NANOlab Center of Excellence literature database -- Query Results

	NANOlab Center of Excellence literature database Home \| Show All \| Simple Search \| Advanced Search	Login Quick Search: Field: contains: ...
	31–60 of 99 records found matching your query (RSS):

Select All Deselect All

<< 1 2 3 4 >>

List View

Citations

Details

	Records
	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
Permanent link to this record



	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
Permanent link to this record



	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
Permanent link to this record



	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
Permanent link to this record



	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
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	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
Permanent link to this record



	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
Permanent link to this record



	Author	Vingerhoets, R.; Spiller, M.; De Backer, J.; Adriaens, A.; Vlaeminck, S.E.; Meers, E.
	Title	Detailed nitrogen and phosphorus flow analysis, nutrient use efficiency and circularity in the agri-food system of a livestock-intensive region			Type	A1 Journal article
	Year	2023	Publication	Journal of cleaner production	Abbreviated Journal
	Volume	410	Issue		Pages	137278-13
	Keywords	A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
	Abstract	The agri-food value chain is a major cause of nitrogen (N) and phosphorus (P) emissions and associated environmental and health impacts. The EU's farm-to-fork strategy (F2F) demands an agri-food value chain approach to reduce nutrient emissions by 50% and fertilizer use by 20%. Substance flow analysis (SFA) is a method that can be applied to study complex systems such as the agri-food chain. A review of 60 SFA studies shows that they often lack detail by not sufficiently distinguishing between nodes, products and types of emissions. The present study aims to assess the added value of detail in SFAs and to illustrate that valuable indicators can be derived from detailed assessments. This aim will be attained by presenting a highly-detailed SFA for the livestock-intensive region of Flanders, Belgium. The SFA distinguishes 40 nodes and 1827 flows that are classified into eight different categories (e.g. by-products, point source emissions) following life cycle methods. Eight novel indicators were calculated, including indicators that assess the N and P recovery potential. Flanders has a low overall nutrient use efficiency (11% N, 18% P). About 55% of the N and 56% of the P embedded in recoverable streams are reused providing 35% and 37% of the total N and P input. Optimized nutrient recycling could replace 45% of N and 48% of P of the external nutrient input, exceeding the target set by the F2F strategy. Detailed accounting for N and P flows and nodes leads to the identification of more recoverable streams and larger N and P flows. More detailed flow accounting is a prerequisite for the quantification of technological intervention options. Future research should focus on including concentration and quality as a parameter in SFAs.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000991013600001	Publication Date	2023-04-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0959-6526	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	11.1	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 11.1; 2023 IF: 5.715
	Call Number	UA @ admin @ c:irua:196227			Serial	7770
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, 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	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	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	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	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	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	Lin, A.; Gorbanev, Y.; De Backer, J.; Van Loenhout, J.; Van Boxem, W.; Lemière, F.; Cos, P.; Dewilde, S.; Smits, E.; Bogaerts, A.
	Title	Non‐Thermal Plasma as a Unique Delivery System of Short‐Lived Reactive Oxygen and Nitrogen Species for Immunogenic Cell Death in Melanoma Cells			Type	A1 Journal article
	Year	2019	Publication	Advanced Science	Abbreviated Journal	Adv Sci
	Volume	6	Issue	6	Pages	1802062
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000462613100001	Publication Date	2019-01-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2198-3844	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	9.034	Times cited	39	Open Access	OpenAccess
	Notes	This study was funded in part by the Flanders Research Foundation (grant no. 12S9218N) and the European Marie Sklodowska-Curie Individual Fellowship within Horizon2020 (LTPAM) grant no. 743151). The microsecond-pulsed power supply was purchased following discussions with the C. & J. Nyheim Plasma Institute at Drexel University. The authors would like to thank Dr. Erik Fransen for his expertise and guidance with the statistical models and analysis used here. The authors would also like to thank Dr. Sander Bekeschus of the Leibniz Institute for Plasma Science and Technology for the discussions at conferences and workshops. A.L. contributed to the design and carrying out of all experiments. A.L. also wrote the manuscript. Y.G. contributed to the design and carrying out of experiments involving chemical measurements. Y.G. also contributed to writing the chemical portions of the manuscript. J.D.B. contributed to the design and carrying out of in vivo experiments. J.D.B. also contributed to writing the portions of the manuscript involving animal experiments and care. J.V.L. contributed to the optimization of the calreticulin protocol used in the experiments. W.V.B. contributed to optimization of colorimetric assays used in the experiments. F.L. contributed to mass spectrometry measurements. P.C., S.D., E.S., and A.B. provided workspace, equipment, and valuable discussions for the project. All authors participated in the review of the manuscript.; Flanders Research Foundation, 12S9218N ; European Marie Sklodowska-Curie Individual Fellowship within Horizon2020, 743151 ;			Approved	Most recent IF: 9.034
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:156548			Serial	5165
Permanent link to this record



	Author	Lin, A.; Sahun, M.; Biscop, E.; Verswyvel, H.; De Waele, J.; De Backer, J.; Theys, C.; Cuypers, B.; Laukens, K.; Berghe, W.V.; Smits, E.; Bogaerts, A.
	Title	Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma			Type	A1 Journal article
	Year	2023	Publication	Drug resistance updates	Abbreviated Journal
	Volume	67	Issue		Pages	100914
	Keywords	A1 Journal article; Pharmacology. Therapy; ADReM Data Lab (ADReM); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	To gain insights into the underlying mechanisms of NTP therapy sensitivity and resistance, using the firstever NTP-resistant cell line derived from sensitive melanoma cells (A375). Methods: Melanoma cells were exposed to NTP and re-cultured for 12 consecutive weeks before evaluation against the parental control cells. Whole transcriptome sequencing analysis was performed to identify differentially expressed genes and enriched molecular pathways. Glucose uptake, extracellular lactate, media acidification, and mitochondrial respiration was analyzed to determine metabolic changes. Cell death inhibitors were used to assess the NTP-induced cell death mechanisms, and apoptosis and ferroptosis was further validated via Annexin V, Caspase 3/7, and lipid peroxidation analysis. Results: Cells continuously exposed to NTP became 10 times more resistant to NTP compared to the parental cell line of the same passage, based on their half-maximal inhibitory concentration (IC50). Sequencing and metabolic analysis indicated that NTP-resistant cells had a preference towards aerobic glycolysis, while cell death analysis revealed that NTP-resistant cells exhibited less apoptosis but were more vulnerable to lipid peroxidation and ferroptosis. Conclusions: A preference towards aerobic glycolysis and ferroptotic cell death are key physiological changes in NTP-resistance cells, which opens new avenues for further, in-depth research into other cancer types.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000925156500001	Publication Date	2022-12-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1368-7646	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	24.3	Times cited		Open Access	OpenAccess
	Notes	The authors would like to thank Dr. Christophe Deben and Ms. Hannah Zaryouh (Center for Oncological Research, University of Antwerp) for the use and their help with the D300e Digital Dispenser and Spark® Cyto, as well as Ms. Rapha¨elle Corremans (Laboratory Pathophysiology, University of Antwerp) for the use of their lactate meter. The authors would also like to acknowledge the help from Ms. Tias Verhezen and Mr. Cyrus Akbari, who was involved at the start of the project but could not continue due to the COVID-19 pandemic. The authors also acknowledge the resources and services provided by the VSC (Flemish Supercomputer Center). This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaerts), and 1S67621N (Hanne Verswyvel). We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr. Willy Floren, and the Vereycken family. We would also like to acknowledge the support from the European Cooperation in Science & Technology (COST) Action on Therapeutical applications of Cold Plasmas (CA20114; PlasTHER).			Approved	Most recent IF: 24.3; 2023 IF: 10.906
	Call Number	PLASMANT @ plasmant @c:irua:193167			Serial	7240
Permanent link to this record



	Author	De Backer, J.; Maric, D.; Zuhra, K.; Bogaerts, A.; Szabo, C.; Vanden Berghe, W.; Hoogewijs, D.
	Title	Cytoglobin Silencing Promotes Melanoma Malignancy but Sensitizes for Ferroptosis and Pyroptosis Therapy Response			Type	A1 Journal article
	Year	2022	Publication	Antioxidants	Abbreviated Journal	Antioxidants
	Volume	11	Issue	8	Pages	1548
	Keywords	A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
	Abstract	Despite recent advances in melanoma treatment, there are still patients that either do not respond or develop resistance. This unresponsiveness and/or acquired resistance to therapy could be explained by the fact that some melanoma cells reside in a dedifferentiated state. Interestingly, this dedifferentiated state is associated with greater sensitivity to ferroptosis, a lipid peroxidation-reliant, iron-dependent form of cell death. Cytoglobin (CYGB) is an iron hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. In this study, we investigated the potential effect of CYGB on the cellular sensitivity towards (1S, 3R)-RAS-selective lethal small molecule (RSL3)-mediated ferroptosis in the G361 melanoma cells with abundant endogenous expression. Our findings show that an increased basal ROS level and higher degree of lipid peroxidation upon RSL3 treatment contribute 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 knockdown also triggers activation of the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome and subsequent induction of pyroptosis target genes. Altogether, we show that silencing of CYGB expression modulates cancer therapy sensitivity via regulation of ferroptosis and pyroptosis cell death signaling pathways.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000846411000001	Publication Date	2022-08-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2076-3921	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	7	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 7
	Call Number	PLASMANT @ plasmant @c:irua:190686			Serial	7102
Permanent link to this record



	Author	De Backer, J.; Lin, A.; Berghe, W.V.; Bogaerts, A.; Hoogewijs, D.
	Title	Cytoglobin inhibits non-thermal plasma-induced apoptosis in melanoma cells through regulation of the NRF2-mediated antioxidant response			Type	A1 Journal article
	Year	2022	Publication	Redox Biology	Abbreviated Journal	Redox Biol
	Volume	55	Issue		Pages	102399
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
	Abstract	Melanoma arises from pigment-producing cells called melanocytes located in the basal layers of the epidermis of the skin. Cytoglobin (CYGB) is a ubiquitously expressed hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. Previously, we showed that non-thermal plasma (NTP)-produced reactive oxygen and nitrogen species (RONS) lead to the formation of an intra molecular disulfide bridge that would allow CYGB to function as a redox-sensitive protein. Here, we investigate the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels, and we explore the role of CYGB in determining treatment outcome. Our findings are consistent with previous studies supporting that NTP cytotoxicity is mediated through the production of RONS and leads to apoptotic cell death in melanoma cells. Furthermore, we show that NTP-treated solutions elicit an antioxidant response through the activation of nuclear factor erythroid 2–related factor 2 (NRF2). The knock down and overexpression of CYGB respectively sensitizes and protects melanoma cells from RONS-induced apoptotic cell death. The presence of CYGB enhances heme-oxygenase 1 (HO-1) and NRF2 protein expression levels, whereas the absence impairs their expression. Moreover, analysis of the CYGB-dependent transcriptome demonstrates the tumor suppressor long non-coding RNA maternally expressed 3 (MEG3) as a hitherto unde scribed link between CYGB and NRF2. Thus, the presence of CYGB, at least in melanoma cells, seems to play a central role in determining the therapeutic outcome of RONS-inducing anticancer therapies, like NTP-treated solutions, possessing both tumor-suppressive and oncogenic features. Hence, CYGB expression could be of in terest either as a biomarker or as a candidate for future targeted therapies in melanoma.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000844595100002	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2213-2317	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	11.4	Times cited		Open Access	OpenAccess
	Notes	This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work include: 12S9221 N (Abraham Lin) and G044420 N (Abraham Lin and Annemie Bogaerts). Joey De Backer acknowledges a visiting fellowship from the University of Fribourg. David Hoogewijs acknowledges support by the Swiss National Science Foundation (grants 31003A173000 and 310030207460).			Approved	Most recent IF: 11.4
	Call Number	PLASMANT @ plasmant @c:irua:190635			Serial	7101
Permanent link to this record



	Author	Lin, A.; De Backer, J.; Quatannens, D.; Cuypers, B.; Verswyvel, H.; De La Hoz, E.C.; Ribbens, B.; Siozopoulou, V.; Van Audenaerde, J.; Marcq, E.; Lardon, F.; Laukens, K.; Vanlanduit, S.; Smits, E.; Bogaerts, A.
	Title	The effect of local non‐thermal plasma therapy on the<scp>cancer‐immunity</scp>cycle in a melanoma mouse model			Type	University Hospital Antwerp
	Year	2022	Publication	Bioengineering & Translational Medicine	Abbreviated Journal	Bioengineering & Transla Med
	Volume		Issue		Pages
	Keywords	University Hospital Antwerp; A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; ADReM Data Lab (ADReM); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES)
	Abstract	Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000784103500001	Publication Date	2022-04-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2380-6761	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	Vlaamse regering, 1S67621N 1S76421N G044420N 12S9221N 12S9218N ; The authors would like to thank and acknowledge Christophe Hermans, Ho Wa Lau, and Hilde Lambrechts for their help with sectioning and preparing the IHC slides. The authors would also like to thank Dani Banner for designing the ergonomic NTP applicator handle and Hasan Baysal for 3D printing the pieces used in this experiment. We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr Willy Floren, and the Vereycken family. Some of the resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) The data that support the findings of this study are available from the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9218N (Abraham Lin), 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaert, and Steve Vanlanduit), 1S76421N (Delphine Quatannens), and 1S67621N (Hanne Verswyvel). Figure 7 was created with BioRender.com.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:187909			Serial	7056
Permanent link to this record



	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
Permanent link to this record



	Author	Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A.
	Title	Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma			Type	A1 Journal article
	Year	2021	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	13	Issue	3	Pages	579
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
	Abstract	Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000614960600001	Publication Date	2021-02-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2072-6694	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:176455			Serial	6709
Permanent link to this record



	Author	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
Permanent link to this record



	Author	Biscop,; Lin,; Boxem,; Loenhout,; Backer,; Deben,; Dewilde,; Smits,; Bogaerts,
	Title	Influence of Cell Type and Culture Medium on Determining Cancer Selectivity of Cold Atmospheric Plasma Treatment			Type	A1 Journal article
	Year	2019	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	11	Issue	9	Pages	1287
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Increasing the selectivity of cancer treatments is attractive, as it has the potential to reduce side-effects of therapy. Cold atmospheric plasma (CAP) is a novel cancer treatment that disrupts the intracellular oxidative balance. Several reports claim CAP treatment to be selective, but retrospective analysis of these studies revealed discrepancies in several biological factors and culturing methods. Before CAP can be conclusively stated as a selective cancer treatment, the importance of these factors must be investigated. In this study, we evaluated the influence of the cell type, cancer type, and cell culture medium on direct and indirect CAP treatment. Comparison of cancerous cells with their non-cancerous counterparts was performed under standardized conditions to determine selectivity of treatment. Analysis of seven human cell lines (cancerous: A549, U87, A375, and Malme-3M; non-cancerous: BEAS-2B, HA, and HEMa) and five different cell culture media (DMEM, RPMI1640, AM, BEGM, and DCBM) revealed that the tested parameters strongly influence indirect CAP treatment, while direct treatment was less affected. Taken together, the results of our study demonstrate that cell type, cancer type, and culturing medium must be taken into account before selectivity of CAP treatment can be claimed and overlooking these parameters can easily result in inaccurate conclusions of selectivity.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000489719000072	Publication Date	2019-09-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2072-6694	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	9	Open Access
	Notes	the Research Foundation Flanders, 12S9218N – ; Universiteit Antwerpen, – ;			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:162097			Serial	5360
Permanent link to this record



	Author	De Backer, J.; Razzokov, J.; Hammerschmid, D.; Mensch, C.; Hafideddine, Z.; Kumar, N.; van Raemdonck, G.; Yusupov, M.; Van Doorslaer, S.; Johannessen, C.; Sobott, F.; Bogaerts, A.; Dewilde, S.
	Title	The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor			Type	A1 Journal article
	Year	2018	Publication	Redox Biology	Abbreviated Journal	Redox Biol
	Volume	19	Issue		Pages	1-10
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
	Abstract	Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000449722100002	Publication Date	2018-07-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2213-2317	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.337	Times cited		Open Access	OpenAccess
	Notes	M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. 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). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:152818			Serial	5006
Permanent link to this record



	Author	Vermeylen, S.; De Waele, J.; Vanuytsel, S.; De Backer, J.; Van der Paal, J.; Ramakers, M.; Leyssens, K.; Marcq, E.; Van Audenaerde, J.; L. J. Smits, E.; Dewilde, S.; Bogaerts, A.
	Title	Cold atmospheric plasma treatment of melanoma and glioblastoma cancer cells			Type	A1 Journal article
	Year	2016	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	13	Issue	13	Pages	1195-1205
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper, two types of melanoma and glioblastoma cancer cell lines are treated with cold atmospheric plasma to assess the effect of several parameters on the cell viability. The cell viability decreases with treatment duration and time until analysis in all cell lines with varying sensitivity. The majority of dead cells stains both AnnexinV (AnnV) and propidium iodide, indicating that the plasma-treated non-viable cells are mostly late apoptotic or necrotic. Genetic mutations might be involved in the response to plasma. Comparing the effects of two gas mixtures, as well as indirect plasma-activated medium versus direct treatment, gives different results per cell line. In conclusion, this study confirms the potential of plasma for cancer therapy and emphasizes the influence of experimental parameters on therapeutic outcome.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000393131600007	Publication Date	2016-10-31
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1612-8850	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.846	Times cited	26	Open Access
	Notes	The authors acknowledge the University of Antwerp for providing research funds. The authors are very grateful to V. Schulz-von der Gathen and J. Benedikt (Bochum University) for providing the COST RF plasma jet. The authors would also like to thank Eva Santermans (University of Hasselt) for statistical advice. J. De Waele, J. Van Audenaerde and J. Van der Paal are research fellows of the Research Foundation Flanders (fellowship numbers: 1121016N, 1S32316N and 11U5416N), E. Marcq of Flanders Innovation & Entrepreneurship (fellowship number: 141433).			Approved	Most recent IF: 2.846
	Call Number	PLASMANT @ plasmant @ c:irua:138722			Serial	4328
Permanent link to this record



	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
Permanent link to this record