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	Author	Yusupov, M.; Razzokov, J.; Cordeiro, R.M.; Bogaerts, A.
	Title	Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture			Type	A1 Journal article
	Year	2019	Publication	Oxidative medicine and cellular longevity	Abbreviated Journal	Oxid Med Cell Longev
	Volume	2019	Issue		Pages	1-11
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Aquaporins (AQPs) are transmembrane proteins that conduct not only water molecules across the cell membrane but also other solutes, such as reactive oxygen and nitrogen species (RONS), produced (among others) by cold atmospheric plasma (CAP). These RONS may induce oxidative stress in the cell interior, which plays a role in cancer treatment. The underlying mechanisms of the transport of RONS across AQPs, however, still remain obscure. We apply molecular dynamics simulations to investigate the permeation of both hydrophilic (H<sub>2</sub>O<sub>2</sub>and OH) and hydrophobic (NO<sub>2</sub>and NO) RONS through AQP1. Our simulations show that these RONS can all penetrate across the pores of AQP1. The permeation free energy barrier of OH and NO is lower than that of H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>, indicating that these radicals may have easier access to the pore interior and interact with the amino acid residues of AQP1. We also study the effect of RONS-induced oxidation of both the phospholipids and AQP1 (i.e., sulfenylation of Cys<sub>191</sub>) on the transport of the above-mentioned RONS across AQP1. Both lipid and protein oxidation seem to slightly increase the free energy barrier for H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>permeation, while for OH and NO, we do not observe a strong effect of oxidation. The simulation results help to gain insight in the underlying mechanisms of the noticeable rise of CAP-induced RONS in cancer cells, thereby improving our understanding on the role of AQPs in the selective anticancer capacity of CAP.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000492999000001	Publication Date	2019-06-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1942-0900	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.593	Times cited	5	Open Access	OpenAccess
	Notes	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. M.Y. gratefully acknowledges Dr. U. Khalilov for the fruitful discussions. This work was ﬁnancially supported by the Research Foundation Flanders (FWO) (grant number 1200219N).			Approved	Most recent IF: 4.593
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:160118			Serial	5180
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	Author	Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A.
	Title	Transport of cystine across xC-antiporter			Type	A1 Journal article
	Year	2019	Publication	Archives of biochemistry and biophysics	Abbreviated Journal	Arch Biochem Biophys
	Volume	664	Issue		Pages	117-126
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Up to now, the molecular level mechanism of the CYC uptake by xC antiporter has not been studied in detail. In this study, we applied several different simulation techniques to investigate the transport of CYC through xCT, the light subunit of the xC antiporter, which is responsible for the CYC and glutamate translocation. Specifically, we studied the permeation of CYC across three model systems, i.e., outward facing (OF), occluded (OCC) and inward facing (IF) configurations of xCT. We also investigated the effect of mutation of Cys327 to Ala within xCT, which was also studied experimentally in literature. This allowed us to qualitatively compare our computation results with experimental observations, and thus, to validate our simulations. In summary, our simulations provide a molecular level mechanism of the transport of CYC across the xC antiporter, more specifically, which amino acid residues in the xC antiporter play a key role in the uptake, transport and release of CYC.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000461411200014	Publication Date	2019-02-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.165	Times cited	3	Open Access	OpenAccess
	Notes	Research Foundation − FlandersResearch Foundation − Flanders (FWO), 1200216N 1200219N ; Hercules FoundationHercules Foundation; Flemish GovernmentFlemish Government (department EWI); UAUA; M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant numbers 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript.			Approved	Most recent IF: 3.165
	Call Number	PLASMANT @ plasmant @UA @ admin @ c:irua:158571			Serial	5183
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	Author	Khalilov, U.; Vets, C.; Neyts, E.C.
	Title	Catalyzed growth of encapsulated carbyne			Type	A1 Journal article
	Year	2019	Publication	Carbon	Abbreviated Journal	Carbon
	Volume	153	Issue		Pages	1-5
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Carbyne is a novel material of current interest in nanotechnology. As is typically the case for nanomaterials, the growth process determines the resulting properties. While endohedral carbyne has been successfully synthesized, its catalyst and feedstock-dependent growth mechanism is still elusive. We here study the nucleation and growth mechanism of different carbon chains in a Ni-containing double walled carbon nanotube using classical molecular dynamics simulations and ﬁrst-principles calculations. We ﬁnd that the understanding the competitive role of the metal catalyst and the hydrocarbon is important to control the growth of 1-dimensional carbon chains, including Ni or H-terminated carbyne. Also, we ﬁnd that the electronic property of the Ni-terminated carbyne can be tuned by steering the H concentration along the chain. These results suggest catalyst-containing carbon nanotubes as a possible synthesis route for carbyne formation.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000485054200001	Publication Date	2019-07-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0008-6223	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.337	Times cited		Open Access	Not_Open_Access
	Notes	Fund of Scientific Research Flanders (FWO), Belgium, 12M1318N 1S22516N ; Flemish Supercomputer Centre VSC; Hercules Foundation; Flemish Government; University of Antwerp; The authors gratefully acknowledge the ﬁnancial support from the Fund of Scientiﬁc Research Flanders (FWO), Belgium, Grant numbers 12M1318N and 1S22516N. The work was carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp.			Approved	Most recent IF: 6.337
	Call Number	PLASMANT @ plasmant @c:irua:160695			Serial	5187
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	Author	Heyne, M.H.; Marinov, D.; Braithwaite, N.; Goodyear, A.; de Marneffe, J.-F.; Cooke, M.; Radu, I.; Neyts, E.C.; De Gendt, S.
	Title	A route towards the fabrication of 2D heterostructures using atomic layer etching combined with selective conversion			Type	A1 Journal article
	Year	2019	Publication	2D materials	Abbreviated Journal	2D Mater
	Volume	6	Issue	3	Pages	035030
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Heterostructures of low-dimensional semiconducting materials, such as transition metal dichalcogenides (MX2), are promising building blocks for future electronic and optoelectronic devices. The patterning of one MX2 material on top of another one is challenging due to their structural similarity. This prevents an intrinsic etch stop when conventional anisotropic dry etching processes are used. An alternative approach consist in a two-step process, where a sacrificial silicon layer is pre-patterned with a low damage plasma process, stopping on the underlying MoS2 film. The pre-patterned layer is used as sacrificial template for the formation of the top WS2 film. This study describes the optimization of a cyclic Ar/Cl-2 atomic layer etch process applied to etch silicon on top of MoS2, with minimal damage, followed by a selective conversion of the patterned Si into WS2. The impact of the Si atomic layer etch towards the MoS2 is evaluated: in the ion energy range used for this study, MoS2 removal occurs in the over-etch step over 1-2 layers, leading to the appearance of MoOx but without significant lattice distortions to the remaining layers. The combination of Si atomic layer etch, on top of MoS2, and subsequent Si-to-WS2 selective conversion, allows to create a WS2/MoS2 heterostructure, with clear Raman signals and horizontal lattice alignment. These results demonstrate a scalable, transfer free method to achieve horizontally individually patterned heterostacks and open the route towards wafer-level processing of 2D materials.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000468335500004	Publication Date	2019-04-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2053-1583	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.937	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 6.937
	Call Number	UA @ admin @ c:irua:160229			Serial	5266
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	Author	Dabral, A.; Lu, A.K.A.; Chiappe, D.; Houssa, M.; Pourtois, G.
	Title	A systematic study of various 2D materials in the light of defect formation and oxidation			Type	A1 Journal article
	Year	2019	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	21	Issue	3	Pages	1089-1099
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The thermodynamic aspects of various 2D materials are explored using Density Functional Theory (DFT). Various metal chalcogenides (MX2, M = metal, chalcogen X = S, Se, Te) are investigated with respect to their interaction and stability under different ambient conditions met in the integration process of a transistor device. Their interaction with high- dielectrics is also addressed, in order to assess their possible integration in Complementary Metal Oxide Semiconductor (CMOS) field effect transistors. 2D materials show promise for high performance nanoelectronic devices, but the presence of defects (vacancies, grain boundaries,...) can significantly impact their electronic properties. To assess the impact of defects, their enthalpies of formation and their signature levels in the density of states have been studied. We find, consistently with literature reports, that chalcogen vacancies are the most likely source of defects. It is shown that while pristine 2D materials are in general stable whenever set in contact with different ambient atmospheres, the presence of defective sites affects the electronic properties of the 2D materials to varying degrees. We observe that all the 2D materials studied in the present work show strong reactivity towards radical oxygen plasma treatments while reactivity towards other common gas phase chemical such as O-2 and H2O and groups present at the high- surface varies significantly between species. While energy band-gaps, effective masses and contact resistivities are key criteria in selection of 2D materials for scaled CMOS and tunneling based devices, the phase and ambient stabilities might also play a very important role in the development of reliable nanoelectronic applications.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000456147000009	Publication Date	2018-12-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076; 1463-9084	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	1	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 4.123
	Call Number	UA @ admin @ c:irua:156715			Serial	5267
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	Author	Trenchev, G.; Nikiforov, A.; Wang, W.; Kolev, S.; Bogaerts, A.
	Title	Atmospheric pressure glow discharge for CO₂ conversion : model-based exploration of the optimum reactor configuration			Type	A1 Journal article
	Year	2019	Publication	Chemical engineering journal	Abbreviated Journal	Chem Eng J
	Volume	362	Issue	362	Pages	830-841
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We investigate the performance of an atmospheric pressure glow discharge (APGD) reactor for CO2 conversion in three different configurations, through experiments and simulations. The first (basic) configuration utilizes the well-known pin-to-plate design, which offers a limited conversion. The second configuration improves the reactor performance by employing a vortex-flow generator. The third, “confined” configuration is a complete redesign of the reactor, which encloses the discharge in a limited volume, significantly surpassing the conversion rate of the other two designs. The plasma properties are investigated using an advanced plasma model.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000457863500084	Publication Date	2019-01-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1385-8947; 1873-3212	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.216	Times cited	4	Open Access	Not_Open_Access: Available from 15.10.2019
	Notes				Approved	Most recent IF: 6.216
	Call Number	UA @ admin @ c:irua:157459			Serial	5269
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	Author	Wang, L.; Wen, D.-Q.; Zhang, Q.-Z.; Song, Y.-H.; Zhang, Y.-R.; Wang, Y.-N.
	Title	Disruption of self-organized striated structure induced by secondary electron emission in capacitive oxygen discharges			Type	A1 Journal article
	Year	2019	Publication	Plasma sources science and technology	Abbreviated Journal	Plasma Sources Sci T
	Volume	28	Issue	5	Pages	055007
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Self-organized striated structure has been observed experimentally and numerically in CF4 plasmas in radio-frequency capacitively coupled plasmas recently (Liu et al 2016 Phys. Rev. Lett. 116 255002). In this work, the striated structure is investigated in a capacitively coupled oxygen discharge with the introduction of the effect from the secondary electron emission, based on a particle-in-cell/Monte Carlo collision model. As we know, the transport of positive and negative ions plays a key role in the formation of striations in electronegative gases, for which, the electronegativity needs to be large enough. As the secondary electron emission increases, electrons in the sheaths gradually contribute more ionization to the discharge. Meanwhile, the increase of the electron density, especially in the plasma bulk, leads to an increased electrical conductivity and a reduced bulk electric field, which would shield the ions' mobility. These changes result in enlarged striation gaps. And then, with more emitted electrons, obvious disruption of the striations is observed accompanied with a transition of electron heating mode. Due to the weakened field, the impact ionization in the plasma bulk is attenuated, compared with the enhanced ionization caused by secondary electrons. This would lead to the electron heating mode transition from striated (STR) mode to gamma-mode. Besides, our investigation further reveals that gamma-mode is more likely to dominate the discharge under high gas pressures or driving voltages.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000467827800001	Publication Date	2019-04-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0963-0252	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.302	Times cited	2	Open Access	Not_Open_Access: Available from 13.05.2020
	Notes				Approved	Most recent IF: 3.302
	Call Number	UA @ admin @ c:irua:160365			Serial	5270
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	Author	Jia, W.-Z.; Zhang, Q.-Z.; Wang, X.-F.; Song, Y.-H.; Zhang, Y.-Y.; Wang, Y.-N.
	Title	Effect of dust particle size on the plasma characteristics in a radio frequency capacitively coupled silane plasma			Type	A1 Journal article
	Year	2019	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	52	Issue	1	Pages	015206
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Compared with dust-free plasmas, the existence of dust particles in plasmas may greatly influence the plasma properties. such as the plasma density, electron temperature, sheath properties, electron energy distribution function (EEDF) as well as the heating mechanism. In this work, a 1D hybrid fluid/MC model has been developed to investigate the interaction between dust and plasma in a low-pressure silane discharge sustained in a radio frequency capacitively coupled plasma, in which we assume spherical dust particles with a given radius are generated by taking the sum of the production rate of Si2H4- and Si2H5- as the nucleation rate. From our simulation, the plasma may experience definite perturbation by dust particles with a certain radius (more than 50nm) with an increase in electron temperature first, which further induces a rapid rise in the positive and negative ion densities. Then, the densities begin to decline due to the gradual lack of sufficient seed electrons. In addition, as the dust radius increases, the high energy tails of the EEDFs will be enhanced for discharge maintenance, accompanied by a decline in the population of low-energy electrons in comparison with those of pristine plasma. Furthermore, an obvious bulk heating is observed apart from the a-mode and local field reversal heating. This may contribute to the enhanced bulk electric field (also called the drift field) as a result of electron depletion via the dust. In addition, large-sized dust particles that accumulate near the sheaths tend to form two stable density peaks with their positions largely influenced by the time-averaged sheath thickness. A detailed study of the effects of the external parameters, including pressure, voltage and frequency, on the spatial distribution of dust particles is also conducted.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000448423800002	Publication Date	2018-10-02
	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	OpenAccess
	Notes				Approved	Most recent IF: 2.588
	Call Number	UA @ admin @ c:irua:155361			Serial	5271
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	Author	Grubova, I.Y.; Surmeneva, M.A.; Huygh, S.; Surmenev, R.A.; Neyts, E.C.
	Title	Effects of silicon doping on strengthening adhesion at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study			Type	A1 Journal article
	Year	2019	Publication	Computational materials science	Abbreviated Journal	Comp Mater Sci
	Volume	159	Issue	159	Pages	228-234
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this paper we employ first-principles calculations to investigate the effect of substitutional Si doping in the amorphous calcium-phosphate (a-HAP) structure on the work of adhesion, integral charge transfer, charge density difference and theoretical tensile strengths between an a-HAP coating and amorphous titanium dioxide (a-TiO2) substrate systemically. Our calculations demonstrate that substitution of a P atom by a Si atom in a-HAP (a-Si-HAP) with the creation of OH-vacancies as charge compensation results in a significant increase of the bonding strength of the coating to the substrate. The work of adhesion of the optimized Si-doped interfaces reaches a value of up to -2.52 J m(-2), which is significantly higher than for the stoichiometric a-HAP/a-TiO2. Charge density difference analysis indicates that the dominant interactions at the interface have significant covalent character, and in particular two Ti-O and three Ca-O bonds are formed for a-Si-HAP/a-TiO2 and one Ti-O and three Ca-O bonds for a-HAP/a-TiO2. From the stress-strain curve, the Young's modulus of a-Si-HAP/a-TiO2 is calculated to be about 25% higher than that of the a-HAP/a-TiO2, and the yielding stress is about 2 times greater than that of the undoped model. Our calculations therefore demonstrate that the presence of Si in the a-HAP structure strongly alters not only the bioactivity and resorption rates, but also the mechanical properties of the a-HAP/a-TiO2 interface. The results presented here provide an important theoretical insight into the nature of the chemical bonding at the a-HAP/a-TiO2 interface, and are particularly significant for the practical medical applications of HAP-based biomaterials.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000457856900023	Publication Date	2018-12-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0927-0256	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.292	Times cited	1	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.292
	Call Number	UA @ admin @ c:irua:157480			Serial	5272
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	Author	Gu, J.-G.; Zhang, Y.; Gao, M.-X.; Wang, H.-Y.; Zhang, Q.-Z.; Yi, L.; Jiang, W.
	Title	Enhancement of surface discharge in catalyst pores in dielectric barrier discharges			Type	A1 Journal article
	Year	2019	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	125	Issue	15	Pages	153303
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The generation of high-density plasmas on the surface of porous catalysts is very important for plasma catalysis, as it determines the active surface of the catalyst that is available for the reaction. In this work, we investigate the mechanism of surface and volume plasma streamer formation and propagation near micro-sized pores in dielectric barrier discharges operating in air at atmospheric pressure. A two-dimensional particle-in-cell/ Monte Carlo collision model is used to model the individual kinetic behavior of plasma species. Our calculations indicate that the surface discharge is enhanced on the surface of the catalyst pores compared with the microdischarge inside the catalyst pores. The reason is that the surface ionization wave induces surface charging along the catalyst pore sidewalls, leading to a strong electric field along the pore sidewalls, which in turn further enhances the surface discharge. Therefore, highly concentrated reactive species occur on the surfaces of the catalyst pores, indicating high-density plasmas on the surface of porous catalysts. Indeed, the maximum electron impact excitation and ionization rates occur on the pore surface, indicating the more pronounced production of excited state and electron-ion pairs on the pore surface than inside the pore, which may profoundly affect the plasma catalytic process. Published under license by AIP Publishing.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000465441200022	Publication Date	2019-04-15
	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	4	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.068
	Call Number	UA @ admin @ c:irua:160397			Serial	5273
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	Author	Vohra, A.; Khanam, A.; Slotte, J.; Makkonen, I.; Pourtois, G.; Loo, R.; Vandervorst, W.
	Title	Evolution of phosphorus-vacancy clusters in epitaxial germanium			Type	A1 Journal article
	Year	2019	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	125	Issue	2	Pages	025701
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The E centers (dopant-vacancy pairs) play a significant role in dopant deactivation in semiconductors. In order to gain insight into dopant-defect interactions during epitaxial growth of in situ phosphorus doped Ge, positron annihilation spectroscopy, which is sensitive to open-volume defects, was performed on Ge layers grown by chemical vapor deposition with different concentrations of phosphorus (similar to 1 x 10(18)-1 x 10(20) cm(-3)). Experimental results supported by first-principles calculations based on the two component density-functional theory gave evidence for the existence of mono-vacancies decorated by several phosphorus atoms as the dominant defect type in the epitaxial Ge. The concentration of vacancies increases with the amount of P-doping. The number of P atoms around the vacancy also increases, depending on the P concentration. The evolution of P-n-V clusters in Ge contributes significantly to the dopant deactivation. Published under license by AIP Publishing.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000455922100057	Publication Date	2019-01-08
	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	5	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 2.068
	Call Number	UA @ admin @ c:irua:156722			Serial	5274
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	Author	Dhayalan, S.K.; Nuytten, T.; Pourtois, G.; Simoen, E.; Pezzoli, F.; Cinquanta, E.; Bonera, E.; Loo, R.; Rosseel, E.; Hikavyy, A.; Shimura, Y.; Vandervorst, W.
	Title	Insights into the C Distribution in Si:C/Si:C:P and the Annealing Behavior of Si:C Layers			Type	A1 Journal article
	Year	2019	Publication	ECS journal of solid state science and technology	Abbreviated Journal	Ecs J Solid State Sc
	Volume	8	Issue	4	Pages	P209-P216
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Si:C and Si:C:P alloys are potential candidates for source-drain stressor applications in n-type Fin Field Effect Transistors (FinFETs). Increasing the C content to achieve high strain results in the arrangement of C atoms as third nearest neighbors (3nn) in the Si: C lattice. During thermal annealing, the presence of C atoms as 3nn may promote clustering at the interstitial sites, causing loss of stress. The concentration of C atoms as 3nn is reduced by the incorporation of a small amount of Ge atoms during the growth, whereas in-situ P doping does not influence this 3nn distribution [J Solid State Sci. Technol vol 6, p 755, 2017]. Small amounts of Ge are provided during low temperature selective epitaxial growth scheme, which are based on cyclic deposition and etching (CDE). In this work, we aim to provide physical insights into the aforementioned phenomena, to understand the behavior of 3nn C atoms and the types of defects that are formed in the annealed Si: C films. Using ab-initio simulations, the Ge-C interaction in the Si matrix is investigated and this insight is used to explain how the Ge incorporation leads to a reduced 3nn distribution of the C atoms. The interaction between C and P in the Si: C: P films is also investigated to explain why the P incorporation has not led to a reduction in the 3nn distribution. We then report on the Raman characterization of Si: C layers subjected to post epi annealing. As the penetration depth of the laser is dependent on the wavelength, Raman measurements at two different wavelengths enable us to probe the depth distribution of 3nn C atoms after applying different annealing conditions. We observed a homogeneous loss in 3nn C throughout the layer. Whereas in the kinematic modeling of high resolution X-ray diffraction spectra, a gradient in the substitutional C loss was observed close to the epitaxial layer/substrate interface. This gradient can be due to the out diffusion of C atoms into the Si substrate or to the formation of interstitial C clusters, which cannot be distinguished in HR-XRD. Deep Level Transient Spectroscopy indicated that the prominent out-diffusing species was interstitial CO complex while the interstitial C defects were also prevalent in the epi layer. (c) 2019 The Electrochemical Society.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000465069200001	Publication Date	2019-04-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2162-8769; 2162-8777	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	1.787	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 1.787
	Call Number	UA @ admin @ c:irua:160399			Serial	5275
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	Author	Brault, P.; Chamorro-Coral, W.; Chuon, S.; Caillard, A.; Bauchire, J.-M.; Baranton, S.; Coutanceau, C.; Neyts, E.
	Title	Molecular dynamics simulations of initial Pd and PdO nanocluster growth in a magnetron gas aggregation source			Type	A1 Journal article
	Year	2019	Publication	Frontiers of Chemical Science and Engineering	Abbreviated Journal	Front Chem Sci Eng
	Volume	13	Issue	2	Pages	324-329
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Molecular dynamics simulations are carried out for describing growth of Pd and PdO nanoclusters using the ReaxFF force field. The resulting nanocluster structures are successfully compared to those of nanoclusters experimentally grown in a gas aggregation source. The PdO structure is quasi-crystalline as revealed by high resolution transmission microscope analysis for experimental PdO nanoclusters. The role of the nanocluster temperature in the molecular dynamics simulated growth is highlighted.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000468848400009	Publication Date	2019-03-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2095-0179	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.712	Times cited	3	Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 1.712
	Call Number	UA @ admin @ c:irua:160278			Serial	5276
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	Author	Wardenier, N.; Vanraes, P.; Nikiforov, A.; Van Hulle, S.W.H.; Leys, C.
	Title	Removal of micropollutants from water in a continuous-flow electrical discharge reactor			Type	A1 Journal article
	Year	2019	Publication	Journal of hazardous materials	Abbreviated Journal	J Hazard Mater
	Volume	362	Issue	362	Pages	238-245
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The emergence of micropollutants into our aquatic resources is regarded as an issue of increasing environmental concern. To protect the aquatic environment against further contamination with micropollutants, treatment with advanced oxidation processes (AOPs) is put forward as a promising technique. In this work, an innovative AOP based on electrical discharges in a continuous-flow pulsed dielectric barrier discharge (DBD) reactor with falling water film over activated carbon textile is examined for its potential application in water treatment. The effect of various operational parameters including feed gas type, gas flow rate, water flow rate and power on removal and energy efficiency has been studied. To this end, a synthetic micropollutant mixture containing five pesticides (atrazine, alachlor, diuron, dichlorvos and pentachlorophenol), two pharmaceuticals (carbamazepine and 1,7-alpha-ethinylestradiol), and 1 plasticizer (bisphenol A) is used. While working under optimal conditions, energy consumption was situated in the range 2.42-4.25 kW h/m(3), which is about two times lower than the economically viable energy cost of AOPs (5 kW h/m(3)). Hence, the application of non-thermal plasma could be regarded as a promising alternative AOP for (industrial) wastewater remediation.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000449127500027	Publication Date	2018-08-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3894	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.065	Times cited	13	Open Access	OpenAccess
	Notes				Approved	Most recent IF: 6.065
	Call Number	UA @ admin @ c:irua:155358			Serial	5279
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	Author	Shaw, P.; Kumar, N.; Hammerschmid, D.; Privat-Maldonado, A.; Dewilde, S.; Bogaerts, A.
	Title	Synergistic Effects of Melittin and Plasma Treatment: A Promising Approach for Cancer Therapy			Type	A1 Journal article
	Year	2019	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	11	Issue	8	Pages	1109
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Melittin (MEL), a small peptide component of bee venom, has been reported to exhibit anti-cancer effects in vitro and in vivo. However, its clinical applicability is disputed because of its non-specific cytotoxicity and haemolytic activity in high treatment doses. Plasma-treated phosphate buffered saline solution (PT-PBS), a solution rich in reactive oxygen and nitrogen species (RONS) can disrupt the cell membrane integrity and induce cancer cell death through oxidative stress-mediated pathways. Thus, PT-PBS could be used in combination with MEL to facilitate its access into cancer cells and to reduce the required therapeutic dose. The aim of our study is to determine the reduction of the effective dose of MEL required to eliminate cancer cells by its combination with PT-PBS. For this purpose, we have optimised the MEL threshold concentration and tested the combined treatment of MEL and PT-PBS on A375 melanoma and MCF7 breast cancer cells, using in vitro, in ovo and in silico approaches. We investigated the cytotoxic effect of MEL and PT-PBS alone and in combination to reveal their synergistic cytological effects. To support the in vitro and in ovo experiments, we showed by computer simulations that plasma-induced oxidation of the phospholipid bilayer leads to a decrease of the free energy barrier for translocation of MEL in comparison with the non-oxidized bilayer, which also suggests a synergistic effect of MEL with plasma induced oxidation. Overall, our findings suggest that MEL in combination with PT-PBS can be a promising combinational therapy to circumvent the non-specific toxicity of MEL, which may help for clinical applicability in the future.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000484438000069	Publication Date	2019-08-03
	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	1	Open Access
	Notes	We gratefully acknowledge financial support from the Research Foundation—Flanders (FWO), grant number 12J5617N. We are thankful to Maksudbek Yusupov for his valuable discussions, and to the Center for Oncological Research (CORE), for providing the facilities for the experimental work. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the University Antwerp, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the University of Antwerp.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:161630			Serial	5286
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	Author	Gorbanev, Y.; Golda, J.; Gathen, V.S.; Bogaerts, A
	Title	Applications of the COST Plasma Jet: More than a Reference Standard			Type	A1 Journal article
	Year	2019	Publication	Plasma	Abbreviated Journal	Plasma
	Volume	2	Issue	3	Pages	316-327
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The rapid advances in the field of cold plasma research led to the development of many plasma jets for various purposes. The COST plasma jet was created to set a comparison standard between different groups in Europe and the world. Its physical and chemical properties are well studied, and diagnostics procedures are developed and benchmarked using this jet. In recent years, it has been used for various research purposes. Here, we present a brief overview of the reported applications of the COST plasma jet. Additionally, we discuss the chemistry of the plasma-liquid systems with this plasma jet, and the properties that make it an indispensable system for plasma research.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2019-07-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2571-6182	ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes	We would like to thank Deborah O’Connell (York Plasma Institute, Department of Physics, University of York, United Kingdom) and Angela Privat-Maldonado (PLASMANT, University of Antwerp) for useful discussions.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:161628			Serial	5287
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	Author	Wardenier, N.; Gorbanev, Y.; Van Moer, I.; Nikiforov, A.; Van Hulle, S.W.H.; Surmont, P.; Lynen, F.; Leys, C.; Bogaerts, A.; Vanraes, P.
	Title	Removal of alachlor in water by non-thermal plasma: Reactive species and pathways in batch and continuous process			Type	A1 Journal article
	Year	2019	Publication	Water research	Abbreviated Journal	Water Res
	Volume	161	Issue		Pages	549-559
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Pesticides are emerging contaminants frequently detected in the aquatic environment. In this work, a novel approach combining activated carbon adsorption, oxygen plasma treatment and ozonation was studied for the removal of the persistent chlorinated pesticide alachlor. A comparison was made between the removal efﬁciency and energy consumption for two different reactor operation modes: batchrecirculation and single-pass mode. The kinetics study revealed that the insufﬁcient removal of alachlor by adsorption was signiﬁcantly improved in terms of degradation efﬁciency and energy consumption when combined with the plasma treatment. The best efﬁciency (ca. 80% removal with an energy cost of 19.4 kWh mÀ3) was found for the single-pass operational mode of the reactor. In the batch-recirculating process, a complete elimination of alachlor by plasma treatment was observed after 30 min of treatment. Analysis of the reactive species induced by plasma in aqueous solutions showed that the decomposition of alachlor mainly occurred through a radical oxidation mechanism, with a minor contribution of long-living oxidants (O3, H2O2). Investigation of the alachlor oxidation pathways revealed six different oxidation mechanisms, including the loss of aromaticity which was never before reported for plasma-assisted degradation of aromatic pesticides. It was revealed that the removal rate and energy cost could be further improved with more than 50% by additional O3 gas bubbling in the solution reservoir.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000475999400054	Publication Date	2019-06-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0043-1354	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.942	Times cited	2	Open Access
	Notes	PlasmaTex project IWT, 1408/2 ; the European Marie Sklodowska-Curie Individual Fellowship within Horizon2020, 743151 ; Flemish Knowledge Centre Water; This work was ﬁnancially supported by the PlasmaTex project IWT 1408/2 and the European Marie Sklodowska-Curie Individual Fellowship within Horizon2020 (‘LTPAM’, grant no. 743151). This research was initiated within the LED H2O project which is ﬁnancially supported by the Flemish Knowledge Centre Water (Vlakwa).			Approved	Most recent IF: 6.942
	Call Number	PLASMANT @ plasmant @c:irua:161173			Serial	5288
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	Author	Bekeschus, S.; Freund, E.; Spadola, C.; Privat-Maldonado, A.; Hackbarth, C.; Bogaerts, A.; Schmidt, A.; Wende, K.; Weltmann, K.-D.; von Woedtke, T.; Heidecke, C.-D.; Partecke, L.-I.; Käding, A.
	Title	Risk Assessment of kINPen Plasma Treatment of Four Human Pancreatic Cancer Cell Lines with Respect to Metastasis			Type	A1 Journal article
	Year	2019	Publication	Cancers	Abbreviated Journal	Cancers
	Volume	11	Issue	9	Pages	1237
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Cold physical plasma has limited tumor growth in many preclinical models and is, therefore, suggested as a putative therapeutic option against cancer. Yet, studies investigating the cells’ metastatic behavior following plasma treatment are scarce, although being of prime importance to evaluate the safety of this technology. Therefore, we investigated four human pancreatic cancer cell lines for their metastatic behavior in vitro and in chicken embryos (in ovo). Pancreatic cancer was chosen as it is particularly metastatic to the peritoneum and systemically, which is most predictive for outcome. In vitro, treatment with the kINPen plasma jet reduced pancreatic cancer cell activity and viability, along with unchanged or decreased motility. Additionally, the expression of adhesion markers relevant for metastasis was down-regulated, except for increased CD49d. Analysis of 3D tumor spheroid outgrowth showed a lack of plasma-spurred metastatic behavior. Finally, analysis of tumor tissue grown on chicken embryos validated the absence of an increase of metabolically active cells physically or chemically detached with plasma treatment. We conclude that plasma treatment is a safe and promising therapeutic option and that it does not promote metastatic behavior in pancreatic cancer cells in vitro and in ovo.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000489719000022	Publication Date	2019-08-23
	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	4	Open Access
	Notes	The authors acknowledge that this work was supported by grants funded by the German Federal Ministry of Education and Research (BMBF), grant number 03Z22DN11. We want to thank the Research Foundation – Flanders (FWO) for providing funding to APM under the “long stay abroad” scheme (grant code V415618N). APM and AB acknowledge financial support from the Methusalem project. Technical support by Felix Niessner and Antje Janetzko is gratefully acknowledged.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:162106			Serial	5357
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	Author	Vanmeert, M.; Razzokov, J.; Mirza, M.U.; Weeks, S.D.; Schepers, G.; Bogaerts, A.; Rozenski, J.; Froeyen, M.; Herdewijn, P.; Pinheiro, V.B.; Lescrinier, E.
	Title	Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins			Type	A1 Journal article
	Year	2019	Publication	Nucleic acids research	Abbreviated Journal	Nucleic Acids Res
	Volume	47	Issue	13	Pages	7130-7142
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000490556600047	Publication Date	2019-07-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0305-1048	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	10.162	Times cited	1	Open Access
	Notes	European Research Council, FP7/2007-2013 ERC-2012-ADG 20120216/320683 ; KU Leuven, OT/14/128 ; Biotechnology and Biosciences Research Council, BB/N01023X/1 BB/N010221/1 ; Authors are grateful to Prof. Dr A.M.J.J. (Alexandre) Bonvin from the University of Utrecht and the WeNMR institute for his expert contribution. We have greatly benefited from discussions and help from numerous postdocs over the years (in particular, Dr E. Groaz, Dr E. Eremeeva, Dr J. Masschelein, Dr S. Xiaoping and Dr M. Renders) as well as graduate student D. Kestemont and undergraduate student M. Abdel Fattah Ismail. We express our gratitude to L. Margamuljana for helpful discussions and excellent technical assistance on in vitro experiments.			Approved	Most recent IF: 10.162
	Call Number	PLASMANT @ plasmant @c:irua:162105			Serial	5359
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	Author	Bogaerts, A.; Zhang, Q.-Z.; Zhang, Y.-R.; Van Laer, K.; Wang, W.
	Title	Burning questions of plasma catalysis: Answers by modeling			Type	A1 Journal article
	Year	2019	Publication	Catalysis today	Abbreviated Journal	Catal Today
	Volume	337	Issue		Pages	3-14
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma catalysis is promising for various environmental, energy and chemical synthesis applications, but the underlying mechanisms are far from understood. Modeling can help to obtain a better insight in these mechanisms. Some burning questions relate to the plasma behavior inside packed bed reactors and whether plasma can penetrate into catalyst pores. In this paper, we try to provide answers to these questions, by means of both ﬂuid modeling and particle-in-cell/Monte Carlo collision simulations. We present a short overview of recent ﬁndings obtained in our group by means of modeling, i.e., the enhanced electric ﬁeld near the contact points and the streamer propagation through the packing in packed bed reactors, as well as the plasma behavior in catalyst pores, to determine the minimum pore size in which plasma streamers can penetrate.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000482179500002	Publication Date	2019-04-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0920-5861	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.636	Times cited	7	Open Access
	Notes	University of Antwerp, the European Marie Skłodowska-Curie Individual Fellowships “GlidArc”; “CryoEtch” within Horizon2020, 657304 702604 ;We would like to thank H.-H. Kim for performing experiments to validate the modeling of streamer propagation in packed bed reactors. We acknowledge ﬁnancial support from the TOP-BOF project of the University of Antwerp, the European Marie Skłodowska-Curie Individual Fellowships “GlidArc” and “CryoEtch” within Horizon2020 (Grant Nos. 657304 and 702604).			Approved	Most recent IF: 4.636
	Call Number	PLASMANT @ plasmant @c:irua:161775			Serial	5356
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	Author	Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A.
	Title	Effect of oxidative stress on cystine transportation by xC‾ antiporter			Type	A1 Journal article
	Year	2019	Publication	Archives of biochemistry and biophysics	Abbreviated Journal	Arch Biochem Biophys
	Volume	674	Issue		Pages	108114
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We performed computer simulations to investigate the eﬀect of oxidation on the extracellular cystine (CYC) uptake by the xC− antiporter. The latter is important for killing of cancer cells. Speciﬁcally, applying molecular dynamics (MD) simulations we studied the transport of CYC across xCT, i.e., the light subunit of the xC− antiporter, in charge of bidirectional transport of CYC and glutamate. We considered the outward facing (OF) conﬁguration of xCT, and to study the eﬀect of oxidation, we modiﬁed the Cys327 residue, located in the vicinity of the extracellular milieu, to cysteic acid (CYO327). Our computational results showed that oxidation of Cys327 results in a free energy barrier for CYC translocation, thereby blocking the access of CYC to the substrate binding site of the OF system. The formation of the energy barrier was found to be due to the conformational changes in the channel. Analysis of the MD trajectories revealed that the reorganization of the side chains of the Tyr244 and CYO327 residues play a critical role in the OF channel blocking. Indeed, the calculated distance between Tyr244 and either Cys327 or CYO327 showed a narrowing of the channel after oxidation. The obtained free energy barrier for CYC translocation was found to be 33.9kJmol−1, indicating that oxidation of Cys327, by e.g., cold atmospheric plasma, is more eﬀective in inhibiting the xC− antiporter than in the mutation of this amino acid to Ala (yielding a barrier of 32.4kJmol−1). The inhibition of the xC− antiporter may lead to Cys starvation in some cancer cells, eventually resulting in cancer cell death.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000525439700011	Publication Date	2019-09-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0003-9861	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.165	Times cited		Open Access
	Notes	Ministry of Science, Research and Technology of Iran; University of Antwerp; Research Foundation − Flanders, 1200219N ; Universiteit Antwerpen; Hercules Foundation; Flemish Government; UA; M. G. acknowledges funding from the Ministry of Science, Research and Technology of Iran and from the University of Antwerp in Belgium. M. Y. gratefully acknowledges ﬁnancial support from the Research Foundation − Flanders (FWO), grant number 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. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript.			Approved	Most recent IF: 3.165
	Call Number	PLASMANT @ plasmant @c:irua:163474			Serial	5372
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	Author	Privat-Maldonado, A.; Schmidt, A.; Lin, A.; Weltmann, K.-D.; Wende, K.; Bogaerts, A.; Bekeschus, S.
	Title	ROS from Physical Plasmas: Redox Chemistry for Biomedical Therapy			Type	A1 Journal article
	Year	2019	Publication	Oxidative medicine and cellular longevity	Abbreviated Journal	Oxid Med Cell Longev
	Volume	2019	Issue		Pages	1-29
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Physical plasmas generate unique mixes of reactive oxygen and nitrogen species (RONS or ROS). Only a bit more than a decade ago, these plasmas, operating at body temperature, started to be considered for medical therapy with considerably little mechanistic redox chemistry or biomedical research existing on that topic at that time. Today, a vast body of evidence is available on physical plasma-derived ROS, from their spatiotemporal resolution in the plasma gas phase to sophisticated chemical and biochemical analysis of these species once dissolved in liquids. Data from<italic>in silico</italic>analysis dissected potential reaction pathways of plasma-derived reactive species with biological membranes, and<italic>in vitro</italic>and<italic>in vivo</italic>experiments in cell and animal disease models identified molecular mechanisms and potential therapeutic benefits of physical plasmas. In 2013, the first medical plasma systems entered the European market as class IIa devices and have proven to be a valuable resource in dermatology, especially for supporting the healing of chronic wounds. The first results in cancer patients treated with plasma are promising, too. Due to the many potentials of this blooming new field ahead, there is a need to highlight the main concepts distilled from plasma research in chemistry and biology that serve as a mechanistic link between plasma physics (how and which plasma-derived ROS are produced) and therapy (what is the medical benefit). This inevitably puts cellular membranes in focus, as these are the natural interphase between ROS produced by plasmas and translation of their chemical reactivity into distinct biological responses.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000493001000003	Publication Date	2019-10-08
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1942-0900	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.593	Times cited		Open Access
	Notes	KW and SB acknowledge funding by the German Federal Ministry of Education and Research (grant numbers 03Z22DN11 and 03Z22DN12). The work of SB is further supported by the European Social Fund (grant number ESF/14-BM-A55-0006). APM and AB acknowledge funding by the Methusalem Project. AL acknowledges funding from the Research Foundation Flanders (grant number 12S9218N). APM thanks Yury Gorbanev for his assistance with the preparation of this review.			Approved	Most recent IF: 4.593
	Call Number	PLASMANT @ plasmant @c:irua:163476			Serial	5373
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	Author	Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M.
	Title	Molecular dynamics simulations of mechanical stress on oxidized membranes			Type	A1 Journal article
	Year	2019	Publication	Biophysical chemistry	Abbreviated Journal	Biophys Chem
	Volume	254	Issue		Pages	106266
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. In this study, we investigated the effects of mechanical stress on oxidized phospholipid bilayers (PLBs). Model bilayers were stretched until pore formation (or poration) using nonequilibrium molecular dynamics simulations. We studied single-component homogeneous membranes composed of lipid oxidation products, as well as two-component heterogeneous membranes with coexisting native and oxidized domains. In homogeneous membranes, the oxidation products with —OH and —OOH groups reduced the areal strain required for pore formation, whereas the oxidation product with ]O group behaved similarly to the native membrane. In heterogeneous membranes composed of oxidized and non-oxidized domains, we tested the hypothesis according to which poration may be facilitated at the domain interface region. However, results were inconclusive due to their large statistical variance and sensitivity to simulation setup parameters. We pointed out important technical issues that need to be considered in future simulations of mechanically-induced poration of heterogeneous membranes. This research is of interest for photodynamic therapy and plasma medicine, because ruptured and intact plasma membranes are experimentally considered hallmarks of necrotic and apoptotic cell death.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000502890900015	Publication Date	2019-09-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0301-4622	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.402	Times cited		Open Access
	Notes	São Paulo Research Foundation, 2012/50680-5 ; National Counsel of Technological and Scientific Development, 459270/2014-1 ; We are thankful for the financial support received from the São Paulo Research Foundation (FAPESP) (grant no. 2012/50680-5) and from the National Counsel of Technological and Scientific Development (CNPq) (grant no. 459270/2014-1). MCO acknowledges UFABC for the Master's scholarship granted.			Approved	Most recent IF: 2.402
	Call Number	PLASMANT @ plasmant @c:irua:163477			Serial	5374
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	Author	Kang, T.-Y.; Kwon, J.-S.; Kumar, N.; Choi, E.; Kim, K.-M.
	Title	Effects of a Non-Thermal Atmospheric Pressure Plasma Jet with Different Gas Sources and Modes of Treatment on the Fate of Human Mesenchymal Stem Cells			Type	A1 Journal article
	Year	2019	Publication	Applied Sciences	Abbreviated Journal	Appl Sci-Basel
	Volume	9	Issue	22	Pages	4819
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Despite numerous attempts to use human mesenchymal stem cells (hMSCs) in the field of tissue engineering, the control of their differentiation remains challenging. Here, we investigated possible applications of a non-thermal atmospheric pressure plasma jet (NTAPPJ) to control the differentiation of hMSCs. An air- or nitrogen-based NTAPPJ was applied to hMSCs in culture media, either directly or by media treatment in which the cells were plated after the medium was exposed to the NTAPPJ. The durations of exposure were 1, 2, and 4 min, and the control was not exposed to the NTAPPJ. The initial attachment of the cells was assessed by a water-soluble tetrazolium assay, and the gene expression in the cells was assessed through reverse-transcription polymerase chain reaction and immunofluorescence staining. The results showed that the gene expression in the hMSCs was generally increased by the NTAPPJ exposure, but the enhancement was dependent on the conditions of the exposure, such as the source of the gas and the treatment method used. These results were attributed to the chemicals in the extracellular environment and the reactive oxygen species generated by the plasma. Hence, it was concluded that by applying the best conditions for the NTAPPJ exposure of hMSCs, the control of hMSC differentiation was possible, and therefore, exposure to an NTAPPJ is a promising method for tissue engineering.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000502570800096	Publication Date	2019-11-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2076-3417	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.679	Times cited		Open Access
	Notes	The plasma source was kindly provided by the Plasma Bioscience Research Center, Kwangwoon University.			Approved	Most recent IF: 1.679
	Call Number	PLASMANT @ plasmant @c:irua:164893			Serial	5435
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	Author	Rezaei, F.; Vanraes, P.; Nikiforov, A.; Morent, R.; De Geyter, N.
	Title	Applications of plasma-liquid systems : a review			Type	A1 Journal article
	Year	2019	Publication	Materials	Abbreviated Journal	Materials
	Volume	12	Issue	17	Pages	2751
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Plasma-liquid systems have attracted increasing attention in recent years, owing to their high potential in material processing and nanoscience, environmental remediation, sterilization, biomedicine, and food applications. Due to the multidisciplinary character of this scientific field and due to its broad range of established and promising applications, an updated overview is required, addressing the various applications of plasma-liquid systems till now. In the present review, after a brief historical introduction on this important research field, the authors aimed to bring together a wide range of applications of plasma-liquid systems, including nanomaterial processing, water analytical chemistry, water purification, plasma sterilization, plasma medicine, food preservation and agricultural processing, power transformers for high voltage switching, and polymer solution treatment. Although the general understanding of plasma-liquid interactions and their applications has grown significantly in recent decades, it is aimed here to give an updated overview on the possible applications of plasma-liquid systems. This review can be used as a guide for researchers from different fields to gain insight in the history and state-of-the-art of plasma-liquid interactions and to obtain an overview on the acquired knowledge in this field up to now.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000488880300104	Publication Date	2019-08-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1996-1944	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.654	Times cited	4	Open Access
	Notes				Approved	Most recent IF: 2.654
	Call Number	UA @ admin @ c:irua:163805			Serial	6285
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	Author	Van der Paal, J.; Fridman, G.; Bogaerts, A.
	Title	Ceramide cross-linking leads to pore formation: Potential mechanism behind CAP enhancement of transdermal drug delivery			Type	A1 Journal article
	Year	2019	Publication	Plasma processes and polymers	Abbreviated Journal	Plasma Process Polym
	Volume	16	Issue	16	Pages	1900122
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In recent years, cold atmospheric plasma (CAP) has been proposed as a novel method to enhance transdermal drug delivery, while avoiding tissue damage. However, the underlying mechanism for the increasing skin permeability upon CAP treatment is still undefined. We propose a mechanism in which CAP-generated reactive species induce cross-linking of skin lipids, leading to the generation of nanopores, thereby facilitating the permeation of drug molecules. Molecular dynamics simulations support this proposed mechanism. Furthermore, our results indicate that to achieve maximum enhancement of the permeability, the optimal treatment will depend on the exact lipid composition of the skin, as well as on the CAP source used.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000479747500001	Publication Date	2019-07-30
	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		Open Access
	Notes				Approved	Most recent IF: 2.846
	Call Number	UA @ admin @ c:irua:161874			Serial	6287
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	Author	Nematollahi, P.; Neyts, E.C.
	Title	Direct methane conversion to methanol on M and MN₄ embedded graphene (M = Ni and Si): a comparative DFT study			Type	A1 Journal article
	Year	2019	Publication	Applied surface science	Abbreviated Journal	Appl Surf Sci
	Volume	496	Issue	496	Pages	143618
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The ever increasing global production and dispersion of methane requires novel chemistry to transform it into easily condensable energy carriers that can be integrated into the chemical infrastructure. In this context, single atom catalysts have attracted considerable interest due to their outstanding catalytic activity. We here use density functional theory (DFT) computations to compare the reaction and activation energies of M and MN4 embedded graphene (M = Ni and Si) on the methane-to-methanol conversion near room temperature. Thermodynamically, conversion of methane to methanol is energetically favorable at ambient conditions. Both singlet and triplet spin state of the studied systems are considered in all of the calculations. The DFT results show that the barriers are significantly lower when the complexes are in the triplet state than in the singlet state. In particular, Si-G with the preferred spin multiplicity of triplet seems to be viable catalysts for methane oxidation thanks to the corresponding lower energy barriers and higher stability of the obtained configurations. Our results provide insights into the nature of methane conversion and may serve as guidance for fabricating cost-effective graphene-based single atom catalysts.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000488957400004	Publication Date	2019-08-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-4332	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	3.387	Times cited	2	Open Access
	Notes				Approved	Most recent IF: 3.387
	Call Number	UA @ admin @ c:irua:163695			Serial	6294
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	Author	Vohra, A.; Khanam, A.; Slotte, J.; Makkonen, I.; Pourtois, G.; Porret, C.; Loo, R.; Vandervorst, W.
	Title	Heavily phosphorus doped germanium : strong interaction of phosphorus with vacancies and impact of tin alloying on doping activation			Type	A1 Journal article
	Year	2019	Publication	Journal of applied physics	Abbreviated Journal	J Appl Phys
	Volume	125	Issue	22	Pages	225703
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	We examined the vacancy trapping proficiency of Sn and P atoms in germanium using positron annihilation spectroscopy measurements, sensitive to the open-volume defects. Epitaxial Ge1 xSnx films were grown by chemical vapor deposition with different P concentrations in the 3: 0 1019-1: 5 1020 cm 3 range. We corroborate our findings with first principles simulations. Codoping of Ge with a Sn concentration of up to 9% is not an efficient method to suppress the free vacancy concentration and the formation of larger phosphorus-vacancy complexes. Experimental results confirm an increase in the number of P atoms around the monovacancy with P-doping, leading to dopant deactivation in epitaxial germanium-tin layers with similar Sn content. Vice versa, no impact on the improvement of maximum achieved P activation in Ge with increasing Sn-doping has been observed. Theoretical calculations also confirm that Pn-V (vacancy) complexes are energetically more stable than the corresponding SnmPn-V and Snm-V defect structures with the same number of alien atoms (Sn or P) around the monovacancy. he strong attraction of vacancies to the phosphorus atoms remains the dominant dopant deactivation mechanism in Ge as well as in Ge1 xSnx. Published under license by AIP Publishing.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000471698600044	Publication Date	2019-06-10
	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	1	Open Access
	Notes				Approved	Most recent IF: 2.068
	Call Number	UA @ admin @ c:irua:161333			Serial	6300
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	Author	Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A.
	Title	How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study			Type	A1 Journal article
	Year	2019	Publication	Physical chemistry, chemical physics	Abbreviated Journal	Phys Chem Chem Phys
	Volume	21	Issue	35	Pages	19327-19341
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000486175400045	Publication Date	2019-08-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1463-9076; 1463-9084	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.123	Times cited	1	Open Access
	Notes				Approved	Most recent IF: 4.123
	Call Number	UA @ admin @ c:irua:162782			Serial	6303
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	Author	Katiyar, K.S.; Lin, A.; Fridman, A.; Keating, C.E.; Cullen, D.K.; Miller, V.
	Title	Non-thermal plasma accelerates astrocyte regrowth and neurite regeneration following physical trauma in vitro			Type	A1 Journal article
	Year	2019	Publication	Applied Sciences	Abbreviated Journal	Appl Sci-Basel
	Volume	9	Issue	18	Pages	3747
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Non-thermal plasma (NTP), defined as a partially ionized gas, is an emerging technology with several biomedical applications, including tissue regeneration. In particular, NTP treatment has been shown to activate endogenous biological processes to promote cell regrowth, differentiation, and proliferation in multiple cell types. However, the effects of this therapy on nervous system regeneration have not yet been established. Accordingly, the current study explored the effects of a nanosecond-pulsed dielectric barrier discharge plasma on neural regeneration. Following mechanical trauma in vitro, plasma was applied either directly to (1) astrocytes alone, (2) neurons alone, or (3) neurons or astrocytes in a non-contact co-culture. Remarkably, we identified NTP treatment intensities that accelerated both neurite regeneration and astrocyte regrowth. In astrocyte cultures alone, an exposure of 20-90 mJ accelerated astrocyte re-growth up to three days post-injury, while neurons required lower treatment intensities (<= 20 mJ) to achieve sub-lethal outgrowth. Following injury to neurons in non-contact co-culture with astrocytes, 20 mJ exposure of plasma to only neurons or astrocytes resulted in increased neurite regeneration at three days post-treatment compared to the untreated, but no enhancement was observed when both cell types were treated. At day seven, although regeneration further increased, NTP did not elicit a significant increase from the control. However, plasma exposure at higher intensities was found to be injurious, underscoring the need to optimize exposure levels. These results suggest that growth-promoting physiological responses may be elicited via properly calibrated NTP treatment to neurons and/or astrocytes. This could be exploited to accelerate neurite re-growth and modulate neuron-astrocyte interactions, thereby hastening nervous system regeneration.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000489115200107	Publication Date	2019-09-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2076-3417	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.679	Times cited	2	Open Access
	Notes				Approved	Most recent IF: 1.679
	Call Number	UA @ admin @ c:irua:163799			Serial	6312
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