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Author Bekeschus, S.; Lin, A.; Fridman, A.; Wende, K.; Weltmann, K.-D.; Miller, V.
Title A comparison of floating-electrode DBD and kINPen jet : plasma parameters to achieve similar growth reduction in colon cancer cells under standardized conditions Type A1 Journal article
Year 2018 Publication Plasma chemistry and plasma processing Abbreviated Journal Plasma Chem Plasma P
Volume 38 Issue 1 Pages (down) 1-12
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract A comparative study of two plasma sources (floating-electrode dielectric barrier discharge, DBD, Drexel University; atmospheric pressure argon plasma jet, kINPen, INP Greifswald) on cancer cell toxicity was performed. Cell culture protocols, cytotoxicity assays, and procedures for assessment of hydrogen peroxide (H2O2) were standardized between both labs. The inhibitory concentration 50 (IC50) and its corresponding H2O2 deposition was determined for both devices. For the DBD, IC50 and H2O2 generation were largely dependent on the total energy input but not pulsing frequency, treatment time, or total number of cells. DBD cytotoxicity could not be replicated by addition of H2O2 alone and was inhibited by larger amounts of liquid present during the treatment. Jet plasma toxicity depended on peroxide generation as well as total cell number and amount of liquid. Thus, the amount of liquid present during plasma treatment in vitro is key in attenuating short-lived species or other physical effects from plasmas. These in vitro results suggest a role of liquids in or on tissues during plasma treatment in a clinical setting. Additionally, we provide a platform for correlation between different plasma sources for a predefined cellular response.
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Corporate Author Thesis
Publisher Place of Publication New York Editor
Language Wos 000419479000001 Publication Date 2017-09-06
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0272-4324 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.355 Times cited 12 Open Access OpenAccess
Notes Approved Most recent IF: 2.355
Call Number UA @ lucian @ c:irua:155653 Serial 5084
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Author Chai, Z.-N.; Wang, X.-C.; Yusupov, M.; Zhang, Y.-T.
Title Unveiling the interaction mechanisms of cold atmospheric plasma and amino acids by machine learning Type A1 Journal article
Year 2024 Publication Plasma processes and polymers Abbreviated Journal
Volume Issue Pages (down) 1-26
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Plasma medicine has attracted tremendous interest in a variety of medical conditions, ranging from wound healing to antimicrobial applications, even in cancer treatment, through the interactions of cold atmospheric plasma (CAP) and various biological tissues directly or indirectly. The underlying mechanisms of CAP treatment are still poorly understood although the oxidative effects of CAP with amino acids, peptides, and proteins have been explored experimentally. In this study, machine learning (ML) technology is introduced to efficiently unveil the interaction mechanisms of amino acids and reactive oxygen species (ROS) in seconds based on the data obtained from the reactive molecular dynamics (MD) simulations, which are performed to probe the interaction of five types of amino acids with various ROS on the timescale of hundreds of picoseconds but with the huge computational load of several days. The oxidative reactions typically start with H-abstraction, and the details of the breaking and formation of chemical bonds are revealed; the modification types, such as nitrosylation, hydroxylation, and carbonylation, can be observed. The dose effects of ROS are also investigated by varying the number of ROS in the simulation box, indicating agreement with the experimental observation. To overcome the limits of timescales and the size of molecular systems in reactive MD simulations, a deep neural network (DNN) with five hidden layers is constructed according to the reaction data and employed to predict the type of oxidative modification and the probability of occurrence only in seconds as the dose of ROS varies. The well-trained DNN can effectively and accurately predict the oxidative processes and productions, which greatly improves the computational efficiency by almost ten orders of magnitude compared with the reactive MD simulation. This study shows the great potential of ML technology to efficiently unveil the underpinning mechanisms in plasma medicine based on the data from reactive MD simulations or experimental measurements. In this study, since reactive molecular dynamics simulation can currently only describe interactions between a few hundred atoms in a few hundred picoseconds, deep neural networks (DNN) are introduced to enhance the simulation results by predicting more data efficiently. image
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001202061200001 Publication Date 2024-04-15
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850 ISBN Additional Links UA library record; WoS full record
Impact Factor 3.5 Times cited Open Access
Notes Approved Most recent IF: 3.5; 2024 IF: 2.846
Call Number UA @ admin @ c:irua:205512 Serial 9181
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Author Yan, M.; Bogaerts, A.; Gijbels, R.
Title Kinetic modeling of relaxation phenomena after photodetachment in a rf electronegative SiH4 discharge Type A1 Journal article
Year 2001 Publication Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics Abbreviated Journal Phys Rev E
Volume 63 Issue 2Part 2 Pages (down)
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The global relaxation process after pulsed laser induced photodetachment in a rf electronegative SIH4 discharge is studied by a self-consistent kinetic one-dimensional particle-in-cell-Monte Carlo model. Our results reveal a comprehensive physical picture of the relaxation process, including the main plasma variables, after a perturbation up to the full recovery of the steady state. A strong influence of the photodetachment on the discharge is found, which results from an increase of the electron density, leading to a weaker bulk field, and hence to a drop in the high energy tail of the electron energy distribution function (EEDF), a reduction of the reaction rates of electron impact attachment and ionization, and a subsequent decrease of the positive and negative ion densities. All the plasma quantities related to electrons recover synchronously. The recovery time of the ion densities is about 1-2 orders of magnitude longer than that of the electrons due to different recovery mechanisms. The modeled behavior of all the charged particles agrees very well with experimental results from the literature. In addition, our work clarifies some unclear processes assumed in the literature, such as the relaxation of the EEDF, the evolution of the electric field, and the recovery of negative ions.
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Corporate Author Thesis
Publisher American Institute of Physics Place of Publication Woodbury (NY) Editor
Language Wos 000167022500057 Publication Date 2002-07-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1063-651X;1095-3787; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.366 Times cited 4 Open Access
Notes Approved Most recent IF: 2.366; 2001 IF: 2.235
Call Number UA @ lucian @ c:irua:34148 Serial 1757
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Author Piacente, G.; Peeters, F.M.; Betouras, J.J.
Title Normal modes of a quasi-one-dimensional multichain complex plasma Type A1 Journal article
Year 2004 Publication Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics Abbreviated Journal Phys Rev E
Volume 70 Issue 3Part 2 Pages (down)
Keywords A1 Journal article; Condensed Matter Theory (CMT)
Abstract We studied equally charged particles, suspended in a complex plasma, which move in a plane and interact with a screened Coulomb potential (Yukawa type) and with an additional external confining parabolic potential in one direction, which makes the system quasi-one-dimensional (Q1D). The normal modes of the system are studied in the presence of dissipation. We also investigated how a perpendicular magnetic field couples the phonon modes with each other. Two different ways of exciting the normal modes are discussed: (1) a uniform excitation of the Q1D lattice, and (2) a local forced excitation of the system in which one particle is driven by, e.g., a laser. Our results are in very good agreement with recent experimental findings on a finite single chain system [Liu , Phys. Rev. Lett. 91, 255003 (2003)]. Predictions are made for the normal modes of multichain structures in the presence of damping.
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Corporate Author Thesis
Publisher Place of Publication Lancaster, Pa Editor
Language Wos 000224302300081 Publication Date 2004-09-21
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1539-3755;1550-2376; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.366 Times cited 18 Open Access
Notes Approved Most recent IF: 2.366; 2004 IF: NA
Call Number UA @ lucian @ c:irua:69417 Serial 2369
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Author Razzokov, J.; Yusupov, M.; Bogaerts, A.
Title Possible Mechanism of Glucose Uptake Enhanced by Cold Atmospheric Plasma: Atomic Scale Simulations Type A1 Journal article
Year 2018 Publication Plasma Abbreviated Journal
Volume 1 Issue 1 Pages (down)
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Cold atmospheric plasma (CAP) has shown its potential in biomedical applications, such as wound healing, cancer treatment and bacterial disinfection. Recent experiments have provided evidence that CAP can also enhance the intracellular uptake of glucose molecules which is important in diabetes therapy. In this respect, it is essential to understand the underlying mechanisms of intracellular glucose uptake induced by CAP, which is still unclear. Hence, in this study we try to elucidate the possible mechanism of glucose uptake by cells by performing computer simulations. Specifically, we study the transport of glucose molecules through native and oxidized membranes. Our simulation results show that the free energy barrier for the permeation of glucose molecules across the membrane decreases upon increasing the degree of oxidized lipids in the membrane. This indicates that the glucose permeation rate into cells increases when the CAP oxidation level in the cell membrane is increased.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date 2018-06-08
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 OpenAccess
Notes 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 Universiteit Antwerpen. Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @ plasma1010011c:irua:152176 Serial 4990
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Author Bogaerts, A.; Snoeckx, R.; Trenchev, G.; Wang, W.
Title Modeling for a Better Understanding of Plasma-Based CO2 Conversion Type H1 Book Chapter
Year 2018 Publication Plasma Chemistry and Gas Conversion Abbreviated Journal
Volume Issue Pages (down)
Keywords H1 Book Chapter; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Abstract This chapter discusses modeling efforts for plasma-based CO2 conversion, which are needed to obtain better insight in the underlying mechanisms, in order to improve this application. We will discuss two types of (complementary) modeling efforts that are most relevant, that is, (i) modeling of the detailed plasma chemistry by zero-dimensional (0D) chemical kinetic models and (ii) modeling of reactor design, by 2D or 3D fluid dynamics models. By showing some characteristic calculation results of both models, for CO2 splitting and in combination with a H-source, and for packed bed DBD and gliding arc plasma, we can illustrate the type of information they can provide.
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Corporate Author Thesis
Publisher IntechOpen Place of Publication Rijeka Editor Britun, N.; Silva, T.
Language Wos Publication Date 2018-12-19
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 Not_Open_Access
Notes Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @ Bogaerts18c:irua:155915 Serial 5142
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Author Duan, J.; Ma, M.; Yusupov, M.; Cordeiro, R.M.; Lu, X.; Bogaerts, A.
Title The penetration of reactive oxygen and nitrogen species across the stratum corneum Type A1 Journal article
Year 2020 Publication Plasma Processes And Polymers Abbreviated Journal Plasma Process Polym
Volume Issue Pages (down)
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The penetration of reactive oxygen and nitrogen species (RONS) across the stratum corneum (SC) is a necessary and crucial process in many skin‐related plasma medical applications. To gain more insights into this penetration behavior, we combined experimental measurements of the permeability of dry and moist SC layers with computer simulations of model lipid membranes. We measured the permeation of relatively stable molecules, which are typically generated by plasma, namely H2O2, NO3−, and NO2−. Furthermore, we calculated the permeation free energy profiles of the major plasma‐generated RONS and their derivatives (i.e., H2O2, OH, HO2, O2, O3, NO, NO2, N2O4, HNO2, HNO3, NO2−, and NO3−) across native and oxidized SC lipid bilayers, to understand the mechanisms of RONS permeation across the SC. Our results indicate that hydrophobic RONS (i.e., NO, NO2, O2, O3, and N2O4) can translocate more easily across the SC lipid bilayer than hydrophilic RONS (i.e., H2O2, OH, HO2, HNO2, and HNO3) and ions (i.e., NO2− and NO3−) that experience much higher permeation barriers. The permeability of RONS through the SC skin lipids is enhanced when the skin is moist and the lipids are oxidized. These findings may help to understand the underlying mechanisms of plasma interaction with a biomaterial and to optimize the environmental parameters in practice in plasma medical applications.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000536892900001 Publication Date 2020-06-02
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 3.5 Times cited Open Access
Notes National Natural Science Foundation of China, 51625701 51977096 ; Fonds Wetenschappelijk Onderzoek, 1200219N ; China Scholarship Council, 201806160128 ; M. Y. acknowledges the Research Foundation Flanders (FWO) for financial support (Grant No. 1200219N). This study was partially supported by the National Natural Science Foundation of China (Grant No: 51625701 and 51977096) and the China Scholarship Council (Grant No: 201806160128). All computational work was performed using 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. Approved Most recent IF: 3.5; 2020 IF: 2.846
Call Number PLASMANT @ plasmant @c:irua:169709 Serial 6372
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Author Bogaerts, A.; Neyts, E.C.; Guaitella, O.; Murphy, A.B.
Title Foundations of plasma catalysis for environmental applications Type A1 Journal article
Year 2022 Publication Plasma Sources Science & Technology Abbreviated Journal Plasma Sources Sci T
Volume Issue Pages (down)
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Plasma catalysis is gaining increasing interest for various applications, but the underlying mechanisms are still far from understood. Hence, more fundamental research is needed to understand these mechanisms. This can be obtained by both modelling and experiments. This foundations paper describes the fundamental insights in plasma catalysis, as well as efforts to gain more insights by modelling and experiments. Furthermore, it discusses the state-of-the-art of the major plasma catalysis applications, as well as successes and challenges of technology transfer of these applications.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000804396200001 Publication Date 2022-03-21
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 3.8 Times cited Open Access OpenAccess
Notes H2020 Marie Skłodowska-Curie Actions, 823745 ; H2020 European Research Council, 810182 ; We acknowldege financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation programme (Grant Agreement No. 810182 – SCOPE ERC Synergy project) and the European Union’s Horizon 2020 Research and Innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 813393 (PIONEER). Approved Most recent IF: 3.8
Call Number PLASMANT @ plasmant @c:irua:188539 Serial 7070
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Author Yusupov, M.; Dewaele, D.; Attri, P.; Khalilov, U.; Sobott, F.; Bogaerts, A.
Title Molecular understanding of the possible mechanisms of oligosaccharide oxidation by cold plasma Type A1 Journal article
Year 2022 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
Volume Issue Pages (down)
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Cold atmospheric plasma (CAP) is a promising technology for several medical applications, including the removal of biofilms from surfaces. However, the molecular mechanisms of CAP treatment are still poorly understood. Here we unravel the possible mechanisms of CAP‐induced oxidation of oligosaccharides, employing reactive molecular dynamics simulations based on the density functional‐tight binding potential. Specifically, we find that the interaction of oxygen atoms (used as CAP‐generated reactive species) with cellotriose (a model system for the oligosaccharides) can break structurally important glycosidic bonds, which subsequently leads to the disruption of the oligosaccharide molecule. The overall results help to shed light on our experimental evidence for cellotriose CAP. This oxidation by study provides atomic‐level insight into the onset of plasma‐induced removal of biofilms, as oligosaccharides are one of the main components of biofilm.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000865844800001 Publication Date 2022-10-11
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 3.5 Times cited Open Access OpenAccess
Notes Fonds Wetenschappelijk Onderzoek, 1200219N ; They also 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. This study was financially supported by the Research Foundation–Flanders (FWO) (grant number 1200219N). Approved Most recent IF: 3.5
Call Number PLASMANT @ plasmant @c:irua:191404 Serial 7113
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Author Morais, E.; Bogaerts, A.
Title Modelling the dynamics of hydrogen synthesis from methane in nanosecond‐pulsed plasmas Type A1 Journal article
Year 2024 Publication Plasma processes and polymers Abbreviated Journal Plasma Processes & Polymers
Volume 21 Issue 1 Pages (down)
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract A chemical kinetics model was developed to characterise the gas‐phase dynamics of H<sub>2</sub>production in nanosecond‐pulsed CH<sub>4</sub>plasmas. Pulsed behaviour was observed in the calculated electric field, electron temperature and species densities at all pressures. The model agrees reasonably with experimental results, showing CH<sub>4</sub>conversion at 30% and C<sub>2</sub>H<sub>2</sub>and H<sub>2</sub>as major products. The underlying mechanisms in CH<sub>4</sub>dissociation and H<sub>2</sub>formation were analysed, highlighting the large contribution of vibrationally excited CH<sub>4</sub>and H<sub>2</sub>to coupling energy from the plasma into gas‐phase heating, and revealing that H<sub>2</sub>synthesis is not affected by applied pressure, with selectivity remaining unchanged at ~42% in the 1–5 bar range.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001091258700001 Publication Date 2023-10-27
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 3.5 Times cited Open Access Not_Open_Access
Notes We gratefully acknowledge financial support by the Flemish Government through the Moonshot cSBO project “Power‐to‐Olefins” (P2O; HBC.2020.2620) and funding from the Independent Research Fund Denmark (project nr. 0217‐00231B). Approved Most recent IF: 3.5; 2024 IF: 2.846
Call Number PLASMANT @ plasmant @c:irua:201192 Serial 8983
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Author Bercx, M.; Mayda, S.; Depla, D.; Partoens, B.; Lamoen, D.
Title Plasmonic effects in the neutralization of slow ions at a metallic surface Type A1 Journal Article
Year 2023 Publication Contributions to Plasma Physics Abbreviated Journal Contrib. Plasma Phys
Volume Issue Pages (down)
Keywords A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
Abstract Secondary electron emission is an important process that plays a significant role in several plasma‐related applications. As measuring the secondary electron yield experimentally is very challenging, quantitative modelling of this process to obtain reliable yield data is critical as input for higher‐scale simulations. Here, we build upon our previous work combining density functional theory calculations with a model originally developed by Hagstrum to extend its application to metallic surfaces. As plasmonic effects play a much more important role in the secondary electron emission mechanism for metals, we introduce an approach based on Poisson point processes to include both surface and bulk plasmon excitations to the process. The resulting model is able to reproduce the yield spectra of several available experimental results quite well but requires the introduction of global fitting parameters, which describe the strength of the plasmon interactions. Finally, we use an in‐house developed workflow to calculate the electron yield for a list of elemental surfaces spanning the periodic table to produce an extensive data set for the community and compare our results with more simplified approaches from the literature.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001067651300001 Publication Date 2023-09-16
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0863-1042 ISBN Additional Links UA library record; WoS full record
Impact Factor 1.6 Times cited Open Access Not_Open_Access
Notes We acknowledge the financial support of FWO-Vlaanderen through project G.0216.14N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) and the HPC infrastructure of the University of Antwerp (CalcUA), both funded by the FWO-Vlaanderen and the Flemish Government-department EWI. Approved Most recent IF: 1.6; 2023 IF: 1.44
Call Number EMAT @ emat @c:irua:200330 Serial 8962
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