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Author | Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S. | ||||
Title | Atom counting from a combination of two ADF STEM images | Type | A1 Journal article | ||
Year | 2024 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume | 255 | Issue | Pages | 113859 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 001089064200001 | Publication Date | 2023-09-23 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). | Approved | Most recent IF: 2.2; 2024 IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:201008 | Serial | 8964 | ||
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Author | Şentürk, D.G.; De Backer, A.; Van Aert, S. | ||||
Title | Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination | Type | A1 Journal Article | ||
Year | 2024 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume | 259 | Issue | Pages | 113941 | |
Keywords | A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ; | ||||
Abstract | In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2024-02-19 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record | |
Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N, GOA7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). | Approved | Most recent IF: 2.2; 2024 IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:204353 | Serial | 8996 | ||
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Author | De Backer, A.; Bals, S.; Van Aert, S. | ||||
Title | A decade of atom-counting in STEM: From the first results toward reliable 3D atomic models from a single projection | Type | A1 Journal article | ||
Year | 2023 | Publication | Ultramicroscopy | Abbreviated Journal | |
Volume | Issue | Pages | 113702 | ||
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted. | ||||
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Language | Wos | 000953765800001 | Publication Date | 2023-02-10 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.2 | Times cited | 3 | Open Access | OpenAccess |
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert, Grant 815128 REALNANO to S. Bals, 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 EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF) . The authors also thank the colleagues who have contributed to this work over the years, including T. Altantzis, E. Arslan Irmak, K.J. Batenburg, E. Bladt, A. De wael, R. Erni, C. Faes, B. Goris, L. Jones, L.M. Liz-Marzán, I. Lobato, G.T. Martinez, P.D. Nellist, M.D. Rosell, A. Rosenauer, K.H.W. van den Bos, A. Varambhia, and Z. Zhang.; esteem3reported; esteem3JRA | Approved | Most recent IF: 2.2; 2023 IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:195896 | Serial | 7236 | ||
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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. | ||||
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. |
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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 | 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 | Zhang, Z.; Lobato, I.; De Backer, A.; Van Aert, S.; Nellist, P. | ||||
Title | Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions | Type | A1 Journal article | ||
Year | 2023 | Publication | Ultramicroscopy | Abbreviated Journal | |
Volume | 246 | Issue | Pages | 113671 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core–shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements. | ||||
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Corporate Author | Zezhong Zhang | Thesis | |||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000995063900001 | Publication Date | 2022-12-28 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | European Research Council 770887 PICOMETRICS; Fonds Wetenschappelijk Onderzoek No.G.0502.18N; Horizon 2020, 770887 ; Horizon 2020 Framework Programme; European Research Council, 823717 ESTEEM3 ; esteem3reported; esteem3JRa | Approved | Most recent IF: 2.2; 2023 IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:195890 | Serial | 7251 | ||
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Author | De Backer, J. | ||||
Title | The versatile nature of cytoglobin, the Swiss army knife among globins, with a preference for oxidative stress | Type | Doctoral thesis | ||
Year | 2023 | Publication | Abbreviated Journal | ||
Volume | Issue | Pages | XVIII, 232 p. | ||
Keywords | Doctoral thesis; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES) | ||||
Abstract | Since its discovery 20 years ago, many studies have been performed to gain insight into the functional role of cytoglobin (Cygb). However, Cygb has been proven to be a promiscuous protein. Yet, there is a consensus that Cygb is a cytoprotective protein involved in redox homeostasis. CYGB is a ubiquitously expressed hexacoordinated globin that is highly expressed in melanocytes and is often found to be downregulated during melanocyte-to-melanoma transition. In Chapter III, we investigated the molecular mechanism through which CYGB could be involved in redox regulation. Here, we showed that CYGB contains two redox-sensitive cysteine residues and that the formation of an intramolecular disulfide bridge resulted in the heme group becoming more accessible to external ligands. This supports the hypothesis that Cys38 and Cys83 serve as sensitive redox sensors. In Chapter IV we showed that CYGB mRNA and protein levels were elevated upon exposure to hypoxia. Interestingly, this upregulation was most likely HIF-2α-dependent. We propose that in melanoma, HIF-2α, rather than HIF-1α, positively regulates CYGB under hypoxic conditions in a cell type specific way. In Chapter V, the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels was investigated. We confirmed that NTP endows cytotoxicity that induces cell death through apoptosis and that this was mediated through the production of ROS. Moreover, we showed that CYGB protects melanoma cells from ROS-induced apoptosis by the scavenging of ROS. Interestingly, CYGB expression influenced the expression of NRF2 and HO-1. We identified the lncRNA MEG3 as a possible mechanism through which NRF2 expression and its downstream target HO-1 can be regulated by CYGB. In chapter VI, increased basal ROS levels and higher degree of lipid peroxidation upon RSL3 treatment contributed to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB expression regulation was identified as a critical determinant of the ferroptosis–pyroptosis therapy response. This suggests that CYGB is involved in the regulation of multiple modes of programmed cell death. FInally, we sought to delineate the RONS that are responsible for plasma-induced ICD. Our results highlight the importance of the short-lived species. Furthermore, we are first to demonstrate that NTP-created vaccine is safely prepared and offers complete protection. Moreover, we provide conclusive evidence that direct application of NTP induces ICD in melanoma. | ||||
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Language | Wos | Publication Date | |||
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ISSN | ISBN | Additional Links | UA library record | ||
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Notes | Approved | Most recent IF: NA | |||
Call Number | UA @ admin @ c:irua:193568 | Serial | 7277 | ||
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Author | Vingerhoets, R.; Spiller, M.; De Backer, J.; Adriaens, A.; Vlaeminck, S.E.; Meers, E. | ||||
Title | Detailed nitrogen and phosphorus flow analysis, nutrient use efficiency and circularity in the agri-food system of a livestock-intensive region | Type | A1 Journal article | ||
Year | 2023 | Publication | Journal of cleaner production | Abbreviated Journal | |
Volume | 410 | Issue | Pages | 137278-13 | |
Keywords | A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) | ||||
Abstract | The agri-food value chain is a major cause of nitrogen (N) and phosphorus (P) emissions and associated environmental and health impacts. The EU's farm-to-fork strategy (F2F) demands an agri-food value chain approach to reduce nutrient emissions by 50% and fertilizer use by 20%. Substance flow analysis (SFA) is a method that can be applied to study complex systems such as the agri-food chain. A review of 60 SFA studies shows that they often lack detail by not sufficiently distinguishing between nodes, products and types of emissions. The present study aims to assess the added value of detail in SFAs and to illustrate that valuable indicators can be derived from detailed assessments. This aim will be attained by presenting a highly-detailed SFA for the livestock-intensive region of Flanders, Belgium. The SFA distinguishes 40 nodes and 1827 flows that are classified into eight different categories (e.g. by-products, point source emissions) following life cycle methods. Eight novel indicators were calculated, including indicators that assess the N and P recovery potential. Flanders has a low overall nutrient use efficiency (11% N, 18% P). About 55% of the N and 56% of the P embedded in recoverable streams are reused providing 35% and 37% of the total N and P input. Optimized nutrient recycling could replace 45% of N and 48% of P of the external nutrient input, exceeding the target set by the F2F strategy. Detailed accounting for N and P flows and nodes leads to the identification of more recoverable streams and larger N and P flows. More detailed flow accounting is a prerequisite for the quantification of technological intervention options. Future research should focus on including concentration and quality as a parameter in SFAs. | ||||
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Language | Wos | 000991013600001 | Publication Date | 2023-04-21 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0959-6526 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 11.1 | Times cited | Open Access | OpenAccess | |
Notes | Approved | Most recent IF: 11.1; 2023 IF: 5.715 | |||
Call Number | UA @ admin @ c:irua:196227 | Serial | 7770 | ||
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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. | ||||
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. | ||||
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Language | Wos | 001037058500022 | Publication Date | 2023-07-25 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 2041-1723 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 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 | Lobato, I.; De Backer, A.; Van Aert, S. | ||||
Title | Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network | Type | A1 Journal article | ||
Year | 2023 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume | 251 | Issue | Pages | 113769 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag, Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS values for a wide range of input parameters that are commonly used for aberration-corrected transmission electron microscopes. |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 001011617200001 | Publication Date | 2023-06-01 | |
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ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N and G0A7723N) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF), Belgium. | Approved | Most recent IF: 2.2; 2023 IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:197275 | Serial | 8812 | ||
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Author | Lin, A.; De Backer, J.; Quatannens, D.; Cuypers, B.; Verswyvel, H.; De La Hoz, E.C.; Ribbens, B.; Siozopoulou, V.; Van Audenaerde, J.; Marcq, E.; Lardon, F.; Laukens, K.; Vanlanduit, S.; Smits, E.; Bogaerts, A. | ||||
Title | The effect of local non‐thermal plasma therapy on the<scp>cancer‐immunity</scp>cycle in a melanoma mouse model | Type | University Hospital Antwerp | ||
Year | 2022 | Publication | Bioengineering & Translational Medicine | Abbreviated Journal | Bioengineering & Transla Med |
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Keywords | University Hospital Antwerp; A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; ADReM Data Lab (ADReM); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES) | ||||
Abstract | Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy. | ||||
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Language | Wos | 000784103500001 | Publication Date | 2022-04-21 | |
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ISSN | 2380-6761 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | OpenAccess | ||
Notes | Vlaamse regering, 1S67621N 1S76421N G044420N 12S9221N 12S9218N ; The authors would like to thank and acknowledge Christophe Hermans, Ho Wa Lau, and Hilde Lambrechts for their help with sectioning and preparing the IHC slides. The authors would also like to thank Dani Banner for designing the ergonomic NTP applicator handle and Hasan Baysal for 3D printing the pieces used in this experiment. 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. Some of the resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) The data that support the findings of this study are available from the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9218N (Abraham Lin), 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaert, and Steve Vanlanduit), 1S76421N (Delphine Quatannens), and 1S67621N (Hanne Verswyvel). Figure 7 was created with BioRender.com. | Approved | Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:187909 | Serial | 7056 | ||
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Author | De Backer, J.; Lin, A.; Berghe, W.V.; Bogaerts, A.; Hoogewijs, D. | ||||
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. | ||||
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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 | 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, J.; Maric, D.; Zuhra, K.; Bogaerts, A.; Szabo, C.; Vanden Berghe, W.; Hoogewijs, D. | ||||
Title | Cytoglobin Silencing Promotes Melanoma Malignancy but Sensitizes for Ferroptosis and Pyroptosis Therapy Response | Type | A1 Journal article | ||
Year | 2022 | Publication | Antioxidants | Abbreviated Journal | Antioxidants |
Volume | 11 | Issue | 8 | Pages | 1548 |
Keywords | A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES) | ||||
Abstract | Despite recent advances in melanoma treatment, there are still patients that either do not respond or develop resistance. This unresponsiveness and/or acquired resistance to therapy could be explained by the fact that some melanoma cells reside in a dedifferentiated state. Interestingly, this dedifferentiated state is associated with greater sensitivity to ferroptosis, a lipid peroxidation-reliant, iron-dependent form of cell death. Cytoglobin (CYGB) is an iron hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. In this study, we investigated the potential effect of CYGB on the cellular sensitivity towards (1S, 3R)-RAS-selective lethal small molecule (RSL3)-mediated ferroptosis in the G361 melanoma cells with abundant endogenous expression. Our findings show that an increased basal ROS level and higher degree of lipid peroxidation upon RSL3 treatment contribute to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB knockdown also triggers activation of the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome and subsequent induction of pyroptosis target genes. Altogether, we show that silencing of CYGB expression modulates cancer therapy sensitivity via regulation of ferroptosis and pyroptosis cell death signaling pathways. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000846411000001 | Publication Date | 2022-08-10 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2076-3921 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7 | Times cited | Open Access | OpenAccess | |
Notes | Approved | Most recent IF: 7 | |||
Call Number | PLASMANT @ plasmant @c:irua:190686 | Serial | 7102 | ||
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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. | ||||
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. | ||||
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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 | 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 | De Backer, A.; Van Aert, S.; Faes, C.; Arslan Irmak, E.; Nellist, P.D.; Jones, L. | ||||
Title | Experimental reconstructions of 3D atomic structures from electron microscopy images using a Bayesian genetic algorithm | Type | A1 Journal article | ||
Year | 2022 | Publication | N P J Computational Materials | Abbreviated Journal | npj Comput Mater |
Volume | 8 | Issue | 1 | Pages | 216 |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | We introduce a Bayesian genetic algorithm for reconstructing atomic models of monotype crystalline nanoparticles from a single projection using Z-contrast imaging. The number of atoms in a projected atomic column obtained from annular dark field scanning transmission electron microscopy images serves as an input for the initial three-dimensional model. The algorithm minimizes the energy of the structure while utilizing a priori information about the finite precision of the atom-counting results and neighbor-mass relations. The results show promising prospects for obtaining reliable reconstructions of beam-sensitive nanoparticles during dynamical processes from images acquired with sufficiently low incident electron doses. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000866500900001 | Publication Date | 2022-10-12 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2057-3960 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | OpenAccess | ||
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A. 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. L.J. acknowledges Science Foundation Ireland (SFI – grant number URF/RI/191637), the Royal Society, and the AMBER Centre. The authors acknowledge Aakash Varambhia for his assistance and expertise with the experimental recording and use of characterization facilities within the David Cockayne Centre for Electron Microscopy, Department of Materials, University of Oxford, and in particular the EPSRC (EP/K040375/1 South of England Analytical Electron Microscope).; esteem3reported; esteem3JRA | Approved | Most recent IF: NA | ||
Call Number | EMAT @ emat @c:irua:191398 | Serial | 7114 | ||
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Author | De wael, A.; De Backer, A.; Yu, C.-P.; Sentürk, D.G.; Lobato, I.; Faes, C.; Van Aert, S. | ||||
Title | Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM | Type | A1 Journal article | ||
Year | 2022 | Publication | Microscopy and microanalysis | Abbreviated Journal | Microsc Microanal |
Volume | Issue | Pages | 1-9 | ||
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000854930500001 | Publication Date | 2022-09-19 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1431-9276 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 2.8 | Times cited | Open Access | OpenAccess | |
Notes | This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp. The authors are grateful to L.M. Liz-Marzán (CIC biomaGUNE and Ikerbasque) for providing the samples. esteem3reported; esteem3jra | Approved | Most recent IF: 2.8 | ||
Call Number | EMAT @ emat @c:irua:190585 | Serial | 7119 | ||
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Author | Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S. | ||||
Title | Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors | Type | A1 Journal article | ||
Year | 2022 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume | 242 | Issue | Pages | 113626 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose. |
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000873778100001 | Publication Date | 0000-00-00 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra | Approved | Most recent IF: 2.2 | ||
Call Number | EMAT @ emat @c:irua:190925 | Serial | 7118 | ||
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Author | Attri, P.; Kaushik, N.K.; Kaushik, N.; Hammerschmid, D.; Privat-Maldonado, A.; De Backer, J.; Shiratani, M.; Choi, E.H.; Bogaerts, A. | ||||
Title | Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells | Type | A1 Journal Article | ||
Year | 2021 | Publication | International Journal Of Biological Macromolecules | Abbreviated Journal | Int J Biol Macromol |
Volume | 182 | Issue | Pages | 1724-1736 | |
Keywords | A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
Abstract | Bacterial and mammalian proteins, such as lysozyme, are gaining increasing interest as anticancer drugs. This study aims to modify the lysozyme structure using cold atmospheric plasma to boost its cancer cell killing effect. We investigated the structure at acidic and neutral pH using various experimental techniques (circular dichroism, fluorescence, and mass spectrometry) and molecular dynamics simulations. The controlled structural modification of lysozyme at neutral pH enhances its activity, while the activity was lost at acidic pH at the same treatment conditions. Indeed, a larger number of amino acids were oxidized at acidic pH after plasma treatment, which results in a greater distortion of the lysozyme structure, whereas only limited structural changes were observed in lysozyme after plasma treatment at neutral pH. We found that the plasma-treated lysozyme significantly induced apoptosis to the cancer cells. Our results reveal that plasma-treated lysozyme could have potential as a new cancer cell killing drug. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000675794700005 | Publication Date | 2021-05-27 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0141-8130 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.671 | Times cited | Open Access | OpenAccess | |
Notes | Japan Society for the Promotion of Science; We gratefully acknowledge the European H2020 Marie SkłodowskaCurie Actions Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. NK thanks to National Research Foundation of Korea under Ministry of Science and ICT (NRF2021R1C1C1013875) of Korean Government. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. | Approved | Most recent IF: 3.671 | ||
Call Number | PLASMANT @ plasmant @c:irua:178813 | Serial | 6792 | ||
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Author | Liu, P.; Arslan Irmak, E.; De Backer, A.; De wael, A.; Lobato, I.; Béché, A.; Van Aert, S.; Bals, S. | ||||
Title | Three-dimensional atomic structure of supported Au nanoparticles at high temperature | Type | A1 Journal article | ||
Year | 2021 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
Volume | 13 | Issue | Pages | ||
Keywords | A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) | ||||
Abstract | Au nanoparticles (NPs) deposited on CeO2 are extensively used as thermal catalysts since the morphology of the NPs is expected to be stable at elevated temperatures. Although it is well known that the activity of Au NPs depends on their size and surface structure, their three-dimensional (3D) structure at the atomic scale has not been completely characterized as a function of temperature. In this paper, we overcome the limitations of conventional electron tomography by combining atom counting applied to aberration-corrected scanning transmission electron microscopy images and molecular dynamics relaxation. In this manner, we are able to perform an atomic resolution 3D investigation of supported Au NPs. Our results enable us to characterize the 3D equilibrium structure of single NPs as a function of temperature. Moreover, the dynamic 3D structural evolution of the NPs at high temperatures, including surface layer jumping and crystalline transformations, has been studied. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000612999200029 | Publication Date | 2020-12-29 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2040-3364 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.367 | Times cited | 13 | Open Access | OpenAccess |
Notes | This work was supported by the European Research Council (Grant 815128 REALNANO to SB, Grant 770887 PICOMETRICS to SVA, Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A. D. w. and A. D. B. and project funding G.0267.18N.; sygma; esteem3JRA; esteem3reported | Approved | Most recent IF: 7.367 | ||
Call Number | EMAT @ emat @c:irua:174858 | Serial | 6665 | ||
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Author | Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A. | ||||
Title | Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma | Type | A1 Journal article | ||
Year | 2021 | Publication | Cancers | Abbreviated Journal | Cancers |
Volume | 13 | Issue | 3 | Pages | 579 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE) | ||||
Abstract | Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000614960600001 | Publication Date | 2021-02-02 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2072-6694 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | OpenAccess | ||
Notes | We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. | Approved | Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:176455 | Serial | 6709 | ||
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Author | Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S. | ||||
Title | Atom column detection | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 177-214 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | By combining statistical parameter estimation and model-order selection using a Bayesian framework, the maximum a posteriori (MAP) probability rule is proposed in this chapter as an objective and quantitative method to detect atom columns from high-resolution scanning transmission electron microscopy (HRSTEM) images. The validity and usefulness of this approach is demonstrated to both simulated and experimental annular dark-field (ADF) STEM images, but also to simultaneously acquired annular bright-field (ABF) and ADF STEM image data. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177531 | Serial | 6775 | ||
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Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
Title | Atom counting | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 91-144 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | In this chapter, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. We show that this method can be applied to nanocrystals of arbitrary shape, size, and atom type. The validity of the atom-counting results is confirmed by means of detailed image simulations and it is shown that the high sensitivity of our method enables us to count atoms with single atom sensitivity. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177529 | Serial | 6776 | ||
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Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
Title | Efficient fitting algorithm | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 73-90 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT) | ||||
Abstract | An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic-resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177528 | Serial | 6778 | ||
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Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
Title | General conclusions and future perspectives | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 243-253 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | This chapter provides an overview of statistical and quantitative methodologies that have pushed (scanning) transmission electron microscopy ((S)TEM) toward accurate and precise measurements of unknown structure parameters for understanding the relation between the structure of a material and its properties. Hereby, statistical parameter estimation theory has extensively been used which enabled not only measuring atomic column positions, but also quantifying the number of atoms, and detecting atomic columns as accurately and precisely as possible from experimental images. As a general conclusion, it can be stated that advanced statistical techniques are ideal tools to perform quantitative electron microscopy at the atomic scale. In the future, statistical methods will continue to be developed and novel quantification procedures will open up new possibilities for studying material structures at the atomic scale. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177533 | Serial | 6781 | ||
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Author | Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S. | ||||
Title | Image-quality evaluation and model selection with maximum a posteriori probability | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 215-242 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | The maximum a posteriori (MAP) probability rule for atom column detection can also be used as a tool to evaluate the relation between scanning transmission electron microscopy (STEM) image quality and atom detectability. In this chapter, a new image-quality measure is proposed that correlates well with atom detectability, namely the integrated contrast-to-noise ratio (ICNR). Furthermore, the working principle of the MAP probability rule is described in detail showing a close relation to the principles of model-selection methods. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177532 | Serial | 6782 | ||
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Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
Title | Introduction | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 1-28 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT) | ||||
Abstract | |||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177525 | Serial | 6784 | ||
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Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
Title | Optimal experiment design for nanoparticle atom counting from ADF STEM images | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 145-175 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | In this chapter, the principles of detection theory are used to quantify the probability of error for atom counting from high-resolution scanning transmission electron microscopy (HRSTEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom counting using the expression of the probability of error. We show that for very thin objects the low-angle annular dark-field (LAADF) regime is optimal and that for thicker objects the optimal inner detector angle increases. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177530 | Serial | 6785 | ||
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Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
Title | Statistical parameter estimation theory : principles and simulation studies | Type | H2 Book chapter | ||
Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
Volume | Issue | Pages | 29-72 | ||
Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | In this chapter, the principles of statistical parameter estimation theory for a quantitative analysis of atomic-resolution electron microscopy images are introduced. Within this framework, electron microscopy images are described by a parametric statistical model. Here, parametric models are introduced for different types of electron microscopy images: reconstructed exit waves, annular dark-field (ADF) scanning transmission electron microscopy (STEM) images, and simultaneously acquired ADF and annular bright-field (ABF) STEM images. Furthermore, the Cramér-Rao lower bound (CRLB) is introduced, i.e. a theoretical lower bound on the variance of any unbiased estimator. This CRLB is used to quantify the precision of the structure parameters of interest, such as the atomic column positions and the integrated atomic column intensities. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2021-03-06 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | 217 | Series Issue | Edition | ||
ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
Call Number | UA @ admin @ c:irua:177527 | Serial | 6788 | ||
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Author | De wael, A.; De Backer, A.; Lobato, I.; Van Aert, S. | ||||
Title | Modelling ADF STEM images using elliptical Gaussian peaks and its effects on the quantification of structure parameters in the presence of sample tilt | Type | A1 Journal article | ||
Year | 2021 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume | Issue | Pages | 113391 | ||
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | A small sample tilt away from a main zone axis orientation results in an elongation of the atomic columns in ADF STEM images. An often posed research question is therefore whether the ADF STEM image intensities of tilted nanomaterials should be quantified using a parametric imaging model consisting of elliptical rather than the currently used symmetrical peaks. To this purpose, simulated ADF STEM images corresponding to different amounts of sample tilt are studied using a parametric imaging model that consists of superimposed 2D elliptical Gaussian peaks on the one hand and symmetrical Gaussian peaks on the other hand. We investigate the quantification of structural parameters such as atomic column positions and scattering cross sections using both parametric imaging models. In this manner, we quantitatively study what can be gained from this elliptical model for quantitative ADF STEM, despite the increased parameter space and computational effort. Although a qualitative improvement can be achieved, no significant quantitative improvement in the estimated structure parameters is achieved by the elliptical model as compared to the symmetrical model. The decrease in scattering cross sections with increasing sample tilt is even identical for both types of parametric imaging models. This impedes direct comparison with zone axis image simulations. Nonetheless, we demonstrate how reliable atom-counting can still be achieved in the presence of small sample tilt. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000704334200001 | Publication Date | 2021-09-24 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.843 | Times cited | Open Access | OpenAccess | |
Notes | This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp.; esteem3JRA; esteem3reported | Approved | Most recent IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:181462 | Serial | 6810 | ||
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Author | Hudry, D.; De Backer, A.; Popescu, R.; Busko, D.; Howard, I.A.; Bals, S.; Zhang, Y.; Pedrazo‐Tardajos, A.; Van Aert, S.; Gerthsen, D.; Altantzis, T.; Richards, B.S. | ||||
Title | Interface Pattern Engineering in Core‐Shell Upconverting Nanocrystals: Shedding Light on Critical Parameters and Consequences for the Photoluminescence Properties | Type | A1 Journal article | ||
Year | 2021 | Publication | Small | Abbreviated Journal | Small |
Volume | Issue | Pages | 2104441 | ||
Keywords | A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT) | ||||
Abstract | Advances in controlling energy migration pathways in core-shell lanthanide (Ln)-based hetero-nanocrystals (HNCs) have relied heavily on assumptions about how optically active centers are distributed within individual HNCs. In this article, it is demonstrated that different types of interface patterns can be formed depending on shell growth conditions. Such interface patterns are not only identified but also characterized with spatial resolution ranging from the nanometer- to the atomic-scale. In the most favorable cases, atomic-scale resolved maps of individual particles are obtained. It is also demonstrated that, for the same type of core-shell architecture, the interface pattern can be engineered with thicknesses of just 1 nm up to several tens of nanometers. Total alloying between the core and shell domains is also possible when using ultra-small particles as seeds. Finally, with different types of interface patterns (same architecture and chemical composition of the core and shell domains) it is possible to modify the output color (yellow, red, and green-yellow) or change (improvement or degradation) the absolute upconversion quantum yield. The results presented in this article introduce an important paradigm shift and pave the way toward the emergence of a new generation of core-shell Ln-based HNCs with better control over their atomic-scale organization. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000710758000001 | Publication Date | 2021-10-25 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1613-6810 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.643 | Times cited | 17 | Open Access | OpenAccess |
Notes | The authors would like to acknowledge the financial support provided by the Helmholtz Recruitment Initiative Fellowship (B.S.R.) and the Helmholtz Association's Research Field Energy (Materials and Technologies for the Energy Transition program, Topic 1 Photovoltaics and Wind Energy). The authors would like to thank the Karlsruhe Nano Micro Facility (KNMF) for STEM access. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme (Grant agreement no. 770887 PICOMETRICS to S.V.A. and Grant agreement no. 815128 REALNANO to S.B.). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through Projects no. G.0502.18N, G.0267.18N, and a postdoctoral grant to A.D.B. T.A. acknowledges funding from the University of Antwerp Research fund (BOF). This project had received funding (EUSMI proposal #E181100205) from the European Union's Horizon 2020 Research and Innovation Programme under Grant agreement no 731019 (EUSMI). D.H. would like to thank “CGFigures” for helpful tutorials on 3D graphics with Blender.; sygmaSB | Approved | Most recent IF: 8.643 | ||
Call Number | EMAT @ emat @c:irua:183285 | Serial | 6817 | ||
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Author | De wael, A.; De Backer, A.; Jones, L.; Varambhia, A.; Nellist, P.D.; Van Aert, S. | ||||
Title | Measuring Dynamic Structural Changes of Nanoparticles at the Atomic Scale Using Scanning Transmission Electron Microscopy | Type | A1 Journal article | ||
Year | 2020 | Publication | Physical Review Letters | Abbreviated Journal | Phys Rev Lett |
Volume | 124 | Issue | 10 | Pages | 106105 |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | We propose a new method to measure atomic scale dynamics of nanoparticles from experimental high-resolution annular dark field scanning transmission electron microscopy images. By using the so-called hidden Markov model, which explicitly models the possibility of structural changes, the number of atoms in each atomic column can be quantified over time. This newly proposed method outperforms the current atom-counting procedure and enables the determination of the probabilities and cross sections for surface diffusion. This method is therefore of great importance for revealing and quantifying the atomic structure when it evolves over time via adatom dynamics, surface diffusion, beam effects, or during in situ experiments. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000519718100015 | Publication Date | 2020-03-13 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0031-9007 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.6 | Times cited | Open Access | OpenAccess | |
Notes | This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N and EOS 30489208. L.J. acknowledges the SFI AMBER Centre for support. A.V. and P.D.N. acknowledge the UK Engineering and Physical Sciences Council (EPSRC) for support (EP/K040375/1 and 1772738). A.V. also acknowledges Johnson-Matthey for support. We would like to thank Brian Theobald and Jonathan Sharman from JMTC Sonning for provision of the Pt sample. | Approved | Most recent IF: 8.6; 2020 IF: 8.462 | ||
Call Number | EMAT @ emat @c:irua:167148 | Serial | 6347 | ||
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