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	Author	de Backer, J.; Vanderveken, O.; Vos, W.; Devolder, A.; Verhulst, S.; Verbraecken, J.
	Title	Functional imaging to predict treatment success of mandibular advancement devices in sleep-disordered breathing			Type	H3 Book chapter
	Year	2008	Publication		Abbreviated Journal
	Volume		Issue		Pages	141-155
	Keywords	H3 Book chapter; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Antwerpen	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:72885			Serial	1298
Permanent link to this record



	Author	Parizel, P.M.; Corthouts, B.; Snoeckx, A.; de Backer, J.; de Backer, W.
	Title	Klinische semiologie en radiologie			Type	H3 Book chapter
	Year	2007	Publication		Abbreviated Journal
	Volume		Issue		Pages	133-146
	Keywords	H3 Book chapter; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Acco	Place of Publication	Leuven	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:63801			Serial	1765
Permanent link to this record



	Author	de Backer, A.
	Title	Quantitative atomic resolution electron microscopy using advanced statistical techniques			Type	Doctoral thesis
	Year	2015	Publication		Abbreviated Journal
	Volume		Issue		Pages
	Keywords	Doctoral thesis; Electron microscopy for materials research (EMAT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Antwerpen	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:125636			Serial	2747
Permanent link to this record



	Author	De Backer, J.
	Title	The versatile nature of cytoglobin, the Swiss army knife among globins, with a preference for oxidative stress			Type	Doctoral thesis
	Year	2023	Publication		Abbreviated Journal
	Volume		Issue		Pages	XVIII, 232 p.
	Keywords	Doctoral thesis; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
	Abstract	Since its discovery 20 years ago, many studies have been performed to gain insight into the functional role of cytoglobin (Cygb). However, Cygb has been proven to be a promiscuous protein. Yet, there is a consensus that Cygb is a cytoprotective protein involved in redox homeostasis. CYGB is a ubiquitously expressed hexacoordinated globin that is highly expressed in melanocytes and is often found to be downregulated during melanocyte-to-melanoma transition. In Chapter III, we investigated the molecular mechanism through which CYGB could be involved in redox regulation. Here, we showed that CYGB contains two redox-sensitive cysteine residues and that the formation of an intramolecular disulfide bridge resulted in the heme group becoming more accessible to external ligands. This supports the hypothesis that Cys38 and Cys83 serve as sensitive redox sensors. In Chapter IV we showed that CYGB mRNA and protein levels were elevated upon exposure to hypoxia. Interestingly, this upregulation was most likely HIF-2α-dependent. We propose that in melanoma, HIF-2α, rather than HIF-1α, positively regulates CYGB under hypoxic conditions in a cell type specific way. In Chapter V, the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels was investigated. We confirmed that NTP endows cytotoxicity that induces cell death through apoptosis and that this was mediated through the production of ROS. Moreover, we showed that CYGB protects melanoma cells from ROS-induced apoptosis by the scavenging of ROS. Interestingly, CYGB expression influenced the expression of NRF2 and HO-1. We identified the lncRNA MEG3 as a possible mechanism through which NRF2 expression and its downstream target HO-1 can be regulated by CYGB. In chapter VI, increased basal ROS levels and higher degree of lipid peroxidation upon RSL3 treatment contributed to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB expression regulation was identified as a critical determinant of the ferroptosis–pyroptosis therapy response. This suggests that CYGB is involved in the regulation of multiple modes of programmed cell death. FInally, we sought to delineate the RONS that are responsible for plasma-induced ICD. Our results highlight the importance of the short-lived species. Furthermore, we are first to demonstrate that NTP-created vaccine is safely prepared and offers complete protection. Moreover, we provide conclusive evidence that direct application of NTP induces ICD in melanoma.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date
	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 @ admin @ c:irua:193568			Serial	7277
Permanent link to this record



	Author	de Backer, J.W.; Vos, W.G.; Germonpré, P.; Salgado, R.; Parizel, P.M.; de Backer, W.
	Title	Clinical applications of image-based airway computational fluid dynamics: assessment of inhalation medication and endobronchial devices			Type	A3 Journal article
	Year	2009	Publication	Proceedings of the Society of Photo-optical Instrumentation Engineers	Abbreviated Journal
	Volume	7262	Issue		Pages	72621p,1-72621p,9
	Keywords	A3 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	Computational fluid dynamics (CFD) is a technique that is used increasingly in the biomedical field. Solving the flow equations numerically provides a convenient way to assess the efficiency of therapies and devices, ranging from cardiovascular stents and heart valves to hemodialysis workflows. Also in the respiratory field CFD has gained increasing interest, especially through the combination of three dimensional image reconstruction which results in highend patient-specific models. This paper provides an overview of clinical applications of CFD through image based modeling, resulting from recent studies performed in our center. We focused on two applications: assessment of the efficiency of inhalation medication and analysis of endobronchial valve placement. In the first application we assessed the mode of action of a novel bronchodilator in 10 treated patients and 4 controls. We assessed the local volume increase and resistance change based on the combination of imaging and CFD. We found a good correlation between the changes in volume and resistance coming from the CFD results and the clinical tests. In the second application we assessed the placement and effect of one way endobronchial valves on respiratory function in 6 patients. We found a strong patientspecific result of the therapy where in some patients the therapy resulted in complete atelectasis of the target lobe while in others the lobe remained inflated. We concluded from these applications that CFD can provide a better insight into clinically relevant therapies.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2009-02-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:79497			Serial	374
Permanent link to this record



	Author	Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S.
	Title	Atom column detection			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	177-214
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	By combining statistical parameter estimation and model-order selection using a Bayesian framework, the maximum a posteriori (MAP) probability rule is proposed in this chapter as an objective and quantitative method to detect atom columns from high-resolution scanning transmission electron microscopy (HRSTEM) images. The validity and usefulness of this approach is demonstrated to both simulated and experimental annular dark-field (ADF) STEM images, but also to simultaneously acquired annular bright-field (ABF) and ADF STEM image data.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177531			Serial	6775
Permanent link to this record



	Author	de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
	Title	Atom counting			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	91-144
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	In this chapter, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. We show that this method can be applied to nanocrystals of arbitrary shape, size, and atom type. The validity of the atom-counting results is confirmed by means of detailed image simulations and it is shown that the high sensitivity of our method enables us to count atoms with single atom sensitivity.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177529			Serial	6776
Permanent link to this record



	Author	de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
	Title	Efficient fitting algorithm			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	73-90
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT)
	Abstract	An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic-resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177528			Serial	6778
Permanent link to this record



	Author	de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
	Title	General conclusions and future perspectives			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	243-253
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	This chapter provides an overview of statistical and quantitative methodologies that have pushed (scanning) transmission electron microscopy ((S)TEM) toward accurate and precise measurements of unknown structure parameters for understanding the relation between the structure of a material and its properties. Hereby, statistical parameter estimation theory has extensively been used which enabled not only measuring atomic column positions, but also quantifying the number of atoms, and detecting atomic columns as accurately and precisely as possible from experimental images. As a general conclusion, it can be stated that advanced statistical techniques are ideal tools to perform quantitative electron microscopy at the atomic scale. In the future, statistical methods will continue to be developed and novel quantification procedures will open up new possibilities for studying material structures at the atomic scale.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177533			Serial	6781
Permanent link to this record



	Author	Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S.
	Title	Image-quality evaluation and model selection with maximum a posteriori probability			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	215-242
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	The maximum a posteriori (MAP) probability rule for atom column detection can also be used as a tool to evaluate the relation between scanning transmission electron microscopy (STEM) image quality and atom detectability. In this chapter, a new image-quality measure is proposed that correlates well with atom detectability, namely the integrated contrast-to-noise ratio (ICNR). Furthermore, the working principle of the MAP probability rule is described in detail showing a close relation to the principles of model-selection methods.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177532			Serial	6782
Permanent link to this record



	Author	de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
	Title	Introduction			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	1-28
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177525			Serial	6784
Permanent link to this record



	Author	de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
	Title	Optimal experiment design for nanoparticle atom counting from ADF STEM images			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	145-175
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	In this chapter, the principles of detection theory are used to quantify the probability of error for atom counting from high-resolution scanning transmission electron microscopy (HRSTEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom counting using the expression of the probability of error. We show that for very thin objects the low-angle annular dark-field (LAADF) regime is optimal and that for thicker objects the optimal inner detector angle increases.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177530			Serial	6785
Permanent link to this record



	Author	de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
	Title	Statistical parameter estimation theory : principles and simulation studies			Type	H2 Book chapter
	Year	2021	Publication	Advances in imaging and electron physics T2 – Advances in imaging and electron physics	Abbreviated Journal
	Volume		Issue		Pages	29-72
	Keywords	H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	In this chapter, the principles of statistical parameter estimation theory for a quantitative analysis of atomic-resolution electron microscopy images are introduced. Within this framework, electron microscopy images are described by a parametric statistical model. Here, parametric models are introduced for different types of electron microscopy images: reconstructed exit waves, annular dark-field (ADF) scanning transmission electron microscopy (STEM) images, and simultaneously acquired ADF and annular bright-field (ABF) STEM images. Furthermore, the Cramér-Rao lower bound (CRLB) is introduced, i.e. a theoretical lower bound on the variance of any unbiased estimator. This CRLB is used to quantify the precision of the structure parameters of interest, such as the atomic column positions and the integrated atomic column intensities.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume	217	Series Issue		Edition
	ISSN		ISBN	978-0-12-824607-8; 1076-5670	Additional Links	UA library record
	Impact Factor		Times cited		Open Access	Not_Open_Access
	Notes	ERC Consolidator project funded by the European Union grant #770887 Picometrics			Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:177527			Serial	6788
Permanent link to this record



	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
Permanent link to this record



	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
Permanent link to this record



	Author	Van Holsbeke, C.S.; Leemans, G.; Vos, W.G.; de Backer, J.W.; Vinchurkar, S.C.; Geldof, M.; Verdonck, P.R.; Parizel, P.M.; van Schil, P.E.; de Backer, W.A.
	Title	Functional Respiratory Imaging as a tool to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis			Type	A1 Journal article
	Year	2013	Publication	Respiratory care	Abbreviated Journal	Resp Care
	Volume		Issue		Pages	1-20
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract	In two subjects with a unilateral diaphragmatic paralysis and complaints of dyspnea, a completely different treatment approach was chosen despite similar anatomical and physiological abnormalities. These decisions were supported by the results generated by Functional Respiratory Imaging (FRI). FRI was able to generate functional information with respect to lobar ventilation and local drug deposition. In one subject, it was found that some lobes were poorly ventilated and drug deposition simulation showed that some regions were undertreated. This subject underwent a diaphragm plication to restore the ventilation. In the other subject, it was found that all lobes were still ventilated. A conservative approach with regular follow-up was chosen to wait for spontaneous recovery of the diaphragmatic function. Both subjects improved subjectively and objectively. These cases demonstrate how novel medical imaging techniques such as FRI can be used to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Dallas, Tex.	Editor
	Language		Wos	000349200100024	Publication Date	2013-12-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0020-1324;1943-3654;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.733	Times cited	5	Open Access
	Notes	; ;			Approved	Most recent IF: 1.733; 2013 IF: 1.840
	Call Number	UA @ lucian @ c:irua:112982			Serial	1303
Permanent link to this record



	Author	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.; Devolder, A.; Verhulst, S.L.; Germonpré, P.; Wuyts, F.L.; Parizel, P.M.; de Backer, W.
	Title	Computational fluid dynamics can detect changes in airway resistance in asthmatics after acute bronchodilation			Type	A1 Journal article
	Year	2008	Publication	Journal of biomechanics	Abbreviated Journal	J Biomech
	Volume	41	Issue	1	Pages	106-113
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000253062100014	Publication Date	2007-08-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9290;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.664	Times cited	53	Open Access
	Notes				Approved	Most recent IF: 2.664; 2008 IF: 2.784
	Call Number	UA @ lucian @ c:irua:64859			Serial	456
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	Author	Vos, W.; de Backer, J.; Devolder, A.; Vanderveken, O.; Verhulst, S.; Salgado, R.; Germonpré, P.; Partoens, B.; Wuyts, F.; Parizel, P.; de Backer, W.
	Title	Correlation between severity of sleep apnea and upper airway morphology based on advanced anatomical and functional imaging			Type	A1 Journal article
	Year	2007	Publication	Journal of biomechanics	Abbreviated Journal	J Biomech
	Volume	40	Issue	10	Pages	2207-2213
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000248468000011	Publication Date	2006-12-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9290;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.664	Times cited	86	Open Access
	Notes				Approved	Most recent IF: 2.664; 2007 IF: 2.897
	Call Number	UA @ lucian @ c:irua:62425			Serial	523
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	Author	de Backer, J.W.; Vanderveken, O.M.; Vos, W.G.; Devolder, A.; Verhulst, S.L.; Verbraecken, J.A.; Parizel, P.M.; Braem, M.J.; van de Heyning, P.H.; de Backer, W.A.
	Title	Functional imaging using computational fluid dynamics to predict treatment success of mandibular advancement devices in sleep-disordered breathing			Type	A1 Journal article
	Year	2007	Publication	Journal of biomechanics	Abbreviated Journal	J Biomech
	Volume	40	Issue	16	Pages	3708-3714
	Keywords	A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	New York, N.Y.	Editor
	Language		Wos	000251845100020	Publication Date	2007-08-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-9290;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.664	Times cited	66	Open Access
	Notes				Approved	Most recent IF: 2.664; 2007 IF: 2.897
	Call Number	UA @ lucian @ c:irua:64860			Serial	1299
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	Author	van den Bos, K.H. W.; De Backer, A.; Martinez, G.T.; Winckelmans, N.; Bals, S.; Nellist, P.D.; Van Aert, S.
	Title	Unscrambling Mixed Elements using High Angle Annular Dark Field Scanning Transmission Electron Microscopy			Type	A1 Journal article
	Year	2016	Publication	Physical review letters	Abbreviated Journal	Phys Rev Lett
	Volume	116	Issue	116	Pages	246101
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	The development of new nanocrystals with outstanding physicochemical properties requires a full threedimensional (3D) characterization at the atomic scale. For homogeneous nanocrystals, counting the number of atoms in each atomic column from high angle annular dark field scanning transmission electron microscopy images has been shown to be a successful technique to get access to this 3D information. However, technologically important nanostructures often consist of more than one chemical element. In order to extend atom counting to heterogeneous materials, a new atomic lensing model is presented. This model takes dynamical electron diffraction into account and opens up new possibilities for unraveling the 3D composition at the atomic scale. Here, the method is applied to determine the 3D structure of Au@Ag core-shell nanorods, but it is applicable to a wide range of heterogeneous complex nanostructures.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000378059500010	Publication Date	2016-06-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0031-9007	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.462	Times cited	46	Open Access	OpenAccess
	Notes	The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through Projects No. G.0374.13N, No. G.0368.15N, and No. G.0369.15N, and by grants to K. H.W. van den Bos and A. De Backer. S. Bals and N. Winckelmans acknowledge funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant No. 312483—ESTEEM2. The authors are grateful to A. Rosenauer for providing the STEMsim program.; esteem2jra2; ECASSara; (ROMEO:green; preprint:; postprint:can ; pdfversion:can);			Approved	Most recent IF: 8.462
	Call Number	c:irua:133954 c:irua:133954			Serial	4084
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	Author	Van Aert, S.; De Backer, A.; Jones, L.; Martinez, G.T.; Béché, A.; Nellist, P.D.
	Title	Control of Knock-On Damage for 3D Atomic Scale Quantification of Nanostructures: Making Every Electron Count in Scanning Transmission Electron Microscopy			Type	A1 Journal article
	Year	2019	Publication	Physical review letters	Abbreviated Journal	Phys Rev Lett
	Volume	122	Issue	6	Pages	066101
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Understanding nanostructures down to the atomic level is the key to optimizing the design of advancedmaterials with revolutionary novel properties. This requires characterization methods capable of quantifying the three-dimensional (3D) atomic structure with the highest possible precision. A successful approach to reach this goal is to count the number of atoms in each atomic column from 2D annular dark field scanning transmission electron microscopy images. To count atoms with single atom sensitivity, a minimum electron dose has been shown to be necessary, while on the other hand beam damage, induced by the high energy electrons, puts a limit on the tolerable dose. An important challenge is therefore to develop experimental strategies to optimize the electron dose by balancing atom-counting fidelity vs the risk of knock-on damage. To achieve this goal, a statistical framework combined with physics-based modeling of the dose-dependent processes is here proposed and experimentally verified. This model enables an investigator to theoretically predict, in advance of an experimental measurement, the optimal electron dose resulting in an unambiguous quantification of nanostructures in their native state with the highest attainable precision.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000458824200008	Publication Date	2019-02-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0031-9007	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.462	Times cited	3	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). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (WO.010.16N, G.0934.17N, G.0502.18N, G.0267.18N), and a grant to A. D. B. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement No. 312483— ESTEEM2 (Integrated Infrastructure Initiative-I3) and the UK EPSRC (Grant No. EP/M010708/1).			Approved	Most recent IF: 8.462
	Call Number	EMAT @ emat @UA @ admin @ c:irua:157175			Serial	5156
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	Author	De wael, A.; De Backer, A.; Jones, L.; Varambhia, A.; Nellist, P.D.; Van Aert, S.
	Title	Measuring Dynamic Structural Changes of Nanoparticles at the Atomic Scale Using Scanning Transmission Electron Microscopy			Type	A1 Journal article
	Year	2020	Publication	Physical Review Letters	Abbreviated Journal	Phys Rev Lett
	Volume	124	Issue	10	Pages	106105
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	We propose a new method to measure atomic scale dynamics of nanoparticles from experimental high-resolution annular dark field scanning transmission electron microscopy images. By using the so-called hidden Markov model, which explicitly models the possibility of structural changes, the number of atoms in each atomic column can be quantified over time. This newly proposed method outperforms the current atom-counting procedure and enables the determination of the probabilities and cross sections for surface diffusion. This method is therefore of great importance for revealing and quantifying the atomic structure when it evolves over time via adatom dynamics, surface diffusion, beam effects, or during in situ experiments.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000519718100015	Publication Date	2020-03-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0031-9007	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.6	Times cited		Open Access	OpenAccess
	Notes	This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N and EOS 30489208. L.J. acknowledges the SFI AMBER Centre for support. A.V. and P.D.N. acknowledge the UK Engineering and Physical Sciences Council (EPSRC) for support (EP/K040375/1 and 1772738). A.V. also acknowledges Johnson-Matthey for support. We would like to thank Brian Theobald and Jonathan Sharman from JMTC Sonning for provision of the Pt sample.			Approved	Most recent IF: 8.6; 2020 IF: 8.462
	Call Number	EMAT @ emat @c:irua:167148			Serial	6347
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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
Permanent link to this record



	Author	Attri, P.; Park, J.-H.; De Backer, J.; Kim, M.; Yun, J.-H.; Heo, Y.; Dewilde, S.; Shiratani, M.; Choi, E.H.; Lee, W.; Bogaerts, A.
	Title	Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study			Type	A1 Journal article
	Year	2020	Publication	International Journal Of Biological Macromolecules	Abbreviated Journal	Int J Biol Macromol
	Volume	163	Issue		Pages	2405-2414
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, ﬁrstly we puriﬁed the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, ﬂuorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modiﬁcation/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000579839600233	Publication Date	2020-09-19
	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	8.2	Times cited		Open Access
	Notes	European Marie Skłodowska-Curie Individual Fellowship, 743546 ; JSPS, 20K14454 ; National Research Foundation of Korea, 2019M3A9F6021810 NRF-2017M3A9F6029753 NRF-2019M3E5D6063903 NRF-2016R1A6A3A04010213 ; Brain Korea 21; MSIT, NRF-2016K1A4A3914113 ; Hercules Foundation; Flemish Government; UA; We gratefully acknowledge the European Marie SkłodowskaCurie Individual Fellowship “Anticancer-PAM” within Horizon 2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. Additionally, work was supported by several grants (2019M3A9F6021810, NRF2017M3A9F6029753, NRF-2019M3E5D6063903 to W. Lee), Basic Science Research Program (NRF-2016R1A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea and in part by the Brain Korea 21 (BK21) PLUS program (J.H.P.). EHC is thankful to National Research Foundation (NRF) of Korea, funded by the Korea government (MSIT) under the grant number (NRF2016K1A4A3914113). 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: 8.2; 2020 IF: 3.671
	Call Number	PLASMANT @ plasmant @c:irua:172451			Serial	6419
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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	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
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	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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