“Atom counting from a combination of two ADF STEM images”. Şentürk DG, Yu CP, De Backer A, Van Aert S, Ultramicroscopy 255, 113859 (2024). http://doi.org/10.1016/j.ultramic.2023.113859
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.2
DOI: 10.1016/j.ultramic.2023.113859
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“Preventing cation intermixing enables 50% quantum yield in sub-15 nm short-wave infrared-emitting rare-earth based core-shell nanocrystals”. Arteaga Cardona F, Jain N, Popescu R, Busko D, Madirov E, Arús BA, Gerthsen D, De Backer A, Bals S, Bruns OT, Chmyrov A, Van Aert S, Richards BS, Hudry D, Nature communications 14, 4462 (2023). http://doi.org/10.1038/s41467-023-40031-4
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 16.6
Times cited: 1
DOI: 10.1038/s41467-023-40031-4
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“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”. Lobato I, De Backer A, Van Aert S, Ultramicroscopy 251, 113769 (2023). http://doi.org/10.1016/j.ultramic.2023.113769
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.2
DOI: 10.1016/j.ultramic.2023.113769
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“Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions”. Zhang Z, Lobato I, De Backer A, Van Aert S, Nellist P, Ultramicroscopy 246, 113671 (2023). http://doi.org/10.1016/j.ultramic.2022.113671
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.2
DOI: 10.1016/j.ultramic.2022.113671
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“Detailed nitrogen and phosphorus flow analysis, nutrient use efficiency and circularity in the agri-food system of a livestock-intensive region”. Vingerhoets R, Spiller M, De Backer J, Adriaens A, Vlaeminck SE, Meers E, Journal of cleaner production 410, 137278 (2023). http://doi.org/10.1016/J.JCLEPRO.2023.137278
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 11.1
DOI: 10.1016/J.JCLEPRO.2023.137278
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“A decade of atom-counting in STEM: From the first results toward reliable 3D atomic models from a single projection”. De Backer A, Bals S, Van Aert S, Ultramicroscopy , 113702 (2023). http://doi.org/10.1016/j.ultramic.2023.113702
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.2
Times cited: 3
DOI: 10.1016/j.ultramic.2023.113702
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“Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma”. Lin A, Sahun M, Biscop E, Verswyvel H, De Waele J, De Backer J, Theys C, Cuypers B, Laukens K, Berghe WV, Smits E, Bogaerts A, Drug resistance updates 67, 100914 (2023). http://doi.org/10.1016/j.drup.2022.100914
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.
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)
Impact Factor: 24.3
DOI: 10.1016/j.drup.2022.100914
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“Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors”. Sentürk DG, De Backer A, Friedrich T, Van Aert S, Ultramicroscopy 242, 113626 (2022). http://doi.org/10.1016/j.ultramic.2022.113626
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.2
DOI: 10.1016/j.ultramic.2022.113626
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“Experimental reconstructions of 3D atomic structures from electron microscopy images using a Bayesian genetic algorithm”. De Backer A, Van Aert S, Faes C, Arslan Irmak E, Nellist PD, Jones L, N P J Computational Materials 8, 216 (2022). http://doi.org/10.1038/s41524-022-00900-w
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
DOI: 10.1038/s41524-022-00900-w
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“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”. De Backer A, Zhang Z, van den Bos KHW, Bladt E, Sánchez‐Iglesias A, Liz‐Marzán LM, Nellist PD, Bals S, Van Aert S, Small methods , 2200875 (2022). http://doi.org/10.1002/smtd.202200875
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 12.4
Times cited: 5
DOI: 10.1002/smtd.202200875
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“Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM”. De wael A, De Backer A, Yu C-P, Sentürk DG, Lobato I, Faes C, Van Aert S, Microscopy and microanalysis , 1 (2022). http://doi.org/10.1017/S1431927622012284
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.8
DOI: 10.1017/S1431927622012284
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“Cytoglobin Silencing Promotes Melanoma Malignancy but Sensitizes for Ferroptosis and Pyroptosis Therapy Response”. De Backer J, Maric D, Zuhra K, Bogaerts A, Szabo C, Vanden Berghe W, Hoogewijs D, Antioxidants 11, 1548 (2022). http://doi.org/10.3390/antiox11081548
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.
Keywords: A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
Impact Factor: 7
DOI: 10.3390/antiox11081548
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“Cytoglobin inhibits non-thermal plasma-induced apoptosis in melanoma cells through regulation of the NRF2-mediated antioxidant response”. De Backer J, Lin A, Berghe WV, Bogaerts A, Hoogewijs D, Redox Biology 55, 102399 (2022). http://doi.org/10.1016/j.redox.2022.102399
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
Impact Factor: 11.4
DOI: 10.1016/j.redox.2022.102399
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Lin A, De Backer J, Quatannens D, Cuypers B, Verswyvel H, De La Hoz EC, Ribbens B, Siozopoulou V, Van Audenaerde J, Marcq E, Lardon F, Laukens K, Vanlanduit S, Smits E, Bogaerts A (2022) The effect of local non‐thermal plasma therapy on the<scp>cancer‐immunity</scp>cycle in a melanoma mouse model
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.
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)
DOI: 10.1002/btm2.10314
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“Interface Pattern Engineering in Core‐Shell Upconverting Nanocrystals: Shedding Light on Critical Parameters and Consequences for the Photoluminescence Properties”. Hudry D, De Backer A, Popescu R, Busko D, Howard IA, Bals S, Zhang Y, Pedrazo‐Tardajos A, Van Aert S, Gerthsen D, Altantzis T, Richards BS, Small , 2104441 (2021). http://doi.org/10.1002/smll.202104441
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT)
Impact Factor: 8.643
Times cited: 17
DOI: 10.1002/smll.202104441
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“Modelling ADF STEM images using elliptical Gaussian peaks and its effects on the quantification of structure parameters in the presence of sample tilt”. De wael A, De Backer A, Lobato I, Van Aert S, Ultramicroscopy , 113391 (2021). http://doi.org/10.1016/j.ultramic.2021.113391
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
DOI: 10.1016/j.ultramic.2021.113391
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“Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells”. Attri P, Kaushik NK, Kaushik N, Hammerschmid D, Privat-Maldonado A, De Backer J, Shiratani M, Choi EH, Bogaerts A, International Journal Of Biological Macromolecules 182, 1724 (2021). http://doi.org/10.1016/j.ijbiomac.2021.05.146
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.
Keywords: A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 3.671
DOI: 10.1016/j.ijbiomac.2021.05.146
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“Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma”. 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, Cancers 13, 579 (2021). http://doi.org/10.3390/cancers13030579
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
DOI: 10.3390/cancers13030579
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“Three-dimensional atomic structure of supported Au nanoparticles at high temperature”. Liu P, Arslan Irmak E, De Backer A, De wael A, Lobato I, Béché, A, Van Aert S, Bals S, Nanoscale 13 (2021). http://doi.org/10.1039/D0NR08664A
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 7.367
Times cited: 13
DOI: 10.1039/D0NR08664A
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“Hidden Markov model for atom-counting from sequential ADF STEM images: Methodology, possibilities and limitations”. De wael A, De Backer A, Van Aert S, Ultramicroscopy 219, 113131 (2020). http://doi.org/10.1016/j.ultramic.2020.113131
Abstract: We present a quantitative method which allows us to reliably measure dynamic changes in the atomic structure of monatomic crystalline nanomaterials from a time series of atomic resolution annular dark field scanning transmission electron microscopy images. The approach is based on the so-called hidden Markov model and estimates the number of atoms in each atomic column of the nanomaterial in each frame of the time series. We discuss the origin of the improved performance for time series atom-counting as compared to the current state-of-the-art atom-counting procedures, and show that the so-called transition probabilities that describe the probability for an atomic column to lose or gain one or more atoms from frame to frame are particularly important. Using these transition probabilities, we show that the method can also be used to estimate the probability and cross section related to structural changes. Furthermore, we explore the possibilities for applying the method to time series recorded under variable environmental conditions. The method is shown to be promising for a reliable quantitative analysis of dynamic processes such as surface diffusion, adatom dynamics, beam effects, or in situ experiments.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.2
DOI: 10.1016/j.ultramic.2020.113131
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“Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study”. Attri P, Park J-H, De Backer J, Kim M, Yun J-H, Heo Y, Dewilde S, Shiratani M, Choi EH, Lee W, Bogaerts A, International Journal Of Biological Macromolecules 163, 2405 (2020). http://doi.org/10.1016/j.ijbiomac.2020.09.120
Abstract: NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, firstly we purified the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, fluorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modification/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 8.2
DOI: 10.1016/j.ijbiomac.2020.09.120
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“Measuring Dynamic Structural Changes of Nanoparticles at the Atomic Scale Using Scanning Transmission Electron Microscopy”. De wael A, De Backer A, Jones L, Varambhia A, Nellist PD, Van Aert S, Physical Review Letters 124, 106105 (2020). http://doi.org/10.1103/PhysRevLett.124.106105
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 8.6
DOI: 10.1103/PhysRevLett.124.106105
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“Quantifying Strain and Dislocation Density at Nanocube Interfaces after Assembly and Epitaxy”. Agrawal H, Patra BK, Altantzis T, De Backer A, Garnett EC, Acs Applied Materials &, Interfaces 12, 8788 (2020). http://doi.org/10.1021/acsami.9b17779
Abstract: Nanoparticle self-assembly and epitaxy are utilized extensively to make 1D and 2D structures with complex shapes. High-resolution transmission electron microscopy (HRTEM) has shown that single-crystalline interfaces can form, but little is known about the strain and dislocations at these interfaces. Such information is critically important for applications: drastically reducing
dislocation density was the key breakthrough enabling widespread implementation of light-emitting diodes, while strain engineering has been fundamental to modern high-performance transistors, solar cells, and thermoelectrics. In this work, the interfacial defect and strain formation after selfassembly and room temperature epitaxy of 7 nm Pd nanocubes capped with polyvinylpyrrolidone (PVP) is examined. It is observed that, during ligand removal, the cubes move over large distances on the substrate, leading to both spontaneous self-assembly and epitaxy to form single crystals. Subsequently, atomically resolved images are used to quantify the strain and dislocation density at the epitaxial interfaces between cubes with different lateral and angular misorientations. It is shown that dislocation- and strain-free interfaces form when the nanocubes align parallel to each other. Angular misalignment between adjacent cubes does not necessarily lead to grain boundaries but does cause dislocations, with higher densities associated with larger rotations.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT)
Impact Factor: 9.5
DOI: 10.1021/acsami.9b17779
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“Locating and controlling the Zn content in In(Zn)P quantum dots”. Kirkwood N, De Backer A, Altantzis T, Winckelmans N, Longo A, Antolinez FV, Rabouw FT, De Trizio L, Geuchies JJ, Mulder JT, Renaud N, Bals S, Manna L, Houtepen AJ, Chemistry of materials 32, 557 (2019). http://doi.org/10.1021/acs.chemmater.9b04407
Abstract: Zinc is routinely employed in the synthesis of InP quantum dots (QDs) to improve the photoluminescence efficiency and carrier mobility of the resulting In(Zn)P alloy nanostructures. The exact location of Zn in the final structures and the mechanism by which it enhances the optoelectronic properties of the QDs is debated. We use synchrotron X-ray absorbance spectroscopy to show that the majority of Zn in In(Zn)P QDs is located at their surface as Zn-carboxylates. However, a small amount of Zn is present inside the bulk of the QDs with the consequent contraction of their lattice, as confirmed by combining high resolution high-angle annular dark-field imaging scanning transmission electron microscopy (HAADF-STEM) with statistical parameter estimation theory. We further demonstrate that the Zn content and its incorporation into the QDs can be tuned by the ligation of commonly employed Zn carboxylate precursors: the use of highly reactive Zn-acetate leads to the formation of undesired Zn3P2 and the final nanostructures being characterized by broad optical features, whereas Zn-carboxylates with longer carbon chains lead to InP crystals with much lower zinc content and narrow optical features. These results can explain the differences between structural and optical properties of In(Zn)P samples reported across the literature, and provide a rational method to tune the amount of Zn in InP nanocrystals and to drive the incorporation of Zn either as surface Zn-carboxylate, as a substitutional dopant inside the InP crystal lattice, or even predominantly as Zn3P2.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 9.466
Times cited: 39
DOI: 10.1021/acs.chemmater.9b04407
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“Influence of Cell Type and Culture Medium on Determining Cancer Selectivity of Cold Atmospheric Plasma Treatment”. Biscop, Lin, Boxem, Loenhout, Backer, Deben, Dewilde, Smits, Bogaerts, Cancers 11, 1287 (2019). http://doi.org/10.3390/cancers11091287
Abstract: Increasing the selectivity of cancer treatments is attractive, as it has the potential to reduce side-effects of therapy. Cold atmospheric plasma (CAP) is a novel cancer treatment that disrupts the intracellular oxidative balance. Several reports claim CAP treatment to be selective, but retrospective analysis of these studies revealed discrepancies in several biological factors and culturing methods. Before CAP can be conclusively stated as a selective cancer treatment, the importance of these factors must be investigated. In this study, we evaluated the influence of the cell type, cancer type, and cell culture medium on direct and indirect CAP treatment. Comparison of cancerous cells with their non-cancerous counterparts was performed under standardized conditions to determine selectivity of treatment. Analysis of seven human cell lines (cancerous: A549, U87, A375, and Malme-3M; non-cancerous: BEAS-2B, HA, and HEMa) and five different cell culture media (DMEM, RPMI1640, AM, BEGM, and DCBM) revealed that the tested parameters strongly influence indirect CAP treatment, while direct treatment was less affected. Taken together, the results of our study demonstrate that cell type, cancer type, and culturing medium must be taken into account before selectivity of CAP treatment can be claimed and overlooking these parameters can easily result in inaccurate conclusions of selectivity.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Times cited: 9
DOI: 10.3390/cancers11091287
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“The atomic lensing model: new opportunities for atom-by-atom metrology of heterogeneous nanomaterials”. van den Bos KHW, Janssens L, De Backer A, Nellist PD, Van Aert S, Ultramicroscopy 203, 155 (2019). http://doi.org/10.1016/j.ultramic.2018.12.004
Abstract: The atomic lensing model has been proposed as a promising method facilitating atom-counting in heterogeneous nanocrystals [1]. Here, image simulations will validate the model, which describes dynamical diffraction as a superposition of individual atoms focussing the incident electrons. It will be demonstrated that the model is reliable in the annular dark field regime for crystals having columns containing dozens of atoms. By using the principles of statistical detection theory, it will be shown that this model gives new opportunities for detecting compositional differences.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 4
DOI: 10.1016/j.ultramic.2018.12.004
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“Non‐Thermal Plasma as a Unique Delivery System of Short‐Lived Reactive Oxygen and Nitrogen Species for Immunogenic Cell Death in Melanoma Cells”. Lin A, Gorbanev Y, De Backer J, Van Loenhout J, Van Boxem W, Lemière F, Cos P, Dewilde S, Smits E, Bogaerts A, Advanced Science 6, 1802062 (2019). http://doi.org/10.1002/advs.201802062
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
Impact Factor: 9.034
Times cited: 39
DOI: 10.1002/advs.201802062
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“Control of Knock-On Damage for 3D Atomic Scale Quantification of Nanostructures: Making Every Electron Count in Scanning Transmission Electron Microscopy”. Van Aert S, De Backer A, Jones L, Martinez GT, Béché, A, Nellist PD, Physical review letters 122, 066101 (2019). http://doi.org/10.1103/PhysRevLett.122.066101
Abstract: Understanding nanostructures down to the atomic level is the key to optimizing the design of advancedmaterials with revolutionary novel properties. This requires characterization methods capable of quantifying the three-dimensional (3D) atomic structure with the highest possible precision. A successful approach to reach this goal is to count the number of atoms in each atomic column from 2D annular dark field scanning transmission electron microscopy images. To count atoms with single atom sensitivity, a minimum electron dose has been shown to be necessary, while on the other hand beam damage, induced by the high energy electrons, puts a limit on the tolerable dose. An important challenge is therefore to develop experimental strategies to optimize the electron dose by balancing atom-counting fidelity vs the risk of knock-on damage. To achieve this goal, a statistical framework combined with physics-based modeling of the dose-dependent processes is here proposed and experimentally verified. This model enables an investigator to theoretically predict, in advance of an experimental measurement, the optimal electron dose resulting in an unambiguous quantification of nanostructures in their native state with the highest attainable precision.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 8.462
Times cited: 3
DOI: 10.1103/PhysRevLett.122.066101
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“Three-Dimensional Quantification of the Facet Evolution of Pt Nanoparticles in a Variable Gaseous Environment”. Altantzis T, Lobato I, De Backer A, Béché, A, Zhang Y, Basak S, Porcu M, Xu Q, Sánchez-Iglesias A, Liz-Marzán LM, Van Tendeloo G, Van Aert S, Bals S, Nano letters 19, 477 (2019). http://doi.org/10.1021/acs.nanolett.8b04303
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 12.712
Times cited: 82
DOI: 10.1021/acs.nanolett.8b04303
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“The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor”. De Backer J, Razzokov J, Hammerschmid D, Mensch C, Hafideddine Z, Kumar N, van Raemdonck G, Yusupov M, Van Doorslaer S, Johannessen C, Sobott F, Bogaerts A, Dewilde S, Redox Biology 19, 1 (2018). http://doi.org/10.1016/j.redox.2018.07.019
Abstract: Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
Impact Factor: 6.337
DOI: 10.1016/j.redox.2018.07.019
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