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Manikandan, Rakshith (author)Fibre-reinforced laminated composites are constructed layer-by-layer, allowing their material properties to be easily tailored relative to their isotropic counterparts (metallic alloys). Moreover, a composite structure with variable stiffness (VS) can be made by spatially tailoring stiffness across a laminate. This permits better load...master thesis 2023
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Representations of DNA Sequence Context and Mutational Spectra for Prediction of Repair DeficienciesBorg, Jonathan (author)Double-strand break (DSB) repair is a critical cellular process which repairs breaks in both strands of the DNA double helix. Different repair mechanisms are tasked with repairing such breaks. Predicting deficiencies in repair mechanisms has been widely used for therapeutic purposes, such as targeting cancer cells that have specific DNA repair...master thesis 2023
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Stol, Madelon (author)Understanding the role of genes and genetic variants is a key challenge in unraveling the driving mechanisms of Alzheimer's disease (AD). Single-cell RNA sequencing is a technique that quantifies gene expression at the cell (type) level enabling investigation of the roles of different cell types in disease. We analyzed changes in gene (co-...master thesis 2023
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Lansu, Mike (author)The use of multi-axis additive manufacturing has enabled the possiblity to fabricate parts using curved layer deposition. Compared to the traditional deposition using planar layers of a fixed thickness, multiaxis additive manufacturing significantly increases the number of possible fabrication sequences. With the introduction of a time component...master thesis 2023
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Golik, Bartek (author)Analysing single-cell RNA sequencing data is becoming an increasingly tedious task as the size of data sets grows. As a proposed solution, recent discoveries suggest that these data sets can be binarized without losing much information. This in turn should allow for memory and time efficient methods of storage and computation. Numerous analyses...bachelor thesis 2023
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Nagtegaal, M.A. (author)Magnetic Resonance Imaging (MRI) is a flexible medical imaging technique that facilitates measurement of a wide range of contrasts particularly in soft tissue (e.g. brain and heart). Conventionally, qualitative images are acquired in which certain physical tissue properties are emphasized such as the transverse and longitudinal relaxation times....doctoral thesis 2023
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Smit, Jean-Paul (author)Deep-learning (DL) models could greatly advance the automation of fact-checking, yet have not widely been adopted by the public because of their hard-to-explain nature. Although various techniques have been proposed to use local explanations for the behaviour of DL models, little attention has been paid to global explanations. <br/>In response,...bachelor thesis 2023
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Wang, W. (author), van Keulen, A. (author), Wu, J. (author)Additive manufacturing of metal parts involves phase transformations and high temperature gradients which lead to uneven thermal expansion and contraction, and, consequently, distortion of the fabricated components. The distortion has a great influence on the structural performance and dimensional accuracy, e.g., for assembly. It is therefore...journal article 2023
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Dekking, F.M. (author)We discuss the base 3/2 representation of the natural numbers. We prove that the sum-of-digits function of the representation is a fixed point of a 2-block substitution on an infinite alphabet, and that this implies that sum-of-digits function modulo 2 of the representation is a fixed point x<sub>3/2</sub> of a 2-block substitution on {0,1}....journal article 2023
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Li, Q. (author), Finn, Adrian J. (author), Doyle, Stephen J. (author), Smith, Robin (author), Kiss, A.A. (author)This paper explores the basis on which reliable screening of distillation sequences for energy-efficient separation of zeotropic multicomponent mixtures can be carried out. A case study for the separation of natural gas liquids is used to demonstrate the approach. To solve this generic problem, a screening algorithm has been developed using...journal article 2023
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Dekking, F.M. (author), Keane, M.S. (author)We consider in general two-block substitutions and their fixed points. We prove that some of them have a simple structure: their fixed points are morphic sequences. Others are intrinsically more complex, such as the Kolakoski sequence. We prove this for the Thue-Morse sequence in base 3/2.journal article 2023
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Koppensteiner, Sarah (author), van Velthoven, J.T. (author), Voigtlaender, Felix (author)This paper provides maximal function characterizations of anisotropic Triebel–Lizorkin spaces associated to general expansive matrices for the full range of parameters p∈ (0 , ∞) , q∈ (0 , ∞] and α∈ R. The equivalent norm is defined in terms of the decay of wavelet coefficients, quantified by a Peetre-type space over a one-parameter dilation...journal article 2023
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van der Sluis, Tetje C. (author), Beyrend, Guillaume (author), van der Gracht, Esmé T.I. (author), Abdelaal, T.R.M. (author), Jochems, Simon P. (author), Belderbos, Robert A. (author), Wesselink, Thomas H. (author), van Duikeren, Suzanne (author), Arens, Ramon (author)Immune checkpoint therapy (ICT) has the power to eradicate cancer, but the mechanisms that determine effective therapy-induced immune responses are not fully understood. Here, using high-dimensional single-cell profiling, we interrogate whether the landscape of T cell states in the peripheral blood predict responses to combinatorial targeting...journal article 2023
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Gil Jimenez, A. (author), van Dorp, Jeroen (author), Contreras-Sanz, Alberto (author), van der Vos, Kristan (author), Vis, Daniel J. (author), Braaf, Linde (author), Broeks, Annegien (author), Kerkhoven, Ron (author), van Kessel, Kim E.M. (author), Wessels, L.F.A. (author)Cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy is recommended for patients with muscle-invasive bladder cancer (MIBC). It has been shown that somatic deleterious mutations in ERCC2, gain-of-function mutations in ERBB2, and alterations in ATM, RB1, and FANCC are correlated with pathological response to NAC in...journal article 2023
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Koster, C.C. (author), Kleefeldt, Askar A. (author), van den Broek, M.A. (author), Luttik, M.A.H. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)Mitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or posttranscriptional processing and splicing. Due to the inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene...journal article 2023
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Li, Q. (author), Finn, Adrian J. (author), Doyle, Stephen J. (author), Smith, Robin (author), Kiss, A.A. (author)The synthesis of heat-integrated distillation sequences for energy-efficient separation of zeotropic multicomponent mixtures is complex due to the many interconnected design degrees of freedom. This paper explores the basis on which reliable screening can be carried out. To solve this problem, a screening algorithm has been developed using...book chapter 2023
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Koppensteiner, Sarah (author), van Velthoven, J.T. (author), Voigtlaender, Felix (author)Continuing previous work, this paper provides maximal characterizations of anisotropic Triebel-Lizorkin spaces F˙p,qα for the endpoint case of p= ∞ and the full scale of parameters α∈ R and q∈ (0 , ∞]. In particular, a Peetre-type characterization of the anisotropic Besov space B˙∞,∞α=F˙∞,∞α is obtained. As a consequence, it is shown that...journal article 2023
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Hendriks, Kasper P. (author), Al-Shehbaz, Ihsan A. (author), Bailey, C. Donovan (author), Hooft van Huysduynen, Alex (author), Nauheimer, Lars (author), Zuntini, Alexandre R. (author), Franzke, Andreas (author), Schranz, M. Eric (author), Ly, E. (author)The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the...journal article 2023
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Ma, Huidong (author), Zhong, Cheng (author), Sun, Hui (author), Chen, Danyang (author), Lin, H.X. (author)The mobile element variant is a very important structural variant, accounting for a quarter of structural variants, and it is closely related to many issues such as genetic diseases and species diversity. However, few detection algorithms of mobile element variants have been developed on third-generation sequencing data. We propose an...conference paper 2023
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Depuydt, Lore (author), Renders, Luca (author), Abeel, T.E.P.M.F. (author), Fostier, Jan (author)Background: Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, as their graph topology naturally reveals similarity and divergence within the pan-genome. Most state-of-the-art pan-genome...journal article 2023