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Saputera, D. H. (author), Jakobsen, M. (author), van Dongen, K.W.A. (author), Jahani, N. (author), Eikrem, K. S. (author), Alyaev, S. (author)The deployment of electromagnetic (EM) induction tools while drilling is one of the standard routines for assisting the geosteering decision-making process. The conductivity distribution obtained through the inversion of the EM induction log can provide important information about the geological structure around the borehole. To image the 3-D...journal article 2024
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Karakaslar, E.O. (author), Severens, J.F. (author), Sánchez-López, Elena (author), van Veelen, Peter A. (author), Zlei, Mihaela (author), van Dongen, Jacques J.M. (author), Otte, Annemarie M. (author), Reinders, M.J.T. (author), van den Akker, E.B. (author)The diagnostic spectrum for AML patients is increasingly based on genetic abnormalities due to their prognostic and predictive value. However, information on the AML blast phenotype regarding their maturational arrest has started to regain importance due to its predictive power for drug responses. Here, we deconvolute 1350 bulk RNA-seq...journal article 2024
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Saputera, D.H. (author), Jakobsen, M. (author), Jahani, N. (author), Alyaev, S. (author), Eikrem, K.S. (author), van Dongen, K.W.A. (author)Real-time 3D imaging of the induction log is essential for improving the decision-making process in geosteering. To fulfill this need, we investigated various strategies for reducing the computational cost for 3D modelling of induction logs using the integral equation (IE) method, including the use of iterative Krylov solver, convolution with...conference paper 2023
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van der Neut, J.R. (author), Hoogerbrugge, L.A. (author), van Dongen, K.W.A. (author), Verschuur, D.J. (author)Full Wavefield Migration (FWMig) is an inversion-based seismic imaging modality that incorporates multiple reflections via one-way wave propagation. The flexible Full Wavefield Modelling (FWMod) engine that undergirds FWMig can be extended to address both compressional and converted waves. To take care of the angle-dependent nature of reflection...conference paper 2023
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Linders, D. G.J. (author), Deken, M. M. (author), van Dam, M. A. (author), Wasser, M. N.J.M. (author), Voormolen, E. M.C. (author), Kroep, J. R. (author), van Dongen, G. A.M.S. (author), Vugts, D. (author), de Geus-Oei, L.F. (author)Background: Approximately 20% of invasive ductal breast malignancies are human epidermal growth factor receptor 2 (HER2)-positive. These patients receive neoadjuvant systemic therapy (NAT) including HER2-targeting therapies. Up to 65% of patients achieve a pathological complete response (pCR). These patients might not have needed surgery....journal article 2023
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Jakobsen, Morten (author), Xiang, Kui (author), van Dongen, K.W.A. (author)We present an iterative nonlinear inverse scattering algorithm for high-resolution acoustic imaging of density and velocity variations. To solve the multi-parameter nonlinear direct scattering problem, the acoustic wave equation for inhomogeneous media in the frequency domain is transformed into a vectorial integral equation of the Lippmann...journal article 2023
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Zhao, Wenzhao (author), Fan, Yuling (author), Wang, Hongjian (author), Gemmeke, Hartmut (author), van Dongen, K.W.A. (author), Hopp, Torsten (author), Hesser, Jürgen (author)Objective. The image reconstruction of ultrasound computed tomography is computationally expensive with conventional iterative methods. The fully learned direct deep learning reconstruction is promising to speed up image reconstruction significantly. However, for direct reconstruction from measurement data, due to the lack of real labeled...journal article 2023
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Zhu, P. (author), Papadimitriou, V. (author), van Dongen, Jeanne E. (author), Cordeiro, Julia (author), Neeleman, Yannick (author), Santoso, A. (author), Chen, Shuyi (author), Eijkel, Jan C.T. (author), Rwei, A.Y. (author)Endotoxin is a deadly pyrogen, rendering it crucial to monitor with high accuracy and efficiency. However, current endotoxin detection relies on multistep processes that are labor-intensive, time-consuming, and unsustainable. Here, we report an aptamer-based biosensor for the real-time optical detection of endotoxin. The endotoxin sensor...journal article 2023
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Cordes, Martijn (author), Canté-Barrett, Kirsten (author), van den Akker, E.B. (author), Moretti, Federico A. (author), Kiełbasa, Szymon M. (author), Vloemans, Sandra A. (author), Garcia-Perez, Laura (author), Teodosio, Cristina (author), van Dongen, Jacques J.M. (author), Pike-Overzet, K. (author), Reinders, M.J.T. (author), Staal, F.J.T. (author)T cell development in the mouse thymus has been studied extensively, but less is known regarding T cell development in the human thymus. We used a combination of single-cell techniques and functional assays to perform deep immune profiling of human T cell development, focusing on the initial stages of prelineage commitment. We identified...journal article 2022
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Scherders, Eva M.L. (author), Verschuur, D.J. (author), van Dongen, K.W.A. (author)Imaging by inversion of acoustic or electromagnetic wave fields have applications in a wide variety of areas, such as non-destructive testing, biomedical applications, and geophysical exploration. Unfortunately, each modality suffers from its own application-specific limitations, typically being difficulties in distinguishing different...conference paper 2022
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Ramirez, Ana B. (author), Abreo, Sergio A. (author), van Dongen, K.W.A. (author)With full waveform inversion (FWI) all available information enclosed in the recorded wavefield - including multiple scattering, dispersion, and diffraction - is used to obtain accurate images showing quantitative information of the tissue parameters. These non-linear inversion methods are implemented either in the time or in the frequency...conference paper 2022
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Hoogerbrugge, L.A. (author), van Dongen, K.W.A. (author), Verschuur, D.J. (author)Conventional Full Wavefield Migration (FWM) is a full-wavefield inversion method based on recursively applying one-way convolutional propagation and reflection operators in the space-frequency domain at every depth level. Therefore, it struggles to model diving waves and image steep reflectors accurately. In this paper, the Interface Contrast...conference paper 2022
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Taskin, U. (author), Suzuki, Atsuro (author), Terada, Takahide (author), Tsubota, Yushi (author), van Dongen, K.W.A. (author)Quantitative images showing the speed of sound proffle of the breast may be obtained by employing full-waveform inversion (FWI) methods on the measured data. These reconstruction methods work well for both dense and normal breasts. Contrast source inversion (CSI) is a frequency domain FWI method. In literature, many examples of successful...conference paper 2022
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Dekker, J.J. (author), van Dongen, Jacques J.M. (author), Reinders, M.J.T. (author), Khatri, Indu (author)The IMGT database profiles the TR germline alleles for all four TR loci (TRA, TRB, TRG and TRD), however, it does not comprise of the information regarding population specificity and allelic frequencies of these germline alleles. The specificity of allelic variants to different human populations can, however, be a rich source of information...journal article 2022
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Khatri, I. (author), Diks, Annieck M. (author), van den Akker, E.B. (author), Oosten, Liesbeth E. M. (author), Zwaginga, Jaap Jan (author), Reinders, M.J.T. (author), van Dongen, Jacques J. M. (author), Berkowska, Magdalena A. (author)To mount an adequate immune response against pathogens, stepwise mutation and selection processes are crucial functions of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single-cell transcriptome as well as the B...journal article 2021
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Duque, Anouk F. (author), Bessa, Vânia S. (author), van Dongen, L.G.J.M. (author), de Kreuk, M.K. (author), Mesquita, Raquel B.R. (author), Rangel, António O.S.S. (author), van Loosdrecht, Mark C.M. (author), Castro, Paula M.L. (author)The presence of toxic compounds in wastewater can cause problems for organic matter and nutrient removal. In this study, the long-term effect of a model xenobiotic, 2-fluorophenol (2-FP), on ammonia-oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and phosphate accumulating organisms (PAO) in aerobic granular sludge was investigated...journal article 2021
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Khatri, I. (author), Berkowska, Magdalena A. (author), van den Akker, E.B. (author), Teodosio, Cristina (author), Reinders, M.J.T. (author), van Dongen, Jacques J. M. (author)Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be...journal article 2021
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- Khatri, Indu (author), Berkowska, Magdalena A. (author), van den Akker, E.B. (author), Teodosio, Cristina (author), Reinders, M.J.T. (author), van Dongen, Jacques J.M. (author) journal article 2021
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Wit, Renate F. (author), Lucassen, Desiree A. (author), Beulen, Yvette H. (author), Faessen, Janine P. M. (author), Bos-de Vos, M. (author), van Dongen, Johanna M. (author), Feskens, Edith J. M. (author), Wagemakers, Annemarie (author), Brouwer-Brolsma, Elske M. (author)Prenatal nutrition is a key predictor of early-life development. However, despite mass campaigns to stimulate healthy nutrition during pregnancy, the diet of Dutch pregnant women is often suboptimal. Innovative technologies offer an opportunity to develop tailored tools, which resulted in the release of various apps on healthy nutrition...journal article 2021
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Taskin, U. (author), van der Neut, J.R. (author), Gemmeke, Hartmut (author), van Dongen, K.W.A. (author)Whole breast ultrasound scanning systems are used to screen a women’s breast for suspicious lesions. Typically, the transducers are located at fixed positions at relatively large distances from the breast to avoid any contact with the breast. Unfortunately, these large distances give rise to large spatial domains to be imaged. These large...journal article 2020