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Blanch Jover, A. (author), De Franceschi, N. (author), Fenel, Daphna (author), Weissenhorn, Winfried (author), Dekker, C. (author)The Cdv proteins constitute the cell division system of the Crenarchaea, a machinery closely related to the ESCRT system of eukaryotes. Using a combination of TEM imaging and biochemical assays, we here present an in vitro study of Metallosphaera sedula CdvB1, the Cdv protein that is believed to play a major role in the constricting ring that...journal article 2022
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Bengtson, M.L. (author), Bharadwaj, M. (author), Franch, O. (author), van der Torre, J. (author), Meerdink, V.E.E. (author), Schallig, Henk (author), Dekker, C. (author)Nucleic-acid detection is crucial for basic research as well as for applications in medicine such as diagnostics. In resource-limited settings, however, most DNA-detection diagnostic schemes are inapplicable since they rely on expensive machinery, electricity, and trained personnel. Here, we present an isothermal DNA detection scheme for the...journal article 2022
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Boskeljon-Horst, L. (author), Sillem, S. (author), Dekker, S.W.A. (author)There is little empirical evidence on the predictive value of safety culture assessments (SCAs) in relation to how accident-prone an organisation might be. Recently, Antonsen not just demonstrated how a quantitative SCA mispredicted future safety outcomes, but actually showed an inverse relationship between the assessment and subsequent critical...journal article 2022
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Chakrabarty, Sanjiban (author), Quiros Solano, W.F. (author), Kuijten, Maayke M.P. (author), Haspels, Ben (author), Mallya, Sandeep (author), van de Stolpe, Anja (author), Odijk, Hanny (author), van Weerden, Wytske M. (author), Dekker, R. (author)Optimal treatment of cancer requires diagnostic methods to facilitate therapy choice and prevent ineffective treatments. Direct assessment of therapy response in viable tumor specimens could fill this diagnostic gap. Therefore, we designed a microfluidic platform for assessment of patient treatment response using tumor tissue slices under...journal article 2022
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Tišma, M. (author), Panoukidou, Maria (author), Antar, Hammam (author), Soh, Young Min (author), Barth, R. (author), Pradhan, B. (author), Barth, A. (author), van der Torre, J. (author), Dekker, C. (author)The ParABS system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzzling how this large-distance spreading can occur along DNA loaded with hundreds of proteins. Using in...journal article 2022
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Wen, C. (author), Bertosin, E. (author), Shi, X. (author), Dekker, C. (author), Schmid, Sonja (author)Nanopores are versatile single-molecule sensors offering a simple label-free readout with great sensitivity. We recently introduced the nanopore electro-osmotic trap (NEOtrap) which can trap and sense single unmodified proteins for long times. The trapping is achieved by the electro-osmotic flow (EOF) generated from a DNA-origami sphere...journal article 2022
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Saccher, M. (author), Kawasaki, S. (author), Proietti Onori, Martina (author), van Woerden, Geeske M. (author), Giagka, Vasiliki (author), Dekker, R. (author)Background<br/>Microelectrode arrays (MEA) enable the measurement and stimulation of the electrical activity of cultured cells. The integration of other neuromodulation methods will significantly enhance the application range of MEAs to study their effects on neurons. A neuromodulation method that is recently gaining more attention is focused...journal article 2022
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Shi, X. (author), Pumm, Anna Katharina (author), Isensee, Jonas (author), Zhao, W. (author), Verschueren, D.V. (author), Martin Gonzalez, A. (author), Golestanian, Ramin (author), Dietz, Hendrik (author), Dekker, C. (author)Flow-driven rotary motors such as windmills and water wheels drive functional processes in human society. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has remained challenging. Here we demonstrate flow-driven rotary motion of a self-organized DNA nanostructure...journal article 2022
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Mc Cluskey, K.A. (author), van Veen, E.N.W. (author), Cnossen, J.P. (author), Wesselink, W.J. (author), Asscher, F.M. (author), Smith, C.S. (author), Dekker, N.H. (author)Accurate image alignment is critical in multicolor single-molecule fluorescence microscopy. Global alignment using affine transformations leaves residual errors due to the nonlinearity of the distortions, which decreases the effective field of view. Subsequent local refinement demands either large amounts of reference data and processing time...journal article 2021
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Dekker, Mireille (author), de Koning, Judith PM (author), Melles, M. (author), Sonneveld, M.H. (author), van Mansfeld, Rosa (author), Jongerden, Irene P (author)Background: Patient information provision about isolation measures is often not standardized. Moreover, it is unclear what information patients and informal caregivers need to optimize their knowledge and actual experience of contact isolation. We explored opportunities for improving the experience of patients in contact isolation from a human...journal article 2021
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Martins Da Ponte, R. (author), Gaio, N. (author), van Zeijl, H.W. (author), Vollebregt, S. (author), Dijkstra, Paul (author), Dekker, R. (author), Serdijn, W.A. (author), Giagka, Vasiliki (author)One of the many applications of organ-on-a-chip (OOC) technology is the study of biological processes in human induced pluripotent stem cells (iPSCs) during pharmacological drug screening. It is of paramount importance to construct OOCs equipped with highly compact in situ sensors that can accurately monitor, in real time, the extracellular...journal article 2021
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Yang, W.W.W. (author), Radha, Boya (author), Choudhary, Adnan (author), You, Yi (author), Mettela, Gangaiah (author), Geim, Andre K. (author), Aksimentiev, Aleksei (author), Keerthi, Ashok (author), Dekker, C. (author)2D nanoslit devices, where two crystals with atomically flat surfaces are separated by only a few nanometers, have attracted considerable attention because their tunable control over the confinement allows for the discovery of unusual transport behavior of gas, water, and ions. Here, the passage of double-stranded DNA molecules is studied...journal article 2021
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Mouter, N. (author), Koster, Paul (author), Dekker, Thijs (author)Participatory Value Evaluation (PVE) is a new method to assess the desirability of government projects. In a PVE, individuals select their preferred portfolio of government projects given a constrained public budget. Individuals’ preferences for (the impacts of) government projects can be determined based on these choices. The obtained...journal article 2021
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Dekker, Mark M. (author), van Lieshout, Rolf N. (author), Ball, Robin C. (author), Bouman, Paul C. (author), Dekker, Stefan C. (author), Dijkstra, Henk A. (author), Goverde, R.M.P. (author), Huisman, Dennis (author), Panja, Debabrata (author), Schaafsma, Alfons A.M. (author), van den Akker, Marjan (author)Railway systems occasionally get into a state of being out-of-control, meaning that barely any train is running, even though the required resources (infrastructure, rolling stock and crew) are available. Because of the large number of affected resources and the absence of detailed, timely and accurate information, currently existing...journal article 2021
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Mouter, N. (author), Koster, Paul (author), Dekker, Thijs (author)Participatory Value Evaluation (PVE) is a new survey method which elicits citizens' preferences over the allocation of public budgets as well as their private income. In a PVE, citizens are asked to choose the best portfolio of projects given a governmental and a private budget constraint. First, this paper aligns PVE with the traditional Kaldor...journal article 2021
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Schmid, S. (author), Stömmer, Pierre (author), Dietz, Hendrik (author), Dekker, C. (author)Many strategies have been pursued to trap and monitor single proteins over time to detect the molecular mechanisms of these essential nanomachines. Single-protein sensing with nanopores is particularly attractive because it allows label-free high-bandwidth detection on the basis of ion currents. Here we present the nanopore electro-osmotic...journal article 2021
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Hulleman, C.N. (author), Thorsen, R.Ø. (author), Kim, E. (author), Dekker, C. (author), Stallinga, S. (author), Rieger, B. (author)Estimating the orientation and 3D position of rotationally constrained emitters with localization microscopy typically requires polarization splitting or a large engineered Point Spread Function (PSF). Here we utilize a compact modified PSF for single molecule emitter imaging to estimate simultaneously the 3D position, dipole orientation, and...journal article 2021
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Fragasso, A. (author), De Franceschi, N. (author), Stömmer, Pierre (author), van der Sluis, E.O. (author), Dietz, Hendrik (author), Dekker, C. (author)Molecular traffic across lipid membranes is a vital process in cell biology that involves specialized biological pores with a great variety of pore diameters, from fractions of a nanometer to >30 nm. Creating artificial membrane pores covering similar size and complexity will aid the understanding of transmembrane molecular transport in...journal article 2021
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Dekker, W.J.C. (author), Ortiz Merino, R.A. (author), Kaljouw, Astrid (author), Battjes, Julius (author), Wiering, Frank W. (author), Mooiman, C. (author), de la Torre, P. (author), Pronk, J.T. (author)Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae,...journal article 2021
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Brinkerhoff, H.D. (author), Kang, A.S.W. (author), Liu, Jingqian (author), Aksimentiev, Aleksei (author), Dekker, C. (author)A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive to single-amino acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA...journal article 2021