Searched for: author:"Lelieveldt, B.P.F."
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Lähnemann, David (author), Köster, Johannes (author), Robinson, Mark D. (author), Vallejos, Catalina A. (author), Campbell, Kieran R. (author), Beerenwinkel, Niko (author), Pinello, Luca (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven...
review 2020
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Pezzotti, N. (author), Thijssen, J.G.L. (author), Mordvinstev, Alexander (author), Höllt, T. (author), Van Lew, B. (author), Lelieveldt, B.P.F. (author), Eisemann, E. (author), Vilanova Bartroli, A. (author)
In recent years the t-distributed Stochastic Neighbor Embedding (t-SNE) algorithm has become one of the most used and insightful techniques for exploratory data analysis of high-dimensional data. It reveals clusters of high-dimensional data points at different scales while only requiring minimal tuning of its parameters. However, the...
journal article 2020
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Keo, D.L. (author), Mahfouz, A.M.E.T.A. (author), Ingrassia, Angela M.T. (author), Meneboo, Jean Pascal (author), Villenet, Celine (author), Mutez, Eugénie (author), Comptdaer, Thomas (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)
The molecular mechanisms underlying caudal-to-rostral progression of Lewy body pathology in Parkinson’s disease remain poorly understood. Here, we identified transcriptomic signatures across brain regions involved in Braak Lewy body stages in non-neurological adults from the Allen Human Brain Atlas. Among the genes that are indicative of...
journal article 2020
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Shahzad, Rahil (author), Shankar, Arun (author), Amier, Raquel (author), Nijveldt, Robin (author), Westenberg, Jos J.M. (author), de Roos, Albert (author), Lelieveldt, B.P.F. (author), van der Geest, R.J. (author)
Background: Aortic pulse wave velocity (PWV) is an indicator of aortic stiffness and is used as a predictor of adverse cardiovascular events. PWV can be non-invasively assessed using magnetic resonance imaging (MRI). PWV computation requires two components, the length of the aortic arch and the time taken for the systolic pressure wave to...
journal article 2019
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Suwandi, Jessica S. (author), Laban, Sandra (author), Vass, Kincsὅ (author), Joosten, Antoinette (author), van Unen, Vincent (author), Lelieveldt, B.P.F. (author), Höllt, T. (author), Zwaginga, Jaap Jan (author), Nikolic, Tatjana (author), Roep, Bart O. (author)
Induction of antigen-specific regulatory T cells (Tregs) in vivo is the holy grail of current immune-regulating therapies in autoimmune diseases, such as type 1 diabetes. Tolerogenic dendritic cells (tolDCs) generated from monocytes by a combined treatment with vitamin D and dexamethasone (marked by CD52<sup>hi</sup> and CD86<sup>lo</sup>...
journal article 2019
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Qiao, Yuchuan (author), Jagt, Thyrza (author), Hoogeman, M.S. (author), Lelieveldt, B.P.F. (author), Staring, M. (author)
Objective: Our goal was to investigate the performance of an open source deformable image registration package, elastix, for fast and robust contour propagation in the context of online-adaptive intensity-modulated proton therapy (IMPT) for prostate cancer. Methods: A planning and 7–10 repeat CT scans were available of 18 prostate cancer...
journal article 2019
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Li, Na (author), van Unen, Vincent (author), Guo, Nannan (author), Abdelaal, T.R.M. (author), Somarakis, Antonios (author), Eggermont, Jeroen (author), Mahfouz, Ahmed (author), Chuva de Sousa Lopes, Susana M. (author), Lelieveldt, B.P.F. (author), Koning, Frits (author)
The human fetal immune system must protect the infant against the sudden exposure to a large variety of pathogens upon birth. While it is known that the fetal immune system develops in sequential waves, relatively little is known about the composition of the innate and adaptive immune system in the tissues. Here, we applied high-dimensional...
journal article 2019
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de Vries, N.L. (author), Van Unen, Vincent (author), Ijsselsteijn, Marieke E. (author), Abdelaal, T.R.M. (author), Van Der Breggen, Ruud (author), Farina Sarasqueta, Arantza (author), Mahfouz, A.M.E.T.A. (author), Peeters, Koen C.M.J. (author), Höllt, T. (author), Lelieveldt, B.P.F. (author), Koning, Frits (author), De Miranda, Noel F.C.C. (author)
Objective: A comprehensive understanding of anticancer immune responses is paramount for the optimal application and development of cancer immunotherapies. We unravelled local and systemic immune profiles in patients with colorectal cancer (CRC) by high-dimensional analysis to provide an unbiased characterisation of the immune contexture of...
journal article 2019
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Höllt, T. (author), Vilanova Bartroli, A. (author), Pezzotti, N. (author), Lelieveldt, B.P.F. (author), Hauser, H. (author)
Hierarchical embeddings, such as HSNE, address critical visual and computational scalability issues of traditional techniques for dimensionality reduction. The improved scalability comes at the cost of the need for increased user interaction for exploration. In this paper, we provide a solution for the interactive visual Focus+Context...
journal article 2019
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Abdelaal, T.R.M. (author), Höllt, T. (author), van Unen, Vincent (author), Lelieveldt, B.P.F. (author), Koning, Frits (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)
Motivation: High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single-cell level, providing a comprehensive view of cell compositions.<br/>However, the power of CyTOF to explore the full heterogeneity of a biological sample at the singlecell level is currently limited by the number of...
journal article 2019
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Liu, Shengnan (author), Dzyubachyk, Oleh (author), Eggermont, Jeroen (author), Nakatani, Shimpei (author), Lelieveldt, B.P.F. (author), Dijkstra, Jouke (author)
Purpose: Intravascular optical coherence tomography (OCT) is widely used for analysis of the coronary artery disease. Its high spatial resolution allows for visualization of arterial tissue components in detail. There are different OCT systems on the market, each of which produces data characterized by its own intensity range and distribution...
journal article 2018
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Aizenberg, Evgeni (author), Roex, Edgar A.H. (author), Nieuwenhuis, Wouter P. (author), Mangnus, Lukas (author), van der Helm-Mil, Annette H.M. (author), Reijnierse, Monique (author), Bloem, Johan L. (author), Lelieveldt, B.P.F. (author), Stoel, Berend G. (author)
Purpose: To investigate the feasibility of automatic quantification of bone marrow edema (BME) on MRI of the wrist in patients with early arthritis. <br clear="none"/>Methods: For 485 early arthritis patients (clinically confirmed arthritis of one or more joints, symptoms for less than 2 years), MR scans of the wrist were processed in three...
journal article 2018
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Abdelmoula, Walid M. (author), Pezzotti, N. (author), Höllt, T. (author), Dijkstra, Jouke (author), Vilanova Bartroli, A. (author), McDonnell, Liam A. (author), Lelieveldt, B.P.F. (author)
Technological advances in mass spectrometry imaging (MSI) have contributed to growing interest in 3D MSI. However, the large size of 3D MSI data sets has made their efficient analysis and visualization and the identification of informative molecular patterns computationally challenging. Hierarchical stochastic neighbor embedding (HSNE), a...
journal article 2018
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Laban, Sandra (author), Suwandi, Jessica S. (author), van Unen, Vincent (author), Pool, Jos (author), Wesselius, Joris (author), Höllt, T. (author), Pezzotti, N. (author), Vilanova Bartroli, A. (author), Lelieveldt, B.P.F. (author), Roep, Bart O. (author)
Auto-reactive CD8 T-cells play an important role in the destruction of pancreatic β-cells resulting in type 1 diabetes (T1D). However, the phenotype of these auto-reactive cytolytic CD8 T-cells has not yet been extensively described. We used high-dimensional mass cytometry to phenotype autoantigen- (pre-proinsulin), neoantigen- (insulin-DRIP)...
journal article 2018
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Li, Na (author), van Unen, Vincent (author), Höllt, T. (author), Thompson, Allan (author), van Bergen, Jeroen (author), Pezzotti, N. (author), Eisemann, E. (author), Vilanova Bartroli, A. (author), Chuva de Sousa Lopes, S.M. (author), Lelieveldt, B.P.F. (author), Koning, Frits (author)
Innate lymphoid cells (ILCs) are abundant in mucosal tissues and involved in tissue homeostasis and barrier function. Although several ILC subsets have been identified, it is unknown if additional heterogeneity exists, and their differentiation pathways remain largely unclear. We applied mass cytometry to analyze ILCs in the human fetal...
journal article 2018
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Sun, Zhuo (author), Qiao, Yuchuan (author), Lelieveldt, B.P.F. (author), Staring, M. (author)
In recent years, machine learning approaches have been successfully applied to the field of neuroimaging for classification and regression tasks. However, many approaches do not give an intuitive relation between the raw features and the diagnosis. Therefore, they are difficult for clinicians to interpret. Moreover, most approaches treat the...
journal article 2018
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Pezzotti, N. (author), Höllt, T. (author), van Gemert, J.C. (author), Lelieveldt, B.P.F. (author), Eisemann, E. (author), Vilanova Bartroli, A. (author)
Deep neural networks are now rivaling human accuracy in several pattern recognition problems. Compared to traditional classifiers, where features are handcrafted, neural networks learn increasingly complex features directly from the data. Instead of handcrafting the features, it is now the network architecture that is manually engineered. The...
journal article 2018
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Liu, Shengnan (author), Sotomi, Yohei (author), Eggermont, Jeroen (author), Nakazawa, Gaku (author), Torii, Sho (author), Ijichi, Takeshi (author), Onuma, Yoshinobu (author), Serruys, Patrick W. (author), Lelieveldt, B.P.F. (author), Dijkstra, J. (author)
An important application of intravascular optical coherence tomography (IVOCT) for atherosclerotic tissue analysis is using it to estimate attenuation and backscatter coefficients. This work aims at exploring the potential of the attenuation coefficient, a proposed backscatter term, and image intensities in distinguishing different...
journal article 2017
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Dzyubachyk, Oleh (author), Staring, M. (author), Reijnierse, Monique (author), Lelieveldt, B.P.F. (author), van der Geest, Rob J. (author)
Purpose To develop and validate a method for performing inter-station intensity standardization in multispectral whole-body MR data. Methods Different approaches for mapping the intensity of each acquired image stack into the reference intensity space were developed and validated. The registration strategies included: “direct” registration to...
journal article 2017
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Keo, D.L. (author), Aziz, N. Ahmad (author), Dzyubachyk, Oleh (author), Van Der Grond, Jeroen (author), van Roon-Mom, Willeke M.C. (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)
Cytosine-adenine-guanine (CAG) repeat expansions in the coding regions of nine polyglutamine (polyQ) genes (HTT, ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATN1, AR, and TBP) are the cause of several neurodegenerative diseases including Huntington’s disease (HD), six different spinocerebellar ataxias (SCAs), dentatorubral-pallidoluysian atrophy, and...
journal article 2017
Searched for: author:"Lelieveldt, B.P.F."
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