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Author de Backer, J.W.; Vos, W.G.; Devolder, A.; Verhulst, S.L.; Germonpré, P.; Wuyts, F.L.; Parizel, P.M.; de Backer, W.
  Title Computational fluid dynamics can detect changes in airway resistance in asthmatics after acute bronchodilation Type A1 Journal article
  Year 2008 Publication Journal of biomechanics Abbreviated Journal J Biomech
  Volume 41 Issue 1 Pages 106-113
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York, N.Y. Editor
  Language Wos 000253062100014 Publication Date 2007-08-15
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0021-9290; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.664 Times cited 53 Open Access
  Notes Approved Most recent IF: 2.664; 2008 IF: 2.784
  Call Number UA @ lucian @ c:irua:64859 Serial 456
Permanent link to this record
 
 
Author Vos, W.; de Backer, J.; Devolder, A.; Vanderveken, O.; Verhulst, S.; Salgado, R.; Germonpré, P.; Partoens, B.; Wuyts, F.; Parizel, P.; de Backer, W.
  Title Correlation between severity of sleep apnea and upper airway morphology based on advanced anatomical and functional imaging Type A1 Journal article
  Year 2007 Publication Journal of biomechanics Abbreviated Journal J Biomech
  Volume 40 Issue 10 Pages 2207-2213
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York, N.Y. Editor
  Language Wos 000248468000011 Publication Date 2006-12-19
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0021-9290; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.664 Times cited 86 Open Access
  Notes Approved Most recent IF: 2.664; 2007 IF: 2.897
  Call Number UA @ lucian @ c:irua:62425 Serial 523
Permanent link to this record
 
 
Author de Backer, J.W.; Vanderveken, O.M.; Vos, W.G.; Devolder, A.; Verhulst, S.L.; Verbraecken, J.A.; Parizel, P.M.; Braem, M.J.; van de Heyning, P.H.; de Backer, W.A.
  Title Functional imaging using computational fluid dynamics to predict treatment success of mandibular advancement devices in sleep-disordered breathing Type A1 Journal article
  Year 2007 Publication Journal of biomechanics Abbreviated Journal J Biomech
  Volume 40 Issue 16 Pages 3708-3714
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York, N.Y. Editor
  Language Wos 000251845100020 Publication Date 2007-08-01
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0021-9290; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.664 Times cited 66 Open Access
  Notes Approved Most recent IF: 2.664; 2007 IF: 2.897
  Call Number UA @ lucian @ c:irua:64860 Serial 1299
Permanent link to this record
 
 
Author Guzzinati, G.; Altantzis, T.; Batuk, M.; De Backer, A.; Lumbeeck, G.; Samaee, V.; Batuk, D.; Idrissi, H.; Hadermann, J.; Van Aert, S.; Schryvers, D.; Verbeeck, J.; Bals, S.
  Title Recent Advances in Transmission Electron Microscopy for Materials Science at the EMAT Lab of the University of Antwerp Type A1 Journal article
  Year 2018 Publication Materials Abbreviated Journal Materials
  Volume 11 Issue 11 Pages 1304
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract The rapid progress in materials science that enables the design of materials down to the nanoscale also demands characterization techniques able to analyze the materials down to the same scale, such as transmission electron microscopy. As Belgium’s foremost electron microscopy group, among the largest in the world, EMAT is continuously contributing to the development of TEM techniques, such as high-resolution imaging, diffraction, electron tomography, and spectroscopies, with an emphasis on quantification and reproducibility, as well as employing TEM methodology at the highest level to solve real-world materials science problems. The lab’s recent contributions are presented here together with specific case studies in order to highlight the usefulness of TEM to the advancement of materials science.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000444112800041 Publication Date 2018-07-28
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1996-1944 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.654 Times cited 15 Open Access OpenAccess
  Notes Fonds Wetenschappelijk Onderzoek, G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N AUHA13009 ; European Research Council, COLOURATOM 335078 ; Universiteit Antwerpen, GOA Solarpaint ; G. Guzzinati, T. Altantzis and A. De Backer have been supported by postdoctoral fellowship grants from the Research Foundation Flanders (FWO). Funding was also received from the European Research Council (starting grant no. COLOURATOM 335078), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 770887), the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N, G.0401.16N) and from the University of Antwerp through GOA project Solarpaint. Funding for the TopSPIN precession system under grant AUHA13009, as well as for the Qu-Ant-EM microscope, is acknowledged from the HERCULES Foundation. H. Idrissi is mandated by the Belgian National Fund for Scientific Research (F.R.S.-FNRS). (ROMEO:green; preprint:; postprint:can ; pdfversion:can); saraecas; ECAS_Sara; Approved Most recent IF: 2.654
  Call Number EMAT @ emat @c:irua:153737UA @ admin @ c:irua:153737 Serial 5064
Permanent link to this record
 
 
Author Van Holsbeke, C.S.; Verhulst, S.L.; Vos, W.G.; de Backer, J.W.; Vinchurkar, S.C.; Verdonck, P.R.; van Doorn, J.W.D.; Nadjmi, N.; de Backer, W.A.
  Title Change in upper airway geometry between upright and supine position during tidal nasal breathing Type A1 Journal article
  Year 2014 Publication Journal Of Aerosol Medicine And Pulmonary Drug Delivery Abbreviated Journal J Aerosol Med Pulm D
  Volume 27 Issue 1 Pages 51-57
  Keywords A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000331144500007 Publication Date 2013-03-19
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1941-2711;1941-2703; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.528 Times cited 16 Open Access
  Notes ; ; Approved Most recent IF: 2.528; 2014 IF: 2.798
  Call Number UA @ lucian @ c:irua:115759 Serial 308
Permanent link to this record
 
 
Author De wael, A.; De Backer, A.; Van Aert, S.
  Title Hidden Markov model for atom-counting from sequential ADF STEM images: Methodology, possibilities and limitations Type A1 Journal article
  Year 2020 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 219 Issue Pages 113131
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000594770500003 Publication Date 2020-10-03
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.2 Times cited Open Access OpenAccess
  Notes This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N and EOS 30489208. Approved Most recent IF: 2.2; 2020 IF: 2.843
  Call Number EMAT @ emat @c:irua:172449 Serial 6417
Permanent link to this record
 
 
Author Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S.
  Title Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors Type A1 Journal article
  Year 2022 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 242 Issue Pages 113626
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In

addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000873778100001 Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.2 Times cited Open Access OpenAccess
  Notes This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra Approved Most recent IF: 2.2
  Call Number EMAT @ emat @c:irua:190925 Serial 7118
Permanent link to this record
 
 
Author De Backer, A.; Bals, S.; Van Aert, S.
  Title A decade of atom-counting in STEM: From the first results toward reliable 3D atomic models from a single projection Type A1 Journal article
  Year 2023 Publication Ultramicroscopy Abbreviated Journal
  Volume Issue Pages 113702
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000953765800001 Publication Date 2023-02-10
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.2 Times cited 3 Open Access OpenAccess
  Notes This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert, Grant 815128 REALNANO to S. Bals, and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N, and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF) . The authors also thank the colleagues who have contributed to this work over the years, including T. Altantzis, E. Arslan Irmak, K.J. Batenburg, E. Bladt, A. De wael, R. Erni, C. Faes, B. Goris, L. Jones, L.M. Liz-Marzán, I. Lobato, G.T. Martinez, P.D. Nellist, M.D. Rosell, A. Rosenauer, K.H.W. van den Bos, A. Varambhia, and Z. Zhang.; esteem3reported; esteem3JRA Approved Most recent IF: 2.2; 2023 IF: 2.843
  Call Number EMAT @ emat @c:irua:195896 Serial 7236
Permanent link to this record
 
 
Author Zhang, Z.; Lobato, I.; De Backer, A.; Van Aert, S.; Nellist, P.
  Title Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions Type A1 Journal article
  Year 2023 Publication Ultramicroscopy Abbreviated Journal
  Volume 246 Issue Pages 113671
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core–shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements.
  Address
  Corporate Author Zezhong Zhang Thesis
  Publisher Place of Publication Editor
  Language Wos 000995063900001 Publication Date 2022-12-28
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.2 Times cited Open Access OpenAccess
  Notes European Research Council 770887 PICOMETRICS; Fonds Wetenschappelijk Onderzoek No.G.0502.18N; Horizon 2020, 770887 ; Horizon 2020 Framework Programme; European Research Council, 823717 ESTEEM3 ; esteem3reported; esteem3JRa Approved Most recent IF: 2.2; 2023 IF: 2.843
  Call Number EMAT @ emat @c:irua:195890 Serial 7251
Permanent link to this record
 
 
Author Lobato, I.; De Backer, A.; Van Aert, S.
  Title Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network Type A1 Journal article
  Year 2023 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 251 Issue Pages 113769
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms

of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In

order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for

a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such

simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently

parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most

research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will

only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and

present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as

a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag,

Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope

parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS

values for a wide range of input parameters that are commonly used for aberration-corrected transmission

electron microscopes.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 001011617200001 Publication Date 2023-06-01
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record
  Impact Factor (down) 2.2 Times cited Open Access OpenAccess
  Notes This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N and G0A7723N) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF), Belgium. Approved Most recent IF: 2.2; 2023 IF: 2.843
  Call Number EMAT @ emat @c:irua:197275 Serial 8812
Permanent link to this record
 
 
Author Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S.
  Title Atom counting from a combination of two ADF STEM images Type A1 Journal article
  Year 2024 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 255 Issue Pages 113859
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 001089064200001 Publication Date 2023-09-23
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 2.2 Times cited Open Access OpenAccess
  Notes This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). Approved Most recent IF: 2.2; 2024 IF: 2.843
  Call Number EMAT @ emat @c:irua:201008 Serial 8964
Permanent link to this record
 
 
Author Şentürk, D.G.; De Backer, A.; Van Aert, S.
  Title Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination Type A1 Journal Article
  Year 2024 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 259 Issue Pages 113941
  Keywords A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
  Abstract In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2024-02-19
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0304-3991 ISBN Additional Links UA library record
  Impact Factor (down) 2.2 Times cited Open Access OpenAccess
  Notes This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N, GOA7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). Approved Most recent IF: 2.2; 2024 IF: 2.843
  Call Number EMAT @ emat @c:irua:204353 Serial 8996
Permanent link to this record
 
 
Author Martinez, G.T.; de Backer, A.; Rosenauer, A.; Verbeeck, J.; Van Aert, S.
  Title The effect of probe inaccuracies on the quantitative model-based analysis of high angle annular dark field scanning transmission electron microscopy images Type A1 Journal article
  Year 2014 Publication Micron Abbreviated Journal Micron
  Volume 63 Issue Pages 57-63
  Keywords A1 Journal article; Engineering Management (ENM); Electron microscopy for materials research (EMAT)
  Abstract Quantitative structural and chemical information can be obtained from high angle annular dark field scanning transmission electron microscopy (HAADF STEM) images when using statistical parameter estimation theory. In this approach, we assume an empirical parameterized imaging model for which the total scattered intensities of the atomic columns are estimated. These intensities can be related to the material structure or composition. Since the experimental probe profile is assumed to be known in the description of the imaging model, we will explore how the uncertainties in the probe profile affect the estimation of the total scattered intensities. Using multislice image simulations, we analyze this effect for Cs corrected and non-Cs corrected microscopes as a function of inaccuracies in cylindrically symmetric aberrations, such as defocus and spherical aberration of third and fifth order, and non-cylindrically symmetric aberrations, such as 2-fold and 3-fold astigmatism and coma.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Oxford Editor
  Language Wos 000338402500011 Publication Date 2014-01-02
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0968-4328; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 1.98 Times cited 25 Open Access
  Notes FWO (G.0393.11; G.0064.10; G.0374.13; G.0044.13); European Research Council under the 7th Framework Program (FP7); ERC GrantNo. 246791-COUNTATOMS and ERC Starting Grant No. 278510-VORTEX. A.R. thanks the DFG under contract number RO2057/8-1.The research leading to these results has received funding fromthe European Union 7th Framework Programme [FP7/2007-2013]under grant agreement no. 312483 (ESTEEM2).; esteem2ta ECASJO; Approved Most recent IF: 1.98; 2014 IF: 1.988
  Call Number UA @ lucian @ c:irua:113857UA @ admin @ c:irua:113857 Serial 831
Permanent link to this record
 
 
Author de Backer, J.W.; Vos, W.G.; Gorlé, C.D.; Germonpré, P.; Partoens, B.; Wuyts, F.L.; Parizel, P.M.; de Backer, W.
  Title Flow analyses in the lower airways: patient-specific model and boundary conditions Type A1 Journal article
  Year 2008 Publication Medical engineering and physics Abbreviated Journal Med Eng Phys
  Volume 30 Issue 7 Pages 872-879
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract Computational fluid dynamics (CFD) is increasingly applied in the respiratory domain. The ability to simulate the flow through a bifurcating tubular system has increased the insight into the internal flow dynamics and the particular characteristics of respiratory flows such as secondary motions and inertial effects. The next step in the evolution is to apply the technique to patient-specific cases, in order to provide more information about pathological airways. This study presents a patient-specific approach where both the geometry and the boundary conditions (BC) are based on individual imaging methods using computed tomography (CT). The internal flow distribution of a 73-year-old female suffering from chronic obstructive pulmonary disease (COPD) is assessed. The validation is performed through the comparison of lung ventilation with gamma scintigraphy. The results show that in order to obtain agreement within the accuracy limits of the gamma scintigraphy scan, both the patient-specific geometry and the BC (driving pressure) play a crucial role. A minimal invasive test (CT scan) supplied enough information to perform an accurate CFD analysis. In the end it was possible to capture the pathological features of the respiratory system using the imaging and computational fluid dynamics techniques. This brings the introduction of this new technique in the clinical practice one step closer.
  Address
  Corporate Author Thesis
  Publisher Place of Publication London Editor
  Language Wos 000259768300009 Publication Date 2007-12-26
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1350-4533; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 1.819 Times cited 82 Open Access
  Notes Approved Most recent IF: 1.819; 2008 IF: 2.216
  Call Number UA @ lucian @ c:irua:71693 Serial 1224
Permanent link to this record
 
 
Author Vinchurkar, S.; De Backer, L.; Vos, W.; Van Holsbeke, C.; de Backer, J.; de Backer, W.
  Title A case series on lung deposition analysis of inhaled medication using functional imaging based computational fluid dynamics in asthmatic patients : effect of upper airway morphology and comparison with in vivo data Type A1 Journal article
  Year 2012 Publication Inhalation Toxicology Abbreviated Journal Inhal Toxicol
  Volume 24 Issue 2 Pages 81-88
  Keywords A1 Journal article; Pharmacology. Therapy; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract Context: Asthma affects 20 million Americans resulting in an economic burden of approximately $18 billion in the US alone (Allergies and Asthma Foundation 2000; National Center for Environmental Health (NCEH) 1999). Research studies based on differences in patient-specific airway morphology for asthma and the associated effect on deposition of inhaled aerosols are currently not available in the literature. Therefore, the role of morphological variations such as upper airway (extrathoracic) occlusion is not well documented. Objective: Functional imaging based computational fluid dynamics (CFD) of the respiratory airways for five asthmatic subjects is performed in this study using computed tomography (CT) based patient-specific airway models and boundary conditions. Methods: CT scans for 5 asthma patients were used to reconstruct 3D lung models using segmentation software. An averaged inhalation profile and patient-specific lobar flow distribution were used to perform the simulation. The simulations were used to obtain deposition for BDP/Formoterol (R) HFA pMDI in the patient-specific airway models. Results: The lung deposition obtained using CFD was in excellent agreement with available in vivo data using the same product. Specifically, CFD resulted in 30% lung deposition, whereas in vivo lung deposition was reported to be approximately 31%. Conclusion: It was concluded that a combination of patient-specific airway models and lobar boundary conditions can be used to obtain accurate lung deposition estimates. Lower lung deposition can be expected for patients with higher extrathoracic resistance. Novel respiratory drug delivery devices need to accommodate population subgroups based on these morphological and anatomical differences in addition to subject age.
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York, N.Y. Editor
  Language Wos 000299744800001 Publication Date 2012-01-20
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0895-8378;1091-7691; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 1.751 Times cited 36 Open Access
  Notes ; ; Approved Most recent IF: 1.751; 2012 IF: 1.894
  Call Number UA @ lucian @ c:irua:96238 Serial 286
Permanent link to this record
 
 
Author Van Holsbeke, C.S.; Leemans, G.; Vos, W.G.; de Backer, J.W.; Vinchurkar, S.C.; Geldof, M.; Verdonck, P.R.; Parizel, P.M.; van Schil, P.E.; de Backer, W.A.
  Title Functional Respiratory Imaging as a tool to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis Type A1 Journal article
  Year 2013 Publication Respiratory care Abbreviated Journal Resp Care
  Volume Issue Pages 1-20
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract In two subjects with a unilateral diaphragmatic paralysis and complaints of dyspnea, a completely different treatment approach was chosen despite similar anatomical and physiological abnormalities. These decisions were supported by the results generated by Functional Respiratory Imaging (FRI). FRI was able to generate functional information with respect to lobar ventilation and local drug deposition. In one subject, it was found that some lobes were poorly ventilated and drug deposition simulation showed that some regions were undertreated. This subject underwent a diaphragm plication to restore the ventilation. In the other subject, it was found that all lobes were still ventilated. A conservative approach with regular follow-up was chosen to wait for spontaneous recovery of the diaphragmatic function. Both subjects improved subjectively and objectively. These cases demonstrate how novel medical imaging techniques such as FRI can be used to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Dallas, Tex. Editor
  Language Wos 000349200100024 Publication Date 2013-12-11
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0020-1324;1943-3654; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 1.733 Times cited 5 Open Access
  Notes ; ; Approved Most recent IF: 1.733; 2013 IF: 1.840
  Call Number UA @ lucian @ c:irua:112982 Serial 1303
Permanent link to this record
 
 
Author de Backer, J.W.; Vos, W.G.; Burnell, P.; Verhulst, S.L.; Salmon, P.; de Clerck, N.; de Backer, W.
  Title Study of the variability in upper and lower airway morphology in Sprague-Dawley rats using modern micro-CT scan-based segmentation techniques Type A1 Journal article
  Year 2009 Publication The anatomical record: advances in integrative anatomy and evolutionary biology Abbreviated Journal Anat Rec
  Volume 292 Issue 5 Pages 720-727
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract Animal models are being used extensively in pre-clinical and safety assessment studies to assess the effectiveness and safety of new chemical entities and delivery systems. Although never entirely replacing the need for animal testing, the use of computer simulations could eventually reduce the amount of animals needed for research purposes and refine the data acquired from the animal studies. Computational fluid dynamics is a powerful tool that makes it possible to simulate flow and particle behavior in animal or patient-specific respiratory models, for purposes of inhaled delivery. This tool requires an accurate representation of the respiratory system, respiration and dose delivery attributes. The aim of this study is to develop a representative airway model of the Sprague-Dawley rat using static and dynamic micro-CT scans. The entire respiratory tract was modeled, from the snout and nares down to the central airways at the point where no distinction could be made between intraluminal air and the surrounding tissue. For the selection of the representative model, variables such as upper airway movement, segmentation length, airway volume and size are taken into account. Dynamic scans of the nostril region were used to illustrate the characteristic morphology of this region in anaesthetized animals. It could be concluded from this study that it was possible to construct a highly detailed representative model of a Sprague-Dawley rat based on imaging modalities such as micro-CT scans
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York, N.Y. Editor
  Language Wos 000265766000010 Publication Date 2009-03-25
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1932-8486;1932-8494; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) 1.431 Times cited 16 Open Access
  Notes Approved Most recent IF: 1.431; 2009 IF: 1.490
  Call Number UA @ lucian @ c:irua:76455 Serial 3342
Permanent link to this record
 
 
Author de Backer, J.W.; Vos, W.G.; Germonpré, P.; Salgado, R.; Parizel, P.M.; de Backer, W.
  Title Clinical applications of image-based airway computational fluid dynamics: assessment of inhalation medication and endobronchial devices Type A3 Journal article
  Year 2009 Publication Proceedings of the Society of Photo-optical Instrumentation Engineers Abbreviated Journal
  Volume 7262 Issue Pages 72621p,1-72621p,9
  Keywords A3 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract Computational fluid dynamics (CFD) is a technique that is used increasingly in the biomedical field. Solving the flow equations numerically provides a convenient way to assess the efficiency of therapies and devices, ranging from cardiovascular stents and heart valves to hemodialysis workflows. Also in the respiratory field CFD has gained increasing interest, especially through the combination of three dimensional image reconstruction which results in highend patient-specific models. This paper provides an overview of clinical applications of CFD through image based modeling, resulting from recent studies performed in our center. We focused on two applications: assessment of the efficiency of inhalation medication and analysis of endobronchial valve placement. In the first application we assessed the mode of action of a novel bronchodilator in 10 treated patients and 4 controls. We assessed the local volume increase and resistance change based on the combination of imaging and CFD. We found a good correlation between the changes in volume and resistance coming from the CFD results and the clinical tests. In the second application we assessed the placement and effect of one way endobronchial valves on respiratory function in 6 patients. We found a strong patientspecific result of the therapy where in some patients the therapy resulted in complete atelectasis of the target lobe while in others the lobe remained inflated. We concluded from these applications that CFD can provide a better insight into clinically relevant therapies.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2009-02-27
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor (down) Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:79497 Serial 374
Permanent link to this record
 
 
Author de Backer, J.; Vanderveken, O.; Vos, W.; Devolder, A.; Verhulst, S.; Verbraecken, J.
  Title Functional imaging to predict treatment success of mandibular advancement devices in sleep-disordered breathing Type H3 Book chapter
  Year 2008 Publication Abbreviated Journal
  Volume Issue Pages 141-155
  Keywords H3 Book chapter; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Antwerpen Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor (down) Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:72885 Serial 1298
Permanent link to this record
 
 
Author Parizel, P.M.; Corthouts, B.; Snoeckx, A.; de Backer, J.; de Backer, W.
  Title Klinische semiologie en radiologie Type H3 Book chapter
  Year 2007 Publication Abbreviated Journal
  Volume Issue Pages 133-146
  Keywords H3 Book chapter; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Acco Place of Publication Leuven Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor (down) Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:63801 Serial 1765
Permanent link to this record
 
 
Author de Backer, A.
  Title Quantitative atomic resolution electron microscopy using advanced statistical techniques Type Doctoral thesis
  Year 2015 Publication Abbreviated Journal
  Volume Issue Pages
  Keywords Doctoral thesis; Electron microscopy for materials research (EMAT)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Antwerpen Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor (down) Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:125636 Serial 2747
Permanent link to this record
 
 
Author De Backer, A.; De Wael, A.; Gonnissen, J.; Martinez, G.T.; Béché, A.; MacArthur, K.E.; Jones, L.; Nellist, P.D.; Van Aert, S.
  Title Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting: What are the limits? Type P1 Proceeding
  Year 2015 Publication Journal of physics : conference series Abbreviated Journal
  Volume 644 Issue 644 Pages 012034
  Keywords P1 Proceeding; Electron microscopy for materials research (EMAT)
  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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000366826200034 Publication Date 2015-10-13
  Series Editor Series Title Abbreviated Series Title Electron Microscopy and Analysis Group Conference (EMAG), JUN 02-JUL 02, 2015, Manchester, ENGLAND
  Series Volume Series Issue Edition
  ISSN 1742-6588 ISBN Additional Links UA library record; WoS full record
  Impact Factor (down) Times cited Open Access
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0368.15N, G.0369.15N, and G.0374.15N) and a PhD research grant to A De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3), ERC Starting Grant 278510 Vortex, and the UK Engineering and Physical Sciences Research Council (EP/K032518/1). The authors acknowledge Johnson-Matthey for providing the sample and PhD funding to K E MacArthur. A Rosenauer is acknowledged for providing the STEMsim program.; esteem2jra2; ECASJO; Approved Most recent IF: NA
  Call Number c:irua:130314 c:irua:130314 Serial 4050
Permanent link to this record
 
 
Author de Backer, A.; De wael, A.; Gonnissen, J.; Martinez, G.T.; Béché, A.; MacArthur, K.E.; Jones, L.; Nellist, P.D.; Van Aert, S.
  Title Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting : what are the limits? Type A1 Journal article
  Year 2015 Publication Journal of physics : conference series Abbreviated Journal
  Volume 644 Issue Pages 012034-4
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Bristol Editor
  Language Wos Publication Date
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1742-6588; 1742-6596 ISBN Additional Links UA library record
  Impact Factor (down) Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:129198 Serial 4506
Permanent link to this record
 
 
Author De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S.
  Title StatSTEM: An efficient program for accurate and precise model-based quantification of atomic resolution electron microscopy images Type P1 Proceeding
  Year 2017 Publication Journal of physics : conference series T2 – Electron Microscopy and Analysis Group Conference 2017 (EMAG2017), 3-6 July 2017, Manchester, UK Abbreviated Journal J. Phys.: Conf. Ser.
  Volume 902 Issue Pages 012013
  Keywords P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab
  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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000416370700013 Publication Date 2017-10-16
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1742-6588 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) Times cited 1 Open Access OpenAccess
  Notes The authors acknowledge nancial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0374.13N, G.0368.15N, G.0369.15N, WO.010.16N) and a PhD research grant to K H W van den Bos, and a postdoctoral research grant to A De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). A Rosenauer is acknowledged for providing the STEMsim program. Approved Most recent IF: NA
  Call Number EMAT @ emat @c:irua:147188 Serial 4764
Permanent link to this record
 
 
Author van den Bos, K.H.W.; Altantzis, T.; De Backer, A.; Van Aert, S.; Bals, S.
  Title Recent breakthroughs in scanning transmission electron microscopy of small species Type A1 Journal article
  Year 2018 Publication Advances in Physics: X Abbreviated Journal Advances in Physics: X
  Volume 3 Issue 3 Pages 1480420
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract Over the last decade, scanning transmission electron microscopy has become one of the most powerful tools to characterise nanomaterials at the atomic scale. Often, the ultimate goal is to retrieve the three-dimensional structure, which is very challenging since small species are typically sensitive to electron irradiation. Nevertheless, measuring individual atomic positions is crucial to understand the relation between the structure and physicochemical properties of these (nano)materials. In this review, we highlight the latest approaches that are available to reveal the 3D atomic structure of small species. Finally, we will provide an outlook and will describe future challenges where the limits of electron microscopy will be pushed even further.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000441619500001 Publication Date 2018-08-13
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2374-6149 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) Times cited 8 Open Access OpenAccess
  Notes This work was supported by the Research Foundation Flanders (FWO, Belgium) under Grant G.0368.15N, G.0369.15N, and G.0267.18N, by personal FWO Grants to K. H. W. van den Bos, T. Altantzis, and A. De Backer, and the European Research Council under Grant 335078 COLOURATOM to S. Bals. The authors would like to thank the colleagues who have contributed to this work over the years, including A. M. Abakumov, K. J. Batenburg, E. Countiño-Gonzalez, C. de Mello Donega, R. Erni, J. J. Geuchies, B. Goris, J. Hofkens, L. Jones, P. Lievens, L. M. Liz-Marzán, I. Lobato, G. T. Martinez, P. D. Nellist, B. Partoens, M. B. J. Roeffaers, M.D. Rossell, B. Schoeters, M. J. Van Bael, W. van der Stam, M. van Huis, G. Van Tendeloo, D. Vanmaekelbergh, and N. Winckelmans. (ROMEO:green; preprint:; postprint:can ; pdfversion:can); saraecas; ECAS_Sara; Approved Most recent IF: NA
  Call Number EMAT @ emat @c:irua:152820UA @ admin @ c:irua:152820 Serial 5007
Permanent link to this record
 
 
Author Biscop,; Lin,; Boxem,; Loenhout,; Backer,; Deben,; Dewilde,; Smits,; Bogaerts,
  Title Influence of Cell Type and Culture Medium on Determining Cancer Selectivity of Cold Atmospheric Plasma Treatment Type A1 Journal article
  Year 2019 Publication Cancers Abbreviated Journal Cancers
  Volume 11 Issue 9 Pages 1287
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
  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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000489719000072 Publication Date 2019-09-01
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2072-6694 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) Times cited 9 Open Access
  Notes the Research Foundation Flanders, 12S9218N – ; Universiteit Antwerpen, – ; Approved Most recent IF: NA
  Call Number PLASMANT @ plasmant @c:irua:162097 Serial 5360
Permanent link to this record
 
 
Author Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A.
  Title Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma Type A1 Journal article
  Year 2021 Publication Cancers Abbreviated Journal Cancers
  Volume 13 Issue 3 Pages 579
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
  Abstract Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000614960600001 Publication Date 2021-02-02
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2072-6694 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor (down) Times cited Open Access OpenAccess
  Notes We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. Approved Most recent IF: NA
  Call Number PLASMANT @ plasmant @c:irua:176455 Serial 6709
Permanent link to this record
 
 
Author Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S.
  Title Atom column detection Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 177-214
  Keywords H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract By combining statistical parameter estimation and model-order selection using a Bayesian framework, the maximum a posteriori (MAP) probability rule is proposed in this chapter as an objective and quantitative method to detect atom columns from high-resolution scanning transmission electron microscopy (HRSTEM) images. The validity and usefulness of this approach is demonstrated to both simulated and experimental annular dark-field (ADF) STEM images, but also to simultaneously acquired annular bright-field (ABF) and ADF STEM image data.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor (down) Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177531 Serial 6775
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Atom counting Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 91-144
  Keywords H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In this chapter, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. We show that this method can be applied to nanocrystals of arbitrary shape, size, and atom type. The validity of the atom-counting results is confirmed by means of detailed image simulations and it is shown that the high sensitivity of our method enables us to count atoms with single atom sensitivity.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor (down) Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177529 Serial 6776
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Efficient fitting algorithm Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 73-90
  Keywords H2 Book chapter; Electron microscopy for materials research (EMAT)
  Abstract An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic-resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor (down) Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177528 Serial 6778
Permanent link to this record
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