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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, R. (author)
The world is currently in a severe man-made climate crisis, creating the need for using renewable energy sources such as offshore wind farms. Offshore wind turbines do not take up any valuable space on land and can use the greater wind resource at sea. The downside is, however, that they are exposed to a much harsher environment at sea, which...
doctoral thesis 2021
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Dekker, W.J.C. (author)
Saccharomyces cerevisiae is a natural producer of ethanol and industrial strains can produce ethanol at high volumetric rates and near-theoretical yields. In addition to its fast fermentative metabolism, its GRAS (generally recognized as safe) status, ease of genetic engineering, tolerance to low pH and high ethanol concentrations contribute to...
doctoral thesis 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
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Kluba, M.M. (author), Li, J. (author), Parkkinen, Katja (author), Louwerse, Marcus (author), Snijder, Jaap (author), Dekker, R. (author)
Several Silicon on Insulator (SOI) wafer manufacturers are now offering products with customer‐defined cavities etched in the handle wafer, which significantly simplifies the fabrication of MEMS devices such as pressure sensors. This paper presents a novel cavity buried oxide (BOX) SOI substrate (cavity‐BOX) that contains a patterned BOX...
journal article 2021
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Kawasaki, S. (author), Subramaniam, Indulakshmi (author), Saccher, M. (author), Dekker, R. (author)
Implantable medical devices are becoming smaller and more deeply implanted in the human body for various applications (i.e., neurostimulation, drug delivery, bone fracture monitoring). Therefore, an efficient ultrasound power transfer link is needed to charge these devices. However, this is challenging because each ultrasound transducer has...
conference paper 2021
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Saccher, M. (author), Kawasaki, S. (author), Dekker, R. (author)
Recently, focused ultrasound has been proposed to power deeply implanted medical devices. Almost exclusively, lead zirconate titanate (PZT) transducers are used to convert acoustic energy into electrical energy. Unfortunately, these lead containing devices cannot be hermetically encapsulated since that would block the ultrasound. We propose the...
conference paper 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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de Koning, Judith (author), Dekker, Mireille (author), Jongerden, Irene (author), Melles, M. (author)
poster 2021
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Dekker, M.C. (author), van Egmond, R. (author), Molenbroek, J.F.M. (author), Vink, P. (author)
BACKGROUND: Former studies on work-related upper limb disorders (WRULD) within university education report substantial prevalence rates. In this study, developments in WRULD amongst students in the period 2004-2014 were investigated. Our findings can be a benchmark for future studies, in particular when there are major societal changes as in...
journal article 2021
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Mastrangeli, Massimo (author), Aydogmus, H. (author), Dostanic, M. (author), Motreuil-Ragot, P.A. (author), Revyn, N. (author), de Wagenaar, B. (author), Dekker, R. (author), Sarro, Pasqualina M (author)
Stemming from the convergence of tissue engineering and microfluidics, organ-on-chip (OoC) technology can reproduce in vivo-like dynamic microphysiological environments for tissues in vitro. The possibility afforded by OoC devices of realistic recapitulation of tissue and organ (patho)physiology may hold the key to bridge the current...
conference paper 2021
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Kawasaki, S. (author), Westhoek, Y. (author), Subramaniam, I. (author), Saccher, M. (author), Dekker, R. (author)
Using ultrasound to power deeply implanted biomedical devices is a promising technique due to its low attenuation in body tissue and its short wavelength that allows precise focusing of the energy. Ultrasound energy harvesting conventionally has been done using lead zirconate titanate (PZT) ultrasound transducers, which uses the piezoelectric...
conference paper 2021
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Bharadwaj, M. (author), Bengtson, M.L. (author), Golverdingen, Mirte (author), Waling, Loulotte (author), Dekker, C. (author)
Inadequate and nonintegrated diagnostics are the Achilles' heel of global efforts to monitor, control, and eradicate neglected tropical diseases (NTDs). While treatment is often available, NTDs are endemic among marginalized populations, due to the unavailability or inadequacy of diagnostic tests that cause empirical misdiagnoses. The need of...
review 2021
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Mooiman, C. (author), Bouwknegt, J. (author), Dekker, W.J.C. (author), Wiersma, S.J. (author), Ortiz Merino, R.A. (author), de Hulster, A.F. (author), Pronk, J.T. (author)
All known facultatively fermentative yeasts require molecular oxygen for growth. Only in a small number of yeast species, these requirements can be circumvented by supplementation of known anaerobic growth factors such as nicotinate, sterols and unsaturated fatty acids. Biosynthetic oxygen requirements of yeasts are typically small and,...
journal article 2021
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Perli, T. (author), Vos, A.M. (author), Bouwknegt, J. (author), Dekker, W.J.C. (author), Wiersma, S.J. (author), Mooiman, C. (author), Ortiz Merino, R.A. (author), Daran, J.G. (author), Pronk, J.T. (author)
Neocallimastigomycetes are unique examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycetes proteomes identified a candidate...
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 Vries, Hendrik W. (author), Andersson, John (author), van der Sluis, E.O. (author), van der Giessen, Erik (author), Dahlin, Andreas (author), Onck, Patrick R. (author), Dekker, C. (author)
Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is...
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), van Dijk, M.C. (author), Primavera, Christian (author), Dekker, C. (author)
We have developed a fabrication methodology for label-free optical trapping of individual nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of these nanoapertures can be reliably produced using focused ion beam (FIB) milling with gap sizes of 10–20 nm, single-nanometer variation, and with a remarkable stability...
journal article 2021
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Janissen, R. (author), Woodman, Andrew (author), Shengjuler, Djoshkun (author), Vallet, Thomas (author), Lee, Kuo Ming (author), Kuijpers, L.C. (author), Moustafa, Ibrahim M. (author), Fitzgerald, Fiona (author), Dekker, N.H. (author)
Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics...
journal article 2021
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