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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
Permanent link to this record



	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	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		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:125636			Serial	2747
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	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		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:129198			Serial	4506
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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	de Backer, W.; Vos, W.; Van Holsbeke, C.; Vinchurkar, S.; Claes, R.; Hufkens, A.; Parizel, P.M.; Bedert, L.; de Backer, J.
	Title	The effect of roflumilast in addition to LABA/LAMA/ICS treatment in COPD patients			Type	L1 Letter to the editor
	Year	2014	Publication	European Respiratory Journal	Abbreviated Journal	Eur Respir J
	Volume	44	Issue	2	Pages	527-529
	Keywords	L1 Letter to the editor; Biophysics and Biomedical Physics; 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	Copenhagen	Editor
	Language		Wos	000340017300029	Publication Date	2014-05-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0903-1936;1399-3003;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	10.569	Times cited	26	Open Access
	Notes	; ;			Approved	Most recent IF: 10.569; 2014 IF: 7.636
	Call Number	UA @ lucian @ c:irua:117335			Serial	832
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	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	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
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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	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	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
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	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	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
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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	Goris, B.; de Backer, A.; Van Aert, S.; Gómez-Graña, S.; Liz-Marzán, L.M.; Van Tendeloo, G.; Bals, S.
	Title	Three-dimensional elemental mapping at the atomic scale in bimetallic nanocrystals			Type	A1 Journal article
	Year	2013	Publication	Nano letters	Abbreviated Journal	Nano Lett
	Volume	13	Issue	9	Pages	4236-4241
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	A thorough understanding of the three-dimensional (3D) atomic structure and composition of coreshell nanostructures is indispensable to obtain a deeper insight on their physical behavior. Such 3D information can be reconstructed from two-dimensional (2D) projection images using electron tomography. Recently, different electron tomography techniques have enabled the 3D characterization of a variety of nanostructures down to the atomic level. However, these methods have all focused on the investigation of nanomaterials containing only one type of chemical element. Here, we combine statistical parameter estimation theory with compressive sensing based tomography to determine the positions and atom type of each atom in heteronanostructures. The approach is applied here to investigate the interface in coreshell Au@Ag nanorods but it is of great interest in the investigation of a broad range of nanostructures.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Washington	Editor
	Language		Wos	000330158900043	Publication Date	2013-08-16
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1530-6984;1530-6992;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	12.712	Times cited	90	Open Access
	Notes	FWO; 246791 COUNTATOMS; 267867 PLASMAQUO; 262348 ESMI; 312483 ESTEEM2; Hercules 3; esteem2_jra4			Approved	Most recent IF: 12.712; 2013 IF: 12.940
	Call Number	UA @ lucian @ c:irua:110036			Serial	3650
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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	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	Vos, W.; de Backer, J.; Poli, G.; De Volder, A.; Ghys, L.; Van Holsbeke, C.; Vinchurkar, S.; De Backer, L.; de Backer, W.
	Title	Novel functional imaging of changes in small airways of patients treated with extrafine beclomethasone/formoterol			Type	A1 Journal article
	Year	2013	Publication	Respiration	Abbreviated Journal	Respiration
	Volume	86	Issue	5	Pages	393-401
	Keywords	A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Background: Inhaled formulations using extrafine particles of long-acting beta(2)-agonists and corticosteroids were developed to optimize asthma treatment. Findings that these combinations reach and treat smaller airways more effectively are predominantly based on general non-specific outcomes with little information on regional characteristics. Objectives: This study aims to assess long-term effects of extrafine beclomethasone/formoterol on small airways of asthmatic patients using novel functional imaging methods. Methods: Twenty-four stable asthma patients were subdivided into three groups (steroid naive, n = 7; partially controlled, n = 6; well controlled, n = 11). Current treatment was switched to a fixed combination of extrafine beclomethasone/formoterol (Foster (R); Chiesi Pharmaceuticals, Parma, Italy). Patients underwent lung function evaluation and thorax high-resolution computerized tomography (HRCT) scan. Local airway resistance was obtained from computational fluid dynamics (CFD). Results: After 6 months, the entire population showed improvement in pre-bronchodilation imaging parameters, including small airway volume (p = 0.0007), resistance (p = 0.011), and asthma control score (p = 0.016). Changes in small airway volume correlated with changes in asthma control score (p = 0.004). Forced expiratory volume in 1 s (p = 0.044) and exhaled nitric oxide (p = 0.040) also improved. Functional imaging provided more detail and clinical relevance compared to lung function tests, especially in the well-controlled group where only functional imaging parameters showed significant improvement, while the correlation with asthma control score remained. Conclusions: Extrafine beclomethasone/formoterol results in a significant reduction of small airway obstruction, detectable by functional imaging (HRCT/CFD). Changes in imaging parameters correlated significantly with clinically relevant improvements. This indicates that functional imaging is a useful tool for sensitive assessment of changes in the respiratory system after asthma treatment. Copyright (C) 2013 S. Karger AG, Basel
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Basel	Editor
	Language		Wos	000329046200006	Publication Date	2013-04-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1423-0356;0025-7931;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.772	Times cited	30	Open Access
	Notes	; ;			Approved	Most recent IF: 2.772; 2013 IF: 2.924
	Call Number	UA @ lucian @ c:irua:113762			Serial	2376
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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	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	Horemans, B.; Van Holsbeke, C.; Vos, W.; Darchuk, L.; Novakovic, V.; Fontan, A.C.; de Backer, J.; van Grieken, R.; de Backer, W.; De Wael, K.
	Title	Particle deposition in airways of chronic respiratory patients exposed to an urban aerosol			Type	A1 Journal article
	Year	2012	Publication	Environmental science and technology	Abbreviated Journal	Environ Sci Technol
	Volume	46	Issue	21	Pages	12162-12169
	Keywords	A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Urban atmospheres in modern cities carry characteristic mixtures of particulate pollution which are potentially aggravating for chronic respiratory patients (CRP). Although air quality surveys can be detailed, the obtained information is not always useful to evaluate human health effects. This paper presents a novel approach to estimate particle deposition rates in airways of CRP, based on real air pollution data. By combining computational fluid dynamics with physical-chemical characteristics of particulate pollution, deposition rates are estimated for particles of different toxicological relevance, that is, minerals, iron oxides, sea salts, ammonium salts, and carbonaceous particles. Also, it enables some qualitative evaluation of the spatial, temporal, and patient specific effects on the particle dose upon exposure to the urban atmosphere. Results show how heavy traffic conditions increases the deposition of anthropogenic particles in the trachea and lungs of respiratory patients (here, +0.28 and +1.5 μg·h1, respectively). In addition, local and synoptic meteorological conditions were found to have a strong effect on the overall dose. However, the pathology and age of the patient was found to be more crucial, with highest deposition rates for toxic particles in adults with a mild anomaly, followed by mild asthmatic children and adults with severe respiratory dysfunctions (7, 5, and 3 μg·h1, respectively).
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Easton, Pa	Editor
	Language		Wos	000310665000082	Publication Date	2012-10-04
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0013-936X;1520-5851;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.198	Times cited	5	Open Access
	Notes	; We are grateful for the financial support of n.v. Vooruitzicht. Furthermore, co-workers at the environmental analysis research group are acknowledged for their help in the fieldwork. ;			Approved	Most recent IF: 6.198; 2012 IF: 5.257
	Call Number	UA @ lucian @ c:irua:101411			Serial	2557
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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	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	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
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	Author	De Backer, L.A.; Vos, W.; de Backer, J.; Van Holsbeke, C.; Vinchurkar, S.; de Backer, W.
	Title	The acute effect of budesonide/formoterol in COPD : a multi-slice computed tomography and lung function study			Type	A1 Journal article
	Year	2012	Publication	European Respiratory Journal	Abbreviated Journal	Eur Respir J
	Volume	40	Issue	2	Pages	298-305
	Keywords	A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	The Global Initiative for Chronic Obstructive Lung Disease (GOLD) classification of chronic obstructive pulmonary disease (COPD) does not always match with other clinical disease descriptors such as exacerbation frequency and quality of life, indicating that forced expiratory volume in 1 s (FEV1) is not a perfect descriptor of the disease. The aim of this study was to find out whether changes in airway geometry after inhalation of the most commonly used inhalation therapy in severe COPD can more adequately be described with an image-based approach than with spirometry. 10 COPD GOLD stage III patients were assessed in a double-blind crossover study. Airway volumes were analysed using segmentation of multi-slice computed tomography (MSCT) images; airway resistance was determined using computational fluid dynamics (CFD). Distal airway volume significantly increased (p=0.011) in patients 4 h after receiving a budesonide/formoterol combination from 9.6+/-4.67 cm(3) to 10.14+/-4.81 cm(3). Also CFD-determined airway resistance significantly decreased (p=0.047) from 0.051+/-0.021 kPa.s.L-1 to 0.043+/- 0.019 kPa.s.L-1. None of the lung function parameters showed a significant change. Only functional residual capacity (FRC) showed a trend to decline (p=0.056). Only the image-based parameters were able to predict the visit at which the combination product was administered. This study showed that imaging is a sensitive, complementary tool to describe changes in airway structure.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Copenhagen	Editor
	Language		Wos	000307291700006	Publication Date	2011-12-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0903-1936;1399-3003;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	10.569	Times cited	37	Open Access
	Notes	; ;			Approved	Most recent IF: 10.569; 2012 IF: 6.355
	Call Number	UA @ lucian @ c:irua:101113			Serial	3568
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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, 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, 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	van Holsbeke, C.; de Backer, J.; Vos, W.; Verdonck, P.; van Ransbeeck, P.; Claessens, T.; Braem, M.; Vanderveken, O.; de Backer, W.
	Title	Anatomical and functional changes in the upper airways of sleep apnea patients due to mandibular repositioning: a large scale study			Type	A1 Journal article
	Year	2011	Publication	Journal of biomechanics	Abbreviated Journal	J Biomech
	Volume	44	Issue	3	Pages	442-449
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
	Abstract	The obstructive sleep apnea-hypopnea syndrome (OSAHS) is a sleep related breathing disorder. A popular treatment is the use of a mandibular repositioning appliance (MRA) which advances the mandibula during the sleep and decreases the collapsibility of the upper airway. The success rate of such a device is, however, limited and very variable within a population of patients. Previous studies using computational fluid dynamics have shown that there is a decrease in upper airway resistance in patients who improve clinically due to an MRA. In this article, correlations between patient-specific anatomical and functional parameters are studied to examine how MRA induced biomechanical changes will have an impact on the upper airway resistance. Low-dose computed tomography (CT) scans are made from 143 patients suffering from OSAHS. A baseline scan and a scan after mandibular repositioning (MR) are performed in order to study variations in parameters. It is found that MR using a simulation bite is able to induce resistance changes by changing the pharyngeal lumen. The change in minimal cross-sectional area is the best parameter to predict the change in upper airway resistance. Looking at baseline values, the ideal patients for MR induced resistance decrease seem to be women with short airways, high initial resistance and no baseline occlusion.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000287551000014	Publication Date	2010-10-23
	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	2.664	Times cited	23	Open Access
	Notes	; ;			Approved	Most recent IF: 2.664; 2011 IF: 2.434
	Call Number	UA @ lucian @ c:irua:85305			Serial	112
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	Author	de Backer, J.W.; Vos, W.G.; Vinchurkar, S.C.; Claes, R.; Drollmann, A.; Wulfrank, D.; Parizel, P.M.; Germonpré, P.; de Backer, W.
	Title	Validation of computational fluid dynamics in CT-based airway models with SPECT/CT1			Type	A1 Journal article
	Year	2010	Publication	Radiology	Abbreviated Journal	Radiology
	Volume	257	Issue	3	Pages	854-862
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Purpose: To compare the results obtained by using numerical flow simulations with the results of combined single photon emission computed tomography (SPECT) and computed tomography (CT) and to demonstrate the importance of correct boundary conditions for the numerical methods to account for the large amount of interpatient variability in airway geometry. Materials and Methods: This study was approved by all relevant institutional review boards. All patients gave their signed informed consent. In this study, six patients with mild asthma (three men; three women; overall mean age, 46 years ± 17 [standard deviation]) underwent CT at functional residual capacity and total lung capacity, as well as SPECT/CT. CT data were used for segmentation and computational fluid dynamics (CFD) simulations. A comparison was made between airflow distribution, as derived with (a) SPECT/CT through tracer concentration analysis, (b) CT through lobar expansion measurement, and (c) CFD through flow computer simulation. Also, the heterogeneity of the ventilation was examined. Results: Good agreement was found between SPECT/CT, CT, and CFD in terms of airflow distribution and hot spot detection. The average difference for the internal airflow distribution was less than 3% for CFD and CT versus SPECT/CT. Heterogeneity in ventilation patterns could be detected with SPECT/CT and CFD. Conclusion: This results of this study show that patient-specific computer simulations with appropriate boundary conditions yield information that is similar to that obtained with functional imaging tools, such as SPECT/CT.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Easton, Pa	Editor
	Language		Wos	000284469300031	Publication Date	2010-11-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0033-8419;1527-1315;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7.296	Times cited	100	Open Access
	Notes	; Supported by Novartis. ;			Approved	Most recent IF: 7.296; 2010 IF: 6.069
	Call Number	UA @ lucian @ c:irua:85379			Serial	3831
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	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	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
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	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		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:79497			Serial	374
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	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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