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See detailFinite-Element Modeling of Thin Wires Including Skin- and Proximity Effects
Velasco, Jonathan ULiege

Doctoral thesis (2022)

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See detailRessources territoriales et productivité des entreprises : approches d'analyse spatiale et d'économétrie. Une application sur les entreprises wallonnes
Wilmotte, Pierre-François ULiege

Doctoral thesis (2021)

Productivity determinants are a central research topic. Among these determinants, the impact of territorial resources (especially at sub-national scales) has been under-researched and relatively neglected ... [more ▼]

Productivity determinants are a central research topic. Among these determinants, the impact of territorial resources (especially at sub-national scales) has been under-researched and relatively neglected by mainstream scientific research. Moreover, many productivity studies deal with it at an aggregate level, which may lead to ecological errors in the conclusions related to public policies and regional development. This doctoral research aims to answer three questions to tackle these gaps and issues. To start with, what are the territorial resources that significantly influence firms’ productivity? Methodologically, can we avoid the bias of the ecological error influencing interpretations and conclusions outlined by studies conducted at aggregated levels? And about policy mix, what specific lessons can we learn from improved understanding of the relationship between territorial resources and firm productivity? The thesis was developed in three research areas to address the research questions. Firstly, two systematic literature reviews were conducted to identify the leading productivity indicators, the most appropriate statistical methods and the relevant territorial resources. Then, the spatial structures of several productivity indicators were identified using spatial autocorrelation indexes. Spatial analysis and cartography are suitable tools to identify geographies of firm productivity, but they are currently underused. Finally, based on the spatial structures and the literature, we developed an explanatory model of Walloon firms’ Total Factor Productivity (TFP) by territorial resources. The results underline agglomeration economies’ central role: an imbalance does exist between economies and diseconomies in the major Walloon urban areas. The economies (linked to urban size) are too small by comparison with the structural difficulties related to the industrial decline of these urban areas. In addition, labour markets of nearby metropolises like Brussels or Luxembourg seem to put pressure on Walloon local labour markets (higher wages) and Walloon firms TFP (lower than expected by literature review). Finally, analyses seem to converge in confirming that dense and multifunctional locations are associated with a higher firms’ TFP, invalidating the link between firm competitiveness and cheap land. [less ▲]

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See detailHow evolved that mouth: a functional morphological approach to unravel the evolutionary history of trophic shift between herbivory and carnivory in Serrasalmidae (Teleostei: Characiformes)
Huby, Alessia ULiege

Doctoral thesis (2021)

In jawed vertebrates, a diet transition between herbivory and carnivory is predicted to result in a change in functional constraints on the feeding system. Curiously, in this context, few studies have ... [more ▼]

In jawed vertebrates, a diet transition between herbivory and carnivory is predicted to result in a change in functional constraints on the feeding system. Curiously, in this context, few studies have explored the phenotypic evolution of the feeding system as an integrated functional system including teeth, bones and muscles. The Neotropical family Serrasalmidae (pacus, piranhas and relatives) is a highly successful group of South American characiform fishes having a large diversity of feeding habits and tooth morphologies. Feeding habits vary from the predominantly frugivorous and granivorous pacus having molariform teeth to the primarily piscivorous piranhas having caniniform teeth. More importantly, serrasalmids are atypical among teleosts because they feed only by biting on various types of plant and animal foods while using only the oral jaw system. All these specificities make serrasalmids the ideal study group to understand how the biting system evolves under a trophic shift, and in particular, how oral teeth, oral jaws and associated jaw muscles evolve in relation to each other. The main objectives of this research thesis were to determine, in a phylogenetic context, the impact of a diet transition between herbivory and carnivory on the feeding performance and functional morphology of the biting system, along with evolutionary patterns of phenotypic integration and modularity between the different dental and musculoskeletal structures of this system in serrasalmids. To this end, we recorded for the first time bite forces in many species of the family, we generated functional and morphological (geometric morphometric) datasets for each structure of the biting system, and we performed the first comparative analysis of function and microstructure of oral teeth between herbivorous and carnivorous serrasalmids. Our results demonstrate that the evolutionary history of serrasalmids is characterized by a main trophic shift from herbivory to carnivory, which is associated with a major phenotypic shift in the biting system enhancing bite performance. Sharper teeth, longer jaws, a jaw joint more in line with teeth and a larger jaw muscle changed the entire configuration of the biting system to generate more efficient and stronger bite forces for animal foods in a scissor-like strategy. In addition to these phenotypic adaptations, our results provide evidence of a shift in tooth attachment and microscopic adaptations at the level of oral teeth. Teeth of piranhas attach by their base to the jawbone to better withstand extreme bite forces and have an increased mineral content that most likely improves their stiffness. Our results also reveal that the biting system evolves as a modular system by having a certain degree of independence between oral teeth, oral jaws and associated jaw muscles. Our results also highlight, for the first time, a sequence of phenotypic adaptations in which oral teeth, oral jaws and then the adductor mandibulae muscle shift in morphology and function. Altogether, our findings suggest that oral teeth might be a key structure in the adaptive evolution of the biting system in serrasalmids in relation to trophic shift. However, their stronger phenotypic integration with oral jaws compared to adductor mandibulae muscle suggest that oral teeth and oral jaws, together, might enable the shift between the herbivorous and carnivorous adaptive zones and ecological diversification within these zones. [less ▲]

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See detailUrban flooding modelling: role of geometric distortion in scale models and influence of urban forms
Li, Xuefang ULiege

Doctoral thesis (2021)

Urban flood risk is increasing worldwide as a result of environmental changes such as more frequent hydro-climatic extremes and due to rapid urbanization. Accurate and reliable tools are critically needed ... [more ▼]

Urban flood risk is increasing worldwide as a result of environmental changes such as more frequent hydro-climatic extremes and due to rapid urbanization. Accurate and reliable tools are critically needed for managing this risk and enhancing flood resilience. Such tools rely on numerical models for computing flood hazard and flood risk. However, the accuracy and applicability of these models still remain hampered by a lack of suitable validation data. Data generated from laboratory experiments is a valuable complement to field observations for validating these flood risk management tools. Through a comprehensive review of the 45+ available experimental studies of urban flooding, a few gaps in current experimental knowledge of urban flooding were identified. Firstly, laboratory studies of urban flooding often use geometrically distorted scale models due to the multi-scale nature of these specific flow pattern The possible bias induced by geometric distortion has never been thoroughly investigated with dedicated laboratory experiments. To address this issue, we firstly carried out a preliminary assessment of these biases based on the reanalysis of two recent experimental datasets related to urban flooding. Then, combining two-dimensional numerical modelling and dedicated laboratory experiments, we provided a first systematic quantification of this bias in the case of a synthetic urban layout, involving models at three horizontal scales, models for different geometries and various flooding conditions. The results indicate the direction and magnitude of the bias induced by geometric distortion for a broad range of flow cases, which is valuable for offsetting these effects in practical laboratory studies of urban flooding. Secondly, water-sensitive urban design is an integral part of flood risk management. Based on numerical modelling, we investigated the influence of various urban forms on flood severity at an urban block scale in the case of long-duration urban flooding. The upstream flow depths, downstream discharge partition and flow exchange through the urban forms were examined. Moreover, the computational model was verified against laboratory observations, which constitute a novel valuable dataset for the validation of other urban flooding models. [less ▲]

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See detailApprendre à maitriser la temporalité historienne: étude de l’efficacité d’un dispositif partiellement non chronologique
Pirard, Gaël ULiege

Doctoral thesis (2021)

Résumé : Depuis le XVIIe siècle, l’histoire s’enseigne dans l’ordre chronologique. Il s’agit là d’une tradition encore respectée aujourd’hui en Belgique francophone. Cependant, ces dernières années, des ... [more ▼]

Résumé : Depuis le XVIIe siècle, l’histoire s’enseigne dans l’ordre chronologique. Il s’agit là d’une tradition encore respectée aujourd’hui en Belgique francophone. Cependant, ces dernières années, des débats concernant le meilleur ordre à adopter pour apprendre l’histoire, et plus particulièrement, pour apprendre le temps, ont vu le jour en Belgique. Notre thèse de doctorat a pour objectif de vérifier empiriquement s’il existe, comme l’affirment de nombreux didacticiens, professeurs et acteurs de l’enseignement de l’histoire, un mode de mise à disposition des savoirs enseignés à privilégier pour permettre aux élèves de maitriser certaines dimensions de la temporalité historienne. Pour ce faire, nous avons mené une recherche quasi expérimentale dans laquelle la variable dépendante correspond à la maitrise de la temporalité historienne tandis que la variable indépendante concerne l’organisation des contenus à apprendre (organisation strictement chronologique ou « parcours chronologiques emboités »). Cette recherche a été menée en province de Liège, en Belgique francophone et a porté sur un échantillon d’élèves (n=369) de 3e année secondaire de l’enseignement qualifiant (technique ou professionnel). Notre recherche ne démontre pas une différence significative (p=0,9832) entre les deux modes d’enseignement lorsque l’on tente d’apprendre aux élèves les connaissances procédurales liées aux trois dimensions que nous avons retenues comme constitutives de la temporalité historienne (causes-conséquences, changements-continuités-périodisation et synchronies). Nous avons également observé qu’en moyenne, il existe une faible diminution des résultats entre le pré-test et le post-test dans les deux groupes. Enfin, nous tirons un certain nombre de conclusions par rapport aux variables secondaires influençant le niveau de maitrise de la temporalité historienne chez des élèves de l’enseignement qualifiant. Nous avons ainsi repéré l’existence d’un lien significatif entre le niveau de maitrise de la temporalité historienne de l’élève et son niveau de compréhension à la lecture, sa filière, l’indice socio-économique de son école, son niveau d’intérêt pour l’histoire et la nationalité de sa mère. Abstract: Since the seventeenth century, history has been taught in a chronological order. In this way, it is a tradition still respected nowadays in francophone Belgium. Nevertheless, these last years, debates about the best way to teach history, and more particularly, to teach time in general, have arisen in Belgium. The aim of our thesis is to check empirically if there is, as a lot of professors and professional stakeholders in history and didactic claim it, a way to introduce historical knowledge that we should opt for in order to allow the students to master some dimensions of historical temporality. In that sense, we have led an quasi-experimental research in which the dependent variable is the mastering of historical temporality, and the independent variable is linked to the organisation of historical understanding (strictly chronological organization or « slotted chronological process »). This research has been led in the province of Liege, in francophone Belgium, and has been built on a sample of 3rd year secondary school students (n=369), from the technical and vocational education. Our research does not show a significant difference (p=0,9832) between the two modes of teaching when we try to teach the students the procedural knowledge linked to the three dimensions that we have kept as constitutive of historical temporality (causes and consequences, changes-continuities-periodisations and synchronies). We have also observed that, in average, there is a slight decrease of the results between the pre-test and the post-test in the two groups. Finally, we have come to several conclusions according to the secondary variables which influence the level of mastering of historical temporality for students of technical and vocational education. We have thus spotted the existence of a significant link between the student’s level of mastering of historical temporality and his level of reading comprehension, his pathway, the socio-economic status of his school, his interest in history and his mother’s nationality. [less ▲]

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See detailOptimal Inspection and Maintenance Planning for Deteriorating Structures via Markov Decision Processes and Deep Reinforcement Learning. Application to Offshore Wind Substructures.
Morato Dominguez, Pablo Gabriel ULiege

Doctoral thesis (2021)

Safeguarding engineering infrastructures in a healthy condition is of paramount importance to sustain the economic and societal growth of most countries. Deterioration mechanisms and mechanical stressors ... [more ▼]

Safeguarding engineering infrastructures in a healthy condition is of paramount importance to sustain the economic and societal growth of most countries. Deterioration mechanisms and mechanical stressors have a detrimental effect on structural performance, inducing a risk of failure that might lead, in some cases, to considerable economic, societal, and environmental consequences. Although the estimation of deterioration processes is associated with significant uncertainties, information from inspections and monitoring can be collected, at a cost, in order to dictate more informed maintenance decisions. Inspection and Maintenance (I&M) planning thus demands methods capable of identifying optimal management strategies in stochastic environments and under imperfect information. Addressing the aforementioned needs, this thesis is devoted to the exploration of efficient methods with the objective of controlling the risk of adverse events by timely planning inspections and optimally dictating maintenance actions. Throughout the investigation, the I&M planning decision-making problem is formally formulated as a Partially Observable Markov Decision Process (POMDP), constituting the underlying principled mathematical foundation of the stochastic control optimization. From medium to high-dimensional state space settings, infinite and finite horizon policies are efficiently computed via POMDP point based solvers, whereas for higher dimensional state, action, and observation space settings, POMDPs are integrated with a multi-agent actor critic deep reinforcement learning approach. Besides overcoming dimensionality limitations by approximating both policy and value functions with artificial neural networks, the formulation of the POMDPs through conditional formations enables the treatment of structural systems under deterioration, reliability, and cost dependence. Sequential monitoring decisions, influenced by the condition of the sensors, can also be aptly allotted through the proposed approach. Extensive numerical experiments have been conducted for both traditional and detailed I&M planning settings with a strong emphasis on offshore wind substructures, thoroughly comparing POMDP policies against corrective, calendar, and heuristic based strategies. The results reveal that POMDP-based policies offer substantial savings compared to their counterparts in all the tested settings. [less ▲]

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See detailGenetic Algorithm as a New Design Tool for MEMS Devices with Freeform Geometries
Wang, Chen ULiege

Doctoral thesis (2021)

The vast majority of micro-electro-mechanical systems (MEMS) devices rely in their mechanical design on very simple geometrical layouts comprising only a few primitives such as beams, rectangular masses ... [more ▼]

The vast majority of micro-electro-mechanical systems (MEMS) devices rely in their mechanical design on very simple geometrical layouts comprising only a few primitives such as beams, rectangular masses and – more rarely – rings or disk-shaped structures. The beams and rectangular structures are typically combined in a Manhattan grid structure to form a suspension system, resonating structures, the proof mass of inertial sensors, comb drives, pick-off capacitive electrodes, etc. However, practically all MEMS devices having movable structures (physical sensors such as inertial sensors, force sensors, pressure sensors, actuators, as well as biochemical sensors based on resonators or beams exhibiting stress induced static deflections) are compliant devices. In other words, they don’t rely on linear or rotational joints as commonly used in macroscopic mechanical designs. However, for compliant devices, orthogonal designs based only on the combination of rectangles may not be the best design approach. Depending on the parameter of interest for a particular device, much more complex geometrical shapes may result in superior performance. Parameters to be maximized could be the deflection of a proof mass in response to an input (e.g. inertial) force, the linear travel range of an electrostatic actuator for a given input voltage, the force in response to an electrostatic drive (e.g. for a micro-gripper), the pull-in voltage, the linearity of a mechanical suspension system, etc. Such a design approach requires substantially higher degrees of freedom for the shapes of the mechanical geometry, rather than restricting it to very few simple primitives. Using simple geometrical shapes is a reminiscence of early MEMS design: the designer had to intuitively understand the design and being able to model it analytically using linear approximations. With modern design tools such as MEMS+, this requirement is no longer a limiting constraint, as these tools can predict the behavior (including nonlinear effects) of virtually arbitrarily complex shapes and designs by multi-physics FEM (finite element modelling) simulations. This offers the exciting possibility for geometrical shape optimization for certain goal parameters for a wide range of MEMS devices. The presented work aims to introduce a novel and powerful design methodology for a wide range of MEMS devices relying on compliant mechanism. The proposed optimization relies on a GA that has already been successfully employed for optimizing the electronic parameters of closed-loop, electro-mechanical sigma-delta modulator control systems for inertial sensors [1]. The primary objective of this thesis is to apply, for the first time, a GA to MEMS devices for freeform geometries. The GA based algorithm running within MEMS+ is capable of quickly and efficiently designing high performance, near optimal freeform compliant mechanisms for many MEMS devices. The semi-automated design procedure is expected to result in rather unusual geometrical shapes that have not been seen in MEMS designs to date and is therefore likely to establish an entirely new research area for MEMS. It is expected that important performance indicators for many MEMS devices will be substantially improved. In the thesis, firstly, a the novel, semi-automated design methodology based on a genetic algorithm (GA) using freeform geometries for MEMS devices is introduced. A detailed description of the optimization process is presented including, mechanical model building, figure of merit, robustness analysis. As a first demonstrator, a MEMS a MEMS accelerometer comprising a mechanical motion amplifier, is presented to validate the effectiveness of the design approach. Experimental results show an improvement of the product of sensitivity and bandwidth by 100% and a sensitivity improvement by 141% compared to a device designed in a conventional way. Furthermore, excellent immunities to fabrication tolerance and parameter mismatch were achieved. As a second demonstrator an actuator, specifically a MEMS microgripper, is designed with this novel methodology. The use of freeform geometries significantly improved the performance of the microgripper. Experimental data shows that the designed microgripper has a large displacement ( 91.5 μm) with a low actuation voltage (47.5 V), which agrees well with theoretical and simulation results. The microgripper has a large actuation displacement and can handle micro-objects with a size from 10 μm to 100 μm. A grasping experiment on human hair with a diameter of 77 μm was performed to prove the functionality of the gripper. The result confirmed the superior performance of the new design methodology enabling freeform geometries. [less ▲]

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See detailThe changes of rural livelihood: the case of the coastal sandy zone in Thua Thien Hue Province, Vietnam
Dao Duy Minh, ULiege

Doctoral thesis (2021)

Similar to other regions of Vietnam, the Coastal Sandy Zone of Thua Thien Hue province has recently achieved many desired outcomes. However, these regions are still facing numerous problems such as ... [more ▼]

Similar to other regions of Vietnam, the Coastal Sandy Zone of Thua Thien Hue province has recently achieved many desired outcomes. However, these regions are still facing numerous problems such as recurring impacts of climate change, increasing frequency of various diseases in many sub-agricultural sectors, considerable fluctuations about market prices, persisting water management issues and challenging stakeholder-collaboration concerns. This study analyses the livelihood changes of rural households and proposes solutions and recommendations for reducing vulnerabilities while strengthening sustainable livelihood strategy. The recommendations of this study are intended for researchers and policy makers who are doing impact assessment studies and development process planning in a multi-level, farm-level approach. Two frameworks of analysis, the original and the advanced Sustainable Livelihood Frameworks (Hao ND, 2009) guided the author in evaluating the livelihood changes through a ten-year time. To view changes in the proportion of households in each block and the income generated from the livelihood strategies, the author divided the households into six categories. A mixed method of Participatory Rapid Appraisal, Focus Group Discussion and household survey were used to identify the reasons for the current livelihood selection, the vulnerability for each specific strategy and the potential strategy adaptation to reduce the vulnerabilities. The driving factors affecting the adaptation of climate change/climate extreme events were assessed by analyzing the indicators and variables of the Livelihood Vulnerability Index with a Multi Logit Regression model. In addition, the author documented the households’ explanations as to why they changed their livelihoods. Findings indicate significant improvements in five types of capital for 2007_2008 to 2017_2018. These include, among others, but not limited to: 1. Households investing more money on increasing their educational level; thus positively changing the occupational structure towards better working conditions, higher salary and more diversified job opportunities; 2. Households experiencing better quality of life because of a well-controlled population growth; 3. Households being exposed to a wider room of credit providers and credit categories; 4. Households improving more of their physical/housing conditions; 5. Households investing more heavily in new machines and technologies resulting in more efficient time and cost of production, lower potential risks from the weather, more time to participate in social and cultural activities and preserve traditional values. 6. Women taking more action in production and marketing aspects, and getting easier access to education, healthcare, information, technology, credit, and land; and 7. Households possessing higher adaptive capacity due to good collaboration among local governments in narrowing the impacts of extreme weather events related to Climate Change. However, of the seven improvements enumerated above, some related concerns also surfaced in this province, namely: 1. The low quality and fragmented land pose an important challenge to increasing the production scale, even with the use of modern technologies and advanced models; 2. The low access to credit despite its increasing outreach because households avoid the exposure to frequently occurring agricultural risks and the threats associated with unpredictable extreme weather impacts (e.g., financial and human losses) and labor shortages in the agricultural sector in the coming years; 3. The many barriers continuing to persist locally, such as managerial capacity, local budgets, and not using updated techniques for estimating and mitigating impacts of extreme events related to climate change. Livelihood Vulnerability and Climate adaptation. Household reduced significantly their vulnerability in almost aspects of human, financial, social and physical capitals while increase exposure in terms of natural hazards. About 27% of the households did not implement any adaptation method; nearly half of them applied a reactive adaptation method and 28% implemented the proactive adaptation method. Livelihood changes. After 10 years, households depended less on agriculture and earned more from migration and off-farm activities. The nominal value of total household income had increased almost 3 times, from 38 million to 97 million. Big changes in the structure of household income were observed. Agriculture remains one of the main livelihood activities of the household economy, with over 30% income increase each for crops and livestock. Agricultural activities related to paddy crops, potatoes, nuts farming did not show many changes. But household income has been largely increased from vegetables and other plants despite the many difficulties in cultivating vegetable. Meanwhile, livestock activities are operating under the impact of market prices as well as diseases. Although the number of households going into livestock breeding is decreasing, the scale of pig and poultry population, in particular, has increased. To reduce the risks in aquaculture, households have adopted the mixed model (shrimp, fish and crab) instead of the mono model (shrimp only) due to water quality issues. This transformation ensures that households can maintain safe operations, but the low net profit results in less contribution from this activity compared to ten years ago. Several modern models, which promise high economic efficiency gain, are in the process of being developed and transferred. Those could be seen as the potential method of aquaculture in the study site. A lot of households have been engaged in migration and, in fact, this strategy has contributed significantly to household reimbursement, supporting family members to find more suitable employment. However, the migration waves have also resulted in some rebound effects, including the labor shortage in the local region. Hence, industrial zones, which have brought many changes in livelihood strategy of the household, were established. With households using new machinery and technology in the agricultural sector, many of the population have found stable jobs with better salaries, balancing the choices of the population structure under the recent impact of migrating waves to the developed cities. More importantly, income from wages also increased significantly, further contributing to the reduction of the urban-rural gap in education as well as in the urbanization process. Lastly, based on the research findings, each livelihood activity still faces pressing difficulties and more vulnerabilities. By comparing the results of empirical studies, along with screening and in-depth assessment of the current state of internal and external aspects related to livelihood and trends, this study strongly proposes a package of recommendations as follows: 1. Strengthening capacity to adapt to Climate extreme events; 2. Mitigating the impacts of climate extreme events; 3. Adopting ecological innovations based on local knowledge under the support of multiple stakeholder levels; 4. Recultivation of aquaculture distribution and restriction of pond extension by issuing a certification of right to participate in this activity; 5. Applying Internet of Things in aquaculture; 6. Promoting the adoption of appropriate land use planning and management system; 7. Applying pest management platform for stored products; 8. Improving labor quality regarding migration strategy; and 9. Incentivizing the application of digital managements on migrants. [less ▲]

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See detailImpact of endophytic entomopathogenic fungi in Plant–aphid–virus relationships
Fingu Mabola, Junior Corneille ULiege

Doctoral thesis (2021)

Entomopathogenic fungi (EPF) are biological control agents widely used as alternatives to synthetic chemicals to protect plants against pests. Particularly, filamentous EPF are sometimes applied by ... [more ▼]

Entomopathogenic fungi (EPF) are biological control agents widely used as alternatives to synthetic chemicals to protect plants against pests. Particularly, filamentous EPF are sometimes applied by inundative method and are effective to control phloem-feeding insects, including aphids, most important vector of plant viruses. These EPF infect their hosts cutaneously, invade their internal cavity until death, then sporulate on the cadaver and spread to reach other insect hosts. Several studies have highlighted the endophytic behaviour of filamentous EPF. Indeed, they colonise plant tissues spending at least a part of their life cycle without symptoms appearance. Thus, several studies report that endophytic entomopathogenic fungi (EEPF) improves plant growth, enhance the immune system and interact with plant enemies including plant pathogens, insect pests, but also beneficials. The objective of this thesis was to evaluate the impact of EEPF on a vector-borne plant virus pathosystem. This, was based on the hypothesis that physiological changes in the plant as a result of EEPF colonisation of its tissues would have an impact on aphid (vector) behaviour and then influence the plant virus spread. Two pathosystems were used: (1) tobacco (Nicotiana tabacum L.), one of the host plants of potato leafroll virus (PLRV) transmitted by Myzus persicae Sulzer (Hemiptera: Aphididae) and (2) wheat (Triticum aestivum L.), host of barley yellow dwarf virus (BYDV) transmitted by Rhopalosiphum padi L. (Hemiptera: Aphididae); and two EPF species: (1) Beauveria bassiana GHA and (2) Metarhizium acridum IMI330189. The study was carried out in three research axis described in the following paragraphs. Previously, (1) the functioning of the plant–aphid–virus pathosystem was studied in order to identify the targets to be analysed in the context of the interaction between the pathosystem and the EPF. Then, the host-seeking behaviour (HSB), life history traits (LHT) and vectorial transmission efficiency (VTE) of the vector were selected for further investigations. Then, (2) experiments were conducted trying to inoculate the EPF on model plants of the pathosystems under study and techniques have been optimised. Knowing that the HSB of aphids justifies in large part their capacity to spread plant viruses, the first axis of the study aimed to evaluate the aphid behaviour when carrying or not carrying plant viruses in response to three plant modalities: healthy, virus-infected and EEPF-colonised. Choice tests in Petri dishes arena were carried out on the two pathosystems, but also sampling and analysis of volatile organic compound (VOC) profiles of the three plant modalities were performed in order to assess the aphid preferences observed during choice tests. We found that aphids were influenced by their infection status when choosing between virus-infected and non-infected plants. In contrast, aphids carrying and not carrying plant virus were all attracted to EEPF-colonised compared to non-colonised plants. Finally, the aphids that were not carrying plant virus had no preference between a virus-infected and an EEPF-colonised plant, whereas the aphids carrying plant virus maintained their choice on EEPF-colonised plants. The VOC analysis confirmed that the volatile profile emitted by the plants was altered as a consequence of EEPF colonisation in their tissues. In the second research axis, aphid life history traits when settled on EEPF-colonised host plant were evaluated. Furthermore, analyses were carried out to compare the efficacy of the systemic effect due to endophytism, the classical contact treatment of EPF and a potential interaction between the two modes of action and the infectious status of the plant virus vector. A synergistic effect between the presence of EEPF in plant tissues and the infectious status of the insect was found. Indeed, aphids carrying plant viruses were more vulnerable in relation with EPF treatment than those not carrying plant viruses. In addition, fecundity and mortality rate of nymphs were negatively and positively correlated with the EEPF-colonisation rate of leaf tissue, respectively. The third research axis focused on plant viruses spread on EEPF-colonised compared to non-colonised plants. The objective was to analyse the impact of EEPF on aphid vectorial competence in relation to its host plant and the plant virus it carries. Experiments implemented with the Tobacco – M. persicae – PLRV pathosystem consisted in releasing aphids on source plants previously inoculated with EEPF or not and then transferring them to EEPF-colonised or not-colonised recipient plants. Samples were collected in three incubation periods to assess the virus spread rate in the different plant treatments. We found that the rate of infection was low for EEPF-colonised plants at the early incubation time compared to not-colonised plants, and evolved over time to have similar results at the late incubation time. At the end of the experiment, almost all plants were positive for plant virus regardless of the treatment. This study is among the first to focus on the impact of the endophytic behaviour of EPF in a plant virus pathosystem, especially on plant virus spread. It provides interesting results on aphid behaviour in response to an EEPF-colonised plant, especially their host-seeking behaviour, their performance when settled on these plants and their ability to transmit virus on the same plants. [less ▲]

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See detailA Tale of Europe(anness): Interpretations of the "European State" in the Discourse of the Political Institutions of the European Union
Niessen, Annie ULiege

Doctoral thesis (2021)

Article 49 of the Treaty on the European Union enshrines that any “European State” may apply for membership in the European Union (EU). As a primary eligibility condition, the “European State” formulation ... [more ▼]

Article 49 of the Treaty on the European Union enshrines that any “European State” may apply for membership in the European Union (EU). As a primary eligibility condition, the “European State” formulation has defined the nature and scope of the EU since the inception of European integration. While the term “European” holds various meanings, there has been no clear definition in EU law of that which makes a state “European”. In the absence of such a definition, the EU political institutions – the European Commission, European Council, European Parliament, and Council of the European Union – have needed to interpret states’ European character amid, among others, membership requests. This thesis aims to investigate the various interpretations that have been provided by the EU political institutions amid European integration; in other words, it aims to tell a tale of Europe(anness), as the “European State” formulation is embedded in wider narratives and representations pertaining to the idea of Europe and Europeanness. Furthermore, the formulation is profoundly ingrained in processes such as enlargement legitimation, the EU’s self-understanding – or even perhaps collective identity – and the institutions’ construction of the public debate. Building on a corpus of various archival resources, the research uncovers four main interpretations of the “European State” formulation – and, by extension, of Europe(anness) – in the discourse of the EU political institutions. These are the geographical, cultural, historical, and political interpretations. Each interpretation is critically addressed by analyzing thematically and statistically its substance, and considering illustrative enlargement cases. The thesis is divided into six chapters. While Chapter 1 explores the legal logics surrounding the membership clause and the “European State” eligibility condition, Chapter 2 dives into the three contextual dynamics – Europe, Europeanness, and enlargement – in which this condition occurs. Chapter 3 engages in a critical review of the institutional interpretations previously identified by scholars, asserting the relevance of the representations and narratives in which these interpretations are firmly rooted. Chapter 4 details the theoretical and methodological frameworks of the thesis’s corpus-based thematic analysis of the four institutional interpretations, which are presented in Chapter 5. Finally, Chapter 6 offers statistical insights into the salience of the interpretations according to various aspects that further allow for a comprehensive understanding of the various dimensions surrounding the studied formulation. This thesis provides a comprehensive understanding of the “European State” formulation and the dynamics and logics surrounding notions of Europe(anness). It highlights how these notions have been constructed at the EU level and instrumentalized toward strategic and legitimation ends, relying on cherry-picked practices and on representations and narratives of Europe(anness) that percolate in the public space. Beyond the construction of the EU institutional discourse on Europe(anness) surrounding European integration, this thesis explores the complexity of the intertwined meanings underpinning the EU’s self-understanding, offering further insights into the fields of enlargement, European collective identity, and European integration. [less ▲]

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See detailIntervenir sur les édifices historiques en Belgique au XIXe siècle
Baudry, Antoine ULiege

Doctoral thesis (2021)

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See detailAppreciating the little things. Possibilities and challenges of stone tool residue analysis in reconstructing Late Pleistocene technologies.
Cnuts, Dries ULiege

Doctoral thesis (2021)

Stone tool residue analysis has been used for reconstructing different aspects of prehistoric human behaviour, including tool use and subsistence, in a wide range of geographical and chronological ... [more ▼]

Stone tool residue analysis has been used for reconstructing different aspects of prehistoric human behaviour, including tool use and subsistence, in a wide range of geographical and chronological settings since its initial development over forty years ago. Despite its frequent and versatile application and the potential it offers for better understanding past technologies and behaviours, residue analysis still suffers from methodological issues that mainly stem from an insufficient understanding of its possibilities and limitations. This study was designed to overcome some of these issues and to refine and reinforce the existing analytical methods in order to increase their interpretative power. The focus was here particularly on exploring the potential of optical microscopy and scanning electron microscopy in addressing the three crucial aspects of residue analysis: the identification of different residues, the attribution of the residues to different anthropogenic and natural processes, and the recognition of the impact of various taphonomic processes on residue preservation. Extensive experimentation and large-scale analysis of Late Pleistocene lithic material from six sites in Africa and Europe (Bushman Rock Shelter, Caours, Fumane Cave, Ifri n'Ammar, Les Cottés and Les Prés de Laure) were applied to reach these goals. The results provided valuable new data on stone tool production, hafting and use as well as site formation processes, and highlighted the need for a well-established theoretical and experimental framework in archaeological residue studies. The insights gained through the analysis of the experimental and archaeological material allowed concluding that residues are best studied using a flexible approach where optical microscopy plays a central role, where the initial hypotheses it provides are further investigated using methods selected for each case individually, and where use-wear data aids both in narrowing down research questions and analysed samples and in improving the reliability of residue interpretations. [less ▲]

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See detailLa vie comme concept et comme expérience de soi. Essai sur la genèse sensorielle de la conscience : Hegel – Plessner – Straus
Rizzo, Rémy ULiege

Doctoral thesis (2021)

Canguilhem a rappelé que la vie contient deux composantes majeures. Elle désigne d’abord la forme – l’a priori objectif – du corps en tant que vivant. Telle constitue la vie comme concept, dont les ... [more ▼]

Canguilhem a rappelé que la vie contient deux composantes majeures. Elle désigne d’abord la forme – l’a priori objectif – du corps en tant que vivant. Telle constitue la vie comme concept, dont les premiers développements remontent à Aristote. Par ailleurs, la vie traduit l’expérience d’une subjectivité en relation avec le monde ainsi qu’avec elle-même. Notre projet rend compte de l’unité de ces deux déterminations à l’aune de la manifestation de la vie. Helmuth Plessner, un des pères de l’Anthropologie philosophique, aborde le mouvement dialectique de cet a priori matériel tandis que le psychiatre et phénoménologue Erwin Straus assume la question de l’apparaître du sensible comme fond de l’expérience. Plessner restitue, à travers le concept de positionnalité, l’axiomatique des catégories de la vie grâce auxquelles est fondée la relation du Soi à son environnement extérieur d’après une légalité d’ordre transcendantal. Straus, de son côté, dévoile les lois psychologiques de la vie dont la principale réside dans l’épreuve corporelle du sentir et du se-mouvoir. Historiquement, c’est à Hegel que revient la paternité de notre paradigme. D’une part, il offre une riche description de l’expérience du Soi en tant qu’être charnel, tant au niveau humain qu’au niveau animal. D’autre part, il définit la vie comme forme immédiate de l’existence du Logos à titre de sens immanent de l’auto-organisation finalisée du vivant. Aussi, ambitionnant d’unifier la phénoménologie et l’approche spéculative de la vie, notre étude réhabilite les trois sciences que Husserl et Heidegger reléguèrent dans le champ ontique pour mieux en abolir leur portée fondatrice : la psychologie, l’anthropologie, et la biologie. Une appréhension dialectique de ces disciplines aura alors permis de répondre à la question que Fichte assigna à la métaphysique : Comment un être est-il pour nous possible ? [less ▲]

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See detailCaractérisation génétique, performances zootechniques et étude des mécanismes de la thermosensibilité du déterminisme environnemental du sexe des populations béninoises de Tilapia du Nil, Oreochromis niloticus
Fagbemi, Mohammed Nambyl Adéoti ULiege

Doctoral thesis (2021)

Au sein des vertébrés, les poissons présentent la plus grande diversité que ce soit dans leur structure génétique populationnelle, leur biotope, leur biologie, leur performance de croissance, leur mode de ... [more ▼]

Au sein des vertébrés, les poissons présentent la plus grande diversité que ce soit dans leur structure génétique populationnelle, leur biotope, leur biologie, leur performance de croissance, leur mode de reproduction jusque dans leurs systèmes de déterminisme du sexe. L’objectif de notre thèse est d’identifier une souche locale béninoise de tilapia du Nil (Oreochromis niloticus) présentant de bonnes performances de croissance et de reproduction pour le développement de l’aquaculture locale, ainsi qu’une thermosensibilité sexuelle suffisante pour pratiquer du monosexage mâle suivant une méthode plus respectueuse de l’environnement. Pour ce faire, nous avons travaillé en 4 étapes : Une caractérisation de la structure génétique des populations locales béninoises, Une étude de comparaison des performances de croissance et de reproduction des différentes populations locales, Une étude comparative de la thermosensibilité sexuelle des populations, Une étude transcriptomique (RNA-seq) pour investiguer et expliquer les mécanismes impliqués dans cette thermosensibilité. Grâce à la technologie des SNPs, nous avons caractérisé la structure génétique de 13 populations de O. niloticus collectées dans les bassins hydrographiques du Mono, l’Ouémé, la Volta, dans les fermes d’élevage du CRIAB et Yohan-Esteve au Bénin puis dans le Centre de Formation et de Recherche d’Aquaculture de Tihange en Belgique. Cette étude a permis d’identifier la population de Nangbéto du bassin du Mono comme celle étant la plus différenciée comparativement aux autres populations. La population de la ferme CRIAB était génétiquement proche de la population sauvage de la Pendjari du bassin de la Volta tandis que les populations de la ferme Yohan-Esteve avaient une proximité génétique avec les populations de Togbadji, Djonougoui et Toho du Mono et de Gbassa du bassin du Niger. Sur base de ces résultats, nous avons sélectionné cinq populations représentatives pour la suite de notre étude : Nangbéto, Sohoumè et Togbadji (Mono), Gbassa (Niger) et Gobé (Ouémé). Ces cinq populations ont fait l’objet d’une étude visant à identifier les populations les plus thermosensibles, puis à étudier l’expression des gènes impliqués dans le déterminisme et la différenciation sexuelle. Vingt progénitures issues de ces populations ont été soumises à une température de masculinisation (36,5°C) de 10 à 30 jours post-fécondation (jpf). Les sexages effectués à 90 jpf ont montré que les populations de Sohoumè, Togbadji et Gobé étaient les plus thermosensibles. Des prélèvements de têtes et de gonades effectués à 15 et 40 jpf ont permis d’étudier des gènes différentiellement exprimés (DEG), différentiellement épissés (DSG), corrélés avec le taux d’inversion (Corr), les termes d’ontologie des gènes associés et les voies de signalisation KEGG impliquées dans la cascade de réactions génétiques conduisant à l’inversion du sexe chez cette espèce. Il ressort de cette étude qu’il existe un groupe de gènes exprimés dans les gonades (abhd4, kmt5c, aebp2), susceptibles d’être impliqués à travers le phénomène d’apoptose dans la résistance de certaines femelles à l’inversion du sexe et dans la différenciation sexuelle. Aussi dans les têtes, les gènes jarid2b, serpin2, crabp2b et psmd10 ont été identifiés comme étant potentiellement impliqués dans la différenciation testiculaire et dans la stimulation du développement des spermatogonies. L’étude des performances de reproduction et de croissance des cinq populations a permis de montrer que les populations de Sohoumè et de Togbadji présentent les meilleures performances de reproduction et de croissance comparativement aux populations de Nangbéto, Gbassa et Gobé. Globalement, nous pouvons conclure que les populations de Sohoumè et Togbadji se révèlent être les plus intéressantes d’un point de vue zootechnique pouvant faire l’objet d’un programme de sélection pour le développement d’une souche d’élevage au Bénin. Grâce à l’étude de la thermosensibilité et de transcriptomique, nous avons identifié pour la première fois un groupe de gènes qui semble être impliqué dans la différenciation sexuelle par le phénomène d’apoptose cellulaire et dans la stimulation de la prolifération des spermatogonies. [less ▲]

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See detailMethods and applications for forensic odor profiling
Dubois, Lena ULiege

Doctoral thesis (2021)

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See detailAlcohol Organosolv Pretreatment: Toward an Efficient Lignin Extraction
Schmetz, Quentin ULiege

Doctoral thesis (2021)

Context: For several decades now that an increasing amount of research has emrged from a common interest to face the fossil-fuels reserves depletion and the greenhouse gas emission increase. This context ... [more ▼]

Context: For several decades now that an increasing amount of research has emrged from a common interest to face the fossil-fuels reserves depletion and the greenhouse gas emission increase. This context has given rise to a growing interest to move from an oil economy towards a sustainable and circular bio-based economy. One of the solutions is to replace part of the fossil resources by renewable ones based on lignocellulosic biomass. The development of biorefineries, using plant material that does not compete with food/feed (lignocellulose) to produce bio based products (biofuels and biomaterials), is in constant evolution. In order to break the complex structure and allow the use of lignocellulosic biomass, an additional fractionation step called pretreatment is necessary before valorizing its constituents. Organosolv treatment, fractionation processes using organic solvent, are among the most promising strategies for valorising lignocellulosic biomass and could facilitate the transition towards efficient utilization of renewable feedstocks. Scientific research: The present thesis aims at broadening the knowledge and opening new perspectives in terms of Organosolv treatment with alcohol in order to extract a lignin with high valorization potential. In particular, it allowed to study an emerging strategy constituted by a sulfuric acid (H2SO4) catalyzed process in a biphasic system using a hydrophobic alcohol (n-butanol) and water. Therefore, the first exploratory work focuses on a conventional organosolv using high ratio of ethanol to dissolve lignin from a crop dedicated for biofuel production: tall fescue. This “lignin-first” approach was limited as it seriously degraded cellulose, produced non-fermentable sugars derivatives and required large amount of water to recover lignin. The second work opens perspectives for improvements in terms of efficiency of lignocellulosic fractionation on the one hand, and on the other hand on the possibility of recycling the solvent and the isolation of the products solubilized in the "liquor". The butanol/water biphasic system was proposed and studied on six different biomasses in order to assess to what extend the process was suitable on a wide variety of heterogeneous biomasses as versatility of process being of great importance. The process is efficient in term of delignification and improves enzymatic saccharification significantly, however, Japanese cedar was too recalcitrant.   Furthermore, the lack of knowledge regarding lignin partition in butanol/water biphasic systems constituted a major limitation for further optimization. The third work is focused on the study of the partition in “aqueous/hydrophobic organic solvent” of three technical lignins originating from various biomasses (grass, hardwood, softwood). They were performed in aqueous/alcohol systems of varying pH and organic phase. Partition coefficients and analyzes of recovered fractions were investigated. Among the investigated alcohols, n-butanol is viewed as a promising solvent for lignin separation considering its ability to solubilize a wider range of lignin polymer. Results provide valuable information regarding the chemical structure and polymer size of recovered lignin based on the setting of medium parameters. This will be helpful for both separation of homogenous lignin fractions from pulp & paper industries and biorefineries byproducts and to understand solubility and partition mechanisms of lignin in pretreatment performed in biphasic systems. A fourth and final work explores the possibilities of optimizing butanol treatment on Japanese cedar. The recovery of butanol after treatment as well as several parameters (solid/liquid ratio, butanol/water ratio, temperature, time, type of acid catalyst...), were investigated. The solid/liquid and butanol/water ratios appear to be the most important factors in the opitimization of the treatment. Moreover, the addition of an acid hydrolysis catalyst (Lewis acid) FeCl3 gives promising results. Conclusion and perspectives: The development of a biphasic process allowed the separation of high purity cellulose, the hydrolysis of hemicellulose and the recovery and isolation of lignin, in three distinct phases. The “in-situ” homogenization of the lignin structure by varying the extraction/solubilization conditions appears promising. The treatment has good perspectives in terms of solvent recycling and is effective in destabilizing the biomass for subsequent saccharification (and potential valorization into biofuel). Several improvements can be envisaged, namely: the implementation of a (semi-)continuous process and further optimization of the softwood fractionation to increase its versatility, in particular by investigating Lewis acids (e.g. FeCl3). Finally, the economic viability of the process should be thoroughly evaluated, by promoting the cascade valorization of the whole plant and maximizing the potential of each component (cellulose, furanic derivatives, lignin, secondary metabolites...). [less ▲]

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See detailCaractérisation fonctionnelle du facteur d’épissage SR45 d’Arabidopsis thaliana
Fanara, Steven ULiege

Doctoral thesis (2021)

Les protéines SR constituent une famille de facteurs d’épissage conservés chez les eucaryotes multicellulaires. Elles sont qualifiées d’essentielles pour assurer les processus épissage (constitutif et ... [more ▼]

Les protéines SR constituent une famille de facteurs d’épissage conservés chez les eucaryotes multicellulaires. Elles sont qualifiées d’essentielles pour assurer les processus épissage (constitutif et alternatif) par l’influence qu’elles ont sur le choix des sites d’épissage le long du pré-ARNm. Ces protéines présentent une organisation modulaire comprenant un à deux domaines de liaison à l’ARN (RRM, pour RNA recognition motif) généralement en position N-terminale et un domaine riche en dipeptides sérine/arginine (SR) ou arginine/sérine (RS) en position C-terminale. Certaines protéines SR bénéficient d’une dynamique nucléocytoplasmique et sont connues pour jouer des rôles additionnels dans le traitement de l’ARN (pré-)messager chez les mammifères, incluant la transcription, l’export de l’ARNm, la surveillance de la « qualité » (maturation) de l’ARNm et le contrôle de la traduction. Les travaux antérieurs au laboratoire ont montré que le génome d’Arabidopsis thaliana présente 19 gènes encodant des protéines SR réparties en 7 sous-familles. Dans le cadre de cette thèse de doctorat, nous avons entrepris l’étude fonctionnelle de la sous-famille SR45, qui ne comprend qu’un seul gène chez A. thaliana et dont le pré-ARNm produit deux protéines fonctionnellement distinctes par épissage alternatif. SR45 serait l’orthologue de la protéine animale RNPS1. Le mutant perte-de-fonction sr45-1 présente un retard de développement des parties aériennes et racinaires, un délai de la floraison et un nombre anormal d’organes floraux. De nombreuses études fonctionnelles ont mis en évidence l’implication de ce facteur dans la régulation de la biogenèse et de la signalisation de l’acide abscissique (ABA), dans les réponses immunitaires ou encore dans le contrôle de mécanismes épigénétiques. Elle participerait à la formation de l’EJC (exon-exon junction complex) et, conséquemment, à la dégradation des ARNms non-sens (NMD, nonsense-mediated decay). Nous avons tout d’abord étudié chez des lignées transgéniques le profil d’expression de ce gène SR (fusion transcriptionnelle pSR45:EGFP), qui se démarque dans les embryons, les plantules, les tissus à croissance rapide et les inflorescences (gynécée, androcée, calice et corolle). Ce profil d’expression se corrèle aux expériences de quantification des ARNms (qRT-PCR) réalisées sur les différents organes de la plante, ainsi qu’à l’étude de la localisation protéique par fusion traductionnelle à l’EGFP (enhanced green fluorescent protein). La méta-analyse de l’enrichissement fonctionnel des substrats ARN de SR45 nous a permis de mettre en évidence le rôle potentiel de cette protéine dans la régulation de l’homéostasie du fer. Nous nous sommes donc concentrés sur l’étude et la caractérisation du mutant sr45-1 lors de conditions hydroponiques déplétées et supplémentées en fer, mettant en évidence de profondes perturbations de l’homéostasie du fer chez le mutant (notamment au niveau racinaire et dans la production de siliques et graines). En effet, le mutant sr45-1 tend à accumuler des fortes concentrations en fer dans les racines, résultant subséquemment en l’émergence de stress oxydatifs. Cette accumulation racinaire de fer s’accompagne d’une diminution de la concentration en fer dans les parties aériennes accompagnée d’une chlorose accrue. Nous avons également constaté que le mutant sr45-1 présentait des phénotypes aggravés lorsqu’exposé à des concentrations accrues de cuivre ou de cadmium (résultats non publiés). Nous nous sommes ensuite intéressés au réseau d’interaction protéine-protéine que SR45 établit grâce à des expériences de double-hybride en levures, avec comme point focal l’élucidation de sa possible intervention dans l’édification de l’EJC – un rôle particulièrement bien étudié chez son orthologue métazoaire (RNPS1). Certaines des interactions identifiées ont été par la suite confirmées in planta. Pour étayer davantage l’étude de ce facteur d’épissage, nous avons également poursuivi l’identification de motifs ARN reconnus par le domaine RRM, et ce grâce à des approches de SELEX (systematic evolution of ligands by exponential enrichment). Nous avons conclu que le domaine RRM de SR45 reconnaît deux motifs ARN. [less ▲]

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See detailEssays on Exports and Investment in Vietnam
Nguyen Thi Phuong Thao, ULiege

Doctoral thesis (2021)

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See detailSelective disruption of histone deacetylase complexes by small-molecule inhibitors of protein interactions
Olivet, Julien ULiege

Doctoral thesis (2021)

This thesis is divided into four chapters, including an introduction, and three research articles. Chapter one positions this work in the context of the druggability of protein-protein interactions (PPIs ... [more ▼]

This thesis is divided into four chapters, including an introduction, and three research articles. Chapter one positions this work in the context of the druggability of protein-protein interactions (PPIs) and inhibition of histone deacetylase (HDAC) complexes. Chapter two describes a framework to maximize PPI detection by combining a minimal number of binary interaction assays. It also describes the development of a versatile assay, NanoLuc 2-Hybrid (N2H), to test PPIs in different experimental conditions to recover as many interactions as when various assays are combined. This chapter appears as published in Nature Communications 10:3907 (2019). Chapter three demonstrates the ability of binary interaction assays to comprehensively map directly interacting subunits within multiprotein complexes supported by 3D structures. It also positions binary PPI assays as powerful complementary tools to increase the resolution of affinity purification-mass-spectrometry (AP-MS)-based maps, by systematically distinguishing direct interactions from indirect associations within complexes. Chapter four describes the functional disruption of the yeast S. cerevisiae Rpd3L histone deacetylase (HDAC) complex by small molecules, and exploits findings from chapters two and three to test compounds against binary PPIs between subunits of the complex. In particular, it presents the discovery and validation of a functional inhibitor that does not affect HDAC enzymatic activity, but rather acts by binding to a large scaffold protein, ultimately inhibiting its interactions with transcription factors at specific chromosomal loci. The pieces of evidence presented in this chapter also suggest the mode of action of the PPI inhibitor is conserved in human cells and in mice since it confers physiologically-relevant phenotypes (e.g. antipsychotic effect) identical to that of wellestablished enzymatic inhibitors, or knockouts of the catalytic HDAC component, while perturbing expression of an order of magnitude fewer genes. Our results highlight the potential clinical relevance of such higher-selectivity HDAC complex PPI inhibitors. [less ▲]

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See detailCaractérisation de RBcel1: une endoglucanase dotée d'activité transglycosylase
Collet, Laetitia ULiege

Doctoral thesis (2021)

The role of glycans in biological processes has raised awareness of oligosaccharides and glycoconjugates as important therapeutic targets for a wide range of diseases. Despite the technological ... [more ▼]

The role of glycans in biological processes has raised awareness of oligosaccharides and glycoconjugates as important therapeutic targets for a wide range of diseases. Despite the technological advancement over the last decades, the diversity and complexity of these glycans remain a major challenge to their production. In nature, the synthesis of glycans is generally attributed to glycosyltransferases (GTs), which carry out the formation of most glycosidic bonds. Their use on an industrial scale, however, is limited because they are often difficult to produce and require activated sugars as substrates. Although glycoside hydrolases (GHs) are generally associated with the hydrolysis of plant biomass, some of them are also able to catalyze the synthesis of glycosidic bonds from simple saccharides via transglycosylation. The ability of GHs to transglycosylate has aroused interest in glycan synthesis as these enzymes are abundant and cover a wide range of substrate specificity. The overall mechanism of transglycosylation is well known and follows the same reaction scheme as hydrolysis. After a first step called glycosylation, the donor sugar is covalently bound to the enzyme. Transglycosylation occurs when a hydroxyl group of an acceptor sugar is used instead of a water molecule in the deglycosylation step. Most transglycosylating GHs can therefore perform both reactions, but their transglycosylation yield is reduced since the newly formed products are concomitantly hydrolyzed. Although knowledge about transglycosylating GHs is still increasing, there is no unique strategy to direct to transglycosylation yield. Thus, obtaining efficient enzymatic tools for glycan synthesis using GHs remains dependent on a better understanding of the molecular factors controlling the balance between hydrolysis and transglycosylation. This work aims to show such factors through the enzymatic and structural study of RBcel1, a family 5 GH endowed with transglycosylase activity. The main goal of this work is to perform an in-depth study of the catalytic mechanism in RBcel1 via the identification of residues involved in catalysis as well as in substrate binding. Several variants of the enzyme were characterized to understand the roles attributed to different residues of the active site, in both catalysis and transglycosylation. The structural study of these variants allowed to obtain the structure of different reaction intermediates allowing to identify residues involved in the binding of substrate and, potentially, transglycosylation. The results obtained in this work confirm partly some widely known mechanistic elements. They also highlighted new elements in the catalytic mechanism such as the key role of the non-catalytic residue tyrosine 201 in glycosylation and deglycosylation. Furthermore, this study presents a novel method to trap reaction intermediates in the presence of natural substrates while maintaining the catalytic residues. Different elements influencing transglycosylation have been highlighted, such as the size of the acceptor sugar or the reaction medium pH. The latter offers interesting perspectives for orienting the reaction towards transglycosylation since transglycosylation products tend to accumulate at basic pH. [less ▲]

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See detailPredicting the dynamics of range shifts under climate change: assumptions and applications to the European bryophyte flora
Collart, Flavien ULiege

Doctoral thesis (2021)

Climate change has and will have a dramatic impact on species ranges. Terrestrial species have accordingly already migrated poleward at a median speed of 16.9km per decade since the beginning of the ... [more ▼]

Climate change has and will have a dramatic impact on species ranges. Terrestrial species have accordingly already migrated poleward at a median speed of 16.9km per decade since the beginning of the industrial era. However, many species are not equipped to efficiently track the geographic changes of the conditions matching their climatic niche, and are consequently prone to extinction. No less than about 20% of land plant species are hence threatened with extinction in the future, with major consequences on human food resources and health. In this context, Species distribution models (SDMs) offer an appealing framework to test the potential effects of climate change on species ranges. Like many biodiversity analyses, SDMs have traditionally been conducted at the species level. Cryptic speciation, which results in taxa that cannot rapidly be distinguished morphologically, but underwent divergent evolutionary histories, has been, however, increasingly reported, raising the question of whether SDMs should be fitted at the level of species (clade models), cryptic species or intraspecific lineages (subclade models). Projecting models through time further raises several questions and relies on several assumptions. In particular, projecting species potential ranges in the future based on their niche inferred from extant climate conditions onto future climatic layers involves that (I) species climatic niches are conserved through time (niche conservatism hypothesis) and that (ii) species are at equilibrium with their environment (i.e. their entire niche is filed), implying that they are not limited by their dispersal capacities, and are immediately able to colonize any newly suitable area. Focusing on bryophytes, whose ecophysiological characteristics, such as poikilohydry and reliance on rainfall for water uptake, make them excellent candidates to study the impact of climate change, but which exhibit reduced morphologies, raising concerns about broadly defined morphological species concepts, we address here the following questions: 1 At which taxonomic level should SDMs be computed? We compare the extent to which model projections generated at the level of species differ from those obtained for intraspecific lineages. Modelling at the level of infraspecific lineages raises a second issue, which is associated with the very small sample sizes that typically characterize molecularly defined lineages, that is: how can ensemble of small models calibrated from very small datasets be evaluated? In the light of analyses of niche overlap, we finally determine whether models should be calibrated at the level of the species or intraspecific lineages. 2 Is there climatic niche conservatism in bryophytes, and how does the tendency for closely related taxa to share the same climatic niche vary at increasing taxonomic depth? 3 To what extent will such efficient dispersers as bryophytes successfully track the shift of their suitable areas during the next decades? To address Q1, Ensembles of Small Models were evaluated by null models calibrated from randomly sampled presence points. We compared the extent of suitable area predicted by the projections of clade and subclade models. Niche overlaps were quantified using Schoener's D and Hellinger's I metrics, and the significance of these metrics in terms of niche conservatism or divergence was assessed by niche similarity tests. Combined predictions from subclade models contributed, on average, five times more than clade models to the total suitable area predicted by the combination of both subclade and clade models. Niche overlap was 0.71 on average, with evidence for niche conservatism in half of the species and no signal for niche divergence. Given the poor performance of models based on small datasets, we pragmatically suggest that, in the absence of evidence for niche divergence during diversification of closely related intraspecific lineages, SDMs should be based on all available occurrence data at the species level. The hypothesis of climatic niche conservatism and its evolutionary ‘labillity’ was further tested at the level of an entire phylum of land plants, the Marchantiophyta, through analyses of the relationship between the spatial turnover of floras and macroclimatic variation. Phylogenetic turnover among floras was quantified through πst statistics. πst-through-time profiles were generated at 1 myr intervals along the phylogenetic time-scale and were correlated with current geographic distance and macroclimatic variation with Mantel tests based on Moran spectral randomization to control for spatial autocorrelation. The contribution of macroclimatic variation to phylogenetic turnover was about four-times higher than that of geographic distance. The correlation between phylogenetic turnover and geographic distance rapidly decayed at increasing phylogenetic depth, whereas the relationship with macroclimatic variation remained constant until 100 myrs. Our analyses reveal that changes in the phylogenetic composition among liverwort floras across the globe are primarily shaped by macroclimatic variation. They demonstrate the relevance of macroclimatic niche conservatism for the assembly of liverwort floras over very large spatial and evolutionary time scales, which may explain why such a pervasive biodiversity pattern as the increase of species richness towards the tropics also applies to organisms with high dispersal capacities. Finally, we developed a newly designed spatially-explicit model of dispersal by wind in the context of changing climate and presented an example of application in the case of the European flora. A grid of pixel-specific environmental conditions and dispersal kernels, combining information on species dispersal traits, local wind conditions, as well as landscape features affecting dispersal by wind, was generated and used as input in simulations of species dispersal in the landscape under changing climate conditions. In European bryophytes, the median ratios between predicted range loss vs expansion by 2050 across species and climate change scenarios ranged from 1.6 to 3.3 when only shifts in climatic suitability were considered, but increased to 34.7–96.8 when species dispersal abilities were added to our models. This highlights the importance of accounting for dispersal restrictions when projecting future distribution ranges and suggests that even highly dispersive organisms like bryophytes are not equipped to fully track the rates of ongoing climate change in the course of the next decades. [less ▲]

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See detailStray light control in space instruments: overcoming the conventional limits
Clermont, Lionel ULiege

Doctoral thesis (2021)

Stray light is a critical problem for space telescopes. It these aspects could be solved, we could develop space instruments with far better performances. This would open the door to new applications and ... [more ▼]

Stray light is a critical problem for space telescopes. It these aspects could be solved, we could develop space instruments with far better performances. This would open the door to new applications and scientific discoveries, from monitoring Earth atmosphere composition better than ever to observing fainter objects in the galaxy. This work aspired to solve this problem. It started by the application of state of the art methods of control by design, then new approaches were proposed to overcome the conventional limits. One of them consists in removing complex stray light features by post-processing, where an improvement by two orders of magnitude is demonstrated. Next, a major limitation of traditional approaches is the inability to measure and identify individual stray light contributors in an instrument. Ultrafast time-of-flight characterization is introduced to solve this decades-old problem, enabling unprecedented understanding and control of stray light in space telescopes. [less ▲]

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See detailGeneralized sweeping preconditioners for domain decomposition methods applied to Helmholtz problems
Dai, Ruiyang ULiege

Doctoral thesis (2021)

The main part of this thesis explores a family of generalized sweeping preconditionners for Helmholtz problems with non-overlapping checkerboard partition of the computational domain. The domain ... [more ▼]

The main part of this thesis explores a family of generalized sweeping preconditionners for Helmholtz problems with non-overlapping checkerboard partition of the computational domain. The domain decomposition procedure relies on high-order transmission conditions and cross-point treatments, which cannot scale without an efficient preconditioning technique when the number of subdomains increases. With the proposed approach, existing sweeping preconditioners, such as the symmetric Gauss-Seidel and parallel double sweep preconditioners, can be applied to checkerboard partitions with different sweeping directions (e.g. horizontal and diagonal). Several directions can be combined thanks to the flexible version of GMRES, allowing for the rapid transfer of information in the different zones of the computational domain, then accelerating the convergence of the final iterative solution procedure. Several two-dimensional finite element results are proposed to study and to compare the sweeping preconditioners, and to illustrate the performance on cases of increasing complexity. [less ▲]

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See detailModelling the hydrodynamics and sediment transport in the Southern Bight of the North Sea for assessing offshore wind farms impacts on the sedimentary environment
Ivanov, Evgeny ULiege

Doctoral thesis (2021)

This PhD thesis is devoted to the study of the environmental impact of artificial marine structures, such as offshore wind farms (OWF), on the bottom deposition of organic and inorganic matter. This study ... [more ▼]

This PhD thesis is devoted to the study of the environmental impact of artificial marine structures, such as offshore wind farms (OWF), on the bottom deposition of organic and inorganic matter. This study aims to connect the local and regional scales using numerical modeling. Living on the foundations of turbines, filter feeders (like the blue mussel) filter suspended particulate matter (SPM) from the water column to produce fecal pellets, rich in carbon, that sink to the bottom. Thus, through biodeposition, fouling organisms living on wind turbines are able to modify the distribution of the carbon flux to the bottom, and the distribution of organic matter and the oxygen consumption in the sediment. Quantification of local effects at the scale of the Southern Bight of the North Sea (SBNS) is necessary within the framework of European strategies of the Blue growth and protection of biodiversity. A hydrodynamic model of the SBNS coupled with a sediment and wave model (COAWST) has been developed. This model has been extended with a model representing the filtration and biodeposition by fouling filter feeders. The model covers the entire SBNS with a coarse resolution (CR) of 5 km while the Belgian coastal zone (BCZ) is covered by a high resolution (HR) model of 1 km. The HR model is forced at the borders by the CR model, while the results of the latter at the level of the BCZ are updated with the results of the HR model. Model simulations of hydrodynamic variables including tides and waves and sediments have been validated against existing data for the region. The impact of variability of atmospheric conditions and tidal regimes on variability of hydrodynamics has been analyzed. This validation effort has shown that the HR model has better performance for the simulation of residual currents, the extension of the river plume and the variability in response to atmospheric forcings and tidal regimes. However, the CR model has better performance for the simulation of overtidal constituents. Regarding the impact of the biodeposition by fouling organisms on the flux of sedimentary particles, it has been shown that the impact of fouling fauna extends beyond the boundaries of the OWFs with an increase in the flux of sedimentary carbon (up to 50%) near (< 5 km) turbines and a slight decrease up to 30 km away. The model has then been used to provide recommendations on the design of a new OWF planned in a new concession area (NCA), located near a site of the Natura 2000 network according to the Marine Spatial Plan 2020. In particular, the impact of the number and position of turbines on the carbon flux to the sediment has been simulated. Placing the NCA turbine foundations over the protected gravel beds of the Natura 2000 network would result in a drastic increase (> 50%) in carbon deposition on them; while if turbines were placed at least 2 km away, the increase in carbon deposition would only be about 10%. The number of turbines plays a marginal role in altering the biodeposition flux. [less ▲]

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See detailSoil-plant silicon dynamics in natural ecosystems and agroecosystems
de Tombeur, Félix ULiege

Doctoral thesis (2021)

Silicon (Si) is widely recognized as an important regulator of the global carbon (C) cycle via its effect on diatom productivity in oceans, and as a beneficial plant nutrient, improving resistance to ... [more ▼]

Silicon (Si) is widely recognized as an important regulator of the global carbon (C) cycle via its effect on diatom productivity in oceans, and as a beneficial plant nutrient, improving resistance to herbivory and pathogens and mitigating the negative effects of several abiotic stresses. This thesis explores the long-term dynamics of Si in terrestrial ecosystems, and investigates some factors driving soil-plant Si dynamics in agroecosystems. The main study sites are three 2-million-years dune chronosequences located on a climatic gradient in southwestern Australia. Within a chronosequence, plant productivity is limited by nitrogen (N), then by phosphorus (P), as soils age. We show that soil Si dynamics is primarily driven by geochemical processes in young and middle-aged soils (carbonates dissolution, clay formation, quartz enrichment), but increasingly by biological processes (silica formation in plants followed by its dissolution in soils) in old and highly-weathered soils. A climate-driven increase in biomass production along the climatic gradient seems to enhance this biological Si feedback loop. Besides, the continuous increase in community-level leaf Si concentrations with increasing soil age and P depletion might reflect the importance of silica-based defenses in P-poor environments. This increase is associated with a decrease in leaf total phenol concentrations, suggesting a tradeoff between both defense strategies along N-P gradients. We also propose that the increase in nutrient-acquisition carboxylate-releasing strategies with increasing soil age might explain the increase in leaf Si concentrations, with carboxylates not only mobilizing rhizosphere P, but also Si. Based on the above results and a literature review, we then summarized the biotic and abiotic controls on soil Si dynamics, and wondered whether they could be exploited in agroecosystems. We particularly stress the importance of mycorrhizal associations, silicate-solubilizing bacteria, soil macrofauna, root exudates and large herbivores on soil-plant Si dynamics. These ecological processes might in turn be exploited in cereal-legume intercropping, cover crops implementation, or integrated crop-livestock systems. We finally demonstrate that soil properties and recycling crop residues strongly influence the foliar silicification and its beneficial effects for two crop species (rice and sugarcane) through two case studies in Burkina Faso and Guadeloupe, respectively. This thesis highlights the major influence of soil age and weathering degree on soil-plant Si dynamics, from both a biogeochemical and ecological perspective, and demonstrate that knowledge from complex natural systems might help to improve the Si-use efficiency and subsequent sustainability of modern agroecosystems. Besides, this thesis stresses the need to develop multidisciplinary approaches to better understand elements mobility in natural ecosystems and agroecosystems. [less ▲]

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See detailFatigue Assessment of Hydraulic Steel Structures
Dang Van Thuong, ULiege

Doctoral thesis (2021)

This research consists of assessing and updating the remaining fatigue life of hydraulic steel structures when a fatigue crack has been discovered or is postulated. Due to constraints linked to inspection ... [more ▼]

This research consists of assessing and updating the remaining fatigue life of hydraulic steel structures when a fatigue crack has been discovered or is postulated. Due to constraints linked to inspection practices, cracks are generally rather large when detected. The research aim is to provide an optimum planning of repairs, in the best conditions for different input data. The study targets optimization of inspection schedule based on probability of failure, repair policies and cost of repairs. Risk-based inspection and maintenance of a hydraulic steel structure are performed based on a critical component or multiple critical components. The study provides an innovative approach for calculating the reliability of hydraulic steel structures, giving strategies and solutions to mitigate risk under corrosion and fatigue fracture failure. The influence of general corrosion and pitting corrosion for assessing and updating the remaining fatigue life of hydraulic steel structures are included in this research. [less ▲]

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See detailOn the k-binomial equivalence of finite words and k-binomial complexity of infinite words
Lejeune, Marie ULiege

Doctoral thesis (2021)

Complexity functions are well-studied objects in combinatorics on words. They encode some information about an infinite word: they count, for every non-negative integer n, the number of factors of length ... [more ▼]

Complexity functions are well-studied objects in combinatorics on words. They encode some information about an infinite word: they count, for every non-negative integer n, the number of factors of length n present in the infinite word. One may take variations of the classical factor complexity, by counting not all factors, but only those which are different enough one from the other. To this aim one can define an equivalence relation and count, for any n, the number of equivalence classes among all factors of length n of a given infinite word. In this thesis we are interested into the k-binomial equivalence and its associated complexity. This latter equivalence involves the notion of binomial coefficient of words, counting, given two words u and x, the number of times (u,x) that x appears in u as a subword. Two words u and v are k-binomially equivalent if (u,x)= (v,x) for every word x of length up to k. In this manuscript we first count the number of k-binomial equivalence classes and give an algorithm generating the 2-binomial class of a finite word. We also show that the monoid A^* / ~2 is isomorphic to the submonoid, generated by A , of the nil-2 group N_2 (A) . We then compute the exact values of the k-binomial complexity of the Thue–Morse word and the Tribonacci word, and we discuss the techniques employed, in an aim of generalizing it to larger families of words. Finally, we study a variant of the classical reconstruction problem and show that, proceeding in a sequential way, knowing n/2 + 1 well-chosen binomial coefficients is sufficient for reconstructing any binary word of length n. We also treat the case of an arbitrary alphabet and show that our bounds are better than what was known in the classical reconstruction case. [less ▲]

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See detailThermal Properties and Molecular Conformation of Peanut Protein Fractions and Its Application
Liu, Li ULiege

Doctoral thesis (2021)

Peanut proteins have been widely used as an important ingredient in food products, due to its high nutritional value, functional properties, and low cost. Arachin and conarachin, the major component of ... [more ▼]

Peanut proteins have been widely used as an important ingredient in food products, due to its high nutritional value, functional properties, and low cost. Arachin and conarachin, the major component of peanut proteins, which account for about 90% of total seed proteins is responsible for functional properties of peanut proteins. Although it is known that different protein subunit compositions contribute to different protein properties, and that heat treatment is a widespread unit operation in the food industry, there are only very few studies on structure and properties characterization of arachin and conarachin with different subunit compositions during thermal processing. In order to contribute to this knowledge, the aim of this work was to study the subunit composition, thermal properties and interfacial properties of peanut protein fractions and their application in film formation. Firstly, the effect of heat treatment on secondary structure and interfacial properties of arachin and conarachin were analyzed by infrared spectroscopy, circular dichroism and Langmuir trough technique. For native sample, arachin mainly consist of β-sheet structure, α-helix, random coil while conarachin is predominantly composed by α-helix and β-sheet. With the temperature increasing, arachin shows a decrease of sheet structure while for conarachin, the component of secondary structure was changed irregularly with temperature. The shape of the compression isotherm recorded for arachin is typical of liquid expanded monolayers, while for conarachin, the isotherm exhibits the typical phase transition from liquid expand state, to liquid condensed state, and solid state. Arachin seemed more stable to temperature treatment than conarachin. Secondly, in order to get more information on arachin, the subunit composition and the thermal stability, steady flow properties, surface hydrophobicity and sulfhydryl content of arachin from six peanut varieties were determined. Two groups of arachin were identified: one containing the 35.5kDa subunit, was more heat-sensitive (Tonset <100℃), had a significant lower initial denaturation temperature, less disulfide bonds and more hydrophobic groups; and the other one without this specific subunit, was less heat-sensitive to temperature, and presented a more compact globular structure. The presence or absence of the 35.5kDa subunit in arachin significantly influenced the thermal and conformation properties of arachin. Furthermore, the 35.5 kDa subunit was sequenced by quadrupole-time of flight and identified as an isoform of Ara h3. Thirdly, Thermal properties and molecular conformation of two types of arachin was further evaluated. The surface hydrophobicity and sulfhydryl content were determined, the protein interactions were characterized by SDS-PAGE electrophoresis, and the molecule size was measured by SEC-MALLS. Heat treatment at 90 ℃ induced an increase in surface hydrophobicity and sulfhydryl groups due to a partial unfolding of the peanut protein structure and the formation of aggregates linked by disulfide bonds. While heat treatment at 120℃ led to lower surface hydrophobicity due to intramolecular hydrophobic binding of protein lateral chains and burying of the sulfhydryl groups inside the protein. The presence of the 35.5 kDa subunit or not of arachin showed the different molecular structure upon heat treatment, arachin without 35.5 kDa subunit exhibited a more compact structure and a higher ability to suppress the thermal processing than did arachin with 35.5kDa subunit. Then, a protocol for the 35.5 kDa subunit purification from arachin was developed. Secondary structure and interfacial properties of the arachin subunit upon heat treatment were investigated using circular dichroism and Langmuir trough technique. Heating resulted in a decrease of α-helix content in the subunit with a corresponding increase in random coil. It also led to a decrease in surface pressure of the monolayer film indicating a decrease of the interfacial stability, a similar trend to the one observed for arachin. Finally, in order to evaluate the film forming property of peanut protein, the structure and mechanical properties of peanut protein isolates film, and the effects of xylose content on protein film were analyzed. According to the above results, heat treatment at 90℃ is beneficial for structure unfolding of protein, and does not affect the interfacial property of peanut fractions. The protein films were successfully developed from peanut protein, but the mechanical properties need to be improved. Compared to pure peanut protein isolate, the incorporation of xylose markedly enhances the mechanical properties and the water resistance of films by increasing the degree of glycosylation and surface hydrophobicity of xylose-modified peanut protein isolate. Globally, this research contributes to identify peanut varieties with specific functionalities and to provide useful information for the processing of peanut protein products with good thermal stability. It will help to the development and utilization of peanut protein resources. [less ▲]

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See detailA numerical model based on cellular automata to assess travelling fires
Gamba, Antonio ULiege

Doctoral thesis (2021)

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See detailLiquid feeding regime and plant extracts affect rumen fermentation and bacterial community in calves
Zhang, Rong ULiege

Doctoral thesis (2021)

Liquid feeding regime and nutrition of calves may produce long-term effect on growth, health, and milk production performance of the adults by influencing the establishment of ruminal microbiota. The ... [more ▼]

Liquid feeding regime and nutrition of calves may produce long-term effect on growth, health, and milk production performance of the adults by influencing the establishment of ruminal microbiota. The objective of this thesis was to investigative the effect of early feeding regime and nutrition on rumen fermentation and bacterial community in calves, and then we follow calves for 6 or 9 months of age to detect any persistence of microbial programming effects. In experiment 1, fifty-four Holstein calves were randomly allocated to one of three treatments and fed pasteurized waste milk (WM), whole milk (M), or milk replacer (MR) during 7 to 63 days of age. Male calves were slaughtered at age 2 months to measure the organ development of forestomach. Female calves were followed for 6 months to determine body weight, blood indices, rumen fermentation, and ruminal bacterial community. The results indicated that the average daily gain was lower but the concentration of total volatile fatty acids was higher in calves fed MR at 2 months of age. This may induce a microbial programming effect at 6 months of age that the ruminal propionate molar proportion was lower, but the ruminal pH and acetate/propionate ratio were higher, for the MR group. Calves fed WM had lower starter intake, rumen weight, but higher concentration of isovalerate at 2 months of age. Meanwhile, the concentrations of serum growth hormone, insulin-like growth factor 1, and the growth hormone to insulin ratio were higher, but the levels of insulin and nonesterified fatty acids were lower, for the WM group, at 2 months of age. Calves fed WM had a different ruminal bacterial composition at age 2 months. No difference was observed in growth, blood indices, rumen fermentation and microbiota between WM and M at 6 months of age. In experiment 2, fifty-four female Holstein calves were randomly assigned to three treatments consisting of basal diet alone or supplemented with sanguinarine or resveratrol during 7 days to 6 months of age. Body weight was measured at the beginning of the experiment and 2 or 6 months of age. Ruminal liquids were sampled at 1, 2, 3, 4, 5, 6, and 9 months of age to monitor rumen fermentation parameters, and samples at 3 and 6 months of age were used to analyze the bacterial community by high-throughput sequencing. The copy number of Desulfovibrio and methanogenic archaea were quantified using droplet digital PCR. Supplementing the basal diet with plant extracts affected rumen fermentation parameters as well as the bacterial community. In addition, the Desulfovibrio population increased after addition of sanguinarine or resveratrol, whereas the methanogenic archaea population decreased after addition of resveratrol. However, no difference were observed in rumen fermentation parameters and bacteria community structure among treatments at 6 months of age. To sum up, liquid feeding regime and nutrition can affect rumen fermentation and bacterial community in calves. Calves fed WM had a different rumen fermentation and bacterial community at 2 months of age. However, this alteration can not persist to 6 months of age. Similarly, supplementation of sanguinarine or resveratrol to calves altered rumen fermentation parameters and microbiota during 3-5 months of age. But, no difference was detected at 6-9 months of age once the dietary treatment was ceased. It is noteworthy that calves fed MR had a higher concentration of TVFA in rumen, which might be a key factor that induced a more long-lasting effect on the rumen environment. [less ▲]

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See detailCaractérisation des céramiques des monuments historiques de la région de Marrakech et prospection des matériaux de restauration
El Halim, Mouhssin ULiege

Doctoral thesis (2021)

Archaeological ceramics from El Badi Palace, Saadian Tombs and Aghmat historical sites located in the region of Marrakech were analyzed by a multi-analytical approach based on Xray diffraction ... [more ▼]

Archaeological ceramics from El Badi Palace, Saadian Tombs and Aghmat historical sites located in the region of Marrakech were analyzed by a multi-analytical approach based on Xray diffraction, fluorescence and microscopic analyzes to study their physical, chemical and textural characteristics. Clay samples were also collected from different quarries in the Marrakesh and Fez region, and then analyzed using the same techniques. The aim is to determine the manufacturing technology, properties and origin of the raw materials used by the Almoravide and Saadian dynasties in construction. Experimental cooking tests on ceramic bodies were also carried out in order to determine the firing temperatures used in traditional ovens during these times. According to the results obtained, the Saadians used carbonated clay to make the zellige, one of the key elements of decorative ceramics; the raw material used comes from the region of Fez. The estimated firing temperature for these materials is between 700 and 800 °C for the El Badi palace and between 800 and 900 °C for the Saadian tombs in an oxidizing atmosphere. The glaze is mainly composed of lead and silica, the coloring agents are conventional, iron (Fe3+) for the yellow glaze, manganese (Mn3+) for the black glaze, copper (Cu2+) and phosphorus (P) for the blue glaze. The texture of the glaze/shard interface was studied using optical microscope and cathodoluminescence; results show that the glaze was applied directly to the ceramic support without slip or intermediate layer. The utility ceramics (irrigation channels) and structural ceramics (red bricks) were made from a local clay rich in iron from the Marrakech region, the firing temperature was around 700 °C for the channels and 900 °C for bricks. The archaeological ceramics collected at the Aghmat site are composed of fragments of tiles, bricks, irrigation channels and pottery. The structural ceramic was made from a local non-carbonated clay rich in iron, fired at a temperature above 900 °C, on the other hand the utility ceramics come from a carbonated raw material collected in the surroundings of the village of Aghmat , the estimated cooking temperature for these materials is between 700 °C and 900 °C. In order to improve the quality of the materials used in the restoration of the studied monuments, we have also made experimental briquettes by varying composition of raw materials and the cooking parameters. The results obtained show that the Benjlikh site clays in Fez are the most suitable for the restoration of these buildings; the appropriate cooking temperature is around 850 °C to 950 °C, with a slow firing cycle and a bearing of at least 4 hours. These parameters provide good quality materials which combine strength, durability and cutting ability. [less ▲]

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See detailExploring virus ecology and diversity in cultivated and wild Poaceae communities in Belgium
Maclot, François ULiege

Doctoral thesis (2021)

Ecology of plant viruses examines complex interactions among plant-associated viruses, their hosts and their vectors, and the environment. Starting at the end of the 19th century, virus ecology followed ... [more ▼]

Ecology of plant viruses examines complex interactions among plant-associated viruses, their hosts and their vectors, and the environment. Starting at the end of the 19th century, virus ecology followed the development of new technologies for virus detection and characterization, from host symptomatology to biochemistry, microscopy, serological and molecular techniques. Most recently, high throughput sequencing (HTS) technologies allowed for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present, that is the study of the viral metagenome or virome. This thesis reviewed the major advances in virus ecology, in relation to the development of virus detection technologies. It focused on the viral metagenomics and detailed the opportunities and challenges associated to each step of a virome-based study using HTS technologies (field sampling, laboratory work and bioinformatics analyses). The research conducted in the framework of this thesis explored the diversity and ecology of viruses infecting a plant family of economical and ecological importance: the Poaceae plants or grasses. The study was performed in the region of the Belgian National Park “Burdinale-Mehaigne”. Combining untargeted HTS-based analysis and targeted virus detection by RT-PCR in thousands of grass samples, virome characterization was unrolled down to the species taxonomical rank to support an analysis at three different levels: in global plant communities, in plant populations from same species, and in individual plants. A global view of the Poaceae virome and its ecology could be obtained through various ecological and epidemiological analyses: examination of virus richness, prevalence and co-infection, network and clustering analyses, Akaike information corrected criterion (AICc) calculation, or Spatial Analysis by Distance IndicEs (SADIE). First, we investigated the virome in three different Poaceae communities presenting a contrasted biodiversity (in terms of grass species richness) and a gradient of human management (i.e. cereal crops, grazed pastures and mowed grasslands). A diversified and largely unknown virome was identified in cultivated and non-cultivated Poaceae, with at least seventy virus species, among which fifty previously unknown, from to eighteen virus families and twenty-nine genera. Viruses with persistent lifestyles belonging to Alphachrysovirus, Partitivirus and Totivirus genera represented a large part of this virome, reaching 60% of the viruses detected and mostly novel virus species. A positive correlation was found between virus species and grass species richness in the plant communities, with very few or no virus species detected in cereal crops while a diversified virome was observed in wilder communities with up 26 virus species in grasslands. It illustrated the influence of plant diversity and land use on the distribution of viral communities. In addition, virome comparison over years revealed complex virus-plant relationships within the Poaceae community, separating plant virus and mycovirus models. Second, virome was characterized and compared among Poaceae species, investigating the influence of plant traits (i.e. lifespan, height, occurrence) on virus richness observed. Significant higher virus richness was determined in perennial grasses compared to annuals, and low occurrence species presented specific virus species that were not observed in dominant species. Virome network and clustering analysis revealed the presence of both ubiquitous (or generalist) virus species and specialist viruses limited to one or a few host species, with specialist viruses dominating the Poaceae virome. Among all plant species examined, the perennial ryegrass (Lolium perenne) was demonstrated to represent an important virus reservoir and will thus constitute an interesting model for future studies in virus ecology. Analysis in individual plants showed contrasted prevalences, co-infections and spatial distributions among plant communities, plant species and virus species. Interactions between viruses were also explored and revealed positive and negative viral associations depending on the grass species. Third, a more-in-depth analysis was performed for two novel virus species belonging to Secoviridae family that were identified in abundance in Poaceae communities and species: Poaceae Liege nepovirus A (PoLNVA) and Poaceae Liege virus 1 (PoLV1). The analysis focused on rough bluegrass (Poa trivialis L.) for which almost complete virus genomes from both viruses could be obtained. Sequence and phylogenetic analyses placed PoLNVA in the genus Nepovirus, while low levels of amino acid identity for both Pro-Pol and CP regions could define PoLV1 as an unclassified secovirid, between the genera Waikavirus and Sequivirus. PoLNVA and PoLV1 were detected in eleven wild Poaceae species, sometimes with high prevalence (e.g. 86% of L. perenne and 74% of P. trivialis samples infected by PoLNVA), highlighting their significant presence and large host range within Poaceae. Virus transmission was also investigated and PoLNVA was found to be seed-transmitted. In summary, this thesis revealed the complex structure of viral communities in nature (in terms of richness, prevalence, co-infection, host range, spatial distribution and genetic structure) and improved our understanding of virus diversity ecology in agro-ecological landscapes, illustrated here with the Poaceae family. A couple of virus species were further characterized but dozens of other novel virus species remains to be examined and will likely provide new insights about the ecology and phylogeny of Poaceae viruses. Other fields of investigation concern the diversity of virus transmission agents and other plant pathogens (i.e. bacteria, fungi), in order to obtain a holistic view of the Poaceae phytobiome. A particular attention should be paid to fungi due to the abundance of so-called mycoviruses in Poaceae. Much remains to be done to unravel the secrets of the virus ecology in wild and cultivated Poaceae, a domain still in its infancy. [less ▲]

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See detailStratospheric circulation changes: investigations using multidecadal observations and simulations of inorganic fluorine
Prignon, Maxime ULiege

Doctoral thesis (2021)

The intense human activity of the past two hundred years has perturbed the subtle balance existing between the spheres of the Earth system. The atmospheric composition has been modified with massive ... [more ▼]

The intense human activity of the past two hundred years has perturbed the subtle balance existing between the spheres of the Earth system. The atmospheric composition has been modified with massive emissions of greenhouse gases and substances depleting the life-essential ozone layer (ODSs). The most known to the general public resulting changes are certainly the global warming of the troposphere and the dramatic formation of the Antarctic ozone hole. However, it is less generally known that the most robustly modelled response to the increase of greenhouse gases, and the resulting global warming, is a speeding-up of the transport circulation occurring in the stratosphere, the atmospheric layer that is situated well above our head, between 10 and 50 km. This transport circulation, referred to as the Brewer-Dobson circulation (BDC), controls the distribution of ozone and other long-lived gaseous constituents of the stratosphere. Therefore, it is crucial to characterize the BDC and its changes to assess precisely the healing of the ozone layer, expected to occur gradually in the twenty-first century as most of ODS emissions have been successfully phased out by the Montreal Protocol on Substances that Deplete the Ozone Layer, including its Amendments and Adjustments. In this work, we investigated BDC changes through their impact on multidecadal time-series of stratospheric fluorine. To this end, we include ground-based Fourier transform infrared time-series from Jungfraujoch (Switzerland, 46°N) and Lauder (New Zealand, 45°S), Atmospheric Chemistry Experiment – Fourier Transform Spectrometer (ACE-FTS) satellite time-series and five simulations performed by the BASCOE chemical-transport model (CTM). These simulations are driven by the five modern meteorological reanalyses of the atmosphere. Thus, we assess the representation of the investigated BDC changes in state-of-the-art reanalyses which are designed to represent at best the atmospheric state over the past 30 years. We first improved the retrieval strategy of HCFC-22 (CHF2Cl), the most abundant hydrochlorofluorocarbon (HCFC) and the second source of fluorine in the stratosphere, using infrared solar spectra recorded at Jungfraujoch. We showed that HCFC-22 accumulation rates are progressively decreasing in the last decade, highlighting the success of the Montreal Protocol. Furthermore, this first step allowed us to demonstrate the validity of our BASCOE CTM set-up. Indeed, it is the first time that this model is used for such simulations, hence new features were implemented just before and during this thesis project and needed to be validated. The investigations on the impact of BDC changes on the time-series of stratospheric fluorine showed that, for the past twenty years, the BDC has been changing asymmetrically, with the Southern Hemisphere branch getting stronger relative to that of the Northern Hemisphere. Observational datasets and all of the five reanalyses are qualitatively in agreement with this change. However, this important finding is opposed to all model projections, notably used to project ozone recovery, modelling a weakening of the southern branch, in response to increases in greenhouse gases and to decreases in ODSs, calling for further investigations. Superimposed to this 20 year-trend, we have further confirmed a 5-to-7-year variability of the stratosphere, a feature which allows to put into perspective recent studies questioning specific stratospheric variabilities and associated hemispheric asymmetries. [less ▲]

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See detailClimate Change, planned relocation and land governance in the Pacific region
Gharbaoui, Dalila ULiege

Doctoral thesis (2021)

The adverse effects of climate change in the Pacific are increasingly forcing people to relocate in order to cope with the threats to their livelihoods. Relocations such as retreating from coastal areas ... [more ▼]

The adverse effects of climate change in the Pacific are increasingly forcing people to relocate in order to cope with the threats to their livelihoods. Relocations such as retreating from coastal areas in response to changing environmental conditions have long been a part of the adaptive strategies, culture and practice of Pacific Island communities. Relocation processes are particularly complex, as most of the land is under customary tenure and land is a common cause of conflict. Yet customary land tenure as a factor in relocation is seldom mooted in discussions on adaptation strategies in the Pacific. This dissertation explores the complex relationships between relocation and land tenure, in particular how cultural norms associated with land ownership impact on sustainability of population movements resulting from climate change in the Pacific, focusing on Fiji as case study. The conceptual framework explored on Hybridity and the use of Pluralism as aspect of Hybridity through the “nuanced approach” suggested that the interaction between state and community governance need to be captured through complex dynamics including tensions, challenges and synergies. One way of capturing those tensions and synergies is to look at theoretical frameworks that study barriers to the governance of adaptation such as Biesbroek’s (2013b) theoretical framework. Key results underline the need to reframe the role of traditional community leadership in planned relocations through the “middle-ground approach to relocation”, a “nuanced approach” where, rather than being limited to participation and consultation, their role in the relocation process should be central and active. The thesis proposes a re-conceptualisation of the role of traditional authorities in the relocation process and a conceptual framework including the “typology of planned relocation.” It proposes to redefine the role of customary chiefs and land owners as central in land acquisition while considering “resilience,” “perceptions” and “immobility” as key concepts for conceptualising planned relocation as an adaptation strategy to climate change in order to develop appropriate policy responses that would address challenges associated with land. Starting with the observation that the way land is accessed, negotiated and secured in planned relocation is central, results from our study suggest that land acquisition based on the “nuanced approach” emerging from the examination of pluralism as aspect of hybridity strongly echoes the need for addressing relocation through a “middle-ground approach”. Both approaches are key to determine Dalila Gharbaoui Page xv mobility and immobility outcomes approached through Carling’s aspiration-capability model (2002). Barriers that might undermine “ability” to relocate and therefore limit adaptation include “staggered or partial relocation” of the community to the new destination site that would leave part of the community “trapped” as “involuntary relocatees” in their site of origin and strongly affect community cohesion minimizing opportunities for sustainable relocation as opposed to “whole or full community relocation”. After putting in perspective field study results with the political frameworks at work in the region, the study finds that regional governance is a promising venue to address planned relocation through the “nuanced approach to relocation” as it allows specific challenges and cultural features the region holds to be addressed, including specific issues surrounding customary ownership of the land, directly conditioning water access and security. The thesis also argues that land management in the context of climate-induced relocation in the Pacific would benefit greatly from a strong and coherent regional framework that would support national and local governance specific to each country. Ultimately, the dissertation provides specific policy recommendations that could serve as tool for future policy in the region while proposing directions for future research on climate change, human mobility and land tenure. [less ▲]

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See detailMethodology for the design of climate-responsive houses for improved thermal comfort in cold semi-arid climates
Mahar, Waqas Ahmed ULiege

Doctoral thesis (2021)

Pakistan is facing a severe energy crisis which results in power cuts across the country. This situation seriously disturbs everyday life, business, and economic activities. The household sector in ... [more ▼]

Pakistan is facing a severe energy crisis which results in power cuts across the country. This situation seriously disturbs everyday life, business, and economic activities. The household sector in Pakistan is the primary consumer of electricity. A reasonable sum of this electricity is used for heating and cooling residential buildings, which can be reduced by adopting passive design strategies. This PhD research aims to provide informed decision support to design and construct climate-responsive houses in the cold semi-arid climate of Quetta, considering the appropriate and locally adapted low-tech solutions to improve residential buildings' indoor thermal comfort. Firstly, a literature review was done to understand the existing housing, comfort, and energy situation in Pakistan. An inventory of the current housing stock was then created to identify housing characteristics, construction types, and materials. The most common housing type was analysed for indoor climate, including monitoring indoor temperature and humidity, comfort perception and energy usage behaviour. Semi-structured interviews were conducted with the residents to get insights on their comfort perception, clothing, behavioural adaptations, lifestyle etc. Then a benchmark study was performed by selecting the most representative house. The representative house's virtual model was analysed using dynamic simulation and calibrated based on actual monitored data. Four comfort models were compared to identify the best fit-t-context model. A parametric analysis was done using passive design strategies to improve indoor thermal comfort. A sensitivity analysis of 21 design variables was performed to identify the most influential passive design strategies, which can be used in the climate of Quetta. A materialization survey was done to determine the locally available and manufactured materials. Based on this PhD research analysis and findings, a prescriptive guide was developed to provide informed decision support for architects to design comfortable and climate-responsive houses. The prescriptive guide was then tested and validated. A usability test was performed among the architects and architecture. The results show that the prescriptive guide provides enhanced decision support compared to the Building Code of Pakistan. In the end, recommendations are made for the regulators and further research. [less ▲]

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See detailBiological Roles & Evolution of Triterpenoids in Holothuroids
Claereboudt, Emily ULiege

Doctoral thesis (2021)

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See detailPositional Numeration Systems: Ultimate Periodicity, Complexity and Automatic Sequences
Massuir, Adeline ULiege

Doctoral thesis (2021)

This dissertation thesis is made up of three distinct parts, connected especially by complexity notion, factorial complexity as well as state complexity. We study positional numeration systems and ... [more ▼]

This dissertation thesis is made up of three distinct parts, connected especially by complexity notion, factorial complexity as well as state complexity. We study positional numeration systems and recognizable sets through decision problems and automatic sequences. The first part is devoted to the following problem: given a numeration system U and a finite automaton accepting U-representations of a set X ⊆ N, can we decide whether the set X is ultimately periodic (i.e. a finite union of arithmetic progressions)? We prove that this problem is decidable for a large class of numeration systems based on linear recurrent sequences. Thanks to the given automaton, we bound the possible periods of X via an arithmetical study of the linear recurrent sequence, as well as p-adic methods. The second part is dealing with the set of non-negative integers whose base-2 representation contains an even number of 1, called the Thue-Morse set and denoted by T. We study of the minimal automaton of the base-2^p expansions of sets of the form mT+r, where m and p are positive integers and r a remainder between 0 and m−1. In particular, we give the state complexity of such sets. The proposed method is constructive and general for any b-recognizable set of integers. As an application, we get a procedure to decide whether a 2^p-recognizable set given via an automaton is a set of the form mT+r. Finally, in the third part, we study properties of automatic sequences based on Parry and Bertrand numeration systems. We show that Parry-automatic sequences, like Pisot-automatic sequences (and thus in particular like b-automatic sequences) have a sublinear factor complexity. Furthermore, we exhibit a Bertrand-automatic sequence whose factor complexity is quadratic. We also prove that, contrarily to Pisot-automatic sequences, the image of a Parry-automatic sequence under a uniform morphism is not always a Parry-automatic sequence. The same happens for periodic deletion of letters. Last, we give the generalization to multidimensional sequences of a well-known result: a sequence is U-automatic if and only if its U-kernel is finite, U being such that the numeration language is regular. [less ▲]

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See detailEtude phytochimique et biologique de deux plantes médicinales de Côte d’Ivoire : Lantana camara et Lantana rhodesiensis (Verbenaceae)
Nea, Fatimata ULiege

Doctoral thesis (2021)

Cette thèse a pour but de contribuer à l’étude phytochimique de Lantana camara Lin et Lantana rhodesiensis Moldenke, et de justifier leurs utilisations dans la médecine traditionnelle ivoirienne. La ... [more ▼]

Cette thèse a pour but de contribuer à l’étude phytochimique de Lantana camara Lin et Lantana rhodesiensis Moldenke, et de justifier leurs utilisations dans la médecine traditionnelle ivoirienne. La première partie a consisté à la détermination de la composition chimique et à l’évaluation des activités biologiques de l’huile essentielle des organes de ces plantes. Les échantillons d’huile essentielle ont été obtenus par hydrodistillation et analysés par CPG-SM, CPG-FID-IR et RMN 13C. Les résultats ont montré que la composition chimique de l’huile essentielle des organes est majoritairement dominée par l’(E)-β-caryophyllène et l’α-humulène. Les monoterpènes tels que le thymol, le sabinène et le 1,8-cinéole y sont parfois majoritaires. L'analyse statistique des échantillons d’huile essentielle a révélé une variabilité de la composition chimique des organes. En outre, l'impact de la variabilité due au stade phénologique sur la composition de l’huile essentielle des organes de L. camara a été démontré. Il ressort que la proportion de thymol est plus élevée pendant les mois de floraison et de fructification intense. La variation chimique de l’huile essentielle de L. camara serait également liée aux facteurs biogéographiques et génétiques. L’huile essentielle des feuilles et des fleurs présente des activités insecticide, antioxydante et anti-inflammatoire intéressantes. La deuxième partie a consisté à l’exploration phytochimique bio-guidée des organes de L. rhodesiensis. Le screening phytochimique a permis de mettre en lumière une plus grande richesse des feuilles en polyphénols et flavonoïdes. L’extrait des feuilles présente une activité antioxydante et antiplasmodiale plus élevée par rapport à l’extrait des tiges et des racines. Plusieurs fractions de l’extrait des feuilles ont révélé une activité antiplasmodiale intéressante (15 ˃ CI50 ˂ 3 µg/mL). À partir des feuilles, une nouvelle flavone (1) et trois autres flavones ont été isolés, il s’agit de : rhodescine ou 5,6,3’,5’-tétrahydroxy-7,4’-diméthoxyflavone (1); 5-hydroxy-6,7,3’,4’,5’-penta-méthoxyflavone (2); 5-hydroxy-6,7,3’,4’-tétramethoxy-flavone (3) et 5,6,3'-trihydroxy-7,4'-diméthoxyflavone (4). La structure de chacun de ces composés a été élucidée par les méthodes spectrales de RMN 1H, 13C, COSY, HSQC, HMBC et LC-MS. Les composés 1, 3 et 4 ont été identifiés pour la première fois à partir de cette espèce. Le pourcentage d’inhibition (%I) du radical DPPH de chaque composé (1mg/mL) a été déterminé. La rhodescine (1) (%I = 97,92 ± 0,20) présente un pourcentage d’inhibition proche de celui de l’acide ascorbique (%I = 98,50 ± 0,56) et de la quercétine (%I = 98,89 ± 0,74). Le pourcentage d’inhibition du composé 4 est moyen (%I = 61,77 ± 3,53) tandis que celui des composés 2 et 3 est faible. Les résultats de ces travaux de recherche permettent de justifier l’usage de ces deux plantes dans la médecine traditionnelle, notamment dans le traitement du rhumatisme et de la malaria. Ces travaux ouvrent des perspectives sur d’autres investigations scientifiques qui pourraient aboutir à l’identification de nouveaux métabolites secondaires à potentialité antioxydante et antipaludique. [less ▲]

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See detailPhytochemical study of plants used traditionally for cosmetics and medicine in the island of Mayotte.
Saive, Matthew ULiege

Doctoral thesis (2021)

The Indian ocean is one of the biggest source of botanical diversity in the world, 25% of the world’s flora can be found in those islands. In addition, people living in that area, have been using what ... [more ▼]

The Indian ocean is one of the biggest source of botanical diversity in the world, 25% of the world’s flora can be found in those islands. In addition, people living in that area, have been using what nature has to offer to treat themselves for centuries. In this work we focused on the Comoros archipelago and more precisely on the island of Mayotte. The socio-economic situation of the area has been precarious since the end of the Ylang-ylang (Cananga odorata (Lam.) Hook.f. & Thomson) industry. The aim of this thesis is to provide the inhabitants with an analysis of plant species with the potential for the development of local cosmetic products. Through the analysis of the traditional knowledge we were hoping to find the ideal species for this project. First, a preliminary study was conducted leading to the identification of more than 200 different species which could be useful. Following this first work, an infield ethnobotanical study was conducted allowing for the identification of 69 species which were interesting. By cross referencing the previously gathered information 21 different species were identified for collection and the analysis so as to validate their real biological activity: the lipoxygenase inhibition potential, the tyrosinase inhibition potential and the DPPH (2,2-diphenyl-1-picrylhydrazyl) reduction potential. The most active species then underwent a selection process based on current knowledge-to-date and availability. Following this selection, we focused on the roots of the litchi plant (Litchi chinensis Sonn.). The last step of this work consisted of the identification of the compound responsible for the observed activities. This was achieved by submitting the crude extract of L. chinensis to a bio-guided fractionation until only a single compound remained. The purified compound then went through the following molecular identification process: UV, IR, MS, RMN and colorimetric analysis. Finally, these process allowed us to identify a compound from the polyphenol family: cinnamtannin D2 (CAS number : 97233-47-1). [less ▲]

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See detailLe financement basé sur les résultats au Bénin et au Sénégal : Un levier pérenne de changement de pratiques des agents de santé ?
Bodson, Oriane ULiege

Doctoral thesis (2021)

Performance-based financing (PBF) has been widely implemented in low- and middle-income countries with the aim of incentivizing health service providers and the health workforce to improve the quantity ... [more ▼]

Performance-based financing (PBF) has been widely implemented in low- and middle-income countries with the aim of incentivizing health service providers and the health workforce to improve the quantity and quality of care for nearly twenty years now. However, the PBF approach continues to face a lack of (relevant) evidence regarding its effects, and a limited understanding of the motivational factors that explain the presence or absence of its effects. This doctoral research intends to address this gap. It aims to explore the potential for change in health workers’ practices through PBF in Benin and Senegal, and uncover the multiple explanatory factors underlying these changes. The originality of our research is manifold. It combines two study countries, analyzes several PBF programs and does so, with an original emphasis on the question of the sustainability of PBF effects in Benin. The research is based on the articulation of qualitative (documentary research, participant observation, semi-structured interviews) and quantitative (statistical analyzes) research methods, and mobilizes an original and dynamic analytical framework - the I-Change model. Our field study shows that, according to the health workers interviewed, PBF allows to change some of their practices, even if the observed changes are not systematic. In the case of Senegal, these changes are not accompanied by a systematic improvement of health indicators, even when the PBF is combined with demand-side programs through a conditional cash transfer (CCT) scheme. From our study, it also emerges that the potential of PBF to change health workers’ practices cannot be only explained by the financial incentive, which is central in results-based approaches dissemination strategy. Indeed, many levers for changing health workers’ practices - both tangible and intangible - have been identified, while other potential levers of change have not been activated, at least not always fully. The second field study conducted in Benin, 9 and 12 months after the end of PBF programs respectively, showed a general trend towards a gradual “relaxation” of “seriousness”, of professional “rigor”, and a deactivation of certain levers for change of PBF. The PBF programs in Benin did not have lasting effects. In addition, our field studies have shown that the context in which PBF programs are implemented plays a crucial role - which can be facilitating or hindering - in achieving and sustaining the results of PBF programs. Taken together, these observations challenge the idea that PBF can constitute an effective approach to respond to dysfunctional health systems – or at least they call for the implementation of PBF programs coordinated with the various reforms initiated or to be initiated within the national health systems (particularly relating to human resources for health remuneration and technical equipment funding), and forming part of an in-depth reflection on supply and demand of care challenges. [less ▲]

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See detailEffect of the Boundary Conditions Applied to the Liquid Bridge on the Liquid Transfer between Two Solid Surfaces
Tourtit, Youness ULiege

Doctoral thesis (2021)

The trend towards miniaturization requires to handle even smaller micro-components: they must be picked, placed with high accuracy, and then released. This highly challenging process should take into ... [more ▼]

The trend towards miniaturization requires to handle even smaller micro-components: they must be picked, placed with high accuracy, and then released. This highly challenging process should take into account two aspects: the yield of successful placements and the minimized risk of damaging the manipulated micrometer-sized objects due to contact forces. Despite the advantages of the latest gripping technologies, including low complexity, high accuracy, and high reliability, the component is subjected to high contact forces that could damage it. As a consequence, there is a need of developing new and innovative ways to manipulate micro-sized components with respect to the requirements mentioned above. Gripping based on capillary bridges is a promising technique to handle components at the micrometric scale. This technique offers many advantages: flexibility and reliability, self-centering effect, the capability of grasping small and delicate components in a wide range of shapes and materials thanks to the “bumper” effect of the mediated liquid bridge. Nevertheless, the liquid residue on the component after breaking up the bridge is undesirable. As a consequence, there is a need to design a capillary gripping system that can retain all the liquid after the breakup of the bridge. Understanding the formation, the stretching, and the liquid distribution after the breakup of the liquid bridge is mandatory. In this thesis and in the first place, we studied the rupture of a liquid bridge confined between different geometries of the gripper and the substrate: plane/plane, cone/plane, and cavity/plane. We developed, based on the resolution of the Young-Laplace equation, an operational quasi-static criterion to predict the rupture gap of the bridge. We also investigated the effect of the geometry on the liquid distribution after the breakup. Optimal geometries are found to retain up to 90% of the liquid after the breakup of the bridge. In the second place, we investigated the secretion dispensing in green dock beetles Gastrophysa viridula. Their ability to walk upside-down on any kind of surfaces rely on mediated secretion between their hairy pad and the surface they walk on. We studied the mechanism of the secretion dispensing from the source where it is produced to the contact zone. Experimental setups have been designed, with advancing 3D printing and micro-fabrication techniques. Models have been developed, discussed, and compared to experimental data. [less ▲]

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See detailPiezoelectric Digital Vibration Absorbers for Multimodal Vibration Mitigation of Complex Mechanical Structures
Raze, Ghislain ULiege

Doctoral thesis (2021)

Engineering structures are becoming lighter and more complex to accommodate the ever-increasing demand for performance and to comply with stringent environmental regulations. This trend comes with several ... [more ▼]

Engineering structures are becoming lighter and more complex to accommodate the ever-increasing demand for performance and to comply with stringent environmental regulations. This trend comes with several challenges, one of which is the increased susceptibility to high-amplitude vibrations. These vibrations can be detrimental to structural performance and lifetime, and may sometimes even threaten safety. Passive and active vibration reduction techniques can provide a solution to this issue. Among the possibilities, piezoelectric damping is an attractive option, due to its compact and lightweight character, its reduced cost and its tunability. This technique uses the ability of a piezoelectric transducer to transform part of its mechanical energy into electrical energy. The converted energy can then be dissipated by connecting a shunt circuit to the transducer. However, the difficulty of realizing such circuits limits the broad applicability of piezoelectric shunting. This doctoral thesis investigates the potential of replacing the electrical circuit comprising classical components such as resistors and inductors by a digital unit and a current source, thereby creating a digital vibration absorber (DVA). Virtually any circuit can be emulated with a digital controller, providing this approach with an extreme versatility for vibration mitigation of complex mechanical structures. In this regard, the DVA is first analyzed in terms of power consumption and stability of the controlled system. Then, effective and easy-to-use tuning approaches for the control of multiple structural modes either with passive electrical circuits or a DVA are proposed, namely a passivity-based tuning of shunt circuits, a modal-based synthesis of electrical networks interconnecting multiple piezoelectric transducers, and a numerical norm-homotopy optimization resulting in an all-equal-peak design. These techniques are eventually applied and adapted to real-life structures with potentially complex dynamics. Specifically, effective vibration mitigation is demonstrated on structures exhibiting nonlinear behaviors and high modal density. [less ▲]

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See detailAutumn to spring inorganic carbon processes in pack and landfast sea ice in the Ross Sea, Antarctica
Van der Linden, Fanny ULiege

Doctoral thesis (2021)

The Ross Sea, the southernmost sea on Earth, presents several iconic features of polar seas: sites of deep water formation, high summer primary production, floating ice shelves, the annual cycle of ... [more ▼]

The Ross Sea, the southernmost sea on Earth, presents several iconic features of polar seas: sites of deep water formation, high summer primary production, floating ice shelves, the annual cycle of advance and retreat of sea ice, polynyas and katabatic winds. Furthermore, sea ice in McMurdo sound (western Ross Sea) is one of the most productive marine environments. However, sea ice inorganic carbon dynamics and related air-ice CO2 fluxes have never been documented in the Ross Sea. Two surveys were carried out in the western Ross Sea to bridge over a critical gap in the current understanding of sea ice: autumn and winter processes. The land-based YROSIAE project was a temporal survey from late winter to summer within landfast sea ice. The ship-based PIPERS project was an unique opportunity to study the early stages of sea ice formation (in polynyas) and more common consolidated pack ice in autumn. Based on these two consistent surveys, this work aims to (i) examine the bulk ice pCO2 dynamics in landfast sea ice from late winter to summer (ii) investigate the seasonal pattern (net source vs net sink) and diurnal pattern of air-ice CO2 fluxes (iii) analyse the depth-dependent physical and biogeochemical processes involved in inorganic carbon dynamics (iv) assess the precipitation of calcium carbonate in autumn and during a full bloom season. CO2 fluxes were measured using the chamber technique in autumn, late winter and spring, over open surface water, frazil ice patch, grey unconsolidated ice and consolidated first-year ice. These new autumn and winter data provide a first step to set up the budget of air-ice CO2 fluxes over the year and evaluate the large-scale influence of these fluxes on the annual uptake of CO2 by ice-covered oceans. Our results confirm that sea ice acts as a CO2 source for the atmosphere during ice growth, with enhanced fluxes reported at the early stages of sea ice formation, and shifts to a sink in spring. In late spring, diel pattern superimposed upon this seasonal pattern and was potentially assigned to either ice skin freeze-thaw cycles or diel changes in net community production. The snowpack plays a complex role in CO2 exchanges and can no longer be considered as an inert reservoir lying at the sea ice surface. The main features of the normalized DIC distribution (DIC35) through the ice column were: (i) a marked depletion at the surface from autumn to spring induced by the CO2 releases to the atmosphere (ii) bubble-driven gas enrichment below or within impermeable layers and (iii) an initial DIC35 enrichment in the bottom layer disappearing in spring when the seasonal peak in biomass occurs.At the bottom of landfast ice, in spring, a particular assemblage of microorganisms, the biofilm, led to a massive biomass build-up counterintuitively associated with nutrients accumulation. This biofilm formation may also promote calcium carbonate precipitation. However, in young pack ice or in cold landfast ice in early spring, limited calcium carbonate precipitation was reported. This suggests that calcium carbonate precipitation is not an ubiquitous process, especially in winter and autumn Antarctic sea ice. Comparison of calcium carbonate precipitation and pCO2 measurements advocates that the calcium carbonate precipitation is rather controlled by pCO2 than temperature. [less ▲]

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See detailPrecision of auditory-verbal working memory performance: A behavioral and neuroimaging investigation
Bouffier, Marion ULiege

Doctoral thesis (2021)

This thesis investigated the precision of auditory-verbal working memory (WM) at phonetic, phonological and semantic levels using probe recognition tasks; in these tasks, participants were presented with ... [more ▼]

This thesis investigated the precision of auditory-verbal working memory (WM) at phonetic, phonological and semantic levels using probe recognition tasks; in these tasks, participants were presented with auditory lists of words or nonwords. After each list, a probe item was presented, and participants were invited to determine whether that item had been in the list. We manipulated the levels of phonetic, phonological or semantic proximity between target and probe items to assess the precision with which items were stored in WM. We showed that phonological WM precision is limited when single-phoneme level resolution is needed, with rejection accuracy strongly declining when target and probe items differ by only one phoneme. We also showed that phonological WM precision declines when multilingual speakers are tested in their less proficient language, suggesting that precision further depends upon the precision of underlying language representations. The fragility of phonological WM traces has furthermore been highlighted in our functional magnetic resonance imaging (fMRI) study, which revealed robust discrimination of phonologically non-overlapping nonwords maintained in WM, but not of phonologically overlapping nonwords. At the phonetic level, we showed that precision for subtle phonetic information tended not to be reliably represented in WM, in line with evidence suggesting that fine-grained phonetic codes are not systematically contained in WM under more naturalistic listening conditions. At the semantic level, we observed high rejection accuracy for probes highly related to target items presented at initial list positions. This suggests that semantic variables influence precision in a time-dependent manner, with early list items being more strongly activated, allowing for optimal discrimination between the target item and a semantically highly related probe item. Hence, while advancing our understanding of the limits and nature of auditory-verbal WM precision, this thesis also highlights the close association of auditory-verbal WM and language domains. [less ▲]

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See detailEffect Of Magnetic Reconnection Over The Earth’s Space Environment
Matar, Jessy ULiege

Doctoral thesis (2021)

The majestic spectacle of polar aurora has fascinated the humankind since the dawn of time. It was understood, already several centuries ago, that the auroral and concurrent magnetic activities were ... [more ▼]

The majestic spectacle of polar aurora has fascinated the humankind since the dawn of time. It was understood, already several centuries ago, that the auroral and concurrent magnetic activities were related to solar activity, which was later understood as the source of the resulting solar wind, which carries a frozen-in magnetic field and interacts with the magnetic field of the Earth. Major progresses were realized towards the understanding of the coupled solar wind - magnetosphere - ionosphere system after the beginning of the space era. Since 1958, around thirty satellites were sent to orbit the Earth and to observe the resulting auroral and geomagnetic disturbances and the different processes governing the solar wind - magnetosphere coupling. Space based observations also led to the discovery of a population of electrically charged particles trapped in the geomagnetic field, forming the plasmasphere. Under suitable conditions, interaction between the solar wind and the Earth’s geomagnetic environment causes a reconfiguration of the magnetic field that connects the interplanetary magnetic field to the geomagnetic field producing so-called open magnetic field lines. The solar wind flow then drags these open field lines, giving the magnetotail its elongated shape. Previously opened field lines eventually reconnect in the central region of the magnetotail, releasing energy and reconfiguring the field back again to a closed configuration. This cycle of magnetic field line opening and closure is now understood to be at the heart of the dynamics of the Earth’s space environment and its auroral and magnetic activity, producing auroral substorms and global geomagnetic storms. We investigate several storm and substorm cases in order to understand how the various regions of the magnetosphere and upper atmosphere interact with each other under different solar wind conditions. This thesis consists of two distinct studies: the first study examines in situ measurements of magnetic reconnection and their relation with remote sensing auroral observations, whilst the second examines the plasmaspheric and auroral responses during storm time. The aim of the first part of the thesis is to study the coupling between the solar wind and the magnetosphere and identify how its consequences materialize in different regions of the system, from the aurora to the space environment of the Earth, with a particular attention being given to the effects of magnetic reconnection. A combination of data from different origins, including satellites, magnetometers and radars, was used to achieve this aim. We combine the NASA-IMAGE satellite observations of the proton aurora with ground based measurements of the ionospheric convection from SuperDARN to analyse the cycle of magnetic flux opening and closure in the Earth’s magnetosphere. The ESA-Cluster mission provided in situ measurements of the plasma properties at reconnection sites which were concurrent with auroral observations from IMAGE and SuperDARN, and therefore allowed us to investigate the ionospheric consequences of reconnection occurring in the magnetotail on the nightside and at the magnetopause on the dayside. We demonstrated that the reconnection rate, expressed as an electric voltage, determined from ionospheric observation, reliably reflects the physical process occurring in the distant space both on the dayside and on the nightside, a result of fundamental importance. The impact of intense solar wind coupling with the magnetosphere makes up the second part of my project, devoted to the contrasted storm time response of the plasmasphere density and boundary on one hand, and the ionospheric auroral dynamics on the other hand. The satellite observations of the aurora from IMAGE-FUV and of the plasmasphere from IMAGE-EUV were used in addition to SuperDARN, OMNI, GOES data, and ground-based magnetometer-derived activity indices. We reach several conclusions highlighting the interplay of the different elements of the system: the plasmasphere responds directly to changes in the solar wind properties, the ionospheric convection boundary HMB is magnetically related to the plasmapause reflecting the topology of the system, the plasmasphere density correlates with the open magnetic flux but does not with the dayside and nightside reconnection rates owing to the fact that reconnection varies over shorter time scales. The analysis showed that some parameters can correlate better during the most active phase of the storm and therefore, better describe the direct response of the magnetosphere than the recovery phase. [less ▲]

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See detailMechanical unfolding of individual bimolecular G-quadruplexes by AFM
Hubert, Sandrine ULiege

Doctoral thesis (2021)

G‑quadruplexes (GQ) are non-canonical nucleic acids structures that form sequences rich in guanines, either in DNA or RNA. The prevalence of sequences able to form G-quadruplexes in crucial genomic sites ... [more ▼]

G‑quadruplexes (GQ) are non-canonical nucleic acids structures that form sequences rich in guanines, either in DNA or RNA. The prevalence of sequences able to form G-quadruplexes in crucial genomic sites suggests a significant role in important biological processes such as the maintenance of telomere stability and the regulation of transcription. However, some aspects stay unclear about their presence in vivo, the processes behind their potential regulatory role and the favourable conditions to their formation. Our objective is the investigation of the force-driven separation of individual bimolecular G‑quadruplexes by AFM-based single-molecule force spectroscopy (SMFS). Our research aims at contributing to a better understanding of the interactions involved in bimolecular G‑quadruplexes, made of DNA or DNA and RNA, and of the mechanism of their mechanical unfolding. [less ▲]

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See detailImpact des coopératives agricoles des cultures vivrières sur les conditions de vie des ménages ruraux au Burundi : Cas des coopératives de la province de Ngozi
Manirakiza, Dismas ULiege

Doctoral thesis (2021)

For more than two decades, Burundi has experienced a resurgence of interest in agricultural cooperatives following the appeal of humanitarian partners aiming to reorient their intervention. In the regard ... [more ▼]

For more than two decades, Burundi has experienced a resurgence of interest in agricultural cooperatives following the appeal of humanitarian partners aiming to reorient their intervention. In the regard, the Government has given a higher priority to the development of food crops to ensure the supply of the population from national productions. Considering its historical situation of recurring food insecurity, the province of Ngozi has since had a proliferation of agricultural cooperatives around food crops, as well as cash crops, mainly coffee. Most of them are involved in access to low-cost agricultural inputs, markets, agricultural micro-credits, natural resources, training and information. The objective of this study was to assess the impact of food crops cooperatives on the living conditions of rural households in Burundi, particularly in the province of Ngozi. The realization of this study covering a period from 2016 to 2019 combines three methods such as the documentary exploitation, surveys and interviews with different actors of the cooperative movement of Busiga and Gashikanwa communes in Ngozi province. The fist survey was conducted on 90 members randomly selected in cooperatives of three main organizations present in each commune. The second survey was carried out on a comparison group of 60 non-members, who were selected by using the purposive sampling technique in the same social group and geographical area as cooperatives’ members. This study highlights various services offered by cooperatives to their members and to the surrounding community. Depending on their size, cooperatives are a preferred channel for supplying agricultural inputs and learning new farming techniques. The valuation of production (storage, processing, sale and inventory credit) is part of their concern. Facing the challenge to get agricultural financing, the cooperatives are innovating alternatives for accessing small loans. Under of mutual solidarity, members organize a kind of community health insurance. For some, cooperative members benefit from regular training on hygiene, small entrepreneurship, environmental protection, peaceful cohabitation, etc. Regarding of the impact assessment, the analysis shows that cooperatives have effects on the majority of aspects of the living conditions of their members. At the production level, the statistical test shows a significant difference in the yields of bananas between the two groups (p = 0.075) at the significance level of 10%. The impact corresponds to an average yield increase of 640 kg / ha per member household. Considering that the banana is an important crop in consumption and especially in commercialization; the increase in its production brings relatively high income to households, especially in member’s. In the process, the storage also allowed the cooperative members to have a capital gain on the production and an inventory credit. Regarding of the livestock, the impact is estimated at an average increase of 0.40 cattle and 0.46 goats per household of members. This situation expresses a great opportunity for fertilization, a social esteem and a wealth with an average value of 160,000 BIF (cattle) and 46,000 BIF (goat) The comparative analysis reveals a significant difference between the average amounts of loans taken out by the two groups. The average difference of 28,500 BIF would therefore constitute an impact induced by membership in cooperatives. Regarding of the habitat, the difference is significant for the quality of materials of the walls, access to safe water and the quality of latrines. Indeed, the impact corresponds to a 13% decrease in the level of possession of houses whose walls are built with wood covered of mud, a 9% decrease in the level of unsafe water consumption and a 7% increase in the level of possession of fitted latrines among members. In this respect, members appear less exposed to precarious hygienic conditions than non-members. In addition, the mutual health insurance within the cooperative offers them financial and physical accessibility to health care. The difference is also significant in the number of houses owned by households. The impact obtained is 0.5 houses corresponding to an additional number of houses owned by a household of cooperators. In relation to the equipment of the house, the impact appears in the possession of the cupboard and the dining room. An additional house and the possession of "complementary" equipment would enhance the comfort of a household. For the other material means, the impact appears in the possession of the bicycle and the radio in the households of the members. The bicycle plays a major role in the speed and cost of activities carried out in the households and the radio allows them to be constantly informed. The analysis of early school leaving reveals an impact corresponding to an average decrease of 0.15 school dropouts in member households. Although the difference is small, the 15% drop in eating just one meal per day among the low-income group could also be an impact. Coming out of the crisis, the cooperatives have succeeded in gathering together people living on the same hills around a common ideal. The social harmony observed in farmers’ cooperatives studied is reflected in mutual aid in many situations. [less ▲]

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See detailRenouveau des approches participatives pour la fabrique de la Smart City
Schelings, Clémentine ULiege

Doctoral thesis (2021)

Facing demographic and environmental challenges, the Smart City model increasingly becomes the chosen strategy to guide future urban developments. Initially essentially technocratic, this new urban ... [more ▼]

Facing demographic and environmental challenges, the Smart City model increasingly becomes the chosen strategy to guide future urban developments. Initially essentially technocratic, this new urban “ideal” very soon raised social acceptability issues vis-à-vis the top-down imposition of standardized solutions. Often overlooked in favour of technological optimization, citizens are actually the key for the Smart City model’s success or failure, because they have the power to accept or reject the solutions deployed on their territory. Noting the importance of citizen participation for the making of the Smart City and the recurring limits of participatory approaches developed since the 1970s, the thesis aims to equip urban professionals (engineers, architects, urban planners), decision makers and citizens with new theoretical, methodological and decision-support frameworks in order to include end-users within the design process of our future urban environments. In practice, the thesis is structured in three main phases. A first diagnosis phase focuses on citizens’ perceptions of the Smart City and on their willingness to participate to its design process. A second multiple-case study phase seeks to better understand which forms of participation are implemented in various Smart Cities, recognized for their citizen-driven dynamic. The third experiment phase consists in concretely implementing a participatory methodology in Wallonia, on the basis of the previously collected data and best practices. In a cross-cutting way, we also studied three participatory approaches, which are often observed in the Smart era: the e-participation platform (online), the co-design workshop (face-to-face) and the participatory budget (mixed). The thesis contributes to the state of knowledge and to the study of participatory approaches for the making of the Smart City in several regards. First, this work provides an essential clarification between three participatory modes that coexist and intertwine: co-decision, co-design and data co-production processes. Beyond those three dimensions, which reflect the purpose of participatory processes, the thesis also affirms the intrinsic value of citizen participation in terms of solutions’ ownership, cohesion among citizens and acquisition of new skills. The thesis then develops the roles of the professional designers and the non-designer participants throughout the participatory processes, highlighting the emergence of new intermediate positions (“professionals of participation” and “citizen ambassadors”). The citizens’ responsibility is nuanced by the criticism of a utopian “super citizen”, supposedly at the same time engaged, creative and connected. Moreover, this work relativizes the participatory imperative and identifies an upstream-downstream switchover of the citizen participation at the Smart era. The thesis eventually seeks to question Arnstein’s participatory ladder (1969) and proposes an adaptation of Fung’s democratic cube (2006) in the form of a multidimensional radar chart, which is better adapted to the participatory context and the complexity of the Smart City, and supports researchers, designers, city officials and citizens in the implementation of participatory approaches at the Smart era. [less ▲]

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See detailDevelopment of multidimensional approaches for metabolomics
Di Giovanni, Nicolas ULiege

Doctoral thesis (2021)

Metabolomics in a clinical context faces many analytical challenges. GC×GC-TOFMS has much higher sensitivity and resolution, therefore much higher untargeted capabilities than GC-MS but is still largely ... [more ▼]

Metabolomics in a clinical context faces many analytical challenges. GC×GC-TOFMS has much higher sensitivity and resolution, therefore much higher untargeted capabilities than GC-MS but is still largely neglected in comparison. In front of that situation, the aim of the thesis was to develop methods to exploit the performances of GC×GC-(HR)TOF-MS in untargeted metabolomics in a clinical context, with the underlying goal of extending its use relatively to 1D GC-MS. [less ▲]

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See detailMulti-Degree-of-Freedom Hybrid Fire Testing in a Non-Linear Environment
Mergny, Elke ULiege

Doctoral thesis (2021)

Hybrid Fire Testing (HFT) is a performance-based approach for structures in fire based on substructuring method. A complete structure is divided in two substructures, one being in a fire test laboratory ... [more ▼]

Hybrid Fire Testing (HFT) is a performance-based approach for structures in fire based on substructuring method. A complete structure is divided in two substructures, one being in a fire test laboratory (physical substructure [PS]), and one being numerically simulated (numerical substructure [NS]). By reducing the number of elements to be tested, this method overcome the huge costs of large-scale tests. Some hybrid fire tests have been successfully performed in the last decades, showing that this technique is promising. However, as HFT is still in its infancy, these hybrid tests were limited to one-degree-of-freedom (DOF) tests. In parallel with the tests, the stability of the HFT process has been studied and algorithms have been developed. These algorithms have been validated numerically but few have been used in experimental tests. This research aims first to propose a new framework based on linear control system theory and proportional integral controller to address identified stability issues and control the time properties in HFT. The final objective consists in performing multi-DOF tests based on this methodology. [less ▲]

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See detailContribution to the study of the links between consciousness and swallowing
Mélotte, Evelyne ULiege

Doctoral thesis (2021)

Following severe brain injuries (e.g., traumatic or anoxic brain injury, stroke), a small proportion of patients will remain in an altered state of consciousness. Patients with prolonged (> 28 days post ... [more ▼]

Following severe brain injuries (e.g., traumatic or anoxic brain injury, stroke), a small proportion of patients will remain in an altered state of consciousness. Patients with prolonged (> 28 days post-insult) disorders of consciousness (DOC) can open their eyes (sometimes showing electrophysiological sleep/wake cycles) and the majority no longer need invasive ventilation. However, most of them receive artificial feeding, suggesting that consciousness affects swallowing capacities. The aim of this thesis is to contribute to the study of the links between consciousness and swallowing. The hypotheses are that swallowing capacities are linked to level of consciousness, and that the presence of some components of swallowing constitutes a possible sign of consciousness. Based on a literature review, we show that the sequencing of the components of swallowing falls on a continuum of voluntary to reflex behaviors. Components of the oral phase may be considered as voluntary behaviors because they are controllable and suppressible (although largely automated), components of the pharyngeal phase as somatic reflexes, and components of the esophageal phase as autonomic reflexes. The triggering of the swallowing reflex inhabits the border region between voluntary behaviors and somatic reflexes, while the opening of the upper esophageal sphincter divides somatic from autonomic reflexes. If voluntary behaviors are considered possible signs of consciousness, the presence of components of the oral phase of swallowing should be considered as revealing conscious behaviors. Moreover, we show that a range of cortical areas (mainly the primary sensorimotor cortex, premotor cortex and supplementary motor area, anterior part of the cingulate cortex, insula and cerebellum) are involved in both volitional and non-volitional swallowing tasks. In two retrospective studies analyzing swallowing in patients with DOC diagnosed by means of repeated behavioral assessment and neuroimaging, we demonstrate that almost all such patients present at least one dysfunction in the oral and/or pharyngeal phase. Patients who do not show behavioral signs of consciousness (unresponsive wakefulness syndrome – UWS) do not present an efficient oral phase of swallowing allowing oral feeding with solid food. Consequently, the preservation of components of the oral phase of swallowing should be considered as a sign of consciousness and be one of the diagnostic criteria for consciousness. The absence of an efficient oral phase of swallowing in patients with UWS and its presence in only a small proportion of minimally conscious (MCS) patients explain why no “typical” patients with UWS (i.e., with behavioral and neuroimaging assessments pointing in the same direction) can be fed entirely orally while no patients with MCS can eat ordinary textured food. Furthermore, in the studied group, level of consciousness is linked to components of the pharyngeal phase (reflected by the absence of a tracheostomy, pharyngo-laryngeal secretions or saliva aspiration) and to the cough reflex. Indeed, more patients with MCS than UWS present efficient spontaneous saliva management and a cough reflex, although these components are present in some patients with UWS. For that reason, these components seem to represent cortically mediated behavior but do not constitute signs of consciousness as such. Finally, this work highlights the lack of appropriate tools to assess and treat swallowing for patients with DOC. A protocol study for the validation of a swallowing assessment tool for patients with DOC is therefore proposed. [less ▲]

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See detailPituitary Gigantism
ROSTOMYAN, Liliya ULiege

Doctoral thesis (2021)

Pituitary gigantism is a rare but important form of overgrowth due to GH/IGF-1 excess. The initial aim of the present research was to design and implement a comprehensive cohort study of the etiology ... [more ▼]

Pituitary gigantism is a rare but important form of overgrowth due to GH/IGF-1 excess. The initial aim of the present research was to design and implement a comprehensive cohort study of the etiology, clinical diagnosis and management of this rare disease. This work describes the findings of an international collaborative study involving the largest pituitary gigantism population described to date (208 patients) from 47 centers across the globe to explore the specific characteristics of these patients and the genetic background of pituitary gigantism. Overall, the work undertaken has permitted us to identify the clinical phenotype and treatment outcomes in patients with pituitary gigantism; these features differ significantly from those in adult somatotropinoma patients with acromegaly. Patients with gigantism presented clear a male predominance (95%) and differ in their presentation based on gender, with females presenting significantly earlier than males. Increased somatic growth in pituitary gigantism is associated with an early onset form of GH/IGF-1 hypersecretion due to pituitary tumors that are highly resistant to treatment. These characteristics point to specific molecular mechanisms in pituitary tumor formation. Until recently, pituitary gigantism has been a well-known disease but poorly understood from genetic point of view. Underlying genetic causes have been studied comprehensively and identified in half of the cases in our large international series. While complex multi-organ syndromes (such as McCune-Albright syndrome (MAS), MEN1 and Carney Complex) counted only for rare cases of pituitary gigantism (7% in total), the most frequent genetic etiologies appear to be those leading to disease isolated to the pituitary, such as AIP mutations (29%) and X-linked acrogigantism syndrome (X-LAG) (10%). The latter is a new genetic form of infant-onset acrogigantism, occurring sporadically and in familial setting, which was described for the first time during the course of this work. X-LAG remains rare and only about 33 genetically confirmed cases have been published to date. X-LAG is a dramatically aggressive disorder affecting children from a very young age (usually during the first year), who are predominantly female (70%). Despite the very young age at disease onset, X-LAG patients develop large pituitary lesions (frequently mixed GH and prolactin secreting adenomas and/or hyperplasia) with extremely elevated hormonal levels. This contributes certainly to excessively rapid somatic growth leading to severe overgrowth. The remarkable phenotype of X-LAG syndrome is underlined by an unusual genetic mechanism; it is due to a microduplication on Xq26.3 including always GPR101 gene, whereas previously described genetic mechanisms in pituitary tumorigenesis are mainly triggered by a point mutation or deletions in a single gene. Additionally, a novel genetic technology (digital droplet PCR (ddPCR)) revealed that males with X-LAG syndrome can be mosaics for the GPR101 duplication, and as few as 16% of duplicated cells could lead to severe overgrowth. Many of the tallest giants in history had a clinical history that exactly mirrors this phenotype. The molecular diagnosis of X-LAG due to a duplication in GPR101 was made using paleogenetic extraction techniques in combination with modern ddPCR on DNA successfully isolated from the century-old remains of the historical case of The Giant Constantin (2.59m) who had autopsy findings of a pituitary adenoma. It can be considered as the tallest genetically proven case of gigantism available. It was also noted that more than 50% of cases remain genetically unexplained. Importantly, these genetic subgroups have statistically significant differences in terms of features at presentation/diagnosis, however all pituitary giants, including the genetically negative group, have aggressive clinical characteristics. Further studies were focused on the association of genetic events, in particular AIP mutations, with the aggressive phenotype of somatotropinomas that are resistant to conventional treatment. The clinical experience in patients with pituitary gigantism that have failed previous therapy with first generation somatostatin analogues, showed the role of other treatment options (pegvisomant, paseriotide) in hormonal and tumoral control in genetically negative and AIP mutated cases. A severe disease burden was highlighted in a comprehensive autopsy and genetic analysis in an adult male patient with a complex clinical profile of MAS including pituitary gigantism. The pathological findings and the presence of GNAS1 mutation in a mosaic state in different endocrine and non-endocrine tissues, combined with the clinical description of this case in the medical records, illustrated the challenges in treatment and consequences of disease activity. Crucially, the results derived from our large pituitary gigantism cohort and our further studies in specific genetically predisposed forms (such as X-LAG, AIP mutation– or MAS– related cases) pointed out that pituitary gigantism is a severe therapeutic challenge, requiring a multimodal treatment approach. However, one of the major findings of our research shows that early recognition and effective management in terms of sustained hormonal control and pituitary tumor shrinkage are essential for limiting the pathological effects on height and multi-organ disease burden. [less ▲]

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See detailContribution des concessions agricoles périurbaines à l’approvisionnement alimentaire de la ville de Kinshasa
Masiala Bode, Mabu ULiege

Doctoral thesis (2021)

The challenges of the demographic evolution of Kinshasa town and its food needs have led this doctoral research to focus on the case of peri-urban agricultural concessions. Two specific objectives have ... [more ▼]

The challenges of the demographic evolution of Kinshasa town and its food needs have led this doctoral research to focus on the case of peri-urban agricultural concessions. Two specific objectives have been assigned to this doctoral thesis. The first was to analyze the land security of farm who use agricultural concessions. The second focused on the analysis of the production systems of these peri-urban agricultural concessions. These two objectives were operationalized separately and integrated together through the adaptation of the evolving theory of property rights over rural agricultural land in Kinshasa. The development of this thesis required the adoption of an inductive scientific approach based on the analysis of documentary resources, interviews with key ressources persons, surveys of agricultural concessions and observations, with agricultural concessions of the peri-urban commune of Mont-Ngafula in Kinshasa as area study. It emerges from the results of this thesis that: - The area of the municipality of Mont-Ngafula devoted to agricultural concessions between 1975 and 2015 is to nearly 5,491.65 ha, or 15.3% of the total area of this municipality; - The rural lands of Mont-Ngafula are managed by administrative authorities and customary chiefs. This cohabitation pushes the purchasers of agricultural concessions to formalize their land status in two phases. First by contacting the customary chief and with the Conservator of land titles. This double validation of the land status gives the security of land tenure use to the agricultural concessions ; - The users of agricultural concessions are mostly natural persons active in non-agricultural sectors. They are not agricultural professionals and do not reside in their agricultural concessions. They use few and unskilled labor force and the rudimentary production equipment. The rate of valuation of land agricultural concessions is low. This level decreases with the increase in the area of agricultural concessions; - The foodstuffs produced are of plant and animal origin. Crop yields are far lower than theoretically conceivable minima. The rearing of backyard animals, livestock and fish farming are of less importance. The holders of agricultural concessions prioritize arboriculture. This is to quickly obtain the empyteose contract and to keep it. This contract is the only officially recognized land title in the DRC; - Income from agricultural production is predominantly negative in all categories of agricultural concessions. When these incomes are positive, they represent absolutely nothing compared to the plus-value of land in Mont-Ngafula. Access to this plus-value is facilitate by the possibility of obtaining an authorization to change the destination of land acquired under agricultural concessions to residential land. It emerges from the investigations carried out that the security of the agricultural land concessions does not have incentives for agricultural investment. Indeed, the majority of agricultural concessions in the Municipality of Mont-Ngafula benefit from land security which, unfortunately, does not benefit the food supply of the city of Kinshasa, but rather serves to hoard land capital whose surplus value in the peri-urban areas of Kinshasa only increases because of the continuous horizontal extension of Kinshasa town. Faced with this paradox and to preserve the agricultural vocation of agricultural concessions on the outskirts of Kinshasa, the following recommendations are proposed: the subordination of the emphyteutic rental contract by the agricultural contract, the professionalization of agriculture in agricultural concessions (profile of the manager, production system and technical services), access to credits for financing agricultural activities and, the application of a property tax at differentiated rates according to the level of development of the agricultural concessions acquired. Finally, research on the contribution of peri-urban agriculture to the food supply of the city of Kinshasa, in particular the contribution of agricultural concessions, should continue and intensify. [less ▲]

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See detailEnhanced Efficacy and Economic Feasibility of Anaerobic Soil Disinfestation Combined with Carbon Source and Cover Tarps in Controlling Strawberry Soil-borne Diseases
Song, Zhaoxin ULiege

Doctoral thesis (2021)

Pre-planting soil fumigation is a common practice for controlling strawberries (Fragaria×ananassa Duchesne) soil-borne diseases worldwide. Methyl bromide was the preferred fumigant for growers until it ... [more ▼]

Pre-planting soil fumigation is a common practice for controlling strawberries (Fragaria×ananassa Duchesne) soil-borne diseases worldwide. Methyl bromide was the preferred fumigant for growers until it was classified as an ozone-depleting substance, and its utilization was gradually restricted and legally phased out in 2015 in China. Chloropicrin or 1, 3-dichloropropene as the main alternative fumigants for methyl bromide are not sustainable. These kinds of broad-spectrum fumigants require a commercially licensed application, are costly, and are potentially hazardous to agricultural workers and the environment. These negative side-effects have promoted the search for alternatives that growers can use to control soil-borne diseases. Anaerobic soil disinfestation (ASD) is widely evaluated to suppress soil-borne diseases economically in numerous crops. The efficacy of the ASD technique varies with the form of the carbon source and its quantity, the soil properties, the temperature, and the cover tarps. The influence of different tarps on ASD efficacy is not documented. The structure of the thesis was divided into three parts: 1) the first part focused on optimizing ASD technologies by testing several carbon sources, cover tarps, soil moisture, and air temperature to reduce ASD cost while maintaining the efficacy; 2) using high-throughput sequencing (HTS) technologies to monitor the soil microbial communities before and after ASD treatments; 3) organizing field trials to evaluate the effect of ASD on control strawberry soil-borne diseases and the responses of plant growth, yield, and grower’s income. In the laboratory experiments, we evaluated the efficacy of three films used for ASD. The films included: polyethylene (PE), totally impermeable film (TIF), and virtually impermeable film (VIF). Water irrigation was used as a blank control. The result indicated that the combined factors of maltose, 28℃ temperature, and 30% of soil moisture carried out for ASD were more efficient than the other conditions by orthogonal experimental studies. Also, ASD using maltose as an organic amendment and sealing with TIF obtained the higher suppression against Fusarium spp. (> 99.5%) and Phytophthora spp. (> 99.3%). In the field trials, the efficacy of ASD using 6 and 9 t/ha maltose and sealing with TIF was evaluated and compared with reference treatment with chloropicrin (Pic), soil solarization (Sol), or untreated control. Compared with the untreated soil, ASD treatments highly reduced the colony number of Fusarium spp. and Phytophthora spp., and successfully controlled the damage caused by root rot wilt disease. ASD significantly increased the soil’s nutrition which promoted plant growth. Also, it significantly increased strawberry yield, which was similar to the Pic but better than the solar energy treatment. The analyzed fungal and bacterial microbiota did not show significant differences in the taxonomic richness and diversity between the compared treatments. Nevertheless, compared with the blank control, ASD treatments seemed to cause a modification change of the soil bacterial and fungi taxonomy composition at the class and genus levels even though the shift was not significant. In the second field trial, to reduce the cost of ASD and to promote its commercial application, the impact of 6 tons/ha composted chicken manure (CCM, CCM6) or 12 tons/ha CCM (CCM12) and TIF against soil-borne pests was evaluated. The results showed that the colonies of Fusarium spp. and Phytophthora spp. reduced significantly after ASD. With ASD treatment, the concentration of ammonium nitrogen, nitrate-nitrogen, and organic matter was significantly increased, but the oxidation-reduction potential was decreased in the soil. Besides, the strawberry plant height, stem thickness, and yield were significantly higher than the control. The strawberry marketable income was higher with ASD, the economic benefit could be due to the suppression of soil-borne disease reduction and the improvement of soil nutrition. The soil bacterial and fungal diversity and richness increased after CCM 6 treatment, but there was no significant difference between the CCM12 and the control. The increased biological control agents lead to the suppression of soil-borne pathogens. In summary, the results of the three experiments showed that adding maltose or compost chicken manure as a carbon source and coupling it with TIF for ASD has a great potential to replace chloropicrin for soil-borne diseases control in commercial strawberries production. [less ▲]

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See detailUnraveling Neurod1 mechanism of action in the differentiation of the intestinal secretory lineages in zebrafish
Reuter, Anne-Sophie ULiege

Doctoral thesis (2021)

The bHLH transcription factors belonging to the ARP/Ascl superfamily are key regulators of cell differentiation in a wide range of tissues. We noticed a striking diversity among these ARP/Ascl factors ... [more ▼]

The bHLH transcription factors belonging to the ARP/Ascl superfamily are key regulators of cell differentiation in a wide range of tissues. We noticed a striking diversity among these ARP/Ascl factors when involved in the determination and differentiation of the endocrine cells. In this study, we first assessed whether different members of the ARP/Ascl family could rescue the gut phenotype of the ascl1a-/- zebrafish mutant, that presents a loss of all intestinal secretory cells. We showed that Neurod1 is the only factor of the family able to rescue the enteroendocrine cells while the others only rescue goblet cells in ascl1a-/- mutant intestine, and highlighted that this role is modulated by an Evolutionary Conserved Domain (ECD) in the protein. Additionally, RNA-sequencing analysis suggest that ECD domain acts as a repressor of the goblet lineage. Furthermore, we investigated the role of ECD domain within the endogenous gene by creating a zebrafish mutant line by CRISPR/Cas9 and performed loss of function studies. Finally, we introduced insights on interacting partners of Neurod1. Altogether, the results of our study provide new understanding in Neurod1 mechanism of action, especially through the highlight of a conserved domain present after the bHLH domain that seems important for target gene repression. [less ▲]

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See detailMonitoring the activity and composition of comets with TRAPPIST telescopes
Moulane, Youssef ULiege

Doctoral thesis (2021)

Comets are remnants of the early stages of the Solar System and the most primitive Solar System bodies. Understanding their nature and evolution history provides important clues about the formation of the ... [more ▼]

Comets are remnants of the early stages of the Solar System and the most primitive Solar System bodies. Understanding their nature and evolution history provides important clues about the formation of the Solar System and the planets. Comets contain complex organic molecules, and may have played a key role in delivering water, organics and noble gases from the interstellar medium to the early Earth, contributing to the origin of life. The strong scientific interest in the Solar System small bodies is well demonstrated by numerous space missions in the recent years, such as Stardust, Deep Impact, Dawn and New Horizon etc. Particularly, ESA’s very successful Rosetta mission recently visited comet 67P/Churyumov–Gerasimenko and made several ground-breaking discoveries that have dramatically increased our knowledge about comets. However, most of the space missions can only perform short-term studies over a narrow time window of single objects. We are currently lacking long-term observations to study variations in the activity and composition in the coma of a comet and how it evolves along its orbit around the Sun. We regularly use the two robotic TRAPPIST telescopes to observe relatively bright comets (V<12 mag) that are visible in both hemispheres. These telescopes are equipped with narrow-band cometary filters that allow us to collect images of a comet at wavelengths where the light is emitted by the main gaseous species accessible in the optical (OH, NH, CN, C2, and C3). In addition, we observe comets in three continuum windows (scattered sunlight) that allow us to characterize the dust component of the comet. Thanks to the large amount of telescope time available on both telescopes for this project, we collected a unique data set of thousands of photometric measurements of 35 comets including 18 Jupiter-family Comets (hereafter JFCs) and 16 Long Period Comets (hereafter LPCs) in addition to the first active interstellar comet 2I/Borisov which was discovered in 2019. Each comet is monitored along an important part of its inner solar system orbit, starting at 3 au from the Sun (where water start to sublimate) and all the way to its perihelion. Post perihelion, we followed the comet again all the way out to 3 au at least. Then, through cometary coma models, the abundances of the main chemical species (accessible in the optical part of the spectrum) and dust production proxy (known as Afrho) and its color were determined. These measurements, thanks to the high quality and homogeneity of the observations and of the verified analysis procedure, allowed us to address important and long debated questions like the existence of comet compositional classes (comet taxonomy), the changes of molecular abundance ratios with the distance to the Sun and the link between chemical composition and dynamical origins, which is a fundamental step in understanding the formation of comets and the Solar System itself. Among 29 comets for which the gas emissions were detected (at least CN and C2), we identified three depleted comets in carbon-chain elements. These comets are 21P/Giacobini–Zinner, 260P/McNaught and 398P/Boattini in addition to the first interstellar comet 2I/Borisov. 21P is known as a depleted comet for a long time , but we confirm its depletion in its 2018 passage. The other three comets were found to be depleted in C2 and C3 for the first time with TRAPPIST. We made an extensive monitoring of the activity of the first interstellar comet 2I/Borisov. We presented an initial characterization of its activity including magnitude, Afrho dust parameter and dust colours during our observation period. 2I/Borisov was found to be depleted in C2 with respect to CN similar to the Solar System comets carbon-depleted group. No LPC was found to be depleted in carbon-chain elements, except for comet C/2019 Y4 which was at the limit of depleted comets before its fragmentation where we see a significant change in its coma composition. We also found four comets (21P, C/2015 V2, C/2017 T2 and C/2018 W2) depleted in NH with respect to OH and CN. In term of dust activity, most comets show a normal dust/gas activity with respect to the heliocentric distance, except for comet C/2017 O1 which shows a higher dust/gas ratio (especially for Afrho/OH) and comet C/2018 Y1 that shows a lower dust/gas ratio (in both Afrho/OH and Afrho/CN) with respect to most comets. We made a follow-up of five JFCs that showed outbursts. These comets include 29P/Schwassmann-Wachmann 1, 123P/West-Hartley, 155P/Shoemaker, 243P/NEAT, and 260P/McNaught. Comet 29P, as usual, shows multiple outbursts with various amplitudes while other comets show an unique outburst. We discussed the evolution of the outbursts for each comet, by measuring the magnitude, Afrho parameter and dust colours. The dense monitoring of comets allows us to investigate new topics like the heterogeneity of the nuclei composition and the determination of their rotation period through the analysis of the flux variations and of the coma features (jets). We found that the rotation period of comet 41P was surprisingly changed by 26 hr in just two months while the rotation period of comet 46P did not change on both sides of perihelion with an average value of 9.10±0.05 hr. The regular measurements of the comets activity and composition from optical measurements are also invaluable to support observing programs on larger ground based or space telescopes that we plan with our collaborators or other groups to perform complementary studies of the most interesting objects through optical and IR spectrometers (e.g, 21P and 66P/du Toit). In this work, we also discussed the reactive collision of electrons with molecular cations in cometary coma. In order to improve our understanding of the kinetics of the cometary coma, theoretical studies of the major reactive collisions in these environments are needed. Deep in the collisional coma, inelastic collisions between thermal electrons and molecular ions result in dissociation and vibrational excitation of the ions, the rates of these processes are especially elevated due to the high ion and electron densities in the inner cometary coma. We presented the study of reactive collisions of electrons with CO+ and H2+ molecular cations using the multi channel quantum defect theory (MQDT), such as dissociative recombination (DR), vibrational excitation (VE) and vibrational de-excitation (VdE), to understand the importance of these reactive collisions in producing carbon, oxygen and hydrogen atoms in cometary activity. The results shows that among all reactive collisions taking place between low energy electrons and CO+/H2+, the dissociative recombination is the most important process at electronic temperatures characteristic of comets, which can be a major source of atoms in the cometary coma at small cometocentric distances. [less ▲]

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See detailLeaving Europe: Emigration, aspirations and pathways of incorporation of Maghrebi French and Belgians in Montréal
Mandin, Jérémy ULiege

Doctoral thesis (2021)

When it comes to migration, Western European countries such as Belgium and France are typically described as destination countries. Yet, emigration remains an important phenomena in most of European ... [more ▼]

When it comes to migration, Western European countries such as Belgium and France are typically described as destination countries. Yet, emigration remains an important phenomena in most of European societies. This emigration is often portrayed as somehow different from migrations ‘from the South.’ The western European migrant – sometimes referred to as ‘expat’ – is generally depicted as a dynamic individual characterized by an entrepreneurial spirit and a taste for adventure. At a time where many European societies experience both the consequences of financial and economic crisis and growing tensions about cultural and religious diversity, very few attention has been given to the relation between such structural dynamics and the emergence of emigration practices among young Europeans. This research is an attempt to explore such a relation by focusing on the migration practices of Belgians and French youngsters of Maghrebi origins leaving Europe for the Canadian city of Montréal. More precisely, the research focuses on the aspirations - defined as socially situated representations of the future – that inform the emigration practices of Maghrebi Europeans. Building on an ethnographic field research conducted in France, Belgium and in the city of Montréal, the thesis is an exploration of migration related aspirations and their evolution at three stages of the migration process: before departure, during migration and once arrived at destination. The goal of the research is to understand the factors that inform the development of emigration aspirations among Maghrebi European people, how these aspirations are channeled during migration and how they evolve after migration. Through the focus on migrants’ aspirations, the research questions how perspectives for a desirable future are distributed both in Europe and in Montréal and how this distribution is highly dependent of one social position. The collection of biographic interviews with Maghrebi European migrants allows to understand the various representations of the future that inform the emergence of migration desires. This highlights a set of various experiences – experiences of ‘existential stuckedness’ or of ‘existential mobility’ – that evolve during the migration process. The ethnographic data also allows to explore the various pathways of incorporation that are carved out by Maghrebi Europeans in Montreal in order to sustain possibilities for a desirable future. These pathways, sometimes constitutes alternatives to the types of incorporation promoted by the Canadian and Québec authorities. In this sense, looking at how migrants think about their future and how they try to organize it also highlights forms of agency that exceed societal expectations. [less ▲]

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See detailLe rôle du théier dans les petites exploitations familiales au Burundi : le cas des complexes théicoles de Teza et d’Ijenda
Bitama, Pierre ULiege

Doctoral thesis (2021)

Since its introduction in 1963, the tea plant has been the heart of a strategic sector in Burundi. Tea cultivation is of paramount importance in the socio-economic life of more than 60,000 tea farmers. It ... [more ▼]

Since its introduction in 1963, the tea plant has been the heart of a strategic sector in Burundi. Tea cultivation is of paramount importance in the socio-economic life of more than 60,000 tea farmers. It creates employment and provides foreign exchange export earnings for the country. The main objective of the research was to emphasize the importance of the tea plant in the means of subsistence of the tea farmers. The specific objectives are: (i) to identify all the resources of tea farmers that enable them to ensure their livelihood, (ii) to highlight the risks and constraints faced by tea farmers, (iii) to analyse the strategies developed by tea farmers to ensure their survival, (iv) to highlight the contribution of tea in the livelihood of tea farmers, (v) to identify and discuss the challenges and constraints in the country's tea sector. To achieve the specific objectives, the study used an analytical model - the livelihood model - to understand the farming system as a whole before a specific study on the tea plant through the analysis of the value chain of the sector on its technoeconomic and governance aspects. The study was carried out through the analysis of primary data and secondary data via a desk research. The primary data were collected in 2018 and 2019 from actors (managers) responsible for tea production, processing and marketing, as well as from a random sample of 120 tea farmers in the Teza and Ijenda areas. The results showed that tea farmers depend on complementary resources. They are facing a wide range of risks and constraints, particularly with regard to food and vegetable crops, a threat to tea farmers who mainly rely on agriculture even though adaptation strategies are being developed. On the other hand, the exploitation of the tea plant in the study area has demonstrated a particularity of the plant and the results highlighted the intrinsic characteristics and virtues of the tea plant. The regular income from the tea plant throughout the year enables tea farmers to purchase food on a regular basis, to overcome the lean season and to meet other needs. This regularity of income classifies smallholders in the zone into a poverty typology of financially secure farmers who are likely to fall into the " wealthy " category if their non-monetary means of survival improve. In addition, the plant's perennial nature and resilience to the country's climatic hazards mean that it is exploited from generation to generation. It provides a pension for tea farmers in old age and is the only guarantee of credit. Implementation of the recommendations developed (gradual replacement of nonproductive tea plants, continuous reforestation, product diversification, etc.) to address the challenges identified in the tea sector would increase yield, profitability and strengthen the resilience of tea farmers. [less ▲]

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See detailAbout some notions of regularity for functions
Loosveldt, Laurent ULiege

Doctoral thesis (2021)

Given a function, a first natural desire is to know its ``behaviour''. To achieve this goal, different notions, such as differentiability, Lipschitz or Hölderian conditions, have been introduced through ... [more ▼]

Given a function, a first natural desire is to know its ``behaviour''. To achieve this goal, different notions, such as differentiability, Lipschitz or Hölderian conditions, have been introduced through the time, with more and more preciseness. In this thesis, we aim at characterizing the regularity of functions from different points of view that generalize the precited ones, and using different associated functional spaces. First, we focus on uniform regularity, investigated through Besov spaces of generalized smoothness. These spaces were originally defined in terms of Littlewood-Paley decompositions and, quickly afterwards, a characterization using finite differences was given. Using this last one, we present some alternative definitions for Besov spaces of generalized smoothness, involving elementary objects: (weak) derivatives, polynomials and convolution. This is made in order to understand as precisely as possible what means the belonging to a given Besov space. Initially, these spaces are known to be interpolation spaces between Sobolev spaces. A first generalization was obtained by introducing a function parameter in the interpolation formula. The spaces we consider here are even more general and, as an intent to ``close the circle'', we define a new method of interpolation for which Besov spaces of generalized smoothness are still linked to Sobolev spaces. Then, we study pointwise regularity by defining functional spaces that generalize both the ones of Hölder and Calderón and Zygmund. After nearly characterizing them by the mean of wavelet coefficients, we establish a multifractal formalism particularly well adapted to explore the pointwise regularity through our new spaces. In fact, as their definition is a kind of localization around the point of interest of generalized Besov conditions, it is not a surprise that Besov spaces of generalized smoothness play a major role in this formalism. After investigating the multifractal nature of pointwise spaces of generalized smoothness, we focus, in a more functional analysis point of view, on their interaction with partial differential equations. This follows the trail of Calderón and Zygmund as we link generalized pointwise smoothness with some families of operators. This leads to a theorem that allows to give the regularity of the solution of an elliptic partial differential equation by formulating it from the regularity of the coefficients and the right-hand side of the equation. Finally, at a midpoint between uniform and pointwise regularites, we study functions that are continuously differentiable on a compact set. Even if the question seems naive and harmless at first look, all good habits from open sets are missing and a whole new theory needs to be established. Based on deep results of functional analysis, we characterize the completeness of the defined functional space and show that, for any compact set, the restrictions on it of the continuously differentiable functions on $\R^d$ are dense in our space. Finally, the latter is compared with other spaces, more frequently met in the literature. [less ▲]

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See detailEtude phytochimique et biologique de trois plantes du genre Zanthoxylum
Tanoh, Amenan Evelyne ULiege

Doctoral thesis (2021)

The genus Zanthoxylum (Rutaceae) includes plants known for their uses in traditional medicine around the world. In Côte d'Ivoire, nine species have been identified (Zanthoxylum atchoum, Z. leprieurii, Z ... [more ▼]

The genus Zanthoxylum (Rutaceae) includes plants known for their uses in traditional medicine around the world. In Côte d'Ivoire, nine species have been identified (Zanthoxylum atchoum, Z. leprieurii, Z. macrophilum, Z. mezoneurispinosum, Z. parvifoliolum, Z. psammophilum, Z. rusbescens, Z. gelletii and Z. zantoxyloides). Zanthoxylum geniuscontains several plant exhibitingbiological properties (antioxidant, anti-inflammatory, anticancer, antifungal, antitumor and antimicrobial etc.). The present research focuses on three species of Zanthoxylum harvested in Côte d'Ivoire: Z. leprieurii, Z. psammphilum and Z. mezoneurispinosum. Its goal is to valorize these plants through their volatile and non-volatile secondary metabolites. The first species Z. leprieurii is extensively used in traditional medicine because of its numerous biological properties. However, to date, no traditional use is known for the last two species endemic to Côte d'Ivoire. The lack of knowledge, especially on Z. psammophilum and Z. mezoneurispinosum, led to the realization of a phytochemical study for the determination and confirmation of biological activities of the constituents of various organs (leaves, trunk bark, roots and fruits) of these plants. The analyses of the chemical composition of essential oils and the biological properties of the various organs were realized. From a hydrodistillation with a Clevenger-type apparatus, the essential oils are extracted and analyzed by gas chromatography coupled with mass spectrometry (GC/MS). For the Z. leprieurii species, a study of the effect of the season on the chemical composition of the various organs of the essential oils was carried out. The statistical analysis of the results obtained made it possible to group the chemical compositions into three classes. The first class is characterized by constituents from fruits dominated by β-myrcene and citronellol. The second class was composed by compounds extracted from bark with an abundance of tridecan-2-one. The last class includes tridecan-2-one, (E) β-caryophyllene and dendrolasin which are derived from essential oils extracted from the leaves. In Z. psammophilum, the chemical compounds extracted from the essential oil of the bark are mainly characterized by methylketones and dominated by tridecan-2-one. However, essential oils from the leaves and roots are represented by methylketone and sesquiterpenes respectively. The main characteristics of essential oils isolated from Z. mezoneurispinosum are monoterpenes (α-pinene) in the aerial parts, while the underground part has an abundance of sesquiterpenes (γ-elemene and cyclosativene). The essential oils extracted from the three plants have satisfactory biological activities. These are antioxidant, anti-inflammatory, insecticidal and anti-plasmodial activities. In addition, the phytochemical study of the leaves of Z. mezoneurispinosum carried out by column chromatography, high pressure liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) allowed the isolation of a total of eight compounds. They consist of four alkaloids (1-hydroxy-3,4-diméthoxy-N-méthylacridone, chelerythrin, skimmianine and xanthoxoline), one triterpene (lupeol), a cinnamic acid derivative (methyl 4-coumarate), a carboxylic acid derivative ((E)-4-isobutylamino-4-butenoic acid) and a flavonoid (4'-methoxy-5,7-dihydroxyflavone or acacetine). The different results indicate that these plants can be useful to human. Indeed, a better knowledge of the chemical composition of the different essential oils, their biological activities and their isolated compounds, can promote greater use in perfumery, food, cosmetics, medicine, etc [less ▲]

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See detailSmart Regulation for Distribution Networks – Modelling New Local Electricity Markets and Regulatory Frameworks for the Integration of Distributed Electricity Generation Resources
Manuel de Villena Millan, Miguel ULiege

Doctoral thesis (2021)

Growing awareness of the effects of man-made global warming is leading societies worldwide to re-evaluate our seemingly ever-increasing energy requirements. The need to understand and mitigate the issues ... [more ▼]

Growing awareness of the effects of man-made global warming is leading societies worldwide to re-evaluate our seemingly ever-increasing energy requirements. The need to understand and mitigate the issues brought about by our current use of the world's resources has thus become a pivotal element in the political agendas of most regions. Accordingly, curbing anthropogenic greenhouse gas emissions has been the goal of many of the political decisions of the past decade. In this context, the electricity sector is undergoing deep structural changes to accommodate intermittent renewable electricity generation resources into a system originally designed to rely on dispatchable power plants to supply our energy needs. One of the main changes consists of a decentralisation of the sector, bringing the generation assets closer to the place of final consumption. This creates regulatory challenges that may jeopardise the integration of distributed renewable energy resources (DER). This PhD dissertation presents several research contributions dealing with these challenges. In the first part of our work, we have created a simulation-based approach to study the effects of different regulatory frameworks on the deployment of DER installations. DER deployment, in turn, is shown to have a notable impact on the revenue of the distribution system operator (DSO), which is also assessed with our simulator. Our approach is designed so as to offer a tool for policy makers and regulators to discriminate between different regulatory frameworks depending on their impact on the distribution network, before implementing them in real life. The second part of our dissertation models different decentralised electricity markets where consumers may exchange electricity, focusing on the concept of renewable energy communities (REC). We have designed a model of interaction that simulates an REC where its members can offer flexibility services by means of a centralised agent such as the REC manager. In addition, we analyse the allocation of local electricity generation among the REC members, and propose an algorithm based on \emph{repartition keys} to minimise the total electricity costs of the REC. The modelling tools developed in this thesis highlight a trade-off between promoting the integration of DER and containing their impact on the DSO revenue. In addition, they show that creating RECs may help maximise the use of local production and, therefore, lower the electricity costs of these communities. Despite having been studied for a few decades now, the promotion of DER is still very much in the political agenda in many regions. Unstable policies concerning these technologies, along with an insufficient understanding of the challenges they pose to the traditional electricity system, have hindered their natural integration into the electricity networks. These problems, though deeply studied in this thesis, call for further research to fight man-made global warming. [less ▲]

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See detailStudy of chemical and enzymatic functionalization of lignocellulosic natural fibers
Morin, Sophie ULiege

Doctoral thesis (2021)

Within the commercially available materials, composites are a class of hybrid material constituted of at least two components. Used for structural and semi- structural applications, glass-fibers ... [more ▼]

Within the commercially available materials, composites are a class of hybrid material constituted of at least two components. Used for structural and semi- structural applications, glass-fibers composites are widely spread. Due to environmental concerns regarding the final glass-fibers reinforced composites, natural plant fibers have been identified as a potential ersatz. Natural fibers are selected on the base of their intrinsic mechanical resistance, similar nay enhanced than glass-fibers. Local fibers suitable for such application could be found all around the world. In Europe, natural fibers market is singularly different from the rest of the world. Instead of being ruled by cotton cultivation and trade, flax and hemp represent the main part of the fibers culture and market in Europe. Their physico-chemical properties turn them suitable for use as reinforcement agent in plastic matrix. To elaborate composite, many steps are required from fibers harvesting to the obtaining of a final functional material. Each step includes multiple parameters to control which affect the resulting composite mechanical properties. Different parameters of the composite elaboration were evaluated to determine which affect the most the final material mechanical properties. Constitutive biopolymers of the fibers were found to play a crucial role in the improvement of the polypropylene and thermoplastic starch reinforcement. In heterogeneous materials such as composites, an optimal load transfer is researched to fully exploit the properties of both initial components. Interface quality between fibers and matrix determine this load transfer. In order to improve the fibers-matrices compatibility, fibers treatments exist such as chemical modification or enzymatic functionalization. The effects of these treatments were evaluated at the fibers level and the resulting composite. This manuscript describes and studies the design of functional natural fibers as plastic reinforcement agent. [less ▲]

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See detailThe impact of fat formulation and emulsifiers on the macro- and microscopic physical properties of palm oil-based puff pastry margarines
Detry, Roxane ULiege

Doctoral thesis (2021)

This work presents advances in vegetable fat crystallization for puff pastry margarine applications

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See detailRegional variation in the Coffin Texts: A study of sentence structure, verbal structure and graphical forms
Grotenhuis, Jorke ULiege

Doctoral thesis (2021)

In the pursuit of regional variation in Ancient Egypt on a linguistic level, this thesis proposes to use the mortuary liturgy of the Coffin Texts as a base from which to extract signs of regionally ... [more ▼]

In the pursuit of regional variation in Ancient Egypt on a linguistic level, this thesis proposes to use the mortuary liturgy of the Coffin Texts as a base from which to extract signs of regionally conditioned variation in the language. In this thesis, three approaches were used in order to visualize the existence of regional variation in the Middle Egyptian language. In the first approach, the sentence structure was compared. Using the metaphor that spells could be treated as proteins, biomedical algorithms were used for cluster analysis of the structure. The second approach tackles the verbal structure of the sentences instead, applying the same method which was used for the sentence structure. Finally, the graphical form of the verbal lemmas was studied in order to show preferences for spelling and written structure. Additionally, the graphical form of morphological features of verbal constructions was studied. The approaches used in this thesis were able to visualize that regional conditioned patterns exist within the Coffin Texts. [less ▲]

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See detailStatistical analysis of vertical land motions and sea level measurements at the coast
Gobron, Kevin ULiege

Doctoral thesis (2021)

Ensuring the long-term stability of sea-level measurements at the coast is essential for the sustainable management of coastal territories. To do this, scientists mainly rely on two complementary ... [more ▼]

Ensuring the long-term stability of sea-level measurements at the coast is essential for the sustainable management of coastal territories. To do this, scientists mainly rely on two complementary measurement techniques: tide-gauges, which measure changes in sea-level with respect to the coast, and space geodesy, which allows measuring the vertical movements of the coast itself, with respect to the centre of the Earth. These two techniques are complementary because the correction of the vertical land motions estimated using geodetic techniques allows estimating geocentric sea-level change at the coast, and thereby to understand the origin of sea-level change better. To estimate and improve the stability and quality of these two sources of information, this thesis proposes methodological developments dedicated to the estimation of the precision of each type of observation and investigates the potential sources of errors. [less ▲]

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See detailPerennial crop systems in Dak Lak province, Vietnam: Practices and socio-economic analysis
Phan Thi Thuy, ULiege

Doctoral thesis (2021)

Perennial crops play a valuable role in agricultural economics, as they provide goods for export and jobs for the workforce as well as contribute significantly to economic prosperity at the national level ... [more ▼]

Perennial crops play a valuable role in agricultural economics, as they provide goods for export and jobs for the workforce as well as contribute significantly to economic prosperity at the national level. Vietnam has a high potential for perennial crop development, and thereby achieve an explosive growth in agricultural commodities. In terms of perennial crops, Vietnam now ranks among the top five international exporters of coffee, pepper and cashew. Vietnam is the second-largest producer of coffee worldwide, while it is the leading exporter of pepper globally. In 2018, the planted area of the dominant perennial crops (coffee, pepper, rubber, tea and cashew nut) reached around 2.2 million hectares (ha) nationwide, an increase of 9,000 ha compared to 2017. The Western Highlands has the largest region of perennial crop production with an area of 1.151 million ha. Dak Lak province has favorable conditions of soil (1,450 ha of basaltic soils of volcanic origin, which equals two thirds of the total basaltic soil area nationwide), as well as weather and amount of arable land, which creates an advantageous situation for the culture of perennial crops. Remarkably, the planted area of coffee and pepper dominated production at about 30% of the whole country’s production in 2018, respectively. Over the years, perennial crops have changed considerably being usual dynamics of requirements. Despite its advantages and positive development trends, provincial perennial crop production has faced numerous constraints due to price fluctuation, unpredictable climatic trends, and incidence of pests and diseases. Thus, perennial crop production needs further research to ensure more evidence. Based on a systematic survey, focus group discussion, key informant interviews and participatory observation, this research project was undertaken to evaluate the practices and socio-economics of perennial crop systems in Dak Lak province, namely monocultures and intercropping systems. The aims of this project are to understand the distinct stages of perennial crop systems and to identify the socio-economic benefits of different systems concentrating on coffee and pepper crops. Additionally, the remaining aim of the study finds determinants affecting the farm’s decision of adoption. The results provide critical references for farmers and policymakers on implementation or decision to plant a particular perennial crop and strategies. The findings show that the type of crop that was planted by the farmers evolved considerably in terms of crop types, crops grown, farm size, type of system and an increase of total cultivated surface. In addition, under driving forces including socio-economic transformation, political changes and ecological movement, perennial crop systems are well changed. Indeed, for many years, perennial crop systems have experienced an evolution through five stages, namely large-scale coffee and rubber plantations; perennial crop systems which are state-owned farms and cooperatives; intensified perennial crop systems; mixed crop systems, and the specialized and diversified perennial crop systems. At present, perennial crop systems are put into practice which take into account climate change, marketing and losses of fertile lands. These systems include monocultures and intercropping, which are two representative models of perennial crop systems which are investigated in this study. Simultaneously, a comparative assessment of the socio-economic benefits between two monocultures (coffee and pepper mono cropping) and an intercropping system (coffee and pepper intercropping) is presented in which the intercropping is more efficient than the monoculture under the context of constraints on key resources, risk and uncertainty. Respectively, intercropping is not only demonstrated to have high economic returns and limitations of economic risk due to the volatile market but also to have the benefits of extended seasonal employment and attraction for women as farmworkers on small farms. In other words, coffee and pepper intercropping is the most desirable option to obtain socio-economic benefits in perennial crop systems. In addition, the classifications in different approaches and groups producing are also organized to clarify these economic performances by cost-benefit analysis. The further results are obtained that intercropped farm approaches, especially in intercropped coffee farms (ICFs) generate more economic earnings than intercropped pepper farms (IPFs) while group producing coffee (GpC) appears to be more appropriate for smallholders than group producing pepper (GpP) does. At the same time, conclusions from binary and multiple logistic regression analysis highlight factors affecting decision-making of farms’ decision in adopting. These factors include household characteristics, farm profits and crop profiles. This study supplies information that will allow farmers to develop productive planning with respect to choosing suitable perennial crop systems, and assist policymakers in forming small-scale perennial crop production strategies in Dak Lak province. In addition, the factors highlighted here are taken into account in the development of perennial crops. [less ▲]

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See detailIntegrated Structural-Geophysical-Geomechanical Models of Landslides in Seismic Regions
Mreyen, Anne-Sophie ULiege

Doctoral thesis (2021)

Slopes in hilly or mountainous regions can present complex morphologies due to erosional, gravitational and seismotectonic processes. In seismically active regions, mountain ranges are usually ... [more ▼]

Slopes in hilly or mountainous regions can present complex morphologies due to erosional, gravitational and seismotectonic processes. In seismically active regions, mountain ranges are usually characterised by numerous slope failures in the form of shallow to deep-seated landslides; yet, their origin is often not clearly established and must not necessarily be seismic. This thesis investigates deep-seated landslides of unknown origin (and age) that hint at a probable co-seismic development in regard to their regional seismotectonic context, site-related structural and geological setting, and distinct geomorphological shape. Such investigations include the reconnaissance of surface as well as subsurface structures with a variety of methods; here, we analyse landslide surfaces with satellite imagery, through geomorphological observations and structural measurements, while multiple geophysical techniques are used to reveal subsurface structures and to infer geotechnical properties of the ground. The work is focused on two study areas presenting rather ancient slope failures: the seismogenic Hockai Fault Zone in East-Belgium, with the Bévercé and the Pays de Herve landslides, and the seismic Vrancea-Buzau region in the Carpathian Mountains of Romania, with the Eagle's Lake and Balta landslides. A third study area, the Longmenshan Fault Zone in Central China with the Daguangbao and the Qinglincun landslides, is used as reference site to discuss landslides actually triggered by a recent earthquake, i.e. the 2008 Wenchuan event, and highlights mechanisms leading to co-seismic slope failure. A decisive approach of this work is the integration of the collected data into 3D geomodels of the respective sites; these allow to link the geophysical subsurface information to observed surface structures, as well as to assess landslide dimensions and to estimate the volume of landslide debris still in place. For two study areas, the Bévercé and Balta landslides, we present a numerical back-analysis with distinct element modelling in the 2D and 3D domain, respectively, to further comprehend mechanisms influencing the genesis and development of slope collapses possibly induced by earthquakes. These computations are based on geomodelled pre-failure slope shapes, structural settings derived from field measurements and geotechnical properties inferred from geophysical measurements. For both sites, numerical computations indicate the necessity of ground acceleration to achieve similar failure patterns as observed in their actual post-failure state. At last, we introduce conclusive key elements that link the observed markers deduced from the field measurements and numerical analyses to distinctive processes that are crucial components to comprehend the development of slope failures in seismic regions. The larger interest beyond the direct scope of this study is the deeper comprehension of regional seismotectonic processes that were active in the past to allow for better constrained seismic hazard evaluations in the future. [less ▲]

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See detailÉtude de l’influence de l’état de stress posttraumatique sur la vulnérabilité aux drogues chez la souris DBA/2J
Matonda Ma Nzuzi, ULiege

Doctoral thesis (2021)

Posttraumatic stress disorder (PTSD) and drug addiction are two comorbid conditions bound in a complex bidirectional relationship. On one hand, the mechanisms by which PTSD promotes the occurrence of drug ... [more ▼]

Posttraumatic stress disorder (PTSD) and drug addiction are two comorbid conditions bound in a complex bidirectional relationship. On one hand, the mechanisms by which PTSD promotes the occurrence of drug addiction are not fully understood. On the other hand, methodological and ethical limitations inherent to human studies do not allow a full understanding of the influence of drug addiction on the expression of PTSD symptoms. In an effort to contribute to the resolution of these two issues, the present thesis based on an animal model with DBA/2J mice, combined sequentially, in both directions, a drug-induced locomotor sensitization procedure and an animal model of PTSD based on an electric shock. Locomotor sensitization was achieved by repeated administrations of ethanol or cocaine at the same dose over several days. The PTSD-like symptoms were assessed several weeks after the electric shock with conditioned fear, sensitized fear and anxiety tests. Overall, the various experiments have shown, on one hand, that a PTSD-like experience in mice does not significantly increase the intensity of drug-induced locomotor sensitization. However, this PTSD-like experience indirectly strengthen drug sensitization through an interaction with some of its modulating factors. On the other hand, drug-induced locomotor sensitization does not directly affect the expression of PTSD in this animal model. However, drug sensitization can be considered as a form of stress sensitization. It induces on its own stress behaviors that add to the effects of the PTSD experience. Further studies on the subject would provide a better understanding of the co-morbidity between PTSD and drug addiction. [less ▲]

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See detailStructural, physicochemical and functional properties of cumin (Cuminum cyminum) proteins
Chen, Jingwang ULiege

Doctoral thesis (2021)

Nowadays, there is an increasing number of plant candidates for protein extraction as an alternative for animal sources. The investigation of new plant protein sources and the study of the effects of ... [more ▼]

Nowadays, there is an increasing number of plant candidates for protein extraction as an alternative for animal sources. The investigation of new plant protein sources and the study of the effects of processing methods on their structure, physicochemical, and functional properties obtain more attention and become necessary. Cumin (Cuminum cyminum) is a traditional and worldwide culinary spice. After the extraction of essential oils and oleoresin, a relatively important amount of defatted cumin residues is produced, which are rich in protein (28.33%) and constitute a good substrate for protein extraction. In this thesis, the composition of protein fractions from cumin seeds and their principal characteristics were studied, as well as the effects of different environmental conditions (pH and NaCl) and processing treatments (heat and high hydrostatic pressure treatment) on the structural, physicochemical and functional properties of cumin protein isolate (CPI) were assessed. First of all, the protein fractions and CPI were extracted from defatted cumin residues, and their characteristics were investigated. The protein fractions of cumin seeds were albumin (62.29%), glutelin (25.16%) globulin (11.12%), and prolamin (1.43%). The CPI presented most bands of albumin, globulin and glutelin, and had more disulfide bonds than major protein fractions when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The glutamic acid and aspartic acid were the predominant amino acids in cumin proteins, furthermore, more hydrophobic and aromatic amino acids were found in CPI than in protein fractions, and the content of essential amino acids in CPI and globulin were higher than in albumin and glutelin. The glutelin displayed greater exposure of tyrosine and tryptophan residues and bigger particle size compared to albumin and CPI, while CPI presented more α-helix (14.4%) and less β-strand (30.7%) than albumin and glutelin. These differences in structure and amino acid composition for CPI, albumin, and glutelin significantly influenced their hydrophobicity (Ho) and zeta-potential (ζ) (p<0.05), and as a consequence their emulsifying and gelling property. Albumin exhibited the highest emulsifying activity (EAI) and stability (ESI) and the smallest emulsion particle size (4.29 μm), followed by CPI and glutelin. The CPI was efficient in forming a gel at 80.6 °C, and glutelin could form the hardest gel at 92.6 °C. CPI and albumin could thus be potential candidates as emulsifying agents, and CPI and glutelin could be used for gelation in food industry. Overall, CPI displayed better amino acid composition and characteristics than the major protein fractions of cumin seeds, and therefore a deep investigation of CPI would be carried out for the application in food industry. Secondly, the effects of pH and NaCl on the structural, physicochemical, and functional properties of CPI were evaluated. The structure of CPI was greatly influenced by the pH adjustment and NaCl addition. The fluorescence intensity (FI) of CPI was reduced as pH reached a value close to 5.0 and the highest α-helix content (18.3%) in CPI was obtained at pH 5.0. The addition of NaCl led to a decrease in the α-helix content and an increase in the β-sheet for CPI. The ζ, Ho, and solubility of CPI were significantly reduced as pH reached 5.0 (p<0.05), whereas the addition of 0.5 and 1.0 M NaCl caused an increase in Ho and a decrease in solubility. CPI showed higher EAI and ESI at pH 7.0 and pH 9.0 with small emulsion droplet size, and the addition of 0.1 M NaCl produced an increase in ESI. At lower NaCl concentration (0.1 M), the EAI wasn’t affected, while the ESI was improved significantly (p<0.05). However, as pH changed to pH 5.0 or the addition of 0.5 M and 1.0 M NaCl, the emulsifying properties of CPI were reduced. All CPI emulsions showed pseudo-plastic behavior, and the apparent viscosity and viscosity coefficient (k) of the CPI emulsions at pH 5.0 were significantly higher than those for the other pH values, and increasing k values were found after the addition of NaCl. The desired emulsifying property of CPI might be obtained at neutral and alkali conditions with the addition of a lower concentration of NaCl. Thirdly, effects of heat treatments at 65, 75, 85 and 95 °C for 30 min on the structure and the emulsifying properties of CPI were investigated. The structure of CPI was remarkably influenced as heating temperature increased while fluorescence intensity decreased. After heat treatments at different temperatures, more protein molecules were unfolded and more compact conformations were formed, the α-helix content of CPI was increased, while the β-sheet content was decreased. A significant increase in the Ho of CPI was found after heat treatments, and the Ho reached 1030.6 for heated CPI at 95 °C. Heat treatments induced the formation of high molecular mass aggregates of CPI, which led to a decrease in the EAI and ESI of heated CPI at different protein concentrations (0.1%, 0.5% and 1.0%). However, the protein absorption in emulsions stabilized by heated CPI gradually increased with heating temperature increasing. Both emulsions stabilized by native and heated CPI showed shear-thinning behavior and exhibited a decrease in their viscosities with protein concentration increasing. Thermal treatments produced different effects on the flow behavior of emulsions formed by various protein concentrations. Indeed, the flow index (n) for heated CPI emulsions decreased for a 0.1% concentration, but increased for protein concentrations of 0.5% and 1.0%. More heated CPI absorbed on the surface of the oil droplet will be helpful for the production of emulsion gel with higher protein concentrations. Furthermore, the effects of high hydrostatic pressure (HHP) treatments (200, 400 and 600 MPa, 15 min) on the structural, physicochemical, and functional properties of CPI were studied. HHP treatments could result in the formation of more aggregates, more pores, irregular conformations, and bigger particle size from the results of SDS-PAGE, atomic force microscope (AFM), and scanning electron microscope (SEM). With pressure increasing, more protein aggregates with large protein molecular mass were formed which influenced the microenvironment of protein and led to a decrease in fluorescence intensity and an increase in α-helix content, a decrease in β-strand for CPI. Surface hydrophobicity of CPI significantly increased after HHP treatments, from 343.35 for native CPI to 906.22 at 600 MPa (p<0.05). HHP treatment at 200 MPa reduced the zeta-potential and solubility of CPI, while having a little effect at 400 and 600 MPa. After HHP treatments, the EAI and ESI of CPI were decreased with a significant increase in droplet size of emulsions (p<0.05). HHP-treated CPI at 400 and 600 MPa could form a heat-induced gel at lower Tgel (68.5 °C and 70.9 °C) with higher storage modulus (G') of 4100 Pa and 4170 Pa, respectively. HHP treatments might be a potential processing method in order to modify CPI making them potential candidates as gelation agent in food matrices. [less ▲]

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See detailPrediction of feed efficiency based on test-day liveweight of dairy cows estimated using animal characteristics and milk mid-infrared spectra
Zhang, Lei ULiege

Doctoral thesis (2021)

Due to the increasing world population, the consumption of milk and dairy products is raising. Optimizing the production of milk under the economic and environmental constraints is a challenge. In this ... [more ▼]

Due to the increasing world population, the consumption of milk and dairy products is raising. Optimizing the production of milk under the economic and environmental constraints is a challenge. In this context, knowing the feed efficiency (FE) of dairy cow is a key issue. Unfortunately, the acquisition of such records at individual and large scales is unfeasible. So, the current thesis aims to fill this gap by developing a FE predictive tool for dairy sector available at large and individual scales. To achieve this objective, the FE was assessed by calculating the ratio of fat and protein corrected milk (FPCM) to dry matter intake (DMI). Although FPCM is already routinely available, this is not the case for DMI. However, a literature equation exists to predict DMI from FCM, live bodyweight (BW) and the number of weeks of lactation. Recently, a methodology using the milk mid-infrared (MIR) spectrometry combined with the animal characteristics was developed to predict test-day BW records, leading to open new perspectives about the use of FE related traits for management and breeding purposes. So, the final achievement of this thesis is the development and the implementation of a FE prediction tool from traits easily recorded by dairy herd improvement (DHI) organizations, including namely the BW estimation. To achieve this objective, 3 main research activities were conducted in this thesis. The first research aimed to increase the calibration set and to apply feature selection algorithms during the modeling in order to improve the BW models' robustness and accuracy. Indeed, the presence of less informative variables in a prediction equation could impact negatively its robustness. Three feature selection algorithms were applied on 280 predictors to select the most informative ones from a dataset containing 5,920 records: partial least squares regression (PLS) combined with sum of ranking difference (SRD), PLS combined with uninformative variables elimination (UVE), and the output of Elastic net regression (EN). Parity, days in milk (DIM), milk yield (MY), and two MIR spectral points were selected as the most relevant variables to predict BW. Validation root mean square errors (RMSEp) of 60 kg were obtained for both PLS and EN regressions employing these 5 predictors, suggesting a better robustness of these models compared to the ones without MIR or using all 277 MIR variables. The RMSE values of validation set coming from another brand of spectrometer were around 64 kg. The second research work focused on the implementation of a BW equation in practice. Indeed, some poor quality BW predictions can be obtained using poor quality spectral data or by applying the model on samples for which the variability was not included in the calibration set. So, the objective of this work was to develop data cleaning methods easy to implement by DHI to ensure the quality of BW predictions. So, 3 data cleaning procedures and their combinations were tested on a DHI dataset containing 346,818 records: the deletion of 1% of extreme high and low predicted values (M1), the deletion of records when the global-H (GH) distance was greater than 5 (M2), and the deletion of records if the absolute fat residual value was higher than 0.30 g/dL of milk (M3). The interest of those procedures was assessed by estimating the root mean square differences (RMSD) between fat, protein, and fatty acids traits predicted by the MIR spectrometry internally and externally. All methods allowed to decrease RMSD, the gain ranged from 0.32% to 41.39%. Based on the obtained results, the “M1 and M2” combination should be preferred to be more parsimonious in the data loss as it had the higher ratio of RMSD gain to data loss. However, to ensure the lowest RMSD, the “M2 or M3” combination was the most relevant. Based on these 2 first works, FE records were easily obtained at large and individual scales and cleaned appropriately. Then, in order to assess the relevancy of the FE tool, the final work of this thesis consisted to study the behaviors of BW and FE predictions obtained from the 5 developed equations within and between lactations as well as per test month and compared them to the ones observed in the literature using reference values. Subsets of Hebei (N=288,607) and Walloon (N=379,472) DHI datasets were used. Even if the BW equations did not differ a lot based on the prediction performances, differences were observed on the DHI datasets and clustered the equations within 2 groups: the ones including 5 predictors and the one using the parity, DIM, MY, and the full MIR spectral data. The final one depicted a more expected evolution within lactation with a drop of BW around 30-50 days in milk and then an increase. This was not observed for the other equations suggesting a lack of MIR information to take into account sufficiently the individual variability of BW. The annual trend observed for this equation was also more expected with a BW drop during the grazing period. However, the differences in FE predictions obtained using BW estimated from different equations were less marked, suggesting a low sensibility of FE predictions to a moderate variation of BW. The validation RMSE reached 0.05 suggesting a good accuracy for this FE indicator. In conclusion, the FE tool developed in this thesis can be implemented by DHI organizations based on the BW equation including milk, parity, DIM, and the 277 MIR spectral points. However, some additional investigations are still needed before the use of a such tool by DHI. Indeed, even if preliminary results obtained in this thesis suggested a moderate heritability of FE trait, a study with the newly developed BW equations could be done as we have observed that the past BW equation tended to overestimate BW. Moreover, knowing the relationships between FE predictions with other traits having economic interest is required before any use. A reflection about the best way to communicate the results to the farmers must be also started. Finally, the FE tool was based on an equation predicting DMI. For the future, it could be also of interest to measure the relevancy of this equation by using DMI reference data. [less ▲]

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See detailSynthesis of furan derivatives from monosaccharides in reaction media based on choline chloride
Istasse, Thibaut ULiege

Doctoral thesis (2021)

In the context of fossil resources dependence and climate change due to green-house gas emissions, increasing efforts are devoted to the synthesis of plastic materials from renewable resources using less ... [more ▼]

In the context of fossil resources dependence and climate change due to green-house gas emissions, increasing efforts are devoted to the synthesis of plastic materials from renewable resources using less energy consuming processes. A possible path to produce plastic resins precursors is the transformation of plant saccharides to furan derivatives like 5-hydroxymethylfurfural (5-HMF) and 2-furfural (2-F). Furan derivatives are obtained through acid-catalyzed dehydration of saccharides and can be converted to new and more performant plastic materials. Their selective synthesis at moderate temperature remains however an important challenge and is the focus of this work. The first part of the research consists in an extensive review of monosaccharides dehydration mechanisms. Monosaccharides can be separated into two categories: ketoses (e.g. fructose) possessing a ketose moiety under acyclic form and aldoses (e.g. glucose) possessing an aldehyde moiety under acyclic form. The dehydration of ketoses through cyclic intermediates and their different reactivities are clarified. The reaction medium components required for their selective conversion to furan derivatives are methodically examined. Aldoses are more abundant in plants than ketoses and also more difficult to convert to furan derivatives. The study reveals why aldoses structure limits their dehydration and how catalysts and reaction media can be combined to enable a selective transformation. Given the promising results achieved with imidazolium chloride ionic liquids according to the literature, reaction media based on melted mixtures of choline chloride and organic acids were investigated as a possibly cheaper alternative. The dehydration of a ketose, fructose, was attempted at 90 °C in different mixtures with the aim to understand the role of each reaction medium components. Through reduction of the amount of organic acid and by increasing the acid strength, an 80% 5-HMF yield could be achieved in only 1h at 90 °C. The addition of small amount of an organic solvent like isopropanol enabled the reaction at 60 °C with a similar selectivity. The potential of choline chloride/organic acids melted mixtures for aldoses dehydration (glucose, mannose, galactose, xylose, arabinose) was then explored. To enable the formation of furan derivatives, boric acid was required for the prior isomerization of aldoses to ketoses. Aldoses transformation remained limited (e.g. 5% 5-HMF yield and 23% glucose conversion after one hour at 90 °C with maleic acid). Combined with α-hydroxyacids however, the reaction was faster and more selective (e.g. 19% 5-HMF yield and 61% glucose conversion after one hour at 90 °C). The synergy between α-hydroxyacids and boric acid was explained by formation of tetrahydroxyborate esters (THBE). Compared to boric acid, THBE reaction with glucose is energetically favored. THBE formation is associated with H3O+ release in the medium increasing its acidity. Dark polymers called humins were the main observed side-product of the reaction and are a major hurdle to the development of selective 5-HMF and 2-F synthesis processes. To better understand and inhibit their formation, humins were produced from different monosaccharides (hexoses, pentoses, 2-deoxyglucose) and analyzed by infrared spectroscopy and nuclear magnetic resonance. Humins formation during ketoses dehydration can be limited using organic solvents but humins production from aldoses persists even in organic reaction media. Those polymers are suspected to form from acyclic monosaccharides after one or several dehydration steps leading to a conjugated structure. The resulting conjugated product is sensitive to aldol addition/condensation with monosaccharides and furan derivatives. The experiments suggest that isomerization catalysts required for furan derivatives synthesis also exacerbate humins formation in two ways: they stabilize monosaccharides acyclic form and therefore expose their carbonyl moiety; humins possess functional groups which interact evenly or more strongly with the catalyst than reaction medium components or monosaccharides. Based on humins structure and a better understanding of their formation, advices are provided regarding the design of new catalysts including transition metals or boronic acids. We suggest that the catalyst should be strongly bonded to an organic structure which must prevent simultaneous interactions of several molecules with the catalytic site. The bulkiness of the organic structure must be precisely controlled to prevent humins of large size to inhibit the catalyst but still enable interaction with monosaccharides. The provided strategy should be valid for choline chloride-based medium as well as other solvents. This research supports the possibility to perform selective dehydration of abundant aldoses (e.g. glucose, xylose) at moderate temperature in commercially available and relatively cheap reaction media based on choline chloride. If polysaccharides depolymerization can be achieved in such media, they will certainly represent a promising path to generate bio-based monomers from renewable resources. [less ▲]

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See detailContribution à l'évaluation du programme de contrôle de l’échinococcose kystique au Maroc
Saadi, Aouatif ULiege

Doctoral thesis (2021)

Cystic echinococcosis (CE) is a major zoonosis, however, it is neglected. It is endemic in several countries around the world, particularly around the Mediterranean. In Morocco, despite the efforts ... [more ▼]

Cystic echinococcosis (CE) is a major zoonosis, however, it is neglected. It is endemic in several countries around the world, particularly around the Mediterranean. In Morocco, despite the efforts carried out within the framework of a national hydatidosis control program (NHCP), initiated in 2007, this zoonosis still presents a major cause of morbidity. Faced with this situation, the establishment of an effective proposal to improve the NHCP is necessary. Our study is based on the principle that, in order to improve the NHCP, we must first analyze and understand its different issues and facets. A multidisciplinary approach was followed, based on the estimation of monetary and non-monetary losses caused by this zoonosis, as well as participatory analyzes of its stakeholders, its implementation and ways of improving it. We were able to raise the multiple challenges facing the NHCP and studied the possibility of establishing a new control strategy, based on the vaccination of sheep and the treatment of dogs. Theoretically capable of eliminating this zoonosis in 15 years, the success of this strategy will indeed depend on the ability of the national program to carry it out and on its acceptability among the population directly concerned. Accurate assessment of the burden disease is essential for sensitizing decision-makers, as it helps prioritize funding for timely control measures. In this objective, a first study was carried out to estimate the economic losses caused by this zoonosis at the national and provincial level by combining financial and non-financial methods. In terms of human health, loss of disability-adjusted life years (DALY), medical costs and productivity losses were estimated. For animals, organ seizure losses at slaughterhouses and production losses caused by reducing milk, fertility, carcass weight and wool production were also estimated. The zDALY indicator, modifying the DALY indicator to include the animal health impacts of zoonotic diseases, was calculated to combine these two components. Monte-Carlo simulations were used to calculate the approximate numerical values. Total losses range from USD 222 million to USD 234 million. DALYs were estimated nationally at 0.5 years per 100,000 person and zDALY at 55 years per 100,000 person. According to these assessments, perceived losses are only the tip of the iceberg, with most of the losses being caused by loss of human productivity in undiagnosed cases and losses in animal production. This study highlighted the enormous losses caused by this zoonosis, throughout Morocco, indicating the need for improved prevention and control measures. The results of the first study showed the persistence of CE in Morocco and the failure that meet NHCP objectives. This prompted us to ask the question of the causes of this failure. To answer this question, a second study on the issues and obstacles that hindered the success of the NHCP was conducted. A qualitative approach was carried out in five regions of Morocco: Rabat-Salé-Kénitra; Béni Mellal-Khénifra; Sous-Masaa; Laâyoune-Sakia El Hamra and Guelmim-Oued Noun. We made the choice for this study to open the framework for application beyond hydatidosis alone, namely rabies and bovine tuberculosis, in order to highlight the common challenges that the control of these zoonoses presents. Participatory observations and 81 individual interviews were conducted with veterinarians, local authorities and slaughterers. The recordings were fully transcribed and the narratives analyzed with R software, using the RQDA package. The study revealed a lack of professional rigor, a lack of legislative framework, as well as an overlap of powers and interests between the different structures, while the multisectoral strategy is essential in the fight against zoonoses. This analysis led to our third study, which analyzed NHCP stakeholders to deepen our understanding of each stakeholder relationship with the program. The third study, therefore aims to analyze the actors of the NHCP in order to identify avenues for improvement and to propose more suitable ways. Stakeholders were identified, and a total of 163 semi-structured interviews were conducted in the same regions as the second study, as well as an inter-ministerial workshop in Rabat. The classic categories of stakeholder analysis, i.e. involvement, interest, importance, influence, priority and power, have been semi-quantified. An analytical framework was proposed combining these categories to evaluate the actors by three attributes: the appropriation of the measures, the political agency and the socio-technical agency. The study highlighted a deficient organization of the diversity of the actors involved, resulting in a deficiency in the three attributes mobilized. This study proposed an analytical and informative approach, particularly useful for an orientation of the fight against zoonoses in which multisectoral coordination is essential. In the search for new CE control strategies, sheep vaccination trials (EG95 vaccine) associated with anthelmintic treatment of dogs were carried out in the Middle Atlas, the region of the country with the highest prevalence. This study presents the analysis of the feasibility and social acceptability of this strategy, the aim of which is to outline an approach for the development of a guide for carrying out such an intervention in the future. Eleven focus groups and sixteen in-depth individual interviews were conducted with breeders, women, local authorities, private doctors and veterinarians, as well as officials from the structures responsible for the potential implementation of the NHCP in parallel with the trials of the vaccine. Recordings were transcribed and analyzed with R software, using RQDA software package. This study highlighted various reservations expressed by the players on the feasibility of the strategy. The study made it possible to collect participants' proposals for a better implementation of this new strategy. These reservations and proposals must imperatively be taken into account for the development of a renewed plan. In conclusion, the study highlighted the impact of CE throughout the Moroccan territory, which causes losses reaching 0.07% of Morocco's GDP. Thus, the qualitative approach allowed us first to understand the functioning of the NHCP in the field, and to propose a scheme for the establishment of a new control strategy, which theoretically, could control this zoonosis in 15 years. [less ▲]

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See detailUne nouvelle hypothèse sur le mécanisme de pacemaking dans les neurones dopaminergiques de la substance noire compacte
Jehasse, Kevin ULiege

Doctoral thesis (2021)

Substantia Nigra pars compacta dopamine neurons are integrated in the nigrostriatal pathways of the basal ganglia. They release dopamine in the striatum to modulate the activity of the different nuclei ... [more ▼]

Substantia Nigra pars compacta dopamine neurons are integrated in the nigrostriatal pathways of the basal ganglia. They release dopamine in the striatum to modulate the activity of the different nuclei from the basal ganglia. Thus, those neurons are involved in motor control, as well as exploration and motivation behaviors. Dopamine release disruption, due to neurodegeneration, leads to various motor impairment (Parkinson Disease) and behavioral diseases. Dopamine release is controlled by the electrical activity of dopamine neurons. The firing pattern of these neurons is controlled by synaptic activity in vivo. They can present a regular firing called “pacemaking”, an irregular firing or a bursting firing. Only the pacemaking activity remains in vitro. This regular firing is therefore sustained and controlled by intrinsic conductances. However, the exact mechanism underlying Substantia Nigra pars compacta dopamine neurons pacemaking activity remains unclear. In fact, blocking one or few conductances only affects the firing frequency but it does not fully inhibit the spontaneous activity. In order to sustain such activity, it has been showed that a small inward current is activated during the slow depolarization phase between two action potentials in ventral tegmental area dopamine neurons (Khaliq and Bean, 2008). Given the similar properties within midbrain dopamine neurons being heterogenous, it is not excluded that their pacemaking is mediated by one and same conductance. We investigated several potential candidates, including the unconventional conductance mediated by ω pores. We used the only known blockers of such pores, 1-(2,4-xylyl)guanidine (XG), in order to verify our hypothesis. We observed that this compound is able to selectively inhibit midbrain dopamine neurons pacemaking activity by blocking one target, without affecting either the burst activity nor the ion channels underlying action potentials. We also observed that the effect of XG still persists even when the pacemaking main modulators are being blocked. These results demonstrate that the XG-sensitive conductance is crucial to sustain the spontaneous activity in midbrain dopamine neurons. We next investigated the presence of ω pores but we did not observe evidence in favor of this hypothesis. However, we managed to isolate a XG-sensitive current occurring during the interspike interval corresponding the pacemaker current described by Khaliq and Bean. We characterized this current and found that it is sustained by Na+ and Cl-. Finally, we investigated whether this current was sustained by the dopamine transporter because it displays similar properties. We used transgenic mice lacking the dopamine transporter in dopamine neurons. We found that the absence of the transporter did not affect either the firing frequency nor XG effect on those neurons. To conclude, even though we did not manage to identify the molecular target of XG, we emphasized a new conductance crucial to sustain pacemaking activity in midbrain dopamine neurons. [less ▲]

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See detailGeneration and data-driven upscaling of open foam representational volume elements
Kilingar, Nanda Gopala ULiege

Doctoral thesis (2021)

In this work, a Representative Volume Element (RVE) generator based on the distance fields of arbitrary shaped inclusion packing is used to obtain morphologies of open-foam materials. When the inclusions ... [more ▼]

In this work, a Representative Volume Element (RVE) generator based on the distance fields of arbitrary shaped inclusion packing is used to obtain morphologies of open-foam materials. When the inclusions are spherical, the tessellations of the resultant packing creates morphologies that are similar to physical foam samples in terms of their face-to-pore ratio, edge-to-face ratio and strut length distribution among others. Functions that combine the distance fields can be used to obtain the tessellations along with the necessary variations in the strut geometry and extract these open-foam morphologies. It is also possible to replace the inclusion packing with a predefined set of inclusions that are directly extracted from CT-scan based images. The use of discrete level-set functions results in steep discontinuities in the distance function derivatives. A multiple level-set based approach is presented that can appropriately capture the sharp edges of the open-foam struts from the resultant distance fields. Such an approach can circumvent the discontinuities presented by the distance fields which might lead to spurious stress concentrations in a material behavior analysis. The individual cells are then extracted as inclusion surfaces based on said combinations of the distance functions and their modifications. These surfaces can be joined together to obtain the final geometry of the open-foam morphologies. The physical attributes of the extracted geometries are compared to the experimental data. A statistical comparison is presented outlining the various features. The study is extended to morphologies that have been extracted using CT-scan images. With the help of mesh optimization tools, surface triangulations can be obtained, merged and developed as finite element (FE) models. The models are ready to use in a multi-scale study to obtain the homogenized material behavior. The upscaling can help assess the practical applications of these models by comparing with experimental data of physical samples. The material behavior of the RVEs are also compared with the experimental observations. To increase the computational efficiency of the study, a neural network based surrogate is presented that can replace the micro-scale boundary value problem (BVP) in the multi-scale analysis. The neural networks are built with the help of modules that are specifically designed to predict history dependent behavior and are called Recurrent Neural Networks (RNN). The surrogates are trained to take into account the randomness of the loading that complex material undergo during any given material behavior analysis. [less ▲]

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See detailReduced tillage increases grain yield through improving soil properties and water use efficiency
Li, Shengping ULiege

Doctoral thesis (2021)

A primary challenge of our time is to attain high food security for a growing world population with reduced investment and ensuring environmental sustainability. Conservation tillage practices have ... [more ▼]

A primary challenge of our time is to attain high food security for a growing world population with reduced investment and ensuring environmental sustainability. Conservation tillage practices have received wide international attention to address this challenge because of their effect on soil physical properties and grain yield. However, there is a lack of knowledge about the relationships between soil physical properties and grain yield, especially for soil water repellency. The dynamic of soil physical properties during the growth period is also seldom taken into account to understand a suitable soil physical environment for plant growth. Moreover, although it is well known that conservation tillage practices could affect soil water repellency through hydrophobic substances and pore structure, most of the studies have only focused on hydrophobic substances due to the complexity of soil pore structure measurement and quantification. This results in limited knowledge about the relationship between soil pore structure and soil water repellency. In this study, we used a long-term field experiment located at the Dryland Farming Experimental Station in Shouyang, Shanxi Province, in northern China to study the seasonal changes of soil physical properties (e.g. bulk density, penetration resistance, porosity, mean weight diameter, least limiting water range, and plant available water). We also assessed how these soil physical properties influence grain yield, especially reveal the mechanism of how soil water repellency affects grain yield from the perspective of soil water availability. To better understand the effects of hydrophobic substances and pore structure on soil water repellency, another long-term experimental location was conducted in Gongzhuling, Jinlin Province, northeast China. The treatments were conventional tillage with residue removal (CT), reduced tillage with residue incorporation (RT), and no-tillage with residue mulching (NT) in both of the fields. The main results of this thesis are as follows: (1) Soil physical properties (e.g. bulk density, penetration resistance, pore size distribution, mean weight diameter, least limiting water range, and plant available water) were significantly influenced by tillage management, soil depth, and growth period (P < 0.05). At 0-5 cm layer, NT was the highest in soil bulk density on April 27th, but there was no significant difference among the three tillage management on July 7th, and NT was lower than RT and CT on September 10th. In addition, bulk density, porosity, S index, and mean weight diameter showed irregular and different relationships with grain yield during the growth period, especially there were no significant relationships between these soil physical properties and grain yield (P > 0.05). These results suggested that these soil physical properties were ineffective indicators for grain yield. Besides, the range of least limiting water range was narrower than plant available water during the growth period and more sensitive to assess soil water availability under the three treatments. NT significantly increased the lower limit of LLWR, which made it more difficult for root water uptake. Hence, RT presented higher corn yield compared to NT, even if the water content remained lower. Redundancy analysis further indicated that maize yield was mainly driven by a lower limit of LLWR and penetration resistance. (2) Soil organic carbon and microbial biomass carbon, both of which are hydrophobic substances, were higher in RT and NT treatments than in CT treatment. Microbial biomass carbon had a closer relationship with the water repellency index than soil organic carbon and more fully explained the impact of tillage on soil water repellency. The RT and NT treatments increased the porosity of pores that were 55-165 μm in diameter and it had a positive relationship with ethanol sorptivity and the water repellency index, respectively. However, there was no significant link with soil water repellency properties when the pores were greater than165 μm in diameter. The RT and NT treatments increased sorptivity by enhancing porosity and connectivity, and decreased water sorptivity by increasing soil surface area, which occurred because the area and possibility of contact between hydrophobic substances and soil water increased. (3) Both water sorptivity and water repellency index had effects on soil water availability (e.g. plant available water, least limiting water range, and soil water storage) that could affect plant growth. The effect of soil water repellency on soil water content became more obvious with the decrease in soil moisture following rainfall, which was also influenced by rainfall intensity. Although both water repellency index and water sorptivity can reflect the nature of soil water repellency, soil water sorptivity had a significant influence on grain yield, whereas water repellency index had no direct effect on grain yield. In addition, water sorptivity was the most favorable for grain yield improvement compared with soil organic carbon, mean weight diameter, penetration resistance, and total porosity. In conclusion, the thesis reveals the mechanism of how soil tillage management affects grain yield by changing soil physical properties. We found that grain yield was mainly driven by a lower limit of least limiting water range and penetration resistance. LLWR was an aggregative indicator including not only soil penetration resistance but also air porosity and soil water potential, which can better explain the change of grain yield under the long-term tillage management in the semi-arid region. Furthermore, the effect of conservation tillage on SWR is a result of the interactions between pore structure and hydrophobic substances. It is necessary to take into account both pore structure and hydrophobic substances when studying the impacts of SWR on soil processes. SWR also had the potential influence on grain yield by changing soil water availability and the effect of SWR on crop yield was worthy of further study under conservation tillage practices. The grain yield under RT treatment was highest by increasing water sorptivity, LLWR, and WUE. From this, we conclude that RT treatment is the most effective tillage practice compared to CT and NT treatments from the perspective of grain yield. [less ▲]

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See detailContribution of Mycobacterium bovis gene Rv3671c in acid resistance and replication
Lin, Weidong ULiege

Doctoral thesis (2021)

The survival of Mycobacterium in the host is largely attributed to its ability to resist the acidic environment. Recently, it has been found that a Mycobacteria tuberculosis mutant cannot maintain ... [more ▼]

The survival of Mycobacterium in the host is largely attributed to its ability to resist the acidic environment. Recently, it has been found that a Mycobacteria tuberculosis mutant cannot maintain intracellular pH in phagosomes in the absence of Rv3671c, which encodes Mycobacterial acid resistance protease (Marp). The aim of this study is to study the effect of Marp in acid resistance and the growth performance of Mycobacterium bovis and decipher the underlying working mechanisms. We have expressed the periplasmic domain of Marp in Escherichia coli and prepared monoclonal antibodies (MAb) against Marp. The serine proteinase activity of Marp was verified by using β-casein as a substrate. Monoclonal antibodies were tested with recombinant or and natural Marp protein from M. bovis. Meanwhile, we have constructed a knockout mutant (ΔMarp) using a mycobacteriophage, and validated its integrity by PCR and western blot. Besides,a complemented strain (ΔMarpComp) and a strain overexpressing the Rv3671c gene (PmvRv3671) were built by using plasmid pMV261. The growth rates of these strains were compared to that of the wild type M. bovis An5. Raw264.7 macrophages were infected at multiplicities of infections of 10 (MOI=10). After culture in standard 7H9 medium to the early logarithmic phase, the strains were transferred into 7H9 medium at pH 6.6 and pH 5.0 and maintenance solution at pH 6.6 and pH 4.5. The results show that while they all survive in 7H9 medium at pH 5.0 or pH 6.6 and maintenance buffer at pH 4.5, the viability at day 14th of the over-expressing strain PmvRv3671 is significantly higher than that of wild-type strain M. bovis, ΔMarpComp and ΔMarp. After comparing their corrected survival rates, it can be observed that the acid resistance abilities of all strains significantly decrease between days 5 and 14. When exposed to pH 4.5-citrate maintenance solution for a long time, their acid-resistance abilities become weaker. In Raw264.7 macrophages stimulated with IFNγ, the replication rate of the PmvRv3671 is significantly higher than that of An5, ΔMarp and ΔMarpComp. So, Rv3671c over-expressing strain shows a better growth ability than the other three strains under acidic environments. In conclusion, the Rv3671c gene is not only related to acid resistance but also affects the growth of M. bovis. To understand the panorama of the working mechanisms of Marp, we investigated proteins interacting with Marp. We used Mycobacteria tuberculosis Protein Chip to screen the proteins binding to Marp. The bacterial two-hybrid system was then used to validate the interacting proteins. The results show that among 295 interacting proteins, 52 displayed stronger binding. Interactions of seven candidates were verified by using the bacterial two-hybrid system. The biological functions were analyzed with String, Uniprot, BioCyc, and Gene Ontology databases. We concluded that these 7 proteins are mainly responsible for two biological functions: the growth of M. bovis and the binding of GDP or ATP. Therefore, we hypothesize that the mechanisms of the acid resistance are associated with these Marp interactants. The results of the present study provide a basis for further deciphering the complete model and working mechanisms of Marp in M. bovis. [less ▲]

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See detailUnveiling the specialized metabolism of Streptomyces lunaelactis spp.
Martinet, Loïc ULiege

Doctoral thesis (2021)

The decline in the number of new antibiotics discoveries, related in parallel with an acceleration and generalization of the bacterial resistance phenomenon, the unfolding of the global health crisis ... [more ▼]

The decline in the number of new antibiotics discoveries, related in parallel with an acceleration and generalization of the bacterial resistance phenomenon, the unfolding of the global health crisis, linked to the emergence of new viral pandemics, as well as the agro-industrial needs for new natural products less impacting the environment and human health, are examples of current driving elements that encourage research of new natural products. Over the past ten years or so, technological innovations allowing on one hand, the high-throughput and low-cost sequencing of bacterial genomes, and on the other, the high-resolution detection and identification of compounds, have offered an unmatched framework for discovery. During last decade, many innovative strategies have emerged, with the aim of providing access to biomolecules buried in nature. One of them is the bioprospecting of new microorganisms in ecological niches, described as extreme and so far unexplored, in order to maximize the chances of discovering new biomolecules. Streptomyces are soil bacteria, which actively participate in the recycling of organic biomass, and are also known to have an extremely developed secondary metabolism. Indeed, these Actinobacteria provide more than 50% of natural molecules of microbial origin used in human or animal medicine (antibacterial, antifungal, anti-tumor, etc) and in agro-industry (herbicides, insecticides, etc). The search for microorganisms native to karstic habitat called moonmilk, has led to the discovery of new strains of Streptomyces, including the recently described Streptomyces lunaelactis species. The aim of this work is to characterize the specialized metabolome associated with the Streptomyces lunaelactis species, including identification of the molecules produced by this microorganism and determination of the genes responsible for their biosynthesis. Through a comparative metabologenomic approach using 18 bacterial strains belonging to the S. lunaelactis species, this work has revealed their ability to produce bioactive molecules. Accordingly, the results of genome mining study of S. lunaelactis, combined with metabolomics studies, made it possible to evaluate the genetic predispositions of this species to produce specialized metabolites, as well as to experimentally validate some of these predictions. This work provides an overview on this species’ specialized metabolome and confirms that not only this microorganism, but also other Streptomyces derived from moonmilk, are abundant sources of new natural products. In addition, this work also exposes the risks associated with the dereplication of bacterial strain banks and investigates an innovative approach, which focuses on the evaluation of biosynthetic potential of strains within a single species, which shows a great promise in the search for new natural products. [less ▲]

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See detailDesign, optimization and control by condensation pressure manipulation of an ORC based waste heat recovery system in heavy-duty trucks
Galuppo, Francesco ULiege

Doctoral thesis (2021)

The new European regulation about the CO2 emissions of long-haul heavy duty trucks pushed the manufacturers to study and implement solutions that can limit the CO2 emissions by reducing the fuel ... [more ▼]

The new European regulation about the CO2 emissions of long-haul heavy duty trucks pushed the manufacturers to study and implement solutions that can limit the CO2 emissions by reducing the fuel consumption of the vehicle. Considering the limited efficiency of the inter- nal combustion engines and the thermal losses that are encountered, the waste heat recovery technologies have gained much interest in the heavy-duty trucks industry; in particular ther- modynamic bottoming cycles, as the Organic Rankine cycle, are considered suitable to reduce the fuel consumption and, consequently, the CO2 emissions. However, several obstacles are encountered in the implementation of a safe system that can ensure high standards of per- formance as long as possible, reducing the total cost of ownership of the vehicle. In the last decade, a large scientific community studied intensely this topic related to the working fluid selection, component modeling and testing, control and optimization. Another important aspect of this application derives from the fact that the heat is recovered from an heat source characterized by a transient behavior. This is taken into account in the system architecture definition, as well as in the implementation of suitable control strategies, intended to the maximization of the performance. In this thesis the exhaust gas and the engine coolant flow are investigated as heat sources; in both cases modeling and control strategies are implemented, in the latter an experimental campaign is performed. Although the heat source is often considered as the main secondary fluid in the Rankine system, the heat sink is often characterized by a transient behavior as well, that can limit the performance of the system and pushes to further control development in the cold side of the system. In this thesis, the control problems related to the working fluid conditions at the inlet of the expander (the controlled variable is called superheat) and the pump (the controlled variable is called subcooling) are addressed, studying the dynamics of the evaporator and condenser, in specific selected operating points, chosen by means of a specific algorithm (published in Galuppo et al. 2018a). For both the heat sources that have been analyzed, the manipulation of the condensation pressure is shown to be not only recommendable, but it is necessary, in order to ensure component safety and high standards of performance of the system. The utilization of the condensation pressure as and addi- tional manipulated variable leads to the definition of a MISO (Multiple Input Single Output) problem to control the subcooling at the inlet of the pump and, consequently, to improve performance (published in Galuppo et al. 2021). Another potential control improvement is identified in the utilization of a deep neural network, trained on-line, to replace the weighting estimators and determine, in an adaptive way, a representative model to design the controller (published in Peralez et al. 2020). [less ▲]

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See detailStudy on extraction technics of sweet potato leaf flavonoids, sustained release of its nanoparticles, and sweet potato leaf fortified bread
Liu, Jiang ULiege

Doctoral thesis (2021)

The previous studies of sweet potato leaf polyphenols were mainly focus on the non-flavonoids part (phenolic acids), there weren’t enough study on the flavonoids part. Chemically, flavonoids have the ... [more ▼]

The previous studies of sweet potato leaf polyphenols were mainly focus on the non-flavonoids part (phenolic acids), there weren’t enough study on the flavonoids part. Chemically, flavonoids have the specific structure of a 15-carbon skeleton, which consists of two phenyl rings (A and B) and a heterocyclic ring (C), and can be abbreviated as C6-C3-C6 structure. Firstly, ultrasonic-microwave synergistic extraction (UMSE) was used to extract flavonoids from sweet potato leaves (SPL) by response surface methodology (RSM). The optimal conditions for flavonoids extraction were 1:40 (g/mL) of solid-liquid ratio, 57 °C of extraction temperature, 76 s of extraction time and 72 % (v/v) ethanol for 2 times of extraction, and the highest flavonoids yield from SPL was 5.1 %. After purification, the flavonoids purity reached up to 76.1 (%, DW). The result of high performance liquid chromatography (HPLC) revealed 11 compounds including astragalin, quercetrin, 4,5-chlorogenic acid, isoquercitrin, tiliroside, quercetin, 3,4,5-chlorogenic acid, caffeic acid, kaempferol, myricetrin and rhamnetin in sweet potato leaf flavonoids (SPLF), which possessed good antioxidant activity compared to soy isoflavones, Ginkgo biloba extract and propolis flavone. Secondly, the effect of heat treatment, high hydrostatic pressure (HHP) treatment, pH, light, temperature and simulated digestion on the stability of SPLF was studied. Heat treatment at 75 °C for 90 min or HHP treatment at 600 MPa for 30 min didn’t cause significant effect on SPLF. Heat treatment at 100 °C for 60 min and 90 min led to a decrease in antioxidant activity by 20 % and 25 % respectively, while pH 7.0 and 8.0 significantly decreased amount of SPLF by approximately 75 %, decreased antioxidant activity by about 30 % and 47 % separately. Light treated samples recorded a decrease in SPLF by 52 % and antioxidant activity by 24 %. No significant effect on SPLF was observed for samples stored at -18, 4 °C or room temperature (RT) (≈ 20 °C). The retention of flavonoids and antioxidant activity was 45 % and 56 %, individually in SPLF after simulated digestion. Thirdly, nanoparticles of SPLF were prepared by freeze-drying encapsulation using 2 % (g/mL) maltodextrin, which showed the highest stability with high absolute zeta potential (-41.6 mV) and encapsulation efficiency (EE) (59.0 %), low mean particle size (277.4 nm) and polydispersity index (PDI) (0.417). Confocal laser scanning microscopy (CLSM) and infrared spectrum provided the evidence. After simulated oral, gastric and intestinal digestion, nanoparticles additionally reserved 16, 31, 28 % of flavonoids and 16, 16, 10 % of antioxidant activity, separately, compared with the sample without encapsulation, which could be intuitively demonstrated by scanning electron microscopy (SEM). Finally, SPL was used to substitute 1, 2, 3.5 and 5 % (w/w) of wheat flour to make bread. 1 % SPL could change the bread color significantly, which could be clearly distinguished by human eyes. The hardness and chewiness of the crumb increased with increased SPL level. When adding 5 % of SPL to the flour, specific volume of the bread shrank in half, compared with the control. Pores in the crumb became deteriorating and disintegrating when the adding of SPL was higher than 3.5 %. Total polyphenols content (TPC) and total flavonoids content (TFC) of the bread increased 6-fold and 10-fold, and antioxidant activity enhanced 10-fold, separately when adding 5 % SPL to the flour. The addition of SPL won’t alter volatile compounds of the bread, but suppressed the generation of typical bread odors significantly. Overall, SPL (no more than 1 %) could be supplemented to the flour to make bread with high TPC (2-fold), TFC (2.5-fold), excellent antioxidant activity (3-fold), and no significant adverse effect on the physical characteristics and flavor. [less ▲]

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See detailStudy on extraction technics of sweet potato leaf flavonoids, sustained release of its nanoparticles, and sweet potato leaf fortified bread
Liu, Jiang ULiege

Doctoral thesis (2021)

The previous studies of sweet potato leaf polyphenols were mainly focus on the non-flavonoids part (phenolic acids), there weren’t enough study on the flavonoids part. Chemically, flavonoids have the ... [more ▼]

The previous studies of sweet potato leaf polyphenols were mainly focus on the non-flavonoids part (phenolic acids), there weren’t enough study on the flavonoids part. Chemically, flavonoids have the specific structure of a 15-carbon skeleton, which consists of two phenyl rings (A and B) and a heterocyclic ring (C), and can be abbreviated as C6-C3-C6 structure. Firstly, ultrasonic-microwave synergistic extraction (UMSE) was used to extract flavonoids from sweet potato leaves (SPL) by response surface methodology (RSM). The optimal conditions for flavonoids extraction were 1:40 (g/mL) of solid-liquid ratio, 57 °C of extraction temperature, 76 s of extraction time and 72 % (v/v) ethanol for 2 times of extraction, and the highest flavonoids yield from SPL was 5.1 %. After purification, the flavonoids purity reached up to 76.1 (%, DW). The result of high performance liquid chromatography (HPLC) revealed 11 compounds including astragalin, quercetrin, 4,5-chlorogenic acid, isoquercitrin, tiliroside, quercetin, 3,4,5-chlorogenic acid, caffeic acid, kaempferol, myricetrin and rhamnetin in sweet potato leaf flavonoids (SPLF), which possessed good antioxidant activity compared to soy isoflavones, Ginkgo biloba extract and propolis flavone. Secondly, the effect of heat treatment, high hydrostatic pressure (HHP) treatment, pH, light, temperature and simulated digestion on the stability of SPLF was studied. Heat treatment at 75 °C for 90 min or HHP treatment at 600 MPa for 30 min didn’t cause significant effect on SPLF. Heat treatment at 100 °C for 60 min and 90 min led to a decrease in antioxidant activity by 20 % and 25 % respectively, while pH 7.0 and 8.0 significantly decreased amount of SPLF by approximately 75 %, decreased antioxidant activity by about 30 % and 47 % separately. Light treated samples recorded a decrease in SPLF by 52 % and antioxidant activity by 24 %. No significant effect on SPLF was observed for samples stored at -18, 4 °C or room temperature (RT) (≈ 20 °C). The retention of flavonoids and antioxidant activity was 45 % and 56 %, individually in SPLF after simulated digestion. Thirdly, nanoparticles of SPLF were prepared by freeze-drying encapsulation using 2 % (g/mL) maltodextrin, which showed the highest stability with high absolute zeta potential (-41.6 mV) and encapsulation efficiency (EE) (59.0 %), low mean particle size (277.4 nm) and polydispersity index (PDI) (0.417). Confocal laser scanning microscopy (CLSM) and infrared spectrum provided the evidence. After simulated oral, gastric and intestinal digestion, nanoparticles additionally reserved 16, 31, 28 % of flavonoids and 16, 16, 10 % of antioxidant activity, separately, compared with the sample without encapsulation, which could be intuitively demonstrated by scanning electron microscopy (SEM). Finally, SPL was used to substitute 1, 2, 3.5 and 5 % (w/w) of wheat flour to make bread. 1 % SPL could change the bread color significantly, which could be clearly distinguished by human eyes. The hardness and chewiness of the crumb increased with increased SPL level. When adding 5 % of SPL to the flour, specific volume of the bread shrank in half, compared with the control. Pores in the crumb became deteriorating and disintegrating when the adding of SPL was higher than 3.5 %. Total polyphenols content (TPC) and total flavonoids content (TFC) of the bread increased 6-fold and 10-fold, and antioxidant activity enhanced 10-fold, separately when adding 5 % SPL to the flour. The addition of SPL won’t alter volatile compounds of the bread, but suppressed the generation of typical bread odors significantly. Overall, SPL (no more than 1 %) could be supplemented to the flour to make bread with high TPC (2-fold), TFC (2.5-fold), excellent antioxidant activity (3-fold), and no significant adverse effect on the physical characteristics and flavor. [less ▲]

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See detailMulti-scale characterization of transport in heterogeneous porous and fractured aquifer media using innovative heat and solute tracer tests
Hoffmann, Richard ULiege

Doctoral thesis (2021)

Characterization of subsurface mass and energy transport in heterogeneous porous and fractured aquifer media is particularly challenging due to existence of preferential flowpaths and dynamic matrix ... [more ▼]

Characterization of subsurface mass and energy transport in heterogeneous porous and fractured aquifer media is particularly challenging due to existence of preferential flowpaths and dynamic matrix processes at multiple scales. The main contribution of the present work is to combine solute and highly diffusive tracer information with the objective to improve the understanding of the actual transport processes and the predictive capacity of models. The use of innovative tracers such as heat or inert dissolved gases leads to different sensitivities to preferential flowpaths and matrix processes due to the broad variation of their diffusion coefficient values. This in turn allows a more realistic consideration of the heterogeneity patterns in the geological media and a better quantification of the associated uncertainty in model predictions. Field campaigns were performed in different geological formations with injections of: (1) heat and a solute in alluvial sediments; (2) dissolved gases, heat and uranine in a porous/fractured chalk system, (3) salt and water with higher and lower temperature (than the natural groundwater background temperature) in a weathered and fissured granite system in India. These field campaigns provided information on the evolution of concentration and temperature as function of time (breakthrough curves). The observations were interpreted with regards to peak time, peak value and slope of the tailing, taking into account the variation of the diffusion coefficient value of the different tracers. First, a joint heat and solute tracer experiment, previously carried out in alluvial sediments, was used to study the heterogeneity and for prior (i.e., parameter) uncertainty investigation. Monte Carlo simulations were used to revisit the current state of knowledge. For example, an increase in hydraulic conductivity with depth (due to the local spatial heterogeneity of the sediments) could now be realistically implemented in the aquifer simulation using the numerical calculator HydroGeoSphere (HGS). The Monte Carlo simulations were also used for a Euclidean distance-based sensitivity analysis relating model input and output uncertainty. It was shown that heat transport is more sensitive to heterogeneous patterns compared to solute tracer transport. Second, the joint injection of uranine and dissolved gases and their recovery (forced gradient experiment) in a porous/fractured chalk emphasized the influence of the specific (i.e., fracturing) aquifer heterogeneity on higher diffusive tracers. A channel model (analytical solution with explicit fracture numbers and apertures) was used to simulate the transport of helium, the gas with the highest diffusion coefficient tested. Then, using HGS, the simulation of flow, transport of solutes and heat transfer allowed to test the influence of matrix diffusion at different time and spatial scales by varying the diffusion coefficient of the tracer species. Third, the injection of hot and cold water in a weathered and fissured granite system in India, allowed the study of the actual and differential release of heat from the matrix to the fracture fluid and vice versa. A deterministic model solution using HGS showed that the width of the discrete fracture that is supposed to represent the fracture tested in the field had a significant effect on the temperature simulations. The results of the present PhD thesis clearly emphasize the importance and usefulness of these new tracers as well as their added value for an advanced aquifer characterization, to obtain a realistic assessment of the inherent heterogeneity of the different investigated groundwater systems. The latter is required for reliable simulations of mass and energy transport in the dynamic subsurface. [less ▲]

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See detailReconstruction of the Gulf Stream variability since 1940 using a variational inverse method and study of its interaction with the North Atlantic Oscillation
Watelet, Sylvain ULiege

Doctoral thesis (2021)

In this study, the Gulf Stream’s (GS) response to the North Atlantic oscillation (NAO) is investigated by generating an observation-based reconstruction of the GS path between 70° and 50°W since 1940 ... [more ▼]

In this study, the Gulf Stream’s (GS) response to the North Atlantic oscillation (NAO) is investigated by generating an observation-based reconstruction of the GS path between 70° and 50°W since 1940. Using in situ data from WOD, SeaDataNet, ICES, Hydrobase3 and ARGO floats, a harmonized database of more than 40 million entries is created. A variational inverse method implemented in the software DIVA (Data-Interpolating Variational Analysis) allows the production of time series of monthly analyses of temperature and salinity over the North Atlantic (NA). These time series are used to derive two GS indices: the GS North Wall (GSNW) index for position and the GS Delta (GSD) index as a proxy of its transport. We find a significant correlation (0.37) between the GSNW and the NAO at a lag of 1 year (NAO preceding GS) since 1940 and significant correlations (0.50 and 0.43) between the GSD and the NAO at lags of 0 and 2 years between 1960–2014. We suggest this 2-year lag is due to Rossby waves, generated by NAO variability, that propagate westwards from the center of the NA. This is the first reconstruction of GS indices over a 75-year period based on an objective method using the largest in situ dataset so far. This enhanced tracking and quantification of the GS confirms and extends the temporal scope of this property: NAO+ phases lead to a stronger and more northward GS, and conversely for NAO− phases. The teleconnections between the NAO and the variability of the GS were extensively studied these last years, often exhibiting time delays between both phenomena. These time lags, usually ranging between 0–2 years, are sometimes explained by the hypothesis of baroclinic Rossby waves generated by the NAO in the central NA and travelling westward before interacting with the GS. In this study, we use a numerical hindcast at an eddy-resolving resolution (1/12°) from the DRAKKAR project to examine the occurrence and properties of such Rossby waves between 1970–2015, thus including a large pre-TOPEX/Poseidon period. Through the use of a two-dimensional Radon Transform (2D-RT) on Hovmöller diagrams of the Sea Surface Height (SSH), a methodology easily portable to other oceanic model outputs, we show evidence of baroclinic Rossby waves travelling at 39°N at a speed of 4.17 cm/s. This study extends the period over which Rossby waves have been found that far north to a much longer period, which reinforces the findings of previous works. These results are consistent with the time lags observed between the NAO and the GS transport while the GS latitudinal shifts might obey additional processes. The Barents Sea, located between the Norwegian Sea and the Arctic Ocean, is one of the main pathways of the Atlantic Meridional Overturning Circulation. Changes in the water mass transformations in the Barents Sea potentially affect the thermohaline circulation through the alteration of the dense water formation process. In order to investigate such changes, we present here a seasonal atlas of the Barents Sea including both temperature and salinity for the period 1965–2016. The atlas is built as a compilation of datasets from the World Ocean Database, the Polar Branch of Russian Federal Research Institute of Fisheries and Oceanography, and the Norwegian Polar Institute using the DIVA tool. DIVA allows for a minimization of the expected error variance with respect to the true field. The atlas is used to provide a volumetric analysis of water mass characteristics and an estimation of the ocean heat and freshwater contents. The results show a recent "Atlantification" of the Barents Sea, that is a general increase of both temperature and salinity, while its density remains stable. The atlas is made freely accessible as handy NetCDF files to encourage further research in the Barents Sea physics. [less ▲]

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See detailEfficient and flexible implementation of an interfacing Python-based tool for numerical simulations of fluid-structure interaction problems
Thomas, David ULiege

Doctoral thesis (2021)

Applications involving a solid structure actively interacting with a surrounding fluid, referred to as fluid-structure interaction (FSI), are constantly gaining interest in fundamental or industrial ... [more ▼]

Applications involving a solid structure actively interacting with a surrounding fluid, referred to as fluid-structure interaction (FSI), are constantly gaining interest in fundamental or industrial research and development. Such a multi-physics system is characterized by a complex dynamics which requires technically advanced methods to be studied. An accurate understanding of FSI systems becomes a key factor in the current trend of producing lighter and more flexible industrial designs. Nowadays, numerical simulations are extensively used to produce high-fidelity FSI models for various engineering applications. The typical approach considered in this thesis performs the coupling between two independent solvers, each of them being specifically designed to solve the governing equations for one particular physics. In this context, this thesis presents the development of an original coupling environment called CUPyDO. It is designed for the coupling of independent single-physics solvers within a unified architecture based on a Python wrapping methodology. The development of CUPyDO has been conducted with the aim of producing a tool that leverages computing efficiency and accuracy, coupling flexibility and user-friendliness while circumventing some limitations and improving some other aspects of the existing solutions. The tool gathers state-of-the-art coupling methods which are deeply reviewed in this work. This includes major capabilities such as under-relaxed coupling algorithms, non-matching interface meshes and multi-core parallelization. The modern Python wrapping technology used in CUPyDO provides easy access to all the features through a high-level API which can be further customized and extended with minimal effort. Furthermore, the same wrapping technology provides a flexible black-box coupling with various existing standalone solvers without any architectural or algorithmic adaptation to be performed in the coupling environment. The implementation and the capabilities of CUPyDO are demonstrated and verified by simulating several FSI test cases for transonic aeroelastic flutter, vortex-induced vibrations and conjugate heat transfer. The test cases are also used to assess the coupling tool in terms of robustness, efficiency and accuracy. The results are successfully validated against experimental and numerical reference data found in the literature, and some usability guidelines are drawn. Furthermore, the coupling flexibility is highlighted by using various structural solvers through the different test cases. The coupling tool is used for the aeroelastic study of a very flexible flat plate wing with various geometrical configurations. In a first step, the linear flutter velocity and frequency are sought and compared with experimental data with good agreement. In a second step, the post-flutter aeroelastic response is simulated for some configurations of the plate and it is found that the system is characterized by a supercritical Hopf bifurcation. For one particular plate configuration, two distinct post-flutter limit cycle oscillations are observed depending on the initial structural perturbation and on the occurrence of aerodynamic nonlinearities. This further highlights the importance of using high-fidelity coupled models for representing nonlinear aeroelastic solution that reduced-order linear models are not able to predict. [less ▲]

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See detailDeep Reinforcement Learning for the Control of Energy Storage in Grid-Scale and Microgrid Applications
Boukas, Ioannis ULiege

Doctoral thesis (2021)

The European and worldwide directives and targets for renewable energy integration, motivated by the imminent need to decarbonize the electricity sector, are imposing severe changes to the conventional ... [more ▼]

The European and worldwide directives and targets for renewable energy integration, motivated by the imminent need to decarbonize the electricity sector, are imposing severe changes to the conventional electrical power system. The inherent unpredictability of the instantaneous energy production from variable renewable energy sources (VRES) is expected to make the reliable and secure operation of the system, a challenging task. Flexibility, and in particular, energy storage is expected to assume a key role in the integration of large shares of VRES in the power system, and thus, in the transition towards a carbon-free electricity sector. One of the main storage mechanisms that can facilitate the integration of VRES is energy arbitrage, i.e. the transfer of electrical energy from a period of low demand to another period of high demand. In this thesis, we investigate and develop novel operating strategies for maximizing the value of energy arbitrage from storage units at different scales (i.e. grid-scale or distributed) and in different settings (i.e. interconnected or off-grid). The decision-making process of an operator optimizing the energy arbitrage value of storage is an inherently complex problem, mainly due to uncertainties induced by: i) the stochasticity of market prices and ii) the variability of renewable generation. In view of the great successes of deep reinforcement learning (DRL) in solving challenging tasks, the goal of this thesis is to investigate its potential in solving problems related to the control of storage in modern energy systems. Firstly, we address the energy arbitrage problem of a storage unit that participates in the European Continuous Intraday (CID) market. We develop an operational strategy in order to maximize its arbitrage value. A novel modeling framework for the strategic participation of energy storage in the European CID market is proposed, where exchanges occur through a process similar to the stock market. A detailed description of the market mechanism and the storage system management is provided. A set of necessary simplifications that constitutes the problem tractable are described. The resulting problem is solved using a state-of-the-art DRL algorithm. The outcome of the proposed method is compared with the state-of-the-art industrial practices and the resulting policy is found able to outperform this benchmark. Secondly, we address the energy arbitrage problem faced by an off-grid microgrid operator in the context of rural electrification. In particular, we propose a novel model-based reinforcement learning algorithm that is able to control the storage device in order to accommodate the different changes that might occur over the microgrid lifetime. The algorithm demonstrates generalisation properties, transfer capabilities and better robustness in case of fast-changing system dynamics. The proposed algorithm is compared against two benchmarks, namely a rule-based and a model predictive controller (MPC). The results show that the trained agent is able to outperform both benchmarks in the lifelong setting where the system dynamics are changing over time. In the context of an off grid-microgrid, the optimal size of the components (i.e. the capacity of photovoltaic (PV) panels, storage) depends heavily on the control policy applied. In this thesis, we propose a new methodology for jointly sizing a system and designing its control law that is based on reinforcement learning. The objective of the optimization problem is to jointly find a control policy and an environment over the joint hypothesis space of parameters such that the sum of the initial investment and the operational cost are minimized. The optimization problem is then addressed by generalizing the direct policy search algorithms to an algorithm we call Direct Environment Search with (projected stochastic) Gradient Ascent (DESGA). We illustrate the performance of DESGA on two benchmarks. First, we consider a parametrized space of Mass-Spring-Damper (MSD) environments and control policies. Then, we use our algorithm for optimizing the size of the components and the operation of a small-scale autonomous energy system, i.e. a solar off-grid microgrid, composed of photovoltaic panels, batteries. On both benchmarks, we show that DESGA results in a set of parameters for which the expected return is nearly equal to its theoretical upper-bound. Finally, we provide the general conclusions and remarks of this thesis and we propose a list of future research directions that emerge as an outcome of this work. [less ▲]

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See detailPresent and future sensitivity of the Antarctic surface mass balance to oceanic and atmospheric forcings: insights with the regional climate model MAR
Kittel, Christoph ULiege

Doctoral thesis (2021)

Recent Global Warming has caused widespread ice losses from the Antarctic Ice Sheet (AIS) leading to an increase in mean sea level. By influencing the ice dynamics and the mass of water that accumulates ... [more ▼]

Recent Global Warming has caused widespread ice losses from the Antarctic Ice Sheet (AIS) leading to an increase in mean sea level. By influencing the ice dynamics and the mass of water that accumulates on the continent, the surface mass balance (SMB, i.e, the difference between snow accumulation and ablation at the surface of the ice sheet) contributes to sea-level variations. A better knowledge of how present and future SMB will change is therefore needed to refine sea-level-rise estimates. With the aim of identifying the driving processes from different components of the climate system (from the surface of the ocean to high-elevation clouds), we reconstruct and project the Antarctic SMB using the regional climate model MAR developed at ULiège, over 1980--2100. The results of MAR have been first compared to diverse observations to evaluate its performance. We gathered observations of several types (near-surface climate and snow accumulation) to guarantee the robustness of our results and conclusions based on our climate modeling. A first objective of this thesis was to determine to what extent the recent changes at the ocean surface can exert a direct feedback on the atmosphere and SMB. Our simulations with perturbed sea-ice concentration and sea-surface temperature around Antarctica reveal that strong and persistent katabatic winds prevent most atmospheric changes induced by the ocean to penetrate inland. This suggests a limited influence of the ocean surface on the Antarctic SMB. We focused afterwards on the sensitivity of the SMB to atmospheric warmings projected by global models using high-emission scenarios (RCP8.5 and ssp585). Higher temperatures are projected to increase SMB on the grounded ice as a result of stronger snowfall while the future SMB over the ice shelves should be dominated by higher meltwater-runoff values (compromising the stability of ice shelves) and is consequently projected to decrease. Leaving aside the role of the ocean on the thinning of ice shelves, increasing surface melt should however remain weak under the Paris Agreement limiting potential ice-shelf collapses and accelerated Antarctic ice losses. However, our results suggest a large spread in melt increase over the ice shelves during the 21st century resulting in large uncertainties in their potential disappearance. Given the important role of ice shelves in limiting the acceleration of Antarctic ice losses (as they restrain the grounded ice to flow into the ocean), the third subject of this thesis has been devoted to the physical drivers explaining differences in increased summer melt over the Antarctic ice shelves. Although the melt increase results from higher greenhouse-gas concentrations, differences in projected melt increases arises from liquid-containing clouds. These clouds re-emits more longwave energy towards the surface, increasing melt over the ice shelves and later favouring absorption of solar energy again strengthening melt. In conclusion, we investigate the sensitivity of the Antarctic SMB to different components of the climate system over 1981--2100. Uncertainties linked with the grounded Antarctic SMB essentially depend on the projected increased rates in snowfall associated with higher temperatures while uncertainties in the ice-shelf SMB decrease are related to cloud properties with more liquid-containing clouds leading to a stronger decrease of the ice-shelf SMB. [less ▲]

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