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Author De Backer, J.; Lin, A.; Berghe, W.V.; Bogaerts, A.; Hoogewijs, D. url  doi
openurl 
  Title Cytoglobin inhibits non-thermal plasma-induced apoptosis in melanoma cells through regulation of the NRF2-mediated antioxidant response Type A1 Journal article
  Year 2022 Publication Redox Biology Abbreviated Journal Redox Biol  
  Volume 55 Issue Pages 102399  
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)  
  Abstract Melanoma arises from pigment-producing cells called melanocytes located in the basal layers of the epidermis of the skin. Cytoglobin (CYGB) is a ubiquitously expressed hexacoordinated globin that is highly enriched in me­lanocytes and frequently downregulated during melanomagenesis. Previously, we showed that non-thermal plasma (NTP)-produced reactive oxygen and nitrogen species (RONS) lead to the formation of an intra­ molecular disulfide bridge that would allow CYGB to function as a redox-sensitive protein. Here, we investigate the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels, and we explore the role of CYGB in determining treatment outcome. Our findings are consistent with previous studies supporting that NTP cytotoxicity is mediated through the production of RONS and leads to apoptotic cell death in melanoma cells. Furthermore, we show that NTP-treated solutions elicit an antioxidant response through the activation of nuclear factor erythroid 2–related factor 2 (NRF2). The knock­ down and overexpression of CYGB respectively sensitizes and protects melanoma cells from RONS-induced apoptotic cell death. The presence of CYGB enhances heme-oxygenase 1 (HO-1) and NRF2 protein expression levels, whereas the absence impairs their expression. Moreover, analysis of the CYGB-dependent transcriptome demonstrates the tumor suppressor long non-coding RNA maternally expressed 3 (MEG3) as a hitherto unde­ scribed link between CYGB and NRF2. Thus, the presence of CYGB, at least in melanoma cells, seems to play a central role in determining the therapeutic outcome of RONS-inducing anticancer therapies, like NTP-treated solutions, possessing both tumor-suppressive and oncogenic features. Hence, CYGB expression could be of in­ terest either as a biomarker or as a candidate for future targeted therapies in melanoma.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000844595100002 Publication Date 0000-00-00  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2213-2317 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 11.4 Times cited Open Access OpenAccess  
  Notes This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work include: 12S9221 N (Abraham Lin) and G044420 N (Abraham Lin and Annemie Bogaerts). Joey De Backer acknowledges a visiting fellowship from the University of Fribourg. David Hoogewijs acknowledges support by the Swiss National Science Foundation (grants 31003A173000 and 310030207460). Approved Most recent IF: 11.4  
  Call Number PLASMANT @ plasmant @c:irua:190635 Serial 7101  
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Author De Backer, A.; Zhang, Z.; van den Bos, K.H.W.; Bladt, E.; Sánchez‐Iglesias, A.; Liz‐Marzán, L.M.; Nellist, P.D.; Bals, S.; Van Aert, S. url  doi
openurl 
  Title Element Specific Atom Counting at the Atomic Scale by Combining High Angle Annular Dark Field Scanning Transmission Electron Microscopy and Energy Dispersive X‐ray Spectroscopy Type A1 Journal article
  Year 2022 Publication Small methods Abbreviated Journal Small Methods  
  Volume Issue Pages 2200875  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract A new methodology is presented to count the number of atoms in multimetallic nanocrystals by combining energy dispersive X-ray spectroscopy (EDX) and high angle annular dark field scanning transmission electron microscopy (HAADF STEM). For this purpose, the existence of a linear relationship between the incoherent HAADF STEM and EDX images is exploited. Next to the number of atoms for each element in the atomic columns, the method also allows quantification of the error in the obtained number of atoms, which is of importance given the noisy nature of the acquired EDX signals. Using experimental images of an Au@Ag core–shell nanorod, it is demonstrated that 3D structural information can be extracted at the atomic scale. Furthermore, simulated data of an Au@Pt core–shell nanorod show the prospect to characterize heterogeneous nanostructures with adjacent atomic numbers.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000862072700001 Publication Date 2022-09-30  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2366-9608 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 12.4 Times cited 5 Open Access OpenAccess  
  Notes This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A., Grant 815128 REALNANO to S.B., and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B.; esteem3reported; esteem3JRA Approved Most recent IF: 12.4  
  Call Number EMAT @ emat @c:irua:191570 Serial 7109  
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Author Goris, B.; de Beenhouwer, J.; de Backer, A.; Zanaga, D.; Batenburg, K.J.; Sánchez-Iglesias, A.; Liz-Marzán, L.M.; Van Aert, S.; Bals, S.; Sijbers, J.; Van Tendeloo, G. pdf  url
doi  openurl
  Title Measuring lattice strain in three dimensions through electron microscopy Type A1 Journal article
  Year 2015 Publication Nano letters Abbreviated Journal Nano Lett  
  Volume 15 Issue 15 Pages 6996-7001  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract The three-dimensional (3D) atomic structure of nanomaterials, including strain, is crucial to understand their properties. Here, we investigate lattice strain in Au nanodecahedra using electron tomography. Although different electron tomography techniques enabled 3D characterizations of nanostructures at the atomic level, a reliable determination of lattice strain is not straightforward. We therefore propose a novel model-based approach from which atomic coordinates are measured. Our findings demonstrate the importance of investigating lattice strain in 3D.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington Editor  
  Language Wos 000363003100108 Publication Date 2015-09-04  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1530-6984;1530-6992; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 12.712 Times cited 87 Open Access OpenAccess  
  Notes Fwo; 335078 Colouratom; 267867 Plasmaquo; 312483 Esteem2; 262348 Esmi; esteem2jra4; ECASSara; (ROMEO:white; preprint:; postprint:restricted 12 months embargo; pdfversion:cannot); Approved Most recent IF: 12.712; 2015 IF: 13.592  
  Call Number c:irua:127639 c:irua:127639 Serial 1965  
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Author Goris, B.; de Backer, A.; Van Aert, S.; Gómez-Graña, S.; Liz-Marzán, L.M.; Van Tendeloo, G.; Bals, S. pdf  doi
openurl 
  Title Three-dimensional elemental mapping at the atomic scale in bimetallic nanocrystals Type A1 Journal article
  Year 2013 Publication Nano letters Abbreviated Journal Nano Lett  
  Volume 13 Issue 9 Pages 4236-4241  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract A thorough understanding of the three-dimensional (3D) atomic structure and composition of coreshell nanostructures is indispensable to obtain a deeper insight on their physical behavior. Such 3D information can be reconstructed from two-dimensional (2D) projection images using electron tomography. Recently, different electron tomography techniques have enabled the 3D characterization of a variety of nanostructures down to the atomic level. However, these methods have all focused on the investigation of nanomaterials containing only one type of chemical element. Here, we combine statistical parameter estimation theory with compressive sensing based tomography to determine the positions and atom type of each atom in heteronanostructures. The approach is applied here to investigate the interface in coreshell Au@Ag nanorods but it is of great interest in the investigation of a broad range of nanostructures.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Washington Editor  
  Language Wos 000330158900043 Publication Date 2013-08-16  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1530-6984;1530-6992; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 12.712 Times cited 90 Open Access  
  Notes FWO; 246791 COUNTATOMS; 267867 PLASMAQUO; 262348 ESMI; 312483 ESTEEM2; Hercules 3; esteem2_jra4 Approved Most recent IF: 12.712; 2013 IF: 12.940  
  Call Number UA @ lucian @ c:irua:110036 Serial 3650  
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Author Altantzis, T.; Lobato, I.; De Backer, A.; Béché, A.; Zhang, Y.; Basak, S.; Porcu, M.; Xu, Q.; Sánchez-Iglesias, A.; Liz-Marzán, L.M.; Van Tendeloo, G.; Van Aert, S.; Bals, S. url  doi
openurl 
  Title Three-Dimensional Quantification of the Facet Evolution of Pt Nanoparticles in a Variable Gaseous Environment Type A1 Journal article
  Year 2019 Publication Nano letters Abbreviated Journal Nano Lett  
  Volume 19 Issue 19 Pages 477-481  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract Pt nanoparticles play an essential role in a wide variety of catalytic reactions. The activity of the particles strongly depends on their three-dimensional (3D) structure and exposed facets, as well as on the reactive environment. High-resolution electron microscopy has often been used to characterize nanoparticle catalysts but unfortunately most observations so far have been either performed in vacuum and/or using conventional (2D) in situ microscopy. The latter however does not provide direct 3D morphological information. We have implemented a quantitative methodology to measure variations of the 3D atomic structure of nanoparticles under the flow of a selected gas. We were thereby able to quantify refaceting of Pt nanoparticles with atomic resolution during various oxidation−reduction cycles. In a H2 environment, a more faceted surface morphology of the particles was observed with {100} and {111} planes being dominant. On the other hand, in O2 the percentage of {100} and {111} facets decreased and a significant increase of higher order facets was found, resulting in a more rounded morphology. This methodology opens up new opportunities toward in situ characterization of catalytic nanoparticles because for the first time it enables one to directly measure 3D morphology variations at the atomic scale in a specific gaseous reaction environment.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000455561300061 Publication Date 2019-01-09  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1530-6984 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 12.712 Times cited 82 Open Access OpenAccess  
  Notes This work was supported by the European Research Council (Grant 335078 COLOURATOM to S.B. and Grant 770887 PICOMETRICS to S.V.A.). The authors acknowledge funding from the European Commission Grant (EUSMI 731019 to S.B., L.M.L.-M., and Q.X. and MUMMERING 765604 to S.B. and Q.X.). The authors gratefully acknowledge funding from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15N, G.0369.15N, and G.0267.18N), postdoctoral grants to T.A. and A.D.B, and an FWO [PEGASUS]2 Marie Sklodowska-Curie fellowship to Y.Z. (12U4917N). L.M.L.-M. acknowledges funding from the Spanish Ministerio de Economía y Competitividad (Grant MAT2017-86659-R). We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan X Pascal GPU used for this research. ecas_sara Realnano 815128; sygma Approved Most recent IF: 12.712  
  Call Number EMAT @ emat @UA @ admin @ c:irua:156390 Serial 5150  
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Author Verhulst, S.L.; de Backer, J.; Van Gaal, L.; de Backer, W.; Desager, K. openurl 
  Title Adenotonsillectomy as first-line treatment for sleep-disordered breathing in obese children Type L1 Letter to the editor
  Year 2008 Publication American journal of respiratory and critical care medicine Abbreviated Journal Am J Resp Crit Care  
  Volume 177 Issue 12 Pages 1399  
  Keywords L1 Letter to the editor; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication New York Editor  
  Language Wos Publication Date 0000-00-00  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1073-449x; 1535-4970 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 13.204 Times cited Open Access  
  Notes Approved Most recent IF: 13.204; 2008 IF: 9.792  
  Call Number UA @ lucian @ c:irua:68864 Serial 59  
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Author Arteaga Cardona, F.; Jain, N.; Popescu, R.; Busko, D.; Madirov, E.; Arús, B.A.; Gerthsen, D.; De Backer, A.; Bals, S.; Bruns, O.T.; Chmyrov, A.; Van Aert, S.; Richards, B.S.; Hudry, D. pdf  url
doi  openurl
  Title Preventing cation intermixing enables 50% quantum yield in sub-15 nm short-wave infrared-emitting rare-earth based core-shell nanocrystals Type A1 Journal article
  Year 2023 Publication Nature communications Abbreviated Journal Nat Commun  
  Volume 14 Issue 1 Pages 4462  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract Short-wave infrared (SWIR) fluorescence could become the new gold standard in optical imaging for biomedical applications due to important advantages such as lack of autofluorescence, weak photon absorption by blood and tissues, and reduced photon scattering coefficient. Therefore, contrary to the visible and NIR regions, tissues become translucent in the SWIR region. Nevertheless, the lack of bright and biocompatible probes is a key challenge that must be overcome to unlock the full potential of SWIR fluorescence. Although rare-earth-based core-shell nanocrystals appeared as promising SWIR probes, they suffer from limited photoluminescence quantum yield (PLQY). The lack of control over the atomic scale organization of such complex materials is one of the main barriers limiting their optical performance. Here, the growth of either homogeneous (α-NaYF<sub>4</sub>) or heterogeneous (CaF<sub>2</sub>) shell domains on optically-active α-NaYF<sub>4</sub>:Yb:Er (with and without Ce<sup>3+</sup>co-doping) core nanocrystals is reported. The atomic scale organization can be controlled by preventing cation intermixing only in heterogeneous core-shell nanocrystals with a dramatic impact on the PLQY. The latter reached 50% at 60 mW/cm<sup>2</sup>; one of the highest reported PLQY values for sub-15 nm nanocrystals. The most efficient nanocrystals were utilized for in vivo imaging above 1450 nm.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 001037058500022 Publication Date 2023-07-25  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2041-1723 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 16.6 Times cited 1 Open Access OpenAccess  
  Notes D.H. would like to thank Dominique Ectors (Bruker AXS GmbH, Karlsruhe, Germany) for assistance and discussion on the PXRD data and TOPAS evaluations. The authors would like to acknowledge the financial support provided by the Helmholtz Association via: i) the Professorial Recruitment Initiative Funding (B.S.R.); ii) the Research Field Energy – Program Materials and Technologies for the Energy Transition – Topic 1 Photovoltaics (F.A.C., D.B., E.M., B.S.R., D.H.). This project received funding from the European Union’s Horizon 2020 innovation programme under grant agreement 823717. This work was supported by the European Research Council (grant 770887-PICOMETRICS to S.V.A. and Grant 815128-REALNANO to S.B.). The authors acknowledge financial support from the ResearchFoundation Flanders (FWO, Belgium) through project fundings (G.0346.21 N to S.V.A. and S.B.) and a postdoctoral grant (A.D.B.). The authors (B.A.A., O.T.B. and A.C.) acknowledge funding from the Helmholtz Zentrum München, the DFG-Emmy Noether program (BR 5355/2-1) and from the CZI Deep Tissue Imaging (DTI-0000000248). The authors (O.T.B. and D.H.) would like to thank the Helmholtz Imaging (ZT-I-PF-4-038-BENIGN). Approved Most recent IF: 16.6; 2023 IF: 12.124  
  Call Number EMAT @ emat @c:irua:198158 Serial 8808  
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Author Lin, A.; Sahun, M.; Biscop, E.; Verswyvel, H.; De Waele, J.; De Backer, J.; Theys, C.; Cuypers, B.; Laukens, K.; Berghe, W.V.; Smits, E.; Bogaerts, A. pdf  url
doi  openurl
  Title Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma Type A1 Journal article
  Year 2023 Publication Drug resistance updates Abbreviated Journal  
  Volume 67 Issue Pages 100914  
  Keywords A1 Journal article; Pharmacology. Therapy; ADReM Data Lab (ADReM); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)  
  Abstract To gain insights into the underlying mechanisms of NTP therapy sensitivity and resistance, using the firstever

NTP-resistant cell line derived from sensitive melanoma cells (A375).

Methods: Melanoma cells were exposed to NTP and re-cultured for 12 consecutive weeks before evaluation

against the parental control cells. Whole transcriptome sequencing analysis was performed to identify differentially

expressed genes and enriched molecular pathways. Glucose uptake, extracellular lactate, media acidification,

and mitochondrial respiration was analyzed to determine metabolic changes. Cell death inhibitors were

used to assess the NTP-induced cell death mechanisms, and apoptosis and ferroptosis was further validated via

Annexin V, Caspase 3/7, and lipid peroxidation analysis.

Results: Cells continuously exposed to NTP became 10 times more resistant to NTP compared to the parental cell

line of the same passage, based on their half-maximal inhibitory concentration (IC50). Sequencing and metabolic

analysis indicated that NTP-resistant cells had a preference towards aerobic glycolysis, while cell death analysis

revealed that NTP-resistant cells exhibited less apoptosis but were more vulnerable to lipid peroxidation and

ferroptosis.

Conclusions: A preference towards aerobic glycolysis and ferroptotic cell death are key physiological changes in

NTP-resistance cells, which opens new avenues for further, in-depth research into other cancer types.
 
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000925156500001 Publication Date 2022-12-29  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1368-7646 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 24.3 Times cited Open Access OpenAccess  
  Notes The authors would like to thank Dr. Christophe Deben and Ms. Hannah Zaryouh (Center for Oncological Research, University of Antwerp) for the use and their help with the D300e Digital Dispenser and Spark® Cyto, as well as Ms. Rapha¨elle Corremans (Laboratory Pathophysiology, University of Antwerp) for the use of their lactate meter. The authors would also like to acknowledge the help from Ms. Tias Verhezen and Mr. Cyrus Akbari, who was involved at the start of the project but could not continue due to the COVID-19 pandemic. The authors also acknowledge the resources and services provided by the VSC (Flemish Supercomputer Center). This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaerts), and 1S67621N (Hanne Verswyvel). We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr. Willy Floren, and the Vereycken family. We would also like to acknowledge the support from the European Cooperation in Science & Technology (COST) Action on Therapeutical applications of Cold Plasmas (CA20114; PlasTHER). Approved Most recent IF: 24.3; 2023 IF: 10.906  
  Call Number PLASMANT @ plasmant @c:irua:193167 Serial 7240  
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Author Geuchies, J.J.; van Overbeek, C.; Evers, W.H.; Goris, B.; de Backer, A.; Gantapara, A.P.; Rabouw, F.T.; Hilhorst, J.; Peters, J.L.; Konovalov, O.; Petukhov, A.V.; Dijkstra, M.; Siebbeles, L.D.A.; van Aert, S.; Bals, S.; Vanmaekelbergh, D. url  doi
openurl 
  Title In situ study of the formation mechanism of two-dimensional superlattices from PbSe nanocrystals Type A1 Journal article
  Year 2016 Publication Nature materials Abbreviated Journal Nat Mater  
  Volume 15 Issue 15 Pages 1248-1254  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract Oriented attachment of PbSe nanocubes can result in the formation of two-dimensional (2D) superstructures with long-range nanoscale and atomic order. This questions the applicability of classic models in which the superlattice grows by first forming a nucleus, followed by sequential irreversible attachment of nanocrystals, as one misaligned attachment would disrupt the 2D order beyond repair. Here, we demonstrate the formation mechanism of 2D PbSe superstructures with square geometry by using in situ grazing-incidence X-ray scattering (small angle and wide angle), ex situ electron microscopy, and Monte Carlo simulations. We observed nanocrystal adsorption at the liquid/gas interface, followed by the formation of a hexagonal nanocrystal monolayer. The hexagonal geometry transforms gradually through a pseudo-hexagonal phase into a phase with square order, driven by attractive interactions between the {100} planes perpendicular to the liquid substrate, which maximize facet-to-facet overlap. The nanocrystals then attach atomically via a necking process, resulting in 2D square superlattices.  
  Address Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language English Wos 000389104400011 Publication Date 2016-09-05  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1476-1122 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (up) 39.737 Times cited 182 Open Access OpenAccess  
  Notes This research is part of the programme ‘Designing Dirac Carriers in semiconductor honeycomb superlattices (DDC13),’ which is supported by the Foundation for Fundamental Research on Matter (FOM), which is part of the Dutch Research Council (NWO). J.J.G. acknowledges funding from the Debye and ESRF Graduate Programs. The authors gratefully acknowledge funding from the Research Foundation Flanders (G.036915 G.037413 and funding of postdoctoral grants to B.G. and A.d.B). S.B. acknowledges the European Research Council, ERC grant No 335078—Colouratom. The authors gratefully acknowledge I. Swart and M. van Huis for fruitful discussions. We acknowledge funding from NWO-CW TOPPUNT ‘Superficial Superstructures’. The X-ray scattering measurements were performed at the ID10 beamline at ESRF under proposal numbers SC-4125 and SC-3786. The authors thank G. L. Destri and F. Zontone for their support during the experiments.; ECAS_Sara; (ROMEO:yellow; preprint:; postprint:restricted ; pdfversion:cannot); Approved Most recent IF: 39.737  
  Call Number EMAT @ emat @ c:irua:136165 Serial 4289  
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