Nano Home

NANOlab Center of Excellence literature database

Home |  Show All |  Simple Search |  Advanced Search
Quick Search:
1–30 of 99 records found matching your query (RSS | history):
toggle visibility
Search within Results:
Display Options:
Select All    Deselect All << 1 2 3 4 >>
List View
 | 
Citations
 | 
Details
   print
  Records
Author Lin, A.; De Backer, J.; Quatannens, D.; Cuypers, B.; Verswyvel, H.; De La Hoz, E.C.; Ribbens, B.; Siozopoulou, V.; Van Audenaerde, J.; Marcq, E.; Lardon, F.; Laukens, K.; Vanlanduit, S.; Smits, E.; Bogaerts, A.
  Title The effect of local non‐thermal plasma therapy on the<scp>cancer‐immunity</scp>cycle in a melanoma mouse model Type University Hospital Antwerp
  Year 2022 Publication Bioengineering & Translational Medicine Abbreviated Journal Bioengineering & Transla Med
  Volume Issue Pages
  Keywords (down) University Hospital Antwerp; A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; ADReM Data Lab (ADReM); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES)
  Abstract Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000784103500001 Publication Date 2022-04-21
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2380-6761 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor Times cited Open Access OpenAccess
  Notes Vlaamse regering, 1S67621N 1S76421N G044420N 12S9221N 12S9218N ; The authors would like to thank and acknowledge Christophe Hermans, Ho Wa Lau, and Hilde Lambrechts for their help with sectioning and preparing the IHC slides. The authors would also like to thank Dani Banner for designing the ergonomic NTP applicator handle and Hasan Baysal for 3D printing the pieces used in this experiment. We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr Willy Floren, and the Vereycken family. Some of the resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) The data that support the findings of this study are available from the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9218N (Abraham Lin), 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaert, and Steve Vanlanduit), 1S76421N (Delphine Quatannens), and 1S67621N (Hanne Verswyvel). Figure 7 was created with BioRender.com. Approved Most recent IF: NA
  Call Number PLASMANT @ plasmant @c:irua:187909 Serial 7056
Permanent link to this record
 
 
Author De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S.
  Title StatSTEM: An efficient program for accurate and precise model-based quantification of atomic resolution electron microscopy images Type P1 Proceeding
  Year 2017 Publication Journal of physics : conference series T2 – Electron Microscopy and Analysis Group Conference 2017 (EMAG2017), 3-6 July 2017, Manchester, UK Abbreviated Journal J. Phys.: Conf. Ser.
  Volume 902 Issue Pages 012013
  Keywords (down) P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab
  Abstract An efficient model-based estimation algorithm is introduced in order to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for the overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, is investigated. The highest attainable precision is reached even for low dose images. Furthermore, advantages of the model- based approach taking into account overlap between neighbouring columns are highlighted. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000416370700013 Publication Date 2017-10-16
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1742-6588 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor Times cited 1 Open Access OpenAccess
  Notes The authors acknowledge nancial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0374.13N, G.0368.15N, G.0369.15N, WO.010.16N) and a PhD research grant to K H W van den Bos, and a postdoctoral research grant to A De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). A Rosenauer is acknowledged for providing the STEMsim program. Approved Most recent IF: NA
  Call Number EMAT @ emat @c:irua:147188 Serial 4764
Permanent link to this record
 
 
Author Goris, B.; De Beenhouwer, J.; de Backer, A.; Zanaga, D.; Batenburg, J.; Sanchez-Iglesias, A.; Liz-Marzan, L.; Van Aert, S.; Sijbers, J.; Van Tendeloo, G.; Bals, S.
  Title Investigating lattice strain in Au nanodecahedrons Type P1 Proceeding
  Year 2016 Publication Abbreviated Journal
  Volume Issue Pages 11-12
  Keywords (down) P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2016-12-21
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 978-3-527-80846-5 ISBN Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:145813 Serial 5144
Permanent link to this record
 
 
Author De Backer, A.; De Wael, A.; Gonnissen, J.; Martinez, G.T.; Béché, A.; MacArthur, K.E.; Jones, L.; Nellist, P.D.; Van Aert, S.
  Title Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting: What are the limits? Type P1 Proceeding
  Year 2015 Publication Journal of physics : conference series Abbreviated Journal
  Volume 644 Issue 644 Pages 012034
  Keywords (down) P1 Proceeding; Electron microscopy for materials research (EMAT)
  Abstract Quantitative atomic resolution annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique for nanoparticle atom-counting. However, a lot of nanoparticles provide a severe characterisation challenge because of their limited size and beam sensitivity. Therefore, quantitative ADF STEM may greatly benefit from statistical detection theory in order to optimise the instrumental microscope settings such that the incoming electron dose can be kept as low as possible whilst still retaining single-atom precision. The principles of detection theory are used to quantify the probability of error for atom-counting. This enables us to decide between different image performance measures and to optimise the experimental detector settings for atom-counting in ADF STEM in an objective manner. To demonstrate this, ADF STEM imaging of an industrial catalyst has been conducted using the near-optimal detector settings. For this experiment, we discussed the limits for atom-counting diagnosed by combining a thorough statistical method and detailed image simulations.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000366826200034 Publication Date 2015-10-13
  Series Editor Series Title Abbreviated Series Title Electron Microscopy and Analysis Group Conference (EMAG), JUN 02-JUL 02, 2015, Manchester, ENGLAND
  Series Volume Series Issue Edition
  ISSN 1742-6588 ISBN Additional Links UA library record; WoS full record
  Impact Factor Times cited Open Access
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0368.15N, G.0369.15N, and G.0374.15N) and a PhD research grant to A De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3), ERC Starting Grant 278510 Vortex, and the UK Engineering and Physical Sciences Research Council (EP/K032518/1). The authors acknowledge Johnson-Matthey for providing the sample and PhD funding to K E MacArthur. A Rosenauer is acknowledged for providing the STEMsim program.; esteem2jra2; ECASJO; Approved Most recent IF: NA
  Call Number c:irua:130314 c:irua:130314 Serial 4050
Permanent link to this record
 
 
Author Verhulst, S.L.; de Backer, J.; Van Gaal, L.; de Backer, W.; Desager, K.
  Title Adenotonsillectomy as first-line treatment for sleep-disordered breathing in obese children Type L1 Letter to the editor
  Year 2008 Publication American journal of respiratory and critical care medicine Abbreviated Journal Am J Resp Crit Care
  Volume 177 Issue 12 Pages 1399
  Keywords (down) L1 Letter to the editor; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1073-449x; 1535-4970 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 13.204 Times cited Open Access
  Notes Approved Most recent IF: 13.204; 2008 IF: 9.792
  Call Number UA @ lucian @ c:irua:68864 Serial 59
Permanent link to this record
 
 
Author de Backer, W.; Vos, W.; Van Holsbeke, C.; Vinchurkar, S.; Claes, R.; Hufkens, A.; Parizel, P.M.; Bedert, L.; de Backer, J.
  Title The effect of roflumilast in addition to LABA/LAMA/ICS treatment in COPD patients Type L1 Letter to the editor
  Year 2014 Publication European Respiratory Journal Abbreviated Journal Eur Respir J
  Volume 44 Issue 2 Pages 527-529
  Keywords (down) L1 Letter to the editor; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Copenhagen Editor
  Language Wos 000340017300029 Publication Date 2014-05-03
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0903-1936;1399-3003; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 10.569 Times cited 26 Open Access
  Notes ; ; Approved Most recent IF: 10.569; 2014 IF: 7.636
  Call Number UA @ lucian @ c:irua:117335 Serial 832
Permanent link to this record
 
 
Author de Backer, J.; Vanderveken, O.; Vos, W.; Devolder, A.; Verhulst, S.; Verbraecken, J.
  Title Functional imaging to predict treatment success of mandibular advancement devices in sleep-disordered breathing Type H3 Book chapter
  Year 2008 Publication Abbreviated Journal
  Volume Issue Pages 141-155
  Keywords (down) H3 Book chapter; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Antwerpen Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:72885 Serial 1298
Permanent link to this record
 
 
Author Parizel, P.M.; Corthouts, B.; Snoeckx, A.; de Backer, J.; de Backer, W.
  Title Klinische semiologie en radiologie Type H3 Book chapter
  Year 2007 Publication Abbreviated Journal
  Volume Issue Pages 133-146
  Keywords (down) H3 Book chapter; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Acco Place of Publication Leuven Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:63801 Serial 1765
Permanent link to this record
 
 
Author Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S.
  Title Atom column detection Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 177-214
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract By combining statistical parameter estimation and model-order selection using a Bayesian framework, the maximum a posteriori (MAP) probability rule is proposed in this chapter as an objective and quantitative method to detect atom columns from high-resolution scanning transmission electron microscopy (HRSTEM) images. The validity and usefulness of this approach is demonstrated to both simulated and experimental annular dark-field (ADF) STEM images, but also to simultaneously acquired annular bright-field (ABF) and ADF STEM image data.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177531 Serial 6775
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Atom counting Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 91-144
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In this chapter, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. We show that this method can be applied to nanocrystals of arbitrary shape, size, and atom type. The validity of the atom-counting results is confirmed by means of detailed image simulations and it is shown that the high sensitivity of our method enables us to count atoms with single atom sensitivity.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177529 Serial 6776
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title General conclusions and future perspectives Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 243-253
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract This chapter provides an overview of statistical and quantitative methodologies that have pushed (scanning) transmission electron microscopy ((S)TEM) toward accurate and precise measurements of unknown structure parameters for understanding the relation between the structure of a material and its properties. Hereby, statistical parameter estimation theory has extensively been used which enabled not only measuring atomic column positions, but also quantifying the number of atoms, and detecting atomic columns as accurately and precisely as possible from experimental images. As a general conclusion, it can be stated that advanced statistical techniques are ideal tools to perform quantitative electron microscopy at the atomic scale. In the future, statistical methods will continue to be developed and novel quantification procedures will open up new possibilities for studying material structures at the atomic scale.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177533 Serial 6781
Permanent link to this record
 
 
Author Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S.
  Title Image-quality evaluation and model selection with maximum a posteriori probability Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 215-242
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract The maximum a posteriori (MAP) probability rule for atom column detection can also be used as a tool to evaluate the relation between scanning transmission electron microscopy (STEM) image quality and atom detectability. In this chapter, a new image-quality measure is proposed that correlates well with atom detectability, namely the integrated contrast-to-noise ratio (ICNR). Furthermore, the working principle of the MAP probability rule is described in detail showing a close relation to the principles of model-selection methods.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177532 Serial 6782
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Optimal experiment design for nanoparticle atom counting from ADF STEM images Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 145-175
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In this chapter, the principles of detection theory are used to quantify the probability of error for atom counting from high-resolution scanning transmission electron microscopy (HRSTEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom counting using the expression of the probability of error. We show that for very thin objects the low-angle annular dark-field (LAADF) regime is optimal and that for thicker objects the optimal inner detector angle increases.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177530 Serial 6785
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Statistical parameter estimation theory : principles and simulation studies Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 29-72
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In this chapter, the principles of statistical parameter estimation theory for a quantitative analysis of atomic-resolution electron microscopy images are introduced. Within this framework, electron microscopy images are described by a parametric statistical model. Here, parametric models are introduced for different types of electron microscopy images: reconstructed exit waves, annular dark-field (ADF) scanning transmission electron microscopy (STEM) images, and simultaneously acquired ADF and annular bright-field (ABF) STEM images. Furthermore, the Cramér-Rao lower bound (CRLB) is introduced, i.e. a theoretical lower bound on the variance of any unbiased estimator. This CRLB is used to quantify the precision of the structure parameters of interest, such as the atomic column positions and the integrated atomic column intensities.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177527 Serial 6788
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Efficient fitting algorithm Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 73-90
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT)
  Abstract An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic-resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177528 Serial 6778
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Introduction Type H2 Book chapter
  Year 2021 Publication Advances in imaging and electron physics T2 – Advances in imaging and electron physics Abbreviated Journal
  Volume Issue Pages 1-28
  Keywords (down) H2 Book chapter; Electron microscopy for materials research (EMAT)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2021-03-06
  Series Editor Series Title Abbreviated Series Title
  Series Volume 217 Series Issue Edition
  ISSN ISBN 978-0-12-824607-8; 1076-5670 Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes ERC Consolidator project funded by the European Union grant #770887 Picometrics Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:177525 Serial 6784
Permanent link to this record
 
 
Author De Backer, J.
  Title The versatile nature of cytoglobin, the Swiss army knife among globins, with a preference for oxidative stress Type Doctoral thesis
  Year 2023 Publication Abbreviated Journal
  Volume Issue Pages XVIII, 232 p.
  Keywords (down) Doctoral thesis; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
  Abstract Since its discovery 20 years ago, many studies have been performed to gain insight into the functional role of cytoglobin (Cygb). However, Cygb has been proven to be a promiscuous protein. Yet, there is a consensus that Cygb is a cytoprotective protein involved in redox homeostasis. CYGB is a ubiquitously expressed hexacoordinated globin that is highly expressed in melanocytes and is often found to be downregulated during melanocyte-to-melanoma transition. In Chapter III, we investigated the molecular mechanism through which CYGB could be involved in redox regulation. Here, we showed that CYGB contains two redox-sensitive cysteine residues and that the formation of an intramolecular disulfide bridge resulted in the heme group becoming more accessible to external ligands. This supports the hypothesis that Cys38 and Cys83 serve as sensitive redox sensors. In Chapter IV we showed that CYGB mRNA and protein levels were elevated upon exposure to hypoxia. Interestingly, this upregulation was most likely HIF-2α-dependent. We propose that in melanoma, HIF-2α, rather than HIF-1α, positively regulates CYGB under hypoxic conditions in a cell type specific way. In Chapter V, the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels was investigated. We confirmed that NTP endows cytotoxicity that induces cell death through apoptosis and that this was mediated through the production of ROS. Moreover, we showed that CYGB protects melanoma cells from ROS-induced apoptosis by the scavenging of ROS. Interestingly, CYGB expression influenced the expression of NRF2 and HO-1. We identified the lncRNA MEG3 as a possible mechanism through which NRF2 expression and its downstream target HO-1 can be regulated by CYGB. In chapter VI, increased basal ROS levels and higher degree of lipid peroxidation upon RSL3 treatment contributed to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB expression regulation was identified as a critical determinant of the ferroptosis–pyroptosis therapy response. This suggests that CYGB is involved in the regulation of multiple modes of programmed cell death. FInally, we sought to delineate the RONS that are responsible for plasma-induced ICD. Our results highlight the importance of the short-lived species. Furthermore, we are first to demonstrate that NTP-created vaccine is safely prepared and offers complete protection. Moreover, we provide conclusive evidence that direct application of NTP induces ICD in melanoma.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ admin @ c:irua:193568 Serial 7277
Permanent link to this record
 
 
Author de Backer, A.
  Title Quantitative atomic resolution electron microscopy using advanced statistical techniques Type Doctoral thesis
  Year 2015 Publication Abbreviated Journal
  Volume Issue Pages
  Keywords (down) Doctoral thesis; Electron microscopy for materials research (EMAT)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Antwerpen Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:125636 Serial 2747
Permanent link to this record
 
 
Author de Backer, J.W.; Vos, W.G.; Germonpré, P.; Salgado, R.; Parizel, P.M.; de Backer, W.
  Title Clinical applications of image-based airway computational fluid dynamics: assessment of inhalation medication and endobronchial devices Type A3 Journal article
  Year 2009 Publication Proceedings of the Society of Photo-optical Instrumentation Engineers Abbreviated Journal
  Volume 7262 Issue Pages 72621p,1-72621p,9
  Keywords (down) A3 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract Computational fluid dynamics (CFD) is a technique that is used increasingly in the biomedical field. Solving the flow equations numerically provides a convenient way to assess the efficiency of therapies and devices, ranging from cardiovascular stents and heart valves to hemodialysis workflows. Also in the respiratory field CFD has gained increasing interest, especially through the combination of three dimensional image reconstruction which results in highend patient-specific models. This paper provides an overview of clinical applications of CFD through image based modeling, resulting from recent studies performed in our center. We focused on two applications: assessment of the efficiency of inhalation medication and analysis of endobronchial valve placement. In the first application we assessed the mode of action of a novel bronchodilator in 10 treated patients and 4 controls. We assessed the local volume increase and resistance change based on the combination of imaging and CFD. We found a good correlation between the changes in volume and resistance coming from the CFD results and the clinical tests. In the second application we assessed the placement and effect of one way endobronchial valves on respiratory function in 6 patients. We found a strong patientspecific result of the therapy where in some patients the therapy resulted in complete atelectasis of the target lobe while in others the lobe remained inflated. We concluded from these applications that CFD can provide a better insight into clinically relevant therapies.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2009-02-27
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:79497 Serial 374
Permanent link to this record
 
 
Author De Backer, J.; Lin, A.; Berghe, W.V.; Bogaerts, A.; Hoogewijs, D.
  Title Cytoglobin inhibits non-thermal plasma-induced apoptosis in melanoma cells through regulation of the NRF2-mediated antioxidant response Type A1 Journal article
  Year 2022 Publication Redox Biology Abbreviated Journal Redox Biol
  Volume 55 Issue Pages 102399
  Keywords (down) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
  Abstract Melanoma arises from pigment-producing cells called melanocytes located in the basal layers of the epidermis of the skin. Cytoglobin (CYGB) is a ubiquitously expressed hexacoordinated globin that is highly enriched in me­lanocytes and frequently downregulated during melanomagenesis. Previously, we showed that non-thermal plasma (NTP)-produced reactive oxygen and nitrogen species (RONS) lead to the formation of an intra­ molecular disulfide bridge that would allow CYGB to function as a redox-sensitive protein. Here, we investigate the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels, and we explore the role of CYGB in determining treatment outcome. Our findings are consistent with previous studies supporting that NTP cytotoxicity is mediated through the production of RONS and leads to apoptotic cell death in melanoma cells. Furthermore, we show that NTP-treated solutions elicit an antioxidant response through the activation of nuclear factor erythroid 2–related factor 2 (NRF2). The knock­ down and overexpression of CYGB respectively sensitizes and protects melanoma cells from RONS-induced apoptotic cell death. The presence of CYGB enhances heme-oxygenase 1 (HO-1) and NRF2 protein expression levels, whereas the absence impairs their expression. Moreover, analysis of the CYGB-dependent transcriptome demonstrates the tumor suppressor long non-coding RNA maternally expressed 3 (MEG3) as a hitherto unde­ scribed link between CYGB and NRF2. Thus, the presence of CYGB, at least in melanoma cells, seems to play a central role in determining the therapeutic outcome of RONS-inducing anticancer therapies, like NTP-treated solutions, possessing both tumor-suppressive and oncogenic features. Hence, CYGB expression could be of in­ terest either as a biomarker or as a candidate for future targeted therapies in melanoma.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000844595100002 Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2213-2317 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 11.4 Times cited Open Access OpenAccess
  Notes This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work include: 12S9221 N (Abraham Lin) and G044420 N (Abraham Lin and Annemie Bogaerts). Joey De Backer acknowledges a visiting fellowship from the University of Fribourg. David Hoogewijs acknowledges support by the Swiss National Science Foundation (grants 31003A173000 and 310030207460). Approved Most recent IF: 11.4
  Call Number PLASMANT @ plasmant @c:irua:190635 Serial 7101
Permanent link to this record
 
 
Author De Backer, J.; Razzokov, J.; Hammerschmid, D.; Mensch, C.; Hafideddine, Z.; Kumar, N.; van Raemdonck, G.; Yusupov, M.; Van Doorslaer, S.; Johannessen, C.; Sobott, F.; Bogaerts, A.; Dewilde, S.
  Title The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor Type A1 Journal article
  Year 2018 Publication Redox Biology Abbreviated Journal Redox Biol
  Volume 19 Issue Pages 1-10
  Keywords (down) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
  Abstract Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000449722100002 Publication Date 2018-07-24
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2213-2317 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 6.337 Times cited Open Access OpenAccess
  Notes M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI. Approved Most recent IF: 6.337
  Call Number PLASMANT @ plasmant @c:irua:152818 Serial 5006
Permanent link to this record
 
 
Author Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A.
  Title Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma Type A1 Journal article
  Year 2021 Publication Cancers Abbreviated Journal Cancers
  Volume 13 Issue 3 Pages 579
  Keywords (down) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
  Abstract Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000614960600001 Publication Date 2021-02-02
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2072-6694 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor Times cited Open Access OpenAccess
  Notes We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. Approved Most recent IF: NA
  Call Number PLASMANT @ plasmant @c:irua:176455 Serial 6709
Permanent link to this record
 
 
Author Biscop,; Lin,; Boxem,; Loenhout,; Backer,; Deben,; Dewilde,; Smits,; Bogaerts,
  Title Influence of Cell Type and Culture Medium on Determining Cancer Selectivity of Cold Atmospheric Plasma Treatment Type A1 Journal article
  Year 2019 Publication Cancers Abbreviated Journal Cancers
  Volume 11 Issue 9 Pages 1287
  Keywords (down) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE)
  Abstract Increasing the selectivity of cancer treatments is attractive, as it has the potential to reduce side-effects of therapy. Cold atmospheric plasma (CAP) is a novel cancer treatment that disrupts the intracellular oxidative balance. Several reports claim CAP treatment to be selective, but retrospective analysis of these studies revealed discrepancies in several biological factors and culturing methods. Before CAP can be conclusively stated as a selective cancer treatment, the importance of these factors must be investigated. In this study, we evaluated the influence of the cell type, cancer type, and cell culture medium on direct and indirect CAP treatment. Comparison of cancerous cells with their non-cancerous counterparts was performed under standardized conditions to determine selectivity of treatment. Analysis of seven human cell lines (cancerous: A549, U87, A375, and Malme-3M; non-cancerous: BEAS-2B, HA, and HEMa) and five different cell culture media (DMEM, RPMI1640, AM, BEGM, and DCBM) revealed that the tested parameters strongly influence indirect CAP treatment, while direct treatment was less affected. Taken together, the results of our study demonstrate that cell type, cancer type, and culturing medium must be taken into account before selectivity of CAP treatment can be claimed and overlooking these parameters can easily result in inaccurate conclusions of selectivity.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000489719000072 Publication Date 2019-09-01
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2072-6694 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor Times cited 9 Open Access
  Notes the Research Foundation Flanders, 12S9218N – ; Universiteit Antwerpen, – ; Approved Most recent IF: NA
  Call Number PLASMANT @ plasmant @c:irua:162097 Serial 5360
Permanent link to this record
 
 
Author Vermeylen, S.; De Waele, J.; Vanuytsel, S.; De Backer, J.; Van der Paal, J.; Ramakers, M.; Leyssens, K.; Marcq, E.; Van Audenaerde, J.; L. J. Smits, E.; Dewilde, S.; Bogaerts, A.
  Title Cold atmospheric plasma treatment of melanoma and glioblastoma cancer cells Type A1 Journal article
  Year 2016 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
  Volume 13 Issue 13 Pages 1195-1205
  Keywords (down) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
  Abstract In this paper, two types of melanoma and glioblastoma cancer cell lines are treated with cold atmospheric plasma to assess the effect of several parameters on the cell viability. The cell viability decreases with treatment duration and time until analysis in all cell lines with varying sensitivity. The majority of dead cells stains both AnnexinV (AnnV) and propidium iodide, indicating that the plasma-treated non-viable cells are mostly late apoptotic or necrotic. Genetic mutations might be involved in the response to plasma. Comparing the effects of two gas mixtures, as well as indirect plasma-activated medium versus direct treatment, gives different results per cell line. In conclusion, this study confirms the potential of plasma for cancer therapy and emphasizes the influence of experimental parameters on therapeutic outcome.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000393131600007 Publication Date 2016-10-31
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1612-8850 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 2.846 Times cited 26 Open Access
  Notes The authors acknowledge the University of Antwerp for providing research funds. The authors are very grateful to V. Schulz-von der Gathen and J. Benedikt (Bochum University) for providing the COST RF plasma jet. The authors would also like to thank Eva Santermans (University of Hasselt) for statistical advice. J. De Waele, J. Van Audenaerde and J. Van der Paal are research fellows of the Research Foundation Flanders (fellowship numbers: 1121016N, 1S32316N and 11U5416N), E. Marcq of Flanders Innovation & Entrepreneurship (fellowship number: 141433). Approved Most recent IF: 2.846
  Call Number PLASMANT @ plasmant @ c:irua:138722 Serial 4328
Permanent link to this record
 
 
Author Attri, P.; Park, J.-H.; De Backer, J.; Kim, M.; Yun, J.-H.; Heo, Y.; Dewilde, S.; Shiratani, M.; Choi, E.H.; Lee, W.; Bogaerts, A.
  Title Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study Type A1 Journal article
  Year 2020 Publication International Journal Of Biological Macromolecules Abbreviated Journal Int J Biol Macromol
  Volume 163 Issue Pages 2405-2414
  Keywords (down) A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
  Abstract NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, firstly we purified the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, fluorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modification/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000579839600233 Publication Date 2020-09-19
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0141-8130 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 8.2 Times cited Open Access
  Notes European Marie Skłodowska-Curie Individual Fellowship, 743546 ; JSPS, 20K14454 ; National Research Foundation of Korea, 2019M3A9F6021810 NRF-2017M3A9F6029753 NRF-2019M3E5D6063903 NRF-2016R1A6A3A04010213 ; Brain Korea 21; MSIT, NRF-2016K1A4A3914113 ; Hercules Foundation; Flemish Government; UA; We gratefully acknowledge the European Marie SkłodowskaCurie Individual Fellowship “Anticancer-PAM” within Horizon 2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. Additionally, work was supported by several grants (2019M3A9F6021810, NRF2017M3A9F6029753, NRF-2019M3E5D6063903 to W. Lee), Basic Science Research Program (NRF-2016R1A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea and in part by the Brain Korea 21 (BK21) PLUS program (J.H.P.). EHC is thankful to National Research Foundation (NRF) of Korea, funded by the Korea government (MSIT) under the grant number (NRF2016K1A4A3914113). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Approved Most recent IF: 8.2; 2020 IF: 3.671
  Call Number PLASMANT @ plasmant @c:irua:172451 Serial 6419
Permanent link to this record
 
 
Author De Backer, J.; Maric, D.; Zuhra, K.; Bogaerts, A.; Szabo, C.; Vanden Berghe, W.; Hoogewijs, D.
  Title Cytoglobin Silencing Promotes Melanoma Malignancy but Sensitizes for Ferroptosis and Pyroptosis Therapy Response Type A1 Journal article
  Year 2022 Publication Antioxidants Abbreviated Journal Antioxidants
  Volume 11 Issue 8 Pages 1548
  Keywords (down) A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
  Abstract Despite recent advances in melanoma treatment, there are still patients that either do not respond or develop resistance. This unresponsiveness and/or acquired resistance to therapy could be explained by the fact that some melanoma cells reside in a dedifferentiated state. Interestingly, this dedifferentiated state is associated with greater sensitivity to ferroptosis, a lipid peroxidation-reliant, iron-dependent form of cell death. Cytoglobin (CYGB) is an iron hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. In this study, we investigated the potential effect of CYGB on the cellular sensitivity towards (1S, 3R)-RAS-selective lethal small molecule (RSL3)-mediated ferroptosis in the G361 melanoma cells with abundant endogenous expression. Our findings show that an increased basal ROS level and higher degree of lipid peroxidation upon RSL3 treatment contribute to the increased sensitivity of CYGB knockdown G361 cells to ferroptosis. Furthermore, transcriptome analysis demonstrates the enrichment of multiple cancer malignancy pathways upon CYGB knockdown, supporting a tumor-suppressive role for CYGB. Remarkably, CYGB knockdown also triggers activation of the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome and subsequent induction of pyroptosis target genes. Altogether, we show that silencing of CYGB expression modulates cancer therapy sensitivity via regulation of ferroptosis and pyroptosis cell death signaling pathways.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000846411000001 Publication Date 2022-08-10
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2076-3921 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 7 Times cited Open Access OpenAccess
  Notes Approved Most recent IF: 7
  Call Number PLASMANT @ plasmant @c:irua:190686 Serial 7102
Permanent link to this record
 
 
Author Vinchurkar, S.; De Backer, L.; Vos, W.; Van Holsbeke, C.; de Backer, J.; de Backer, W.
  Title A case series on lung deposition analysis of inhaled medication using functional imaging based computational fluid dynamics in asthmatic patients : effect of upper airway morphology and comparison with in vivo data Type A1 Journal article
  Year 2012 Publication Inhalation Toxicology Abbreviated Journal Inhal Toxicol
  Volume 24 Issue 2 Pages 81-88
  Keywords (down) A1 Journal article; Pharmacology. Therapy; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract Context: Asthma affects 20 million Americans resulting in an economic burden of approximately $18 billion in the US alone (Allergies and Asthma Foundation 2000; National Center for Environmental Health (NCEH) 1999). Research studies based on differences in patient-specific airway morphology for asthma and the associated effect on deposition of inhaled aerosols are currently not available in the literature. Therefore, the role of morphological variations such as upper airway (extrathoracic) occlusion is not well documented. Objective: Functional imaging based computational fluid dynamics (CFD) of the respiratory airways for five asthmatic subjects is performed in this study using computed tomography (CT) based patient-specific airway models and boundary conditions. Methods: CT scans for 5 asthma patients were used to reconstruct 3D lung models using segmentation software. An averaged inhalation profile and patient-specific lobar flow distribution were used to perform the simulation. The simulations were used to obtain deposition for BDP/Formoterol (R) HFA pMDI in the patient-specific airway models. Results: The lung deposition obtained using CFD was in excellent agreement with available in vivo data using the same product. Specifically, CFD resulted in 30% lung deposition, whereas in vivo lung deposition was reported to be approximately 31%. Conclusion: It was concluded that a combination of patient-specific airway models and lobar boundary conditions can be used to obtain accurate lung deposition estimates. Lower lung deposition can be expected for patients with higher extrathoracic resistance. Novel respiratory drug delivery devices need to accommodate population subgroups based on these morphological and anatomical differences in addition to subject age.
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York, N.Y. Editor
  Language Wos 000299744800001 Publication Date 2012-01-20
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0895-8378;1091-7691; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 1.751 Times cited 36 Open Access
  Notes ; ; Approved Most recent IF: 1.751; 2012 IF: 1.894
  Call Number UA @ lucian @ c:irua:96238 Serial 286
Permanent link to this record
 
 
Author Lin, A.; Sahun, M.; Biscop, E.; Verswyvel, H.; De Waele, J.; De Backer, J.; Theys, C.; Cuypers, B.; Laukens, K.; Berghe, W.V.; Smits, E.; Bogaerts, A.
  Title Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma Type A1 Journal article
  Year 2023 Publication Drug resistance updates Abbreviated Journal
  Volume 67 Issue Pages 100914
  Keywords (down) A1 Journal article; Pharmacology. Therapy; ADReM Data Lab (ADReM); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
  Abstract To gain insights into the underlying mechanisms of NTP therapy sensitivity and resistance, using the firstever

NTP-resistant cell line derived from sensitive melanoma cells (A375).

Methods: Melanoma cells were exposed to NTP and re-cultured for 12 consecutive weeks before evaluation

against the parental control cells. Whole transcriptome sequencing analysis was performed to identify differentially

expressed genes and enriched molecular pathways. Glucose uptake, extracellular lactate, media acidification,

and mitochondrial respiration was analyzed to determine metabolic changes. Cell death inhibitors were

used to assess the NTP-induced cell death mechanisms, and apoptosis and ferroptosis was further validated via

Annexin V, Caspase 3/7, and lipid peroxidation analysis.

Results: Cells continuously exposed to NTP became 10 times more resistant to NTP compared to the parental cell

line of the same passage, based on their half-maximal inhibitory concentration (IC50). Sequencing and metabolic

analysis indicated that NTP-resistant cells had a preference towards aerobic glycolysis, while cell death analysis

revealed that NTP-resistant cells exhibited less apoptosis but were more vulnerable to lipid peroxidation and

ferroptosis.

Conclusions: A preference towards aerobic glycolysis and ferroptotic cell death are key physiological changes in

NTP-resistance cells, which opens new avenues for further, in-depth research into other cancer types.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000925156500001 Publication Date 2022-12-29
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 1368-7646 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 24.3 Times cited Open Access OpenAccess
  Notes The authors would like to thank Dr. Christophe Deben and Ms. Hannah Zaryouh (Center for Oncological Research, University of Antwerp) for the use and their help with the D300e Digital Dispenser and Spark® Cyto, as well as Ms. Rapha¨elle Corremans (Laboratory Pathophysiology, University of Antwerp) for the use of their lactate meter. The authors would also like to acknowledge the help from Ms. Tias Verhezen and Mr. Cyrus Akbari, who was involved at the start of the project but could not continue due to the COVID-19 pandemic. The authors also acknowledge the resources and services provided by the VSC (Flemish Supercomputer Center). This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaerts), and 1S67621N (Hanne Verswyvel). We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr. Willy Floren, and the Vereycken family. We would also like to acknowledge the support from the European Cooperation in Science & Technology (COST) Action on Therapeutical applications of Cold Plasmas (CA20114; PlasTHER). Approved Most recent IF: 24.3; 2023 IF: 10.906
  Call Number PLASMANT @ plasmant @c:irua:193167 Serial 7240
Permanent link to this record
 
 
Author Attri, P.; Kaushik, N.K.; Kaushik, N.; Hammerschmid, D.; Privat-Maldonado, A.; De Backer, J.; Shiratani, M.; Choi, E.H.; Bogaerts, A.
  Title Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells Type A1 Journal Article
  Year 2021 Publication International Journal Of Biological Macromolecules Abbreviated Journal Int J Biol Macromol
  Volume 182 Issue Pages 1724-1736
  Keywords (down) A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
  Abstract Bacterial and mammalian proteins, such as lysozyme, are gaining increasing interest as anticancer drugs. This study aims to modify the lysozyme structure using cold atmospheric plasma to boost its cancer cell killing effect. We investigated the structure at acidic and neutral pH using various experimental techniques (circular dichroism, fluorescence, and mass spectrometry) and molecular dynamics simulations. The controlled structural modification of lysozyme at neutral pH enhances its activity, while the activity was lost at acidic pH at the same treatment conditions. Indeed, a larger number of amino acids were oxidized at acidic pH after plasma treatment, which results in a greater distortion of the lysozyme structure, whereas only limited structural changes were observed in lysozyme after plasma treatment at neutral pH. We found that the plasma-treated lysozyme significantly induced apoptosis to the cancer cells. Our results reveal that plasma-treated lysozyme could have potential as a new cancer cell killing drug.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000675794700005 Publication Date 2021-05-27
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0141-8130 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 3.671 Times cited Open Access OpenAccess
  Notes Japan Society for the Promotion of Science; We gratefully acknowledge the European H2020 Marie SkłodowskaCurie Actions Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. NK thanks to National Research Foundation of Korea under Ministry of Science and ICT (NRF2021R1C1C1013875) of Korean Government. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Approved Most recent IF: 3.671
  Call Number PLASMANT @ plasmant @c:irua:178813 Serial 6792
Permanent link to this record
 
 
Author Vingerhoets, R.; Spiller, M.; De Backer, J.; Adriaens, A.; Vlaeminck, S.E.; Meers, E.
  Title Detailed nitrogen and phosphorus flow analysis, nutrient use efficiency and circularity in the agri-food system of a livestock-intensive region Type A1 Journal article
  Year 2023 Publication Journal of cleaner production Abbreviated Journal
  Volume 410 Issue Pages 137278-13
  Keywords (down) A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
  Abstract The agri-food value chain is a major cause of nitrogen (N) and phosphorus (P) emissions and associated environmental and health impacts. The EU's farm-to-fork strategy (F2F) demands an agri-food value chain approach to reduce nutrient emissions by 50% and fertilizer use by 20%. Substance flow analysis (SFA) is a method that can be applied to study complex systems such as the agri-food chain. A review of 60 SFA studies shows that they often lack detail by not sufficiently distinguishing between nodes, products and types of emissions. The present study aims to assess the added value of detail in SFAs and to illustrate that valuable indicators can be derived from detailed assessments. This aim will be attained by presenting a highly-detailed SFA for the livestock-intensive region of Flanders, Belgium. The SFA distinguishes 40 nodes and 1827 flows that are classified into eight different categories (e.g. by-products, point source emissions) following life cycle methods. Eight novel indicators were calculated, including indicators that assess the N and P recovery potential. Flanders has a low overall nutrient use efficiency (11% N, 18% P). About 55% of the N and 56% of the P embedded in recoverable streams are reused providing 35% and 37% of the total N and P input. Optimized nutrient recycling could replace 45% of N and 48% of P of the external nutrient input, exceeding the target set by the F2F strategy. Detailed accounting for N and P flows and nodes leads to the identification of more recoverable streams and larger N and P flows. More detailed flow accounting is a prerequisite for the quantification of technological intervention options. Future research should focus on including concentration and quality as a parameter in SFAs.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000991013600001 Publication Date 2023-04-21
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0959-6526 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 11.1 Times cited Open Access OpenAccess
  Notes Approved Most recent IF: 11.1; 2023 IF: 5.715
  Call Number UA @ admin @ c:irua:196227 Serial 7770
Permanent link to this record
Select All    Deselect All << 1 2 3 4 >>
List View
 | 
Citations
 | 
Details
   print
toggle visibility
Save Citations:
Export Records:
Home CQL Search  |  Library Search  |  Show Record  |  Extract Citations Help