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	Author	Aghaei, M.; Flamigni, L.; Lindner, H.; Günther, D.; Bogaerts, A.
	Title	Occurrence of gas flow rotational motion inside the ICP torch : a computational and experimental study			Type	A1 Journal article
	Year	2014	Publication	Journal of analytical atomic spectrometry	Abbreviated Journal	J Anal Atom Spectrom
	Volume	29	Issue	2	Pages	249-261
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	An inductively coupled plasma, connected to the sampling cone of a mass spectrometer, is computationally investigated. The occurrence of rotational motion of the auxiliary and carrier gas flows is studied. The effects of operating parameters, i.e., applied power and gas flow rates, as well as geometrical parameters, i.e., sampler orifice diameter and injector inlet diameter, are investigated. Our calculations predict that at higher applied power the auxiliary and carrier gas flows inside the torch move more forward to the sampling cone, which is validated experimentally for the auxiliary gas flow, by means of an Elan 6000 ICP-MS. Furthermore, an increase of the gas flow rates can also modify the occurrence of rotational motion. This is especially true for the carrier gas flow rate, which has a more pronounced effect to reduce the backward motion than the flow rates of the auxiliary and cooling gas. Moreover, a larger sampler orifice (e.g., 2 mm instead of 1 mm) reduces the backward flow of the auxiliary gas path lines. Finally, according to our model, an injector inlet of 2 mm diameter causes more rotations in the carrier gas flow than an injector inlet diameter of 1.5 mm, which can be avoided again by changing the operating parameters.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000329934000005	Publication Date	2013-11-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0267-9477;1364-5544;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.379	Times cited	21	Open Access
	Notes				Approved	Most recent IF: 3.379; 2014 IF: 3.466
	Call Number	UA @ lucian @ c:irua:112896			Serial	2427
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	Author	Bengtson, C.; Bogaerts, A.
	Title	On the Anti-Cancer Effect of Cold Atmospheric Plasma and the Possible Role of Catalase-Dependent Apoptotic Pathways			Type	A1 Journal article
	Year	2020	Publication	Cells	Abbreviated Journal	Cells
	Volume	9	Issue	10	Pages	2330
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold atmospheric plasma (CAP) is a promising new agent for (selective) cancer treatment, but the underlying cause of the anti-cancer effect of CAP is not well understood yet. Among different theories and observations, one theory in particular has been postulated in great detail and consists of a very complex network of reactions that are claimed to account for the anti-cancer effect of CAP. Here, the key concept is a reactivation of two specific apoptotic cell signaling pathways through catalase inactivation caused by CAP. Thus, it is postulated that the anti-cancer effect of CAP is due to its ability to inactivate catalase, either directly or indirectly. A theoretical investigation of the proposed theory, especially the role of catalase inactivation, can contribute to the understanding of the underlying cause of the anti-cancer effect of CAP. In the present study, we develop a mathematical model to analyze the proposed catalase-dependent anti-cancer effect of CAP. Our results show that a catalase-dependent reactivation of the two apoptotic pathways of interest is unlikely to contribute to the observed anti-cancer effect of CAP. Thus, we believe that other theories of the underlying cause should be considered and evaluated to gain knowledge about the principles of CAP-induced cancer cell death.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000584186700001	Publication Date	2020-10-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2073-4409	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	2	Open Access
	Notes	; ;			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:173632			Serial	6429
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	Author	Uytdenhouwen, Y.; Bal, Km.; Neyts, Ec.; Meynen, V.; Cool, P.; Bogaerts, A.
	Title	On the kinetics and equilibria of plasma-based dry reforming of methane			Type	A1 Journal article
	Year	2021	Publication	Chemical Engineering Journal	Abbreviated Journal	Chem Eng J
	Volume	405	Issue		Pages	126630
	Keywords	A1 Journal article; Laboratory of adsorption and catalysis (LADCA); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma reactors are interesting for gas-based chemical conversion but the fundamental relation between the plasma chemistry and selected conditions remains poorly understood. Apparent kinetic parameters for the loss and formation processes of individual components of gas conversion processes, can however be extracted by performing experiments in an extended residence time range (2–75 s) and ﬁtting the gas composition to a ﬁrstorder kinetic model of the evolution towards partial chemical equilibrium (PCE). We speciﬁcally investigated the diﬀerences in kinetic characteristics and PCE state of the CO2 dissociation and CH4 reforming reactions in a dielectric barrier discharge reactor (DBD), how these are mutually aﬀected when combining both gases in the dry reforming of methane (DRM) reaction, and how they change when a packing material (non-porous SiO2) is added to the reactor. We ﬁnd that CO2 dissociation is characterized by a comparatively high reaction rate of 0.120 s−1 compared to CH4 reforming at 0.041 s−1; whereas CH4 reforming reaches higher equilibrium conversions, 82% compared to 53.6% for CO2 dissociation. Combining both feed gases makes the DRM reaction to proceed at a relatively high rate (0.088 s−1), and high conversion (75.4%) compared to CO2 dissociation, through accessing new chemical pathways between the products of CO2 and CH4. The addition of the packing material can also distinctly inﬂuence the conversion rate and position of the equilibrium, but its precise eﬀect depends strongly on the gas composition. Comparing diﬀerent CO2:CH4 ratios reveals the delicate balance of the combined chemistry. CO2 drives the loss reactions in DRM, whereas CH4 in the mixture suppresses back reactions. As a result, our methodology provides some of the insight necessary to systematically tune the conversion process.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000621197700003	Publication Date	2020-08-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1385-8947	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.216	Times cited		Open Access	OpenAccess
	Notes	The authors acknowledge ﬁnancial support from the European Fund for Regional Development through the cross-border collaborative Interreg V program Flanders-the Netherlands (project EnOp), the Fund for Scientiﬁc Research (FWO; grant number: G.0254.14N), a TOP-BOF project and an IOF-SBO (SynCO2Chem) project from the University of Antwerp.			Approved	Most recent IF: 6.216
	Call Number	PLASMANT @ plasmant @c:irua:172458			Serial	6411
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	Author	Eckert, M.; Neyts, E.; Bogaerts, A.
	Title	On the reaction behaviour of hydrocarbon species at diamond (1 0 0) and (1 1 1) surfaces: a molecular dynamics investigation			Type	A1 Journal article
	Year	2008	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	41	Issue		Pages	032006,1-3
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000253177800006	Publication Date	2008-01-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	17	Open Access
	Notes				Approved	Most recent IF: 2.588; 2008 IF: 2.104
	Call Number	UA @ lucian @ c:irua:66107			Serial	2449
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	Author	Martens, T.; Brok, W.J.M.; van Dijk, J.; Bogaerts, A.
	Title	On the regime transitions during the formation of an atmospheric pressure dielectric barrier glow discharge			Type	A1 Journal article
	Year	2009	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	42	Issue	12	Pages	122002,1-122002,5
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The atmospheric pressure dielectric barrier discharge in helium is a pulsed discharge in nature. If during the electrical current pulse a glow discharge is reached, then this pulse will last only a few microseconds in operating periods of sinusoidal voltage with lengths of about 10 to 100 µs. In this paper we demonstrate that right before a glow discharge is reached, the discharge very closely resembles the commonly assumed Townsend discharge structure, but actually contains some significant differing features and hence should not be considered as a Townsend discharge. In order to clarify this, we present calculation results of high time and space resolution of the pulse formation. The results indicate that indeed a maximum of ionization is formed at the anode, but that the level of ionization remains high and that the electric field at that time is significantly disturbed. Our results also show where this intermediate structure comes from.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos	000266639300002	Publication Date	2009-05-22
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727;1361-6463;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	21	Open Access
	Notes				Approved	Most recent IF: 2.588; 2009 IF: 2.083
	Call Number	UA @ lucian @ c:irua:76458			Serial	2450
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	Author	de Bleecker, K.; Herrebout, D.; Bogaerts, A.; Gijbels, R.; Descamps, P.
	Title	One-dimensional modelling of a capacitively coupled rf plasma in silane/helium, including small concentrations of O₂ and N₂			Type	A1 Journal article
	Year	2003	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	36	Issue		Pages	1826-1833
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	London	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited		Open Access
	Notes				Approved	Most recent IF: 2.588; 2003 IF: 1.265
	Call Number	UA @ lucian @ c:irua:44022			Serial	2463
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	Author	Aghaei, M.; Lindner, H.; Bogaerts, A.
	Title	Optimization of operating parameters for inductively coupled plasma mass spectrometry : a computational study			Type	A1 Journal article
	Year	2012	Publication	Spectrochimica acta: part B : atomic spectroscopy	Abbreviated Journal	Spectrochim Acta B
	Volume	76	Issue		Pages	56-64
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	An inductively coupled plasma, connected to a mass spectrometer interface, is computationally investigated. The effect of pressure behind the sampler, injector gas flow rate, auxiliary gas flow rate, and applied power is studied. There seems to be an optimum range of injector gas flow rate for each setup which guaranties the presence and also a proper length of the central channel in the torch. Moreover, our modeling results show that for any specific purpose, it is possible to control that either only the central gas flow passes through the sampler orifice or that it is accompanied by the auxiliary gas flow. It was also found that depending on geometry, the variation of outgoing gas flow rate is much less than the variation of the injector gas flow rate and this causes a slightly higher pressure inside the torch. The general effect of increasing the applied power is a rise in the plasma temperature, which results in a higher ionization in the coil region. However, the negative effect is reducing the length of the cool central channel which is important to transfer the sample substances to the sampler. Using a proper applied power can enhance the efficiency of the system. Indeed, by changing the gas path lines, the power can control which flow (i.e., only from injector gas or also from the auxiliary gas) goes to the sampler orifice. Finally, as also reported from experiments in literature, the pressure behind the sampler has no dramatic effect on the plasma characteristics.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Oxford	Editor
	Language		Wos	000311008600008	Publication Date	2012-06-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0584-8547;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.241	Times cited	18	Open Access
	Notes				Approved	Most recent IF: 3.241; 2012 IF: 3.141
	Call Number	UA @ lucian @ c:irua:101356			Serial	2488
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	Author	Lindner, H.; Autrique, D.; Garcia, C.C.; Niemax, K.; Bogaerts, A.
	Title	Optimized transport setup for high repetition rate pulse-separated analysis in laser ablation-inductively coupled plasma mass spectrometry			Type	A1 Journal article
	Year	2009	Publication	Analytical chemistry	Abbreviated Journal	Anal Chem
	Volume	81	Issue	11	Pages	4241-4248
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	An optimized laser ablation setup, proposed for high repetition rate inductively coupled plasma mass spectrometry (ICPMS) analyses such as 2D imaging or depth profiling, is presented. For such applications, the particle washout time needs to be as short as possible to allow high laser pulse frequencies for reduced analysis time. Therefore, it is desirable to have an ablation setup that operates as a laminar flow reactor (LFR). A top-down strategy was applied that resulted in the present design. In the first step, a previously applied ablation setup was analyzed on the basis of computational fluid dynamics (CFD) results presented by D. Autrique et al. (Spectrochim. Acta, B 2008, 63, 257−270). By means of CFD simulations, the design was modified in such a way that it operated in the LFR regime. Experimental results demonstrate that the current design can indeed be regarded as an LFR. Furthermore, the operation under LFR conditions allowed some insight into the initial radial concentration distribution if the experimental ICPMS signal and analytical expressions are taken into account. Recommendations for a modified setup for more resilient spatial distributions are given. With the present setup, a washout time of 140 ms has been achieved for a 3% signal area criterion. Therefore, 7 Hz repetition rates can be applied with the present setup. Using elementary formulas of the analytical model, an upper bound for the washout times for similar setups can be predicted. The authors believe that the presented setup geometry comes close to the achievable limit for reliable short washout times.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Washington, D.C.	Editor
	Language		Wos	000266601800014	Publication Date	2009-04-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-2700;1520-6882;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.32	Times cited	18	Open Access
	Notes				Approved	Most recent IF: 6.32; 2009 IF: 5.214
	Call Number	UA @ lucian @ c:irua:76935			Serial	2492
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	Author	Deben, C.; Cardenas De La Hoz, E.; Le Compte, M.; Van Schil, P.; Hendriks, J.M.H.; Lauwers, P.; Yogeswaran, S.K.; Lardon, F.; Pauwels, P.; van Laere, S.; Bogaerts, A.; Smits, E.; Vanlanduit, S.; Lin, A.
	Title	OrBITS : label-free and time-lapse monitoring of patient derived organoids for advanced drug screening			Type	A1 Journal article
	Year	2022	Publication	Cellular Oncology (2211-3428)	Abbreviated Journal	Cell Oncol
	Volume		Issue		Pages	1-16
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Center for Oncological Research (CORE)
	Abstract	Background Patient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications. Methods Here, we developed a high-throughput compatible and automated live-cell image analysis software that allows for kinetic monitoring of organoids, named Organoid Brightfield Identification-based Therapy Screening (OrBITS), by combining computer vision with a convolutional network machine learning approach. The OrBITS deep learning analysis approach was validated against current standard assays for kinetic imaging and automated analysis of organoids. A drug screen of standard-of-care lung and pancreatic cancer treatments was also performed with the OrBITS platform and compared to the gold standard, CellTiter-Glo 3D assay. Finally, the optimal parameters and drug response metrics were identified to improve patient stratification. Results OrBITS allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D (R)-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. The obtained organoid Count, Mean Area, and Total Area had a strong correlation with the nuclear staining, Hoechst, following pairwise comparison over a broad range of sizes. By incorporating a fluorescent cell death marker, infra-well normalization for organoid death could be achieved, which was tested with a 10-point titration of cisplatin and validated against the current gold standard ATP-assay, CellTiter-Glo 3D. Using this approach with OrBITS, screening of chemotherapeutics and targeted therapies revealed further insight into the mechanistic action of the drugs, a feature not achievable with the CellTiter-Glo 3D assay. Finally, we advise the use of the growth rate-based normalised drug response metric to improve accuracy and consistency of organoid drug response quantification. Conclusion Our findings validate that OrBITS, as a scalable, automated live-cell image analysis software, would facilitate the use of patient-derived organoids for drug development and therapy screening. The developed wet-lab workflow and software also has broad application potential, from providing a launching point for further brightfield-based assay development to be used for fundamental research, to guiding clinical decisions for personalized medicine.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000898426100001	Publication Date	2022-12-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2211-3428; 2211-3436	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.6	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 6.6
	Call Number	UA @ admin @ c:irua:192698			Serial	7272
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	Author	Razzokov, J.; Yusupov, M.; Bogaerts, A.
	Title	Oxidation destabilizes toxic amyloid beta peptide aggregation			Type	A1 Journal article
	Year	2019	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	9	Issue	1	Pages	5476
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000462990000018	Publication Date	2019-04-02
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	5	Open Access	OpenAccess
	Notes	M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant 1200216N and 1200219N. 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: 4.259
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:159367			Serial	5182
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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
	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
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	Author	Yusupov, M.; Privat-Maldonado, A.; Cordeiro, R.M.; Verswyvel, H.; Shaw, P.; Razzokov, J.; Smits, E.; Bogaerts, A.
	Title	Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy			Type	A1 Journal article
	Year	2021	Publication	Redox Biology	Abbreviated Journal	Redox Biol
	Volume	43	Issue		Pages	101968
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000657371800005	Publication Date	2021-04-14
	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	Fwo; The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, where all computational work was performed.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:177780			Serial	6750
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	Author	Mannaerts, D.; Faes, E.; Cos, P.; Briedé, J.J.; Gyselaers, W.; Cornette, J.; Gorbanev, Y.; Bogaerts, A.; Spaanderman, M.; Van Craenenbroeck, E.; Jacquemyn, Y.; Torrens, C.
	Title	Oxidative stress in healthy pregnancy and preeclampsia is linked to chronic inflammation, iron status and vascular function			Type	University Hospital Antwerp
	Year	2018	Publication	PLoS ONE	Abbreviated Journal	Plos One
	Volume	13	Issue	9	Pages	e0202919
	Keywords	University Hospital Antwerp; A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Translational Pathophysiological Research (TPR)
	Abstract	Background During normal pregnancy, placental oxidative stress (OS) is present during all three trimesters and is necessary to obtain normal cell function. However, if OS reaches a certain level, pregnancy complications might arise. In preeclampsia (PE), a dangerous pregnancy specific hypertensive disorder, OS induced in the ischemic placenta causes a systemic inflammatory response and activates maternal endothelial cells. In this study, we aimed to quantify superoxide concentrations (as a measure of systemic OS) using electron paramagnetic resonance (EPR) and correlate them to markers of systemic inflammation, iron status and vascular function. Methods Fifty-nine women with a healthy pregnancy (HP), 10 non-pregnant controls (NP) and 28 PE patients (32±3.3weeks) were included. During HP, blood samples for superoxide, neutrophil to lymphocyte ratio (NLR), mean platelet volume (MPV) and iron status were taken at 10, 25 and 39 weeks. Vascular measurements for arterial stiffness (carotid-femoral pulse wave velocity (CF-PWV), augmentation index (AIx), augmentation Pressure (AP)) and microvascular endothelial function (reactive hyperemia index (RHI)) were performed at 35 weeks. In PE, all measurements were performed at diagnosis. CMH (1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine) was used as spin probe for EPR, since the formed CM radical corresponds to the amount of superoxide. Results Superoxide concentration remains stable during pregnancy (p = 0.92), but is significantly higher compared to the NP controls (p<0.0001). At 25 weeks, there is a significant positive correlation between superoxide and ferritin concentration. (p = 0.04) In PE, superoxide, systemic inflammation and iron status are much higher compared to HP (all p<0.001). During HP, superoxide concentrations correlate significantly with arterial stiffness (all p<0.04), while in PE superoxide is significantly correlated to microvascular endothelial function (p = 0.03). Conclusions During HP there is an increased but stable oxidative environment, which is correlated to ferritin concentration. If superoxide levels increase, there is an augmentation in arterial stiffness. In PE pregnancies, systemic inflammation and superoxide concentrations are higher and result in a deterioration of endothelial function. Together, these findings support the hypothesis that vascular function is directly linked to the amount of OS and that measurement of OS in combination with vascular function tests might be used in the prediction of PE.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000444355500010	Publication Date	2018-09-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1932-6203	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.806	Times cited	15	Open Access	OpenAccess
	Notes	This study is part of a PhD-thesis which is supported by the University of Antwerp and the Department Obstetrics and Gynaecology of the Antwerp University Hospital. The University of Antwerp provides the earnings for the principal investigator (DM) who is responsible for the design of the study, data collection and interpretation and writing of the manuscript. The Antwerp University Hospital supports the financial part of data collection. EMVC is supported by the fund for scientific research-Flanders (FWO) as senior clinical investigator.			Approved	Most recent IF: 2.806
	Call Number	PLASMANT @ plasmant @c:irua:153802c:irua:153644			Serial	5048
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	Author	Van Loenhout, J.; Peeters, M.; Bogaerts, A.; Smits, E.; Deben, C.
	Title	Oxidative Stress-Inducing Anticancer Therapies: Taking a Closer Look at Their Immunomodulating Effects			Type	A1 Journal article
	Year	2020	Publication	Antioxidants	Abbreviated Journal	Antioxidants
	Volume	9	Issue	12	Pages	1188
	Keywords	A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Cancer cells are characterized by higher levels of reactive oxygen species (ROS) compared to normal cells as a result of an imbalance between oxidants and antioxidants. However, cancer cells maintain their redox balance due to their high antioxidant capacity. Recently, a high level of oxidative stress is considered a novel target for anticancer therapy. This can be induced by increasing exogenous ROS and/or inhibiting the endogenous protective antioxidant system. Additionally, the immune system has been shown to be a significant ally in the fight against cancer. Since ROS levels are important to modulate the antitumor immune response, it is essential to consider the effects of oxidative stress-inducing treatments on this response. In this review, we provide an overview of the mechanistic cellular responses of cancer cells towards exogenous and endogenous ROS-inducing treatments, as well as the indirect and direct antitumoral immune effects, which can be both immunostimulatory and/or immunosuppressive. For future perspectives, there is a clear need for comprehensive investigations of different oxidative stress-inducing treatment strategies and their specific immunomodulating effects, since the effects cannot be generalized over different treatment modalities. It is essential to elucidate all these underlying immune effects to make oxidative stress-inducing treatments effective anticancer therapy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000602288600001	Publication Date	2020-11-27
	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
	Notes	This research was funded by the Olivia Hendrickx Research Fund (21OCL06) and the University of Antwerp (FFB160231).			Approved	Most recent IF: 7; 2020 IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:173865			Serial	6441
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	Author	Biswas, A.N.; Winter, L.R.; Loenders, B.; Xie, Z.; Bogaerts, A.; Chen, J.G.
	Title	Oxygenate Production from Plasma-Activated Reaction of CO₂and Ethane			Type	A1 Journal article
	Year	2021	Publication	Acs Energy Letters	Abbreviated Journal	Acs Energy Lett
	Volume		Issue		Pages	236-241
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Upgrading ethane with CO2 as a soft oxidant represents a desirable means of obtaining oxygenated hydrocarbons. This reaction is not thermodynamically feasible under mild conditions and has not been previously achieved as a one-step process. Nonthermal plasma was implemented as an alternative means of supplying energy to overcome activation barriers, leading to the production of alcohols, aldehydes, and acids as well as C1−C5+ hydrocarbons under ambient pressure, with a maximum total oxygenate selectivity of 12%. A plasma chemical kinetic computational model was developed and found to be in good agreement with the experimental trends. Results from this study illustrate the potential to use plasma for the direct synthesis of value-added alcohols, acids, and aldehydes from ethane and CO2 under mild conditions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000732435700001	Publication Date	2021-12-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2380-8195	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	Basic Energy Sciences, DE-SC0012704 ; Fonds Wetenschappelijk Onderzoek, S001619N ; H2020 European Research Council, 810182 ; National Science Foundation, DGE 16-44869 ; This research was supported by the U.S. Department of Energy, Oﬃce of Basic Energy Sciences, Catalysis Science Program (grant no. DE-SC0012704). L.R.W. acknowledges the U.S. National Science Foundation Graduate Research Fellowship Program grant number DGE 16-44869. B.L. and A.B. acknowledge support from the FWO-SBO project PLASMA240			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:184812			Serial	6897
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	Author	Madani, M.; Bogaerts, A.; Gijbels, R.; Vangeneugden, D.
	Title	Parametric study by means of numerical modelling for a dielectric barrier discharge at atmospheric pressure in nitrogen			Type	P3 Proceeding
	Year	2004	Publication		Abbreviated Journal
	Volume		Issue		Pages	49-52
	Keywords	P3 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	S.l.	Editor
	Language		Wos		Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:82304			Serial	2554
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	Author	Cordeiro, R.M.; Yusupov, M.; Razzokov, J.; Bogaerts, A.
	Title	Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences			Type	A1 Journal article
	Year	2020	Publication	Journal Of Physical Chemistry B	Abbreviated Journal	J Phys Chem B
	Volume	124	Issue	6	Pages	1082-1089
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Nitrogen oxyanions and oxyacids are important agents in atmospheric chemistry and medical biology. Although their chemical behavior in solution is relatively well understood, they may behave very diﬀerently at the water/air interface of atmospheric aerosols or at the membrane/water interface of cells. Here, we developed a fully classical model for molecular dynamics simulations of NO3−, NO2−, HNO3, and HNO2 in the framework of the GROMOS 53A6 and 54A7 force ﬁeld versions. The model successfully accounted for the poorly structured solvation shell and ion pairing tendency of NO3−. Accurate pure-liquid properties and hydration free energies were obtained for the oxyacids. Simulations at the water/air interface showed a local enrichment of HNO3 and depletion of NO3−. The eﬀect was discussed in light of earlier spectroscopic data and ab initio calculations, suggesting that HNO3 behaves as a weaker acid at the surface of water. Our model will hopefully allow for eﬃcient and accurate simulations of nitrogen oxyanions and oxyacids in solution and at microheterogeneous interface environments.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000512222500015	Publication Date	2020-02-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1520-6106	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.3	Times cited		Open Access
	Notes	We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work. This study was ﬁnanced in part by the Coordenaçaõ de Aperfeiçoamento de Pessoal de Nı ́vel Superior – Brasil (CAPES) – Finance Code 001.			Approved	Most recent IF: 3.3; 2020 IF: 3.177
	Call Number	PLASMANT @ plasmant @c:irua:166488			Serial	6340
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	Author	Aghaei, M.; Bogaerts, A.
	Title	Particle transport through an inductively coupled plasma torch: elemental droplet evaporation			Type	A1 Journal article
	Year	2016	Publication	Journal of analytical atomic spectrometry	Abbreviated Journal	J Anal Atom Spectrom
	Volume	31	Issue	31	Pages	631-641
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We studied the transport of copper droplets through an inductively coupled plasma, connected to the sampling cone of a mass spectrometer, by means of a computational model. The sample droplets are followed until they become evaporated. They are inserted as liquid particles from the central inlet and the effects of injection position (i.e. “on” and “off” axis), droplet diameter, as well as mass loading flow rate are investigated. It is shown that more “on-axis” injection of the droplets leads to a more straight path line, so that the droplets move less in the radial direction and are evaporated more on the central axis, enabling a better sample transfer efficiency to the sampler cone. Furthermore, there are optimum ranges of diameters and flow rates, which guarantee the proper position of evaporation along the torch, i.e. not too early, so that the sample can get lost in the torch, and not too late, which reduces the chance of becoming ionized before reaching the sampler.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000372857300003	Publication Date	2015-07-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0267-9477	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.379	Times cited	21	Open Access
	Notes	The authors are very grateful to H. Lindner for the many fundamental and fruitful discussions. They are also gratefully acknowledge nancial support from the Fonds voor Wetenschappelijk Onderzoek (FWO).			Approved	Most recent IF: 3.379
	Call Number	c:irua:133240			Serial	4024
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	Author	Cenian, A.; Chernukho, A.; Bogaerts, A.; Gijbels, R.; Leys, C.
	Title	Particle-in-cell Monte Carlo modeling of Langmuir probes in an Ar plasma			Type	A1 Journal article
	Year	2005	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	97	Issue		Pages	123310,1-10
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000230278100019	Publication Date	2005-06-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	18	Open Access
	Notes				Approved	Most recent IF: 2.068; 2005 IF: 2.498
	Call Number	UA @ lucian @ c:irua:53103			Serial	2560
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	Author	Bultinck, E.; Mahieu, S.; Depla, D.; Bogaerts, A.
	Title	Particle-in-cell/Monte Carlo collisions model for the reactive sputter deposition of nitride layers			Type	A1 Journal article
	Year	2009	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	6	Issue	S:1	Pages	S784-S788
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	A 2d3v Particle-in-cell/Monte Carlo collisions (PIC/MCC) model was constructed for an Ar/N2 reactive gas mixture in a magnetron discharge. A titanium target was used, in order to study the sputter deposition of a TiNx thin film. Cathode currents and voltages were calculated self-consistently and compared with experiments. Also, ion fluxes to the cathode were calculated, which cause sputtering of the target. The sputtered atom fluxes from the target, and to the substrate were calculated, in order to visualize the deposition of the TiNx film.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Weinheim	Editor
	Language		Wos	000272302900149	Publication Date	2009-09-16
	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	2	Open Access
	Notes				Approved	Most recent IF: 2.846; 2009 IF: 4.037
	Call Number	UA @ lucian @ c:irua:79364			Serial	2558
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	Author	Bultinck, E.; Bogaerts, A.
	Title	Particle-in-cell/Monte Carlo collisions treatment of an Ar/O₂ magnetron discharge used for the reactive sputter deposition of TiO_x films			Type	A1 Journal article
	Year	2009	Publication	New journal of physics	Abbreviated Journal	New J Phys
	Volume	11	Issue		Pages	103010-103010,24
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The physical processes in an Ar/O2 magnetron discharge used for the reactive sputter deposition of TiOx thin films were simulated with a 2d3v particle-in-cell/Monte Carlo collisions (PIC/MCC) model. The plasma species taken into account are electrons, Ar+ ions, fast Arf atoms, metastable Arm* atoms, Ti+ ions, Ti atoms, O+ ions, O2+ ions, O− ions and O atoms. This model accounts for plasmatarget interactions, such as secondary electron emission and target sputtering, and the effects of target poisoning. Furthermore, the deposition process is described by an analytical surface model. The influence of the O2/Ar gas ratio on the plasma potential and on the species densities and fluxes is investigated. Among others, it is shown that a higher O2 pressure causes the region of positive plasma potential and the O− density to be more spread, and the latter to decrease. On the other hand, the deposition rates of Ti and O are not much affected by the O2/Ar proportion. Indeed, the predicted stoichiometry of the deposited TiOx film approaches x=2 for nearly all the investigated O2/Ar proportions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Bristol	Editor
	Language		Wos	000270820900001	Publication Date	2009-10-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-2630;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.786	Times cited	24	Open Access
	Notes				Approved	Most recent IF: 3.786; 2009 IF: 3.312
	Call Number	UA @ lucian @ c:irua:78326			Serial	2559
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	Author	Georgieva, V.; Bogaerts, A.; Gijbels, R.
	Title	Particle-in-cell/Monte Carlo simulation of a capacitively coupled radio frequency Ar/Cf₄ discharge: effect of gas composition			Type	A1 Journal article
	Year	2003	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	93	Issue		Pages	2369-2379
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000181307000007	Publication Date	2003-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	57	Open Access
	Notes				Approved	Most recent IF: 2.068; 2003 IF: 2.171
	Call Number	UA @ lucian @ c:irua:44011			Serial	2561
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	Author	Neyts, E.; Yan, M.; Bogaerts, A.; Gijbels, R.
	Title	Particle-in-cell/Monte Carlo simulations of a low-pressure capacitively coupled radio-frequency discharge: effect of adding H₂ to an Ar discharge			Type	A1 Journal article
	Year	2003	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	93	Issue		Pages	5025-5033
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000182296700010	Publication Date	2003-04-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	15	Open Access
	Notes				Approved	Most recent IF: 2.068; 2003 IF: 2.171
	Call Number	UA @ lucian @ c:irua:44012			Serial	2562
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	Author	Attri, P.; Bogaerts, A.
	Title	Perspectives of Plasma-treated Solutions as Anticancer Drugs			Type	A1 Journal article
	Year	2019	Publication	Anti-cancer agents in medicinal chemistry	Abbreviated Journal	Anti-Cancer Agent Me
	Volume	19	Issue	4	Pages	436-438
	Keywords	A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000472726300001	Publication Date	2019-06-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1871-5206	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.598	Times cited	2	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.598
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:160694			Serial	5189
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	Author	Chen, Z.; Bogaerts, A.; Vertes, A.
	Title	Phase explosion in atmospheric pressure infrared laser ablation from water-rich targets			Type	A1 Journal article
	Year	2006	Publication	Applied physics letters	Abbreviated Journal	Appl Phys Lett
	Volume	89	Issue	4	Pages	041503,1-3
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000239376500032	Publication Date	2006-08-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-6951;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.411	Times cited	32	Open Access
	Notes				Approved	Most recent IF: 3.411; 2006 IF: 3.977
	Call Number	UA @ lucian @ c:irua:58732			Serial	2583
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	Author	Wen, D.-Q.; Zhang, Q.-Z.; Jiang, W.; Song, U.-H.; Bogaerts, A.; Wang, Y.-N.
	Title	Phase modulation in pulsed dual-frequency capacitively coupled plasmas			Type	A1 Journal article
	Year	2014	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	115	Issue	23	Pages	233303
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Particle-in-cell/Monte Carlo collision simulations, coupled with an external circuit, are used to investigate the behavior of pulsed dual-frequency (DF) capacitively coupled plasmas (CCPs). It is found that the phase shift θ between the high (or low) frequency source and the pulse modulation has a great influence on the ion density and the ionization rate. By pulsing the high frequency source, the time-averaged ion density shows a maximum when θ = 90∘. The time-averaged ion energy distribution functions (IEDFs) at the driven electrode, however, keep almost unchanged, illustrating the potential of pulsed DF-CCP for independent control of ion density (and flux) and ion energy. A detailed investigation of the temporal evolution of the plasma characteristics indicates that several high frequency harmonics can be excited at the initial stage of a pulse period by tuning the phase shift θ, and this gives rise to strong sheath oscillations, and therefore high ionization rates. For comparison, the pulsing of the low frequency source is also studied. In this case, the ion density changes slightly as a function of time, and the time-averaged ion density shows the same trend as in the HF modulation for different phase shifts θ. Moreover, the time-averaged IEDFs at the driven electrode can be modulated, showing the potential to reduce the maximum ion bombardment energy.
	Address
	Corporate Author				Thesis
	Publisher	American Institute of Physics	Place of Publication	New York, N.Y.	Editor
	Language		Wos	000338106000008	Publication Date	2014-06-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0021-8979;1089-7550;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.068	Times cited	8	Open Access
	Notes				Approved	Most recent IF: 2.068; 2014 IF: 2.183
	Call Number	UA @ lucian @ c:irua:117415			Serial	2585
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	Author	Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A.
	Title	Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling			Type	A1 Journal article
	Year	2017	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	14	Issue	10	Pages	1700013
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000413045800010	Publication Date	2017-04-05
	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	9	Open Access	Not_Open_Access
	Notes	Fonds Wetenschappelijk Onderzoek, 1200216N ;			Approved	Most recent IF: 2.846
	Call Number	PLASMANT @ plasmant @c:irua:149567			Serial	4910
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	Author	Verswyvel, H.; Deben, C.; Wouters, A.; Lardon, F.; Bogaerts, A.; Smits, E.; Lin, A.
	Title	Phototoxicity and cell passage affect intracellular reactive oxygen species levels and sensitivity towards non-thermal plasma treatment in fluorescently-labeled cancer cells			Type	A1 Journal article
	Year	2023	Publication	Journal of physics: D: applied physics	Abbreviated Journal
	Volume	56	Issue	29	Pages	294001
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Live-cell imaging with fluorescence microscopy is a powerful tool, especially in cancer research, widely-used for capturing dynamic cellular processes over time. However, light-induced toxicity (phototoxicity) can be incurred from this method, via disruption of intracellular redox balance and an overload of reactive oxygen species (ROS). This can introduce confounding effects in an experiment, especially in the context of evaluating and screening novel therapies. Here, we aimed to unravel whether phototoxicity can impact cellular homeostasis and response to non-thermal plasma (NTP), a therapeutic strategy which specifically targets the intracellular redox balance. We demonstrate that cells incorporated with a fluorescent reporter for live-cell imaging have increased sensitivity to NTP, when exposed to ambient light or fluorescence excitation, likely through altered proliferation rates and baseline intracellular ROS levels. These changes became even more pronounced the longer the cells stayed in culture. Therefore, our results have important implications for research implementing this analysis technique and are particularly important for designing experiments and evaluating redox-based therapies like NTP.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000978180500001	Publication Date	2023-07-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.4	Times cited		Open Access	OpenAccess
	Notes	This work was partially funded by the Research Foundation— Flanders (FWO) and supported by the following Grants: 1S67621N (H V), 12S9221N (A L), and G044420N (A B and A L). 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.			Approved	Most recent IF: 3.4; 2023 IF: 2.588
	Call Number	PLASMANT @ plasmant @c:irua:196441			Serial	7381
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	Author	Kumar, N.; Perez-Novo, C.; Shaw, P.; Logie, E.; Privat-Maldonado, A.; Dewilde, S.; Smits, E.; Berghe, W.V.; Bogaerts, A.
	Title	Physical plasma-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death			Type	A1 Journal article
	Year	2021	Publication	Free Radical Biology And Medicine	Abbreviated Journal	Free Radical Bio Med
	Volume	166	Issue		Pages	187-200
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
	Abstract	Despite modern therapeutic advances, the survival prospects of pancreatic cancer patients remain poor, due to chemoresistance and dysregulated oncogenic kinase signaling networks. We applied a novel kinome activitymapping approach using biological peptide targets as phospho-sensors to identify vulnerable kinase dependencies for therapy sensitization by physical plasma. Ser/Thr-kinome specific activity changes were mapped upon induction of ferroptotic cell death in pancreatic tumor cells exposed to reactive oxygen and nitrogen species of plasma-treated water (PTW). This revealed a broad kinome activity response involving the CAMK, the AGC and CMGC family of kinases. This systems-level kinome network response supports stress adaptive switches between chemoresistant anti-oxidant responses of Kelch-like ECH-associated protein 1 (KEAP1)/Heme Oxygenase 1 (HMOX1) and ferroptotic cell death sensitization upon suppression of Nuclear factor (erythroid derived 2)-like 2 (NRF2) and Glutathione peroxidase 4 (GPX4). This is further supported by ex vivo experiments in the chicken chorioallantoic membrane assay, showing decreased GPX4 and Glutathione (GSH) expression as well as increased lipid peroxidation, along with suppressed BxPC-3 tumor growth in response to PTW. Taken all together, we demonstrate that plasma treated water-derived oxidants sensitize pancreatic cancer cells to ferroptotic cell death by targeting a NRF2-HMOX1-GPX4 specific kinase signaling network.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000632703400001	Publication Date	2021-02-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0891-5849	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.606	Times cited		Open Access	OpenAccess
	Notes	We gratefully acknowledge the financial support obtained from the Research Foundation Flanders (FWO), Belgium, grant number 12J5617 N and Department of Biotechnology (DBT) Ramalingaswami Re-entry Fellowship, India, grant number D.O.NO.BT/HRD/35/02/2006. We are thankful to the Laboratory of Experimental Hematology, for providing the facilities for the experimental and fluorescence microscopy work. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), Belgium. The Kinome profiling was performed at the Epigenetic Signaling service facility (PPES-UA) funded by the Hercules Foundation and Foundation against cancer Belgium (KOTK 7872).			Approved	Most recent IF: 5.606
	Call Number	PLASMANT @ plasmant @c:irua:176878			Serial	6711
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	Author	Clemen, R.; Heirman, P.; Lin, A.; Bogaerts, A.; Bekeschus, S.
	Title	Physical Plasma-Treated Skin Cancer Cells Amplify Tumor Cytotoxicity of Human Natural Killer (NK) Cells			Type	A1 Journal article
	Year	2020	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	12	Issue	12	Pages	3575
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Skin cancers have the highest prevalence of all human cancers, with the most lethal forms being squamous cell carcinoma and malignant melanoma. Besides the conventional local treatment approaches like surgery and radiotherapy, cold physical plasmas are emerging anticancer tools. Plasma technology is used as a therapeutic agent by generating reactive oxygen species (ROS). Evidence shows that inflammation and adaptive immunity are involved in cancer-reducing effects of plasma treatment, but the role of innate immune cells is still unclear. Natural killer (NK)-cells interact with target cells via activating and inhibiting surface receptors and kill in case of dominating activating signals. In this study, we investigated the effect of cold physical plasma (kINPen) on two skin cancer cell lines (A375 and A431), with non-malignant HaCaT keratinocytes as control, and identified a plasma treatment time-dependent toxicity that was more pronounced in the cancer cells. Plasma treatment also modulated the expression of activating and inhibiting receptors more profoundly in skin cancer cells compared to HaCaT cells, leading to significantly higher NK-cell killing rates in the tumor cells. Together with increased pro-inflammatory mediators such as IL-6 and IL-8, we conclude that plasma treatment spurs stress responses in skin cancer cells, eventually augmenting NK-cell activity.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000601901900001	Publication Date	2020-11-30
	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
	Notes	This work was funded by the German Federal Ministry of Education and Research (BMBF), grant numbers 03Z22DN11 and 03Z22Di1; The authors acknowledge the technical assistance of Eric Freund, Julia Berner, Sanjeev Kumar Sagwal, Christina Wolff, Felix Niessner, Walison Brito, and Lea Miebach.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:173863			Serial	6442
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