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UMC Repository: Recent submissions

  • Supporting reuse of EHR data in healthcare organizations: The CARED research infrastructure framework 
    Menger, Vincent; Spruit, Marco; De Bruin, Jonathan; Kelder, Thomas; Scheepers, Floor (SciTePress, 2019-01-01)
    Healthcare organizations have in recent years started assembling their Electronic Health Record (EHR) data in data repositories to unlock their value using data analysis techniques. There are however a number of technical, ...
  • Cardiovascular Sequels During and After Preeclampsia 
    Paauw, Nina D; Lely, A Titia (Springer, 2018-07-28)
    Preeclampsia is a pregnancy-specific disorder complicating 2%-8% of pregnancies worldwide and characterized by de novo development of hypertension and proteinuria. Current understanding of the pathophysiology of preeclampsia ...
  • Registration of brain CT images to an MRI template for the purpose of lesion-symptom mapping 
    Kuijf, Hugo J.; Biesbroek, J. Matthijs; Viergever, Max A.; Biessels, Geert Jan; Vincken, Koen L. (2013-09-05)
    Lesion-symptom mapping is a valuable tool for exploring the relation between brain structure and function. In order to perform lesion-symptom mapping, lesion delineations made on different brain CT images need to be ...
  • Hemorrhagic lesions of the central nervous system 
    de Vries, LS (Cambridge University Press, 2017-12-21)
  • The added value of diffusion tensor imaging for automated white matter hyperintensity segmentation 
    Kuijf, Hugo J.; Tax, Chantal M W; Zaanen, L. Karlijn; Bouvy, Willem H.; de Bresser, Jeroen; Leemans, Alexander; Viergever, Max A.; Biessels, Geert Jan; Vincken, Koen L. (Springer Berlin Heidelberg, 2014)
    Automatedwhite matter hyperintensity (WMH) segmentation techniques for brain MRI often employ voxel-wise classifiers, trained on traditional features such as: multi-spectral MR image intensities, spatial location, texture, ...
  • IFNγ induces epithelial reprogramming driving CXCL11-mediated T cell migration 
    Cutilli, Alessandro; Jansen, Suze A; Paolucci, Francesca; Mokry, Michal; Mocholi, Enric; Lindemans, Caroline A; Coffer, Paul J (BioRxivCold Spring Harbor Laboratory Press, 2024-02-07)
    The cytokine interferon-gamma (IFNγ) plays a multifaceted role in intestinal immune responses ranging from anti-to pro-inflammatory depending on the setting. Here, using a 3D co-culture system based on human intestinal ...
  • Design of the EPIGENEC Study: Assessing the EPIdemiology and GENetics of Escherichia coli in the Netherlands 
    van Hout, Denise; Verschuuren, Tess; Bruijning-Verhagen, P.; Bosch, Thijs; Reuland, Ascelijn; Fluit, AC; Schürch, Anita; Willems, Rob; de Greeff, Sabine C; van 't Veen, A.; Kluijtmans, Jan; Bonten, Marc (2019-02-07)
    Background: Infections caused by E. coli cause considerable disease burden and range from frequently occurring and relatively innocent urinary tract infection (UTI) to severe bloodstream infection (BSI). The incidence of ...
  • Microvascular Specificity of Spin Echo BOLD fMRI: Impact of EPI Echo Train Length 
    van Horen, Tanya; Siero, J C W; Bhogal, A A; Petridou, N; Báez-Yáñez, M G (BioRxivCold Spring Harbor Laboratory Press, 2023-09-15)
    A spatially specific fMRI acquisition requires specificity to the microvasculature that serves active neuronal sites. Macrovascular contributions will reduce the microvascular specificity but can be reduced by using spin ...
  • Lack of association between HLA and asymptomatic SARS-CoV-2 infection 
    COVID Human Genetic Effort (BMJCold Spring Harbor Laboratory Press, 2023-12-08)
    Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B*15:01 allele and ...
  • Pathogenic variants in SMARCA1 cause an X-linked neurodevelopmental disorder modulated by NURF complex composition 
    Picketts, David; Mirzaa, Ghayda; Yan, Keqin; Relator, Raissa; Timpano, Sara; Yalcin, Binnaz; Collins, Stephan; Ziegler, Alban; Pao, Emily; Oyama, Nora; Brischoux-Boucher, Elise; Piard, Juliette; Monaghan, Kristin; Sacoto, Maria Guillen; Dobyns, William; Park, Kristen; Fernández-Mayoralas, Daniel; Fernández-Jaén, Alberto; Jayakar, Parul; Brusco, Alfredo; Antona, Vincenzo; Giorgio, Elisa; Kvarnung, Malin; Isidor, Bertrand; Conrad, Solène; Cogné, Benjamin; Deb, Wallid; Stuurman, K E; Sterbova, Katalin; Smal, Noor; Weckhuysen, Sarah; Oegema, Renske; Innes, Micheil; Latsko, Maeson; Ben-Omran, Tawfeg; Yeh, Rebecca; Kruer, Michael; Bakhtiari, Somayeh; Papavasiliou, Antigone; Moutton, Sébastien; Nambot, Sophie; Chanprasert, Sirisak; Paolucci, Sarah; Miller, Kait; Burton, Barbara; Kim, Katherine; O'Heir, Emily; Bruwer, Zandre; Donald, Kirsten; Kleefstra, Tjitske; Goldstein, Amy; Angle, Brad; Bontempo, Kelly; Miny, Peter; Joset, Pascal; Demurger, Florence; Hobson, Emma; Pang, Lewis; Carpenter, Lori; Li, Dong; Bonneau, Dominique; Sadikovic, Bekim (Research Square, 2023-09-29)
    Pathogenic variants in ATP-dependent chromatin remodeling proteins are a recurrent cause of neurodevelopmental disorders (NDDs). The NURF complex consists of BPTF and either the SNF2H ( SMARCA5) or SNF2L ( SMARCA1) ...
  • Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study 
    van Boven, Michiel; van Dorp, Christiaan H; Westerhof, Ilse; Jaddoe, Vincent; Heuvelman, Valerie; Duijts, Liesbeth; Fourie, Elandri; Sluiter-Post, Judith; van Houten, Marlies A; Badoux, Paul; Euser, Sjoerd; Herpers, Bjorn; Eggink, Dirk; de Hoog, Marieke; Boom, Trisja; Wildenbeest, Joanne; Bont, Louis; Rozhnova, Ganna; Bonten, Marc J; Kretzschmar, Mirjam E; Bruijning-Verhagen, Patricia (medRxivCold Spring Harbor Laboratory Press, 2023-06-05)
    Household studies provide an efficient means to study transmission of infectious diseases, enabling estimation of individual susceptibility and infectivity. A main inclusion criterion in such studies is often the presence ...
  • EV-Elute: a universal platform for enrichment of functional surface marker-defined extracellular vesicle subpopulations 
    de Voogt, Willemijn; Frunt, Rowan; Leandro, Raul; Triesscheijn, Casper; Monica, Bella; Paspali, Ioanna; Tielemans, Mark; Gitz-Francois, Jerney J. J. M.; Seinen, CW; de Jong, Olivier; Kooijmans, Sander (BioRxiv, 2023-10-29)
    Intercellular communication via extracellular vesicles (EVs) has been identified as a vital component of a steadily expanding number of physiological and pathological processes. To accommodate these roles, EVs are equipped ...
  • Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection 
    Loehr, Amanda R; Timmerman, Dennis M; Liu, Michelle; Gillis, Ad J M; Matthews, Melia; Bloom, Jordana C; Nicholls, Peter K; Page, David C; Miller, Andrew D; Looijenga, Leendert H J; Weiss, Robert S (BioRxivCold Spring Harbor Laboratory Press, 2023-09-12)
    Malignant testicular germ cells tumors (TGCTs) are the most common solid cancers in young men. Current TGCT diagnostics include conventional serum protein markers, but these lack the sensitivity and specificity to serve ...
  • Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People with Type 2 Diabetes Mellitus 
    Kwak, Soo Heon; Hernandez-Cancela, Ryan B; DiCorpo, Daniel A; Condon, David E; Merino, Jordi; Wu, Peitao; Brody, Jennifer A; Yao, Jie; Guo, Xiuqing; Ahmadizar, Fariba; Meyer, Mariah; Sincan, Murat; Mercader, Josep M; Lee, Sujin; Haessler, Jeffrey; Vy, Ha My T; Lin, Zhaotong; Armstrong, Nicole D; Gu, Shaopeng; Tsao, Noah L; Lange, Leslie A; Wang, Ningyuan; Wiggins, Kerri L; Trompet, Stella; Liu, Simin; Loos, Ruth J F; Judy, Renae; Schroeder, Philip H; Hasbani, Natalie R; Bos, Maxime M; Morrison, Alanna C; Jackson, Rebecca D; Reiner, Alexander P; Manson, JoAnn E; Chaudhary, Ninad S; Carmichael, Lynn K; Chen, Yii-Der Ida; Taylor, Kent D; Ghanbari, Mohsen; van Meurs, Joyce; Pitsillides, Achilleas N; Psaty, Bruce M; Noordam, Raymond; Do, Ron; Park, Kyong Soo; Jukema, J Wouter; Kavousi, Maryam; Correa, Adolfo; Rich, Stephen S; Damrauer, Scott M; Hajek, Catherine; Cho, Nam H; Irvin, Marguerite R; Pankow, James S; Nadkarni, Girish N; Sladek, Robert; Goodarzi, Mark O; Florez, Jose C; Chasman, Daniel I; Heckbert, Susan R; Kooperberg, Charles; Dupuis, Josée; Malhotra, Rajeev; de Vries, Paul S; Liu, Ching-Ti; Rotter, Jerome I; Meigs, James B (medRxiv, 2023-07-28)
    BACKGROUND: Type 2 diabetes mellitus (T2D) confers a two- to three-fold increased risk of cardiovascular disease (CVD). However, the mechanisms underlying increased CVD risk among people with T2D are only partially understood. ...
  • EXO1-mediated DNA repair by single-strand annealing is essential for BRCA1-deficient cells 
    van de Kooij, B; Schreuder, A; Pavani, R S; Garzero, V; Van Hoeck, A; San Martin Alonso, M; Koerse, D; Wendel, T J; Callen, E; Boom, J; Mei, H; Cuppen, E; Nussenzweig, A; van Attikum, H; Noordermeer, S M (BioRxiv, 2023-02-24)
    Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be ...
  • Colchicine promotes atherosclerotic plaque stability independently of inflammation 
    Li, Weizhen; Lin, Alexander; Hutton, Michael; Dhaliwal, Harkirat; Nadel, James; Rodor, Julie; Tumanov, Sergey; Örd, Tiit; Hadden, Matthew; Mokry, Michal; Mol, Barend M; Pasterkamp, Gerard; Padula, Matthew P; Geczy, Carolyn L; Ramaswamy, Yogambha; Sluimer, Judith C; Kaikkonen, Minna U; Stocker, Roland; Baker, Andrew H; Fisher, Edward A; Patel, Sanjay; Misra, Ashish (BioRxivCold Spring Harbor Laboratory Press, 2023-10-03)
    Atherosclerosis is a chronic inflammatory disease which is driven in part by the aberrant trans -differentiation of vascular smooth muscle cells (SMCs). No therapeutic drug has been shown to reverse detrimental SMC-derived ...
  • Precise Spatial Tuning of Visually Driven Alpha Oscillations in Human Visual Cortex 
    Yuasa, Kenichi; Groen, Iris I A; Piantoni, Giovanni; Montenegro, Stephanie; Flinker, Adeen; Devore, Sasha; Devinsky, Orrin; Doyle, Werner; Dugan, Patricia; Friedman, Daniel; Ramsey, Nick; Petridou, Natalia; Winawer, Jonathan (BioRxiv, 2023-07-12)
    Neuronal oscillations at about 10 Hz, called alpha oscillations, are often thought to arise from synchronous activity across occipital cortex, reflecting general cognitive states such as arousal and alertness. However, ...
  • Chemotherapy-induced intestinal injury promotes Galectin-9-driven modulation of T cell function 
    Jansen, Suze A; Cutilli, Alessandro; de Koning, Coco; van Hoesel, Marliek; Sierra, Leire Saiz; Nierkens, Stefan; Mokry, Michal; Nieuwenhuis, Edward E S; Hanash, Alan M; Mocholi, Enric; Coffer, Paul J; Lindemans, Caroline A (BioRxivCold Spring Harbor Laboratory Press, 2023-04-30)
    The intestine is vulnerable to chemotherapy-induced toxicity due to its high epithelial proliferative rate, making gut toxicity an off-target effect in several cancer treatments, including conditioning regimens for allogeneic ...
  • Cell type deconvolution of bulk blood RNA-Seq to reveal biological insights of neuropsychiatric disorders 
    Boltz, Toni; Schwarz, Tommer; Bot, Merel; Hou, Kangcheng; Caggiano, Christa; Lapinska, Sandra; Duan, Chenda; Boks, Marco P; Kahn, Rene S; Zaitlen, Noah; Pasaniuc, Bogdan; Ophoff, Roel (BioRxiv, 2023-05-25)
    Genome-wide association studies (GWAS) have uncovered susceptibility loci associated with psychiatric disorders like bipolar disorder (BP) and schizophrenia (SCZ). However, most of these loci are in non-coding regions of ...
  • Leukocytes carrying Clonal Hematopoiesis of Indeterminate Potential (CHIP) Mutations invade Human Atherosclerotic Plaques. 
    von Scheidt, Moritz; Bauer, Sabine; Ma, Angela; Hao, Ke; Kessler, Thorsten; Vilne, Baiba; Wang, Ying; Hodonsky, Chani J; Ghosh, Saikat K B; Mokry, Michal; Gao, Hua; Kawai, Kenji; Sakamoto, Atsushi; Kaiser, Juliane; Bongiovanni, Dario; Fleig, Julia; Oldenbuettel, Lilith; Chen, Zhifen; Moggio, Aldo; Sager, Hendrik B; Hecker, Judith S; Bassermann, Florian; Maegdefessel, Lars; Miller, Clint L; Koenig, Wolfgang; Zeiher, Andreas M; Dimmeler, Stefanie; Graw, Matthias; Braun, Christian; Ruusalepp, Arno; Leeper, Nicholas J; Kovacic, Jason C; Björkegren, Johan L M; Schunkert, Heribert (medRxiv, 2023-07-26)
    BACKGROUND: Leukocyte progenitors derived from clonal hematopoiesis of undetermined potential (CHIP) are associated with increased cardiovascular events. However, the prevalence and functional relevance of CHIP in coronary ...