Amin Jafarzadeh​

• 18/12/2020
  
• 15.00 uur
• ​Online Doctoraatsverdediging​
• Promotoren: Erik Neyts & Annemie Bogaerts
• Departement Chemie

Abstract

The interest in utilizing plasma catalysis for environmental purposes continues to grow. Since a plasma-catalytic reaction can benefit both from the reactivity of the plasma and the high product selectivity induced by the catalyst, it is important to understand the plasma-catalyst interaction at a fundamental level in order to maximize the synergistic effects in practical experiments. Because of the highly complex network of processes happening simultaneously, revealing the entire mechanism is not straightforward. Utilizing computer simulations, we can study each factor separately and obtain detailed information about their effect on the whole reaction network. As part of an integrated multi-scale simulation scheme for understanding plasma catalysis, atomic scale calculations provide valuable insight into the interactions and subsequent changes in the catalyst electronic structure and the reactivity of atoms, molecules, and radical species present in the plasma. In that context, this thesis aims to provide answers to the following questions from the atomistic point of view: (1) How can we model plasma-induced surface charging and its impact on the adsorption of size selected catalytic nanoclusters on a support material? (2), What is the effect of “surface charging” on the activation of molecules, such as CO2 adsorbed on supported metal clusters? (3), How can we model the effect of an externally applied electric field in plasma catalysis? (4), How does the electric field change the activation and chemisorption properties of CO2 molecules adsorbed on Cu surfaces when combined with the effects of surface charging and the catalyst surface morphology? (5), How do plasma-generated radicals affect the plasma-catalytic reactions, especially for the case of ammonia reforming of methane for HCN production on Cu surfaces?, and (6) How can we simulate the reactivity of vibrationally excited species in a plasma-catalytic non-equilibrium environment?

The results of this thesis have demonstrated that the plasma-induced changes in the electronic structure of catalysts and reactants have great potential in steering the plasma-catalytic reactions and the answers to the abovementioned questions could help to adjust and optimize plasma-catalytic processes towards revamping renewable energy resources and mitigating environmental issues arising from greenhouse gas production. ​ ​

William Keustermans​

• 18/12/2020
  
• 16.00 uur
• ​Online Doctoraatsverdediging​
• Promotor: Joris Dirckx
• Departement Fysica

Abstract

Nasal airway obstruction (NAO) is a routinely encountered complaint by ear-nose-throat (ENT) physicians, affecting all age groups. NAOs yearly reduces the overall quality of life for millions of patients and, together with sinus diseases, cost the European healthcare systems billions of euros. The aetiology of NAO is determined by different conditions. If pharmacological treatment fails, as in many cases of anatomic abnormalities, surgery is often the treatment of choice. Nowadays, no proper gold standard currently exists for assessing nasal function impairment. Clinical examination is mainly used to make treatment decisions but frequently fails to pinpoint the cause of the patient’s perceived nasal obstruction. Current routine measurement techniques are found to correlate poorly with patients’ subjective feeling of nasal airway obstruction. However, these methods are used by rhinologists during decision making because no better objective measures are available. Therefore, the decision to proceed to surgery is generally based on the surgeon’s assessment, often without clear objective criteria. The reported surgical correction of nasal anatomic deformities with post-surgical symptom relief is inconsistent, and the range on reported failure rates inordinate. The introduction of a new standard for objective assessment of nasal airway obstruction could reduce the high failure rates by guiding surgical decision making.

Computational fluid dynamics (CFD) models have the potential to fill this gap by providing consistent and accurate information on nasal airflow and function. CFD can also be coupled to different physical laws, such as particle deposition and heat loss. Particle deposition in the nose depends on the airflow and is essential to understand nasal cleansing of airborne particles and for targeted drug delivery. Such physics-based models would enable an accurate diagnosis for each patient individually, together with an evidence-based selection of the most effective therapy while enabling postoperative evaluation. Ideally, and in combination with other techniques, allow taking into account the evolution of the internal nasal anatomy and its effect on airflow.

However, nowadays, some limitations inhibit such an approach becoming viable in the medical setting. Model-creation remains labour-intensive and time-consuming. The manual editing of X-ray tomographic cross-sections is not only tedious but also makes the model-creation prone to errors. On top of this, the numerical model design requires specific technical expertise that is not available for most physicians. In this dissertation, different machine learning and computer vision techniques were researched and combined with CFD to build proof-of-concept solutions to overcome existing limitations.

Charlotte Van Moorleghem​

• 15/12/2020
  
• 17.00 uur
• ​Online Doctoraatsverdediging​
• Promotoren: Katleen Huyghe & Raoul Van Damme
• Departement Biologie

Abstract

For many animals, the ability to detect and recognise predators is crucial for their survival. Accordingly, species have evolved multiple sensory systems warning them of imminent dangers. One of these, the sense of smell, is probably the oldest and most widespread system, but likely also the least understood. This thesis explores the effects of predator type (mammal or snake), origin (native, invasive or allopatric) and insularity (mainland or island prey populations) on chemosensory abilities of lacertid lizards. Additionally, in order to lay bare the mechanics behind chemosensory predator detection in these lizards, I look into the chemical nature of predator-derived cues. Instigated by the alarming spread of the invasive mongoose (Herpestes auropunctatus, a notorious predator of reptiles) in the Balkan, I set out to test whether lacertids were able to interpret its odour. Surprisingly, individuals of the Asian grass lizard (Takydromus sexlineatus), a lacertid from the native range of the mongoose, exhibited no signs of stress when experimentally confronted with mongoose chemicals; chemicals of a sympatric snake predator elicited the behaviours typical for lacertids in dangerous situations. More puzzling, Dalmatian wall lizards (Podarcis melisellensis) from mainland Croatia did mount the typical anti-predatory response when brought into contact with mongoose scent. However, conspecific wall lizards living on islands failed to recognise mongoose chemicals, or ignored them. In fact, island lizards showed signs of chemosensory deprivation in general: they did not respond to a sympatric snake predator, and brain areas involved in the processing of chemical signals tended to be smaller than in mainland specimens. I hypothesise that insular conditions (limited resource availability and predator relaxation) select against chemosensory investment. In the second part of the thesis, I used a well-known study system (recognition of adder, Vipera berus, chemicals by common lizards, Zootoca vivipara) to test the usefulness of two techniques for the identification of kairomones. I found that neutral lipids, extracted with n-hexane from adder skin, provoked the typical fear-response in lizards. Gas Chromatography – Mass Spectrometry revealed a complex cocktail of 165 different molecules, several of which are likely candidate-kairomones. In a subsequent study, I tested a recently developed technique (Proton-Transfer Reaction Time-of-Flight Mass Spectrometry) that allows real-time capture and extremely accurate mass annotation of volatile molecules. Common lizards can detect the presence of adders based on such volatile molecules only. These results emphasise the complexity of the information prey animals can obtain from their predators’ scent. ​ ​

Maxim Pieters

• 14/12/2020
  
• 15.30 uur
• ​Online Doctoraatsverdediging​
• Promotoren: Pierre Van Mechelen & Hans Van Haevermaet
• Departement Fysica

Abstract

A study of inclusive four jet production in proton-proton collisions at a centre-of-mass energy of 13 TeV is presented. The data sample was collected in 2016 with the CMS detector at the LHC during a low intensity run, with an integrated luminosity of 0.042 pb-1. Differential cross sections are measured as a function of the jet transverse momentum, pseudorapidity, and several other observables that exploit angular correlations. The lowest jet transverse momentum cuts required in this paper are 35, 30, 25, and 20 GeV for the first, second, third and fourth leading jet respectively within |η| < 4.7, leading to a fiducial cross section of σ = 2.77 ± 0.02 (stat.)+0.68-0.55(syst.) μb. It is found that the data are very sensitive to different aspects of the underlying event, parton showers, and matrix element calculations. In particular the interplay between the de-correlations caused by parton showers and double parton scattering contributions is shown to be important. Models employing angular ordered parton showers, off-shell initial kinematics, as well as models with higher order matrix element calculations provide a better description of the data in certain observables, compared to standard leading-order models. The ΔS observable, which characterizes the azimuthal angular difference between the hard and soft jet pair, is used to extract a double parton scattering contribution by means of a template fit method. Model dependent values of sigma effective are calculated and compared to previous measurements. While all extracted values of the effective cross section show agreement with measurements performed at lower centre-of-mass energies, a strong model dependence of the double parton scattering contribution is found.

Yannick Uytdenhouwen

• 11/12/2020
  
• 14 uur
• Online doctoraatsverdediging 
• Promotoren: Annemie Bogaerts & Pegie Cool
• Departement Chemie

Abstract

Combatting the ever rising concentrations of greenhouse gases in the atmosphere, in particular CO2 and CH4, is one of the biggest challenges of peoplekind in this century. Reducing emissions and developing innovative solutions for capturing and reusing the gases that are inevitably produced, are the tasks at hand for the next decades. However, novel technologies are required in order to convert these greenhouse gases in a sustainable and efficient way. Plasma technology could offer a viable solution, by directly targeting the molecules in reacting into value-added chemicals. Their quick on-and-off-switching capabilities by electrical energy, in combination with intermittent renewable energy sources, makes them a promising technology to directly convert CO2 and CH4 in a sustainable way. Therefore, in this work, we studied the potential use of the DBD reactor for sustainable CO2 and CH4 conversion. We aimed to improve the reactor performance via different methods, and to develop a technique to gain more fundamental insight on how the kinetics in the reactor change on the macro scale when optimising the performance. First we investigated the influence of micrometre sized discharge gaps and packing materials to enhance CO2 dissociation conversions. The results show that smaller gap sizes are beneficial and that the performance of a packing material greatly depends on the specific combination of material composition, sphere size, and gap size. Further investigation with core-shell structured spheres showed that overall sphere properties can be optimised to a specific use. Next, an apparent first order reversible reaction fit was developed to retrieve more fundamental parameters, such as equilibrium conversion and reaction rate coefficients, on a macro level scale. By tracking the reactor conversion over a wide range of residence times for different cases and matching the results to our fit, we have elucidated how the applied power, reactor pressure, discharge gap size, and the addition of packing materials change the kinetics to influence the reactor performance in CO2 dissociation, CH4 reforming, and dry reforming of methane and their product distribution. Finally, we explored whether the reactor performance can be optimised for bi-component gas mixtures by altering the gas flow design in the reactor. The results assessed the potential of this method for dry reforming of methane and ammonia synthesis and showed room for improvement in conversion and product distribution.

Jonas Buys 

• ​25/11/2020
• 10 uur
• ​Online verdediging ​
• Promotoren: Vincenzo De Florio, Chris Blondia
• Departement Informatica
  

Abstract

Ten eerste kan een statische, context-agnostische redundantieconfiguratie op termijn leiden tot een snellere uitputting van de beschikbare redundantie. Daardoor is het mogelijk dat eventuele verstoringen die de operationele status (context) van de onderliggende componenten niet naar behoren kunnen worden gecompenseerd.

Ten tweede bepaalt de hoeveelheid redundantie, in combinatie met het stemalgoritme, hoeveel simultaan falende versies een NVP-schema kan tolereren. Een vooraf bepaald niveau van redundantie is echter niet kosteneffectief: wanneer het werkelijke aantal storingen lager zou zijn dat wat tijdens de ontwerpfase vooropgesteld werd, dan zou een kleinere hoeveelheid redundantie (tijdelijk) volstaan, waardoor de computationele kost gereduceerd kan worden, en mogelijk tevens de kost van het daaraan geassocieerde energieverbruik.In dit proefschrift wordt een nieuwe betrouwbaarheidsstrategie geïntroduceerd die geavanceerd redundantiebeheer toevoegt aan NVP, met als doel de interne redundantieconfiguratie autonoom af te stemmen op de waargenomen verstoringen. Deze adaptieve fouttolerante strategie is ontworpen om een hoge beschikbaarheid en betrouwbaarheid te handhaven en kan redundantieniveau en de selectie van functioneel equivalente componenten die door het redundantieschema worden gebruikt, dynamisch aanpassen. Daarbij berust het algoritme op een aantal metrieken om de doeltreffendheid van de redundantieconfiguratie en de gebruikte onderliggende componenten te evalueren, op vlak van betrouwbaarheid en tijdigheid. Simulatietechnieken werden aangewend om de kenmerken van het algoritme, het systeem en de omgeving waarin het zal functioneren te modelleren. Hierdoor kon de doeltreffendheid van het algoritme geanalyseerd worden, en werd aangetoond hoe het algoritme de tekortkomingen aanpakt die typisch verbonden zijn aan het gebruik van de conventionele NVP-techniek.

​Dajana Radujkovic​

• 25 november 2020
  
• Tijdstip: 10 uur
• Online doctoraatsverdediging
  
• Departement Biologie 
• Promotoren: Erik Verbruggen en Sara Vicca
  

Abstract

Plants and soil microorganisms are the main components of every terrestrial ecosystem. They drive the cycle of carbon in nature and they form complex, often species-specific interactions with each other shaping both aboveground and belowground communities. Soil is a medium that connects these two worlds and mediates all interactions between them. This work explores the role of soil abiotic properties in predicting plant productivity and microbial (bacterial and fungal) community composition patterns in grassland soils worldwide and the role of plant-soil interactions on the development of soil fungal community composition in heathlands.

Our findings demonstrate that soil properties determining soil fertility and nutrient availability (soil organic matter, cation exchange capacity, percentage of sand, soil Zn concentrations) can explain a substantial amount of variation in global grassland productivity which surpasses the predictive power of commonly used climatic predictors. These same properties are also shown to be the best predictors of the local-scale variation in plant productivity across globally distributed grassland sites.

Regarding soil microbes, we show that there is generality in predictors of microbial community composition along globally replicated, local-scale grassland productivity gradients (where abiotic factors such as pH and base saturation best predict bacterial community composition and plant communities best predict fungal community composition). Furthermore, we find that that different plant productivity levels are consistently associated with distinct soil microbial communities across different grassland sites. Finally, we demonstrate that plant-soil interactions are important factors determining fungal community assembly in heathlands, which can override the importance of abiotic soil conditions.

These findings suggest that considering key soil physicochemical properties when predicting the effect of environmental changes on grassland productivity would not only improve grassland productivity models, but it could also help predict the shifts in soil microbial community composition. Moreover, given that some of the factors and interactions predicting both grassland plant productivity and microbial community composition were found to be universal across contrasting climates, similar general patterns might also hold in other systems. While this remains to be explored, the universal patterns observed in this study provide confidence that making global predictions regarding future changes in plant productivity, soil microbial community composition and, possibly resulting changes in ecosystem functioning, is a feasible task.

Vincent Vermeiren​

• 23 november 2020
  
• Promotor: Annemie Bogaerts
• Departement Chemie
• Locatie: Online doctoraatsverdediging
• Tijdstip: 11 uur

Abstract

In our research, we aim to reveal the conditions at which the most energy efficient dissociation of CO2 takes place, for plasmas in which both vibrational induced dissociation and thermal dissociation become important.

First, a supersonic flow microwave plasma model is investigated. This model reveals the effect of the flow on the plasma performance. The results reveal that the time delay for vibrational induced dissociation to take place, as well as the maximum specific energy input that can be added before the flow is choked are the main limitations to reaching high energy efficiency.

Next, it is shown that pulsing the plasma can increase the vibrational-translational non-equilibrium, that is needed for efficient vibrational induced dissociation. The maximum improvement is reached when the plasma pulse time equals the time at which the vibrational temperature reaches a maximum value, and for long interpulse times, so that the gas can cool down before the next pulse starts.

Finally, the effect of thermal quenching on the plasma performance is investigated for warm and cold plasmas at different specific energy inputs. It is shown that quenching can increase the final CO2 conversion by reducing the recombination mechanisms, and that high efficiencies are reached for thermal plasmas in combination with quenching.
This PhD thesis increases our knowledge of the kinetics in CO2 plasmas, and gives valuable insight for experimentalists.

​​Jennifer Jörissen​

• 20 november 2020
  
• Promotoren: Sarah Lebeer en Olivier Vanderveken
• Departement Bio-Ingenieurswetenschappen

Abstract

Otitis media with effusion (OME) is a common childhood disease characterized by accumulation of fluid in the middle ear without symptoms of an acute infection. Chronic OME, lasting longer than three months, is often treated by placing a drainage tube into the ear drum, and there is an urgent need to develop non-invasive treatment and prevention methods. All bacteria traditionally associated with middle ear diseases are commensals also found in the upper respiratory tract (URT) of healthy individuals. Interaction with the host immune system and other bacteria present in the same niche determine their ability to expand into neighbouring anatomic locations and to express their virulence. Long-term perturbation of the microbiota has been associated with several chronic inflammatory diseases and is also hypothesized to underlie chronic OME. Preventing such perturbation or restoring a perturbed microbiota through addition of beneficial bacteria could therefore be a valuable method for OME prevention, reducing the need for surgical intervention.

This project aimed to identify bacteria associated with or protective against chronic OME. We first compared the microbiome of several URT and ear niches of 70 chronic OME patients and 63 healthy controls by sequencing the diverse V4 region of the bacterial 16S rRNA gene. This allowed us to identify bacterial taxa over-represented in healthy individuals or dominant in OME middle ear effusion. Next, we isolated health-associated bacteria and predicted their beneficial effect, ability to survive in the human URT and their safety through in vitro experimentation and genome analysis.

OME middle ear effusion frequently harboured one of several dominant (>50% relative abundance) taxa likely responsible for OME, which were traced to the URT and the ear canal. In contrast, most healthy middle ear rinses could not be sequenced, indicating very low biomass in or even sterility of this niche. Therefore, potentially health-associated bacteria were identified by comparing the nasopharynx microbiome between OME patients and healthy controls. Salivarius group streptococci and Acinetobacter lwoffi were significantly more abundant in the nasopharynx of healthy children compared to OME patients, but only the Streptococcus taxon was present in ≥50% of children and could be isolated. Seven Streptococcus salivarius isolates were characterized in detail and five were free of known virulence and transferable antibiotic resistance genes, inhibited all tested pathogens and adhered well to respiratory epithelial cells. This makes them promising candidates for further testing and development as potential probiotics or microbiome therapeutics to prevent or treat OME.

​Ignace Van Spilbeeck​

• 17 november 2020
  
• Promotor: Benny Van Houdt
• Departement Informatica

Abstract

Load balancing is one of the key components in many distributed systems as it heavily impacts performance and resource utilization.

This thesis considers heterogeneous systems where servers belong to one of multiple classes, with the speed of an individual server depending on its class.
Two categories of load balancing strategies are considered.

The first category consists of centralized load balancing strategies, where a dispatcher assigns incoming jobs to the servers. Both randomized dispatching and size-based dispatching strategies are considered.

For these strategies, we propose mathematical models to describe the queue lengths over time and validate them through discrete event simulation. We show that the dispatcher's optimal parameter can be determined via convex optimization, if it exists.

Furthermore we also investigate the effects of different system parameters on the achievable mean response time and propose several easier to compute schemes for determining the dispatcher's selection parameter.

Finally, we also discuss the impact of scheduling policies in the nodes in addition to the load balancing strategies.

The second category consists of decentralized load balancing strategies where no dispatcher is used, but servers can exchange jobs through communication by means of probing.
For these load balancing strategies, we use a mean field model to study the queue lengths and the required probe rate to achieve stability. We also develop an iterative algorithm to more easily compute the mean response time.

Finally we study and compare the mean response times for specific "pull" and "push" strategies for different parameter settings.

Nathalie Brenard

• 21 oktober 2020
  
• Promotoren: Herwig Leirs, Rob Moerkens en Vincent Sluydts
• Departement Biologie

Abstract

Biologische bestrijding van plagen is een succesverhaal in de Europese paprikateelt onder glas en de meeste plagen worden onder controle gehouden door het uitzetten van natuurlijke vijanden. Bladluizen vormen echter nog steeds een groot probleem en de gespecialiseerde bladluispredatoren die uitgezet worden, blijken vaak niet in staat om de plaag onder controle te krijgen waardoor men chemisch ingrijpt. Maar door hun hoge voortplantingssnelheid en korte generatietijd zijn bladluizen in staat zeer snel resistentie te ontwikkelen tegen verschillende insecticiden.

Tegenwoordig is er meer aandacht voor het gebruik van generalisten in plaagbestrijding omdat zij ook in het gewas kunnen overleven als er geen plagen zijn. Macrolophus pygmaeus is een generalistische roofwants die reeds veelvuldig wordt ingezet in Europese tomatenserres tegen diverse plagen. In dit doctoraatsonderzoek werd het gebruik van M. pygmaeus in paprikateelt onderzocht.

Allereerst werden uitzetstrategieën met betrekking tot bijvoederen getest. Niet alle generalisten hebben nood aan bijvoederen en verschillende voedseltypes of bijvoederstrategieën kunnen de populatiegroei en verspreiding in het gewas beïnvloeden. Tweewekelijks vollevelds bijvoederen met cysten van pekelkreeftjes bleek de beste strategie voor de vestiging van M. pygmaeus in paprika.

Vervolgens werd onderzocht of de roofwantsen in staat zijn om twee belangrijke plagen in paprika, bladluizen en tripsen, te bestrijden. Het effect van M. pygmaeus op bladluisbestrijding werd bestudeerd in combinatie met het wegsnijden van bladeren tot op verschillende hoogtes. Dit verkleint de verticale lengte van het gebladerte en brengt zo prooi en predator dichter bij elkaar. Bij een lengte korter dan 190 cm konden de roofwantsen bladluizen succesvol bestrijden.

Californische trips wordt momenteel bestreden door het uitzetten van de roofwants Orius laevigatus. Maar M. pygmaeus voedt zich ook met tripsen en kan zo O. laevigatus overbodig maken. Tijdens de drie seizoen van experimenten was M. pygmaeus op zichzelf in staat om trips onder controle te houden.

Deze trips en M. pygmaeus data werden vervolgens gebruikt om prooi-predator modellen op te stellen die op basis van wekelijkse monitoringdata de kans op plaagcontrole voorspellen in de komende week.

Met onze bevindingen kan M. pygmaeus succesvol ingezet worden voor plaagbestrijding in paprikaserres en telers verder op weg helpen naar een pesticiden-arme of zelfs pesticiden-vrije paprikateelt.

Mylène Hendrickx

• 20 oktober 2020
  
• Promotor: Joke Hadermann
• Departement Fysica

Abstract

The type and arrangement of the atoms in a material, called the crystal structure, determine its physical properties. Thus to gain control over materials properties, the first step is to determine these crystal structures. During my PhD, I have investigated the crystal structures of two main groups of materials, perovskites and Li-ion battery cathode materials, to which cation substitution was applied in an attempt to induce and enhance specific properties. For the perovskites, which can have a wide variety of properties depending on small structural changes, we focussed on the magnetic properties, of great importance in nano-electronics. With the Li-ion batteries, we tried to find new cathode materials with enhanced electrochemical performance.

The crystal structures of these new materials were investigated using advanced transmission electron microscopy (TEM) in both reciprocal space (electron diffraction) and direct space (imaging techniques), combined with energy-dispersive X-ray spectroscopy (EDX). Based on these studies, we proposed and refined models for the new structures. With these models, we were able to explain the variations in the properties of these materials. The study of the relation between structure and properties has yielded fundamental knowledge, applicable for the optimization of the properties of the investigated materials as well as of related materials.

Myrthe Pareyn​

• 15 oktober 2020
  
• Promotoren: Herwig Leirs en Simon Shibru
• Departement Biologie

Abstract

Cutaneous leishmaniasis (CL) is a neglected tropical disease characterized by nodular and crusty skin lesions, mainly on people’s face and extremities, resulting in disfiguring scars after healing. It is caused by Leishmania parasites, which are transmitted by female phlebotomine sand flies during blood feeding. The disease is a major public health problem in Ethiopia, where Leishmania aethiopica affects approximately 20,000 to 50,000 people annually and transmission is zoonotic, with hyraxes serving as reservoir hosts.

The first main objective of this thesis was to thoroughly explore the transmission cycle of CL in an endemic hotspot in southwestern Ethiopia and map the distribution of the vector and the infection in a larger surrounding area. We found that aside from hyraxes, humans also play an important role in transmission, hence early diagnosis and treatment of the human reservoir is pivotal for disease management. Furthermore, we show that the vector is mainly biting at night indoors. This information can be used to limit the human-vector contact by for instance the use of bed nets. The distribution of both the vector and the disease is much more widespread than reported, which is calling for better surveillance. The generated distribution map can be used for guidance of control interventions.

The second objective was to comparatively assess the performance of different molecular assays for detection of Leishmania aethiopica in clinical samples and sand flies. We show that the probe-based LC kDNA PCR, which was developed for L. aethiopica detection specifically, performs superior and should be implemented in routine practice for CL diagnosis in case microscopy results are negative. For large entomological or eco-epidemiological studies, however, we recommend the use of a crude high-salt extraction buffer with ethanol precipitation step for DNA isolation in combination with a SYBR Green qPCR assay targeting the spliced leader (SL-)RNA sequence.
For the third objective, we assessed that the recently introduced matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein profiling technique is a suitable alternative for unambiguous sand fly species determination in Ethiopia.

Collectively, this thesis lays groundwork for adequate CL detection and disease control and indicates the use of novel techniques for accurate, cost-effective future entomological surveys in Ethiopia.

Joren Vanherck​

• 15 oktober 2020
  
• Promotoren: Wim Magnus en Bart Sorée
• Departement Fysica

Abstract

De voorbije jaren waren tweedimensionale (2D) materialen niet weg te denken uit de vastestoffysica en -technologie. Pas sinds 2017 zijn er ook experimentele waarnemingen van ferromagnetisme in zulke materialen. Vanuit een technologisch standpunt is het begrijpen van magnetisme in deze ultra-dunne limiet essentieel met het oog op de steeds verder doorgedreven verkleining van geïntegreerde electronicacomponenten, waarbij er gestreefd wordt naar goedkopere, snellere en energiezuinigere apparaten.

Vanuit een wetenschappelijk standpunt is het bestaan van tweedimensionale ferromagneten nog niet goed begrepen aangezien het ogenschijnlijk in tegenspraak is met de bekende stelling van Mermin-Wagner — die onder bepaalde voorwaarden de ferromagnetische ordening in 2D materialen verbiedt. Om deze situatie te verbeteren, hebben we het kwantummechanische Heisenberg model bestudeerd op niet-nul temperaturen en met een uitwisselingsinteractie die anisotroop is en voorbij de naaste buren reikt. Er wordt verwacht dat dit een goed model is voor enkele recent ontdekte 2D ferromagneten zoals CrI3, CrBr3 en MnSe2.

We hebben resultaten bekomen door Zubarev’s Greense functies met het Tyablikov ontkoppelingsschema te gebruiken, waarvan geweten is dat het goede voorspellingen voor de magnetisatie oplevert over het volledige temperatuursinterval. De verkregen resultaten hebben we vergeleken voor twee- en driedimensionale materialen. Verder hebben we het effect van een homogeen aangelegd magnetisch veld in een willekeurige richting onderzocht en de werkwijze uitgebreid om ook magnetische dipool-dipool interactie mee in rekening te kunnen nemen.

We zijn erin geslaagd om de voorspellingen van het Mermin-Wagner theorema te reproduceren en vonden dat spontane magnetisatie op niet-nul temperaturen nog steeds mogelijk is in 2D materialen die een easy-axis anisotropie vertonen. De combinatie van onze resultaten met ab initio berekeningen liet ons bovendien toe om Curietemperaturen te berekenen in overeenstemming met experimentele waarnemingen. Het magnetisatiegedrag van 2D easy-axis materialen blijkt zeer gelijkaardig aan dat van driedimensionale materialen, terwijl er een groot verschil is voor materialen met easy-plane anisotropie. Over het algemeen is er een oplijning van de magnetisatie met de intrinsieke anisotropie bij lage temperaturen en kleine magnetische velden, terwijl deze zich heoriënteert in de richting van het aangelegde veld in de tegenovergestelde regimes. De dipool-dipool interactie kan een extra bijdrage leveren aan de easy-plane anisotropie in dunne materialen, waarbij het bijhorende lange-afstands karakter de magnetisatie mogelijks stabiliseert. Om verder computationeel onderzoek naar monolaag ferromagneten te stimuleren stelden we een computer programma beschikbaar om Curietemperaturen te berekenen op basis van ons formalisme.

Jennifer Jörissen

• 9 oktober 2020
  
• Promotoren: Sarah Lebeer en Olivier Vanderveken​
• Departement Bio-ingenieurswetenschappen

Abstract

Otitis media with effusion (OME) is a common childhood disease characterized by accumulation of fluid in the middle ear without symptoms of an acute infection. Chronic OME, lasting longer than three months, is often treated by placing a drainage tube into the ear drum, and there is an urgent need to develop non-invasive treatment and prevention methods. All bacteria traditionally associated with middle ear diseases are commensals also found in the upper respiratory tract (URT) of healthy individuals. Interaction with the host immune system and other bacteria present in the same niche determine their ability to expand into neighbouring anatomic locations and to express their virulence. Long-term perturbation of the microbiota has been associated with several chronic inflammatory diseases and is also hypothesized to underlie chronic OME. Preventing such perturbation or restoring a perturbed microbiota through addition of beneficial bacteria could therefore be a valuable method for OME prevention, reducing the need for surgical intervention.

This project aimed to identify bacteria associated with or protective against chronic OME. We first compared the microbiome of several URT and ear niches of 70 chronic OME patients and 63 healthy controls by sequencing the diverse V4 region of the bacterial 16S rRNA gene. This allowed us to identify bacterial taxa over-represented in healthy individuals or dominant in OME middle ear effusion. Next, we isolated health-associated bacteria and predicted their beneficial effect, ability to survive in the human URT and their safety through in vitro experimentation and genome analysis.

OME middle ear effusion frequently harboured one of several dominant (>50% relative abundance) taxa likely responsible for OME, which were traced to the URT and the ear canal. In contrast, most healthy middle ear rinses could not be sequenced, indicating very low biomass in or even sterility of this niche. Therefore, potentially health-associated bacteria were identified by comparing the nasopharynx microbiome between OME patients and healthy controls. Salivarius group streptococci and Acinetobacter lwoffi were significantly more abundant in the nasopharynx of healthy children compared to OME patients, but only the Streptococcus taxon was present in ≥50% of children and could be isolated. Seven Streptococcus salivarius isolates were characterized in detail and five were free of known virulence and transferable antibiotic resistance genes, inhibited all tested pathogens and adhered well to respiratory epithelial cells. This makes them promising candidates for further testing and development as potential probiotics or microbiome therapeutics to prevent or treat OME.

Kevin NYS​

• 25 september 2020
  
• Promotor: Sabine Van Doorslaer
• Departement Fysica

Abstract

Heemeiwitten zijn alomtegenwoordig in de verschillende koninkrijken van het leven en vertonen een intrigerende veelzijdigheid. De functie van heemeiwitten wordt grotendeels bepaald door de eiwitopvouwing die de architectuur van de heemzak, de toegang tot de actieve site en de redoxeigenschappen vastlegt. Er is echter geen één-op-één-relatie die een welbepaalde eiwitopvouwing aan een specifieke functie linkt. In dit werk bestudeerde ik dan ook twee types heemeiwitten waarbij ik naging welke structurele elementen en subtiele veranderingen aanleiding geven tot een functie. Hiervoor werd gebruik gemaakt van optische spectroscopie en elektronen paramagnetische resonantie aangezien deze technieken toelaten om de redox-actieve sites van heemeiwitten selectief te bestuderen.

Verfontkleurende peroxidasen zijn heem-bevattende oxidoreductasen die voorkomen in bacteriën en schimmels. Ze katalyseren de oxidatie van grote kleurstofmoleculen en lignine en gebruiken daarbij waterstofperoxide als elektronenacceptor. Een gecombineerde biofysische en biochemische aanpak heeft geleid tot nieuwe inzichten omtrent de katalytische eigenschappen van deze eiwitklasse, wat de deur opent naar toepassingen zoals de biologische afbraak van kleurstofmoleculen in afvalwater of de omzetting van biomassa in biobrandstoffen. De rol van de distale aminozuurresiduen werd ontrafeld voor een subklasse van de verfontkleurende peroxidasen en de toegang tot de actieve site van het eiwit werd grondig bestudeerd. Dit onderzoek heeft zo ook aanleiding gegeven tot enkele technische aanbevelingen voor de studie van heemeiwitten met EPR spectroscopie.
Voorts werd ook een stabiel organisch radicaal in de rusttoestand van een verfontkleurende peroxidase geobserveerd en gekarakteriseerd. Hiertoe werd een zeer succesvolle combinatie gebruikt van computationele voorspellingen en spectroscopische experimenten. De ontdekking van een stabiliserende aminozuurconformatie heeft zo geleid tot de eerste melding van een stabiel radicaal in de rusttoestand van een heem peroxidase.

Een ander heemeiwit dat bestudeerd werd in dit werk is hemoglobine dat gekend is voor zijn rol bij het transport van zuurstof. Het was echter een verrassing dat ook insecten, die ademen via een netwerk van tracheeën, hemoglobine bezitten. Een spectroscopische studie van het hemoglobine van de Europese honingbij en de malariamug kon verschillen onthullen in de heemzak, ligandaffiniteit en voorgestelde functie ondanks de zeer gelijkaardige leefomstandigheden.

Daniel van den Akker​

• 16 september 2020
  
• Promotor: Chris Blondia
• Departement Informatica

Abstract

Leandro Van Langenhove 

• 9 september 2020
  
• Promotoren: Ivan Janssens, Pascal Boeckx en James Weedon
• Departement Biologie

Abstract

Tropical forests are among the most productive ecosystems in the world and play a central role in global biogeochemical cycles due to the high exchange of carbon between biosphere and atmosphere. Nutrient cycles, especially of nitrogen and phosphorus, exert an important control on this exchange and by consequence also on forest growth and dynamics. How nutrients cycle between atmosphere, biosphere and pedosphere in tropical forests remains thus far poorly understood, mainly because a lack of data and a high diversity of tropical forest ecosystem functioning make generalizations difficult. To complicate matters, although tropical forests are very productive, they typically grow on impoverished soils with especially low mineral nutrient availabilities. This begs the question where the required nutrients are coming from. In this thesis, various sampling schemes are coupled with chemical measurements to evaluate how nutrient poor these soils are, and how much nutrients are coming into this system every year. For this, we focused on two topographic gradients with expected soil nutrient heterogeneity situated in two distinct tropical field sites in French Guiana. We measured soil nutrient distribution along the topographic gradients and found that soil phosphorus content differs with topography, a characteristic driven mainly by the soil texture. Additionally, we measured ecosystem nitrogen input through asymbiotic nitrogen fixation and found that these inputs are very low compared to other tropical forest regions, mainly because of the low phosphorus availability. Another nutrient input, namely atmospheric deposition, was also measured and results showed that organic nitrogen, an often-ignored part of the deposition, represented the main fraction of nitrogen deposition in our forest. Phosphorus deposition amounted to only 0.5 kg ha-1 y-1, and was most likely primarily derived from African dust transported across the Atlantic. This arguably low amount of phosphorus deposition, however, amounted to one third of the yearly amount of phosphorus recycled through litterfall, meaning that the amount deposited from the atmosphere is an important contribution to the ecosystem.

Finally, lab and field fertilization studies were conducted that showed that any P added to the soil is rapidly taken up by plant roots, and that plots receiving additional P showed a large increase in nitrogen fixation, indicating that phosphorus availability was severely limiting this process. From these results it becomes clear that phosphorus is in short supply in these forests and that its availability is severely limiting both microbial processes and plant growth.

Davide Di Croce ​

• 3 september 2020
• Promotor: Nick Van Remortel
• Departement Fysica

Abstract

Deze thesis beschrijft het meetproces waarmee Higgs bosonen, geproduceerd in pro-ton-proton botsingen bij de Large Hadron Collider in CERN, worden gedetecteerd. We maken gebruik van het vervalkanaal in twee tegengesteld geladen W bosonen. De W+W- kandidaten worden geselecteerd in botsinggegevens die twee gereconstrueerd leptonen bevatten met hetzelfde leptongetal en tegengestelde lading, in combinatie met een minimale hoeveelheid ontbrekende energue en impuls in het transversale botsingsvlak.

Om de achtergrond processen te wijten aan top quark productie en verval op een juiste manier in rekening te brengen worden de botsingsgegevens vervolgens geklasseerd met behulp van het aantal gereconstrueerde jets en hun kinematische eigenschappen. De dominante bron van achtergrond gebeurtenissen is het Drell-Yan proces. Om hieraan het hoofd te bieden werden zogenaamde machine learning of A.I. technieken gebruikt.

Waar mogelijk worden achtergrond processen gemodelleerd aan de hand van werkelijke botsingsgegevens, in plaats van met gesimuleerde botsingen.
Het gegevensstaal dat hier geanaliseerd wordt komt overeen met proton-proton botsingen uit de LHC bij een massamiddelpuntsenergie van 13 TeV, verzameld met het CMS experiment, over een periode van drie jaar (2016-2018), de LHC Run II dataset.

De waarschijnlijkheid dat het aantal observeerbare Higgs verval kandidaten te wijten aan enkel achtergrond processen hoger of gelijk is aan het geobserveerde aantal kandidaat gebeurtenissen, komt overeen met een verwachte statistische beduidendheid van 3.1 standaard afwijkingen.
Omdat de complete analyse van H->WW vervallen met de Run II dataset nog onder interne pre-publicatie embargo's van het CMS experiment valt, kunnen we de werkelijk geobserveerde beduidendheid nog niet bekend maken. Om die reden presenteren we wel de resultaten bekomen met dezelfde methode, maar toegepast op enkel de 2016 dataset. Dit gegevens staal correspondeert met een ge"integreerde luminositeit van 35.9 fb-1, in vergelijking met 137.1 fb-1 voor de drie jaren samen.

De combinatie van het door ons geanaliseerde vervalkanaal met meer uitgesproken H->WW vervallen, met typisch verschillende soorten leptonen in de eindtoestand, leidt voor de 2016 dataset al tot een geobserveerde statistische beduidendheid van 9.1 standaard afwijkingen te opzichte van de nul-hypothese zonder Higgs productie en verval. Dit resultaat vertaalt zich in een gemeten verhouding van de werkzame doorsnede maal vertakkingsverhouding voor dit verval van 1.28, ten opzichte van de voorspelling van het Stanadaard Model van de deeltjesfysica. Dit resultaat was ook de eerste statistisch significante waarneming van Higgs boson verval in dit kanaal door de CMS collaboratie.

Mats de Jong

• 27 augustus 2020
  
• Promotoren: Karolien De Wael en Nele Samyn
• Departement Chemie

Abstract

Illicit drugs are everywhere in our society. The clandestine market is growing faster than ever before, with record breaking seizures in Europe (and particularly Belgium) concerning cocaine. Cocaine is singled out as a major substance of interest, in Europe and Belgium in particular. Currently used field tests for cocaine detection have several downfalls. They lack specificity, leading to false positive results, and are also easily bypassed by adding other (often colored) compounds, producing many false negative results. This lack of accuracy causes large costs for society: juridical, health-wise and economical. This, combined with the continuously growing drug retail market, presses the need for new and better portable detection devices for cocaine. This PhD thesis aimed at the development of a portable, reliable electrochemical sensor device for cocaine, allowing accurate analysis in field settings such as the Port of Antwerp. The potential of the electrochemical approach to replace other field techniques was tested and evaluated throughout the project. Electrochemical detection, square-wave voltammetry in particular, allows a fast (<40 s) analysis with high sensitivity, specificity and the possibility to detect multiple compounds (illicit drugs, adulterants and diluents) in one measurement scan, making it perfect for on-site screening purposes. In order to obtain this optimized electrochemical approach for cocaine, several fundamental and applied research steps were conducted of which the results are presented in this thesis: (1) determination of methodology and identification of interfering compounds, (2) defining the interfering mechanism of these compounds and provide solutions, (3) test possibility towards polydrug analysis (heroin), and (4) validation and field testing. This approach was followed to guide our fundamental research towards a highly relevant application. This PhD involved close collaboration with the National Institute for Criminalistics and Criminology, as well as with the Netherlands Forensic Institute, the Federal Judicial Police and Belgian Customs. All these agencies provided expert insights into the topic, as well as access to confiscated cocaine street and smuggle samples to help validating the developed technology. Lab validation on 374 samples delivered an accuracy of 98.4 % for the developed sensor, while the field measurements presented clear advantages over other screening tests, certainly concerning the detection of cocaine in colored and mixed smuggle samples. In conclusion, this work includes the research foundations to bring this cocaine detection technology to the market, where it has the potential to replace other commonly used screening techniques.

Eline Berghmans

• 26 augustus 2020
  
• Promotoren: Geert Baggerman en Patrick Pauwels
• Departement Biologie

Abstract

Non-small cell lung cancer (NSCLC), accounting for 80-85% of all lung cancer cases, is generally linked with a poor prognosis and is one of the leading causes of cancer-related deaths worldwide for both women and men. Recently, immunotherapy has changed the landscape of NSCLC treatment. For those who respond, promising results, in terms of acceptable side-effects and antitumor activity by restoring host immunity, have been achieved in NSCLC patients by therapeutic blocking of immune checkpoint programmed cell death protein 1 (PD-1) and its ligand PD-L1. Unfortunately, to date, only a subgroup of patients experiences any long term benefit, while severe immune-related toxicities may occur in patients that do not clinically respond to the therapy. To avoid unnecessary costs and toxicities in patients who will not clinically respond, unique response patterns for anti-PD-(L)1 immunotherapy and additional biomarkers need to be discovered to overcome the limitations of PD-L1 as the sole predictive biomarker in clinical use.

Proteomic approaches, in particular mass spectrometry, have already proven their relevance in discovery of new biomarkers, allowing early diagnosis or prediction of therapy response resulting in a better patient’s quality of life and improvement of health care. In this study, we demonstrated how the combinatorial use of mass spectrometry imaging (MSI) with top-down proteomics on NSCLC tissues was used to discover three candidate predictive biomarkers for anti-PD-(L)1 immunotherapy response in NSCLC patients. Evaluation of these three candidate predictive biomarkers (i.e. neutrophil defensin 1, neutrophil defensin 2 and neutrophil defensin 3) was performed with mass spectrometry imaging and verified with traditional immunohistochemistry and corresponding statistical analysis. The findings reported suggest the possible association between neutrophil defensin expression and response to anti-PD-(L)1 immunotherapy for a more accurate therapy decision for NSCLC patients. Finally, we demonstrated with in vitro physiological data that neutrophil defensin 1, 2 and 3 show an immune-stimulatory effect towards lung cancer.

In conclusion, implementation of MSI and top-down proteomics in lung cancer research has led to the discovery of neutrophil defensins as biomarker to differentiate which NSCLC patients will benefit from anti-PD-(L)1 immunotherapy. MSI has further been used as a successful screening method to evaluate expression levels of these molecules in pretreatment biopsies, confirmed by immunohistochemical analysis. Lastly, the newly discovered neutrophil defensin biomarkers show potential as new molecular targets, essential for designing new effective therapeutic strategies.

Piet Bladt

• 9 juli 2020
  
• Promotoren: Jan Sijbers, Arnold J. den Dekker en Eric Achten
• Departement Fysica

Abstract

Aimeric Teyssier​

• 30 juni 2020
  
• Promotoren: Erik Matthysen, Luc Lens en Joël White
• Departement Biologie

Abstract

The gut microbiota plays a fundamental role for host health and fitness. The gut microbiota is known to be shaped by host traits and environmental factors. One of the dominant causes of contemporary environmental change is the increase in human activity, with urbanisation representing one of the most radical forms of land use alterations in terrestrial ecosystems. These anthropogenic alterations are likely to alter host-associated microbiomes and the interactions between host and microbiota, resulting in adverse effects on hosts. The main aim of this thesis was to investigate the effect of anthropogenic alterations, on the characteristics of the gut microbiota of two passerine hosts, and to further examine the role of specific factors, notably diet and the rearing environment in shaping the gut microbiota.

By studying gut microbiota of free-ranging house sparrows and great tits in habitats with different levels of urbanisation I found that microbial diversity was reduced with urbanisation in house sparrows, but no effect was found in great tits. Urbanisation was also associated with modifications in taxonomic composition and community structure, and changes in functional composition. By exposing wild house sparrows from urban and rural populations to contrasting diets in an experimental set-up, with experimental diets based on a rural vs urban diet, I observed gut microbiota modifications with alterations of both α- and β-diversity and taxonomic composition, with the strongest shifts occurring in individuals exposed to contrasting diets. The influence of the nesting environment on the gut microbiota was investigated by performing a partial cross-fostering experiment in great tits halfway during nestling development. Results showed a significant decrease in microbial diversity between 8 and 15 days after hatching, as well as changes in community composition. In addition, fostered nestlings became more similar to their nest mates, providing evidence that the rearing environment plays a role in shaping the nestlings’ microbiota. Finally, gut microbiota characteristics were found to be related to host condition in both species with an effect of the microbial diversity, taxonomic and functional composition on the body mass and mass gain of the host.

To conclude, this thesis reports new insights on the effect of urbanisation on gut microbiota characteristics and provides experimental evidence for major factors that may induce microbiota changes, notably diet and rearing environment. It also highlights the potential impact of the gut microbiota and its disturbance on the performance of hosts living in cities.

Hans Vanrompay​

• 26 juni 2020
• Promotor: Sara Bals
• Departement Fysica

Abstract

Thais Milagres de Oliveira​

• 25 juni 2020
  
• Promotor: Sara Bals
• Departement Fysica

Abstract

Nanomaterials have attracted enormous attention during the last decades due to their unique physical properties (e.g. optical, thermal, electronic and catalytic properties). This is of importance for an increasing range of applications of nanomaterials, where the characterisation techniques are vital to understand the relationship between their morphology, size, composition or crystallinity and their physical properties. Recent advances in (scanning) transmission electron microscopy ((S)TEM) have enabled a comprehensive characterisation of the chemical composition, size and crystallinity of nanomaterials, from the nanoscale to the atomic level. Nevertheless, images obtained with (S)TEM only correspond to a two-dimensional (2D) projection of a three-dimensional (3D) object, hindering the quantification and interpretation of the material’s shape. To unravel the structure-properties relationship, electron tomography is required. Electron tomography has become an important technique to investigate nanomaterials, but only relatively simple structures (e.g., model-like materials like monocrystalline nanospheres and nanorods) can be investigated in a routinely manner.

During my PhD research, I applied advanced techniques for electron tomography for the investigation of complex nanostructures, such as nanoparticles containing structural defects and beam sensitive nanomaterials. Advanced techniques for electron microscopy were employed for the identification of the defect type as well as the statistical distribution of nanoparticles containing such structural defects. Moreover, an approach for the 3D atomic structure recovery that was recently developed in our laboratory was used for the investigation of different systems containing unknown defects, which prevents the use of any prior information regarding the object under investigation during the tomographic reconstruction. By a thorough characterization of defects at the atomic level (e.g., grain boundaries/dislocations in welded nanorods) in combination with spectroscopic techniques, a better understanding on the relationship of optical properties and crystallinity was achieved. Additionally, the formation mechanisms of hollow nanoparticles induced by ultrafast laser pulses was unveiled by combining advanced approaches for the atomic structure characterization in 3D, methods for the determination of the chemical composition of nanoparticles and techniques for investigation of the dynamical behaviour of nanoparticles in 3D under increasing temperature conditions in in-situ environment. Still, due to the sensitiveness of some nanostructures towards the electron beam, structural modifications can be induced in the nanomaterials during the investigations by electron microscopy, preventing the establishment of a structure-to-properties relationship. Therefore, advanced approaches for the 3D characterization of beam sensitive structures were employed, at the nano and atomic levels.

Shashi Kanth Reddy Singam​

• 25 juni 2020
  
• Promotoren: Etienne Goovaerts en Michele Giugliano
• Departement: Fysica

Abstract

In recent years the nitrogen-vacancy (NV) center in diamond has emerged as an atom-like system with many applications in precision measurements, quantum information processing and quantum fundamental research. In this thesis we focus on characterization of NV centers as a function of optical excitation as well as on a novel technique for local temperature sensing.

In this thesis several factors that affect the spin-dependent fluorescence of NV- centers such as the power of resonant microwave radiation, magnetic field strength and optical excitation intensity are explored. Fluorescence contrast is induced either by spin-resonant microwaves or by a static magnetic field, which can be applied for background free imaging of fluorescent nanodiamonds. Experiments are performed to measure the contrast characteristics of NV- centers under various optical excitation intensities on different types of samples, and the results are backed by an energy level simulation model for estimating population distribution between electronic and spin energy levels. These observations and the model provide good understanding of the contrast in imaging at various optical excitations and a basis for improving NV- detection. Later, by using the knowledge from the experiments, the method is applied to map nanodiamonds seeded in a neuron cell culture by means of the background free imaging technique using the static magnetic field contrast.

A new approach, called the frequency-jump method, is introduced to detect local temperature change on a surface of interest. The method, based on a specific frequency-modulation of the resonant microwaves, is tested first on a single crystal diamond sample and later on deposited nanodiamonds. Finally, this technique is applied on the real-world problem of measuring local temperature change in a GaAs/AlAs microelectronics circuit, by dropcasting nanodiamonds on the chip surface. The local diffusion of heat due to applied power to one of the devices is measured at different spots on the circuit resulting in local temperature detection at multiple points on the same device and in its surrounding. The measurement is time-dependent, which provides information about temperature change at the different spots as a function of time after sudden power switching.

Wouter Verstraelen​

• 24 juni 2020
  
• Promotor: Michiel Wouters
• Departement Fysica

Abstract

Menelia Vasilopoulou-Kampitsi​

• 4 juni 2020
  
• Promotoren: Jana Goyens en Peter Aerts
• Departement Biologie

Abstract

In this thesis, we studied the anatomy of the lacertid vestibular system as well as the manoeuvring capacities of lacertid lizards. When we investigated the interaction between vestibular system size, head size and microhabitat use, we found that lizards with smaller heads housed disproportionally large ears for their size. Since sensitivity of the vestibular system relies on the circulation of the endolymph inside the canals and is positively related to size, a large vestibular system in small animals would ensure the functioning of the ear. The microhabitat lizards occupy did not have an impact on this size relationship, because of spatial constraints of the skull. The shape analysis showed that species living in simple microhabitats possessed more anatomical adaptations linked to enhanced sensitivity than species in more complex habitats, suggesting that the former may benefit from increased sensitivity due to a higher visibility to predators.

Then, we tested the manoeuvrability, turning capacity and running performance of male and female Podarcis erhardi lizards, running on a zigzag and on a straight line racetrack. We used four P. erhardii populations situated at the Greek archipelago. In 2014 lizards were captured from the island of Naxos, Greece (site of Alyko) and were translocated to three experimental islets. The analyses on the microhabitat structure showed that the site of Alyko differed significantly in microhabitat structure from the three islets being covered more by sand rather than rocks and vegetation. We found that lizards from Alyko avoided areas lacking completely in shelters, a behaviour probably relating to thermoregulation and predator avoidance. The experiments performed for the population (males and females) of Alyko two years after the translocation (in 2016) showed that females turned more succesfully than males, however, a similar locomotor performance was observed for both sexes. We found that lizards on the experimental islands increased their size after their introduction, however their locomotor performance did not significantly differ from the performance of the individuals sampled in Alyko, 2016. We found that the average turning speed increased during the first two years of colonization, however two years later, it decreased. Islet lizards became better in avoiding collisions with the walls of the racetrack with time, and used more controlled manoeuvring strategies. We hypothesize that the complexity of the structural habitat on the experimental islets selects for improved manoeuvring capacities, and the lack of predation pressure selects for the use of slower manoeuvring in 2018.

Joy Eliaerts​

• 3 juni 2020
  
• Promotoren: Karolien De Wael, Koen Janssens en Natalie Meert
• Departement Chemie

Abstract

Wereldwijd is cocaïne één van de meest inbeslaggenomen en gebruikte drugs. De huidige screening van cocaïne in inbeslaggenomen poeders wordt uitgevoerd met kleurtesten. De voornaamste nadelen van deze testen zijn een gebrek aan specificiteit en een subjectieve kleureninterpretatie (’50 shades of blue’). De hoge prevalentie van cocaïne en de beperkingen van de kleurtesten hebben ertoe geleid dat er een algemene interesse is in het ontwikkelen van een snelle methode voor identificatie en kwantificatie van cocaïne.

In dit doctoraat werd een nieuwe strategie ontwikkeld met behulp van Midden-InfraRood [MIR] spectroscopie en Support Vector Machines [SVM]. De SVM modellen resulteerden in een duidelijke output (cocaïne gedetecteerd/niet gedetecteerd) en in een betrouwbare schatting van de zuiverheid van cocaïne in verschillende soorten straatstalen. De MIR techniek gecombineerd met SVM is een eenvoudige, gebruiksvriendelijke en snelle methode voor het identificeren en kwantificeren van cocaïne.

De ontwikkelde chemometrische modellen werden in de praktijk toegepast op grote inbeslagnames van cocaïne. Er werd een strategie ontwikkeld om informatie te bekomen over de homogeniteit van loten, de aanwezigheid en de concentratie van cocaïne en zijn meest voorkomend versnijdingsmiddel, levamisol. Deze werkwijze had tot gevolg dat zowel het aantal staalnames als het aantal bevestigende analyses konden worden verminderd.

Verder werd nagegaan of de ontwikkelde modellen konden worden gebruikt bij een ander MIR instrument van hetzelfde merk. Voor het uitvoeren van deze kalibratietransfer werden verschillende mogelijkheden vergeleken. Een gemengd model, opgebouwd met data van beide instrumenten, was het meest succesvol en kon worden gebruikt op beide instrumenten voor het detecteren van cocaïne.

Om na te gaan of andere spectroscopische technieken zoals Raman en Nabij-InfraRood [NIR], naast de MIR techniek, kunnen worden aangewend voor het classificeren en kwantificeren van cocaïne, werd een vergelijkende studie uitgevoerd. In het algemeen presteerden deze technieken gelijkaardig en kunnen ze als goede alternatieven voor de MIR techniek worden beschouwd.

Ten slotte werden de huidige screeningstechnieken (kleurtesten en MIR spectroscopie) geëvalueerd voor de detectie van cocaïne in complexe smokkelstalen. Het detecteren van cocaïne was enkel mogelijk na het uitvoeren van een extractie vóór screeningsanalyse.

Als besluit kan gesteld worden dat de combinatie van spectroscopische technieken met chemometrische methoden een belangrijke meerwaarde biedt voor de initiële screening van cocaïne. Bovendien is een schatting van de zuiverheid mogelijk zonder het toepassen van ‘wet chemistry’. De vergaarde kennis in het kader van dit werk kan ook worden toegepast voor de detectie van andere veelvoorkomende drugs zoals heroïne en amfetamines.

Senne Van Loon​

• 29 mei 2020
• Promotoren: Jacques Tempere en Hadrien Kurkjian
• Departement Fysica

Abstract

Parisa Nematollahi

• 27 mei 2020
• Promotor: Erik Neyts 
  
• Departement Chemie

Abstract

Since the industrial revolution, the global air and sea temperature has increased significantly because of the rise in the concentration of greenhouse gases. Therefore, extensive research is carried out to both minimize the carbon emission from the exhaust of automobiles, petrochemical, agricultural and chemical industries, and reduce the current high levels of greenhouse gases by converting them into carbon-neutral fuels and other value-added industrial chemicals.

Graphene-based nanocatalysts are of great interest to the catalysis community due to their outstanding catalytic activity, surface properties, environmental friendliness, and cost-effectiveness. Surface modification of graphene-based materials is of great interest since it enhances the catalytic activity, electronic property, mechanical strength, and thermal conductivity of the nanocatalyst. The most commonly used surface modification methods are introducing defects, and doping with single metal atoms.

Two promising nanocatalysts are graphene and BC2N nano-flakes. The surface modification includes introducing defects or doping with single metal atoms. Depending on the type of nanocatalyst, the type of defects may change. The exact characteristics of the modified surfaces, the detailed reaction mechanisms, and the potential energy surface of direct conversion of methane to methanol, along with CO and NO oxidation to CO2 and NO2 on these surfaces at ambient conditions are unclear. Therefore, finding the corresponding reactions, detailed mechanisms, and characteristics of the tailored nano-surfaces was the main goal of this Ph.D. All the simulations were carried out using density functional theory (DFT) calculations. Our results reveal that the modified graphene and BC2N nanoflakes hold great promise toward gas conversion. Using these tuned nanostructures is energetically and thermodynamically interesting since they reduce the oxidation steps and their energy barriers, the formation of sub-chemicals, the possibility of surface poisoning with unwanted species, and make the reactions occur at ambient conditions. Our results may serve as guidance for fabricating a cost-effective graphene-based single-atom catalyst.

Wout Van Alphen​

• 25 mei 2020
• Promotor: ​Jacques Tempere 
  
• Departement Fysica

Abstract

Ultracold quantum gases consist of a collection of magnetically or optically trapped atoms cooled down to nanokelvin temperatures. At these ultralow temperatures, the laws of quantum mechanics, which are usually confined to the microscopic world of atoms and particles, now become apparent on the macroscopic scale of the entire cloud. This leads to remarkable behavior, such as the occurrence of flow without friction or “superfluidity”. In addition, these ultracold atomic gases possess a very high experimental tunability, thus making them the ideal systems for the study of quantum phenomena.

Non-linear excitations like dark solitons and quantized vortices play an important role in the dynamics of superfluid systems. A dark soliton is a solitary dip in the density of the fluid which does not change shape while propagating at a constant velocity, while a quantized vortex is the quantum equivalent of a whirlpool in classical hydrodynamics. Although several aspects of these solitary excitations have already been thoroughly examined in bosonic superfluids, much remains to be learned about their properties and dynamics in fermionic superfluids, which possess a more complex but also much richer physics than their bosonic counterparts. The aim of this thesis is to provide a detailed theoretical analysis of solitary excitations in fermionic quantum gases, through the use of a finite-temperature, low-energy effective field theory that was developed specifically for these systems. Our studies on the dynamics, stability and interactions of solitons and vortices throughout the various unique regimes of the superfluid Fermi gas demonstrate the emergence of new and interesting features that are clearly different from the established behavior of solitary excitations in bosonic quantum gases.

Marwa Kavelaars​

• 15 mei 2020
• Promotoren: Wendt Müller en Luc Lens
• Departement Biologie

Abstract

Ik heb onderzocht hoe ouderparen de zorg voor hun nageslacht samen coördineerden en hoe zij de taken onderling verdeelden om te achterhalen wat de optimale ouderlijke strategie is. Hiertoe heb ik eerst onderzocht hoe partners een veelvoorkomende ouderlijke taak verdeelden tijdens de initiële fase van de voortplanting, namelijk het incuberen van eieren, en onderzocht of ouderlijke samenwerking werd gefaciliteerd door communicatie op het moment dat de partners elkaar aflossen op het nest. Vervolgens bestudeerde ik hoe de ouderparen samenwerkten tijdens het grootbrengen van de kuikens en of individuen dan hun investering in de nakomelingen aanpasten aan die van de partner. In tegenstelling tot de incubatiefase hebben beide ouders dan al substantiële investeringen gedaan in het nageslacht en is er een vertrouwensband opgebouwd. Gedurende beide fases van dit onderzoek investeerden partners gelijkwaardig in hun nageslacht, wat suggereert dat ze hun mate van investering actief aan elkaar aanpassen. Ouders wachtten telkens op de terugkeer van hun partner voordat ze het nest verlieten om te foerageren, hetgeen wijst naar een coördinatie van het foerageergedrag. Hoewel ouders tijdens het afwisselen mogelijk informatie vergaren over de ouderlijke investering van de partner, was er geen blijk van dat zij deze informatie gebruikten om hun eigen investering aan te passen. Een mogelijke verklaring hiervoor is dat een onderhandeling over de ouderlijke investering reeds heeft plaatsgevonden tijdens de communicatiemomenten in de incubatiefase.

In aanvulling hierop heb ik bestudeerd hoe veranderingen in het landschap van invloed kan zijn op het aanleveren van voedsel aan het nageslacht. De Kleine Mantelmeeuwen in deze studie broeden en foerageren in een antropogeen landschap en worden derhalve continu onderworpen aan een veranderende omgeving. Na de destructie van hun broedomgeving paste een gedeelte van de meeuwen zich aan door te verplaatsen naar een nabijgelegen kolonie. Ze bleven echter voornamelijk foerageren op plekken waar zij eerder waren geweest, ook al waren deze plekken ver weg en had deze standvastigheid negatieve gevolgen voor hun nageslacht. Aangezien het landschap door toedoen van de mens in rap tempo blijft veranderen, zou meer flexibel, opportunistisch foerageergedrag steeds belangrijker kunnen worden voor een succesvolle voortplanting.

Len Feremans

• 14 mei 2020
• Promotor: Bart Goethals
• Departement Informatica

Abstract

Roberta Sgammato​

• 8 mei 2020
• Promotoren: Wouter Herrebout en Christian Johannessen
• Departement Chemie

Abstract

Globins are haem containing proteins ubiquitously expressed in all kingdoms of life, from bacteria to vertebrates. Thanks to the haem iron, globins can reversibly bind small ligands and can be involved in redox reactions. Nowadays more than 400 globins have been identified and classified into three main lineages and two structural families. Many of the recently discovered globins exhibit quite unusual structural architecture and a still unexplored mechanism of action. Revealing details about their structure-function paradigm can have an important biomedical relevance: a simple interaction between the globin haem iron with an exogenous ligand can eventually change the habits of the host organism and influence its adaptability to the environment, or in some cases its virulence. Moreover, some newly characterised globins are thought to have a neuroprotective function, hence a detailed knowledge of their mechanism of action could be beneficial for pharmacological purposes.

In the present work, we propose a spectroscopic approach to the study of haem-containing proteins, based on a combination of chiroptical techniques. In particular, we base our investigation on the use of resonance Raman optical activity (rROA) and electronic circular dichroism (ECD). While these techniques are routinely employed for the determination of the absolute configuration of natural compounds, their application to the study of the haem chromophore in globins, has been so far very poorly explored. The present thesis represents therefore a first, preliminary approach to relatively simple globins (or globin domains solely), using a non-classical spectroscopic approach. We have highlighted the capability of this methodology to detect conformational modifications of the achiral haem chromophore when placed in a protein matrix, and its fine sensitivity to small perturbations of the haem planarity induced by ligand binding. The early results show the potential of the chiroptical approach, and set the bases for a future investigation of more complex chimeric globins, via rROA and ECD.

Melissa Van Landeghem​

• 7 mei 2020
• Promotoren: Etienne Goovaerts en Sabine Van Doorslaer
• Departement Fysica

Abstract

Jeroen Van Dijck

• 4 mei 2020
• Promotoren: Vera Meynen en Anita Buekenhoudt
• Departement Chemie

Abstract

Stijn Heijkers​

• 27 april 2020
• Promotor: ​Annemie Bogaerts
• Departement Chemie

Abstract

Mariëlle Kaashoek​

• 24 april 2020
• Promotoren: Sandra Nauwelaerts, Peter Aerts en Friedl de Groote
• Departement Biologie

Abstract

Daniel van den Akker

• 25 maart 2020
• Promotor: Chris Blondia
• Departement Informatica

Abstract

Marnik Berckx​

• 20 maart 2020
• Promotoren: Dirk Lamoen en Bart Partoens
  
• Departement Fysica

Abstract

Joy Eliaerts​

• 17 maart 2020
• Promotoren: Karolien De Wael, Koen Janssens en Natalie Meert

Abstract

Wereldwijd is cocaïne één van de meest inbeslaggenomen en gebruikte drugs. De huidige screening van cocaïne in inbeslaggenomen poeders wordt uitgevoerd met kleurtesten. De voornaamste nadelen van deze testen zijn een gebrek aan specificiteit en een subjectieve kleureninterpretatie (’50 shades of blue’). De hoge prevalentie van cocaïne en de beperkingen van de kleurtesten hebben ertoe geleid dat er een algemene interesse is in het ontwikkelen van een snelle methode voor identificatie en kwantificatie van cocaïne.

In dit doctoraat werd een nieuwe strategie ontwikkeld met behulp van Midden-InfraRood [MIR] spectroscopie en Support Vector Machines [SVM]. De SVM modellen resulteerden in een duidelijke output (cocaïne gedetecteerd/niet gedetecteerd) en in een betrouwbare schatting van de zuiverheid van cocaïne in verschillende soorten straatstalen. De MIR techniek gecombineerd met SVM is een eenvoudige, gebruiksvriendelijke en snelle methode voor het identificeren en kwantificeren van cocaïne.

De ontwikkelde chemometrische modellen werden in de praktijk toegepast op grote inbeslagnames van cocaïne. Er werd een strategie ontwikkeld om informatie te bekomen over de homogeniteit van loten, de aanwezigheid en de concentratie van cocaïne en zijn meest voorkomend versnijdingsmiddel, levamisol. Deze werkwijze had tot gevolg dat zowel het aantal staalnames als het aantal bevestigende analyses konden worden verminderd.

Verder werd nagegaan of de ontwikkelde modellen konden worden gebruikt bij een ander MIR instrument van hetzelfde merk. Voor het uitvoeren van deze kalibratietransfer werden verschillende mogelijkheden vergeleken. Een gemengd model, opgebouwd met data van beide instrumenten, was het meest succesvol en kon worden gebruikt op beide instrumenten voor het detecteren van cocaïne.

Om na te gaan of andere spectroscopische technieken zoals Raman en Nabij-InfraRood [NIR], naast de MIR techniek, kunnen worden aangewend voor het classificeren en kwantificeren van cocaïne, werd een vergelijkende studie uitgevoerd. In het algemeen presteerden deze technieken gelijkaardig en kunnen ze als goede alternatieven voor de MIR techniek worden beschouwd.

Ten slotte werden de huidige screeningstechnieken (kleurtesten en MIR spectroscopie) geëvalueerd voor de detectie van cocaïne in complexe smokkelstalen. Het detecteren van cocaïne was enkel mogelijk na het uitvoeren van een extractie vóór screeningsanalyse.

Als besluit kan gesteld worden dat de combinatie van spectroscopische technieken met chemometrische methoden een belangrijke meerwaarde biedt voor de initiële screening van cocaïne. Bovendien is een schatting van de zuiverheid mogelijk zonder het toepassen van ‘wet chemistry’. De vergaarde kennis in het kader van dit werk kan ook worden toegepast voor de detectie van andere veelvoorkomende drugs zoals heroïne en amfetamines.

Frederik Van de Perre

• 9 maart 2020
• Promotoren: Herwig Leirs, Erik Verheyen en Steven Dessein
• Departement Biologie

Abstract

Menselijke handelingen hebben een fundamentele invloed op de diversiteit van het leven op aarde, en de meeste van deze veranderingen leiden tot het verlies van biodiversiteit. Aangezien de biodiversiteit bepalend is voor het functioneren van ecosystemen, zal het verlies aan soorten of de vermindering van de omvang van populaties een negatieve invloed hebben op de diensten die het ecosysteem aan de mensheid levert. Daarom vormen beheerstrategieën die tegelijkertijd de ecosysteemdiensten en het behoud van de biodiversiteit maximaliseren, de beste manier om een efficiënt gebruik van de beperkte hulpbronnen en de beschikbare grond te garanderen. Het regenwoud van het Congobekken is het op één na grootste regenwoud en een van de gebieden met de grootste biodiversiteit op aarde. Toch is over de verspreiding van de biodiversiteit binnen het laaglandregenwoud weinig bekend. We stellen vast dat de klimaatschommelingen van het Plio-Pleistoceen het aantal gewervelde soorten in de ecoregio's hebben bepaald, terwijl de klimaatveranderingen in het Holoceen hun stempel hebben gedrukt op de samenstelling van de spitsmuisgemeenschappen. Dit wil zeggen dat historische, grootschalige verstoringen op lange termijn gevolgen hebben voor de samenstelling van de lokale soortengemeenschappen.

Hoewel het verband tussen de diversiteit van de bomen en koolstofvoorraden in bossen over het algemeen positief is, blijft dit verband onduidelijk voor andere plant- en diergroepen. We hebben deze relatie beoordeeld voor meerdere trofische niveaus in de laaglandregenwouden van het Congobekken. Vergelijkingen tussen secundaire en primaire bossen toonden zoals verwacht een positief verband voor bomen, maar dit was niet het geval voor de meeste andere organismen. Bovendien toonden onze resultaten aan dat de verschillen in soortensamenstelling tussen bossen toenemen met het verschil in bovengrondse koolstofvoorraden. Het feit dat deze verbanden verschillen tussen soortengroepen is in tegenspraak met de veronderstelling dat het behoud van bossen met de hoogste koolstofopslag ook de biodiversiteit optimaal beschermt.

De huidige bosfauna van het Congobekken is veerkrachtig genoeg gebleken om zich te herstellen van de klimaatveranderingen in het verleden die de omvang en de kenmerken van deze laaglandbossen dramatisch hebben beïnvloed. De belangrijkste bedreigingen voor het Centraal-Afrikaanse bos zijn echter de snel voortschrijdende ontbossing door de mens, de klimaatverandering en de jacht op wilde dieren. Aangezien het herstel van de diversiteit van verstoorde gebieden (zowel recentelijk als in het verleden) afhankelijk is van de instroom van gespecialiseerde bossoorten uit ongestoorde gebieden, moet de bescherming van oerbossen en bosrefugia onze hoogste prioriteit zijn.

Constance Fastré​

• 9 maart 2020
• Promotoren: Erik Matthysen en Diederik Strubbe
• Departement Biologie

Abstract

Effective management of protected areas is necessary to ensure they deliver socio-economic benefits to local communities while conserving the biodiversity they contain.
In this thesis, we use targeted monitoring and remote sensing data combined with modeling tools to generate scientifically-based management recommendations designed to ensure the conservation of biodiversity and the delivery of ecosystem services in the Tunari National Park (TNP) in Bolivia. More specifically, we aimed to (1) investigate which characteristics of the remaining Polylepis fragments of the Southern Slope of the TNP are associated with bird species richness and the presence of species of conservation concern, (2) study habitat selection patterns for the most common forest-dependent bird species occurring in a mosaic landscape made of Polylepis fragments, agricultural fields and exotic plantations on the Southern Slope of the TNP, (3) identify, using species distribution models, the areas of highest priority for the conservation of the avifauna occurring in Polylepis forests of the Southern Slope and especially for conservation concern species and (4) use the conservation planning software Marxan with Zones to generate optimal land use plans that maximize the conservation of several bird species, including species of conservation concern, while minimizing opportunity cost for the local communities on the Southern Slope of the TNP. We then use these plans to explore the potential trade-offs between biodiversity conservation and the delivery of water-related ecosystem services, a limited resource in the area and important source of conflicts. Finally, we formulate scientifically-based management recommendations for the conservation of the avifauna of the Polylepis remnants in the TNP and especially on the Southern Slope.

We confirm the importance of the Polylepis patches of the Tunari National Park and especially of its Southern Slope to support rare and/or threatened Andean species. We conclude that, while it is crucial to protect the biodiversity-rich Polylepis patches, managing the entire landscape in which these patches occur is necessary to meet conflicting conservation and socio-economic demands for the Southern Slope of the TNP. Therefore, conservation management should focus on (1) conserving and/or restoring existing Polylepis fragments, (2) establishing a reforestation scheme and (3) promoting agroforestry and silvopastoralism. We make spatially-explicit recommendations of where to prioritize conservation, restoration and reforestation and promote agroforestry and pastoralism to best support biodiversity, ecosystem services delivery and local livelihoods in a tropical protected area.

Ali Pilehvar​

• 28 februari 2020
• Promotoren: Ronny Blust en Raewyn Town
• Departement Biologie

Abstract

Zoetwaterecosystemen worden bedreigd door de effecten van multiple stressoren. Conventionele aquatische toxicologische studies op metaalionen stellen echter enkel organismen bloot aan individuele stoffen onder constante en optimale experimentele condities. Bijgevolg was het doel van het eerste deel van dit doctoraatsproefschrift om na te gaan wat het effect is van de interactie tussen metaalion toxiciteit en omgevingsstressoren (temperatuurstress en ionsterkte van het medium) bij zebravissen (Danio rerio), een veelgebruikt modelorganisme voor vertebraten. Hiervoor werden volwassen zebravissen blootgesteld aan koper (Cu(II)) en cadmium (Cd(II)) in individuele en binaire blootstellingen bij verschillende waterhardheden en temperaturen. De bevindingen benadrukken het belang van het in rekening brengen van het effect van omgevingsfactoren bij het ontwerpen van standaard toxiciteitstesten gebruikt om milieunormen af te leiden die zowel geschikt als beschermend zijn voor milieu-realistische scenario’s. Verder bleken zebravissen ongeacht de omgevingsfactoren gevoeliger te zijn voor Cu(II) dan voor Cd(II) bij individuele metaalion blootstelling. Bovendien onthulden mengsel bootstellingen een robuust synergetisch toxisch effect van Cu(II) en Cd(II) op vlak van mortaliteit bij zebravissen. Ten slotte hebben we een significante daling waargenomen van het Na+ niveau voor het gehele organisme bij dode vissen in vergelijking met nog levende. Zulk effect werd echter niet gevonden voor de andere fysiologisch belangrijke kationen (K+, Mg2+, Ca2+). Overeenkomstig met deze bevinding werd het vermogen om de Na+ homeostase te handhaven geïdentificeerd als een cruciale factor om te overleven bij omstandigheden onder multiple stressoren.

In het tweede deel van dit proefschrift hebben we enkele van de belangrijkstee gedragskenmerken van zebravissen en het effect van Cu(II) blootstelling hierop onderzocht, door gebruik te maken van twee gedragstesten: de “novel tank diving test” en het “T-maze assay”. Vervolgens hebben we ook het effect van Cu(II)-blootstelling op de chemische communicatiepatronen beoordeeld, in het bijzonder de alarmstof respons bij zebravissen. De bevindingen uit onze gedragsbenadering suggereren dat ook gedragstesten voor toxiciteitsbepalingen, mits goed ontworpen, gebruikt kunnen worden in combinatie met de klassieke toxicologische eindpunten (e.g. mortaliteit, cellulaire en biochemische veranderingen en groeisnelheid) om de bewijskracht te vergroten. Algeheel biedt dit proefschrift meer inzicht in het effect van metaalion toxiciteit op het gedrag van zebravissen in de context van multi-stressorscenario's.

Esteban Municio Hernández​

• 25 februari 2020
• Promotoren: Steven Latré en Johann Márquez Barja
• Departement Informatica

Abstract

Nicolas De Neuter

• 21 februari 2020
• Promotoren: Kris Laukens en Arvid Suls

Abstract

Saeid Pourbabak​

• 10 februari 2020
• Promotoren: Nick Schryvers en Bert Verlinden
  
• Departement Fysica

Abstract

The main properties of Ni–Ti alloys, i.e., shape memory and superelasticity, are used in engineering applications usually through a cyclic shape recovery during thermal or strain cycling, respectively. As these properties originate from the martensitic transformation, the functional stability of the material depends on the reversibility of this martensitic transformation. Therefore, the reversibility of martensitic transformation for Ni–Ti material under thermal cycling was investigated for bulk and micro–wire Ni–Ti.

In the first part of this work the effect of low temperature thermal cycling combined with room and elevated temperature aging on the martensitic transformation of some bulk and micro–wire Ni–Ti samples was studied. The cluster model was used to interpret strong structured diffuse intensities condensed in specific periodic loci in selected area electron diffraction patterns which revealed the formation of micro–domains in the shape of needle clusters of pure Ni atoms. Quantitative comparison between samples with and without a differential scanning calorimetry cycle revealed that the more DSC cycles a sample has received, the more condensed the diffuse intensity becomes which is expected to be caused by longer Ni clusters and enhancement of short–range ordering. A novel method to use a conventional twin–jet electropolishing apparatus for thin wires was also introduced.

In the second part of this work in–situ transmission electron microscopy tensile tests on nano–scale single crystals and polycrystalline Ni–Ti specimens was performed. The formation of stress–induced martensite was observed and stress–strain curves were plotted based on the obtained mechanical data. The stress plateau height shows an increase by decreasing specimen thickness but remains independent of the grain size since the latter is, on average, larger than the specimen thickness. Martensitic transformation starts at edges of the specimen for the single crystal and on the edges and grain boundaries for the polycrystalline specimen. When a martensite plate approaches a grain boundary in the polycrystalline specimen, it provokes the transformation in the neighboring grain at the other side of the grain boundary. After releasing the load, depending on the totally induced strain, some residual martensite remains in the specimen indicating the existence of induced plasticity in the martensite at large strains.

Vera Andrejchenko​

• 4 februari 2020
• Promotor: Paul Scheunders
• Departement Fysica

Abstract

Hyperspectral images (HSI) contain rich spectral information, by capturing a wide range of the electromagnetic radiation. Even though this is advantageous and provides the potential of a very detailed characterization of materials, it comes with a number of challenges. Information in HSI is highly redundant due to the high number of spectral bands involved. Another source of redundancy is the large spectral variability between spectral reflectances of the same material. Spatial redundancy is introduced by mixed pixels, containing more than one materials and high correlations between neighboring spectra.

The general research objective in this work is to address these redundancies of the HSI, by employing spectral unmixing techniques. These methods have the capability of describing highly redundant spectra as (linear or nonlinear) mixtures of a very limited amount of pure materials. In this way, they capture the structure of the low-dimensional subspace in which this high redundant data lives.

In this work, we mainly address the redundancy in HSI by developing model-based techniques which employ prior information on the parameters, derived from the data. HSI are high-dimensional but intrinsically lie on a lower-dimensional subspace which will be unraveled by exploiting the proposed priors. Moreover, these low-dimensional representations are employed in a decision fusion framework to improve the classification performance of HSI.

The thesis is organized in such a way that there are three clear subdivisions. The first contains the developed spectral unmixing method with the local low rank and inter-group sparsity prior imposed on its abundance parameters simultaneously. The second embraces the model based method which considers nonlinearities, i.e., multiple reflections and the shadowing at the same time in addition to the estimation of the abundance parameters. And the last consists of two decision fusion frameworks that incorporate the sparse low dimensional feature sets to enhance the HSI classification when limited training data is available. These are naturally preceded by an a) introduction to the hyperspectral imaging area and its active research areas and b) prerequisite key elements required for the forthcoming chapters.

Ana Castanheiro​

• 21 januari 2020
• Promotoren: Roeland Samson en Karolien De Wael
• Departement Bio-ingenieurswetenschappen

Abstract

Particulate matter (PM), the collection of fine respirable particles suspended in the air, is the greatest health-threatening pollutant. To properly monitor the high spatial variability of PM is not possible at the moment, particularly within dynamic, mixed-source urban environments, as conventional air quality monitoring networks have limited spatial resolution and often lack information on PM composition. To use urban vegetation as a bio-indicator for atmospheric PM (biomonitoring), as it provides a natural surface for deposition of particulates, may help filling out those gaps. Iron and other metals are of particular interest within PM. Therefore, biomagnetic monitoring of leaves has been extensively used as a rapid and cost-effective tool to assess urban PM exposure.

Leaves exposed to atmospheric conditions leads to the invariable accumulation of magnetic particles, which are ubiquitously present in PM but allow distinguishing between low and high pollution levels. Throughout this PhD research, the applicability of biomagnetic monitoring as a fingerprinting tool for atmospheric PM was investigated across different environments and source types, using a combination of analytical techniques. Overall this consisted in 1) characterizing major urban source types of PM by means of magnetic, chemical and microscopic techniques, to obtain source-specific magnetic and physicochemical PM fingerprints, 2) investigating potential associations source-specific magnetic and physicochemical PM fingerprints, and 3) evaluating leaf biomagnetic monitoring as a strategy to infer atmospheric PM levels and characteristics of major PM contributing sources.
Leaf-deposited PM from environments mainly exposed to different pollution sources were first investigated microscopically for their morphological characteristics and elemental composition. In a second stage, dedicated particle-analysis was combined with leaf magnetic investigation to discriminate between different source types (small scale) and between urban streets and parks across 20 European cities (large scale). To gain more insight on the leaf accumulation of PM, a multi-approach leaf monitoring campaign was also conducted using plant species with distinct macro- and micro-morphology.

The information gathered on the analytical techniques used and their potential for source characterization were finally applied in a large PM fingerprinting (PMF) project. The PMF project comprised the monitoring and fingerprinting of five different source locations (road, railway and shipping traffic, industry and a background site) based on air-pumped samples (conventional monitoring) and exposed plant leaves, to obtain source-specific signatures and evaluate the applicability of leaf magnetic monitoring of PM. The health-risk potential of the studied source types was also explored in terms of human lung pro-inflammatory response.

Carolien Callaert​

• 20 januari 2020
• Promotoren: Joke Hadermann en Dirk Lamoen
• Departement Fysica

Abstract

Fabio Bottari​

• 20 januari 2020
• Promotoren: Karolien De Wael en Ronny Blust
• Departement Chemie

Abstract

In the broad context of food and environmental safety, the development of selective and sensitive analytical tools for the detection of β-lactam antibiotics in milk down to their Maximum Residues Limits (MRL), is still an open challenge. To address this need, the design of new bio(mimetic) electrochemical sensors was investigated in the present thesis. These sensors are based on the intrinsic electrochemistry of β-lactam antibiotics, taking advantages of the characteristic electrochemical fingerprints of the core structures and redox active side chain groups. Once verified the applicability of a direct electrochemical detection, different sensor configurations were tested mainly focusing on:

- the selection and validation of aptamers to be used as bioreceptors in the development of β-lactam biosensors;
- the design of biomimetic receptors, particularly molecularly imprinted polymers, and other synthetic electrode modifiers compatible with a direct detection strategy.

Lastly, the research activity was directed towards milk sample analysis following two parallel routes: the development of a pre-treatment protocol for raw milk, based on solvent addition and the study of β-lactam antibiotics electrochemistry in undiluted raw milk.

Jeroen Van Dyck

• 16 januari 2020
• Promotoren: Frank Sobott en Dirk Snyders
• Departement Chemie

Abstract

Native mass spectrometry has shown over the past years to be a very useful tool in the investigation of membrane proteins and pores, which provides additional information next to the conventional structural techniques. This information concerns for example the stoichiometry of complexes and structural information. In recent years native mass spectrometry has shown to be very useful for the investigation of large noncovalent, mainly globular structures. In this thesis different projects are presented and discussed showing the versatility of native mass spectrometry; including membrane associated proteins and nanopores build from custom designed DNA strands. To investigate each of the different projects ion mobility and mass spectrometric techniques were used. This also includes the methods of sample preparation required to transfer the samples into the gas phase without disturbing the complexes formed significantly.

The BAX protein revealed to behave differently, when different detergents were present in solution above the critical micelle concentration or when binding the directly activating molecule BAM-7. Ion mobility and mass spectrometry show that it forms oligomers and conformational changes.

Native mass spectrometry turned out to be very useful in the investigation of lipid interactions with membrane proteins. This was shown by MgtA membrane protein revealing a very specific binding of lipids. Native MS has shown to be very useful for observing of specifically bound lipids even when high concentrations of other lipid were present.

DNA origami is a term used for artificial designed nano-structures from DNA building blocks. Within this thesis the formation of such a DNA nano-structure was investigated concerning the formation of a DNA nanopore. This pore is formed from different DNA strands which should only fit together in one possible manner. Using ion mobility mass spectrometry it was shown that the salt concentration, in the form of ammonium acetate, has a profound influence on the actual form of the hexameric pore.

Felipe Sempértegui Maldonado Pires

• 14 januari 2020
• Promotoren: Joris Dirckx en Steve Vanlanduit
• Departement Fysica
  

Abstract

The middle ear system functions as an acoustic impedance transformer, from which energy is transmitted from the air medium to the fluid present in the inner ear. The first transmission of mechanical energy is located between the eardrum and the first of the ossicles. Moreover, it was assumed that most of the energy is efficiently transmitted from the eardrum’s tissues to their attachment to the malleus. No more specific information could be found in literature and it was the aim of this Ph.D. research to quantify the energy flow on human eardrums.

The starting point of this work was based on a well-known technique called the energy flow analysis and it is based on a combination of measured deformations and the stiffness of a sample. These studies were mainly focused on analyzing plate-like structures in the past, which are by no means comparable to the complex morphology of eardrums. Furthermore, the stiffness of individual eardrums may also vary considerably. Therefore, the Ph.D. candidate had 2 challenges to face: expand the current energy flow analysis suited for simple geometries, in order to estimate results from complex ones & develop a method, from which stiffnesses could be identified via measurements of individual eardrums.

The first issue was addressed by developing a method that discretizes the continuous & irregular surface of the eardrum to a collection of individual elements. This choice has shown itself to be efficient and it could provide precise energy transmission data via measurements of an irregular sample’s deformation. Later, the second challenge was overcome by refining the so-called the Virtual Fields Method. The adapted algorithm was validated with synthetic data and the errors of the retrieved stiffnesses were below 3%. Since the stiffness and the energy flow assessments were completed for irregular geometries, it was decided to use the algorithms for the case of an eardrum. Thankfully, after recording some experimental data of the refereed membrane, reasonable stiffness values were estimated and were within the range of what researchers published in the past. By combining the stiffness with the displacement fields of a single eardrum, the energy flow could be finally visualized and the results were in accordance with our expectations. Due to this achievement, not just the main aim of this research was completed, but 2 well-established engineering techniques were refined, so they could be applied on more complex geometries.

Charlotte Vets 

• 10 januari 2020
• Promotor: Erik Neyts
  

Abstract