Searched for: author%3A%22Van+de+Plas%2C+Raf%22
(1 - 16 of 16)
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Gisch, Debora L. (author), Brennan, Michelle (author), Lake, Blue B. (author), Basta, Jeannine (author), Keller, Mark S. (author), P. Gonçalves, Joana (author), Migas, L.G. (author), Van de Plas, Raf (author), Lardenoije, R. (author)
There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a...
journal article 2024
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Bajaj, V. (author), Van de Plas, Raf (author), Wahls, S. (author)
While probabilistic constellation shaping (PCS) enables rate and reach adaption with finer granularity [1] (Cho and Winzer, 2009), it imposes signal processing challenges at the receiver. Since the distribution of PCS-quadrature amplitude modulation (QAM) signals tends to be Gaussian, conventional blind polarization demultiplexing algorithms...
journal article 2024
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Sharman, Kavya (author), Patterson, Nathan Heath (author), Weiss, Andy (author), Neumann, Elizabeth K. (author), Guiberson, Emma R. (author), Ryan, Daniel J. (author), Gutierrez, Danielle B. (author), Spraggins, Jeffrey M. (author), Van de Plas, Raf (author), Skaar, Eric P. (author), Caprioli, Richard M. (author)
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate...
journal article 2023
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Djambazova, Katerina V. (author), Dufresne, Martin (author), Migas, L.G. (author), Kruse, Angela R.S. (author), Van de Plas, Raf (author), Caprioli, Richard M. (author), Spraggins, Jeffrey M. (author)
Gangliosides are acidic glycosphingolipids, containing ceramide moieties and oligosaccharide chains with one or more sialic acid residue(s) and are highly diverse isomeric structures with distinct biological roles. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables the untargeted spatial analysis of...
journal article 2023
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Sharman, Kavya (author), Patterson, Nathan Heath (author), Migas, L.G. (author), Neumann, Elizabeth K. (author), Allen, Jamie (author), Gibson-Corley, Katherine N. (author), Spraggins, Jeffrey M. (author), Van de Plas, Raf (author), Skaar, Eric P. (author), Caprioli, Richard M. (author)
Imaging mass spectrometry (IMS) provides untargeted, highly multiplexed maps of molecular distributions in tissue. Ion images are routinely presented as heatmaps and can be overlaid onto complementary microscopy images that provide greater context. However, heatmaps use transparency blending to visualize both images, obscuring subtle...
journal article 2023
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Esselman, Allison B. (author), Patterson, Nathan Heath (author), Migas, L.G. (author), Dufresne, Martin (author), Djambazova, Katerina V. (author), Colley, Madeline E. (author), Van de Plas, Raf (author), Spraggins, Jeffrey M. (author)
The glomerulus is a multicellular functional tissue unit (FTU) of the nephron that is responsible for blood filtration. Each glomerulus contains multiple substructures and cell types that are crucial for their function. To understand normal aging and disease in kidneys, methods for high spatial resolution molecular imaging within these FTUs...
journal article 2023
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de Almeida Nieto, L.M. (author), Gabrieli, Francesca (author), van Loon, A. (author), Gonzalez, Victor (author), Dik, J. (author), Van de Plas, Raf (author), Alfeld, M.W.E.M. (author)
Macroscopic x-ray fluorescence imaging spectroscopy (MA-XRF) and reflectance imaging spectroscopy (RIS) are important tools in the analysis of cultural heritage objects, both for conservation and art historical research purposes. The elemental and molecular distributions provided by MA-XRF and RIS respectively, are particularly useful for the...
journal article 2023
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Jain, Sanjay (author), Pei, Liming (author), Spraggins, Jeffrey M. (author), Angelo, Michael (author), Carson, James P. (author), Gehlenborg, Niels (author), Ginty, Fiona (author), P. Gonçalves, Joana (author), Van de Plas, Raf (author)
The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the...
journal article 2023
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Anderson, David M G (author), Kotnala, Ankita (author), Migas, L.G. (author), Patterson, N. Heath (author), Tideman, L.E.M. (author), Ach, Thomas (author), Tortorella, Sara (author), Van de Plas, Raf (author), Curcio, Christine A. (author), Schey, Kevin L. (author)
Introduction: Age related macular degeneration (AMD) causes legal blindness worldwide, with few therapeutic targets in early disease and no treatments for 80% of cases. Extracellular deposits, including drusen and subretinal drusenoid deposits (SDD; also called reticular pseudodrusen), disrupt cone and rod photoreceptor functions and strongly...
journal article 2023
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Perry, William J. (author), Grunenwald, Caroline M. (author), Van de Plas, Raf (author), Witten, James C. (author), Martin, Daniel R. (author), Apte, Suneel S. (author), Cassat, James E. (author), Pettersson, Gösta B. (author), Caprioli, Richard M. (author), Skaar, Eric P. (author), Spraggins, Jeffrey M. (author)
Bacterial pathogens have evolved virulence factors to colonize, replicate, and disseminate within the vertebrate host. Although there is an expanding body of literature describing how bacterial pathogens regulate their virulence repertoire in response to environmental signals, it is challenging to directly visualize virulence response within...
journal article 2022
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Rivera, Emilio S. (author), Weiss, Andy (author), Migas, L.G. (author), Freiberg, Jeffrey A. (author), Djambazova, Katerina V. (author), Neumann, Elizabeth K. (author), Van de Plas, Raf (author), Spraggins, Jeffrey M. (author), Skaar, Eric P. (author), Caprioli, Richard M. (author)
Introduction: Although Staphylococcus aureus is the leading cause of biofilm-related infections, the lipidomic distributions within these biofilms is poorly understood. Here, lipidomic mapping of S. aureus biofilm cross-sections was performed to investigate heterogeneity between horizontal biofilm layers. Methods: S. aureus biofilms were...
journal article 2022
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Bajaj, V. (author), Van de Plas, Raf (author), Aref, Vahid (author), Wahls, S. (author)
We propose a novel method for blind polarization-demultiplexing of probabilistically shaped signals for coherent receivers. The method is capable of separating signals with (quasi) Gaussian distributions by exploiting temporal correlations added to the transmit signals. The proposed method is evaluated in challenging mixing scenarios.
conference paper 2022
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Neumann, Elizabeth K. (author), Patterson, Nathan Heath (author), Allen, Jamie L. (author), Migas, L.G. (author), Yang, Haichun (author), Brewer, Maya (author), Anderson, David M. (author), Harvey, Jennifer (author), Harris, Raymond C. (author), Van de Plas, Raf (author)
Here, we describe the preservation and preparation of human kidney tissue for interrogation by histopathology, imaging mass spectrometry, and multiplexed immunofluorescence. Custom image registration and integration techniques are used to create cellular and molecular atlases of this organ system. Through careful optimization, we ensure high...
journal article 2021
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Tideman, L.E.M. (author), Migas, L.G. (author), Djambazova, Katerina V. (author), Patterson, Nathan Heath (author), Caprioli, Richard M. (author), Spraggins, Jeffrey M. (author), Van de Plas, Raf (author)
The search for molecular species that are differentially expressed between biological states is an important step towards discovering promising biomarker candidates. In imaging mass spectrometry (IMS), performing this search manually is often impractical due to the large size and high-dimensionality of IMS datasets. Instead, we propose an...
journal article 2021
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Verbeeck, N. (author), Caprioli, Richard M. (author), Van de Plas, Raf (author)
Imaging mass spectrometry (IMS) is a rapidly advancing molecular imaging modality that can map the spatial distribution of molecules with high chemical specificity. IMS does not require prior tagging of molecular targets and is able to measure a large number of ions concurrently in a single experiment. While this makes it particularly suited...
review 2019
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Marien, Eyra (author), Meister, Michael (author), Muley, Thomas (author), del Pulgar, Teresa Gomez (author), Derua, Rita (author), Spraggins, Jeffrey M. (author), Van de Plas, Raf (author), Vanderhoydonc, Frank (author), Machiels, Jelle (author), Binda, Maria Mercedes (author), Dehairs, Jonas (author), Willette-Brown, Jami (author), Hu, Yinling (author), Dienemann, Hendrik (author), Thomas, Michael (author), Schnabe, Philipp A. (author), Caprioli, Richard M. (author), Lacal, Juan Carlos (author), Waelkens, Etienne (author), Swinnen, Johannes V. (author)
Lung cancer is the leading cause of cancer death. Beyond first line treatment, few therapeutic options are available, particularly for squamous cell carcinoma (SCC). Here, we have explored the phospholipidomes of 30 human SCCs and found that they almost invariably (in 96.7% of cases) contain phospholipids with longer acyl chains compared to...
journal article 2016
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