All living organisms are made out of cells, which serve as the fundamental units of life. Protein molecules, comprised of amino acids, carry out diverse functions across various cellular... Show moreAll living organisms are made out of cells, which serve as the fundamental units of life. Protein molecules, comprised of amino acids, carry out diverse functions across various cellular compartments. Proteins are tightly controlled in their synthesis, folding, localization and degradation to ensure proper functioning. Dysregulation of protein control mechanisms within the cell can lead to cellular dysfunction, disease or eventually cell death. Post-translational modifications (PTMs) are the addition of a chemical group to an existing protein to regulate its function, localization, stability or interaction. In this thesis we will dive deeper into PTMs SUMO and ubiquitin, with the aim to understand the biochemistry of these proteins in different aspects of cellular function and human pathophysiology. An interesting aspect of the conjugation process lies in its reversibility, which is governed by specific proteases known as SENPs in the case of SUMO. However, only SENP6 and SENP7 have the ability to depolymerize SUMO2/3 chains by an insertion in their conserved catalytic domains. We delve into the promising horizon that lies ahead of a small yet profoundly impactful post-translational modifying protein. Despite its modest size, this protein wields a significant influence on fundamental cellular processes Show less
The Dutch reward system in prison (Promoveren en Degraderen) has never been formally evaluated, therewith obscuring its theoretical soundness, application and effects. There are scholarly concerns,... Show moreThe Dutch reward system in prison (Promoveren en Degraderen) has never been formally evaluated, therewith obscuring its theoretical soundness, application and effects. There are scholarly concerns, however, regarding all three of these aspects. Therefore, the current dissertation aims to improve our understanding of reward systems in prisons, by studying the Dutch reward system in prison. Specifically, the soundness of its theoretical assumptions is tested, prior research is mapped, predictors of receiving rewards are identified (e.g. motivation, self-governance ability and behaviour), and the association between rewards and feelings of autonomy is examined.The current dissertation reveals that the theoretical assumptions can only partially be supported by scientific knowledge and that the system is not fully applied as intended. Moreover, the current reward system disadvantages incarcerated individuals low on self-governance ability. Finally, some rewards do increase feelings of autonomy in prison. These results underscore the relevance of promoting intrinsic over extrinsic motivation for compliance, and of adapting the current system to the level of self-governance ability of incarcerated individuals. Policymakers are advised to effectuate such policy changes, and practitioners are advised to look beyond behaviour as the key determinant of who is ‘deserving’ of rewards. Show less
Central to this thesis was the use of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to model a rare form of mitochondrial cardiomyopathy. To model this disease required the... Show moreCentral to this thesis was the use of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to model a rare form of mitochondrial cardiomyopathy. To model this disease required the design of new methodologies, improving upon the current limitations of hiPSC-CMs as model systems, notably the variability and the immature state of the resulting cardiomyocytes. The diseases we were interested in manifest soon after birth. At the outset of the studies, it was unclear whether a phenotype would be evident in our standard immature 2D cultures, or whether more complex models would be required to capture more salient features of the condition. Our focus was on the rare mitochondrial disease Combined Oxidative Phosphorylation Deficiency, caused by mutations in the gene alanyl-tRNA synthetase 2. We refined our emerging 3D cardiac microtissue protocol to improve robustness and reproducibility and reduce cost by basing differentiation on small molecules rather than growth factors without altering the functionality of hiPSC-CMs. We also demonstrated that integrating pH and O2 sensors in a micro-physiological chip was possible for the assessment of metabolic parameters under microfluidic flow. The overall goal of this thesis was to provide additional tools that would have utility in studying mitochondrial and other cardiac diseases. Show less
This thesis explores Breaking of Ensemble Equivalence (BEE) in random graph models by examining the spectral properties of adjacency matrices. The goal is to identify spectral characteristics that... Show moreThis thesis explores Breaking of Ensemble Equivalence (BEE) in random graph models by examining the spectral properties of adjacency matrices. The goal is to identify spectral characteristics that differentiate random graph ensembles, enhancing the understanding of complex network structures and behaviors. The research encompasses both theoretical analysis and practical applications, including a chapter on simulations and sampling methods.Chapter 1 introduces basic random graph theory and emphasizes the importance of maximum entropy models in real-world network modeling. It defines BEE and its characterization within statistical mechanics, highlighting the natural differences between canonical and microcanonical ensembles. It then introduces spectral theory of random graphs and why it is utilized to investigate BEE.Chapter 2 proposes a conjecture linking BEE to a gap between the expectations of the largest eigenvalue in the canonical and microcanonical ensembles, proving it for homogeneous graphs.Chapter 3 examines Chung-Lu random graphs, establishing central limit theorems for the largest eigenvalue and its eigenvector.Chapter 4 verifies the conjecture for inhomogeneous graphs, computing the expected largest eigenvalue of the configuration model.Chapter 5 offers numerical evidence through simulations, after a brief introduction to graph sampling. The thesis concludes with a summary of findings and suggestions for future research. Show less
In this thesis, deep learning is studied from a statistical perspective. Convergence rates for the worst case risk bounds of neural network estimators are obtained in the classification, density... Show moreIn this thesis, deep learning is studied from a statistical perspective. Convergence rates for the worst case risk bounds of neural network estimators are obtained in the classification, density estimation and linear regression model. Special attention is given to the role of input dimension since in practice, neural networks have shown promising results for high dimensional input settings. First, the estimation of conditional class probabilities under the cross-entropy loss is studied. A challenge with this loss is that it becomes unbounded near zero. To deal with this, the loss is truncated. Convergence rates are obtained for a neural network estimator under this truncated loss. The second problem considered is density estimation. A two step procedure is proposed. The first step transforms the density estimation problem into a regression problem by constructing response variables using a kernel density estimator on half of the data. In the second step, a neural network is fitted to this constructed data. Convergence rates for this method are obtained using existing approximation results for compositional functions. Finally, forward gradient descent is studied. This is a biologically motivated alternative for gradient descent. Convergence rates are derived for this method in the linear regression model with random design. Show less
Boeren, A.M.P.; Oei, E.H.G.; Willemze, A.; Jong, P.H.P. de; Mil, A.H.M.V.; Mulligen, E. van 2024
ObjectiveUS can detect subclinical joint-inflammation in patients with clinically suspect arthralgia (CSA), which is valuable as predictor for RA development. In most research protocols both hands... Show moreObjectiveUS can detect subclinical joint-inflammation in patients with clinically suspect arthralgia (CSA), which is valuable as predictor for RA development. In most research protocols both hands and forefeet are scanned, but it is unclear if US of the forefeet has additional value for predicting RA, especially since synovial hypertrophy in MTP-joints of healthy individuals is also common. To explore the possibility to omit scanning of the forefeet we determined if US of the forefeet is of additional predictive value for RA-development in CSA patients.MethodsCSA patients of two independent cohorts underwent US of the hands and forefeet. We analysed the association between RA-development and US-positivity for the full US-protocol, the full US-protocol with correction for gray scale (GS)-findings in the forefeet of healthy and the protocol without forefeet.ResultsIn total, 298 CSA patients were studied. In patients with a positive US, subclinical joint-inflammation was mostly present in the hands (90–86%). Only 10–14% of patients had subclinical joint-inflammation solely in the forefeet. US-positivity was associated with inflammatory arthritis development in both cohorts, with HRs 2.6 (95% CI 0.9–7.5) and 3.1 (95% CI 1.5–6.4) for the full protocol, 3.1 (95% CI 1.3–7.7) and 2.7 (95% CI 1.3–5.4) for the full US-protocol with correction, and 3.1 (95% CI 1.4–6.9) and 2.8 (95% CI 1.4–5.6) without the forefeet. AUROCs were equal across both cohorts.ConclusionThe forefeet can be omitted when US is used for the prediction of RA-development in CSA patients. This is due to the finding that subclinical joint-inflammation in the forefeet without concomitant inflammation in the hands is infrequent. Show less
The studies described in this thesis provide additional evidence that the current Dutch population-based screening programmes (CSPs) can be further optimized, particularly concerning the... Show moreThe studies described in this thesis provide additional evidence that the current Dutch population-based screening programmes (CSPs) can be further optimized, particularly concerning the participation of potential participants from highly urbanized and low socioeconomic status (SES) neighbourhoods. Our findings suggest that non-participation in the CSPs in these low SES-neighbourhoods is associated with more unfavourable, relatively advanced, tumour outcomes. Given that the decision to participate in a CSP is not solely based on rational decision-making processes, primary care providers could play an important role here. This would primarily involve informing and advising potential participants who are hesitant about participating in CSPs. In this thesis, we describe that both potential participants and general practitioners support the idea that primary care should be more involved in the invitation process of the CSPs. Based on our findings, we therefore recommend implementing a proactive, risk-based invitation strategy from primary care regarding the invitation process of the current CSPs. Show less
This dissertation examines various monitoring mechanisms within the International Humanitarian and Human Rights Law frameworks in order to draw lessons learned from their monitoring functions,... Show moreThis dissertation examines various monitoring mechanisms within the International Humanitarian and Human Rights Law frameworks in order to draw lessons learned from their monitoring functions, approaches and practices and assess whether they can be applied to a future compliance system under the four Geneva Conventions of 1949 and their Additional Protocols. The scope of the enquiry includes the existing compliance system of the Geneva Conventions, the compliance systems of other treaties within the International Humanitarian Law framework, the United Nations human rights monitoring system, and a number of mechanisms that supervise respect for humanitarian norms by States and/or armed non-State actors. The dissertation suggests that a future compliance system under the Geneva Conventions should include thematic reporting, a plenary forum for States Parties and an International Humanitarian Law Committee. The establishment of effective compliance mechanisms that are tailored to the specifics of International Humanitarian Law would support and advance the implementation of the Geneva Conventions by States Parties as well as strengthen the capacity to monitor their implementation from within the International Humanitarian Law framework. Show less
This thesis had two main focuses. First, it investigated the mechanisms underlying individual differences in brain structure, developmental changes, and function. Second, it examined how enriched... Show moreThis thesis had two main focuses. First, it investigated the mechanisms underlying individual differences in brain structure, developmental changes, and function. Second, it examined how enriched and deprived environments affect brain development from middle childhood to early adolescence (ages 7-14). The study revealed distinct genetic and environmental influences on the developing brain during this period. Genetic contributions largely explained the variations in brain structure and developmental changes, along with location-specific environmental factors. While studies on genetic and environmental influences on brain regions showed both overlapping and unique outcomes, the interplay between these influences is complex. Using MRI and fMRI provided a comprehensive understanding of how individual differences arise. Additionally, the thesis highlighted the distinct effects of specific environmental influences on brain development. An enriched cognitive environment, such as musical ability, was linked to attenuated development, while a deprived environment, exemplified by the COVID-19 pandemic, accelerated development. Notably, the brain showed resilience to adverse effects, particularly in TPJ growth during the pandemic, suggesting adaptive processes during this developmental phase. Future research should explore whether the relationship between environmental effects and brain maturation pace is linked to positive mental health outcomes. Ultimately, identifying interventions to ensure all children thrive throughout their development is crucial. Show less
It is increasingly common for citizens to take initiatives to improve their immediate living environment. While setting up and implementing these initiatives initiators come into contact with the... Show moreIt is increasingly common for citizens to take initiatives to improve their immediate living environment. While setting up and implementing these initiatives initiators come into contact with the government. Governments are often enthusiastic about these plans, but yet it proves far from easy to get get the initiative off the ground. 'The law' is seen as the main bottleneck. In this dissertation several (legal) bottlenecks are researched and recommendations to facilitate initiators are formulated. Show less
If diversity counteracts solidarity, as welfare state scholarship commonly concludes, then how did the expansion of European welfare states in the postwar period coexist with (post)colonial... Show moreIf diversity counteracts solidarity, as welfare state scholarship commonly concludes, then how did the expansion of European welfare states in the postwar period coexist with (post)colonial migrations? Through a historical-interpretivist lens, this dissertation studies the inclusion of migrants from the Caribbean, Algeria, and present-day Indonesia in post-war British, French, and Dutch welfare setates respectively. It documents a variety of inclusions on inequal terms in French and Dutch welfare states. While those who qualified as repatriates received aid under targeted assistance schemes and expedited access to social security, many who had been disadvantaged under colonial legal codes were directed towards paternalistic arms of the welfare state aimed at surveillance and cultural conversion. In the UK, street-level discrimination and restricitonist immigration law marred the promise of equality under the Beveridgean welfare state for Caribbean citizens. These patterns were racialised, but not inevitable. Ideological efforts to construct certain migrants as deserving cultural insiders have important explanatory power. This dissertation improves the theoretical toolkit available to welfare state scholars interested in inclusion, and elucidates the relationship between race and redistribution. Diversity neither caused retrenchment, nor threatened solidarity. Rather, (post)colonial migrations offered contemporaries an opportunity to consciously and manually create it. Show less
Unsaturated fatty acids (UFA) are crucial for T-cell effector functions, as they can affect the growth, differentiation, survival, and function of T cells. Nonetheless, the mechanisms by which UFA... Show moreUnsaturated fatty acids (UFA) are crucial for T-cell effector functions, as they can affect the growth, differentiation, survival, and function of T cells. Nonetheless, the mechanisms by which UFA affects T-cell behavior are ill-defined. Therefore, we analyzed the processing of oleic acid, a prominent UFA abundantly present in blood, adipocytes, and the fat pads surrounding lymph nodes, in CD4+ T cells. We found that exogenous oleic acid increases proliferation and enhances the calcium flux response upon CD3/CD28 activation. By using a variety of techniques, we found that the incorporation of oleic acid into membrane lipids, rather than regulation of cellular metabolism or TCR expression, is essential for its effects on CD4+ T cells. These results provide novel insights into the mechanism through which exogenous oleic acid enhances CD4+ T-cell function. Show less
Oratie uitgesproken door Prof.dr. Ben S. Kuipers bij de aanvaarding van het ambt van hoogleraar Publiek Leiderschap aan de Universiteit Leiden op vrijdag 14 juni 2024
Lemkes, A.C.; Struijs, S.Y.; Littel, M.; Ekkers, W.D.; Berg, J.F. van den 2024
This research focuses on creating composite biomarkers that can classify diagnoses, estimate symptom severity, and detect treatment effects using data from wearable sensors and smartphone... Show moreThis research focuses on creating composite biomarkers that can classify diagnoses, estimate symptom severity, and detect treatment effects using data from wearable sensors and smartphone applications. The thesis consists of an introduction to machine learning techniques and their use in developing biomarkers for the central nervous system; a narrative review of the relevant literature; and detailed studies on the application of these techniques in various health conditions. Specifically, the research includes observational and cross-sectional studies on facioscapulohumeral muscular dystrophy (FSHD) and major depressive disorder (MDD), demonstrating how smartphone and wearable sensor data can be used to monitor disease severity and progression. Additionally, the research identified the use of a tablet-based finger tapping task to monitor the real-time effects of antiparkinson's drugs on Parkinson's symptom severity. Key findings highlight the potential of mHealth biomarkers to provide continuous, real-time monitoring of patients, which can enhance the accuracy of clinical assessments and potentially reduce the burden on patients and healthcare systems. The thesis also addresses the challenges of variability in mHealth device data and emphasizes the need for robust validation and standardization to ensure the reliability of these biomarkers in clinical settings. Show less
The human body consists of many different cell types. Cell types can be defined by the genes expressed, and unique cell-type-specific transcriptional mechanisms control these expressions. Single... Show moreThe human body consists of many different cell types. Cell types can be defined by the genes expressed, and unique cell-type-specific transcriptional mechanisms control these expressions. Single nucleotide polymorphisms (SNPs) in the DNA can be associated with diseases, but approximately 95% fall in the non-coding region. Usually, it is unknown whether these variants are causal, and which gene and cell type they affect.Advances in single-cell RNA-sequencing improved our understanding of heterogeneous tissues and led to the discovery of many new cell types. This new technology also presents computational challenges including consistent cell-type annotations. It is essential to annotate cells using classification instead of currently practiced clustering methods. To facilitate this transition, we benchmarked cell-type classification methods and developed computational methods to automatically build reference atlases using multiple already labeled single-cell datasets.Next, we establish a relationship between mutations and their effect on gene or isoform expression. We study sequence-to-expression models that can predict an alteration in expression when a mutation is observed. Given that gene expression mechanisms are cell-type specific, we introduce sequence-to-expression models based on single-cell data to make cell-type-specific predictions. We use these models to show that certain mutations are indeed changing expression, increasing our understanding of transcriptional regulation. Show less
Uveal melanoma, as opposed to cutaneous melanoma, is a tumor which is predominantly located in the center of the eye. Given its potential aggressive nature with fatal consequences, it is important... Show moreUveal melanoma, as opposed to cutaneous melanoma, is a tumor which is predominantly located in the center of the eye. Given its potential aggressive nature with fatal consequences, it is important to start treatment in a timely manner. Currently, treatment consists of decreasing the size of the tumor by means of radiation therapy or surgery, but by mapping the genetic makeup of uveal melanoma, personalized treatment potentially becomes possible. In this thesis we tried to solve a piece of this genetic puzzle by focusing on genetic and cellular differences within and between different uveal melanoma. By means of an innovative new technique, digital PCR, we aimed to visualize this so-called heterogeneity. We demonstrate that we can accurately assess which genetic aberrations are present in uveal melanoma. Moreover, we show in what percentage of cells these aberrations are present. Additionally, we illustrate which cell types play an important role in uveal melanoma development. This way, we characterized a substantial amount of different uveal melanoma based on their heterogeneity profile. Lastly, we display whether and how uveal melanomas with a specific heterogeneity profile are susceptible to treatment. Show less
Cardiac arrhythmias are a common cause of sudden death worldwide. However, despite decades of thorough investigation the underlying biophysical mechanisms of cardiac arrhythmias are still... Show moreCardiac arrhythmias are a common cause of sudden death worldwide. However, despite decades of thorough investigation the underlying biophysical mechanisms of cardiac arrhythmias are still insufficiently understood due to incomplete theories and the lack of precise spatiotemporal control in experiments. In the last decade, the problem of insufficient spatiotemporal control has started to be tackled by means of a new technique, called optogenetics. This technique employs expression of light-activated proteins, which are activated or deactivated in time and space by switching on/off light (in the near-ultraviolet to near-infrared wavelength range) in specific patterns thus realizing fully biological spatiotemporal control. However, with a few notable exceptions, cardiac optogenetic studies have only confirmed previously known mechanisms and yielded no or little novel mechanistic insights. In this thesis, to fill this gap, we combined nonlinear dynamics theory, numerical simulations and optogenetic experiments with unique spatiotemporal control to theoretically predict and demonstrate novel arrhythmogenic phenomena in cardiac tissue. Thanks to the robustness of the optogenetics methods and generality of the applied theories and computations, this thesis uncovered novel mechanisms for the biophysics of cardiac tissue that are applicable to the functioning of excitable systems in general. Show less
The ideas underlying this thesis are that lipidomics may improve the diagnosis of liver metabolic diseases, and can provide further insights into the underlying pathophysiology of these diseases.... Show moreThe ideas underlying this thesis are that lipidomics may improve the diagnosis of liver metabolic diseases, and can provide further insights into the underlying pathophysiology of these diseases. However to achieve this, the measurement of lipids should be further improved by enabling comprehensive coverage, accurate identification and quantitation. Therefore, in this thesis, new analytical methodologies using LC-MS for the accurate detection and quantitation of lipids are developed. These methods are then applied to MCADD samples to identify lipid biomarkers, which are further correlated with gene expression analysis to understand the underlying biochemical pathways. Show less
