailed demonstration of a functional coupling between transcription and mRNA decay machineries in humans. We showed that ERG promoted mRNA decay of key mitotic regulators, among which the Aurora kinases Aurora A and B. Depletion of ERG prevented degradation of Aurora A and B mRNAs during mitosis, leading to aberrant levels of Aurora proteins, accumulation of centrosome and mitotic spindle defects, and ultimately mitosis blockage. This consists in a significant advance in understanding of mitosis progression that was until now thought to be exclusively regulated by post-translational modifications and proteasomal degradation of proteins. Our results show that, in the contrary of bulk mRNAs whose decay is inhibited during mitosis, degradation of specific transcripts is a prerequisite for normal mitosis progression. [less ▲]

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See detailFirst-principles study of ferroelectricity in oxide superlattices
Zhao, Jinzhu ULg

Doctoral thesis (2013)

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See detailDesign, performance analysis, and implementation of a positioning system for autonomous mobile robots
Pierlot, Vincent ULg

Doctoral thesis (2013)

Positioning is a fundamental issue in mobile robot applications, and it can be achieved in multiple ways. Among these methods, triangulation based on angle measurements is widely used, robust, and ... [more ▼]

Positioning is a fundamental issue in mobile robot applications, and it can be achieved in multiple ways. Among these methods, triangulation based on angle measurements is widely used, robust, and flexible. In this thesis, we present an original beacon-based angle measurement system, an original triangulation algorithm, and a calibration method, which are parts of an absolute robot positioning system in the 2D plane. Also, we develop a theoretical model, useful for evaluating the performance of our system. In the first part, we present the hardware system, named BeAMS, which introduces several innovations. A simple infrared receiver is the main sensor for the angle measurements, and the beacons are common infrared LEDs emitting an On-Off Keying signal containing the beacon ID. Furthermore, the system does not require an additional synchronization channel between the beacons and the robot. BeAMS introduces a new mechanism to measure angles: it detects a beacon when it enters and leaves an angular window. This allows the sensor to analyze the temporal evolution of the received signal inside the angular window. In our case, this feature is used to code the beacon ID. Then, a theoretical framework for a thorough performance analysis of BeAMS is provided. We establish the upper bound of the variance and its exact evolution as a function of the angular window. Finally, we validate our theory by means of simulated and experimental results. The second part of the thesis is concerned with triangulation algorithms. Most triangulation algorithms proposed so far have major limitations. For example, some of them need a particular beacon ordering, have blind spots, or only work within the triangle defined by the three beacons. More reliable methods exist, but they have an increasing complexity or they require to handle certain spatial arrangements separately. Therefore, we have designed our own triangulation algorithm, named ToTal, that natively works in the whole plane, and for any beacon ordering. We also provide a comprehensive comparison between other algorithms, and benchmarks show that our algorithm is faster and simpler than similar algorithms. In addition to its inherent efficiency, our algorithm provides a useful and unique reliability measure, assessable anywhere in the plane, which can be used to identify pathological cases, or as a validation gate in data fusion algorithms. Finally, in the last part, we concentrate on the biases that affect the angle measurements. We show that there are four sources of errors (or biases) resulting in inaccuracies in the computed positions. Then, we establish a model of these errors, and we propose a complete calibration procedure in order to reduce the final bias. Based on the results obtained with our calibration setup, the angular RMS error of BeAMS has been evaluated to 0.4 deg without calibration, and to 0.27 deg, after the calibration procedure. Even for the uncalibrated hardware, BeAMS has a better performance than other prototypes found in the literature and, when the system is calibrated, BeAMS is close to state of the art commercial systems. [less ▲]

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See detailDesign of sugar-based surface active agents for emulsion polymerization in supercritical carbon dioxide
Boyère, Cédric ULg

Doctoral thesis (2013)

The use of supercritical CO2 (scCO2) as alternative to traditional organic solvents and the valorization of biomass are interesting approaches to reduce the ecological footprint of chemical processes. On ... [more ▼]

The use of supercritical CO2 (scCO2) as alternative to traditional organic solvents and the valorization of biomass are interesting approaches to reduce the ecological footprint of chemical processes. On the other hand, emulsions offers many advantages over bulk and solution processes for polymerization reactions including limited environmental impact, ease of products recovery and increased reaction rate. In this context, this thesis aims to design novel fluorinated sugar-based surfactants able to stabilize water/CO2 (W/C) emulsion systems and explore their potential as template for polymerization reactions. Such surface active agents were prepared either by lipase-catalyzed esterification of mannose with fluorinated acid derivatives or following chemoenzymatic approaches involving very efficient and versatile "click" chemistries like the thiol-Michael addition or the thiol-ene/-yne reactions. The W/C interfacial activity of these novel glycosurfactants was confirmed by tensiometry as well as their ability to form stable W/C microemulsions. Then, we tested a range of these neutral fluorinated carbohydrate esters as stabilizers for the CO2-in-water (C/W) emulsion polymerization. In particular, the radical polymerization of acrylamide was performed in the continuous aqueous phase of a C/W high internal phase emulsion (HIPE) leading to highly interconnected macroporous polymer matrices, also called polyHIPEs. In this case, we emphasized a clear dependence of morphology of the porous structure with the concentration and the structure of the glycosurfactant. Thanks to the electrical neutrality of these fluorinated glycosurfactants which confers them a lower sensitivity to the ionic forces compared to their ionic counterparts, we could extend this system to the polymerization of ionic liquid monomers. Porous poly(ionic liquid)s were thus formed by emulsion polymerization for the first time and exhibit spherical cells interconnected by pores with size (~ 1 μm) among the lowest reported for polyHIPEs produced from C/W emulsions. The emulsion C/W templating methodology based on the designed fluorinated glycosurfactants thus appears as a technique of choice for the preparation of valuable macroporous polymer matrices. [less ▲]

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See detailScalar and fermionic extensions of the Standard Model
Degée, Audrey ULg

Doctoral thesis (2013)

In this thesis several aspects of beyond SM physics schemes have been treated. In particular, two categories of models have been considered: ($i$) models with extra Higgs ElectroWeak (EW) doublets (multi ... [more ▼]

In this thesis several aspects of beyond SM physics schemes have been treated. In particular, two categories of models have been considered: ($i$) models with extra Higgs ElectroWeak (EW) doublets (multi-Higgs-doublet models), ($ii$) models with new fermion EW singlets (type-I seesawmodels). In the first category, two problems associated with the most general two-Higgs-Doublet Model (2HDM) and with the three-Higgs-Doublet Model (3HDM) have been tackled. In the former case the scalar mass spectrum has been derived in a basis-invariant fashion whereas in the later, after introducing a general procedure for the minimization of highly symmetric potentials, the minimization of an $S_4$ and of an $A_4$ 3HDM has been analyzed. In the second category, the possibility of envisaging seesaw-like models yielding sizeable lepton-flavor-violating decay rates has been investigated. With the models at hand, the corresponding charged lepton-flavor-violating phenomenology has been studied focusing on rare muon decays, for which forthcoming lepton-flavor-violating experiments will be able to prove large parts of their parameter space. [less ▲]

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See detailAbsorbing Layers for Wave-Like Time-Dependent Problems - Design, Discretization and Optimization
Modave, Axel ULg

Doctoral thesis (2013)

The numerical simulation of wave-like phenomena occurring in large or infinite domains is a great challenge for a wide range of technological and scientifical problems. A classical way consists in ... [more ▼]

The numerical simulation of wave-like phenomena occurring in large or infinite domains is a great challenge for a wide range of technological and scientifical problems. A classical way consists in considering only a limited computational domain with an artificial boundary that requires a specific treatment. In this thesis, \textit{absorbing layers} are developed and studied for time-dependent problems in order to deal with such artificial boundary. A large part of this thesis is dedicated to the \textit{perfectly matched layers} (PMLs), which exhibit appealing properties. They are first studied in a fundamental case with non-dispersive linear scalar waves. A procedure for building PMLs is proposed for convex domains with regular boundary. It permits a great flexibility when choosing the shape of the computational domain. After, the issue of choosing PML parameters is addressed with the aim of optimizing the PML effectiveness in discrete contexts. The role of each parameter, including the so-called \textit{absorption function}, is highlighted by means of analytical and numerical results. A systematic comparison of different kinds of absorption functions is performed for several classical numerical schemes (based on finite differences, finite volumes or finite elements). Then, while the PMLs do not a priori account for incoming signals generated outside the computational domain, different problem formulations that account for such forcing are detailed and compared. The interest of the whole approach is finally illustrated with two- and three-dimensional numerical examples in electromagnetism and acoustics, using a discontinuous finite element scheme. In regional oceanic models, modeling open-sea boundaries brings new difficulties. Indeed, additional linear/nonlinear dynamics are involved and the external forcing is generally poorly known. In this context, different absorbing layers and the widely used Flather boundary condition are compared by means of classical benchmarks. The choice of the absorption function and the way of prescribing the external forcing are discussed in specific marine cases. [less ▲]

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See detailLes processus d'écologisation entre santé et environnement. Le cas de la maladie de Lyme
Massart, Clémence ULg

Doctoral thesis (2013)

La thèse vise à comprendre comment une diversité de définitions d’une maladie émergente et complexe, la Borréliose de Lyme, se construisent aujourd’hui dans un grand nombre de lieux. Ces définitions sont ... [more ▼]

La thèse vise à comprendre comment une diversité de définitions d’une maladie émergente et complexe, la Borréliose de Lyme, se construisent aujourd’hui dans un grand nombre de lieux. Ces définitions sont parfois concurrentes, parfois étrangères l’une à l’autre ; parfois médiatisées, parfois confinées dans des espaces discrets. Pour comprendre cette diversité, je mobilise le concept de pratique développé par Stengers (2006). J’ai accédé aux processus de connaissance mis en œuvre par les praticiens à travers les deux versants qui définissent une pratique : les obligations, qui renvoient à leur manière spécifique d’interroger l’objet ou l’être dont ils cherchent à apprendre quelque chose ; les exigences qui opèrent des exclusions et tracent des frontières entre pratiques. Cette grille d’analyse s’applique à des groupes de taille variable, professionnels ou non, mandatés ou pas par le politique, de même qu’aux vivants non-humains. La première partie situe la maladie de Lyme dans le champ des maladies et définit sa spécificité en regard des « maladies environnementales » qui ont pour cause les pollutions industrielles. En tant que maladie infectieuse ayant pour vecteur une tique et pour réservoir la faune sauvage, la maladie de Lyme présente davantage les traits d’une « maladie écologique » qui renouvelle l’attribution des responsabilités, les modes de gestion, la nature des entités incriminées ainsi que l’identité des praticiens impliqués. À partir de ce constat, j’ai fait l’hypothèse d’une « écologisation des problèmes sanitaires » : les problématiques environnementales s’immiscent dans d’autres secteurs. J’ai interrogé cette écologisation thématique à la lumière de « l’écologisation des pratiques » que Stengers définit comme un mode de relation entre pratiques qui remplace les exclusions par des coordinations pour produire des savoirs nouveaux, dynamiques et irréductibles à chaque pratique. La deuxième partie expose les pratiques de quatre groupes de praticiens : les malades chroniques qui échangent sur Internet, les infectiologues, les ticologues et les écologues généticiens des populations. L’analyse révèle l’existence de deux espaces de discussions marqués par des relations distinctes : dans le premier, médical, diagnostic et curatif, les définitions de la maladie s’opposent tandis qu’elles se chevauchent dans le second, environnemental, épidémiologique et préventif. Ces deux espaces entretiennent peu de relations entre eux. La troisième partie s’intéresse aux interractions entre praticiens. À travers un groupe de travail, un lieu, un concept et des techniques diagnostiques, j’interroge la rencontre effective entre pratiques environnementales et médicales. L’essentiel des collaborations entre acteurs environnementaux et médicaux portent sur la prévention de la maladie. Les savoirs écologiques, comme ceux des malades, ont pourtant un potentiel pour une autre élaboration du diagnostic de ces maladies. Cette analyse montre que des frictions apparaissent lorsque des praticiens interrogent un même vivant sur des modes différents. À l’inverse, une sympathie se manifeste entre praticiens dès lors qu’ils interrogent sur le même mode des vivants différents. Plus qu’une écologisation du sanitaire, la thèse met en évidence un processus de « sanitarisation de l’écologie ». En effet, ce sont les praticiens rattachés à l’écologie qui s’immiscent dans la thématique des « maladies infectieuses émergentes ». Les savoirs qu’ils produisent tendent à dépeindre un ensemble de maladies variables dans le corps et le milieu, qui rappelle la définition par les malades, sans que ces groupes de praticiens disposent à ce jour d’espace de rencontre. [less ▲]

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See detailRéalisation d'un spectromètre à fluorescence X portable
Carapelle, Alain ULg

Doctoral thesis (2013)

Réalisation d'un spectromètre XRF portable à haute résolution à détecteur X SDD et tube à rayons X. L'utilisation d'algorithmes spécifiques a permis de démontrer l'utilisation dans plusieurs cas pratiques ... [more ▼]

Réalisation d'un spectromètre XRF portable à haute résolution à détecteur X SDD et tube à rayons X. L'utilisation d'algorithmes spécifiques a permis de démontrer l'utilisation dans plusieurs cas pratiques. En particulier la mesure d'épaisseurs de coatings de 0.4 à 1500 nm grâce à une routine d'optimisation de la définition de la ROI du pic. Il a été montré qu'un monitoring d'un étalon pendant la mesure permet, via renormalisation du spectre, d'améliorer la répétabilité des mesures d'un facteur >2. [less ▲]

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See detailVers une méthode de conception de SIG 3D collaboratif
Hajji, Rafika ULg

Doctoral thesis (2013)

Our thesis work focuses on collaborative 3D GIS and considers two main aspects governing their implementation: a conceptual framework for an approach to design these systems and a technical framework ... [more ▼]

Our thesis work focuses on collaborative 3D GIS and considers two main aspects governing their implementation: a conceptual framework for an approach to design these systems and a technical framework dealing with the main issues of integration of multiple data sources from different partners in a 3D collaborative database. [less ▲]

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See detailANTIBODY-COUPLED NANORODS AS BIOSENSOR PLATFORM FOR SPECIFIC CANCER DETECTION
Schol, Daureen ULg

Doctoral thesis (2013)

This work started as part of a Specific Targeted Research Project, ADONIS (FP-6 of the European Commission) and the aim of the project was the development of active targeting gold nanoparticles for ... [more ▼]

This work started as part of a Specific Targeted Research Project, ADONIS (FP-6 of the European Commission) and the aim of the project was the development of active targeting gold nanoparticles for optoacoustic imaging, from chemistry to biology. The establishment of a biosensor composed of antibody-functionalized gold nanorods is achieved on a model of tumor, in our case prostate cancer. Prostate cancer is a major public health problem in our industrialized countries, indeed it is the most frequent cancer and the second leading cause of death by cancer in men [1]. A major challenge in prostate cancer oncology is to develop more accurate, precise and less invasive tools for early stage diagnostic, including more accurate imaging assessments than those currently available. An efficient imaging technique which significantly improves the sensitivity and the specificity of the diagnostic and enables prediction of the cancer behavior would be extremely valuable to oncologists. Briefly the developed biosensor model consists of a gold nanorod – designed to convert a primary optical excitation into a detectable acoustic signal – coupled with a monoclonal antibody that targets prostate cancer cells for a specific recognition. Improved access to the target can be achieved by targeting accessible extracellular domain of a membrane protein, here the Prostate Specific Membrane Antigen (PSMA) [2]. PSMA is a transmembrane protein considered as a suitable biomarker for prostate cancer [3] and which is under intense investigation for use as an imaging and therapeutic target. PSMA is highly expressed in prostate cancers and also expressed in the tumor associated neovasculature of most solid cancers [4]. Before biological assessments the cytotoxic surfactant, essential to form rod-shaped nanoparticles, is exchanged by a mixture of two functionalized polyethylene glycol (PEG) molecules: HS-PEG-OMe for nanoparticle passivation and HS-PEG-NH2 for subsequent coupling with the antibody. The different cytotoxicity assays are achieved to establish the toxic threshold of the surfactant in order to know what CTAB concentration maybe tolerable on the cells. This argument is important during the displacement of the surfactant, based on successive centrifugations, because the whole discard of CTAB seem to be time-consuming or even routinely unfeasible. Once this threshold drawn up, the PEGylated GNRs can be assessed on cancer cells, what seems being a common in vitro investigation. However unexpected issues came up during the experiments and had to be considered due to the properties of the nanomaterial. Nevertheless, after cytotoxicity assessment of PEGylated nanoparticles, the biosensor binding on targeted cells was assessed by fluorescence and scanning electron microscopies, two straightforward and flexible techniques. The antibody coupled to the gold nanorod is specific to the human prostate carcinoma LNCaP cell line, reported to express PSMA which is an admitted biomarker of this cell line [5]. Finally, in order to complete the specific targeting of the biosensor, the antibody-coupled gold nanorods are injected in nude mice to evaluate their biodistribution and bioaccumulation for which inductively coupled plasma mass spectrometry (ICP/MS) is the technique of choice. Preliminary optoacoustic imaging is the ultimate step for the state-of-theart of the developed biosensor. Although the promising end results, particularly biodistribution assays, new questioning swarm and this is more and more discussed in publications due to the in vivo use of nanomaterials. Owing to their increasingly extensive use, their nanometer sizes and their physiological contact (more or less long), controlling the interaction of nanoparticles with biological systems became a fundamental challenge of nanomedicine [6]. Therefore the protein opsonization on the gold nanorods is a tremendous study and is accomplished via mass spectrometry analyses. [less ▲]

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See detailSystems analysis of oscillator models in the space of phase response curves
Sacré, Pierre ULg

Doctoral thesis (2013)

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See detailSélection et caractérisation de Nanobodies inhibiteurs de métallo-β-lactamases
Sohier, Jean ULg

Doctoral thesis (2013)

Les antibiotiques, et notamment les antibiotiques à noyau β-lactame, ont révolutionné la médecine du 20ième siècle, et sauvé un nombre incalculable de vies. Leur efficacité est cependant mise en péril par ... [more ▼]

Les antibiotiques, et notamment les antibiotiques à noyau β-lactame, ont révolutionné la médecine du 20ième siècle, et sauvé un nombre incalculable de vies. Leur efficacité est cependant mise en péril par la dissémination croissante des facteurs de résistance. La production de β-lactamases par des souches infectieuses est le principal mode de résistance aux antibiotiques à noyau β-lactame. Ces enzymes hydrolysent le noyau β-lactame de ces antibiotiques, les empêchant ainsi d’exercer leur action lytique. Parmi les β-lactamases, les métallo-β-lactamases (MβLs) attirent plus particulièrement l’attention en raison de leur capacité à hydrolyser les carbapénèmes, antibiotiques considérés comme les plus efficaces, et parce qu’il n’existe à l’heure actuelle aucun inhibiteur utile d’un point de vue clinique. Avec ce travail, nous avons voulu explorer le potentiel des Nanobodies (Nbs) de camélidé en tant qu’inhibiteurs de β-lactamases, et plus particulièrement de MβLs. Ces fragments d’anticorps correspondent aux domaines variables des anticorps à chaîne lourde produits par les camélidés (HCAbs). Aussi appelés VHHs, ou « single-domain antibodies » (sdAbs), ils sont considérés comme les plus petits fragments fonctionnels dérivés d’anticorps, et peuvent être facilement sélectionnés par phage-display. Des lamas et un dromadaire ont donc été immunisés avec la MβL VIM-4, ainsi qu’avec d’autres β-lactamases choisies comme modèles. Une sélection par phage-display nous a permis d’identifier un Nb inhibiteur de VIM-4, i.e. le Nanobody Nb_VIM38. Ce Nb a été fusionné à la protéine « cherry » pour augmenter sa production. Des concentrations de l’ordre du μM en cherry-NbVIM_38 inhibent l’hydrolyse de toutes les β-lactamines testées. Par ailleurs, un modèle d’inhibition mixte hyperbolique à tendance anticompétitive est proposé. L’épitope de NbVIM_38 a pu être déterminé par immunodétection en faisant usage de peptides chevauchants. Etant donné que le site de fixation de cherry-NbVIM_38 est distant du site actif, ce Nb peut être considéré comme un inhibiteur allostérique de la MβL VIM-4, et de probablement toutes les MβLs de type VIM. Notre hypothèse est que sa fixation interfère avec la dynamique de la boucle L7 du site actif. L’inhibition de la MβL BcII par le Nanobody cAbBcII10 a aussi été étudiée. Ce Nanobody a été obtenu par K. Conrath et al. en 2001. Il a une affinité de l’ordre du nM pour la MβL BcII (« tight-binding »), ce qui devrait être pris en compte si une caractérisation détaillée de l’inhibition devait être réalisée. De manière surprenante, l’inhibition observée est partielle et dépendante du substrat, ce qui suggère un modèle d’inhibition mixte. Ce Nb peut probablement aussi être considéré comme un inhibiteur allostérique. Ces Nanobodies illustrent la possibilité d’une inhibition allostérique des MβLs. Cette piste mériterait peut-être d’être explorée. [less ▲]

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See detailEvaluation échocardiographique de la fonction cardiaque chez le cheval en coliques
Borde, Laura ULg

Doctoral thesis (2013)

Endotoxemia is a common complication of colic in adult horses and its outcome is mainly related to cardiovascular status. Endotoxic shock, like septic shock, involves hypovolemic, cardiogenic and ... [more ▼]

Endotoxemia is a common complication of colic in adult horses and its outcome is mainly related to cardiovascular status. Endotoxic shock, like septic shock, involves hypovolemic, cardiogenic and distributive components leading to tissue hypoperfusion with a high risk for multiple organ failure and an elevated mortality rate in equine and human intensive care units. Via the release of pro-inflammatory mediators, endotoxins induce a fall in systemic vascular resistance (SVR) and a drop of cardiac output (CO) resulting both from reduction in venous return and myocardial depression. First, CO is preserved thanks to a compensatory vasoconstriction and an increase in heart rate (HR), myocardial contractility and venous return. However, a loss of vascular responsiveness to catecholamines and a myocardial depression finally result in a drop of CO and SVR with a progressive hypotension despite a persistent tachycardia. The time point during the course of septic shock when hemodynamic monitoring is used has been proven to influence outcome, allowing early goal-directed therapy in humans. Unfortunately, hemodynamic monitoring in conscious horses is often limited due to animal size, working conditions and lack of patient cooperation. Therefore, such as in human patients, echocardiography could provide useful non invasive information about stroke volume (SV) and CO, systolic and diastolic function as well as fluid status. In human septic shock patients, this technique has emphasised a myocardial depression with both diastolic and systolic dysfunction reversible in survivors. Previous studies in horses focused on quantitative evaluation of hemodynamic parameters after an experimental endotoxin challenge. However, LV function had not been reported in naturally-occurring endotoxemia in horses. The purpose of the first prospective study was to assess the impact of clinically-occuring endotoxic shock on echocardiographic indices of LV systolic function in horses. Fifty horses admitted in clinic on emergency for colic were submitted to an echocardiographic exam on admission. A shock score from 1 to 4 was established for each horse based on clinical evaluation, non invasive systolic blood pressure and blood tests measurements. LV echocardiographic parameters were compared between the 4 groups according to the shock score (SS) (SS1: no or discrete signs of shock, n=11; SS2 : mild, n=17; SS3: moderate, n=12; SS4: severe, n=10) using a multivariable analysis. Significance was set at p < 0.05. Stroke volume, stroke index (SI), ejection time (ET), ejection time index corrected for HR (ETI), aortic velocity time integral (AoVTI), aortic flow acceleration time (TTP) and deceleration time (DTAo) were significantly lower, whereas aortic flow acceleration rate (dv/dtAo) was significantly higher in shocked horses than in SS1. CO was not significantly different between groups. Even if those results were difficult to interpret because of the shock-induced changes in loading conditions of the heart, they suggested that alterations in some indicators of systolic function can be quantified by Doppler echocardiography in horses with colic-induced endotoxemic shock. The aim of the second study was to non invasively assess the impact of colic-related endotoxic shock on equine diastolic cardiac function. Sixty-eight horses admitted in clinic on emergency with colic were included in this study. A similar SS was established for each horse. LV echocardiographic parameters were compared between the 4 groups according to the SS (SS1 n=14; SS2 n=16; SS3 n=27; SS4 n=12) using a multivariable analysis. Significance was set at p < 0.05. Deceleration rate of peak early LV filling velocity, peak late LV filling velocity and E/Em (peak early LV filling velocity (E) to peak early myocardial velocity (Em) ratio) were significantly higher whereas time to Em onset was significantly lower in high shock score groups compared with horses with no or mild signs of shock. The results of this second study could suggest a diastolic dysfunction with a rise of LV filling pressure ocurring with endotoxic shock in horses. Since E/Em has shown to be a very reliable predictor of mortality in human with septic shock, the results of this second study warranted further investigations. To assess the prognostic value of echocardiographic parameters of LV function in horses with endotoxic shock, 41 horses admitted for colic with clinical evidence of systemic inflammatory response syndrome associated to hyperlactatemia or hypotension underwent echocardiographic examination on admission. LV echocardiographic parameters were compared between nonsurvivors (n=29) and horses that survived to discharge (n=12). With comparable heart rate and LV preload estimate, LV SV, AoVTI, DTAo, ET and ETI of aortic flow and Em were lower in the nonsurviving than in the surviving horses while pre-ejection period to ejection time ratio (PEP/ET) of Doppler aortic flow and E/Em ratio were higher (p<0.05). A cut-off value of 0.26 for PEP/ET predicted mortality with 100% sensitivity and 42% specificity (area under the receiver operating characteristic curve (AUC): 0.71), whereas a cut-off value of 2.67 for E/Em predicted mortality with 100% sensitivity and 83% specificity (AUC: 0.89). The results of this third study suggested that echocardiography may provide prognostic information in colic horses with clinical evidence of endotoxic shock. Especially, PEP/ET and E/Em could be useful markers of systolic and diastolic dysfunction, respectively, to detect horses with a high risk of death requiring more intensive cardiovascular monitoring as it has been reported in human patients with septic shock. Finally, to assess LV function after preload restoration in colic horses, 5 horses were followed echocardiographically from admission to at least 24 hours after colic surgery in a preliminary study. Systolic dysfunction was detected in 4/5 horses and diastolic dysfunction assumed in 2/5 horses and suspected in the 3 other horses during hospitalisation. Moreover, echocardiography provided useful diagnosis informations about hemodynamic and fluid status suggesting that ultrasonographic monitoring of cardiovascular function could be of interest in equine intensive care. 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See detailEcotoxicology of Organic and Inorganic Pollutants in Chelonians. Marine Turtle Risk to Pollutant Exposure
Dyc, Christelle ULg

Doctoral thesis (2013)

Marine turtles are oviparous vertebrates subdivided in seven existing species widespread in most of the oceans. They are suffering from human activities and especially from fishery by-catch, egg ... [more ▼]

Marine turtles are oviparous vertebrates subdivided in seven existing species widespread in most of the oceans. They are suffering from human activities and especially from fishery by-catch, egg harvesting, adult poaching, degradation of their habitats, environmental pollution and climate change. While direct threats (e.g. fishery by-catch) are often less challenging to identify and predict, indirect threats associated with environmental pollution often induce more insidious effects that can take longer to manifest and be more significant and lasting. Understanding the marine turtle risks to pollutant exposure is critical because a) pollutants are persistent and ubiquitous in the environment, b) all the marine turtle species are listed on the Red List of Threatened Species by the IUCN and c) pollutants were indicated to adversely threaten the marine turtles’ survival, especially the developing individuals. Despite decades of investigations and evidences of significant pollutant threats, few data is still being available for marine turtles. The present study proposed to assess pollutant exposure in the green Chelonia mydas and hawksbill Eretmochelys imbricata marine turtles nesting in Guadeloupe (French West Indies FWI, Caribbean Sea). Trace elements (e.g. selenium, mercury and cadmium) and organohalogen pollutants OHP (e.g. polychlorobiphenyls PCBs and chlordecone) were determined in dermis collected from the nesting females and in their eggs. A broad range of pollutants was detected in these tissues among which chlordecone. This was quite interesting because of the past history of chlordecone in the FWI. Results suggested that the green and hawksbill marine turtles fed on contaminated foraging ground, accumulated chlordecone in their body and then transferred it into their eggs during the egg formation. Both Guadeloupean marine turtle species appeared less exposed to OHP and trace elements than other marine turtle populations, except for other green marine turtle colonies (i.e. trace elements). The developing embryo risks to pollutant exposure were evaluated as those for the Guadeloupean inhabitants that consume marine turtle eggs. Little threat may be expected for the Guadeloupean inhabitants while some pollutants may affect the marine turtle embryos’ survival of both species (i.e. p,p’-DDE, cadmium, mercury and selenium). The present study was not the first to arise concern about embryo risks to selenium exposure as suggested by previous reptilian studies including marine turtles. As part of the present study, the toxicokinetics and dynamics of selenium were thus approached under laboratory conditions by using the slider turtle Trachemys scripta as model candidate. Juvenile turtles dietary exposed to selenium effectively accumulated selenium in their tissues but appeared unaffected by the exposure. Indeed, their body condition and antioxidant system were unaffected over the feeding trial. This was unexpected since the dietary levels used in the present study were indicated to induce sublethal effects in birds and other reptilian species. Selenium toxicity was initiated by oxidative stress leading to unusual production of oxidant species such as reactive oxygenated species. Therefore, turtles could tolerate high selenium levels due to specific trait of life (e.g. ability to deal with oxygen introduction after anoxic conditions associated with hibernation and/or diving). It is challenging to transpose results obtained from laboratory animals exposed to controlled conditions to wild individuals exposed to many environmental factors, even if species are closely related. The development life-stage further greatly affects the sensitivity of individuals to pollutant exposure. Nevertheless, the green and hawksbill marine turtle embryos could also tolerate high selenium exposure. This would contradict the risk assessment conducted in the present study but would be possible considering the food habits of both marine turtle species. These species are feeding on seagrasses and sponges which may expose the marine turtles to natural toxic compounds. Consequently, they could have developed adaptive strategies to deal with toxics in response to pressure at their foraging ground. To date, more works are needed to better understand the metabolism of selenium in turtles as well as to properly determine toxic thresholds of selenium for marine turtles. Finally, nondestructive collection techniques were tested for their suitability in assessing the turtle exposure to pollutants in both field and laboratory conditions. Keratinized tissues (i.e. carapace and skin) were proposed as promising tools and should warrant further investigations in researches aiming at the conservation of marine turtles. The present study provides several firsts such as the first baseline levels of a) pollutants in green and hawksbill marine turtles nesting in an area not investigated yet (i.e. Guadeloupe), b) OHP in the marine turtle dermis, c) OHP in hawksbill turtle eggs and d) chlordecone in marine turtle tissues. The first toxicological data on e) selenium kinetics and dynamics were further provided in turtles. [less ▲]

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See detailGeometric statistical processing of brain diffusion tensor images
Collard, Anne ULg

Doctoral thesis (2013)

Nowadays, the functioning of the human brain is still one of the biggest mysteries of humanity. The multiple holes in the understanding of the human brain explain why an intensification of brain-oriented ... [more ▼]

Nowadays, the functioning of the human brain is still one of the biggest mysteries of humanity. The multiple holes in the understanding of the human brain explain why an intensification of brain-oriented research can be observed since a few years. One of the most recent techniques to better understand the brain is Diffusion Tensor Imaging (DTI), a noninvasive imaging modality that provides information about orientation of nervous fibers, and their spatial density, with a high resolution. The particular nature of DTI images makes them multi-valued. Their processing therefore requires to adapt state-of-the-art techniques, which are fundamentally tailored to scalar-valued images. The objective of this PhD thesis is to develop a novel framework for the processing of tensor diffusion images. The focus is threefold: first, we adopt a Riemannian geometric framework to generalize image processing from linear to nonlinear spaces. Second, we aim at developing a processing framework that retains the physical information of measurement data. Thirdly, the proposed algorithm must be computationally efficient in order to scale with the data size of clinical applications. The main contribution of this thesis is the development of a novel processing method, which has the particularity to preserve the important features of diffusion tensors, while being computationally affordable. This technique is based on the decoupling between the two types of information conveyed by tensors: the diffusion intensity on one hand, and the orientation of diffusion on the other hand. Moreover, the computational cost is limited thanks to the use of unit quaternions to represent tensors orientation. Another contribution of the thesis lies in the development of a statistical method for group comparison. This method uses the notion of similarity measure between the values, a notion that can be defined for multi-valued images, and which enables to reduce the computational cost. The use, for the statistical tests, of the similarity measure associated to our framework turns out to be efficient and informative. The study of geometric methods for multi-valued images together with the study of potential applications of diffusion tensor images have enabled the introduction of a novel framework, which is particularly appropriate for those images. The basic operations developed in the thesis open the way to more sophisticated processing algorithms, while ensuring the preservation of the main information associated to the tensors. [less ▲]

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See detailImplicit Real Vector Automata
Degbomont, Jean-François ULg

Doctoral thesis (2013)

This thesis introduces a new data structure, the Implicit Real Vector Automaton (IRVA), suited for representing symbolically polyhedra, i.e., regions of n-dimensional space defined by finite Boolean ... [more ▼]

This thesis introduces a new data structure, the Implicit Real Vector Automaton (IRVA), suited for representing symbolically polyhedra, i.e., regions of n-dimensional space defined by finite Boolean combinations of linear inequalities. IRVA can represent exactly arbitrary convex and non-convex polyhedra, including features such as open and closed boundaries, unconnected parts, and non-manifold components. In addition, they provide efficient procedures for deciding whether a point belongs to a given polyhedron, and determining the polyhedron component (vertex, edge, facet, ...) that contains a point. An advantage of IRVA is that they can easily be minimized into a canonical form, which leads to a simple and efficient test for equality between represented polyhedra. Elementary IRVA representing primitive polyhedra, such as linear (in)equations and vector spaces are easily constructed and algorithms have been developed for computing Boolean combinations as well as projections of polyhedra represented by IRVA. These algorithms are illustrated by complete examples of executions as a support for the comprehension of their mechanisms. Another contribution is a first prototype implementation of an IRVA library, containing functions for building and manipulating arbitrary n-dimensional polyhedra. We reinforce the presentation of the implementation by discussing some design choices. Such choices include the use of exact arithmetic. Finally, experimental results are presented and discussed. These experiments pave the way to future adaptations and improvements. [less ▲]

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See detailImmunotoxicology of methylmercury and other contaminants in harbour seals (Phoca vitulina) from the North Sea
Dupont, Aurélie ULg

Doctoral thesis (2013)

Environmental contaminants are suspected to have detrimental effects on marine mammal health. They were notably hypothesised to be involved in the severity and extent of catastrophic viral epidemics that ... [more ▼]

Environmental contaminants are suspected to have detrimental effects on marine mammal health. They were notably hypothesised to be involved in the severity and extent of catastrophic viral epidemics that recently affected the harbour seal (Phoca vitulina) population from the North Sea. High levels were indeed found in their tissues. However, the exact effects of those pollutants on free-ranging harbour seal health are not yet elucidated. In the field of immunotoxicology, in vitro cell culture techniques have been developed and are considered as valuable tools to assess specific toxicity mechanisms. The first objective of this study was to investigate the relationships between environmental contaminant levels found in harbour seal blood and lymphocyte proliferation responses in vitro. Indeed, wild harbour seal cells used in the framework of in vitro culture studies are isolated from the blood of animals that are contaminated, but little is known about the possible relationships between them. They were thus investigated in harbour seals from the North Sea. Peripheral blood leucocytes were isolated and cultured during 72h with Concanavalin A (ConA), a mitogen agent, to evaluate the lymphocyte proliferative responses as a stimulation index. The ConA-induced lymphocyte proliferation assay evaluates their ability to proliferate in response to a polyclonal stimulation, which is considered to reflect the activation of the immune response after an antigenic stimulation in vivo. No statistically significant relationship was found between the lymphocyte stimulation index and blood pollutants or class of pollutants studied (i.e. mercury, lead, persistent organic pollutants, pentachlorophenol, tribromoanisole) in harbour seals sampled while in good body condition and presenting no sign of disease. However, the number of lymphocytes per milliliter of whole blood appeared to be negatively correlated to pentachlorophenol, an organochlorine pesticide. A high interindividual variability of lymphocyte stimulation indexes was observed although cells were isolated in the same way and cultured in identical conditions. This is probably linked to a whole set of parameters such as precise age, sex, life history leading to particular immune status (probably partly related to pollutant loads), physiological parameters and inevitable experimental variability. So, in a general manner, experiments with in vitro immune cell cultures of wild marine mammals should be designed so as to minimise confounding factors in which case they remain a valuable tool to study pollutant effects in vitro. The second objective of this study was to determine underlying mechanisms of methylmercury immunotoxicity. Indeed, among the numerous contaminants found in harbour seal tissues, methylmercury is one of the most hazardous organic compounds known to have numerous detrimental effects on living organisms. It has the property to bioaccumulate and biomagnify in the trophic chain, and can reach very high levels in harbour seal tissues. Peripheral blood leucocytes exposed to relatively low concentrations of methylmercury chloride (MeHg) in vitro revealed a significant decrease of viable cell counts with obvious ultrastructural effects. A higher frequency of apoptosis was observed in lymphocytes, in which mitochondria and nuclei may have been targeted, as demonstrated by ultrastructural analysis. These results were in accordance with the significant decrease of the mitochondrial membrane potential and of lymphocyte proliferation (BrdU assay) observed. The toxicity of this compound was shown to be counteracted by selenium. However, little is known about that interaction in marine mammal blood and the underlying mechanisms still remain unclear. The present study aimed to investigate the in vitro effects of relatively low (0.75 µM) MeHgCl levels on harbour seal ConA-stimulated leucocytes while added concomitantly to Se. Two different forms of Se were studied: selenite and selenomethionine. Their concentrations were within the range of those measured in free-ranging harbour seal blood, and in a Hg:Se ratio of 1:10. Lymphocyte proliferation as well as the mitochondrial membrane potentials were significantly reduced following in vitro exposure to MeHgCl during 72h. No significant difference was found when sodium selenite or selenomethionine was added concomitantly to MeHgCl. Conversely, on average, Se alone did not lead to significant decreased proliferation and mitochondrial membrane potentials. The absence of protection of Se, either in organic or inorganic form, against Hg toxicity in harbour seal blood leucocytes in vitro raises concern as regards the deleterious effects this toxic compound could have on marine mammal immune system. The range of current Hg levels found in free-ranging harbour seals from the North Sea encompasses exposure levels which elicited deleterious effects on lymphocytes in the present study. This highlights the potential for effects on host resistance to disease. [less ▲]

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See detailAnalysis of performance and robustness of biological switches: local tools for non-local dynamical phenomena.
Trotta, Laura ULg

Doctoral thesis (2013)

Biological switches are frequently encountered in mathematical modeling of biological systems because binary decisions are at the core of many cellular processes. A bistable switch presents two stable ... [more ▼]

Biological switches are frequently encountered in mathematical modeling of biological systems because binary decisions are at the core of many cellular processes. A bistable switch presents two stable steady-states, each of them corresponding to a distinct decision. These two decisions are assumed to result from the interactions between biochemical effectors at the molecular level. Because these molecular interactions are particularly complex, involving many effectors, mathematical models of biological switches are often high dimensional and nonlinear. Therefore, an analysis of these systems is challenging. In this dissertation, we try to identify principles and tools to study the performance and robustness of biological switches. Our first contribution is to highlight the dynamical nature of these switches. A biological switch encodes a decision-making process rather than a static binary code. It captures dynamical phenomena that are important for the decision-making process, such as decision latencies and reversibility. Our second contribution is methodological. While most of the classical analysis tools are based on a linearization of the system around a stable steady-state, a switch is a non local phenomenon involving a transition between two stable steady-sates. Rather than studying the system around stable equilibria, we identify the local rulers of the decision-making process in both the state and parameter spaces and propose a local analysis in the vicinity of these particular points. Our third contribution is to emphasize the added value of an abstract (that is, mathematical) framework for the analysis of biological switches. By studying different models, we point out that the same principles can be used to encode dynamical phenomena in very different cellular processes. Physiological processes as different as apoptosis, the cellular choice of death, and action potential, the cellular choice to emit an electrical spike, share common features when regarded as decision-making processes. [less ▲]

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See detailLes forêts à Marantaceae au sein de la mosaïque forestière du Nord de la République du Congo : origines et modalités de gestion
Gillet, Jean-François ULg

Doctoral thesis (2013)

The Marantaceae forests are conspicuous by an unusual physiognomy with a giant herbaceous continuous stratum in association with a scattered tree component regenerating with difficulty. This vegetation ... [more ▼]

The Marantaceae forests are conspicuous by an unusual physiognomy with a giant herbaceous continuous stratum in association with a scattered tree component regenerating with difficulty. This vegetation, arranged as a heterogeneous patchwork within the lowland semi-deciduous forests, is widely extended in the Northern Republic of Congo. The thesis aims to define and describe the vegetation types of this forest patchwork in order to identify the key factors that have shaped it and to recommend an appropriate forestry. To achieve this, the study was conducted in the CIB-OLAM logging concession (Sangha and Likwala departments). Two types of monodominant G. dewevrei forests and three hydromorphic vegetation types have been described trough on ordination multivariate analysis of the woody stand in relation with the hydrological conditions. In addition, a multi-strata classification of mixed terra firma forests has individualized five vegetation types that are defined and characterized. These are: (1.1) open vegetation types with Marantaceae and Aframomum cf. subsericeum, (1.2) sparse Marantaceae forests with Megaphrynium macrostachyum and (1.3) with Haumania liebrechtsiana, (1.4) dense forests with Marantaceae and (2) moist semi-deciduous dense forests (3 forms: (2.1) with Sarcophrynium schweinfurthianum, (2.2) with Haumania danckelmaniana and (2.3) with Triplochiton scleroxylon). They are characterized by their specific richness, floristic composition and/or structural parameters. Thanks to an archaeo-pedological study coupled with 14C dating, we established that the Marantaceae forests suffered the strongest past disturbances. The perturbations were mostly caused by humans and predominated around 1,550 yrs BP. They would be related to an expansion phase of the oil palm Elaeis guineensis and its exploitation by humans. The simultaneous degradation of the forest cover, combined with poor and wet soils, has facilitated the expanding of giant herbs, gradually inhibiting the tree regeneration. The dense forests on the contrary, whose the dominant species are light-demanding and wind-dispersed trees (eg. T. scleroxylon) would have a more recent origin. Indeed, they date back about 7 to 2 centuries and are related to shifting cultivation on richer and well-drained soils. The logging within the open canopy Marantaceae vegetation types results in a recovery of the forest dynamic on skid trails. Thanks to the destruction of the herbaceous understorey by logging equipment. On these trails, an assisted regeneration by selection and freeing of seedlings and an additional planting turns out to be an effective technique for woody species regeneration. The results are especially encouraging for the following species: Canarium schweinfurthii, Terminalia superba, Ricinodendron heudelotii and Nauclea diderrichii whose average height growth is respectively 154, 130, 125 and 124 cm, one year after the silvicultural treatment. Given the evolutionary dynamics of these open canopy Marantaceae vegetation types, systematic reforestation with timber species on skid trails seems to be the most appropriate silvicultural technique to ensure sustainable exploitation. [less ▲]

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See detailLa propriété intellectuelle : nature juridique et régime patrimonial
Vanbrabant, Bernard ULg

Doctoral thesis (2013)

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See detailProduction et caractérisation d'hydrolysats de pectine obtenus par voies enzymatique et thermique(micro-onde)
Combo, Agnan Marie Michel ULg

Doctoral thesis (2013)

L’objectif de cette thèse est de contribuer à étudier d’une part les voies de production des oligosaccharides pectiques (POS) et d’autre part à déterminer leurs principales propriétés physico-chimiques ... [more ▼]

L’objectif de cette thèse est de contribuer à étudier d’une part les voies de production des oligosaccharides pectiques (POS) et d’autre part à déterminer leurs principales propriétés physico-chimiques. Pour ce faire, deux voies de production ont été utilisées : enzymatique et thermique. En ce qui concerne la production de POS par voie enzymatique, six pectinases commerciales de qualité alimentaire (Endopolygalacturonase-M2, Pectinase P-4716, Viscozyme L, Pectinex Ultra SP-L, Pectinase 62L et Macer8 FJ) ont été testées sur une pectine modèle (acide polygalacturonique) pour sélectionner la pectinase capable de produire au mieux des POS. Préalablement, la totalité de ces pectinases a été caractérisée en termes d’activité polygalacturonase et de pureté: toutes possédaient une activité polygalacturonase, mais concernant la pureté, ces préparations commerciales se sont révélées être un mélange de plusieurs activités enzymatiques à l’exception de l’Endopolygalacturonase-M2 (EPG-M2). Cette dernière a présenté, après deux heures d’hydrolyse de l’acide polygalacturonique, les meilleurs résultats pour la production de POS avec 18% et 58% de la masse convertie en acides di et tri-galacturoniques respectivement (contre 0,22 et 0,20% pour la Pectinase P-4716, 0,9 et 0,3% pour la Viscozyme, 2,7 et 9,4% pour la Pectinex Ultra SP-L, 0,4 et 0,3% pour la Pectinase 62L et 0,2 et 0,15% pour la Macer8 FJ). L’EPG-M2 a donc été choisie pour modifier la pectine de betterave dans la suite du travail. Ainsi, en utilisant l’EPG-M2 combinée à une pectine-méthylestérase (Rapidase Smart®), des poudres de POS ont été obtenues par lyophilisation après hydrolyse de la pectine de betterave. Une étude des propriétés chimiques et physico-chimiques de ces POS a été ensuite réalisée par chromatographie liquide haute performance, par analyse thermogravimétrique couplée à la spectroscopie infrarouge à transformée de Fourier, par analyse calorimétrique différentielle et par diffraction des rayons X. Les analyses chromatographiques ont montré que les POS sont composés de mélanges d’oligomères de masses moléculaires (Mw) diverses avec différentes teneurs en acide galacturonique. L'analyse thermique a toutefois révélé que les POS étaient plus sensibles à la dégradation thermique que la pectine native. L'analyse par ATG-IRTF n’a montré aucun changement majeur dans les groupes fonctionnels après hydrolyse enzymatique de la pectine de betterave. La diffraction RX des POS a indiqué une diminution de la cristallinité par rapport à la pectine native. La seconde voie suivie pour la production de POS a été une voie hydro-thermique par utilisation de micro-ondes. Le potentiel des micro-ondes pour produire des POS a été exploré et les conditions optimales conduisant aux meilleures teneurs en POS ont été déterminées. Trois paramètres ont été simultanément étudiés: la température, le temps ainsi que le pH. Un plan expérimental a permis d’évaluer l’effet de ces paramètres sur la production de POS à partir d’une solution de pectine de betterave. Une diminution considérable de la Mw de la pectine de betterave a été observée avec des Mw correspondant à des oligosaccharides de degré de polymérisation (DP) moyen de l’ordre de 24 à 25. Les résultats de cette étude ont montré qu’un pH de 3, une durée supérieure à 15 min et une température comprise entre 140 et 148°C sont les conditions les plus favorables à l’obtention de POS. Ces deux voies d’hydrolyse de la pectine en POS pourraient représenter des méthodes pratiques et fiables pour une production en routine de POS, composés utilisables comme ingrédients additifs pouvant être incorporés dans des formulations alimentaires ayant des propriétés nutritionnelles et/ou technofonctionelles. [less ▲]

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See detailEvaluation de la justesse vocale en contexte mélodique
Larrouy, Pauline ULg

Doctoral thesis (2013)

In order to determine if a vocal performance is “in tune” or “out of tune”, to better understand the causes of poor-pitch singing or to evaluate the quality of a singer, tools are necessary. Two methods ... [more ▼]

In order to determine if a vocal performance is “in tune” or “out of tune”, to better understand the causes of poor-pitch singing or to evaluate the quality of a singer, tools are necessary. Two methods are actually used to evaluate the vocal accuracy of a sung performance. The "subjective" method makes use of judges whereas the "objective" method uses computer tools. While the first method allows a rapid assessment, it lacks precision. The “objective” method seems currently preferred but shows limits that our research aims to overcome. The first step was to develop a functional and objective method, which takes into account the different melodic errors we encounter when using the Western tonal system (i.e. respect of the melodic contours, the pitch intervals, and the tonal center). We then applied this method to sung performances of occasional and professional singers. These first studies confirmed the functionality and legitimacy of our method. However, some limits occurred regarding the evaluation of Western operatic singers. In a second step, we observed the relevance of this method and more specifically the interest to evaluate complete melodies (compared to pitch matching tasks) and the interest to differentiate the possible melodic errors. Finally, the comparison of our method with the evaluation made by music experts has enabled us to examine their perception and definition of vocal accuracy. Through seven studies, we explored the theoretical and methodological aspects of vocal accuracy in a melodic context. Taken together, the results of these studies allow us to clarify the definition of vocal accuracy and to consider the several clinical and experimental perspectives of our objective method for evaluating singing voice accuracy. [less ▲]

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See detailDevelopment of an analytical method to determine the composition of cryolitic baths used in the Hall-Heroult process, by Raman spectroscopy, at 1000°C
Malherbe, Cédric ULg

Doctoral thesis (2013)

Worldwide metallic aluminium production involves the Hall-Héroult process where the metal is electro-deposited from aluminium oxide solubilised in a molten NaF-AlF3-CaF2 mixture at around 950°C. The ... [more ▼]

Worldwide metallic aluminium production involves the Hall-Héroult process where the metal is electro-deposited from aluminium oxide solubilised in a molten NaF-AlF3-CaF2 mixture at around 950°C. The cryolitic melt is conveniently characterised by both the molar NaF/AlF3 ratio and the Al2O3 content. Nowadays the Hall-Héroult process remains the more economically efficient process even if it still suffers from a high consumption of energy. In particular the overvoltage required by the electrolysis is strongly dependent on the melt composition, especially regarding the Al2O3 content. Controlling the industrial baths composition during the process is therefore critical to reduce the energy loss. Unfortunately there is, up to now, no in situ direct analytical method to do so. Considering our experience in the study of such highly corrosive media by Raman spectroscopy, that technique has been applied to directly determine the melt composition. Three sets of reference spectra are considered in this study, each of them recorded with a different setup. The employed setups were developed to reach progressively, at the laboratory scale, a design that is suitable for a plant application. Eventually, a high quality spectrum can be recorded by the top of the melt, in less than 20 seconds. The employed apparatus is found to influence significantly the shape and quality of the spectra, and consequently their involvement in the quantification. A complex digital treatment of the spectral data acquired is necessary because all Raman bands of interest strongly overlap and some are situated close to the Rayleigh decay. Two main quantitative procedures for the melt composition determination are studied. The first one, the AutoAnalysis procedure, developed in the past and adapted here to the new data, gives reliable predictive results for both the NaF/AlF3 molar ratio and the alumina content. They can be determined with an absolute deviation of 0.06 molar ratio unit and 0.5 wt% respectively. However, the intensity normalisation, required for comparing the intensities of different spectra, relies on the Rayleigh decay that is likely to change with the experimental conditions in the plants. In our second quantitative procedure, the NormaAnalysis procedure, the intensity normalisation is based on the equilibria taking place in the melt. Since those equilibria do no differ with the experimental setup, the NormaAnalysis procedure can be imported to the industrial field. The predicted composition is also evaluated with a good precision: the NaF/AlF3 molar ratio and the alumina content can be determined with an absolute deviation of 0.08 cryolitic ratio unit and 0.3 wt% respectively. It is concluded that the composition of the melt can now be determined with our NormaAnalysis procedure, from a single Raman spectrum, recorded with a Raman apparatus exportable for an in situ measurement on the industrial cells. [less ▲]

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See detailEtude des relations pucerons-virus en pomme de terre et perspectives de stratégies alternatives de lutte
Yattara, Almouner Ag Alhamis ULg

Doctoral thesis (2013)

Abstract – Sustainable approach of crop production, including the implementation of biological control is essential in potato pest and disease control in general, and aphids and viruses associated in ... [more ▼]

Abstract – Sustainable approach of crop production, including the implementation of biological control is essential in potato pest and disease control in general, and aphids and viruses associated in particular. In addition, given to the lack of data available for Mali, it was essential to study the aphid and virus actors related to this geographical location. Here we firstly proposed to compare two techniques for trapping aphids. During two growing seasons, the yellow traps were found to be more effective (73.6%) than Malaise traps (26.4%) in the potato aphid survey. The use of trapping techniques and limitations of each of these were discussed in the context of the implementation of a monitoring crop pests in an area or issue of sampling aphids collected. How to efficiently proceed for this purpose was discussed. Then, as very few data documenting the presence and impact of aphids in Mali were available, we followed for three consecutive years, the abundance and diversity of aphids in the fields of potato consumption. Nineteen species of aphids have been identified for the first time in all investigated areas. As a corollary, the presence of potato virus Y and potato leaf roll virus was shown in the two main producing areas of potato. The occurrence of these viral diseases has proved to be very consistent from one year to another with relatively high levels. This study is a first quantification in this region of Mali of the importance of aphid vector- virus couples in cultured potato. Finally, a comparison with the conditions of production in Belgium was performed and higher abundance and richness of aphid species was found in Belgium than in Mali. Unlike Mali, only the potato virus Y detected by RT-PCR in the fields of plant production and consumption in Wallonia with the appearance of PVY-N and PVY-NTN strains. The relationship between the diversity of aphids - abundance and the presence of virus in the potato fields were examined to improve the control strategies of the virus. [less ▲]

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See detailLes facteurs parentaux, les stéréotypes de genre et l'intelligence émotionnelle dans le développement d'une sensibilité à l'anxiété chez l'enfant
Stassart, Céline ULg

Doctoral thesis (2013)

Ce travail de thèse tente de favoriser une meilleure connaissance de l'étude de la sensibilité à l'anxiété chez l'enfant et de sa pertinence, ainsi que de permettre une compréhension plus précise des ... [more ▼]

Ce travail de thèse tente de favoriser une meilleure connaissance de l'étude de la sensibilité à l'anxiété chez l'enfant et de sa pertinence, ainsi que de permettre une compréhension plus précise des facteurs impliqués dans le développement d'une sensibilité à l'anxiété chez l'enfant. De manière plus spécifique, il poursuit trois objectifs précis. (1) Après une description détaillée de la littérature sur la pertinence d'étudier un concept tel que la sensibilité à l'anxiété, il parait important d'être en mesure de posséder une échelle valide permettant de l'investiguer. Le questionnaire de sensibilité à l'anxiété chez l'enfant, intitulé Children Anxiety Sensitivity Index (CASI) de Silverman, Fleisig, Rabian, & Peterson (1991), n’a pas encore fait l'objet d'une validation dans une population belge. Une analyse de la structure factorielle, ainsi qu'une exploration des qualités psychométriques de la version française de la CASI est le premier objectif de cette étude. (2) Le deuxième objectif concerne l'impact de rôle de genre et de l'intelligence émotionnelle dans le développement d'une sensibilité à l'anxiété chez l'enfant. Différents auteurs mettent en avant la pertinence de prendre en compte le rôle de genre, plutôt que le sexe biologique, dans la .prévalence des troubles anxieux. Ceci est davantage documenté dans une population adulte, et n'a jamais été investigué dans la sensibilité à l'anxiété. De plus, les compétences émotionnelles ont montré leur facteur protecteur dans la vie de l'enfant, tant au niveau relationnel, que psychologique et physique. Ce travail investigue si cet effet protecteur est également présent dans la sensibilité à l'anxiété. (3) Enfin, le troisième objectif approfondit la question de l'influence des parents dans le développement d'une sensibilité à l'anxiété chez l'enfant. En effet, la littérature met en évidence l'implication parentale dans la présence des peurs des sensations anxieuses chez l'enfant. En conséquence, la sensibilité à l'anxiété des parents ainsi que les expériences d'apprentissages catastrophiques au sein du milieu familial sont examinées. De plus, l'influence de deux modérateurs est investigué: plus spécifiquement, l'impact d'un facteur de vulnérabilité et de protection, respectivement le niveau de féminité (du parent et de l'enfant) et l'intelligence émotionnelle de l'enfant dans le lien entre les facteurs parentaux et le développement d'une sensibilité à l'anxiété chez l'enfant. [less ▲]

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See detailSynthèse et étude biologique des phosphonopeptides: les rhizocticines, les plumbemycines et leurs analogues
Gahungu, Mathias ULg

Doctoral thesis (2013)

Rhizocticins and Plumbemycins are natural phosphonate antibiotics produced by the bacterial strains Bacillus subtilis ATCC 6633 and Streptomyces plumbeus, respectively. Up to now, these potential ... [more ▼]

Rhizocticins and Plumbemycins are natural phosphonate antibiotics produced by the bacterial strains Bacillus subtilis ATCC 6633 and Streptomyces plumbeus, respectively. Up to now, these potential threonine synthase inhibitors have only been synthesized under enzymatic catalysis. Here we report the chemical stereoselective synthesis of the non-proteinogenic (S,Z)-2-amino-5-phosphonopent-3-enoic acid [(S,Z)-APPA] and its use for the synthesis of Rhizocticin A and Plumbemycin A. In this work, (S,Z)-APPA was synthesized via the Still–Gennari olefination starting from Garner’s aldehyde. The Michaelis–Arbuzov reaction was used to form the phosphorus–carbon bond. Oligopeptides were prepared using liquid phase peptide synthesis (LPPS) and were tested against selected bacteria and fungi. [less ▲]

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See detailVirus transmission efficiency: investigation on Chinese clone diversity of wheat aphids and role of aphid endosymbionts
Yu, Wenjuan ULg

Doctoral thesis (2013)

Clone diversity in aphids (Hemiptera: Aphididae) was known to be related to acceptance and suitability of host plant. Occurrence of particular patterns of bacterial endosymbionts was demonstrated to ... [more ▼]

Clone diversity in aphids (Hemiptera: Aphididae) was known to be related to acceptance and suitability of host plant. Occurrence of particular patterns of bacterial endosymbionts was demonstrated to specific plant – aphid interactions. Barley yellow dwarf virus (BYDY) has a high degree of vector specificity to be transmitted only by specific species of cereal aphids. BYDV and their aphid vectors are associated in a variety of complex interactions. In this context, the main objective of this dissertation was to understand the virus partners in host-aphid interactions, the role of endosymbionts pattern on virus transmission efficiency and (E)-β-farnesene (EBF) production. Aphids were of closely association with bacterial endosymbionts; which substantially affect the physiology, ecology, reproduction and behaviors of aphids in a variety of way. Firstly, endosymbionts were selective eliminated by antibiotic, the EBF production was reduced; from the result of protein analysis, some protein from Buchnera aphidicola were found. It demonstrated that endosymbionts take part in the EBF production. Secondly, Fourteen populations of Sitobion avenae Fabricius (Hemiptera: Aphididae) originating from China were tested for their ability to transmit Barley yellow dwarf virus-PAV (BYDV-PAV, one isolate from Belgium, another from China) using wheat plants. All populations could transmit BYDV-PAV and variation in transmission rates ranged from 24.42% to 66.67% with BYDV-PAV-Belgium and from 23.55% to 56.18% with BYDV-PAV-CN. Significant differences of percentages of transmission between the populations with BYDV-PAV-Belgium and BYDV-PAV-CN were observed. Buchnera and seven S-symbionts (PASS, PABS, PAUS, Rickettsia, Spiroplasma, Wolbachia and Arsenophonus) universally found in different local population with different infection frequencies. The endosymbionts in most and least efficient vector aphid clones were selectively eliminated by antibiotic, the BYDV transmission efficiencies were inhibited. Compared with the result of western blot, Buchnera plays an import role on BYDV transmission. Finally, according to the direct toxic effect of lectins on insect biological parameters but also to the potential competitive effect of lectins towards viral particles in virus transmission by aphids, GNA and PSL incorporated in an artificial diet, the BYDV transmission efficiencies were inhibited. The inhibition rate of GNA-treatment reached to 46.63% in STY-BYDV-PAV-CN treatment and PSL-treatment was 46.47% in STY-BYDV-PAV-CN treatment. It is demonstrated that lectins represent a very promising protein to control aphid pest damages in crops. [less ▲]

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See detailEtude d’impact de l’apprentissage par la vidéo et la radio rurale sur la transformation à petite échelle du riz local au Bénin
Zossou, Enangnon ULg

Doctoral thesis (2013)

La culture du riz a été reconnue par les Nations Unies comme l'une des principales sources de nourriture pouvant favoriser la sécurité alimentaire, l'éradication de la pauvreté et la réalisation à l ... [more ▼]

La culture du riz a été reconnue par les Nations Unies comme l'une des principales sources de nourriture pouvant favoriser la sécurité alimentaire, l'éradication de la pauvreté et la réalisation à l'échelle internationale des objectifs du Millénaire. Au Bénin, beaucoup de réformes ont été faites dans la filière riz pour accroître la production nationale. La production et la transformation du riz sont des tâches souvent réparties sur la base du sexe avec les femmes en grande partie responsables des opérations post-récoltes. La transformation du riz au Bénin est généralement faite à petite échelle et constitue une source non négligeable de revenus. Dans le but d’améliorer l’apprentissage au sein des acteurs du riz, des chercheurs et des partenaires, en collaboration avec les producteurs et transformateurs de riz au Bénin, ont élaboré une série de vidéos sur la production de riz et les activités post-récoltes. Les vidéos ont été utilisées comme une ressource à partir de laquelle des scripts radiophoniques ont été développés. Cette étude s’intéresse à l'impact de l’apprentissage par les vidéos et émissions radiophoniques (relatives à la post-récolte du riz) sur (i) les pratiques des transformateurs, (ii) les caractéristiques physiques et les propriétés de cuisson du riz local, (iii) la valorisation du riz local par les consommateurs et (iv) le capital financier, social et humain des transformateurs du riz local. L'étude a été menée dans le sud et le nord du Bénin avec 240 transformateurs de riz et 270 femmes consommatrices de riz ; et dans le centre du Bénin avec 160 femmes étuveuses de riz et 100 consommatrices de riz. En plus des interviews structurées et des fiches de suivi hebdomadaire, l'évaluation participative utilisant l'approche des moyens d'existence durable a été utilisée pour apprécier l’état du capital financier, social et humain des transformateurs de riz. Pour l’analyse des données, nous avons utilisé le modèle de la double différence « Diff-in-Diff », le modèle de régression OLS (Ordinary Least Squares), le modèle de régression de Poisson et l'effet moyen de traitement (ATE). Pour apprécier la volonté des consommateurs béninois à payer pour le riz local, nous avons mené des enchères expérimentales dans les marchés au nord, centre et sud du Bénin. Avant l’apprentissage par la vidéo ou la radio, les transformateurs de riz avaient moins accès aux sources formelles d'apprentissage et avaient des pratiques peu recommandées. Les méthodes traditionnelles ne conduisant pas à une bonne qualité de riz étaient prédominantes. Par conséquent, l'état général des capitaux des moyens d’existence était faible. Les projections publiques des vidéos et les émissions radiophoniques ont été très bien appréciées par les transformateurs de riz dans les zones d’étude. La radio rurale semble être moins efficace que la vidéo et doit être utilisée avec précaution dans la vulgarisation agricole. Les animateurs des radios rurales ont en effet besoin d’une connaissance suffisante des sujets agricoles et de se familiariser avec le vernaculaire agricole local afin de diffuser des messages appropriés. Les scripts radiophoniques développés à partir des vidéos aident à relever ces défis. Les transformateurs de riz qui ont suivi les vidéos et les émissions radiophoniques ont amélioré leurs pratiques et leur créativité en développant des technologies appropriées à leur environnement. Ce qui a eu un impact positif sur la qualité du riz local transformé ; améliorant ainsi le prix sur le marché. Par rapport au prix du riz étuvé traditionnel, les consommateurs sont prêts à payer un surplus de 9 à 27% pour avoir le riz étuvé avec des technologies d'innovation locale; et 25 à 34% pour avoir le riz étuvé avec la technologie améliorée. Comparativement aux offres du groupe témoin, la sensibilisation par la vidéo et la radio a augmenté respectivement les offres des consommatrices pour le riz étuvé avec la méthode améliorée de 23 à 47F CFA et de 9 à 18 F CFA. vi En 2012, on constate dans les villages vidéo une augmentation du pourcentage de transformateurs de riz qui font la vente dans les marchés régionaux ; ce qui constitue un indicateur de la bonne qualité du riz. Avec l’utilisation du modèle de l'ATE, nous notons pour le riz blanc qu'il n'y a pas eu un impact significatif de la radio sur les revenus parce que le message a été à un moment mal compris. La vidéo par contre a eu un impact significatif sur les revenus des transformateurs aussi bien pour le cas du riz blanc que pour celui du riz étuvé. L’impact de la vidéo sur les revenus des transformateurs de riz étuvé est pratiquement le double de ce qui a été noté dans le cas de la radio rurale. Les transformateurs de riz qui ont suivi la vidéo et les émissions radiophoniques ont perçu une amélioration significative au niveau de leur capital financier, social et humain. Des campagnes d'information sur les technologies améliorées de transformation du riz ont non seulement joué un rôle important au niveau des transformateurs de riz en améliorant la qualité de leurs produits ; mais aussi elles ont permis d’informer les consommateurs sur la valeur du produit final. Les résultats de la présente étude ont été certainement influencés par (i) l’approche participative utilisée lors de la réalisation des vidéos et des émissions radiophoniques ; (ii) le mode d’utilisation des vidéos, c’est-à-dire leurs projections publiques sur des écrans géants ; et (iii) l’utilisation des vidéos comme des ressources à partir desquelles les émissions radiophoniques ont été réalisées. D’autres projets utilisant la vidéo et la radio rurale pourraient ne pas avoir les mêmes résultats si les conditions précitées n’ont pas été remplies. Ce qui nécessite des études ultérieures quant à l’influence du mode de réalisation et d’utilisation des vidéos et émissions radiophoniques dans le monde rural sur leur efficacité et durabilité dans le temps. Dans un contexte de pauvreté généralisée, d’insécurité alimentaire, de fort taux de ruralité et de faible taux d’alphabétisation, l’utilisation dans la vulgarisation agricole de la vidéo et de la radio rurale (fondées sur les principes de base des approches participatives) constitue une opportunité pour favoriser l’accès général des populations rurales à l’information agricole. Ce qui constitue un potentiel pouvant promouvoir une agriculture durable en encourageant les innovations locales. Au regard de l’intérêt que présentent la vidéo et la radio rurale, des suggestions ont été faites à l’endroit de la recherche, du développement et des décideurs politiques afin qu’une attention particulière soit portée sur ces outils de communication dans la vulgarisation agricole. [less ▲]

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See detailStudy of CMV - plant - aphid interactions focusing on Myzus persicae in vegetable crops
Yin, Rongling ULg

Doctoral thesis (2013)

Myzus persicae aphid is a very polyphagous pest found on hundreds of host plants including several vegetable crops. Its role as virus potential vector was cited for many viruses including the ones found ... [more ▼]

Myzus persicae aphid is a very polyphagous pest found on hundreds of host plants including several vegetable crops. Its role as virus potential vector was cited for many viruses including the ones found in vegetable crops. Transmission efficiency of virus such as Cucumber mosaic virus (CMV), transmitted by M. persicae to vegetable crops is the most common model used in many researches. In a non-persistent manner, CMV particles bind on the top of aphid stylet and transmitted in a few minutes, with an efficiency affected by a number of factors, like virus strains, aphid species, source and recipient plant species, and plant species on which the aphid is maintained. Management of vector-borne plant diseases has presented a challenge because of complex dynamics and interactions of host plants, vectors and viruses within natural environment. Lectins as defense proteins in plants are present in large quantities in storage organs and seeds that are especially vulnerable to pathogens or pest insects (Peumans and Van Damme, 1995). Numerous reports in recent years have shown that lectins are toxic to various pest insects belonging to economically important insects such as Lepidoptera, Coleoptera, Diptera or Hemiptera in genetic engineered plants or artificial diets with lectins, which negatively affected the performances of pest insects. In the last decades, some plant lectins were shown to be toxic particularly to several aphids. Plant-aphid-virus interactions have been researched for several decades, and there are some important questions studied, and still being in process. Although there are reports on virus transmission, we focus on transmission efficiency affected by 8 geographic aphid species, virus strains and plant lectins, and finally we performed to get a better understanding of the virus-aphid interactions and to propose new insight of lectins in non-persistent virus transmission control in crop protection. [less ▲]

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See detailBelgian population exposed to furan: from analytical developments to risk assessment
Scholl, Georges ULg

Doctoral thesis (2013)

Since the acrylamide incident in 2002, food authorities such as EFSA, FDA, FAO and Belgian FFSA paid more attention to the food borne contaminants such as furan, glycidyl esters or nitrosamines. As a ... [more ▼]

Since the acrylamide incident in 2002, food authorities such as EFSA, FDA, FAO and Belgian FFSA paid more attention to the food borne contaminants such as furan, glycidyl esters or nitrosamines. As a consequence, authorities support scientific initiatives to gather information about these toxicants. The thesis was conducted in this framework and was specifically dedicated to the furan issue. The fundamental concept behind this work on furan was to include analytical developments, to determine its occurrence in Belgian food and to carry out a risk assessment of the Belgian population. The first section was dedicated to the development of a high sensitive analytical method able to report sub-parts-per-billion (ppb) levels in foodstuffs with the aim to limit the number of unreported results below of the limit of quantification (LOQ). A HS-SPME-GC-MS method has been developed and optimized using the experimental design approach. The developed method has been validated to fulfill the requirements of the European Commission decision regarding the validation of analytical method (2002/657/EC). The second section was dedicated to the achievement of a contamination survey of the foodstuffs available on the Belgian market with a restricted number of samples (n=496). A specific sampling plan was designed to cover every food matrices with regard to the more consumed and/or contaminated items. The analytical method developed in the first section was applied and 78% of results were reported above LOQ. We concluded to a ubiquitous contamination of our food chain with specially high levels in coffee, roasted and long-time cooking foodstuffs. The third section was dedicated to the assessment of the risk linked to the furan ingestion by the Belgian population. A methodology involving the estimation of the furan daily intake (by both deterministic and probabilistic approach) and the calculation of the Margin of Exposure (MoE) was applied to 3 sub-populations namely Adults, Children and Toddlers. The adults and children assessments highlighted that almost none have a “High concern risk level” (MoE < 100), that the risk for health tends to be low (median MoE for adults 5486; median MoE for children 5079), and that the risk for children is slightly higher than for adults. For infants, the assessment showed a higher risk (median MoE 817) compared to children and adults. However, this finding has to be tempered by the current limited knowledge of the furan toxicity for toddlers. In addition, the size of the datasets available for this work was low and limited to ready-to-eat baby foods, which are known to be more contaminated than home-made baby food. It gives however the first benchmark for Belgian infants exposed to furan. Thus, developing consumption survey for infants that are harmonized at European level, and basic research on furan toxicity for toddlers are necessary. [less ▲]

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See detailLa filière avicole de chair dans les zones périurbaines de Hanoï, Vietnam: situation économique et perspectives
Phan Dang, Thang ULg

Doctoral thesis (2013)

In Vietnam, the economic growth in recent years, has brought a strong demand for animal products consumption, particularly poultry meat. This research aims to better understand how the factors in the meat ... [more ▼]

In Vietnam, the economic growth in recent years, has brought a strong demand for animal products consumption, particularly poultry meat. This research aims to better understand how the factors in the meat-producing poultry sector adapt to current economic conditions in Hanoi suburbs by analyzing agricultural product chains. These studies have conducted two surveys from October 2008 to November 2010. As results, three meat-producing poultry systems have been identified. The industrial farms with contract farming have obtained the most important net income (from 28,923,000 VND per farm per year for colored chickens to 67,341,000 VND for standard chickens). The productivity is also very high. The mortality rate is 5 % for colored and standards chickens. But number of these industrial farms is still limited due to a large capital investment and the limitation of available land. The cost price of broiler production is really competitive compared to other chickens. Meat-producing poultry farms on semi-industrial scale have obtained weak productivity. The mortality rate is 13 % for colored chickens and ducks. Agricultural by-products of the farms are generally used for poultry. The net income has varied from 14,279,000 VND per farm per year with colored chickens to 25,424,000 VND with standard chickens. Backyard poultry farms are widely practiced in household farms with low investment. The productivity is very weak. The mortality rate of chickens is high (19 %). The net income of poultry production is also weak in households (4,432,000 VND per farm per year, or equivalent to 9 % of net income in farms). Majority surveyed farms raised various species of chickens and ducks. This is to permit a better risk management and responds to varied market demand according to different consumer tastes. Poultry meat production also aims to satisfy a significant share of the demand for self-consumption with chickens and ducks in small households. [less ▲]

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See detailLe dumping social dans l'Union européenne : Étude à l'aune du droit primaire et de la directive détachement
Defossez, Alexandre ULg

Doctoral thesis (2013)

La dénonciation du risque de « dumping social » que fait courir le processus d’intégration économique européen aux systèmes sociaux des États membres apparaît, en filigrane, tout au long de l’histoire de ... [more ▼]

La dénonciation du risque de « dumping social » que fait courir le processus d’intégration économique européen aux systèmes sociaux des États membres apparaît, en filigrane, tout au long de l’histoire de l’édification du marché intérieur . Les exemples récents de telles dénonciations ont fait l’objet d’une forte médiatisation, qui ne doit toutefois pas masquer l’ancienneté du risque ainsi dénoncé . Plusieurs affaires ont ainsi défrayé la chronique et ont poussé citoyens et syndicats à interpeller les responsables politiques, européens et nationaux. L’objet de cette étude est né de cette interrogation : le risque de dumping social étant une crainte permanente au sein de l’Union, une crainte elle-même associée à la construction et à l’approfondissement du marché intérieur européen, quels mécanismes juridiques le législateur européen a mis (ou pas) en place afin d’en contrer les effets ? L’objectif de cette recherche est, plus précisément, d’identifier la manière dont ces débats, récurrents, ont conduit le législateur européen à adopter des mécanismes de lutte contre le dumping social et d’évaluer les effets des mécanismes ainsi mis en place. Il ne s’agira donc pas d’analyser comment l’espace européen s’intègre lui-même dans le tissu économique mondial et peut, à cette occasion, se protéger contre le risque de concurrence sociale induit par les échanges avec le reste du monde . Le dumping social intra-européen, et la manière dont l’Union européenne cherche (ou pas) à s’en prémunir, forme le cœur, plus modeste, de cette étude. [less ▲]

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See detailCaractérisation structurale des protéines et de complexes non covalents par "footprinting" et MALDI In-Source Decay
Lemaire, Pascale ULg

Doctoral thesis (2013)

La fragmentation de protéines entières dans la source d’un spectromètre de masse (« In-Source Decay » ou « ISD ») lors de l’ionisation-désorption laser assistée par une matrice (« Matrix-Assisted Laser ... [more ▼]

La fragmentation de protéines entières dans la source d’un spectromètre de masse (« In-Source Decay » ou « ISD ») lors de l’ionisation-désorption laser assistée par une matrice (« Matrix-Assisted Laser Desorption/Ionisation » ou « MALDI ») permet leur identification. On parle alors de méthode « Top-down », par opposition à l’approche « Bottom-up » dans laquelle les protéines sont d’abord digérées en peptides. Cette fragmentation étant rapide, elle peut être considérée comme une technique intéressante pour analyser les régions d’une protéine qui sont accessibles au solvant dans des expériences qualifiées de « footprinting ». En effet, les zones non accessibles soit en raison de la conformation d’une protéine soit suite à son interaction avec un ligand seront protégées. En plus d’être rapide, la fragmentation par MALDI-ISD ne nécessite qu’une faible quantité d’échantillon. Les spectres de masse obtenus sont principalement composés d’ions fragments monochargés résultant de la rupture de la liaison peptidique, ce qui permet leur interprétation en termes de séquence. Cette technique peut donc être intégrée dans une stratégie permettant d’obtenir rapidement des données qualitatives concernant la topologie d’une protéine. Dans ce manuscrit, la fragmentation par MALDI-ISD a été utilisée pour localiser les sites qui sont accessibles au solvant et par là, les sites protégés par repliement ou par interaction de protéines avec des ligands non covalents. Les méthodes de footprinting qui utilisent des techniques de marquage oxydatif ou de marquage par le deutérium en solution ont été utilisées. La fragmentation ISD elle même peut être vue comme une méthode de footprinting directe, n’utilisant pas de marquage préalable de protéines en solution. Cette analyse repose sur l’étude des modifications d’accessibilité des groupes carbonyles en comparant le profil de fragmentation des protéines lors d’un changement structural ou lors de leur interaction avec un ligand. Footprinting oxydatif analysé par MALDI-In-Source Decay. N’ayant jamais été exploitée pour l’analyse des données de footprinting oxydatif, la fragmentation par MALDI-ISD a été utilisée pour localiser les sites d’oxydation du peptide amyloïde Aβ(1-40). Une étude de la faisabilité de détection de produits d’oxydation ainsi que l’identification des chaînes latérales oxydées a tout d’abord été effectuée en oxydant le peptide Aβ(1-40) dans une solution de peroxyde d’hydrogène. La modification des profils de fragmentation ISD du peptide oxydéa été expliquée par la probabilité d’intervention de compétitions de réactions d’addition radicalaire et de transfert de charge. Cet effet sur l’aspect global des spectres de masse n’affecte cependant que le rendement des oxydations et non leur localisation. L’oxydation du peptide Aβ(1-40) résultant de son interaction spécifique avec le fer a permis de valider l’utilisation de la méthode pour la localisation des sites d’oxydation. Une corrélation entre l’identité des résidus oxydés et les données d’interaction du métal fournies par la littérature a pu être établie. Le peptide Aβ(1-40) constitue une cible thérapeutique potentielle étant donné son implication dans la toxicité cellulaire observée dans la maladie d’Alzheimer. Les sites d’interaction de molécules bi-aromatiques susceptibles d’inhiber potentiellement l’agrégation du peptide devaient au départ être identifiés par la méthode d’échange hydrogène/deutérium (« hydrogen/deuterium exchange » ou « HDX ») analysé par MALDI-ISD. Les premières expériences ont cependant révélé que les fonctions amides du peptide étaient caractérisées par des cinétiques d’échange isotopique intrinsèques rapides. Le marquage oxydatif par des radicaux hydroxyles produits par photolyse laser du peroxyde d’hydrogène a été la stratégie alternative de choix pour l’étude d’interaction du peptide avec un ligand bi-aromatique leader. Une diminution de la proportion de la forme mono-oxydée du peptide en présence du ligand est observée sur les spectres de masse MALDI. L’identité de l’acide aminé oxydé n’a malheureusement pas été élucidée, cependant, la méthionine 35 pourrait être l’acide aminé oxydé. Footprinting utilisant le deutérium analysé par MALDI-In-Source Decay. La matrice MALDI 1,5-DAN qui est pourtant connue pour présenter un potentiel réducteur élevé, favorisant la production d’ions fragments par MALDI-ISD, n’a cependant jamais été utilisée pour l’analyse des données d’échange H/D de protéines. Les cinétiques d’échange H/D intrinsèques rapides du peptide Aβ(1-40) ont permis de l’utiliser comme modèle pour évaluer l’utilisation de la matrice 1,5-DAN pour le couplage de l’échange H/D à la spectrométrie de masse MALDI. L’homogénéité des profils d’échange isotopique et le degré de rétroéchange moyen observé sur un spot MALDI ont été examinés en comparant les résultats obtenus avec la matrice 1,5-DAN à ceux obtenus avec trois matrices MALDI plus communes. Les résultats révèlent qu’outre son potentiel réducteur élevé, la matrice 1,5-DAN possède une cinétique de cristallisation très rapide. Ceparamètre facilite la mise au point de protocoles robustes. La matrice 1,5-DAN a été utilisée pour l’analyse des données d’échange H/D de la structure tertiaire de l’ubiquitine dans des conditions natives. Les résultats obtenus en ISD sont en accord avec des données préalablement obtenues en ETD et RMN. Cet accord entre les résultats a permis de valider la méthode proposée. Une seconde étude basée sur la caractérisation de structures secondaires a été effectuée avec la β- endorphine. Les profils d’échange H/D de la β-endorphine sous une structure secondaire hélicoïdale, induite par le méthanol, ont été comparés à ceux obtenus lorsque le peptide est sous une conformation en pelote statistique non périodique. Le peptide sous sa conformation hélicoïdale présente systématiquement une accessibilité au solvant plus réduite. Les résultats obtenus sont en accord avec les prédictions qualitatives, sur base de la polarité des acides aminés, de formation d’hélices α induite par le méthanol. Footprinting utilisant la voie de fragmentation radicalaire en MALDI-In- Source Decay. Les résultats de marquage oxydatif du peptide Aβ(1-40) analysé par MALDI-ISD ont révélé une variation considérable de l’intensité relative de signaux ioniques caractéristiques d’une fragmentation induite par les radicaux hydrogènes de la matrice. Le profil de fragmentation est modifié au niveau de l’ion fragment caractérisant la tyrosine 10 du peptide. Ce résidu, selon la littérature, est impliqué dans l’interaction du peptide avec le fer. Nous avons donc évalué l’utilisation de la fragmentation ISD comme méthode de footprinting reposant sur l’étude de l’accessibilité des groupes carbonyles des protéines aux radicaux hydrogènes de matrice. Une comparaison des spectres de fragmentation ISD du lysozyme humain natif ou dénaturé puis alkylé en solution a été réalisée. Les profils de fragmentation ISD des deux conformères du lysozyme sont différents. En particulier, les ions fragments c18, c19 et z14 ont fourni une information pertinente sur la différence d’accessibilité des deux conformères visà- vis des radicaux hydrogènes. Cependant, la différence d’intensité de l’ion fragment z14 observée entre les deux conformères peut aussi être expliquée par un effet de l’alkylation de la cystéine 116 du lysozyme sur le clivage du lien N—Cα du côté C-terminal du résidu. Une étude supplémentaire a été réalisée avec un complexe formé entre le lysozyme humain et un fragment d’anticorps de camélidé, cAb-HuL6. L’objectif était de détecter une modification éventuelle du profil de fragmentation ISD lors de la complexation du lysozyme. Les intensitésrelatives des ions fragments caractérisant des acides aminés de l’interface du complexe lysozyme—cAb-HuL6 sont peu modifiées par rapport à celles du complexe Aβ(1-40)—Fe. Cette observation a conduit la conclusion que l’utilisation de la fragmentation ISD comme méthode de footprinting dépend non seulement de la stabilité du complexe (constante d’affinité, Kaff, et constante de vitesse de dissociation, kd) et des conditions expérimentales utilisées (solvant, additifs et matrice), mais aussi du type d’interactions impliquées dans la formation du complexe. [less ▲]

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See detailTopology optimization of electrostatic MEMS including stability constraints
Lemaire, Etienne ULg

Doctoral thesis (2013)

Among actuation techniques available for MEMS devices, electrostatic actuation is often used as it provides a short response time and is relatively easy to implement. However, these actuators possess a ... [more ▼]

Among actuation techniques available for MEMS devices, electrostatic actuation is often used as it provides a short response time and is relatively easy to implement. However, these actuators possess a limit voltage called pull-in voltage beyond which they are unstable. The pull-in effect, can eventually damage the device since it can be impossible to separate the electrodes afterward. Consequently, pull-in phenomenon should be taken into account during the design process of electromechanical microdevices to ensure that it is avoided within utilization range. In this thesis, a topology optimization procedure which allows controlling pull-in phenomenon during the design process is developed. A first approach is based on a simplified optimization problem where the optimization domain is separated from the electrical domain by a perfectly conducting material layer making the optimization domain purely mechanical. This assumption reduces the difficulty of the optimization problem as the location of the electrostatic forces is then independent from the design. However, it allows us to develop and validate a design function based on pull-in voltage in the framework of a topology optimization problem. Nevertheless, in some applications, the developed pull-in voltage optimization procedure suffers from design oscillations that prevent from reaching solution. In order to solve this issue, we propose to investigate an alternative approach consisting in formulating a linear eigenproblem approximation for the nonlinear stability problem. The first eigenmode of the proposed stability eigenproblem corresponds to the actual pull-in mode while higher order modes allow estimating upcoming instability modes. By including several instability modes into a multiobjective formulation, it is possible to circumvent the oscillations encountered with pull-in voltage design function. Next, the possibility to generalize the pull-in optimization problem by removing the separation between optimization and electrostatic domains is studied. Unlike the original method, the dielectric permittivity has then to depend on the pseudo-density like the Young Modulus to represent the different electrostatic behavior of void and solid. Additionally, in order to render perfect conducting behavior for the structural part of the optimization domain, a fictitious permittivity is also introduced into the material model. Difficulties caused by non-physical local instability modes could be solved by using a force filtering technique which removes electrostatic forces originating from numerical inaccuracies of the modeling method. Thanks to these improvements, the optimization problem based on the pull-in design function can be generalized. As a result, the optimizer is able to adapt the electrostatic force distribution applied on the structure which leads to a higher efficiency of the optimal device. In order to illustrate the interest of the pull-in voltage design function, the pull-in voltage optimization problem is merged with the electrostatic actuator optimization problem. In this new optimization problem, the pull-in voltage does not appear anymore in the objective function but in a constraint which prevents the pull-in voltage to decrease below a given minimal value. Firstly, the new optimization problem is compared to the basic electrostatic actuator design procedure on basis of a numerical application. The pull-in voltage constraint proved to be very useful since it prevents the pull-in voltage of the mechanism to decrease below the driving voltage during the optimization process. Finally, the effect of geometric nonlinearity modeling is also tested on numerical applications of our optimization procedure. [less ▲]

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