“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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“Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure”. Alania M, Altantzis T, De Backer A, Lobato I, Bals S, Van Aert S, Ultramicroscopy 177, 36 (2016). http://doi.org/10.1016/j.ultramic.2016.11.002
Abstract: Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 13
DOI: 10.1016/j.ultramic.2016.11.002
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“How precise can atoms of a nanocluster be located in 3D using a tilt series of scanning transmission electron microscopy images?”.Alania M, De Backer A, Lobato I, Krause FF, Van Dyck D, Rosenauer A, Van Aert S, Ultramicroscopy 181, 134 (2017). http://doi.org/10.1016/j.ultramic.2016.12.013
Abstract: In this paper, we investigate how precise atoms of a small nanocluster can ultimately be located in three dimensions (3D) from a tilt series of images acquired using annular dark field (ADF) scanning transmission electron microscopy (STEM). Therefore, we derive an expression for the statistical precision with which the 3D atomic position coordinates can be estimated in a quantitative analysis. Evaluating this statistical precision as a function of the microscope settings also allows us to derive the optimal experimental design. In this manner, the optimal angular tilt range, required electron dose, optimal detector angles, and number of projection images can be determined.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 3
DOI: 10.1016/j.ultramic.2016.12.013
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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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“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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“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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“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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“Atomic resolution electron tomography”. Bals S, Goris B, de Backer A, Van Aert S, Van Tendeloo G, MRS bulletin 41, 525 (2016). http://doi.org/10.1557/mrs.2016.138
Abstract: Over the last two decades, three-dimensional (3D) imaging by transmission electron microscopy or “electron tomography” has evolved into a powerful tool to investigate a variety of nanomaterials in different fields, such as life sciences, chemistry, solid-state physics, and materials science. Most of these results were obtained with nanometer-scale resolution, but different approaches have recently pushed the resolution to the atomic level. Such information is a prerequisite to understand the specific relationship between the atomic structure and the physicochemical properties of (nano) materials. We provide an overview of the latest progress in the field of atomic-resolution electron tomography. Different imaging and reconstruction approaches are presented, and state-of-the-art results are discussed. This article demonstrates the power and importance of electron tomography with atomic-scale resolution.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 5.199
Times cited: 19
DOI: 10.1557/mrs.2016.138
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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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de Backer A (2015) Quantitative atomic resolution electron microscopy using advanced statistical techniques. Antwerpen
Keywords: Doctoral thesis; Electron microscopy for materials research (EMAT)
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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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“Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting: What are the limits?”.De Backer A, De Wael A, Gonnissen J, Martinez GT, Béché, A, MacArthur KE, Jones L, Nellist PD, Van Aert S, Journal of physics : conference series 644Electron Microscopy and Analysis Group Conference (EMAG), JUN 02-JUL 02, 2015, Manchester, ENGLAND, 012034 (2015). http://doi.org/10.1088/1742-6596/644/1/012034
Abstract: Quantitative atomic resolution annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique for nanoparticle atom-counting. However, a lot of nanoparticles provide a severe characterisation challenge because of their limited size and beam sensitivity. Therefore, quantitative ADF STEM may greatly benefit from statistical detection theory in order to optimise the instrumental microscope settings such that the incoming electron dose can be kept as low as possible whilst still retaining single-atom precision. The principles of detection theory are used to quantify the probability of error for atom-counting. This enables us to decide between different image performance measures and to optimise the experimental detector settings for atom-counting in ADF STEM in an objective manner. To demonstrate this, ADF STEM imaging of an industrial catalyst has been conducted using the near-optimal detector settings. For this experiment, we discussed the limits for atom-counting diagnosed by combining a thorough statistical method and detailed image simulations.
Keywords: P1 Proceeding; Electron microscopy for materials research (EMAT)
DOI: 10.1088/1742-6596/644/1/012034
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“Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting : what are the limits?”.de Backer A, De wael A, Gonnissen J, Martinez GT, Béché, A, MacArthur KE, Jones L, Nellist PD, Van Aert S, Journal of physics : conference series 644, 012034 (2015). http://doi.org/10.1088/1742-6596/644/012034
Abstract: Quantitative atomic resolution annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique for nanoparticle atom-counting. However, a lot of nanoparticles provide a severe characterisation challenge because of their limited size and beam sensitivity. Therefore, quantitative ADF STEM may greatly benefit from statistical detection theory in order to optimise the instrumental microscope settings such that the incoming electron dose can be kept as low as possible whilst still retaining single-atom precision. The principles of detection theory are used to quantify the probability of error for atom-counting. This enables us to decide between different image performance measures and to optimise the experimental detector settings for atom-counting in ADF STEM in an objective manner. To demonstrate this, ADF STEM imaging of an industrial catalyst has been conducted using the near-optimal detector settings. For this experiment, we discussed the limits for atomcounting diagnosed by combining a thorough statistical method and detailed image simulations.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
DOI: 10.1088/1742-6596/644/012034
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“Optimal experimental design for nano-particle atom-counting from high-resolution STEM images”. de Backer A, De wael A, Gonnissen J, Van Aert S, Ultramicroscopy 151, 46 (2015). http://doi.org/10.1016/j.ultramic.2014.10.015
Abstract: In the present paper, the principles of detection theory are used to quantify the probability of error for atom-counting from high resolution scanning transmission electron microscopy (HR STEM) 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 for the probability of error. We show that for very thin objects LAADF is optimal and that for thicker objects the optimal inner detector angle increases.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 24
DOI: 10.1016/j.ultramic.2014.10.015
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“Atom counting”. de Backer A, Fatermans J, den Dekker AJ, Van Aert S Advances in imaging and electron physics
T2 – Advances in imaging and electron physics. page 91 (2021).
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.
Keywords: H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
DOI: 10.1016/BS.AIEP.2021.01.004
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“Efficient fitting algorithm”. de Backer A, Fatermans J, den Dekker AJ, Van Aert S Advances in imaging and electron physics
T2 – Advances in imaging and electron physics. page 73 (2021).
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.
Keywords: H2 Book chapter; Electron microscopy for materials research (EMAT)
DOI: 10.1016/BS.AIEP.2021.01.003
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“General conclusions and future perspectives”. de Backer A, Fatermans J, den Dekker AJ, Van Aert S Advances in imaging and electron physics
T2 – Advances in imaging and electron physics. page 243 (2021).
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.
Keywords: H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
DOI: 10.1016/BS.AIEP.2021.01.008
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“Introduction”. de Backer A, Fatermans J, den Dekker AJ, Van Aert S Advances in imaging and electron physics
T2 – Advances in imaging and electron physics. page 1 (2021).
Keywords: H2 Book chapter; Electron microscopy for materials research (EMAT)
DOI: 10.1016/BS.AIEP.2021.01.001
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“Optimal experiment design for nanoparticle atom counting from ADF STEM images”. de Backer A, Fatermans J, den Dekker AJ, Van Aert S Advances in imaging and electron physics
T2 – Advances in imaging and electron physics. page 145 (2021).
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.
Keywords: H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
DOI: 10.1016/BS.AIEP.2021.01.005
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“Statistical parameter estimation theory : principles and simulation studies”. de Backer A, Fatermans J, den Dekker AJ, Van Aert S Advances in imaging and electron physics
T2 – Advances in imaging and electron physics. page 29 (2021).
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.
Keywords: H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
DOI: 10.1016/BS.AIEP.2021.01.002
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“Three-dimensional atomic models from a single projection using Z-contrast imaging: verification by electron tomography and opportunities”. De Backer A, Jones L, Lobato I, Altantzis T, Goris B, Nellist PD, Bals S, Van Aert S, Nanoscale 9, 8791 (2017). http://doi.org/10.1039/C7NR02656K
Abstract: In order to fully exploit structure–property relations of nanomaterials, three-dimensional (3D) characterization at the atomic scale is often required. In recent years, the resolution of electron tomography has reached the atomic scale. However, such tomography typically requires several projection images demanding substantial electron dose. A newly developed alternative circumvents this by counting the number of atoms across a single projection. These atom counts can be used to create an initial atomic model with which an energy minimization can be applied to obtain a relaxed 3D reconstruction of the nanoparticle. Here, we compare, at the atomic scale, this single projection reconstruction approach with tomography and find an excellent agreement. This new approach allows for the characterization of beam-sensitive materials or where the acquisition of a tilt series is impossible. As an example, the utility is illustrated by the 3D atomic scale characterization of a nanodumbbell on an in situ heating holder of limited tilt range.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 7.367
Times cited: 33
DOI: 10.1039/C7NR02656K
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“Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting”. de Backer A, Martinez GT, MacArthur KE, Jones L, Béché, A, Nellist PD, Van Aert S, Ultramicroscopy 151, 56 (2015). http://doi.org/10.1016/j.ultramic.2014.11.028
Abstract: Quantitative annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique to characterise nano-particles on an atomic scale. Because of their limited size and beam sensitivity, the atomic structure of such particles may become extremely challenging to determine. Therefore keeping the incoming electron dose to a minimum is important. However, this may reduce the reliability of quantitative ADF STEM which will here be demonstrated for nano-particle atom-counting. Based on experimental ADF STEM images of a real industrial catalyst, we discuss the limits for counting the number of atoms in a projected atomic column with single atom sensitivity. We diagnose these limits by combining a thorough statistical method and detailed image simulations.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 29
DOI: 10.1016/j.ultramic.2014.11.028
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“Atom counting in HAADF STEM using a statistical model-based approach : methodology, possibilities, and inherent limitations”. de Backer A, Martinez GT, Rosenauer A, Van Aert S, Ultramicroscopy 134, 23 (2013). http://doi.org/10.1016/j.ultramic.2013.05.003
Abstract: In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 48
DOI: 10.1016/j.ultramic.2013.05.003
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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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“High precision measurements of atom column positions using model-based exit wave reconstruction”. de Backer A, Van Aert S, van Dyck D, Ultramicroscopy 111, 1475 (2011). http://doi.org/10.1016/j.ultramic.2011.07.002
Abstract: In this paper, it has been investigated how to measure atom column positions as accurately and precisely as possible using a focal series of images. In theory, it is expected that the precision would considerably improve using a maximum likelihood estimator based on the full series of focal images. As such, the theoretical lower bound on the variances of the unknown atom column positions can be attained. However, this approach is numerically demanding. Therefore, maximum likelihood estimation has been compared with the results obtained by fitting a model to a reconstructed exit wave rather than to the full series of focal images. Hence, a real space model-based exit wave reconstruction technique based on the channelling theory is introduced. Simulations show that the reconstructed complex exit wave contains the same amount of information concerning the atom column positions as the full series of focal images. Only for thin samples, which act as weak phase objects, this information can be retrieved from the phase of the reconstructed complex exit wave.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 8
DOI: 10.1016/j.ultramic.2011.07.002
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“StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images”. De Backer A, van den Bos KHW, Van den Broek W, Sijbers J, Van Aert S, Ultramicroscopy 171, 104 (2016). http://doi.org/10.1016/j.ultramic.2016.08.018
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 neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 43
DOI: 10.1016/j.ultramic.2016.08.018
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“StatSTEM: An efficient program for accurate and precise model-based quantification of atomic resolution electron microscopy images”. De Backer A, van den Bos KHW, Van den Broek W, Sijbers J, Van Aert S, Journal of physics : conference series
T2 –, Electron Microscopy and Analysis Group Conference 2017 (EMAG2017), 3-6 July 2017, Manchester, UK 902, 012013 (2017). http://doi.org/10.1088/1742-6596/902/1/012013
Abstract: An efficient model-based estimation algorithm is introduced in order 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 the overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, is investigated. The highest attainable precision is reached even for low dose images. Furthermore, advantages of the model- based approach taking into account overlap between neighbouring columns are highlighted. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.
Keywords: P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab
Times cited: 1
DOI: 10.1088/1742-6596/902/1/012013
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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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De Backer J (2023) The versatile nature of cytoglobin, the Swiss army knife among globins, with a preference for oxidative stress. XVIII, 232 p
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.
Keywords: Doctoral thesis; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
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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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