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	Author	Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S.
	Title	Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design			Type	A1 Journal article
	Year	2016	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	170	Issue	170	Pages	128-138
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramer-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms.
	Address	Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium. Electronic address: sandra.vanaert@uantwerpen.be
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000386925500014	Publication Date	2016-07-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	6	Open Access
	Notes	The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15, G.0369.15 and G.0374.13) and a postdoctoral research grant to A. De Backer. The research leading to these results has also received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). The authors would also like to thank A. Rosenauer for providing access to the STEMsim software and Gerardo T. Martinez for fruitful discussions.; esteem2_jra2			Approved	Most recent IF: 2.843
	Call Number	c:irua:135337 c:irua:135337			Serial	4128
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 approach for accurate and precise model-based quantification of atomic resolution electron microscopy images			Type	A1 Journal article
	Year	2016	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	171	Issue	171	Pages	104-116
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000389106200014	Publication Date	2016-09-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	43	Open Access
	Notes	The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0393.11, G.0064.10 and G.0374.13), a Ph.D. 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.; esteem2_jra2			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @ c:irua:135516			Serial	4280
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	Author	Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S.
	Title	Atom-counting in High Resolution Electron Microscopy: TEM or STEM – that's the question			Type	A1 Journal article
	Year	2016	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	174	Issue	174	Pages	112-120
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000403342200013	Publication Date	2016-10-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	2	Open Access
	Notes	The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15N, G.0369.15N, G.0374.13N, and WO.010.16N) and a postdoctoral grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2).			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @ c:irua:137102			Serial	4315
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	Author	Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S.
	Title	Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure			Type	A1 Journal article
	Year	2016	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	177	Issue	177	Pages	36-42
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000401219800006	Publication Date	2016-11-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	13	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. S. Bals acknowledges funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N and G.0368.15N) and a post-doctoral grant to A. De Backer and T. Altantzis. The authors are grateful to Professor Luis M. Liz-Marzán for providing the sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot);			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @ c:irua:138015UA @ admin @ c:irua:138015			Serial	4316
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	Author	Alania, M.; De Backer, A.; Lobato, I.; Krause, F.F.; Van Dyck, D.; Rosenauer, A.; Van Aert, S.
	Title	How precise can atoms of a nanocluster be located in 3D using a tilt series of scanning transmission electron microscopy images?			Type	A1 Journal article
	Year	2017	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	181	Issue	181	Pages	134-143
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000411170800016	Publication Date	2016-12-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	3	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N, G.0368.15N, and WO.010.16N) and a post-doctoral grant to A. De Backer, and from the DFG under contract No. RO-2057/4-2.			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @ c:irua:144432			Serial	4618
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	Author	De wael, A.; De Backer, A.; Jones, L.; Nellist, P.D.; Van Aert, S.
	Title	Hybrid statistics-simulations based method for atom-counting from ADF STEM images			Type	A1 Journal article
	Year	2017	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	177	Issue	177	Pages	69-77
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000401219800010	Publication Date	2017-01-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	8	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0368.15N, G.0369.15N, and WO.010.16N), 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). The authors are grateful to G.T. Martinez for providing image simulations.			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @ c:irua:141718			Serial	4486
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	Author	Schryvers, D.; Salje, E.K.H.; Nishida, M.; De Backer, A.; Idrissi, H.; Van Aert, S.
	Title	Quantification by aberration corrected (S)TEM of boundaries formed by symmetry breaking phase transformations			Type	A1 Journal article
	Year	2017	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	176	Issue		Pages	194-199
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	The present contribution gives a review of recent quantification work of atom displacements, atom site occupations and level of crystallinity in various systems and based on aberration corrected HR(S)TEM images. Depending on the case studied, picometer range precisions for individual distances can be obtained, boundary widths at the unit cell level determined or statistical evolutions of fractions of the ordered areas calculated. In all of these cases, these quantitative measures imply new routes for the applications of the respective materials.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000403992200026	Publication Date	2017-01-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	1	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the Fund for Scientific Research-Flanders (G.0064.10N, G.0393.11N, G.0374.13N, G.0368.15N, G.0369.15N) and the Flemish Hercules 3 program for large infrastructure as well as financial support from the European Union Seventh Framework Programme (FP7/2007 – 2013) under Grant agreement no. 312483 (ESTEEM2). EKHS thanks EPSRC (EP/ K009702/1) and the Leverhulme trust (EM-2016-004) for support. DS and MN acknowledge financial support from the Japan Society for the Promotion of Science (JSPS, Japan) through the Grant-in-Aid for Scientific Research (A: No. 26249090) and the Strategic Young Researcher Overseas Visits Program for Accelerating Brain Circulation (R2408).			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @c:irua:149654			Serial	4914
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	Author	van den Bos, K.H.W.; Janssens, L.; De Backer, A.; Nellist, P.D.; Van Aert, S.
	Title	The atomic lensing model: new opportunities for atom-by-atom metrology of heterogeneous nanomaterials			Type	A1 Journal article
	Year	2019	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	203	Issue		Pages	155
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	The atomic lensing model has been proposed as a promising method facilitating atom-counting in heterogeneous nanocrystals [1]. Here, image simulations will validate the model, which describes dynamical diffraction as a superposition of individual atoms focussing the incident electrons. It will be demonstrated that the model is reliable in the annular dark field regime for crystals having columns containing dozens of atoms. By using the principles of statistical detection theory, it will be shown that this model gives new opportunities for detecting compositional differences.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000465021000020	Publication Date	2018-12-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	4	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0369.15N, G.0502.18N and WO.010.16N), and by personal grants to K.H.W. van den Bos and A. De Backer. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No. 770887).			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @UA @ admin @ c:irua:155721			Serial	5074
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	Author	De wael, A.; De Backer, A.; Lobato, I.; Van Aert, S.
	Title	Modelling ADF STEM images using elliptical Gaussian peaks and its effects on the quantification of structure parameters in the presence of sample tilt			Type	A1 Journal article
	Year	2021	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume		Issue		Pages	113391
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	A small sample tilt away from a main zone axis orientation results in an elongation of the atomic columns in ADF STEM images. An often posed research question is therefore whether the ADF STEM image intensities of tilted nanomaterials should be quantified using a parametric imaging model consisting of elliptical rather than the currently used symmetrical peaks. To this purpose, simulated ADF STEM images corresponding to different amounts of sample tilt are studied using a parametric imaging model that consists of superimposed 2D elliptical Gaussian peaks on the one hand and symmetrical Gaussian peaks on the other hand. We investigate the quantification of structural parameters such as atomic column positions and scattering cross sections using both parametric imaging models. In this manner, we quantitatively study what can be gained from this elliptical model for quantitative ADF STEM, despite the increased parameter space and computational effort. Although a qualitative improvement can be achieved, no significant quantitative improvement in the estimated structure parameters is achieved by the elliptical model as compared to the symmetrical model. The decrease in scattering cross sections with increasing sample tilt is even identical for both types of parametric imaging models. This impedes direct comparison with zone axis image simulations. Nonetheless, we demonstrate how reliable atom-counting can still be achieved in the presence of small sample tilt.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000704334200001	Publication Date	2021-09-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited		Open Access	OpenAccess
	Notes	This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp.; esteem3JRA; esteem3reported			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @c:irua:181462			Serial	6810
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	Author	van den Broek, W.; Verbeeck, J.; de Backer, S.; Scheunders, P.; Schryvers, D.
	Title	Acquisition of the EELS data cube by tomographic reconstruction			Type	A1 Journal article
	Year	2006	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	106	Issue	4/5	Pages	269-276
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	Energy filtered TEM, EFTEM, provides three-dimensional data, two spatial and one spectral dimension. We propose to acquire these data by measuring a series of images with a defocused energy filter. It will be shown that each image is a projection of the data on the detector and that reconstruction of the data out of a sufficient number of such projections using a tomographic reconstruction algorithm is possible. This technique uses only a fraction of the electron dose an energy filtered series (EFS) needs for the same spectral and spatial resolution and the same mean signal-to-noise ratio. (c) 2005 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000236042300003	Publication Date	2005-11-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	6	Open Access
	Notes				Approved	Most recent IF: 2.843; 2006 IF: 1.706
	Call Number	UA @ lucian @ c:irua:56910UA @ admin @ c:irua:56910			Serial	55
Permanent link to this record



	Author	van den Broek, W.; Verbeeck, J.; Schryvers, D.; de Backer, S.; Scheunders, P.
	Title	Tomographic spectroscopic imaging; an experimental proof of concept			Type	A1 Journal article
	Year	2009	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	109	Issue	4	Pages	296-303
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	Recording the electron energy loss spectroscopy data cube with a series of energy filtered images is a dose inefficient process because the energy slit blocks most of the electrons. When recording the data cube by scanning an electron probe over the sample, perfect dose efficiency is attained; but due to the low current in nanoprobes, this often is slower, with a smaller field of view. In W. Van den Broek et al. [Ultramicroscopy, 106 (2006) 269], we proposed a new method to record the data cube, which is more dose efficient than an energy filtered series. It produces a set of projections of the data cube and then tomographically reconstructs it. In this article, we demonstrate these projections in practice, we present a simple geometrical model that allows for quantification of the projection angles and we present the first successful experimental reconstruction, all on a standard post-column instrument.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000265345400003	Publication Date	2008-12-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	1	Open Access
	Notes	Esteem 026019			Approved	Most recent IF: 2.843; 2009 IF: 2.067
	Call Number	UA @ lucian @ c:irua:77271			Serial	3671
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	Author	de Backer, A.; Van Aert, S.; van Dyck, D.
	Title	High precision measurements of atom column positions using model-based exit wave reconstruction			Type	A1 Journal article
	Year	2011	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	111	Issue	9/10	Pages	1475-1482
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000300461200004	Publication Date	2011-07-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	8	Open Access
	Notes	Fwo			Approved	Most recent IF: 2.843; 2011 IF: 2.471
	Call Number	UA @ lucian @ c:irua:91879			Serial	1438
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	Author	de Backer, A.; Martinez, G.T.; Rosenauer, A.; Van Aert, S.
	Title	Atom counting in HAADF STEM using a statistical model-based approach : methodology, possibilities, and inherent limitations			Type	A1 Journal article
	Year	2013	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	134	Issue		Pages	23-33
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000324474900005	Publication Date	2013-05-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	48	Open Access
	Notes	FWO; Esteem2; FP 2007-2013; esteem2_jra2			Approved	Most recent IF: 2.843; 2013 IF: 2.745
	Call Number	UA @ lucian @ c:irua:109916			Serial	162
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	Author	den Dekker, A.J.; Gonnissen, J.; de Backer, A.; Sijbers, J.; Van Aert, S.
	Title	Estimation of unknown structure parameters from high-resolution (S)TEM images : what are the limits?			Type	A1 Journal article
	Year	2013	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	134	Issue		Pages	34-43
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	Statistical parameter estimation theory is proposed as a quantitative method to measure unknown structure parameters from electron microscopy images. Images are then purely considered as data planes from which structure parameters have to be determined as accurately and precisely as possible using a parametric statistical model of the observations. For this purpose, an efficient algorithm is proposed for the estimation of atomic column positions and intensities from high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. Furthermore, the so-called CramérRao lower bound (CRLB) is reviewed to determine the limits to the precision with which continuous parameters such as atomic column positions and intensities can be estimated. Since this lower bound can only be derived for continuous parameters, alternative measures using the principles of detection theory are introduced for problems concerning the estimation of discrete parameters such as atomic numbers. An experimental case study is presented to show the practical use of these measures for the optimization of the experiment design if the purpose is to decide between the presence of specific atom types using STEM images.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000324474900006	Publication Date	2013-06-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	31	Open Access
	Notes	FWO; FP 2007-2013; Esteem2; esteem2_jra2			Approved	Most recent IF: 2.843; 2013 IF: 2.745
	Call Number	UA @ lucian @ c:irua:109240			Serial	1083
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	Author	Martinez, G.T.; Rosenauer, A.; de Backer, A.; Verbeeck, J.; Van Aert, S.
	Title	Quantitative composition determination at the atomic level using model-based high-angle annular dark field scanning transmission electron microscopy			Type	A1 Journal article
	Year	2014	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	137	Issue		Pages	12-19
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000331092200003	Publication Date	2013-11-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	74	Open Access
	Notes	FWO; FP7; ERC Countatoms; ESTEEM2; esteem2_ta			Approved	Most recent IF: 2.843; 2014 IF: 2.436
	Call Number	UA @ lucian @ c:irua:111579UA @ admin @ c:irua:111579			Serial	2749
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	Author	de Backer, A.; Martinez, G.T.; MacArthur, K.E.; Jones, L.; Béché, A.; Nellist, P.D.; Van Aert, S.
	Title	Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting			Type	A1 Journal article
	Year	2015	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	151	Issue	151	Pages	56-61
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000351237800008	Publication Date	2014-12-03
	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	2.843	Times cited	29	Open Access
	Notes	312483 Esteem2; 278510 Vortex; Fwo G039311; G006410; G037413; esteem2ta; ECASJO;			Approved	Most recent IF: 2.843; 2015 IF: 2.436
	Call Number	c:irua:123927 c:irua:123927			Serial	753
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	Author	de Backer, A.; De wael, A.; Gonnissen, J.; Van Aert, S.
	Title	Optimal experimental design for nano-particle atom-counting from high-resolution STEM images			Type	A1 Journal article
	Year	2015	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	151	Issue	151	Pages	46-55
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	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.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000351237800007	Publication Date	2014-11-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	24	Open Access
	Notes	312483 Esteem2; Fwo G039311; G037413; esteem2_jra2			Approved	Most recent IF: 2.843; 2015 IF: 2.436
	Call Number	c:irua:123926 c:irua:123926			Serial	2481
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	Author	Martinez, G.T.; Jones, L.; de Backer, A.; Béché, A.; Verbeeck, J.; Van Aert, S.; Nellist, P.D.
	Title	Quantitative STEM normalisation : the importance of the electron flux			Type	A1 Journal article
	Year	2015	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	159	Issue	159	Pages	46-58
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Annular dark-field (ADF) scanning transmission electron microscopy (STEM) has become widely used in quantitative studies based on the opportunity to directly compare experimental and simulated images. This comparison merely requires the experimental data to be normalised and expressed in units of fractional beam-current. However, inhomogeneities in the response of electron detectors can complicate this normalisation. The quantification procedure becomes both experiment and instrument specific, requiring new simulations for the particular response of each instrument's detector, and for every camera-length used. This not only impedes the comparison between different instruments and research groups, but can also be computationally very time consuming. Furthermore, not all image simulation methods allow for the inclusion of an inhomogeneous detector response. In this work, we propose an alternative method for normalising experimental data in order to compare these with simulations that consider a homogeneous detector response. To achieve this, we determine the electron flux distribution reaching the detector by means of a camera-length series or a so-called atomic column cross-section averaged convergent beam electron diffraction (XSACBED) pattern. The result is then used to determine the relative weighting of the detector response. Here we show that the results obtained by this new electron flux weighted (EFW) method are comparable to the currently used method, while considerably simplifying the needed simulation libraries. The proposed method also allows one to obtain a metric that describes the quality of the detector response in comparison with the ideal detector response.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000366220000006	Publication Date	2015-08-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	27	Open Access
	Notes	246791 Countatoms; 278510 Vortex; 312483 Esteem2; Fwo G036815; G036915; G037413; G004413; esteem2ta ECASJO;			Approved	Most recent IF: 2.843; 2015 IF: 2.436
	Call Number	c:irua:127293 c:irua:127293UA @ admin @ c:irua:127293			Serial	2762
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	Author	Vermeylen, S.; De Waele, J.; Vanuytsel, S.; De Backer, J.; Van der Paal, J.; Ramakers, M.; Leyssens, K.; Marcq, E.; Van Audenaerde, J.; L. J. Smits, E.; Dewilde, S.; Bogaerts, A.
	Title	Cold atmospheric plasma treatment of melanoma and glioblastoma cancer cells			Type	A1 Journal article
	Year	2016	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	13	Issue	13	Pages	1195-1205
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper, two types of melanoma and glioblastoma cancer cell lines are treated with cold atmospheric plasma to assess the effect of several parameters on the cell viability. The cell viability decreases with treatment duration and time until analysis in all cell lines with varying sensitivity. The majority of dead cells stains both AnnexinV (AnnV) and propidium iodide, indicating that the plasma-treated non-viable cells are mostly late apoptotic or necrotic. Genetic mutations might be involved in the response to plasma. Comparing the effects of two gas mixtures, as well as indirect plasma-activated medium versus direct treatment, gives different results per cell line. In conclusion, this study confirms the potential of plasma for cancer therapy and emphasizes the influence of experimental parameters on therapeutic outcome.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000393131600007	Publication Date	2016-10-31
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.846	Times cited	26	Open Access
	Notes	The authors acknowledge the University of Antwerp for providing research funds. The authors are very grateful to V. Schulz-von der Gathen and J. Benedikt (Bochum University) for providing the COST RF plasma jet. The authors would also like to thank Eva Santermans (University of Hasselt) for statistical advice. J. De Waele, J. Van Audenaerde and J. Van der Paal are research fellows of the Research Foundation Flanders (fellowship numbers: 1121016N, 1S32316N and 11U5416N), E. Marcq of Flanders Innovation & Entrepreneurship (fellowship number: 141433).			Approved	Most recent IF: 2.846
	Call Number	PLASMANT @ plasmant @ c:irua:138722			Serial	4328
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	Author	Lin, A.; Sahun, M.; Biscop, E.; Verswyvel, H.; De Waele, J.; De Backer, J.; Theys, C.; Cuypers, B.; Laukens, K.; Berghe, W.V.; Smits, E.; Bogaerts, A.
	Title	Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma			Type	A1 Journal article
	Year	2023	Publication	Drug resistance updates	Abbreviated Journal
	Volume	67	Issue		Pages	100914
	Keywords	A1 Journal article; Pharmacology. Therapy; ADReM Data Lab (ADReM); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	To gain insights into the underlying mechanisms of NTP therapy sensitivity and resistance, using the firstever NTP-resistant cell line derived from sensitive melanoma cells (A375). Methods: Melanoma cells were exposed to NTP and re-cultured for 12 consecutive weeks before evaluation against the parental control cells. Whole transcriptome sequencing analysis was performed to identify differentially expressed genes and enriched molecular pathways. Glucose uptake, extracellular lactate, media acidification, and mitochondrial respiration was analyzed to determine metabolic changes. Cell death inhibitors were used to assess the NTP-induced cell death mechanisms, and apoptosis and ferroptosis was further validated via Annexin V, Caspase 3/7, and lipid peroxidation analysis. Results: Cells continuously exposed to NTP became 10 times more resistant to NTP compared to the parental cell line of the same passage, based on their half-maximal inhibitory concentration (IC50). Sequencing and metabolic analysis indicated that NTP-resistant cells had a preference towards aerobic glycolysis, while cell death analysis revealed that NTP-resistant cells exhibited less apoptosis but were more vulnerable to lipid peroxidation and ferroptosis. Conclusions: A preference towards aerobic glycolysis and ferroptotic cell death are key physiological changes in NTP-resistance cells, which opens new avenues for further, in-depth research into other cancer types.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000925156500001	Publication Date	2022-12-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1368-7646	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	24.3	Times cited		Open Access	OpenAccess
	Notes	The authors would like to thank Dr. Christophe Deben and Ms. Hannah Zaryouh (Center for Oncological Research, University of Antwerp) for the use and their help with the D300e Digital Dispenser and Spark® Cyto, as well as Ms. Rapha¨elle Corremans (Laboratory Pathophysiology, University of Antwerp) for the use of their lactate meter. The authors would also like to acknowledge the help from Ms. Tias Verhezen and Mr. Cyrus Akbari, who was involved at the start of the project but could not continue due to the COVID-19 pandemic. The authors also acknowledge the resources and services provided by the VSC (Flemish Supercomputer Center). This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaerts), and 1S67621N (Hanne Verswyvel). We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr. Willy Floren, and the Vereycken family. We would also like to acknowledge the support from the European Cooperation in Science & Technology (COST) Action on Therapeutical applications of Cold Plasmas (CA20114; PlasTHER).			Approved	Most recent IF: 24.3; 2023 IF: 10.906
	Call Number	PLASMANT @ plasmant @c:irua:193167			Serial	7240
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	Author	De Backer, L.; Vos, W.; Dieriks, B.; Daems, D.; Verhulst, S.; Vinchurkar, S.; Ides, K.; de Backer, J.; Germonpré, P.; de Backer, W.
	Title	The effects of long-term noninvasive ventilation in hypercapnic COPD patients : a randomized controlled pilot study			Type	A1 Journal article
	Year	2011	Publication	International journal of chronic obstructive pulmonary disease	Abbreviated Journal	Int J Chronic Obstr
	Volume	6	Issue		Pages	615-624
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Introduction: Noninvasive ventilation (NIV) is a well-established treatment for acute-on-chronic respiratory failure in hypercapnic COPD patients. Less is known about the effects of a long-term treatment with NIV in hypercapnic COPD patients and about the factors that may predict response in terms of improved oxygenation and lowered CO2 retention.Methods: In this study, we randomized 15 patients to a routine pharmacological treatment (n = 5, age 66 [standard deviation ± 6] years, FEV1 30.5 [±5.1] %pred, PaO2 65 [±6] mmHg, PaCO2 52.4 [±6.0] mmHg) or to a routine treatment and NIV (using the Synchrony BiPAP device [Respironics, Inc, Murrsville, PA]) (n = 10, age 65 [±7] years, FEV1 29.5 [±9.0] %pred, PaO2 59 [±13] mmHg, PaCO2 55.4 [±7.7] mmHg) for 6 months. We looked at arterial blood gasses, lung function parameters and performed a low-dose computed tomography of the thorax, which was later used for segmentation (providing lobe and airway volumes, iVlobe and iVaw) and post-processing with computer methods (providing airway resistance, iRaw) giving overall a functional image of the separate airways and lobes.Results: In both groups there was a nonsignificant change in FEV1 (NIV group 29.5 [9.0] to 38.5 [14.6] %pred, control group 30.5 [5.1] to 36.8 [8.7] mmHg). PaCO2 dropped significantly only in the NIV group (NIV: 55.4 [7.7] → 44.5 [4.70], P = 0.0076; control: 52.4 [6.0] → 47.6 [8.2], NS). Patients actively treated with NIV developed a more inhomogeneous redistribution of mass flow than control patients. Subsequent analysis indicated that in NIV-treated patients that improve their blood gases, mass flow was also redistributed towards areas with higher vessel density and less emphysema, indicating that flow was redistributed towards areas with better perfusion. There was a highly significant correlation between the % increase in mass flow towards lobes with a blood vessel density of >9% and the increase in PaO2. Improved ventilation–perfusion match and recruitment of previously occluded small airways can explain the improvement in blood gases.Conclusion: We can conclude that in hypercapnic COPD patients treated with long-term NIV over 6 months, a mass flow redistribution occurs, providing a better ventilation–perfusion match and hence better blood gases and lung function. Control patients improve homogeneously in iVaw and iRaw, without improvement in gas exchange since there is no improved ventilation/perfusion ratio or increased alveolar ventilation. These differences in response can be detected through functional imaging, which gives a more detailed report on regional lung volumes and resistances than classical lung function tests do. Possibly only patients with localized small airway disease are good candidates for long-term NIV treatment. To confirm this and to see if better arterial blood gases also lead to better health related quality of life and longer survival, we have to study a larger population.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000208709800066	Publication Date	2011-11-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1178-2005;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.157	Times cited	28	Open Access
	Notes	; ;			Approved	Most recent IF: 3.157; 2011 IF: NA
	Call Number	UA @ lucian @ c:irua:93164			Serial	866
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	Author	De Backer, L.A.; Vos, W.G.; Salgado, R.; de Backer, J.W.; Devolder, A.; Verhulst, S.L.; Claes, R.; Germonpré, P.R.; de Backer, W.A.
	Title	Functional imaging using computer methods to compare the effect of salbutamol and ipratropium bromide in patient-specific airway models of COPD			Type	A1 Journal article
	Year	2011	Publication	International journal of chronic obstructive pulmonary disease	Abbreviated Journal	Int J Chronic Obstr
	Volume	6	Issue		Pages	637-646
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Background: Salbutamol and ipratropium bromide improve lung function in patients with chronic obstructive pulmonary disease (COPD). However, their bronchodilating effect has not yet been compared in the central and distal airways. Functional imaging using computational fluid dynamics offers the possibility of making such a comparison. The objective of this study was to assess the effects of salbutamol and ipratropium bromide on the geometry and computational fluid dynamics-based resistance of the central and distal airways.Methods: Five patients with Global Initiative for Chronic Obstructive Lung Disease Stage III COPD were randomized to a single dose of salbutamol or ipratropium bromide in a crossover manner with a 1-week interval between treatments. Patients underwent lung function testing and a multislice computed tomography scan of the thorax that was used for functional imaging. Two hours after dosing, the patients again underwent lung function tests and repeat computed tomography.Results: Lung function parameters, including forced expiratory volume in 1 second, vital capacity, overall airway resistance, and specific airway resistance, changed significantly after administration of each product. On functional imaging, the bronchodilating effect was greater in the distal airways, with a corresponding drop in airway resistance, compared with the central airways. Salbutamol and ipratropium bromide were equally effective at first glance when looking at lung function tests, but when viewed in more detail with functional imaging, hyporesponsiveness could be shown for salbutamol in one patient. Salbutamol was more effective in the other patients.Conclusion: This pilot study gives an innovative insight into the modes of action of salbutamol and ipratropium bromide in patients with COPD, using the new techniques of functional imaging and computational fluid dynamics.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000208709800068	Publication Date	2011-11-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1178-2005;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.157	Times cited	25	Open Access
	Notes	; ;			Approved	Most recent IF: 3.157; 2011 IF: NA
	Call Number	UA @ lucian @ c:irua:93165			Serial	1300
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	Author	de Backer, J.; Vos, W.; Van Holsbeke, C.; Vinchurkar, S.; Claes, R.; Parizel, P.M.; de Backer, W.
	Title	Effect of high-dose N-acetylcysteine on airway geometry, inflammation, and oxidative stress in COPD patients			Type	A1 Journal article
	Year	2013	Publication	International Journal Of Chronic Obstructive Pulmonary Disease	Abbreviated Journal	Int J Chronic Obstr
	Volume	8	Issue		Pages	569-579
	Keywords	A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Background: Previous studies have demonstrated the potential beneficial effect of N-acetylcysteine (NAC) in chronic obstructive pulmonary disease (COPD). However, the required dose and responder phenotype remain unclear. The current study investigated the effect of high-dose NAC on airway geometry, inflammation, and oxidative stress in COPD patients. Novel functional respiratory imaging methods combining multislice computed tomography images and computer-based flow simulations were used with high sensitivity for detecting changes induced by the therapy. Methods: Twelve patients with Global Initiative for Chronic Obstructive Lung Disease stage II COPD were randomized to receive NAC 1800 mg or placebo daily for 3 months and were then crossed over to the alternative treatment for a further 3 months. Results: Significant correlations were found between image-based resistance values and glutathione levels after treatment with NAC (P = 0.011) and glutathione peroxidase at baseline (P = 0.036). Image-based resistance values appeared to be a good predictor for glutathione peroxidase levels after NAC (P = 0.02), changes in glutathione peroxidase levels (P = 0.035), and reduction in lobar functional residual capacity levels (P = 0.00084). In the limited set of responders to NAC therapy, the changes in airway resistance were in the same order as changes induced by budesonide/formoterol. Conclusion: A combination of glutathione, glutathione peroxidase, and imaging parameters could potentially be used to phenotype COPD patients who would benefit from addition of NAC to their current therapy. The findings of this small pilot study need to be confirmed in a larger pivotal trial.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000327537300001	Publication Date	2013-11-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1178-2005;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.157	Times cited	21	Open Access
	Notes	; JDB is a founder/shareholder of FluidDA NV, Kontich, Belgium. WV, SV, and CVH are employed by FluidDA NV, and WDB is the director of FluidDA NV. PMP and RC have no conflicts of interest to report. The study was supported by Zambon SpA, Bresso, Italy. ;			Approved	Most recent IF: 3.157; 2013 IF: NA
	Call Number	UA @ lucian @ c:irua:112799			Serial	813
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	Author	Klingstedt, M.; Sundberg, M.; Eriksson, L.; Haigh, S.; Kirkland, A.; Grüner, D.; de Backer, A.; Van Aert, S.; Tarasaki, O.
	Title	Exit wave reconstruction from focal series of HRTEM images, single crystal XRD and total energy studies on Sb_xWO_3+y (x\sim0.11)			Type	A1 Journal article
	Year	2012	Publication	Zeitschrift für Kristallographie	Abbreviated Journal	Z Krist-Cryst Mater
	Volume	227	Issue	6	Pages	341-349
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	A new tungsten bronze in the SbWO system has been prepared in a solid state reaction from Sb2O3, WO3 and W metal powder. The average structure was determined by single crystal X-ray diffraction. SbxWO3+y (x ∼ 0.11) crystallizes in the orthorhombic space group Pm21n (no. 31), a = 27.8135(9) Å, b = 7.3659(2) Å and c = 3.8672(1) Å. The structure belongs to the (n)-ITB class of intergrowth tungsten bronzes. It contains slabs of hexagonal channels formed by six WO6 octahedra. These slabs are separated by three layers of WO6 octahedra that are arranged in a WO3-type fashion. The WO6 octahedra share all vertices to build up a three-dimensional framework. The hexagonal channels are filled with Sb atoms to ∼80% and additional O atoms. The atoms are shifted out of the center of the channels. Exit-wave reconstruction of focal series of high resolution-transmission-electron-microscope (HRTEM) images combined with statistical paramäeter estimation techniques allowed to study local ordering in the channels. Sb atoms in neighbouring channels tend to be displaced in the same direction, which is in agreement with total energy calculations on ordered structure models, but the ratio of the occupation of the two possible Sb sites varies from channel to channel. The structure of SbxWO3+y exhibits pronounced local modulations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	München	Editor
	Language		Wos	000307314200003	Publication Date	2012-06-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2194-4946;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.179	Times cited	4	Open Access
	Notes	Fwo; Esteem 026019			Approved	Most recent IF: 3.179; 2012 IF: NA
	Call Number	UA @ lucian @ c:irua:101218			Serial	1131
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	Author	Van Holsbeke, C.; Vos, W.; van Hoorenbeeck, K.; Boudewyns, A.; Salgado, R.; Verdonck, P.R.; Ramet, J.; de Backer, J.; De Backer, W.; Verhulst, S.L.
	Title	Functional respiratory imaging as a tool to assess upper airway patency in children with obstructive sleep apnea			Type	A1 Journal article
	Year	2013	Publication	Sleep Medicine	Abbreviated Journal	Sleep Med
	Volume	14	Issue	5	Pages	433-439
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Objective: We aim to investigate if anatomical and functional properties of the upper airway using computerized 3D models derived from computed tomography (CT) scans better predict obstructive sleep apnea (OSA) severity than standard clinical markers. Methods: Consecutive children with suspected OSA underwent polysomnography, clinical assessment of upper airway patency, and a CT scan while awake. A three-dimensional (3D) reconstruction of the pharyngeal airway was built from these images, and computational fluid dynamics modeling of low inspiratory flow was performed using open-source software. Results: Thirty-three children were included (23 boys; mean age, was 6.0 +/- 3.2 y). OSA was diagnosed in 23 patients. Children with OSA had a significantly lower volume of the overlap region between tonsils and the adenoids (median volume, 1408 mm compared to 2173 mm; p = 0.04), a lower mean cross-sectional area at this location (median volume, 69.3 mm(2) compared to 114.3 mm(2); p = 0.04), and a lower minimal cross-sectional area (median volume, 17.9 mm(2) compared to 25.9 mm(2); p = 0.05). Various significant correlations were found between several imaging parameters and the severity of OSA, most pronounced for upper airway conductance (r = -0.46) (p < 0.01) for correlation between upper airway conductance and the apnea-hypopnea index. No differences or significant correlations were observed with clinical parameters of upper airway patency. Preliminary data after treatment showed that none of the patients with residual OSA had their smallest cross-sectional area located in segment 3, and this frequency was significantly lower than in their peers whose sleep study normalized (64%; p = 0.05). Conclusion: Functional imaging parameters are highly correlated with OSA severity and are a more powerful correlate than clinical scores of upper airway patency. Preliminary data also showed that we could identify differences in the upper airway of those subjects who did not benefit from a local upper airway treatment. (c) 2013 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000318612100009	Publication Date	2013-03-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1389-9457;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.391	Times cited	18	Open Access
	Notes	; ;			Approved	Most recent IF: 3.391; 2013 IF: 3.100
	Call Number	UA @ lucian @ c:irua:109015			Serial	1302
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	Author	Gonnissen, J.; de Backer, A.; den Dekker, A.J.; Martinez, G.T.; Rosenauer, A.; Sijbers, J.; Van Aert, S.
	Title	Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images			Type	A1 Journal article
	Year	2014	Publication	Applied physics letters	Abbreviated Journal	Appl Phys Lett
	Volume	105	Issue	6	Pages	063116
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage applications, much effort has been made to optimize the STEM technique in order to detect light elements. Therefore, classical performance criteria, such as contrast or signal-to-noise ratio, are often discussed hereby aiming at improvements of the direct visual interpretability. However, when images are interpreted quantitatively, one needs an alternative criterion, which we derive based on statistical detection theory. Using realistic simulations of technologically important materials, we demonstrate the benefits of the proposed method and compare the results with existing approaches.
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000341188700073	Publication Date	2014-08-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-6951;1077-3118;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.411	Times cited	12	Open Access
	Notes	FWO (G.0393.11; G.0064.10; and G.0374.13); European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement No. 312483 (ESTEEM2); esteem2_jra2			Approved	Most recent IF: 3.411; 2014 IF: 3.302
	Call Number	UA @ lucian @ c:irua:118333			Serial	2482
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	Author	Attri, P.; Kaushik, N.K.; Kaushik, N.; Hammerschmid, D.; Privat-Maldonado, A.; De Backer, J.; Shiratani, M.; Choi, E.H.; Bogaerts, A.
	Title	Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells			Type	A1 Journal Article
	Year	2021	Publication	International Journal Of Biological Macromolecules	Abbreviated Journal	Int J Biol Macromol
	Volume	182	Issue		Pages	1724-1736
	Keywords	A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
	Abstract	Bacterial and mammalian proteins, such as lysozyme, are gaining increasing interest as anticancer drugs. This study aims to modify the lysozyme structure using cold atmospheric plasma to boost its cancer cell killing effect. We investigated the structure at acidic and neutral pH using various experimental techniques (circular dichroism, ﬂuorescence, and mass spectrometry) and molecular dynamics simulations. The controlled structural modiﬁcation of lysozyme at neutral pH enhances its activity, while the activity was lost at acidic pH at the same treatment conditions. Indeed, a larger number of amino acids were oxidized at acidic pH after plasma treatment, which results in a greater distortion of the lysozyme structure, whereas only limited structural changes were observed in lysozyme after plasma treatment at neutral pH. We found that the plasma-treated lysozyme signiﬁcantly induced apoptosis to the cancer cells. Our results reveal that plasma-treated lysozyme could have potential as a new cancer cell killing drug.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000675794700005	Publication Date	2021-05-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0141-8130	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.671	Times cited		Open Access	OpenAccess
	Notes	Japan Society for the Promotion of Science; We gratefully acknowledge the European H2020 Marie SkłodowskaCurie Actions Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. NK thanks to National Research Foundation of Korea under Ministry of Science and ICT (NRF2021R1C1C1013875) of Korean Government. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA.			Approved	Most recent IF: 3.671
	Call Number	PLASMANT @ plasmant @c:irua:178813			Serial	6792
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	Author	Van Aert, S.; de Backer, A.; Martinez, G.T.; Goris, B.; Bals, S.; Van Tendeloo, G.; Rosenauer, A.
	Title	Procedure to count atoms with trustworthy single-atom sensitivity			Type	A1 Journal article
	Year	2013	Publication	Physical review : B : condensed matter and materials physics	Abbreviated Journal	Phys Rev B
	Volume	87	Issue	6	Pages	064107-6
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	We report a method to reliably count the number of atoms from high-angle annular dark field scanning transmission electron microscopy images. A model-based analysis of the experimental images is used to measure scattering cross sections at the atomic level. The high sensitivity of these measurements in combination with a thorough statistical analysis enables us to count atoms with single-atom sensitivity. The validity of the results is confirmed by means of detailed image simulations. We will show that the method can be applied to nanocrystals of arbitrary shape, size, and atom type without the need for a priori knowledge about the atomic structure.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000315144700006	Publication Date	2013-02-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1098-0121;1550-235X;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.836	Times cited	106	Open Access
	Notes	FWO; 262348 ESMI; 312483 ESTEEM2;246791 COUNTATOMS; Hercules 3; esteem2_jra2			Approved	Most recent IF: 3.836; 2013 IF: 3.664
	Call Number	UA @ lucian @ c:irua:105674			Serial	2718
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	Author	Geuchies, J.J.; van Overbeek, C.; Evers, W.H.; Goris, B.; de Backer, A.; Gantapara, A.P.; Rabouw, F.T.; Hilhorst, J.; Peters, J.L.; Konovalov, O.; Petukhov, A.V.; Dijkstra, M.; Siebbeles, L.D.A.; van Aert, S.; Bals, S.; Vanmaekelbergh, D.
	Title	In situ study of the formation mechanism of two-dimensional superlattices from PbSe nanocrystals			Type	A1 Journal article
	Year	2016	Publication	Nature materials	Abbreviated Journal	Nat Mater
	Volume	15	Issue	15	Pages	1248-1254
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Oriented attachment of PbSe nanocubes can result in the formation of two-dimensional (2D) superstructures with long-range nanoscale and atomic order. This questions the applicability of classic models in which the superlattice grows by first forming a nucleus, followed by sequential irreversible attachment of nanocrystals, as one misaligned attachment would disrupt the 2D order beyond repair. Here, we demonstrate the formation mechanism of 2D PbSe superstructures with square geometry by using in situ grazing-incidence X-ray scattering (small angle and wide angle), ex situ electron microscopy, and Monte Carlo simulations. We observed nanocrystal adsorption at the liquid/gas interface, followed by the formation of a hexagonal nanocrystal monolayer. The hexagonal geometry transforms gradually through a pseudo-hexagonal phase into a phase with square order, driven by attractive interactions between the {100} planes perpendicular to the liquid substrate, which maximize facet-to-facet overlap. The nanocrystals then attach atomically via a necking process, resulting in 2D square superlattices.
	Address	Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language	English	Wos	000389104400011	Publication Date	2016-09-05
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1476-1122	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	39.737	Times cited	182	Open Access	OpenAccess
	Notes	This research is part of the programme ‘Designing Dirac Carriers in semiconductor honeycomb superlattices (DDC13),’ which is supported by the Foundation for Fundamental Research on Matter (FOM), which is part of the Dutch Research Council (NWO). J.J.G. acknowledges funding from the Debye and ESRF Graduate Programs. The authors gratefully acknowledge funding from the Research Foundation Flanders (G.036915 G.037413 and funding of postdoctoral grants to B.G. and A.d.B). S.B. acknowledges the European Research Council, ERC grant No 335078—Colouratom. The authors gratefully acknowledge I. Swart and M. van Huis for fruitful discussions. We acknowledge funding from NWO-CW TOPPUNT ‘Superficial Superstructures’. The X-ray scattering measurements were performed at the ID10 beamline at ESRF under proposal numbers SC-4125 and SC-3786. The authors thank G. L. Destri and F. Zontone for their support during the experiments.; ECAS_Sara; (ROMEO:yellow; preprint:; postprint:restricted ; pdfversion:cannot);			Approved	Most recent IF: 39.737
	Call Number	EMAT @ emat @ c:irua:136165			Serial	4289
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	Author	Varambhia, A.M.; Jones, L.; De Backer, A.; Fauske, V.T.; Van Aert, S.; Ozkaya, D.; Nellist, P.D.
	Title	Quantifying a Heterogeneous Ru Catalyst on Carbon Black Using ADF STEM			Type	A1 Journal article
	Year	2016	Publication	Particle and particle systems characterization	Abbreviated Journal	Part Part Syst Char
	Volume	33	Issue	33	Pages	438-444
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	Ru catalysts are part of a set of late transition metal nanocatalysts that have garnered much interest for catalytic applications such as ammonia synthesis and fuel cell production. Their performance varies greatly depending on their morphology and size, these catalysts are widely studied using electron microscopy. Using recent developments in Annular Dark Field (ADF) Scanning Transmission Electron Microscopy (STEM) quantification techniques, a rapid atom counting procedure was utilized to document the evolution of a heterogeneous Ru catalyst supported on carbon black. Areas of the catalyst were imaged for approximately 15 minutes using ADF STEM. When the Ru clusters were exposed to the electron beam, the clusters changed phase from amorphous to crystalline. To quantify the thickness of the crystalline clusters, two techniques were applied (simulation and statistical decomposition) and compared. These techniques show that stable face centredcubic crystal structures in the form of rafts, between 2 and 8 atoms thick, were formed after the initial wetting of the carbon support.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000379970000012	Publication Date	2016-06-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0934-0866	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.474	Times cited	4	Open Access
	Notes	The authors would like to thank the EPSRC and Johnson Matthey for funding this work as part of a CASE-Award studentship. 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). We would like to thank Brian Theobald and Jonathan Sharman from JMTC for provision of the samples The authors gratefully acknowledge the Research Foundation Flanders (FWO, Belgium) for funding and for a postdoctoral grant to ADB. The microscope used was funded by the INFRASTRUKTUR Grant 197405 (NORTEM) program of the Research Council of Norway.; esteem2_jra2			Approved	Most recent IF: 4.474
	Call Number	c:irua:134036 c:irua:134036			Serial	4086
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