This thesis focuses on data found in the field of computational drug discovery. New insight can be obtained by applying machine learning in various ways and in a variety of domains. Two studies... Show moreThis thesis focuses on data found in the field of computational drug discovery. New insight can be obtained by applying machine learning in various ways and in a variety of domains. Two studies delved into the application of proteochemometrics (PCM), a machine learning technique that can be used to find relations in protein-ligand bioactivity data and then predict using a virtual screen whether compounds that had never been tested on a particular protein, or set of proteins. With this, sets of compounds were suggested for experimental validation that were significant in a myriad of ways. Another study investigated the mutational patterns in cancer, applying a large dataset of mutation data and identifying several motifs in G protein-coupled receptors. The thesis also contains the work done on the Papyrus dataset, a large scale bioactivity dataset that focuses on standardising data for computational drug discovery and providing an out-of-the-box set that can be used in a variety of settings. Show less
The sequence-dependence of biomolecular interactions involving nucleic acids and proteins is essential for numerous processes inside the cell. Insights into the underlying molecular mechanisms have... Show moreThe sequence-dependence of biomolecular interactions involving nucleic acids and proteins is essential for numerous processes inside the cell. Insights into the underlying molecular mechanisms have been obtained using various biochemical and biophysical methods on two different levels — bulk and single-molecule. These have complemented each other as single-molecule studies excel in observing multi-state dynamic interactions, but perform only at low throughput; while bulk studies can probe many different sequences simultaneously, but providing limited kinetic information. To unite the strengths of both levels, we developed high-throughput Single-molecule Parallel Analysis for Rapid eXploration of Sequence space (SPARXS), that allows the study of molecular structure, kinetics and interactions for thousands of different sequences simultaneously at the single-molecule level. We, for the first time, combine single-molecule fluorescence with next-generation Illumina sequencing. As a proof of principle we apply SPARXS to study the sequence-dependent kinetics of the four-way DNA Holliday junction, occurring among others during homologous recombination. Using SPARXS we observe the dynamic behavior of 120,000 Holliday junction molecules covering 3750 distinct core sequences, a result unattainable with previous techniques. Overall, the mechanistic insights obtained using SPARXS will give an entirely new view on the relationship between sequence, structure and function. Show less
A strong correlation exists between abdominal aortopathy and atherosclerosis. In thoracic aortopathy however, the prevalence of atherosclerosis and its role in the etiology of thoracic aortopathy... Show moreA strong correlation exists between abdominal aortopathy and atherosclerosis. In thoracic aortopathy however, the prevalence of atherosclerosis and its role in the etiology of thoracic aortopathy remained unknown. This thesis therefore studied the cardiovascular disease burden within this patient group. These results showed that the prevalence of atherosclerosis (i.e. cardiovascular disease burden), in contrast to abdominal aortopathy, is not increased within the thoracic aortopathy population. Show less
This thesis explores North Korea’s influential role in the liberation of Southern Africa. Specifically, it examines the question of how political elites in Southern Africa benefitted from North... Show moreThis thesis explores North Korea’s influential role in the liberation of Southern Africa. Specifically, it examines the question of how political elites in Southern Africa benefitted from North Korean support, from 1960 until 2020. The main argument of this book is that liberation (and not the Cold War) is the leitmotif for African–North Korean relations, as the transition from anticolonial struggles to postcolonial politics is characterised by continuity not change. This approach is based on three assumptions. First, political culture in Southern Africa transcends national boundaries, which is a legacy of the exile dimension of the struggle for liberation. Second, scholarship must shift its lens from states to regimes. Third, the standard periodisation of African history and the Cold War distorts a proper understanding of African–North Korean interactions. Show less
Human vocal communication and music perception represent advanced cognitive skills, seemingly innate and universal. These faculties encompass a range of perceptual and cognitive abilities. Cross... Show moreHuman vocal communication and music perception represent advanced cognitive skills, seemingly innate and universal. These faculties encompass a range of perceptual and cognitive abilities. Cross-species research sheds light on the origins of musicality by investigating whether these traits are shared by nonhuman species. Songbirds, notably zebra finches, serve as valuable models due to their complex vocalizations and similarities to humans in auditory perception. My thesis explored zebra finches' sensitivity to spectral and temporal sound features. Chapter 2 examines the influence of song duration and spectral characteristics on song discrimination, while Chapter 3 tests song preferences. Chapter 4 investigates sequential and spectral feature recognition. Chapter 5 focuses on melody recognition. Zebra finches demonstrate perceptual flexibility, adapting focus based on stimulus characteristics. These findings underscore the importance of training conditions and stimulus nature in shaping auditory perception. Overall, my thesis enhances understanding of auditory cognition and cognitive flexibility among songbirds. Show less
This dissertation explores the impact of international cultural heritage law on individuals and local communities, particularly through the lens of cultural heritage law's use of universalising... Show moreThis dissertation explores the impact of international cultural heritage law on individuals and local communities, particularly through the lens of cultural heritage law's use of universalising language such as the ‘cultural heritage of mankind’. It argues that this rhetoric empowers states to prioritise purportedly common interests over local ones, potentially erasing living heritage value in the process. The dissertation places cultural heritage law in the context of broader international legal trends, in particular the tension between the pursuit of common interests through international law and the enduring influence of state sovereignty as a structuring principle of that law. It argues that contemporary cultural heritage law often fails to effectively limit state powers or protect the interests of individuals and local communities. It thus calls for stronger guarantees of participation within cultural heritage law, drawing upon legal standards developed within environmental law and human rights law. The dissertation suggests a rethinking the concept of ‘universal interest’ in heritage law to qualify the operation of state sovereignty and to better accommodate the interests of individuals and local communities, emphasizing their role as central actors and the need to bridge the gap between local and global interests in cultural heritage protection. Show less
This thesis explores ancient Egyptian descriptions of sicknesses of the inner body, the concepts used to understand them, and the trends in associated therapeutic applications for healing. It... Show moreThis thesis explores ancient Egyptian descriptions of sicknesses of the inner body, the concepts used to understand them, and the trends in associated therapeutic applications for healing. It concludes that the ancient Egyptian system of understanding recorded in writings—while somewhat obscured as the surviving texts were never intended to be descriptive of ideas—can be compared to other ways of thinking and categorising sickness experiences as found in other written cultures. Especially in terms of how such ideas are constructed and how therapies are associated with such concepts. Similarities can be observed in terms of core concepts and associated therapeutic applications recorded in cuneiform compendia of comparable age from Mesopotamia. Rather than using these observations as evidence of an influence of one culture over another, it is argued that these writings include practices and ideas which can instead be considered common to this region of the world, rather than as exclusive and invariably peculiar either the Egyptian and/or Mesopotamian cultures. Show less
Triple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by limited treatment options and unfavorable clinical outcomes. Therefore, the research described in this thesis... Show moreTriple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by limited treatment options and unfavorable clinical outcomes. Therefore, the research described in this thesis focused on the exploration of novel targeted therapies for TNBC. Through high-throughput screening, we assessed the responsiveness of TNBC cells to kinase inhibitors, which indicated a notable sensitivity to cyclin-dependent kinase (CDK) inhibitors. Building upon these findings, this thesis systematically compares the efficacy of targeting various transcription-associated CDKs, with CDK9 and CDK12 emerging as highly potent targets for disrupting TNBC cell proliferation. Transcription-associated CDKs play multiple roles in regulating mRNA transcription. Yet, inhibitors of these CDK’s induced selective, rather than global, changes in gene expression. This provides insights into their mechanisms of action and suggesting potential opportunities for combination therapy. Furthermore, our research elucidated the mechanism underlying the synergistic effects of combining kinase inhibitors with transcriptional CDK inhibitors, by demonstrating that this is mediated through the inhibition of cellular drug efflux by ABCG2. In conclusion, this thesis highlights the potential of transcription-associated CDK inhibitors as a promising avenue for treating TNBC. The insights from this thesis will help to further steer the (pre)clinical development and strategy of using transcription-associated CDK inhibitors for the treatment of TNBC. Show less
Betrokken burgers vormden de ruggengraat van de Republiek. Het dagelijks leven draaide voor een groot deel op buurtorganisaties, gilden en schutterijen – en dat waren juist de stedelijke... Show moreBetrokken burgers vormden de ruggengraat van de Republiek. Het dagelijks leven draaide voor een groot deel op buurtorganisaties, gilden en schutterijen – en dat waren juist de stedelijke instituties waar zij deel van uitmaakten. In 1796 kondigden de Bataafse revolutionairen het einde van sommige van deze instellingen af en introduceerden zij het staatsburgerschap. Maar was daarmee de rol van de stedelijke burger ook uitgespeeld?Dat komen we te weten als we luisteren naar de stadsbewoners zelf. Aan de hand van de levens van Haarlemmers en Groningers tussen 1747 en 1848 illustreert dit boek het voortbestaan van lokaal burgerschap. Zij komen aan het woord via verzoekschriften, kronieken, gelegenheidsgedichten, vergadernotulen en mondelinge klachten op de burgemeesterskamer. Hoe zag de ideale stedelijke gemeenschap er volgens hen uit? Welke rechten en plichten had een burger in hun ogen? En wat waren de dure plichten van een stadsbestuurder? Voor dit burgerschap putten stadsbewoners met souplesse uit traditionele én revolutionaire idealen en praktijken. Show less
Innovation plays an essential role in firms' competitiveness and long-term success. It varies from different types, ranging from run-of-the-mill innovation that brings incremental changes to... Show moreInnovation plays an essential role in firms' competitiveness and long-term success. It varies from different types, ranging from run-of-the-mill innovation that brings incremental changes to existing technologies to radical innovation that breaks from existing trajectories. The aim of this PhD dissertation is to integrate radical innovation and social network literature to broaden theoretical understanding, especially contribute to the literature on social networks, creativity, and innovation, and inform innovation management by unpacking the drivers and effects of radical innovation. Focusing on the long-standing debates in the social network literature regarding which types of networks are more advantageous for innovation, this dissertation starts with investigating how tie strength and structural holes collectively affect innovation radicalness at a location within an innovating firm. Then this dissertation investigates how social structure for producing a creative idea influences the adoption and future use of its innovations and makes a novel contribution by exploring how this effect is contingent on the radical nature of the creative idea. In addition to contributing to this long-standing debate, this dissertation also investigates how radicalness affects the private value for the innovating firm. Show less
This dissertation showed that physicians must be aware of the constraints that allow them to identify or obviate (un)desirable effects most notably if they evaluate these effects in a blinded... Show moreThis dissertation showed that physicians must be aware of the constraints that allow them to identify or obviate (un)desirable effects most notably if they evaluate these effects in a blinded matter. Unblinding might partially mitigate the limitation, but current measurement methods have gaps that we should remain aware of. Detailed measurements of subintervals with characterization of ion channel profiles, concentration QTc modelling, or machine learning might help physicians in their decision making in the future. Show less
Interest groups play an important role within a democratic society. Less is known about their role within the legal system. Meanwhile, interest groups are the driving force behind many high-profile... Show moreInterest groups play an important role within a democratic society. Less is known about their role within the legal system. Meanwhile, interest groups are the driving force behind many high-profile lawsuits against the Dutch government, such as the lawsuits concerning climate change, the quality of asylum facilities, and the Dutch nitrogen policy. This research focuses on the access of interest groups to the courts. How extensive is their access? Does it threaten or protect a democratic society under the rule of law? The access of interest groups to Dutch administrative and civil courts is evaluated in terms of legitimacy and effectiveness. Since interest group litigation is at the intersection of politics and law, the research adopts an interdisciplinary approach. Beyond the boundaries of Dutch legal scholarship, it seeks insights from social sciences regarding the role of interest groups within the political decision-making process. Additionally, it examines, from a legal sociological perspective, the role that interest groups play in public interest litigation in the United States. As a result, the research explores approaches, concepts, and arguments that have largely remained outside of the Dutch legal legal discourse. Ultimately, this leads to a reassessment of both the legitimacy and effectiveness of interest groups' access to the courts. Show less
A complex community of microbes develops in the infant gut shortly after birth. We call this community the infant gut microbiota. The microbiota influences the health of the infant, which makes the... Show moreA complex community of microbes develops in the infant gut shortly after birth. We call this community the infant gut microbiota. The microbiota influences the health of the infant, which makes the composition and function of the infant gut microbiota an important topic to study. It’s not possible to directly study the development of the microbiota inside the infant, so we are limited to information from fecal samples and laboratory experiments. Because it is so difficult to study, the processes and mechanisms that shape the microbiota also remain unclear. Mathematical models can generate hypotheses and predictions about the unseen inner workings of a system such as the infant gut microbiota.In this thesis we develop a mathematical model that makes predictions both on how bacteria are influenced by the environment and on how they influence the environment. By applying this influence to the environment and repeating the technique, the model can make predictions for how the whole system changes over time. We use this model to make predictions on how changes to the environment, such as the presence of oxygen, antibiotic disturbances, or in particular the presence of oligosaccharides, influence the infant gut microbiota, their metabolism, and ultimately the infant. Show less
In this thesis we push the boundaries of high-resolution imaging at radio frequencies between 100 and 200 MHz. Using the International LOFAR Telescope that spans across Europe we achieve sub... Show moreIn this thesis we push the boundaries of high-resolution imaging at radio frequencies between 100 and 200 MHz. Using the International LOFAR Telescope that spans across Europe we achieve sub-arcsecond angular resolution. We demonstrate mapping of the full field of view of the telescope at its native resolution and use the resulting images to study active galactic nuclei in the Lockman Hole field. Show less
This thesis describes a set of excitability measurements -transcranial magnetic stimulation (TMS) combined with electromyography (EMG) and electroencephalography (EEG), nerve excitability threshold... Show moreThis thesis describes a set of excitability measurements -transcranial magnetic stimulation (TMS) combined with electromyography (EMG) and electroencephalography (EEG), nerve excitability threshold tracking (NETT), and muscle velocity recovery cycles (MVRC)- and the applicability of these tools in early phase clinical drug development. We validated the biomarkers in healthy subjects with registered drugs and showed that the measurements are all repeatable and sensitive to pharmacological effects, even in a small number of subjects. Furthermore, we have evaluated effects of a novel AMPA-positive allosteric modulator with TMS-EMG/EEG, and a first-in-class skeletal muscle-specific chloride channel (ClC-1) inhibitor with MVRC, and the findings helped us to confirm proof-of-mechanism of these compounds in healthy subjects. In conclusion, these measurements proved to be valuable pharmacodynamic biomarkers in two drug development programs, encouraging their further use in clinical development of other future drug candidates targeting cortical-, neuronal-, and muscle cell excitability. The use of such clinical pharmacodynamic biomarkers could improve the quality and efficiency of the development process of drugs for e.g. amyotrophic lateral sclerosis, chronic pain, depression, treatment-resistant epilepsy, and neuromuscular diseases. Show less
This work explores the notion of independence as it relates to international civil servants and secretariats. It identifies the fundamental characteristics of the term and examines how the... Show moreThis work explores the notion of independence as it relates to international civil servants and secretariats. It identifies the fundamental characteristics of the term and examines how the independence of international civil service can erode. It describes the acts and omissions of three main actors responsible for preserving this independence: member states, international organizations, and international civil servants. The work concludes by providing concrete recommendations for strengthening the independence of the international civil service. Show less
The healthcare landscape is constantly evolving. eHealth (electronic health) presents opportunities to alleviate pressure in healthcare, for example by empowering patients to take more control over... Show moreThe healthcare landscape is constantly evolving. eHealth (electronic health) presents opportunities to alleviate pressure in healthcare, for example by empowering patients to take more control over their care. This thesis has examined various digital applications that have already been (partially) implemented. The research primarily focuses on the user-friendliness and effectiveness of these digital applications, aiming to promote self-management and accessibility of healthcare. The digital applications in this thesis relate to requesting diagnostic tests, both with and without involvement of healthcare professionals. Diagnostic tests enable the detection of conditions, such as sexually transmitted diseases for instance. Additionally, research has been conducted on the effectiveness of a self-management program for asthma and COPD. The results generally indicate that patients and citizens, particularly the younger generation, are receptive to online applications aimed at supporting their self-management of health and illness. Nevertheless, certain factors influence their acceptance, such as reliability and user-friendliness. Therefore, it is essential to promote collaboration among all stakeholders to enhance usability and ensure that online applications effectively meet their intended purpose and objectives. Show less
Thromboembolic complications remain a major public health burden, making antithrombotic agents one of the most widely prescribed groups of medication, but the treatment is often challenging as it... Show moreThromboembolic complications remain a major public health burden, making antithrombotic agents one of the most widely prescribed groups of medication, but the treatment is often challenging as it at the same time increases risk of bleeding. With nationwide data from Statistics Netherlands, antithrombotic therapy and relevant clinical outcomes were comprehensively examined in the patient population of atrial fibrillation, overall or among those with comorbid cancer. The results suggest the patient population was increasingly receiving anticoagulants, driven by the newly introduced medication- direct oral anticoagulant and guided by the CHA2DS2-VASc score, and meanwhile the patient population experienced fewer ischemic stroke and major bleeding. In spite of these promising changes, suboptimal medication adherence and potential underuse of anticoagulants remain directions for further improvement. Antithrombotic agent use during pregnancy was also examined in the general Dutch pregnant population, which featured a surge in antiplatelet prescriptions, and risk of preeclampsia/eclampsia decreased and several newborn outcomes improved simultaneously. Together, the studies presented in this thesis provide an overview of antithrombotic therapy in the Netherlands in recent years, providing insights for further improving this treatment and relevant patient outcomes. Show less
This dissertation explores the ways in which affective responses to disabled bodies are represented and how this invites us to read these bodies aesthetically. I argue that this affective impact... Show moreThis dissertation explores the ways in which affective responses to disabled bodies are represented and how this invites us to read these bodies aesthetically. I argue that this affective impact can be understood as an affordance, a term I use to describe how the appearance of and interaction with disabled bodies produces affective responses such as fear, wonder, or disgust. I study the relationship between representation and affective reactions through literature and other art forms. Through close readings of literary texts and works of art, this dissertation offers an alternative to so-called model thinking—an approach that emphasizes categorization. Instead, I propose a reading that focuses on how bodily capacities are culturally and socially translated into (dis)abilities. Unlike taxonomic approaches that categorize and generalize, this method allows moving from the particular to the private. Works of art, although prone to generalization, emphasize their unicity and resist categorization. By analyzing how different art forms represent disabled bodies, the dissertation brings a new dimension to understanding our emotional responses and the aesthetic appreciation of bodily diversity. Show less
