Recently added

DSpace/Manakin Repository

UMC Repository: Recent submissions

  • Towards extracting absolute event timelines from english clinical reports 
    Leeuwenberg, Artuur; Moens, Marie Francine (IEEE Advancing Technology for Humanity, 2020)
    Temporal information extraction is a challenging but important area of automatic natural language understanding. Existing approaches annotate and extract various parts of the temporal information conveyed in language like ...
  • Associations between the development of PTSD symptoms and longitudinal changes in the DNA methylome of deployed military servicemen: A comparison with polygenic risk scores 
    van der Wal, Sija J.; Maihofer, Adam X.; Vinkers, Christiaan H.; Smith, Alicia K.; Nievergelt, Caroline M.; Cobb, Dawayland O.; Uddin, Monica; Baker, Dewleen G.; Zuithoff, Nicolaas P.A.; Rutten, Bart P.F.; Vermetten, Eric; Geuze, Elbert; Boks, Marco P. (Elsevier, 2020-11)
    Objective: Military servicemen deployed to war zones are at increased risk of developing posttraumatic stress disorder (PTSD) and successful adaptation to stress is important. Epigenetic alterations in response to trauma ...
  • The Influence of Number and Timing of Pregnancies on Breast Cancer Risk for Women With BRCA1 or BRCA2 Mutations 
    Terry, Mary Beth; Liao, Yuyan; Kast, Karin; Antoniou, Antonis C.; McDonald, Jasmine A.; Mooij, Thea M.; Engel, Christoph; Nogues, Catherine; Buecher, Bruno; Mari, Véronique; Moretta-Serra, Jessica; Gladieff, Laurence; Luporsi, Elisabeth; Barrowdale, Daniel; Frost, Debra; Henderson, Alex; Brewer, Carole; Evans, D. Gareth; Eccles, Diana; Cook, Jackie; Ong, Kai Ren; Izatt, Louise; Ahmed, Munaza; Morrison, Patrick J.; Dommering, Charlotte J.; Oosterwijk, Jan C.; Ausems, Margreet G.E.M.; Kriege, Mieke; Buys, Saundra S.; Andrulis, Irene L.; John, Esther M.; Daly, Mary; Friedlander, Michael; McLachlan, Sue Anne; Osorio, Ana; Caldes, Trinidad; Jakubowska, Anna; Simard, Jacques; Singer, Christian F.; Tan, Yen; Olah, Edith; Navratilova, Marie; Foretova, Lenka; Gerdes, Anne Marie; Roos-Blom, Marie José; Arver, Brita; Olsson, Håkan; Schmutzler, Rita K.; Hopper, John L.; van Leeuwen, Flora E.; on behalf of EMBRACE, GENEPSO, BCFR, HEBON, kConFab and IBCCS (Oxford University Press, 2018-10-01)
    Background: Full-term pregnancy (FTP) is associated with a reduced breast cancer (BC) risk over time, but women are at increased BC risk in the immediate years following an FTP. No large prospective studies, however, have ...
  • Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis 
    Hasaart, Karlijn A L; Manders, Freek; van der Hoorn, Marie-Louise; Verheul, Mark; Poplonski, Tomasz; Kuijk, Ewart; de Sousa Lopes, Susana M Chuva; van Boxtel, Ruben (Nature Publishing Group, 2020-07-31)
    Children show a higher incidence of leukemia compared to young adolescents, yet their cells have less age-related (oncogenic) somatic mutations. Newborns with Down syndrome have an even higher risk of developing leukemia, ...
  • The diagnosis and treatment of invasive aspergillosis in Dutch haematology units facing a rapidly increasing prevalence of azole-resistance. A nationwide survey and rationale for the DB-MSG 002 study protocol 
    Schauwvlieghe, Alexander F A D; de Jonge, Nick; van Dijk, Karin; Verweij, Paul E; Brüggemann, Roger J; Biemond, Bart J; Bart, Aldert; von dem Borne, Peter A; Verbon, Annelies; van der Beek, Martha T; Demandt, Astrid M P; Oudhuis, Guy J; Cornelissen, Jan J; van der Velden, Walter J F M; Span, Lambert F R; Kampinga, Greetje A; Bruns, Anke H; Vonk, Alieke G; Haas, Pieter-Jan A; Doorduijn, Jeanette K; Rijnders, Bart J A (Wiley-Blackwell, 2018-09)
    Patients with haematological malignancies are at risk for invasive fungal diseases (IFD). A survey was conducted in all Dutch academic haematology centres on their current diagnostic, prophylactic and therapeutic approach ...
  • A genetic cluster of MDR Enterobacter cloacae complex ST78 harbouring a plasmid containing bla VIM-1 and mcr-9 in the Netherlands 
    Hendrickx, Antoni P A; Debast, Sylvia; Pérez-Vázquez, María; Schoffelen, Annelot F; Notermans, Daan W; Landman, Fabian; Wielders, Cornelia C H; Cañada Garcia, Javier E; Flipse, Jacky; de Haan, Angela; Witteveen, Sandra; van Santen-Verheuvel, Marga; de Greeff, Sabine C; Kuijper, Ed; Schouls, Leo M; Dutch CPE surveillance Study Group (Oxford, 2021-06)
    BACKGROUND: Carbapenemases produced by Enterobacterales are often encoded by genes on transferable plasmids and represent a major healthcare problem, especially if the plasmids contain additional antibiotic resistance ...
  • Upfront Treatment Influences the Composition of Genetic Alterations in Relapsed Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia 
    Yu, Jiangyan; Waanders, Esmé; van Reijmersdal, Simon V; Antić, Željko; van Bosbeek, Charlotte M; Sonneveld, Edwin; de Groot, Hester; Fiocco, Marta; Geurts van Kessel, Ad; van Leeuwen, Frank N; Pieters, Rob; Hoogerbrugge, Peter M; Kuiper, Roland P (Wolters Kluwer Health, 2020-02)
    Genomic alterations in relapsed B-cell precursor acute lymphoblastic leukemia (BCP-ALL) may provide insight into the role of specific genomic events in relapse development. Along this line, comparisons between the spectrum ...
  • Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs 
    Dobson, Stephanie M; García-Prat, Laura; Vanner, Robert J; Wintersinger, Jeffrey; Waanders, Esmé; Gu, Zhaohui; McLeod, Jessica; Gan, Olga I; Grandal, Ildiko; Payne-Turner, Debbie; Edmonson, Michael N; Ma, Xiaotu; Fan, Yiping; Voisin, Veronique; Chan-Seng-Yue, Michelle; Xie, Stephanie Z; Hosseini, Mohsen; Abelson, Sagi; Gupta, Pankaj; Rusch, Michael; Shao, Ying; Olsen, Scott R; Neale, Geoffrey; Chan, Steven M; Bader, Gary; Easton, John; Guidos, Cynthia J; Danska, Jayne S; Zhang, Jinghui; Minden, Mark D; Morris, Quaid; Mullighan, Charles G; Dick, John E (American Association for Cancer Research Inc., 2020-04)
    Disease recurrence causes significant mortality in B-progenitor acute lymphoblastic leukemia (B-ALL). Genomic analysis of matched diagnosis and relapse samples shows relapse often arising from minor diagnosis subclones. ...
  • Multiclonal complexity of pediatric acute lymphoblastic leukemia and the prognostic relevance of subclonal mutations 
    Antić, Željko; Yu, Jiangyan; Van Reijmersdal, Simon V; Van Dijk, Anke; Dekker, Linde; Segerink, Wouter H; Sonneveld, Edwin; Fiocco, Marta; Pieters, Rob; Hoogerbrugge, Peter M; Van Leeuwen, Frank N; Van Kessel, Ad Geurts; Waanders, Esme; Kuiper, Roland P (Ferrata Storti Foundation, 2021-12-01)
    Genomic studies of pediatric acute lymphoblastic leukemia (ALL) have shown remarkable heterogeneity in initial diagnosis, with multiple (sub)clones harboring lesions in relapse-associated genes. However, the clinical ...
  • Estimation of the Effect of Surrogate Multi-Omic Biomarkers 
    Fuady, Angga M.; Bouhaddani, Said El; Uh, Hae Won; Houwing-Duistermaat, Jeanine (Fabrizio Serra Editore srl, 2021-01)
    Multiple technologies which measure the same omics data set but are based on different aspects of the molecules exist. In practice, studies use different technologies and have therefore different biomarkers. An example is ...
  • Fc engineering strategies to advance IgA antibodies as therapeutic agents 
    van Tetering, Geert; Evers, Mitchell; Chan, Chilam; Stip, Marjolein; Leusen, Jeanette (Multidisciplinary Digital Publishing Institute (MDPI), 2020)
    In the past three decades, a great interest has arisen in the use of immunoglobulins as therapeutic agents. In particular, since the approval of the first monoclonal antibody Rituximab for B cell malignancies, the progress ...
  • Adjustment for unmeasured confounding through informative priors for the confounder-outcome relation 
    Groenwold, Rolf H.H.; Shofty, Inbal; Miočević, Milica; Van Smeden, Maarten; Klugkist, Irene (BioMed Central, 2018-12-22)
    Background: Observational studies of medical interventions or risk factors are potentially biased by unmeasured confounding. In this paper we propose a Bayesian approach by defining an informative prior for the confounder-outcome ...
  • Calculating the sample size required for developing a clinical prediction model 
    Riley, Richard D.; Ensor, Joie; Snell, Kym I.E.; Harrell, Frank E.; Martin, Glen P.; Reitsma, Johannes B.; Moons, Karel G.M.; Collins, Gary; Van Smeden, Maarten (BMJ Publishing Group, 2020-03-18)
  • A workflow for missing values imputation of untargeted metabolomics data 
    Faquih, Tariq; van Smeden, Maarten; Luo, Jiao; Le Cessie, Saskia; Kastenmüller, Gabi; Krumsiek, Jan; Noordam, Raymond; van Heemst, Diana; Rosendaal, Frits R.; Vlieg, Astrid van Hylckama; van Dijk, Ko Willems; Mook-Kanamori, Dennis O. (Multidisciplinary Digital Publishing Institute, 2020-12)
    Metabolomics studies have seen a steady growth due to the development and implementation of affordable and high-quality metabolomics platforms. In large metabolite panels, measurement values are frequently missing and, if ...
  • Clinical practice guidelines on the treatment of patients with cleft lip, alveolus, and palate: An executive summary 
    Mink van der Molen, Aebele B.; van Breugel, Johanna M.M.; Janssen, Nard G.; Admiraal, Ronald J.C.; van Adrichem, Leon N.A.; Bierenbroodspot, Frank; Bittermann, Dirk; van den Boogaard, Marie José H.; Broos, Pieter H.; Dijkstra‐putkamer, Janet J.M.; van Gemert‐Schriks, Martine C.M.; Kortlever, Andrea L.J.; Mouës‐vink, Chantal M.; Swanenburg de Veye, Henriette F.N.; van Tol‐Verbeek, Nanouk; Vermeij‐keers, Christl; de Wilde, Hester; Kuijpers‐jagtman, Anne Marie (Multidisciplinary Digital Publishing Institute (MDPI), 2021-11-01)
    Significant treatment variation exists in the Netherlands between teams treating patients with cleft lip, alveolus, and/or palate, resulting in a confusing and undesirable situation for patients, parents, and practitioners. ...
  • A Note on Applying the BCH Method Under Linear Equality and Inequality Constraints 
    Boeschoten, L.; Croon, M. A.; Oberski, D. L. (Springer New York, 2019-10-01)
    Researchers often wish to relate estimated scores on latent variables to exogenous covariates not previously used in analyses. The BCH method corrects for asymptotic bias in estimates due to these scores’ uncertainty and ...
  • Identifying Heterogeneity in Dynamic Panel Models with Individual Parameter Contribution Regression 
    Arnold, Manuel; Oberski, Daniel L.; Brandmaier, Andreas M.; Voelkle, Manuel C. (Psychology Press Ltd, 2020-07-03)
    Dynamic panel models are a popular approach to study interrelationships between repeatedly measured variables. Often, dynamic panel models are specified and estimated within a structural equation modeling (SEM) framework. ...
  • How linkage error affects hidden Markov model estimates: A sensitivity analysis 
    Pankowska, Paulina; Bakker, Bart F.M.; Oberski, Daniel L.; Pavlopoulos, Dimitris (Oxford University Press, 2020-06-01)
    Hidden Markov models (HMMs) are increasingly used to estimate and correct for classification error in categorical, longitudinal data, without the need for a “gold standard,” error-free data source. To accomplish this, HMMs ...
  • Erratum: How linkage error affects hidden Markov model estimates: A sensitivity analysis (Journal of Survey Statistics and Methodology DOI: 10.1093/jssam/smz011) 
    Pankowska, Paulina; Bakker, Bart F.M.; Oberski, Daniel L.; Pavlopoulos, Dimitris (Oxford University Press, 2020-09-01)
    Upon initial publication, the last column in Table 1 was not consistently rightaligned. Also, the contents of the last column in Table 2 were misaligned and should not have included a % sign. This has now been corrected.
  • Reconciliation of inconsistent data sources using hidden Markov models 
    Pankowska, Paulina; Pavlopoulos, Dimitris; Bakker, Bart; Oberski, Daniel L. (IOS Press, 2020)
    This paper discusses how National Statistical Institutes (NSI's) can use hidden Markov models (HMMs) to produce consistent official statistics for categorical, longitudinal variables using inconsistent sources. Two main ...