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Filius, M. (author), van Wee, R.G. (author), de Lannoy, C.V. (author), Westerlaken, I. (author), Li, Zeshi (author), Kim, S.H. (author), de Agrela Pinto, C. (author), Wu, Yunfei (author), Boons, Geert-Jan (author), Pabst, Martin (author), de Ridder, Dick (author), Joo, C. (author)Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoforms. Mass spectrometric methods, in particular, often provide only ambiguous information on post-translational modification sites, and...journal article 2024
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Zhang, Kaixuan (author), Shi, Zhaochen (author), Zujovic, Jana (author), de Ridder, H. (author), van Egmond, R. (author), Neuhoff, David L. (author), Pappas, T. (author)We present a systematic approach for training and testing structural texture similarity metrics (STSIMs) so that they can be used to exploit texture redundancy for structurally lossless image compression. The training and testing is based on a set of image distortions that reflect the characteristics of the perturbations present in natural...journal article 2024
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Calderon Franco, D. (author), Corbera Rubio, F. (author), Cuesta Sanz, M. (author), Pieterse, Brent (author), de Ridder, David (author), van Loosdrecht, Mark C.M. (author), van Halem, D. (author), Laureni, M. (author), Weissbrodt, D.G. (author)Drinking water treatment plants (DWTPs) are designed to remove physical, chemical, and biological contaminants. However, until recently, the role of DWTPs in minimizing the cycling of antibiotic resistance determinants has got limited attention. In particular, the risk of selecting antibiotic-resistant bacteria (ARB) is largely overlooked in...journal article 2023
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Handula, M. (author), Beekman, Savanne (author), Konijnenberg, Mark (author), Stuurman, Debra (author), de Ridder, Corrina (author), Bruchertseifer, Frank (author), Morgenstern, Alfred (author), Denkova, A.G. (author), de Blois, Erik (author), Seimbille, Y. (author)Background: The [<sup>177</sup>Lu]Lu-DOTA-TATE mediated peptide receptor radionuclide therapy (PRRT) of neuroendocrine tumors (NETs) is sometimes leading to treatment resistance and disease recurrence. An interesting alternative could be the somatostatin antagonist, [<sup>177</sup>Lu]Lu-DOTA-JR11, that demonstrated better biodistribution...journal article 2023
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Zhao, Y. (author), Stumpel, J.F.H.J. (author), de Ridder, H. (author), Wijntjes, M.W.A. (author)Most studies on the perception of style have used whole scenes/entire paintings; in our study, we isolated a single motif (an apple) to reduce or even eliminate the influence of composition, iconography, and other contextual information. In this article, we empirically address two fundamental questions of the existence (Experiment 1) and...journal article 2023
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Chaves-de-Plaza, Nicolas F. (author), Mody, P. (author), Hildebrandt, K.A. (author), Staring, M. (author), Astreinidou, Eleftheria (author), de Ridder, Mischa (author), de Ridder, H. (author), van Egmond, R. (author)Delineation of tumours and organs-at-risk permits detecting and correcting changes in the patients' anatomy throughout the treatment, making it a core step of adaptive external beam radiotherapy. Although auto-contouring technologies have sped up this process, the time needed to perform the quality assessment of the generated contours remains a...book chapter 2022
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Mody, Prerak (author), Chaves-de-Plaza, Nicolas F. (author), Hildebrandt, K.A. (author), van Egmond, R. (author), de Ridder, H. (author), Staring, Marius (author)Deep learning models for organ contouring in radiotherapy are poised for clinical usage, but currently, there exist few tools for automated quality assessment (QA) of the predicted contours. Bayesian models and their associated uncertainty, can potentially automate the process of detecting inaccurate predictions. We investigate two Bayesian...journal article 2022
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de Ridder, Else F. (author), Friedericy, Herman J. (author), van der Eijk, A.C. (author), Dankelman, J. (author), Jansen, F.W. (author)Highlights: What are the main findings? Using the HSMEA, it is possible to systematically reduce operating room waste. The HSMEA identifies carbon hotspots of surgical waste based on waste stream analysis. Solutions for improvement are found by applying the six Rs of waste management. What is the implication of the main finding? A...journal article 2022
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Wapenaar, C.P.A. (author), de Ridder, Sjoerd (author), Dukalski, Marcin (author), Reinicke, Christian (author)Standard Marchenko redatuming and imaging schemes neglect evanescent waves and are based on the assumption that decomposition into downgoing and upgoing waves is possible in the subsurface. Recently we have shown that propagator matrices, which circumvent these assumptions, can be expressed in terms of Marchenko focusing functions. In this paper...conference paper 2022
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de Ridder, M.P. (author), den Bieman, J.P. (author), Gautier, C. (author), van Nieuwkoop, J.C.C. (author)To improve the energy density and directional spectra computed with the SWAN model for the North Sea, a data-driven model is trained to correct the SWAN spectra. After training of the data-driven model on a year of observed and modelled data, the energy density and directional spectrum are corrected for three locations in the North Sea. When...conference paper 2021
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Zijlstra, H. (author), Quist, W.J. (author), Thissen, Paul (author), Pegels, Tom (author), Nijhuis, S. (author), Naldini, S. (author), Lubelli, B. (author), de Ridder, A.C. (author), Remøy, H.T. (author), Clarke, Nicholas (author), van den Dobbelsteen, A.A.J.F. (author), Gommans, L.J.J.H.M. (author), Dang, M.K. (author)Deze publicatie is een weerslag van de uitkomsten van het KaDEr-project (Karakteristiek Duurzaam Erfgoed) dat de TU Delft in opdracht van en in samenwerking met de Provincie Gelderland heeft uitgevoerd. De lezer wordt meegenomen in de zoektocht om invulling te geven aan de relatie wetenschap, praktijk en beleid rondom duurzaam erfgoed op...book 2021
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Dekkers, T. (author), Melles, M. (author), Vehmeijer, S.B.W. (author), de Ridder, H. (author)Background: Web-based patient education is increasingly offered to improve patients’ ability to learn, remember, and apply health information. Efficient organization, display, and structural design, that is, information architecture (IA), can support patients’ ability to independently use web-based patient education. However, the role of IA in...journal article 2021
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- Gonçalves, Joana (author), Clarke, Nicholas (author), de Ridder, A.C. (author) book chapter 2021
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de Lannoy, C.V. (author), Filius, M. (author), Kim, S.H. (author), Joo, C. (author), de Ridder, Dick (author)Förster resonance energy transfer (FRET) is a useful phenomenon in biomolecular investigations, as it can be leveraged for nanoscale measurements. The optical signals produced by such experiments can be analyzed by fitting a statistical model. Several software tools exist to fit such models in an unsupervised manner but lack the flexibility...journal article 2021
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de Lannoy, C.V. (author), Filius, M. (author), van Wee, R.G. (author), Joo, C. (author), de Ridder, Dick (author)Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and...journal article 2021
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Derks, Martijn F.L. (author), Groß, C. (author), Lopes, Marcos S. (author), Reinders, M.J.T. (author), Bosse, Mirte (author), Gjuvsland, Arne B. (author), de Ridder, Dick (author), Megens, Hendrik-Jan (author), Groenen, Martien A.M. (author)The genotype-phenotype link is a major research topic in the life sciences but remains highly complex to disentangle. Part of the complexity arises from the number of genes contributing to the observed phenotype. Despite the vast increase of molecular data, pinpointing the causal variant underlying a phenotype of interest is still challenging...journal article 2021
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de Ridder, M.P. (author), Smit, Pieter B. (author), van Dongeren, Ap R. (author), McCall, Robert T. (author), Nederhoff, Kees (author), Reniers, A.J.H.M. (author)A 2-layer non-hydrostatic model with improved dispersive behaviour is presented. Due to the assumption of a constant non-hydrostatic pressure distribution in the lower layer, the dispersive behaviour is improved without much additional computational time. A comparison with linear wave theory showed that this 2-layer model gives a better...journal article 2021
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Mei, Yanni (author), Li, Jie (author), de Ridder, H. (author), Cesar, Pablo (author)Cake customization services allow clients to collaboratively personalize cakes with pastry chefs. However, remote (e.g., email) and in-person co-design sessions are prone to miscommunication, due to natural restrictions in visualizing cake size, decoration, and celebration context. This paper presents the design, implementation, and expert...conference paper 2021
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Groß, C. (author), Derks, Martijn (author), Megens, Hendrik Jan (author), Bosse, Mirte (author), Groenen, Martien A.M. (author), Reinders, M.J.T. (author), de Ridder, D. (author)Background: In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by...journal article 2020
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Zhang, F. (author), de Ridder, H. (author), Barla, Pascal (author), Pont, S.C. (author)We previously presented a systematic optics-based canonical approach to test material-lighting interactions in their full natural ecology, combining canonical material and lighting modes. Analyzing the power of the spherical harmonics components of the lighting allowed us to predict the lighting effects on material perception for generic...journal article 2020