| Records |
| 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 |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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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 |
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 |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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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 |
| |
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| |
| Author |
de Backer, J.W.; Vos, W.G.; Germonpré, P.; Salgado, R.; Parizel, P.M.; de Backer, W. |
| Title |
Clinical applications of image-based airway computational fluid dynamics: assessment of inhalation medication and endobronchial devices |
Type |
A3 Journal article |
| Year |
2009 |
Publication |
Proceedings of the Society of Photo-optical Instrumentation Engineers |
Abbreviated Journal |
|
| Volume |
7262 |
Issue |
|
Pages |
72621p,1-72621p,9 |
| Keywords |
A3 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) |
| Abstract |
Computational fluid dynamics (CFD) is a technique that is used increasingly in the biomedical field. Solving the flow equations numerically provides a convenient way to assess the efficiency of therapies and devices, ranging from cardiovascular stents and heart valves to hemodialysis workflows. Also in the respiratory field CFD has gained increasing interest, especially through the combination of three dimensional image reconstruction which results in highend patient-specific models. This paper provides an overview of clinical applications of CFD through image based modeling, resulting from recent studies performed in our center. We focused on two applications: assessment of the efficiency of inhalation medication and analysis of endobronchial valve placement. In the first application we assessed the mode of action of a novel bronchodilator in 10 treated patients and 4 controls. We assessed the local volume increase and resistance change based on the combination of imaging and CFD. We found a good correlation between the changes in volume and resistance coming from the CFD results and the clinical tests. In the second application we assessed the placement and effect of one way endobronchial valves on respiratory function in 6 patients. We found a strong patientspecific result of the therapy where in some patients the therapy resulted in complete atelectasis of the target lobe while in others the lobe remained inflated. We concluded from these applications that CFD can provide a better insight into clinically relevant therapies. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
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Publication Date |
2009-02-27 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
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| ISSN |
|
ISBN |
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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 |
de Backer, J.W.; Vos, W.G.; Gorlé, C.D.; Germonpré, P.; Partoens, B.; Wuyts, F.L.; Parizel, P.M.; de Backer, W. |
| Title |
Flow analyses in the lower airways: patient-specific model and boundary conditions |
Type |
A1 Journal article |
| Year |
2008 |
Publication |
Medical engineering and physics |
Abbreviated Journal |
Med Eng Phys |
| Volume |
30 |
Issue |
7 |
Pages |
872-879 |
| Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) |
| Abstract |
Computational fluid dynamics (CFD) is increasingly applied in the respiratory domain. The ability to simulate the flow through a bifurcating tubular system has increased the insight into the internal flow dynamics and the particular characteristics of respiratory flows such as secondary motions and inertial effects. The next step in the evolution is to apply the technique to patient-specific cases, in order to provide more information about pathological airways. This study presents a patient-specific approach where both the geometry and the boundary conditions (BC) are based on individual imaging methods using computed tomography (CT). The internal flow distribution of a 73-year-old female suffering from chronic obstructive pulmonary disease (COPD) is assessed. The validation is performed through the comparison of lung ventilation with gamma scintigraphy. The results show that in order to obtain agreement within the accuracy limits of the gamma scintigraphy scan, both the patient-specific geometry and the BC (driving pressure) play a crucial role. A minimal invasive test (CT scan) supplied enough information to perform an accurate CFD analysis. In the end it was possible to capture the pathological features of the respiratory system using the imaging and computational fluid dynamics techniques. This brings the introduction of this new technique in the clinical practice one step closer. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
London |
Editor |
|
| Language |
|
Wos |
000259768300009 |
Publication Date |
2007-12-26 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1350-4533; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
1.819 |
Times cited |
82 |
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 1.819; 2008 IF: 2.216 |
| Call Number |
UA @ lucian @ c:irua:71693 |
Serial |
1224 |
| Permanent link to this record |
| |
|
| |
| Author |
Vinchurkar, S.; De Backer, L.; Vos, W.; Van Holsbeke, C.; de Backer, J.; de Backer, W. |
| Title |
A case series on lung deposition analysis of inhaled medication using functional imaging based computational fluid dynamics in asthmatic patients : effect of upper airway morphology and comparison with in vivo data |
Type |
A1 Journal article |
| Year |
2012 |
Publication |
Inhalation Toxicology |
Abbreviated Journal |
Inhal Toxicol |
| Volume |
24 |
Issue |
2 |
Pages |
81-88 |
| Keywords |
A1 Journal article; Pharmacology. Therapy; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP) |
| Abstract |
Context: Asthma affects 20 million Americans resulting in an economic burden of approximately $18 billion in the US alone (Allergies and Asthma Foundation 2000; National Center for Environmental Health (NCEH) 1999). Research studies based on differences in patient-specific airway morphology for asthma and the associated effect on deposition of inhaled aerosols are currently not available in the literature. Therefore, the role of morphological variations such as upper airway (extrathoracic) occlusion is not well documented. Objective: Functional imaging based computational fluid dynamics (CFD) of the respiratory airways for five asthmatic subjects is performed in this study using computed tomography (CT) based patient-specific airway models and boundary conditions. Methods: CT scans for 5 asthma patients were used to reconstruct 3D lung models using segmentation software. An averaged inhalation profile and patient-specific lobar flow distribution were used to perform the simulation. The simulations were used to obtain deposition for BDP/Formoterol (R) HFA pMDI in the patient-specific airway models. Results: The lung deposition obtained using CFD was in excellent agreement with available in vivo data using the same product. Specifically, CFD resulted in 30% lung deposition, whereas in vivo lung deposition was reported to be approximately 31%. Conclusion: It was concluded that a combination of patient-specific airway models and lobar boundary conditions can be used to obtain accurate lung deposition estimates. Lower lung deposition can be expected for patients with higher extrathoracic resistance. Novel respiratory drug delivery devices need to accommodate population subgroups based on these morphological and anatomical differences in addition to subject age. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
|
| Language |
|
Wos |
000299744800001 |
Publication Date |
2012-01-20 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0895-8378;1091-7691; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
1.751 |
Times cited |
36 |
Open Access |
|
| Notes |
; ; |
Approved |
Most recent IF: 1.751; 2012 IF: 1.894 |
| Call Number |
UA @ lucian @ c:irua:96238 |
Serial |
286 |
| 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 |
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| Corporate Author |
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Thesis |
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| Publisher |
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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 |
van den Broek, W.; Verbeeck, J.; de Backer, S.; Scheunders, P.; Schryvers, D. |
| Title |
Acquisition of the EELS data cube by tomographic reconstruction |
Type |
A1 Journal article |
| Year |
2006 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| Volume |
106 |
Issue |
4/5 |
Pages |
269-276 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
| Abstract |
Energy filtered TEM, EFTEM, provides three-dimensional data, two spatial and one spectral dimension. We propose to acquire these data by measuring a series of images with a defocused energy filter. It will be shown that each image is a projection of the data on the detector and that reconstruction of the data out of a sufficient number of such projections using a tomographic reconstruction algorithm is possible. This technique uses only a fraction of the electron dose an energy filtered series (EFS) needs for the same spectral and spatial resolution and the same mean signal-to-noise ratio. (c) 2005 Elsevier B.V. All rights reserved. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
Amsterdam |
Editor |
|
| Language |
|
Wos |
000236042300003 |
Publication Date |
2005-11-30 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.843 |
Times cited |
6 |
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 2.843; 2006 IF: 1.706 |
| Call Number |
UA @ lucian @ c:irua:56910UA @ admin @ c:irua:56910 |
Serial |
55 |
| Permanent link to this record |
| |
|
| |
| Author |
Martinez, G.T.; Rosenauer, A.; de Backer, A.; Verbeeck, J.; Van Aert, S. |
| Title |
Quantitative composition determination at the atomic level using model-based high-angle annular dark field scanning transmission electron microscopy |
Type |
A1 Journal article |
| Year |
2014 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| Volume |
137 |
Issue |
|
Pages |
12-19 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| Abstract |
High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
Amsterdam |
Editor |
|
| Language |
|
Wos |
000331092200003 |
Publication Date |
2013-11-09 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.843 |
Times cited |
74 |
Open Access |
|
| Notes |
FWO; FP7; ERC Countatoms; ESTEEM2; esteem2_ta |
Approved |
Most recent IF: 2.843; 2014 IF: 2.436 |
| Call Number |
UA @ lucian @ c:irua:111579UA @ admin @ c:irua:111579 |
Serial |
2749 |
| Permanent link to this record |
| |
|
| |
| Author |
De Backer, A.; Jones, L.; Lobato, I.; Altantzis, T.; Goris, B.; Nellist, P.D.; Bals, S.; Van Aert, S. |
| Title |
Three-dimensional atomic models from a single projection using Z-contrast imaging: verification by electron tomography and opportunities |
Type |
A1 Journal article |
| Year |
2017 |
Publication |
Nanoscale |
Abbreviated Journal |
Nanoscale |
| Volume |
9 |
Issue |
9 |
Pages |
8791-8798 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| Abstract |
In order to fully exploit structure–property relations of nanomaterials, three-dimensional (3D) characterization at the atomic scale is often required. In recent years, the resolution of electron tomography has reached the atomic scale. However, such tomography typically requires several projection images demanding substantial electron dose. A newly developed alternative circumvents this by counting the number of atoms across a single projection. These atom counts can be used to create an initial atomic model with which an energy minimization can be applied to obtain a relaxed 3D reconstruction of the nanoparticle. Here, we compare, at the atomic scale, this single projection reconstruction approach with tomography and find an excellent agreement. This new approach allows for the characterization of beam-sensitive materials or where the acquisition of a tilt series is impossible. As an example, the utility is illustrated by the 3D atomic scale characterization of a nanodumbbell on an in situ heating holder of limited tilt range. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000404614700031 |
Publication Date |
2017-06-09 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
2040-3364 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
7.367 |
Times cited |
33 |
Open Access |
OpenAccess |
| Notes |
The authors gratefully acknowledge funding from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N, G.0368.15N, and WO.010.16N) and postdoctoral grants to T. Altantzis, A. De Backer, and B. Goris. S. Bals acknowledges financial support from the European Research Council (Starting Grant No. COLOURATOM 335078). Funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiatieve-I3) is acknowledged. The authors would also like to thank Luis Liz-Marzán, Marek Grzelczak, and Ana Sánchez-Iglesias for sample provision. (ROMEO:yellow; preprint:; postprint:restricted ; pdfversion:cannot); saraecas; ECAS_Sara; |
Approved |
Most recent IF: 7.367 |
| Call Number |
EMAT @ emat @ c:irua:144436UA @ admin @ c:irua:144436 |
Serial |
4617 |
| 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 |
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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 |
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 |
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Thesis |
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| Publisher |
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Place of Publication |
|
Editor |
|
| Language |
English |
Wos |
000386925500014 |
Publication Date |
2016-07-26 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.843 |
Times cited |
6 |
Open Access |
|
| Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15, G.0369.15 and G.0374.13) and a postdoctoral research grant to A. De Backer. The research leading to these results has also received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). The authors would also like to thank A. Rosenauer for providing access to the STEMsim software and Gerardo T. Martinez for fruitful discussions.; esteem2_jra2 |
Approved |
Most recent IF: 2.843 |
| Call Number |
c:irua:135337 c:irua:135337 |
Serial |
4128 |
| Permanent link to this record |
| |
|
| |
| Author |
de Backer, A.; De wael, A.; Gonnissen, J.; Van Aert, S. |
| Title |
Optimal experimental design for nano-particle atom-counting from high-resolution STEM images |
Type |
A1 Journal article |
| Year |
2015 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| Volume |
151 |
Issue |
151 |
Pages |
46-55 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| Abstract |
In the present paper, the principles of detection theory are used to quantify the probability of error for atom-counting from high resolution scanning transmission electron microscopy (HR STEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom-counting using the expression for the probability of error. We show that for very thin objects LAADF is optimal and that for thicker objects the optimal inner detector angle increases. |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
| Language |
|
Wos |
000351237800007 |
Publication Date |
2014-11-11 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.843 |
Times cited |
24 |
Open Access |
|
| Notes |
312483 Esteem2; Fwo G039311; G037413; esteem2_jra2 |
Approved |
Most recent IF: 2.843; 2015 IF: 2.436 |
| Call Number |
c:irua:123926 c:irua:123926 |
Serial |
2481 |
| 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 |
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 |
Şentürk, D.G.; De Backer, A.; Van Aert, S. |
| Title |
Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination |
Type |
A1 Journal Article |
| Year |
2024 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| Volume |
259 |
Issue |
|
Pages |
113941 |
| Keywords |
A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ; |
| Abstract |
In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy. |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
|
Publication Date |
2024-02-19 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record |
| Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N, GOA7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). |
Approved |
Most recent IF: 2.2; 2024 IF: 2.843 |
| Call Number |
EMAT @ emat @c:irua:204353 |
Serial |
8996 |
| Permanent link to this record |
| |
|
| |
| Author |
de Backer, A.; Van Aert, S.; van Dyck, D. |
| Title |
High precision measurements of atom column positions using model-based exit wave reconstruction |
Type |
A1 Journal article |
| Year |
2011 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| Volume |
111 |
Issue |
9/10 |
Pages |
1475-1482 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
| Abstract |
In this paper, it has been investigated how to measure atom column positions as accurately and precisely as possible using a focal series of images. In theory, it is expected that the precision would considerably improve using a maximum likelihood estimator based on the full series of focal images. As such, the theoretical lower bound on the variances of the unknown atom column positions can be attained. However, this approach is numerically demanding. Therefore, maximum likelihood estimation has been compared with the results obtained by fitting a model to a reconstructed exit wave rather than to the full series of focal images. Hence, a real space model-based exit wave reconstruction technique based on the channelling theory is introduced. Simulations show that the reconstructed complex exit wave contains the same amount of information concerning the atom column positions as the full series of focal images. Only for thin samples, which act as weak phase objects, this information can be retrieved from the phase of the reconstructed complex exit wave. |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
Amsterdam |
Editor |
|
| Language |
|
Wos |
000300461200004 |
Publication Date |
2011-07-28 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.843 |
Times cited |
8 |
Open Access |
|
| Notes |
Fwo |
Approved |
Most recent IF: 2.843; 2011 IF: 2.471 |
| Call Number |
UA @ lucian @ c:irua:91879 |
Serial |
1438 |
| 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 |
Alania, M.; De Backer, A.; Lobato, I.; Krause, F.F.; Van Dyck, D.; Rosenauer, A.; Van Aert, S. |
| Title |
How precise can atoms of a nanocluster be located in 3D using a tilt series of scanning transmission electron microscopy images? |
Type |
A1 Journal article |
| Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| Volume |
181 |
Issue |
181 |
Pages |
134-143 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
| Abstract |
In this paper, we investigate how precise atoms of a small nanocluster can ultimately be located in three dimensions (3D) from a tilt series of images acquired using annular dark field (ADF) scanning transmission electron microscopy (STEM). Therefore, we derive an expression for the statistical precision with which the 3D atomic position coordinates can be estimated in a quantitative analysis. Evaluating this statistical precision as a function of the microscope settings also allows us to derive the optimal experimental design. In this manner, the optimal angular tilt range, required electron dose, optimal detector angles, and number of projection images can be determined. |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000411170800016 |
Publication Date |
2016-12-15 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.843 |
Times cited |
3 |
Open Access |
OpenAccess |
| Notes |
The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N, G.0368.15N, and WO.010.16N) and a post-doctoral grant to A. De Backer, and from the DFG under contract No. RO-2057/4-2. |
Approved |
Most recent IF: 2.843 |
| Call Number |
EMAT @ emat @ c:irua:144432 |
Serial |
4618 |
| Permanent link to this record |
| |
|
| |
| 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 |
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| 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 |
| 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 |
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, L.; Vos, W.; Dieriks, B.; Daems, D.; Verhulst, S.; Vinchurkar, S.; Ides, K.; de Backer, J.; Germonpré, P.; de Backer, W. |
| Title |
The effects of long-term noninvasive ventilation in hypercapnic COPD patients : a randomized controlled pilot study |
Type |
A1 Journal article |
| Year |
2011 |
Publication |
International journal of chronic obstructive pulmonary disease |
Abbreviated Journal |
Int J Chronic Obstr |
| Volume |
6 |
Issue |
|
Pages |
615-624 |
| Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP) |
| Abstract |
Introduction: Noninvasive ventilation (NIV) is a well-established treatment for acute-on-chronic respiratory failure in hypercapnic COPD patients. Less is known about the effects of a long-term treatment with NIV in hypercapnic COPD patients and about the factors that may predict response in terms of improved oxygenation and lowered CO2 retention.Methods: In this study, we randomized 15 patients to a routine pharmacological treatment (n = 5, age 66 [standard deviation ± 6] years, FEV1 30.5 [±5.1] %pred, PaO2 65 [±6] mmHg, PaCO2 52.4 [±6.0] mmHg) or to a routine treatment and NIV (using the Synchrony BiPAP device [Respironics, Inc, Murrsville, PA]) (n = 10, age 65 [±7] years, FEV1 29.5 [±9.0] %pred, PaO2 59 [±13] mmHg, PaCO2 55.4 [±7.7] mmHg) for 6 months. We looked at arterial blood gasses, lung function parameters and performed a low-dose computed tomography of the thorax, which was later used for segmentation (providing lobe and airway volumes, iVlobe and iVaw) and post-processing with computer methods (providing airway resistance, iRaw) giving overall a functional image of the separate airways and lobes.Results: In both groups there was a nonsignificant change in FEV1 (NIV group 29.5 [9.0] to 38.5 [14.6] %pred, control group 30.5 [5.1] to 36.8 [8.7] mmHg). PaCO2 dropped significantly only in the NIV group (NIV: 55.4 [7.7] → 44.5 [4.70], P = 0.0076; control: 52.4 [6.0] → 47.6 [8.2], NS). Patients actively treated with NIV developed a more inhomogeneous redistribution of mass flow than control patients. Subsequent analysis indicated that in NIV-treated patients that improve their blood gases, mass flow was also redistributed towards areas with higher vessel density and less emphysema, indicating that flow was redistributed towards areas with better perfusion. There was a highly significant correlation between the % increase in mass flow towards lobes with a blood vessel density of >9% and the increase in PaO2. Improved ventilation–perfusion match and recruitment of previously occluded small airways can explain the improvement in blood gases.Conclusion: We can conclude that in hypercapnic COPD patients treated with long-term NIV over 6 months, a mass flow redistribution occurs, providing a better ventilation–perfusion match and hence better blood gases and lung function. Control patients improve homogeneously in iVaw and iRaw, without improvement in gas exchange since there is no improved ventilation/perfusion ratio or increased alveolar ventilation. These differences in response can be detected through functional imaging, which gives a more detailed report on regional lung volumes and resistances than classical lung function tests do. Possibly only patients with localized small airway disease are good candidates for long-term NIV treatment. To confirm this and to see if better arterial blood gases also lead to better health related quality of life and longer survival, we have to study a larger population. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000208709800066 |
Publication Date |
2011-11-18 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1178-2005; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.157 |
Times cited |
28 |
Open Access |
|
| Notes |
; ; |
Approved |
Most recent IF: 3.157; 2011 IF: NA |
| Call Number |
UA @ lucian @ c:irua:93164 |
Serial |
866 |
| 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 |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000449722100002 |
Publication Date |
2018-07-24 |
| Series Editor |
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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 |
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 |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000844595100002 |
Publication Date |
0000-00-00 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| 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 |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000784103500001 |
Publication Date |
2022-04-21 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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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.; 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 |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000579839600233 |
Publication Date |
2020-09-19 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| 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 |
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| |
| Author |
Agrawal, H.; Patra, B.K.; Altantzis, T.; De Backer, A.; Garnett, E.C. |
| Title |
Quantifying Strain and Dislocation Density at Nanocube Interfaces after Assembly and Epitaxy |
Type |
A1 Journal article |
| Year |
2020 |
Publication |
Acs Applied Materials & Interfaces |
Abbreviated Journal |
Acs Appl Mater Inter |
| Volume |
12 |
Issue |
7 |
Pages |
8788-8794 |
| Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT) |
| Abstract |
Nanoparticle self-assembly and epitaxy are utilized extensively to make 1D and 2D structures with complex shapes. High-resolution transmission electron microscopy (HRTEM) has shown that single-crystalline interfaces can form, but little is known about the strain and dislocations at these interfaces. Such information is critically important for applications: drastically reducing
dislocation density was the key breakthrough enabling widespread implementation of light-emitting diodes, while strain engineering has been fundamental to modern high-performance transistors, solar cells, and thermoelectrics. In this work, the interfacial defect and strain formation after selfassembly and room temperature epitaxy of 7 nm Pd nanocubes capped with polyvinylpyrrolidone (PVP) is examined. It is observed that, during ligand removal, the cubes move over large distances on the substrate, leading to both spontaneous self-assembly and epitaxy to form single crystals. Subsequently, atomically resolved images are used to quantify the strain and dislocation density at the epitaxial interfaces between cubes with different lateral and angular misorientations. It is shown that dislocation- and strain-free interfaces form when the nanocubes align parallel to each other. Angular misalignment between adjacent cubes does not necessarily lead to grain boundaries but does cause dislocations, with higher densities associated with larger rotations. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000515214300101 |
Publication Date |
2020-02-19 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1944-8244 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
9.5 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
Fonds Wetenschappelijk Onderzoek; H2020 Research Infrastructures, 731019 ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek, 14846 ; The work at AMOLF is part of the research program of the “Nederlandse Organisatie voor Wetenschappelijk Onderzoek” (NWO). This work was supported by the NWO VIDI grant (project no. 14846). The authors would like to thank Reinout Jaarsma and Dr. Sven Askes for helping with the XPS measurements. A.D.B. acknowledges a postdoctoral grant from the research foundation Flanders (FWO). The authors acknowledge financial support from the European Commission under the Horizon 2020 Programme by means of the grant agreement no. 731019 EUSMI. |
Approved |
Most recent IF: 9.5; 2020 IF: 7.504 |
| Call Number |
EMAT @ emat @c:irua:167770 |
Serial |
6398 |
| Permanent link to this record |
| |
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| |
| 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 |
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Thesis |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000614960600001 |
Publication Date |
2021-02-02 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| 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 |
| |
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| |
| Author |
Van Holsbeke, C.; Vos, W.; van Hoorenbeeck, K.; Boudewyns, A.; Salgado, R.; Verdonck, P.R.; Ramet, J.; de Backer, J.; De Backer, W.; Verhulst, S.L. |
| Title |
Functional respiratory imaging as a tool to assess upper airway patency in children with obstructive sleep apnea |
Type |
A1 Journal article |
| Year |
2013 |
Publication |
Sleep Medicine |
Abbreviated Journal |
Sleep Med |
| Volume |
14 |
Issue |
5 |
Pages |
433-439 |
| Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP) |
| Abstract |
Objective: We aim to investigate if anatomical and functional properties of the upper airway using computerized 3D models derived from computed tomography (CT) scans better predict obstructive sleep apnea (OSA) severity than standard clinical markers. Methods: Consecutive children with suspected OSA underwent polysomnography, clinical assessment of upper airway patency, and a CT scan while awake. A three-dimensional (3D) reconstruction of the pharyngeal airway was built from these images, and computational fluid dynamics modeling of low inspiratory flow was performed using open-source software. Results: Thirty-three children were included (23 boys; mean age, was 6.0 +/- 3.2 y). OSA was diagnosed in 23 patients. Children with OSA had a significantly lower volume of the overlap region between tonsils and the adenoids (median volume, 1408 mm compared to 2173 mm; p = 0.04), a lower mean cross-sectional area at this location (median volume, 69.3 mm(2) compared to 114.3 mm(2); p = 0.04), and a lower minimal cross-sectional area (median volume, 17.9 mm(2) compared to 25.9 mm(2); p = 0.05). Various significant correlations were found between several imaging parameters and the severity of OSA, most pronounced for upper airway conductance (r = -0.46) (p < 0.01) for correlation between upper airway conductance and the apnea-hypopnea index. No differences or significant correlations were observed with clinical parameters of upper airway patency. Preliminary data after treatment showed that none of the patients with residual OSA had their smallest cross-sectional area located in segment 3, and this frequency was significantly lower than in their peers whose sleep study normalized (64%; p = 0.05). Conclusion: Functional imaging parameters are highly correlated with OSA severity and are a more powerful correlate than clinical scores of upper airway patency. Preliminary data also showed that we could identify differences in the upper airway of those subjects who did not benefit from a local upper airway treatment. (c) 2013 Elsevier B.V. All rights reserved. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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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 |
