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UMC Repository: Recent submissions

  • Absolute measurement of fast and slow neuronal signals with fluorescence lifetime photometry at high temporal resolution 
    Lodder, Bart; Kamath, Tarun; Savenco, Ecaterina; Röring, Berend; Siegel, Michelle; Chouinard, Julie; Lee, Suk Joon; Zagoren, Caroline; Rosen, Paul; Adan, Roger; Tian, Lin; Sabatini, Bernardo L (BioRxiv, 2025-01-12)
    The concentrations of extracellular and intracellular signaling molecules, such as dopamine and cAMP, change over both fast and slow timescales and impact downstream pathways in a cell-type specific manner. Fluorescence ...
  • The relationship of white matter tract orientation to vascular geometry in the human brain 
    Schilling, Kurt G; Newton, Allen; Tax, Chantal M W; Chamberland, Maxime; Remedios, Samuel W; Gao, Yurui; Li, Muwei; Chang, Catie; Rheault, Francois; Sepherband, Farshid; Anderson, Adam; Gore, John C; Landman, Bennett (BioRxiv, 2025-03-06)
    The white matter of the human brain exhibits highly ordered anisotropic structures of both axonal nerve fibers and cerebral vasculature. Separately, the anisotropic nature of white matter axons and white matter vasculature ...
  • Disturbed Flow Induces Reprogramming of Endothelial Cells to Immune-like and Foam Cells under Hypercholesterolemia during Atherogenesis 
    Park, Christian; Baek, Kyung In; Hung, Ruei-Chun; Choi, Leandro; Jeong, Kiyoung; Kim, Paul; Jahng, Andrew Keunho; Kim, Jung Hyun; Meselhe, Mostafa; Kannan, Ashwin; Chou, Chien-Ling; Kang, Dong Won; Song, Eun Ju; Kim, Yerin; Bowman-Kirigin, Jay Aaron; Clark, Michael David; van der Laan, Sander W; Pasterkamp, Gerard; Villa-Roel, Nicolas; Panitch, Alyssa; Jo, Hanjoong (BioRxiv, 2025-03-06)
    BACKGROUND: Atherosclerosis occurs preferentially in the arteries exposed to disturbed flow (d-flow), while the stable flow (s-flow) regions are protected even under hypercholesterolemic conditions. We recently showed that ...
  • Intraplaque haemorrhage quantification and molecular characterisation using attention based multiple instance learning 
    Cisternino, Francesco; Song, Yipei; Peters, Tim S; Westerman, Roderick; de Borst, Gert J; Diez Benavente, Ernest; van den Dungen, Noortje A M; van der Kraak, Petra H; De Kleijn, Dominique; Mekke, Joost M; Mokry, Michal; Pasterkamp, Gerard; den Ruijter, Hester M; Velema, Evelyn; Miller, Clint L; Glastonbury, Craig A; van der Laan, Sander W (medRxiv, 2025-03-07)
    Intraplaque haemorrhage (IPH) represents a critical feature of plaque vulnerability as it is robustly associated with adverse cardiovascular events, including stroke and myocardial infarction. How IPH drives plaque instability ...
  • Human colon stem cells are the principal epithelial responders to bacterial antigens 
    de Vries, Maaike Hillegonda; Meddens, Claartje; Hijma, Hemme; Berrens, Anne-Claire; Jansen, Suze; Kooiman, Berend; Snapper, Scott; Clevers, Hans; Mokry, Michal; Kuijk, Ewart; Nieuwenhuis, Edward (BioRxiv, 2025-02-08)
    Intestinal epithelial cells (IECs) are capable of mounting an adequate antimicrobial inflammatory response to pathogens while tolerating commensals. The underlying regulatory mechanisms of immune sensitivity remain ...
  • A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer 
    Wassenaar, Emma Ce; Gorelick, Alexander N; Hung, Wei-Ting; Cheek, David M; Kucukkose, Emre; Lee, I-Hsiu; Blohmer, Martin; Degner, Sebastian; Giunta, Peter; Wiezer, Rene Mj; Raicu, Mihaela G; Ubink, Inge; Klaasen, Sjoerd J; Lansu, Nico; Watson, Emma V; Corcoran, Ryan B; Boland, Genevieve; Getz, Gad; Kops, Geert Jpl; Juric, Dejan; Lennerz, Jochen K; Boerma, Djamila; Kranenburg, Onno; Naxerova, Kamila (BioRxiv, 2024-09-27)
    Whether metastasis in humans can be accomplished by most primary tumor cells or requires the evolution of a specialized trait remains an open question. To evaluate whether metastases are founded by non-random subsets of ...
  • Learning immune receptor representations with protein language models 
    Dounas, Andreas; Cotet, Tudor Stefan; Yermanos, Alexander (ArXiv, 2024-02-06)
    Protein language models (PLMs) learn contextual representations from protein sequences and are profoundly impacting various scientific disciplines spanning protein design, drug discovery, and structural predictions. One ...
  • Clonally expanded IgG antibody-secreting cells preferentially target influenza nucleoprotein following homologous and heterologous infections 
    Kuhn, Raphael; Panetti, Camilla; Venerito, Marco; Phandee, Hathaichanok; Stalder, Lucas; Shlesinger, Danielle; D'Arcy, Vittoria Martinolli; Hong, Kai Lin; van Ginneken, Daphne; Genovese, Alessandro; Joller, Nicole; Oxenius, Annette; Reddy, Sai T.; Yermanos, Alexander (BioRxiv, 2024-12-11)
    Infection with influenza virus remains a significant global health concern due to its ability to acquire mutations at key antigenic sites to escape antibody recognition. While germinal center (GC) and memory B cells have ...
  • Protein language model pseudolikelihoods capture features of in vivo B cell selection and evolution 
    van Ginneken, Daphne; Samant, Anamay; Daga-Krumins, Karlis; Agrafiotis, Andreas; Kladis, Evgenios; Reddy, Sai T.; Yermanos, Alexander (BioRxiv, 2024-12-11)
    B cell selection and evolution play crucial roles in dictating successful immune responses. Recent advancements in sequencing technologies and deep-learning strategies have paved the way for generating and exploiting an ...
  • Do Not Lose Sleep Over It: Implanted Brain-computer Interface Functionality During Nighttime in Late-stage Amyotrophic Lateral Sclerosis 
    Leinders, Sacha; Aarnoutse, Erik J; Branco, Mariana P; Freudenburg, Zac V; Geukes, Simon H; Schippers, Anouck; Verberne, Malinda S W; van den Boom, Max; van der Vijgh, Benny; Crone, Nathan E; Denison, Timothy; Ramsey, Nick F; Vansteensel, Mariska J (medRxivCold Spring Harbor Laboratory Press, 2024-10-15)
    BACKGROUND AND OBJECTIVES: Brain-computer interfaces ( BCIs) hold promise as augmentative and alternative communication technology for people with severe motor and speech impairment (locked-in syndrome) due to neural disease ...
  • Novel hepatocyte-like liver organoids recapitulate crucial mature hepatic functions 
    Ardisasmita, Ibrahim; Joore, Indi; Levy, Natacha; Myszczyszyn, A.; Marsee, Ary; Sinnige, Theo; Ruiter, J.; Ferdinandusse, Sacha; Dudaryeva, Oksana; Gruber, E.; Daive, V.; Levato, Riccardo; Spee, Bart; Verstegen, Monique Ma; van der Laan, L.J.W.; Nieuwenhuis , E.E.S.; Schene, Imre; Fuchs, Sabine (BioRxiv, 2024-10-29)
    Accurate liver disease modeling and drug toxicity testing still remain challenging as liver cells in vitro poorly resemble adult hepatocytes, as we previously demonstrated using whole transcriptome and cell identity analysis. ...
  • Adaptation of ACMG/AMP guidelines for clinical classification of BMPR2 variants in Pulmonary Arterial Hypertension resolves variants of unclear pathogenicity in ClinVar 
    Eichstaedt, Christina A; Maldonado-Velez, Gabriel; Machado, Rajiv D; Balachandar, Srimmitha; Coulet, Florence; Day, Kristina; Dooijes, Dennis; Eyries, Melanie; Gräf, Stefan; Macaya, Daniela; Shaukat, Memoona; Southgate, Laura; Tenorio-Castano, Jair; Chung, Wendy K; Welch, Carrie L; Aldred, Micheala A (medRxiv, 2024-11-26)
    PURPOSE: Pulmonary arterial hypertension (PAH) is a rare disease that can be caused by pathogenic variants, most frequently in the bone morphogenetic protein receptor type 2 ( BMPR2 ) gene. We formed a ClinGen variant ...
  • Independent and joint effects of genomic and exposomic loads for schizophrenia on distressing and persisting psychotic experiences in adolescence 
    Vincenzo, Matteo Di; Prachason, Thanavadee; Sampogna, Gaia; Arias-Magnasco, Angelo; Danae Lin, Bochao; Pries, Lotta-Katrin; van Os, Jim; Rutten, Bart P F; Barzilay, Ran; Fiorillo, Andrea; Guloksuz, Sinan (medRxiv, 2024-11-11)
    To assess the longitudinal associations of genomic and exposomic liabilities for schizophrenia, both independently and jointly, with distressing psychotic experiences (PEs) and their persistence in early adolescence. The ...
  • Genomic analysis of intracranial and subcortical brain volumes yields polygenic scores accounting for variation across ancestries 
    García-Marín, Luis M; Campos, Adrian I; Diaz-Torres, Santiago; Rabinowitz, Jill A; Ceja, Zuriel; Mitchell, Brittany L; Grasby, Katrina L; Thorp, Jackson G; Agartz, Ingrid; Alhusaini, Saud; Ames, David; Amouyel, Philippe; Andreassen, Ole A; Arfanakis, Konstantinos; Vasquez, Alejandro Arias; Armstrong, Nicola J; Athanasiu, Lavinia; Bastin, Mark E; Beiser, Alexa S; Bennett, David A; Bis, Joshua C; Boks, Marco Pm; Boomsma, Dorret I; Brodaty, Henry; Brouwer, Rachel M; Buitelaar, Jan K; Burkhardt, Ralph; Cahn, Wiepke; Calhoun, Vince D; Carmichael, Owen T; Chakravarty, Mallar; Chen, Qiang; Ching, Christopher R K; Cichon, Sven; Crespo-Facorro, Benedicto; Crivello, Fabrice; Dale, Anders M; Smith, George Davey; de Geus, Eco Jc; De Jager, Philip L; de Zubicaray, Greig I; Debette, Stéphanie; DeCarli, Charles; Depondt, Chantal; Desrivières, Sylvane; Ikram, M Kamran; Kahn, Rene S; Klein, Marieke; Shen, Li; Weinberger, Daniel R; Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands (GJB, GJER) (medRxivCold Spring Harbor Laboratory Press, 2024-08-15)
    Subcortical brain structures are involved in developmental, psychiatric and neurological disorders. We performed GWAS meta-analyses of intracranial and nine subcortical brain volumes (brainstem, caudate nucleus, putamen, ...
  • Entrustable professional activities and entrustment decision-making in health professions education 
    ten Cate, Olle; Burch, Vanessa C.; Chen, H. Carrie; Chou, Fremen Chihchen; Hennus, Marije P. (Ubiquity Press, 2024-10-29)
    This book discusses the ins and outs of a new approach to competency-based education in the education and training of health professionals, including doctors and medical specialists, but also nurses, dentists, pharmacists, ...
  • Midwifery and Sexuality 
    Geuens, Sam; Mivšek, Ana Polona; Gianotten, Woet L. (Springer International Publishing, 2023-01-01)
    This first open-access book on midwifery and sexuality integrates sexual health into the care for the pregnant and postpartum couple. It addresses sexuality and intimacy from an education and prevention perspective instead ...
  • Clinical Cardiogenetics: Third Edition 
    Baars, Hubert F.; Doevendans, Pieter A.F.M.; Houweling, Arjan C.; van Tintelen, J. Peter (Springer, 2020-01-01)
    This thoroughly revised third edition provides a comprehensive grounding on hereditary heart diseases with special emphasis on the genetic aspects of these conditions. It continues to provide the expertise that all ...
  • Amortized Normalizing Flows for Transcranial Ultrasound with Uncertainty Quantification 
    Orozco, Rafael; Louboutin, Mathias; Siahkoohi, Ali; Rizzuti, Gabrio; van Leeuwen, Tristan; Herrmann, Felix (2023)
    We present a novel approach to transcranial ultrasound computed tomography that utilizes normalizing flows to improve the speed of imaging and provide Bayesian uncertainty quantification. Our method combines physics-informed ...
  • How Consistent are Speech-Based Biomarkers in Remote Tracking of ALS Disease Progression Across Languages? A Case Study of English and Dutch 
    Kothare, Hardik; Neumann, Michael; Zhang, Cathy; Liscombe, Jackson; van Unnik, Jordi W.J.; Botman, Lianne C.M.; van den Berg, Leonard H.; van Eijk, Ruben P.A.; Ramanarayanan, Vikram (2024)
    Previous work has demonstrated the utility of speech-based digital biomarkers for remotely tracking longitudinal progression in people with Amyotrophic Lateral Sclerosis (pALS). Here, we investigate the responsiveness of ...
  • Dynamic modulation of the motor neuron translatome during developmental synapse elimination 
    van der Hoorn, Dinja; Lauria, Fabio; Chaytow, Helena; Faller, Kiterie M E; Huang, Yu-Ting; Kline, Rachel A; Signoria, Ilaria; Morris, Kim; Wishart, Thomas M; Groen, Ewout J N; Viero, Gabriella; Gillingwater, Thomas H (American Association for the Advancement of Science, 2025-04-15)
    The developmental sculpting of neuromuscular circuitry in early postnatal life occurs through the process of synapse elimination: Supernumerary axon inputs are gradually eliminated from the neuromuscular junction (NMJ), ...