Title Promoter Affiliations Abstract "Joint focused ion beam (FIB) facility for nanofabrication and nanocharacterization" "André Vantomme" "Manufacturing Processes and Systems (MaPS), Quantum Solid State Physics (QSP), Universiteit Hasselt" "The dual beam FIB (focused ion beam) system allows the controlled restructuring, removal or deposition of material with a lateral resolution of just a few nanometer. By bombarding a sample with a low-energy, focused ion beam, one can create nanostructure with a specific size and shape, modify their structure, or electrically isolate them from their vicinity. Hence, the properties can be tuned at nanometer scale. Moreover, this process allows to select and prepare a specific nanostructure for further structural, chemical or functional analysis with microscopy, tomography or other techniques. Obviously, excellent control of this process requires continuously monitoring the sample throughout the ion bombardment. This imaging is done by detecting how a focused electron beam interacts with the sample, revealing the exact position of the ion beam, the evolution of the sample shape and composition, etc. The combination of controlled growth and modification with atomic scale characterization of single nanostructures will allow this consortium to disentangling the mechanisms that govern the altered properties when reducing sizes to the nm, which is the backbone of nanotechnology." "CLARIAH-VL: Open Humanities Service Infrastructure." "Dirk Van Hulle" "Power in History - Centre for Political History, Centre for Urban History, Katholieke Universiteit Leuven, Institute for Dutch Language, Flemish Institute for Archives, Ghent University, Vrije Universiteit Brussel, Antwerp Centre for Digital humanities and literary Criticism (ACDC)" "CLARIAH-VL: Open Humanities Service Infrastructure is the Flemish contribution to the European DARIAH and CLARIN infrastructures. It brings together and extends the portfolio of services enabling digital scholarship in the Arts and Humanities offered by the DARIAH-VL Virtual Research Environment Service Infrastructure (VRE-SI; Hercules & FWO 2015-2018) with the digital tools and language data that are offered through CLARIN-DLU/Flanders. The consortium which includes the network of Digital Humanities Research Centres at the universities of Antwerp, Brussels, Ghent and Leuven has been extended with the Dutch Language Institute (INT) – the CLARIN-ERIC certified B-Centre for Flanders. CLARIAH-VL will implement a modular research infrastructure embedding high-quality, user-friendly tools and resources into the workflows of humanities researchers in the five focus areas of linguistics; literature; socio-economic history; media studies; ancient history and archaeology. CLARIAH-VL aims to provide sustainable services, while fostering experimental development and innovation. Offering an open infrastructure which facilitates public humanities is a guiding principle for CLARIAH-VL. It will ensure the accessibility and relevance of the humanities to the general public, specific (heritage) community groups and policy makers. It will make it technically possible to share knowledge, including sharing and co-creating knowledge with non-specialist users, such as facilitating citizen science and crowdsourcing projects. Furthermore, by implementing international best practices in FAIR (Findability, Accessibility, Interoperability and Reusability) Research Data Management (RDM), CLARIAH-VL will pave the way to Flemish participation in the European Open Science Cloud." "CLARIAH: open humanities service infrastructure." "Mark Depauw" "Formal and Computational Linguistics (ComForT), Leuven, Ancient History, Leuven, Universiteit Antwerpen, Vrije Universiteit Brussel, Universiteit Gent" "Open Humanities Service Infrastructure is the Flemish contribution to the European DARIAH and CLARIN infrastructures. It brings together and extends the portfolio of services enabling digital scholarship in the Arts and Humanities offered by the DARIAH-VL Virtual Research Environment Service Infrastructure (VRE-SI; Hercules & FWO 2015-2018) with the digital tools and language data that are offered through CLARIN-DLU/Flanders.The consortium which includes the network of Digital Humanities Research Centres at the universities of Antwerp, Brussels, Ghent and Leuven has been extended with the Dutch Language Institute (INT) – the CLARIN-ERIC certified B-Centre for Flanders. CLARIAH-VL will implement a modular research infrastructure embedding high-quality, user-friendly tools and resources into the workflows of humanities researchers in the five focus areas of linguistics; literature; socio-economic history; media studies; ancient history and archaeology. CLARIAH-VL aims to provide sustainable services, while fostering experimental development and innovation. Offering an open infrastructure which facilitates public humanities is a guiding principle for CLARIAH-VL. It will ensure the accessibility and relevance of the humanities to the general public, specific (heritage) community groups and policy makers. It will make it technically possible to share knowledge, including sharing and co-creating knowledge with non-specialist users, such as facilitating citizen science and crowdsourcing projects.Furthermore, by implementing international best practices in FAIR (Findability, Accessibility, Interoperability and Reusability) Research Data Management (RDM), CLARIAH-VL will pave the way to Flemish participation in the European Open Science Cloud." "Supporting Pregnancy Care Based on Heterogeneous and Longitudinal Data Analysis" "Bart De Moor" "Nephrology and Renal Transplantation Research Group, Woman and Child, Dynamical Systems, Signal Processing and Data Analytics (STADIUS)" "With the advent of information technology in healthcare, data occupy a central place in clinical practice. This digital dependency calls for efficient tools to assist physicians in managing and processing the explosion of data resources. These tools are commonly known as clinical decision support systems (CDSS). They cover a broad range of applications from alerting physicians of drug allergy to the facilitation of administrative data encoding. In this thesis, we focused on diagnostic decision support systems (DDSS), a subtype of CDSS devoted to enhancing the diagnostic decision process with relevant information provided at the patient-level. DDSS often target a very specific medical condition. Therefore, their development largely depends on applied research centered around a predefined medical problem. In this thesis, we expose the research on DDSS initiated by three different medical challenges.The first challenge focuses on patient similarity. Physicians often solve current cases by referring to prior encountered patients. To exploit the valuable clinical databases for similar patient retrieval, proper metrics of inter-patient similarity must first be defined. In this project, we focused on tree-based ensemble algorithms, which consist of combinations of individual decision trees, to learn task-specific patient similarity metrics. While requiring little optimization, the flexibility of these algorithms makes them suitable to learn metrics for various medical outcomes (e.g. diagnosis, prognosis or scoring systems). We demonstrated that these approaches, by natively handling the presence of missing values, provide powerful task-specific patient similarity metrics for heterogeneous clinical databases.Our second use-case targets the problem of viability prediction at the end of the first trimester of pregnancy using early gestation data. Our main contributions consist in the development and the internal validation of two calibrated models to predict the first trimester outcome based on demographics, clinical, sonographic and biomarkers predictors. We also extensively assessed the added value of plasmatic biomarkers variables in the predictive models. In addition, we studied the imputation of incomplete data at prediction time using a modified version of fixed chained equation imputation. This online imputation framework allows to perform accurate model predictions on moderately incomplete queries. Finally, we leveraged a post-hoc interpretability framework, along with relevant visualization plots, to facilitate the understanding of the models’ predictions from the clinical end-users. In the third project, we focus on kidney transplant biopsies and explore another aspect of DDSS. While most of the existing DDSS are based on pre-established diagnostic classifications, we first aimed to improve the existing classification of acute kidney transplant rejection. The current categorization, based on the histological assessment of kidney transplant biopsies, produces categories that are not mutually exclusive and makes use of lesions that are not specific of the disease processes. While this complex classification accurately depicts the observed histological reality, its clinical interpretation remains difficult, leading to potential unstable clinical decisions. In this project, we derived and validated six novel phenotypes of acute rejection by semi-supervised consensus clustering, a special form of clustering where external guidance is added to enforce the creation of clinically meaningful clusters.Finally, the last part of this thesis, as a synthesis of the use cases research, outlines a generic framework for data-driven DDSS. Additional theoretical considerations with regard to DDSS are exposed. In particular, we discuss healthcare-related data and their preprocessing, the choice of appropriate clinical predictive models for DDSS and important notions around clinical model interpretability." "Systematic perturbation and adaptive evolution to build a model for improving industrially relevant complex traits" "Rob Jelier" "Microbial and Plant Genetics (CMPG)" "Loss of gene function is surprisingly common throughout evolution, even though it often leads to lower fitness. Humans for example each carry about 100 loss-of-function variants, some of which underlie severe genetic disorders. Even though it is known that loss-of-function mutations can offer a quick evolutionary advantage during adaptation, it remains unclear how losing a gene influences evolutionary parameters such as the speed of adaptation (~adaptability) or the variability in the outcome of evolution. Additionally, it remains unclear if and how crucial architectural features of an organism’s genetic network, such as modularity and connectivity, influence the adaptive process after gene loss. In this thesis, experimental evolution of budding yeast (Saccharomyces cerevisiae) was used to systematically explore the influence of genetic architecture on adaptation after gene loss and evaluate how gene loss affects evolvability. I systematically evaluated how yeast strains adapt after losing genes that are important for growth under oxidative stress, a trait involved in many disease phenotypes. By evolving, sequencing, and phenotyping over 200 yeast lineages, I found that gene loss can enhance an organism’s capacity to evolve and adapt. Although gene loss often led to an immediate decrease in fitness, many mutants rapidly acquired suppressor mutations that restored fitness. Depending on the strain’s genotype, some ultimately even attained higher fitness levels than similarly adapted wild-type cells. Further, cells with deletions in different modules of the genetic network followed distinct and predictable mutational trajectories. Finally, losing highly connected genes increased evolvability by facilitating the emergence of a more diverse array of phenotypes after adaptation. Together, these findings show that loss of specific parts of a genetic network can facilitate adaptation by opening alternative evolutionary paths." "A license to discriminate: when, how and why do diversity policies affect employment discrimination?" "Karin Proost" "Department of Work and Organisation Studies (main work address Brussels)" "The fields of behavioral ethics and moral psychology have demonstrated the contextual malleability of moral and immoral behavior of people. One particular observation is that people balance moral and immoral behavior on a moment-to-moment base, also referred to as moral balancing. When people engage in moral behavior, their moral self-image increases, which subsequently allows them to engage in immoral behavior (moral licensing). When people engage in immoral behavior, their moral self-image decreases, urging them to subsequently engage in moral behavior (moral cleansing). In this dissertation, we applied these ideas to the domain of discrimination and hiring discrimination in particular. This is particularly novel because current explanations of discrimination mainly focus on stereotypes and preferences of people, but neglect contextual aspects such as the behavioral history of people.First, we assessed moral balancing effects at the individual level. We expected that a previous choice for a candidate with an Arab name in a first selection procedure would increase the chance that a candidate with a Dutch/Belgian name will be selected in the second selection procedure (moral licensing) and vice versa (moral cleansing). Furthermore, we built on construal level theory and expected that a small spatial distance to the candidate in the second selection procedure (employing for the own team) would generally increase the likelihood that a candidate with a Dutch/Belgian name will be selected and facilitate moral licensing. A large spatial distance (employing for the other team) should lead to the opposite effect and facilitate moral cleansing. In one experimental study, we found the expected moral licensing and cleansing pattern. Moreover, a large distance increased the chances that the candidate with the Arab name was employed and vice versa. Moral cleansing and moral licensing were, however, not dependent on spatial distance.Second, we aimed at lifting the idea of moral licensing to the policy level. More specifically, we investigated whether working for an organization that highlights the successful implementation of a diversity policy can lead to hiring discrimination. We argued that this would particularly be the case when discrimination is ambiguous. That is, when the context allows justification of discriminatory hiring preferences. Moreover, we investigated whether moral self-image variations are a likely explanatory mechanism for this effect and whether the mere presence versus the perceived successfulness of diversity policies is likely to promote moral licensing effects. Results of three studies showed that successful diversity policies increased the moral self-image of employees, which in turn increased discrimination in ambiguous contexts.Third, we took an observer`s perspective on moral licensing effects. We argued that observers evaluating a woman`s gender discrimination claim against an organization would perceive this claim less valid after first reading the organization’s diversity (as opposed to mission) statement. Furthermore, we proposed that enhanced perceptions of organizational morality might explain this effect. In addition, we built on social identity theory to predict that female observers should be less influenced by exposure to particular organizational statements. More specifically, women compared to men would generally perceive the organization accused of discrimination as less moral and the discrimination claim as more valid. Two experimental studies demonstrated that reading a diversity statement subsequently decreased the perceived validity of the woman`s gender discrimination claim which was mediated by perceived morality of the organization. This effect did not depend on observer gender. Yet, female observers generally perceived the organization as less moral and perceived the claim as more valid.   " "Unraveling the cell type specific underpinnings that shape collicular mediated visual behaviors" "Karl Farrow" "Animal Physiology and Neurobiology" "Cell types are the building blocks of living organisms, and the brain has the most extensive variety of them. Yet, how (or to what extent) different neuronal cell populations contribute to bringing about behavior remains an open question. The work presented in my thesis aims to advance the understanding of the relationship between specific neuronal cell types, the behaviors they evoke, and the related brain-wide activity. In the first part, I focus on the functional connectivity supported by different neuronal cell types and the behaviors they trigger while optogenetically activated. In the second part, I assess the necessity of two different cell types for a behavioral repertoire in response to various threat-mimicking visual stimuli.As a general approach, I use the mouse superior colliculus and its involvement in visually guided behaviors as a model. The superior colliculus is a midbrain structure crucial in mediating various motor actions by directing visual attention toward or away from ethologically relevant stimuli (such as food, potential partner, or predator). The collicular-dependent behaviors are highly stereotyped and conserved across species. More importantly, there is strong evidence for a relationship between morphologically distinct and genetically targetable collicular cell types and diverse innate behaviors. These features make the superior colliculus a good model for studying cell types as structural and functional channels that support and facilitate quick and reliable sensory-motor transformations.In the first part of my thesis, I focus on answering how specific genetically-targeted cell types of the superior colliculus broadcast behaviorally relevant information across the brain and form brain-wide functional networks. To do that, in a collaborative work, we first demonstrated that optogenetic activation of four different cell populations triggers distinct behaviors. Subsequently, we combined functional ultrasound imaging (fUSI) with optogenetics to reveal the network of 264 brain regions functionally activated by these collicular cell types. Furthermore, stimulating each neuronal group activated distinct sets of brain nuclei. This included areas previously not thought to mediate defensive behaviors, for example, the posterior paralaminar nuclei of the thalamus (PPnT), which we showed to play a role in suppressing habituation. Neuronal recordings with high-density Neuropixels probes showed that (1) patterns of spiking activity and fUSI signals correlate well in space and (2) neurons in downstream nuclei preferentially respond to innately threatening visual stimuli. This work provides insight into the functional organization of the networks that govern innate behaviors (ranging from orienting through different levels of stopping to directed escape) and demonstrates an experimental approach to explore the neuronal activity of the whole brain downstream of targeted cell types.In the second part of my thesis, I focus on the role of two collicular cell types in responding to natural, ethologically relevant visual stimuli. Specifically, I investigated how changes in the saliency of different visual stimuli influence behavioral responses and how these responses are supported by the activity of different cell types in the superior colliculus. To do that, I designed various threat saliency scenarios by manipulating parameters like the size or contrast of two sets of visual stimuli resembling cruising or approaching predators. I demonstrated that (1) the strength of responses to these stimuli increased with the perceived threat intensity; (2) the stimuli previously considered ethologically neutral evoked defensive responses like stopping or hiding in a safe space and (3) these responses appear to be differentially modulated by the activity of two genetically-targetable and morphologically distinct collicular cell types: wide- and narrow-field neurons. Freely-moving behavioral experiments in combination with chemogenetic inhibition of these neuronal populations resulted in a set of impairments of how animals react to potentially dangerous visual stimuli, characterized by a significant drop in their defensive behavior repertoire. More specifically, I demonstrated that inhibition of collicular wide-field neurons significantly decreases the ability of an animal to respond to any stimuli adequately. In contrast, inhibition of narrow-filed neurons resulted in less pronounced behavioral responses to a subset of stimuli. These results highlight the importance of different cell types in the brain and suggest functional specialization in assessing threats. It remains to be discovered how the neural activity facilitated by these cell types engages local neural activity and global brain-wide dynamics to evoke appropriate behavior. Overall, this work stresses the importance of cell types as functional building blocks in the brain and provides insight into how they can facilitate information transfer across the brain to guide behavior." "THE ENVIRONMENTAL CRIMES AND HARMS BEHIND PANDEMICS A green criminological exploration of wildlife trafficking, farms and markets in Vietnam" "Letizia Paoli" "Leuven Institute of Criminology, Faculty of Law and Criminology" "After the breakout of the COVID-19 pandemic, zoonotic diseases -diseases transmitted from animals to humans- have dominated the central stage of the world debate and policy agenda. While its study has traditionally belonged to biomedical sciences, this research project aims to add a criminological view to such literature. Concretely, it aims to understand the nature and cause of harmful and/or law-breaking behaviour leading to zoonotic diseases, and the ways in which wildlife trade, trafficking and farming facilitate the emergence of these diseases. It draws on the emerging field of green criminology, which is the study of environmental crimes and harms. It explores wildlife farms, markets, and trafficking in three selected southern provinces in Vietnam through ethnographic fieldwork, focusing on the trade of high-risk species for zoonotic transmission like rodents or bats. In particular, the study relies on qualitative methods, including both semi-structured interviews and participant observations. This study is urgently needed given the likelihood that the current COVID-19 pandemic was caused by a virus that passed from bats to humans via an intermediary host in a market in Wuhan (China). Therefore, apart from adding a criminological approach to the study of zoonotic diseases, this study will also contribute to prevent future pandemics. In particular, it will do so by providing insights to underpin prevention and regulation of the human actions that facilitate the emergence of zoonotic diseases." "Advancing the Open Humanities Service Infrastructure (CLARIAH-VL)." "Walter Daelemans" "Power in History - Centre for Political History, Centre for Urban History, Katholieke Universiteit Leuven, Ghent University, Vrije Universiteit Brussel, Antwerp Centre for Digital humanities and literary Criticism (ACDC)" "CLARIAH-VL constitutes the Flemish contribution to the European DARIAH (Digital Humanities) and CLARIN (Computational Linguistics) research infrastructures (ERICs). Building on the work of these landmark ERICs, CLARIAH-VL will join the efforts of their respective Flemish consortia towards further development and valorisation of high-quality, modular, user-friendly tools, resources, and services by and for humanities researchers. The infrastructure brings together 22 research teams representing a range of disciplines from the universities of Ghent, Antwerp, Leuven and Brussels and the Dutch Language Institute. CLARIAH-VL will continue catering to the highly diverse and multilingual composition of digital humanities data inherent in European long term history, culture, environment and society. To facilitate and (semi-)automate as many aspects of the workflows of humanities researchers as possible, each service component of the infrastructure will need to take full advantage of the most recent advances in the fields of machine learning, linked data and semantic technologies especially with regard to digital text and image analysis." "CLARIAH-VL: Advancing the Open Humanities Service Infrastructure" "Mark Depauw" "Ancient History, Leuven, Formal and Computational Linguistics (ComForT), Leuven, Archaeology, Leuven, Cultural Studies Research Group" "CLARIAH-VL constitutes the Flemish contribution to the European DARIAH (Digital Humanities)and CLARIN (Computational Linguistics) research infrastructures (ERICs). Building on the work ofthese landmark ERICs, CLARIAH-VL will join the efforts of their respective Flemish consortiatowards further development and valorisation of high-quality, modular, user-friendly tools,resources, and services by and for humanities researchers. The infrastructure brings together 22research teams representing a range of disciplines from the universities of Ghent, Antwerp,Leuven and Brussels and the Dutch Language Institute. CLARIAH-VL will continue catering to thehighly diverse and multilingual composition of digital humanities data inherent in European longterm history, culture, environment and society. To facilitate and (semi-)automate as manyaspects of the workflows of humanities researchers as possible, each service component of theinfrastructure will need to take full advantage of the most recent advances in the fields ofmachine learning, linked data and semantic technologies especially with regard to digital text andimage analysis."