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Author de Backer, J.W.; Vanderveken, O.M.; Vos, W.G.; Devolder, A.; Verhulst, S.L.; Verbraecken, J.A.; Parizel, P.M.; Braem, M.J.; van de Heyning, P.H.; de Backer, W.A. doi  openurl
  Title Functional imaging using computational fluid dynamics to predict treatment success of mandibular advancement devices in sleep-disordered breathing Type A1 Journal article
  Year 2007 Publication Journal of biomechanics Abbreviated Journal J Biomech  
  Volume 40 Issue (up) 16 Pages 3708-3714  
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)  
  Abstract  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication New York, N.Y. Editor  
  Language Wos 000251845100020 Publication Date 2007-08-01  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0021-9290; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.664 Times cited 66 Open Access  
  Notes Approved Most recent IF: 2.664; 2007 IF: 2.897  
  Call Number UA @ lucian @ c:irua:64860 Serial 1299  
Permanent link to this record
 

 
Author Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S. pdf  url
doi  openurl
  Title Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 170 Issue (up) 170 Pages 128-138  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramer-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms.  
  Address Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium. Electronic address: sandra.vanaert@uantwerpen.be  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language English Wos 000386925500014 Publication Date 2016-07-26  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 6 Open Access  
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15, G.0369.15 and G.0374.13) and a postdoctoral research grant to A. De Backer. The research leading to these results has also received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). The authors would also like to thank A. Rosenauer for providing access to the STEMsim software and Gerardo T. Martinez for fruitful discussions.; esteem2_jra2 Approved Most recent IF: 2.843  
  Call Number c:irua:135337 c:irua:135337 Serial 4128  
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Author De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S. pdf  url
doi  openurl
  Title StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 171 Issue (up) 171 Pages 104-116  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  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 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, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. 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 000389106200014 Publication Date 2016-09-09  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 43 Open Access  
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0393.11, G.0064.10 and G.0374.13), a Ph.D. 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.; esteem2_jra2 Approved Most recent IF: 2.843  
  Call Number EMAT @ emat @ c:irua:135516 Serial 4280  
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Author Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S. url  doi
openurl 
  Title Atom-counting in High Resolution Electron Microscopy: TEM or STEM – that's the question Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 174 Issue (up) 174 Pages 112-120  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000403342200013 Publication Date 2016-10-27  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 2 Open Access  
  Notes The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15N, G.0369.15N, G.0374.13N, and WO.010.16N) and a postdoctoral grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). Approved Most recent IF: 2.843  
  Call Number EMAT @ emat @ c:irua:137102 Serial 4315  
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Author Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S. pdf  url
doi  openurl
  Title Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 177 Issue (up) 177 Pages 36-42  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000401219800006 Publication Date 2016-11-09  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 13 Open Access OpenAccess  
  Notes The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. S. Bals acknowledges funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N and G.0368.15N) and a post-doctoral grant to A. De Backer and T. Altantzis. The authors are grateful to Professor Luis M. Liz-Marzán for providing the sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843  
  Call Number EMAT @ emat @ c:irua:138015UA @ admin @ c:irua:138015 Serial 4316  
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Author De wael, A.; De Backer, A.; Jones, L.; Nellist, P.D.; Van Aert, S. pdf  url
doi  openurl
  Title Hybrid statistics-simulations based method for atom-counting from ADF STEM images Type A1 Journal article
  Year 2017 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 177 Issue (up) 177 Pages 69-77  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000401219800010 Publication Date 2017-01-25  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 8 Open Access OpenAccess  
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0368.15N, G.0369.15N, and WO.010.16N), 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). The authors are grateful to G.T. Martinez for providing image simulations. Approved Most recent IF: 2.843  
  Call Number EMAT @ emat @ c:irua:141718 Serial 4486  
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Author Alania, M.; De Backer, A.; Lobato, I.; Krause, F.F.; Van Dyck, D.; Rosenauer, A.; Van Aert, S. pdf  url
doi  openurl
  Title How precise can atoms of a nanocluster be located in 3D using a tilt series of scanning transmission electron microscopy images? Type A1 Journal article
  Year 2017 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 181 Issue (up) 181 Pages 134-143  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract In this paper, we investigate how precise atoms of a small nanocluster can ultimately be located in three dimensions (3D) from a tilt series of images acquired using annular dark field (ADF) scanning transmission electron microscopy (STEM). Therefore, we derive an expression for the statistical precision with which the 3D atomic position coordinates can be estimated in a quantitative analysis. Evaluating this statistical precision as a function of the microscope settings also allows us to derive the optimal experimental design. In this manner, the optimal angular tilt range, required electron dose, optimal detector angles, and number of projection images can be determined.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000411170800016 Publication Date 2016-12-15  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 3 Open Access OpenAccess  
  Notes The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N, G.0368.15N, and WO.010.16N) and a post-doctoral grant to A. De Backer, and from the DFG under contract No. RO-2057/4-2. Approved Most recent IF: 2.843  
  Call Number EMAT @ emat @ c:irua:144432 Serial 4618  
Permanent link to this record
 

 
Author Altantzis, T.; Lobato, I.; De Backer, A.; Béché, A.; Zhang, Y.; Basak, S.; Porcu, M.; Xu, Q.; Sánchez-Iglesias, A.; Liz-Marzán, L.M.; Van Tendeloo, G.; Van Aert, S.; Bals, S. url  doi
openurl 
  Title Three-Dimensional Quantification of the Facet Evolution of Pt Nanoparticles in a Variable Gaseous Environment Type A1 Journal article
  Year 2019 Publication Nano letters Abbreviated Journal Nano Lett  
  Volume 19 Issue (up) 19 Pages 477-481  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract Pt nanoparticles play an essential role in a wide variety of catalytic reactions. The activity of the particles strongly depends on their three-dimensional (3D) structure and exposed facets, as well as on the reactive environment. High-resolution electron microscopy has often been used to characterize nanoparticle catalysts but unfortunately most observations so far have been either performed in vacuum and/or using conventional (2D) in situ microscopy. The latter however does not provide direct 3D morphological information. We have implemented a quantitative methodology to measure variations of the 3D atomic structure of nanoparticles under the flow of a selected gas. We were thereby able to quantify refaceting of Pt nanoparticles with atomic resolution during various oxidation−reduction cycles. In a H2 environment, a more faceted surface morphology of the particles was observed with {100} and {111} planes being dominant. On the other hand, in O2 the percentage of {100} and {111} facets decreased and a significant increase of higher order facets was found, resulting in a more rounded morphology. This methodology opens up new opportunities toward in situ characterization of catalytic nanoparticles because for the first time it enables one to directly measure 3D morphology variations at the atomic scale in a specific gaseous reaction environment.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000455561300061 Publication Date 2019-01-09  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1530-6984 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 12.712 Times cited 82 Open Access OpenAccess  
  Notes This work was supported by the European Research Council (Grant 335078 COLOURATOM to S.B. and Grant 770887 PICOMETRICS to S.V.A.). The authors acknowledge funding from the European Commission Grant (EUSMI 731019 to S.B., L.M.L.-M., and Q.X. and MUMMERING 765604 to S.B. and Q.X.). The authors gratefully acknowledge funding from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15N, G.0369.15N, and G.0267.18N), postdoctoral grants to T.A. and A.D.B, and an FWO [PEGASUS]2 Marie Sklodowska-Curie fellowship to Y.Z. (12U4917N). L.M.L.-M. acknowledges funding from the Spanish Ministerio de Economía y Competitividad (Grant MAT2017-86659-R). We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan X Pascal GPU used for this research. ecas_sara Realnano 815128; sygma Approved Most recent IF: 12.712  
  Call Number EMAT @ emat @UA @ admin @ c:irua:156390 Serial 5150  
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Author Vinchurkar, S.; De Backer, L.; Vos, W.; Van Holsbeke, C.; de Backer, J.; de Backer, W. doi  openurl
  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 (up) 2 Pages 81-88  
  Keywords A1 Journal article; Pharmacology. Therapy; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract Context: Asthma affects 20 million Americans resulting in an economic burden of approximately $18 billion in the US alone (Allergies and Asthma Foundation 2000; National Center for Environmental Health (NCEH) 1999). Research studies based on differences in patient-specific airway morphology for asthma and the associated effect on deposition of inhaled aerosols are currently not available in the literature. Therefore, the role of morphological variations such as upper airway (extrathoracic) occlusion is not well documented. Objective: Functional imaging based computational fluid dynamics (CFD) of the respiratory airways for five asthmatic subjects is performed in this study using computed tomography (CT) based patient-specific airway models and boundary conditions. Methods: CT scans for 5 asthma patients were used to reconstruct 3D lung models using segmentation software. An averaged inhalation profile and patient-specific lobar flow distribution were used to perform the simulation. The simulations were used to obtain deposition for BDP/Formoterol (R) HFA pMDI in the patient-specific airway models. Results: The lung deposition obtained using CFD was in excellent agreement with available in vivo data using the same product. Specifically, CFD resulted in 30% lung deposition, whereas in vivo lung deposition was reported to be approximately 31%. Conclusion: It was concluded that a combination of patient-specific airway models and lobar boundary conditions can be used to obtain accurate lung deposition estimates. Lower lung deposition can be expected for patients with higher extrathoracic resistance. Novel respiratory drug delivery devices need to accommodate population subgroups based on these morphological and anatomical differences in addition to subject age.  
  Address  
  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  
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Author de Backer, W.; Vos, W.; Van Holsbeke, C.; Vinchurkar, S.; Claes, R.; Hufkens, A.; Parizel, P.M.; Bedert, L.; de Backer, J. pdf  doi
openurl 
  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 (up) 2 Pages 527-529  
  Keywords 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  
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Author De Backer, L.A.; Vos, W.; de Backer, J.; Van Holsbeke, C.; Vinchurkar, S.; de Backer, W. pdf  doi
openurl 
  Title The acute effect of budesonide/formoterol in COPD : a multi-slice computed tomography and lung function study Type A1 Journal article
  Year 2012 Publication European Respiratory Journal Abbreviated Journal Eur Respir J  
  Volume 40 Issue (up) 2 Pages 298-305  
  Keywords A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract The Global Initiative for Chronic Obstructive Lung Disease (GOLD) classification of chronic obstructive pulmonary disease (COPD) does not always match with other clinical disease descriptors such as exacerbation frequency and quality of life, indicating that forced expiratory volume in 1 s (FEV1) is not a perfect descriptor of the disease. The aim of this study was to find out whether changes in airway geometry after inhalation of the most commonly used inhalation therapy in severe COPD can more adequately be described with an image-based approach than with spirometry. 10 COPD GOLD stage III patients were assessed in a double-blind crossover study. Airway volumes were analysed using segmentation of multi-slice computed tomography (MSCT) images; airway resistance was determined using computational fluid dynamics (CFD). Distal airway volume significantly increased (p=0.011) in patients 4 h after receiving a budesonide/formoterol combination from 9.6+/-4.67 cm(3) to 10.14+/-4.81 cm(3). Also CFD-determined airway resistance significantly decreased (p=0.047) from 0.051+/-0.021 kPa.s.L-1 to 0.043+/- 0.019 kPa.s.L-1. None of the lung function parameters showed a significant change. Only functional residual capacity (FRC) showed a trend to decline (p=0.056). Only the image-based parameters were able to predict the visit at which the combination product was administered. This study showed that imaging is a sensitive, complementary tool to describe changes in airway structure.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Copenhagen Editor  
  Language Wos 000307291700006 Publication Date 2011-12-20  
  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 37 Open Access  
  Notes ; ; Approved Most recent IF: 10.569; 2012 IF: 6.355  
  Call Number UA @ lucian @ c:irua:101113 Serial 3568  
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Author Horemans, B.; Van Holsbeke, C.; Vos, W.; Darchuk, L.; Novakovic, V.; Fontan, A.C.; de Backer, J.; van Grieken, R.; de Backer, W.; De Wael, K. doi  openurl
  Title Particle deposition in airways of chronic respiratory patients exposed to an urban aerosol Type A1 Journal article
  Year 2012 Publication Environmental science and technology Abbreviated Journal Environ Sci Technol  
  Volume 46 Issue (up) 21 Pages 12162-12169  
  Keywords A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract Urban atmospheres in modern cities carry characteristic mixtures of particulate pollution which are potentially aggravating for chronic respiratory patients (CRP). Although air quality surveys can be detailed, the obtained information is not always useful to evaluate human health effects. This paper presents a novel approach to estimate particle deposition rates in airways of CRP, based on real air pollution data. By combining computational fluid dynamics with physical-chemical characteristics of particulate pollution, deposition rates are estimated for particles of different toxicological relevance, that is, minerals, iron oxides, sea salts, ammonium salts, and carbonaceous particles. Also, it enables some qualitative evaluation of the spatial, temporal, and patient specific effects on the particle dose upon exposure to the urban atmosphere. Results show how heavy traffic conditions increases the deposition of anthropogenic particles in the trachea and lungs of respiratory patients (here, +0.28 and +1.5 μg·h1, respectively). In addition, local and synoptic meteorological conditions were found to have a strong effect on the overall dose. However, the pathology and age of the patient was found to be more crucial, with highest deposition rates for toxic particles in adults with a mild anomaly, followed by mild asthmatic children and adults with severe respiratory dysfunctions (7, 5, and 3 μg·h1, respectively).  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Easton, Pa Editor  
  Language Wos 000310665000082 Publication Date 2012-10-04  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0013-936X;1520-5851; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 6.198 Times cited 5 Open Access  
  Notes ; We are grateful for the financial support of n.v. Vooruitzicht. Furthermore, co-workers at the environmental analysis research group are acknowledged for their help in the fieldwork. ; Approved Most recent IF: 6.198; 2012 IF: 5.257  
  Call Number UA @ lucian @ c:irua:101411 Serial 2557  
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Author van Holsbeke, C.; de Backer, J.; Vos, W.; Verdonck, P.; van Ransbeeck, P.; Claessens, T.; Braem, M.; Vanderveken, O.; de Backer, W. pdf  doi
openurl 
  Title Anatomical and functional changes in the upper airways of sleep apnea patients due to mandibular repositioning: a large scale study Type A1 Journal article
  Year 2011 Publication Journal of biomechanics Abbreviated Journal J Biomech  
  Volume 44 Issue (up) 3 Pages 442-449  
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)  
  Abstract The obstructive sleep apnea-hypopnea syndrome (OSAHS) is a sleep related breathing disorder. A popular treatment is the use of a mandibular repositioning appliance (MRA) which advances the mandibula during the sleep and decreases the collapsibility of the upper airway. The success rate of such a device is, however, limited and very variable within a population of patients. Previous studies using computational fluid dynamics have shown that there is a decrease in upper airway resistance in patients who improve clinically due to an MRA. In this article, correlations between patient-specific anatomical and functional parameters are studied to examine how MRA induced biomechanical changes will have an impact on the upper airway resistance. Low-dose computed tomography (CT) scans are made from 143 patients suffering from OSAHS. A baseline scan and a scan after mandibular repositioning (MR) are performed in order to study variations in parameters. It is found that MR using a simulation bite is able to induce resistance changes by changing the pharyngeal lumen. The change in minimal cross-sectional area is the best parameter to predict the change in upper airway resistance. Looking at baseline values, the ideal patients for MR induced resistance decrease seem to be women with short airways, high initial resistance and no baseline occlusion.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication New York, N.Y. Editor  
  Language Wos 000287551000014 Publication Date 2010-10-23  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0021-9290; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.664 Times cited 23 Open Access  
  Notes ; ; Approved Most recent IF: 2.664; 2011 IF: 2.434  
  Call Number UA @ lucian @ c:irua:85305 Serial 112  
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Author Van Aert, S.; De Backer, A.; Martinez, G.T.; den Dekker, A.J.; Van Dyck, D.; Bals, S.; Van Tendeloo, G. pdf  url
doi  openurl
  Title Advanced electron crystallography through model-based imaging Type A1 Journal article
  Year 2016 Publication IUCrJ Abbreviated Journal Iucrj  
  Volume 3 Issue (up) 3 Pages 71-83  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab; Engineering Management (ENM)  
  Abstract The increasing need for precise determination of the atomic arrangement of non-periodic structures in materials design and the control of nanostructures explains the growing interest in quantitative transmission electron microscopy. The aim is to extract precise and accurate numbers for unknown structure parameters including atomic positions, chemical concentrations and atomic numbers. For this purpose, statistical parameter estimation theory has been shown to provide reliable results. In this theory, observations are considered purely as data planes, from which structure parameters have to be determined using a parametric model describing the images. As such, the positions of atom columns can be measured with a precision of the order of a few picometres, even though the resolution of the electron microscope is still one or two orders of magnitude larger. Moreover, small differences in average atomic number, which cannot be distinguished visually, can be quantified using high-angle annular dark-field scanning transmission electron microscopy images. In addition, this theory allows one to measure compositional changes at interfaces, to count atoms with single-atom sensitivity, and to reconstruct atomic structures in three dimensions. This feature article brings the reader up to date, summarizing the underlying theory and highlighting some of the recent applications of quantitative model-based transmisson electron microscopy.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000368590900010 Publication Date 2015-11-13  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2052-2525; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 5.793 Times cited 30 Open Access OpenAccess  
  Notes The authors gratefully acknowledge the Research Foundation Flanders (FWO, Belgium) for funding and for a PhD grant to ADB. The research leading to these results has received funding from the European Union 7th Framework Program (FP7/20072013) under grant agreement No. 312483 (ESTEEM2). SB and GVT acknowledge the European Research Council under the 7th Framework Program (FP7), ERC grant No. 335078 – COLOURATOMS and ERC grant No. 246791 – COUNTATOMS.; esteem2jra2; ECASSara; (ROMEO:green; preprint:; postprint:can ; pdfversion:can); Approved Most recent IF: 5.793  
  Call Number c:irua:129589 c:irua:129589 Serial 3965  
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Author de Backer, J.W.; Vos, W.G.; Vinchurkar, S.C.; Claes, R.; Drollmann, A.; Wulfrank, D.; Parizel, P.M.; Germonpré, P.; de Backer, W. pdf  doi
openurl 
  Title Validation of computational fluid dynamics in CT-based airway models with SPECT/CT1 Type A1 Journal article
  Year 2010 Publication Radiology Abbreviated Journal Radiology  
  Volume 257 Issue (up) 3 Pages 854-862  
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract Purpose: To compare the results obtained by using numerical flow simulations with the results of combined single photon emission computed tomography (SPECT) and computed tomography (CT) and to demonstrate the importance of correct boundary conditions for the numerical methods to account for the large amount of interpatient variability in airway geometry. Materials and Methods: This study was approved by all relevant institutional review boards. All patients gave their signed informed consent. In this study, six patients with mild asthma (three men; three women; overall mean age, 46 years ± 17 [standard deviation]) underwent CT at functional residual capacity and total lung capacity, as well as SPECT/CT. CT data were used for segmentation and computational fluid dynamics (CFD) simulations. A comparison was made between airflow distribution, as derived with (a) SPECT/CT through tracer concentration analysis, (b) CT through lobar expansion measurement, and (c) CFD through flow computer simulation. Also, the heterogeneity of the ventilation was examined. Results: Good agreement was found between SPECT/CT, CT, and CFD in terms of airflow distribution and hot spot detection. The average difference for the internal airflow distribution was less than 3% for CFD and CT versus SPECT/CT. Heterogeneity in ventilation patterns could be detected with SPECT/CT and CFD. Conclusion: This results of this study show that patient-specific computer simulations with appropriate boundary conditions yield information that is similar to that obtained with functional imaging tools, such as SPECT/CT.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Easton, Pa Editor  
  Language Wos 000284469300031 Publication Date 2010-11-17  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0033-8419;1527-1315; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 7.296 Times cited 100 Open Access  
  Notes ; Supported by Novartis. ; Approved Most recent IF: 7.296; 2010 IF: 6.069  
  Call Number UA @ lucian @ c:irua:85379 Serial 3831  
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Author van den Bos, K.H.W.; Altantzis, T.; De Backer, A.; Van Aert, S.; Bals, S. pdf  url
doi  openurl
  Title Recent breakthroughs in scanning transmission electron microscopy of small species Type A1 Journal article
  Year 2018 Publication Advances in Physics: X Abbreviated Journal Advances in Physics: X  
  Volume 3 Issue (up) 3 Pages 1480420  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract Over the last decade, scanning transmission electron microscopy has become one of the most powerful tools to characterise nanomaterials at the atomic scale. Often, the ultimate goal is to retrieve the three-dimensional structure, which is very challenging since small species are typically sensitive to electron irradiation. Nevertheless, measuring individual atomic positions is crucial to understand the relation between the structure and physicochemical properties of these (nano)materials. In this review, we highlight the latest approaches that are available to reveal the 3D atomic structure of small species. Finally, we will provide an outlook and will describe future challenges where the limits of electron microscopy will be pushed even further.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000441619500001 Publication Date 2018-08-13  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2374-6149 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor Times cited 8 Open Access OpenAccess  
  Notes This work was supported by the Research Foundation Flanders (FWO, Belgium) under Grant G.0368.15N, G.0369.15N, and G.0267.18N, by personal FWO Grants to K. H. W. van den Bos, T. Altantzis, and A. De Backer, and the European Research Council under Grant 335078 COLOURATOM to S. Bals. The authors would like to thank the colleagues who have contributed to this work over the years, including A. M. Abakumov, K. J. Batenburg, E. Countiño-Gonzalez, C. de Mello Donega, R. Erni, J. J. Geuchies, B. Goris, J. Hofkens, L. Jones, P. Lievens, L. M. Liz-Marzán, I. Lobato, G. T. Martinez, P. D. Nellist, B. Partoens, M. B. J. Roeffaers, M.D. Rossell, B. Schoeters, M. J. Van Bael, W. van der Stam, M. van Huis, G. Van Tendeloo, D. Vanmaekelbergh, and N. Winckelmans. (ROMEO:green; preprint:; postprint:can ; pdfversion:can); saraecas; ECAS_Sara; Approved Most recent IF: NA  
  Call Number EMAT @ emat @c:irua:152820UA @ admin @ c:irua:152820 Serial 5007  
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Author Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A. url  doi
openurl 
  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 (up) 3 Pages 579  
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)  
  Abstract Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000614960600001 Publication Date 2021-02-02  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2072-6694 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor Times cited Open Access OpenAccess  
  Notes We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. Approved Most recent IF: NA  
  Call Number PLASMANT @ plasmant @c:irua:176455 Serial 6709  
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Author Kirkwood, N.; De Backer, A.; Altantzis, T.; Winckelmans, N.; Longo, A.; Antolinez, F.V.; Rabouw, F.T.; De Trizio, L.; Geuchies, J.J.; Mulder, J.T.; Renaud, N.; Bals, S.; Manna, L.; Houtepen, A.J. url  doi
openurl 
  Title Locating and controlling the Zn content in In(Zn)P quantum dots Type A1 Journal article
  Year 2019 Publication Chemistry of materials Abbreviated Journal Chem Mater  
  Volume 32 Issue (up) 32 Pages 557-565  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract Zinc is routinely employed in the synthesis of InP quantum dots (QDs) to improve the photoluminescence efficiency and carrier mobility of the resulting In(Zn)P alloy nanostructures. The exact location of Zn in the final structures and the mechanism by which it enhances the optoelectronic properties of the QDs is debated. We use synchrotron X-ray absorbance spectroscopy to show that the majority of Zn in In(Zn)P QDs is located at their surface as Zn-carboxylates. However, a small amount of Zn is present inside the bulk of the QDs with the consequent contraction of their lattice, as confirmed by combining high resolution high-angle annular dark-field imaging scanning transmission electron microscopy (HAADF-STEM) with statistical parameter estimation theory. We further demonstrate that the Zn content and its incorporation into the QDs can be tuned by the ligation of commonly employed Zn carboxylate precursors: the use of highly reactive Zn-acetate leads to the formation of undesired Zn3P2 and the final nanostructures being characterized by broad optical features, whereas Zn-carboxylates with longer carbon chains lead to InP crystals with much lower zinc content and narrow optical features. These results can explain the differences between structural and optical properties of In(Zn)P samples reported across the literature, and provide a rational method to tune the amount of Zn in InP nanocrystals and to drive the incorporation of Zn either as surface Zn-carboxylate, as a substitutional dopant inside the InP crystal lattice, or even predominantly as Zn3P2.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000507721600056 Publication Date 2019-12-13  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0897-4756 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 9.466 Times cited 39 Open Access OpenAccess  
  Notes A.J.H. acknowledges support from the European Research Council Horizon 2020 ERC Grant Agreement No. 678004 (Doping on Demand). This research is supported by the Dutch Technology Foundation TTW, which is part of The Netherlands Organization for Scientific Research (NWO), and which is partly funded by Ministry of Economic Affairs. SB acknowledges funding from the European Research Council (grant 815128 REALNANO). The authors gratefully acknowledge funding from the Research Foundation Flanders (FWO, Belgium) through project funding G.0381.16N and a postdoctoral grant to A.D.B. AJH, LM and JM acknowledge support from the H2020 Collaborative Project TEQ (Grant No. 766900).; sygma Approved Most recent IF: 9.466  
  Call Number EMAT @ emat @c:irua:165234 Serial 5438  
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Author Varambhia, A.M.; Jones, L.; De Backer, A.; Fauske, V.T.; Van Aert, S.; Ozkaya, D.; Nellist, P.D. pdf  url
doi  openurl
  Title Quantifying a Heterogeneous Ru Catalyst on Carbon Black Using ADF STEM Type A1 Journal article
  Year 2016 Publication Particle and particle systems characterization Abbreviated Journal Part Part Syst Char  
  Volume 33 Issue (up) 33 Pages 438-444  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract Ru catalysts are part of a set of late transition metal nanocatalysts that have garnered much interest for catalytic applications such as ammonia synthesis and fuel cell production. Their performance varies greatly depending on their morphology and size, these catalysts are widely studied using electron microscopy. Using recent developments in Annular Dark Field (ADF) Scanning Transmission Electron Microscopy (STEM) quantification techniques, a rapid atom counting procedure was utilized to document the evolution of a heterogeneous Ru catalyst supported on carbon black. Areas of the catalyst were imaged for approximately 15 minutes using ADF STEM. When the Ru clusters were exposed to the electron beam, the clusters changed phase from amorphous to crystalline. To quantify the thickness of the crystalline clusters, two techniques were applied (simulation and statistical decomposition) and compared. These techniques show that stable face centredcubic crystal structures in the form of rafts, between 2 and 8 atoms thick, were formed after the initial wetting of the carbon support.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000379970000012 Publication Date 2016-06-17  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0934-0866 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 4.474 Times cited 4 Open Access  
  Notes The authors would like to thank the EPSRC and Johnson Matthey for funding this work as part of a CASE-Award studentship. 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). We would like to thank Brian Theobald and Jonathan Sharman from JMTC for provision of the samples The authors gratefully acknowledge the Research Foundation Flanders (FWO, Belgium) for funding and for a postdoctoral grant to ADB. The microscope used was funded by the INFRASTRUKTUR Grant 197405 (NORTEM) program of the Research Council of Norway.; esteem2_jra2 Approved Most recent IF: 4.474  
  Call Number c:irua:134036 c:irua:134036 Serial 4086  
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Author van den Broek, W.; Verbeeck, J.; Schryvers, D.; de Backer, S.; Scheunders, P. pdf  doi
openurl 
  Title Tomographic spectroscopic imaging; an experimental proof of concept Type A1 Journal article
  Year 2009 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 109 Issue (up) 4 Pages 296-303  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract Recording the electron energy loss spectroscopy data cube with a series of energy filtered images is a dose inefficient process because the energy slit blocks most of the electrons. When recording the data cube by scanning an electron probe over the sample, perfect dose efficiency is attained; but due to the low current in nanoprobes, this often is slower, with a smaller field of view. In W. Van den Broek et al. [Ultramicroscopy, 106 (2006) 269], we proposed a new method to record the data cube, which is more dose efficient than an energy filtered series. It produces a set of projections of the data cube and then tomographically reconstructs it. In this article, we demonstrate these projections in practice, we present a simple geometrical model that allows for quantification of the projection angles and we present the first successful experimental reconstruction, all on a standard post-column instrument.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Amsterdam Editor  
  Language Wos 000265345400003 Publication Date 2008-12-10  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 1 Open Access  
  Notes Esteem 026019 Approved Most recent IF: 2.843; 2009 IF: 2.067  
  Call Number UA @ lucian @ c:irua:77271 Serial 3671  
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Author van den Broek, W.; Verbeeck, J.; de Backer, S.; Scheunders, P.; Schryvers, D. pdf  doi
openurl 
  Title Acquisition of the EELS data cube by tomographic reconstruction Type A1 Journal article
  Year 2006 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 106 Issue (up) 4/5 Pages 269-276  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract Energy filtered TEM, EFTEM, provides three-dimensional data, two spatial and one spectral dimension. We propose to acquire these data by measuring a series of images with a defocused energy filter. It will be shown that each image is a projection of the data on the detector and that reconstruction of the data out of a sufficient number of such projections using a tomographic reconstruction algorithm is possible. This technique uses only a fraction of the electron dose an energy filtered series (EFS) needs for the same spectral and spatial resolution and the same mean signal-to-noise ratio. (c) 2005 Elsevier B.V. All rights reserved.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Amsterdam Editor  
  Language Wos 000236042300003 Publication Date 2005-11-30  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0304-3991; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.843 Times cited 6 Open Access  
  Notes Approved Most recent IF: 2.843; 2006 IF: 1.706  
  Call Number UA @ lucian @ c:irua:56910UA @ admin @ c:irua:56910 Serial 55  
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Author Bals, S.; Goris, B.; de Backer, A.; Van Aert, S.; Van Tendeloo, G. pdf  url
doi  openurl
  Title Atomic resolution electron tomography Type A1 Journal article
  Year 2016 Publication MRS bulletin Abbreviated Journal Mrs Bull  
  Volume 41 Issue (up) 41 Pages 525-530  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract Over the last two decades, three-dimensional (3D) imaging by transmission electron microscopy or “electron tomography” has evolved into a powerful tool to investigate a variety of nanomaterials in different fields, such as life sciences, chemistry, solid-state physics, and materials science. Most of these results were obtained with nanometer-scale resolution, but different approaches have recently pushed the resolution to the atomic level. Such information is a prerequisite to understand the specific relationship between the atomic structure and the physicochemical properties of (nano) materials. We provide an overview of the latest progress in the field of atomic-resolution electron tomography. Different imaging and reconstruction approaches are presented, and state-of-the-art results are discussed. This article demonstrates the power and importance of electron tomography with atomic-scale resolution.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Pittsburgh, Pa Editor  
  Language Wos 000382508100012 Publication Date 2016-07-07  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0883-7694 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 5.199 Times cited 19 Open Access OpenAccess  
  Notes ; The authors gratefully acknowledge funding from the Research Foundation Flanders (G.0381.16N, G.036915, G.0374.13, and funding of postdoctoral grants to B.G. and A.D.B.). S.B. acknowledges the European Research Council, ERC Grant Number 335078-Colouratom. The research leading to these results received funding from the European Union Seventh Framework Program under Grant Agreements 312483 (ESTEEM2). The authors would like to thank the colleagues who have contributed to this work, including K.J. Batenburg, J. De Beenhouwer, R. Erni, M.D. Rossell, W. Van den Broek, L. Liz-Marzan, E. Carbo-Argibay, S. Gomez-Grana, P. Lievens, M. Van Bael, B. Partoens, B. Schoeters, and J. Sijbers. ; ecas_sara Approved Most recent IF: 5.199  
  Call Number UA @ lucian @ c:irua:135690 Serial 4299  
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Author Van Holsbeke, C.; Vos, W.; van Hoorenbeeck, K.; Boudewyns, A.; Salgado, R.; Verdonck, P.R.; Ramet, J.; de Backer, J.; De Backer, W.; Verhulst, S.L. pdf  doi
openurl 
  Title Functional respiratory imaging as a tool to assess upper airway patency in children with obstructive sleep apnea Type A1 Journal article
  Year 2013 Publication Sleep Medicine Abbreviated Journal Sleep Med  
  Volume 14 Issue (up) 5 Pages 433-439  
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract Objective: We aim to investigate if anatomical and functional properties of the upper airway using computerized 3D models derived from computed tomography (CT) scans better predict obstructive sleep apnea (OSA) severity than standard clinical markers. Methods: Consecutive children with suspected OSA underwent polysomnography, clinical assessment of upper airway patency, and a CT scan while awake. A three-dimensional (3D) reconstruction of the pharyngeal airway was built from these images, and computational fluid dynamics modeling of low inspiratory flow was performed using open-source software. Results: Thirty-three children were included (23 boys; mean age, was 6.0 +/- 3.2 y). OSA was diagnosed in 23 patients. Children with OSA had a significantly lower volume of the overlap region between tonsils and the adenoids (median volume, 1408 mm compared to 2173 mm; p = 0.04), a lower mean cross-sectional area at this location (median volume, 69.3 mm(2) compared to 114.3 mm(2); p = 0.04), and a lower minimal cross-sectional area (median volume, 17.9 mm(2) compared to 25.9 mm(2); p = 0.05). Various significant correlations were found between several imaging parameters and the severity of OSA, most pronounced for upper airway conductance (r = -0.46) (p < 0.01) for correlation between upper airway conductance and the apnea-hypopnea index. No differences or significant correlations were observed with clinical parameters of upper airway patency. Preliminary data after treatment showed that none of the patients with residual OSA had their smallest cross-sectional area located in segment 3, and this frequency was significantly lower than in their peers whose sleep study normalized (64%; p = 0.05). Conclusion: Functional imaging parameters are highly correlated with OSA severity and are a more powerful correlate than clinical scores of upper airway patency. Preliminary data also showed that we could identify differences in the upper airway of those subjects who did not benefit from a local upper airway treatment. (c) 2013 Elsevier B.V. All rights reserved.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Amsterdam Editor  
  Language Wos 000318612100009 Publication Date 2013-03-07  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1389-9457; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.391 Times cited 18 Open Access  
  Notes ; ; Approved Most recent IF: 3.391; 2013 IF: 3.100  
  Call Number UA @ lucian @ c:irua:109015 Serial 1302  
Permanent link to this record
 

 
Author Vos, W.; de Backer, J.; Poli, G.; De Volder, A.; Ghys, L.; Van Holsbeke, C.; Vinchurkar, S.; De Backer, L.; de Backer, W. pdf  doi
openurl 
  Title Novel functional imaging of changes in small airways of patients treated with extrafine beclomethasone/formoterol Type A1 Journal article
  Year 2013 Publication Respiration Abbreviated Journal Respiration  
  Volume 86 Issue (up) 5 Pages 393-401  
  Keywords A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract Background: Inhaled formulations using extrafine particles of long-acting beta(2)-agonists and corticosteroids were developed to optimize asthma treatment. Findings that these combinations reach and treat smaller airways more effectively are predominantly based on general non-specific outcomes with little information on regional characteristics. Objectives: This study aims to assess long-term effects of extrafine beclomethasone/formoterol on small airways of asthmatic patients using novel functional imaging methods. Methods: Twenty-four stable asthma patients were subdivided into three groups (steroid naive, n = 7; partially controlled, n = 6; well controlled, n = 11). Current treatment was switched to a fixed combination of extrafine beclomethasone/formoterol (Foster (R); Chiesi Pharmaceuticals, Parma, Italy). Patients underwent lung function evaluation and thorax high-resolution computerized tomography (HRCT) scan. Local airway resistance was obtained from computational fluid dynamics (CFD). Results: After 6 months, the entire population showed improvement in pre-bronchodilation imaging parameters, including small airway volume (p = 0.0007), resistance (p = 0.011), and asthma control score (p = 0.016). Changes in small airway volume correlated with changes in asthma control score (p = 0.004). Forced expiratory volume in 1 s (p = 0.044) and exhaled nitric oxide (p = 0.040) also improved. Functional imaging provided more detail and clinical relevance compared to lung function tests, especially in the well-controlled group where only functional imaging parameters showed significant improvement, while the correlation with asthma control score remained. Conclusions: Extrafine beclomethasone/formoterol results in a significant reduction of small airway obstruction, detectable by functional imaging (HRCT/CFD). Changes in imaging parameters correlated significantly with clinically relevant improvements. This indicates that functional imaging is a useful tool for sensitive assessment of changes in the respiratory system after asthma treatment. Copyright (C) 2013 S. Karger AG, Basel  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Basel Editor  
  Language Wos 000329046200006 Publication Date 2013-04-12  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1423-0356;0025-7931; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 2.772 Times cited 30 Open Access  
  Notes ; ; Approved Most recent IF: 2.772; 2013 IF: 2.924  
  Call Number UA @ lucian @ c:irua:113762 Serial 2376  
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Author de Backer, J.W.; Vos, W.G.; Burnell, P.; Verhulst, S.L.; Salmon, P.; de Clerck, N.; de Backer, W. doi  openurl
  Title Study of the variability in upper and lower airway morphology in Sprague-Dawley rats using modern micro-CT scan-based segmentation techniques Type A1 Journal article
  Year 2009 Publication The anatomical record: advances in integrative anatomy and evolutionary biology Abbreviated Journal Anat Rec  
  Volume 292 Issue (up) 5 Pages 720-727  
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract Animal models are being used extensively in pre-clinical and safety assessment studies to assess the effectiveness and safety of new chemical entities and delivery systems. Although never entirely replacing the need for animal testing, the use of computer simulations could eventually reduce the amount of animals needed for research purposes and refine the data acquired from the animal studies. Computational fluid dynamics is a powerful tool that makes it possible to simulate flow and particle behavior in animal or patient-specific respiratory models, for purposes of inhaled delivery. This tool requires an accurate representation of the respiratory system, respiration and dose delivery attributes. The aim of this study is to develop a representative airway model of the Sprague-Dawley rat using static and dynamic micro-CT scans. The entire respiratory tract was modeled, from the snout and nares down to the central airways at the point where no distinction could be made between intraluminal air and the surrounding tissue. For the selection of the representative model, variables such as upper airway movement, segmentation length, airway volume and size are taken into account. Dynamic scans of the nostril region were used to illustrate the characteristic morphology of this region in anaesthetized animals. It could be concluded from this study that it was possible to construct a highly detailed representative model of a Sprague-Dawley rat based on imaging modalities such as micro-CT scans  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication New York, N.Y. Editor  
  Language Wos 000265766000010 Publication Date 2009-03-25  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-8486;1932-8494; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 1.431 Times cited 16 Open Access  
  Notes Approved Most recent IF: 1.431; 2009 IF: 1.490  
  Call Number UA @ lucian @ c:irua:76455 Serial 3342  
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Author Klingstedt, M.; Sundberg, M.; Eriksson, L.; Haigh, S.; Kirkland, A.; Grüner, D.; de Backer, A.; Van Aert, S.; Tarasaki, O. pdf  url
doi  openurl
  Title Exit wave reconstruction from focal series of HRTEM images, single crystal XRD and total energy studies on SbxWO3+y (x\sim0.11) Type A1 Journal article
  Year 2012 Publication Zeitschrift für Kristallographie Abbreviated Journal Z Krist-Cryst Mater  
  Volume 227 Issue (up) 6 Pages 341-349  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract A new tungsten bronze in the SbWO system has been prepared in a solid state reaction from Sb2O3, WO3 and W metal powder. The average structure was determined by single crystal X-ray diffraction. SbxWO3+y (x ∼ 0.11) crystallizes in the orthorhombic space group Pm21n (no. 31), a = 27.8135(9) Å, b = 7.3659(2) Å and c = 3.8672(1) Å. The structure belongs to the (n)-ITB class of intergrowth tungsten bronzes. It contains slabs of hexagonal channels formed by six WO6 octahedra. These slabs are separated by three layers of WO6 octahedra that are arranged in a WO3-type fashion. The WO6 octahedra share all vertices to build up a three-dimensional framework. The hexagonal channels are filled with Sb atoms to ∼80% and additional O atoms. The atoms are shifted out of the center of the channels. Exit-wave reconstruction of focal series of high resolution-transmission-electron-microscope (HRTEM) images combined with statistical paramäeter estimation techniques allowed to study local ordering in the channels. Sb atoms in neighbouring channels tend to be displaced in the same direction, which is in agreement with total energy calculations on ordered structure models, but the ratio of the occupation of the two possible Sb sites varies from channel to channel. The structure of SbxWO3+y exhibits pronounced local modulations.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication München Editor  
  Language Wos 000307314200003 Publication Date 2012-06-06  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2194-4946; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.179 Times cited 4 Open Access  
  Notes Fwo; Esteem 026019 Approved Most recent IF: 3.179; 2012 IF: NA  
  Call Number UA @ lucian @ c:irua:101218 Serial 1131  
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Author de Backer, J.W.; Vos, W.G.; Verhulst, S.L.; de Backer, W. doi  openurl
  Title Novel imaging techniques using computer methods for the evaluation of the upper airway in patients with sleep-disordered breathing: a comprehensive review Type A1 Journal article
  Year 2008 Publication Sleep medicine reviews Abbreviated Journal Sleep Med Rev  
  Volume 12 Issue (up) 6 Pages 437-447  
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)  
  Abstract Patients with sleep related breathing disorders (SRBD) can be treated with nasal continuous positive airway pressure (nCPAP) or with several upper airway (UA) interventions. While nCPAP is almost always effective when clinically well tolerated, the therapeutic outcome of UA surgery and UA devices is difficult to predict. The improvement of our capability to perform the latter predictions more accurately is of great clinical importance since it will prevent patients to be treated with ineffective, sometimes irreversible, techniques. In this review we describe the importance of new imaging methods in this respect. We first refer to the most important pathophysiological mechanisms known so far to play a role in SRBD, indicating that functional imaging could elucidate these mechanisms in a patient specific manner. Then we describe the new technologies that make UA imaging more functional referring to the data as they are presently available. Finally we summarise the studies that do indicate that the use of functional imaging of the UA in SRBD patients may significantly help to predict the clinical outcome after UA interventions.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication New York Editor  
  Language Wos 000261904500003 Publication Date 2008-10-16  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1087-0792; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 8.958 Times cited 33 Open Access  
  Notes Approved Most recent IF: 8.958; 2008 IF: 6.143  
  Call Number UA @ lucian @ c:irua:71640 Serial 2378  
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Author Gonnissen, J.; de Backer, A.; den Dekker, A.J.; Martinez, G.T.; Rosenauer, A.; Sijbers, J.; Van Aert, S. pdf  url
doi  openurl
  Title Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images Type A1 Journal article
  Year 2014 Publication Applied physics letters Abbreviated Journal Appl Phys Lett  
  Volume 105 Issue (up) 6 Pages 063116  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage applications, much effort has been made to optimize the STEM technique in order to detect light elements. Therefore, classical performance criteria, such as contrast or signal-to-noise ratio, are often discussed hereby aiming at improvements of the direct visual interpretability. However, when images are interpreted quantitatively, one needs an alternative criterion, which we derive based on statistical detection theory. Using realistic simulations of technologically important materials, we demonstrate the benefits of the proposed method and compare the results with existing approaches.  
  Address  
  Corporate Author Thesis  
  Publisher American Institute of Physics Place of Publication New York, N.Y. Editor  
  Language Wos 000341188700073 Publication Date 2014-08-14  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0003-6951;1077-3118; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.411 Times cited 12 Open Access  
  Notes FWO (G.0393.11; G.0064.10; and G.0374.13); European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement No. 312483 (ESTEEM2); esteem2_jra2 Approved Most recent IF: 3.411; 2014 IF: 3.302  
  Call Number UA @ lucian @ c:irua:118333 Serial 2482  
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Author Van Aert, S.; de Backer, A.; Martinez, G.T.; Goris, B.; Bals, S.; Van Tendeloo, G.; Rosenauer, A. url  doi
openurl 
  Title Procedure to count atoms with trustworthy single-atom sensitivity Type A1 Journal article
  Year 2013 Publication Physical review : B : condensed matter and materials physics Abbreviated Journal Phys Rev B  
  Volume 87 Issue (up) 6 Pages 064107-6  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract We report a method to reliably count the number of atoms from high-angle annular dark field scanning transmission electron microscopy images. A model-based analysis of the experimental images is used to measure scattering cross sections at the atomic level. The high sensitivity of these measurements in combination with a thorough statistical analysis enables us to count atoms with single-atom sensitivity. The validity of the results is confirmed by means of detailed image simulations. We will show that the method can be applied to nanocrystals of arbitrary shape, size, and atom type without the need for a priori knowledge about the atomic structure.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000315144700006 Publication Date 2013-02-20  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1098-0121;1550-235X; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 3.836 Times cited 106 Open Access  
  Notes FWO; 262348 ESMI; 312483 ESTEEM2;246791 COUNTATOMS; Hercules 3; esteem2_jra2 Approved Most recent IF: 3.836; 2013 IF: 3.664  
  Call Number UA @ lucian @ c:irua:105674 Serial 2718  
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Author Van Aert, S.; De Backer, A.; Jones, L.; Martinez, G.T.; Béché, A.; Nellist, P.D. pdf  url
doi  openurl
  Title Control of Knock-On Damage for 3D Atomic Scale Quantification of Nanostructures: Making Every Electron Count in Scanning Transmission Electron Microscopy Type A1 Journal article
  Year 2019 Publication Physical review letters Abbreviated Journal Phys Rev Lett  
  Volume 122 Issue (up) 6 Pages 066101  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract Understanding nanostructures down to the atomic level is the key to optimizing the design of advancedmaterials with revolutionary novel properties. This requires characterization methods capable of quantifying the three-dimensional (3D) atomic structure with the highest possible precision. A successful approach to reach this goal is to count the number of atoms in each atomic column from 2D annular dark field scanning transmission electron microscopy images. To count atoms with single atom sensitivity, a minimum electron dose has been shown to be necessary, while on the other hand beam damage, induced by the high energy electrons, puts a limit on the tolerable dose. An important challenge is therefore to develop experimental strategies to optimize the electron dose by balancing atom-counting fidelity vs the risk of knock-on damage. To achieve this goal, a statistical framework combined with physics-based modeling of the dose-dependent processes is here proposed and experimentally verified. This model enables an investigator to theoretically predict, in advance of an experimental measurement, the optimal electron dose resulting in an unambiguous quantification of nanostructures in their native state with the highest attainable precision.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000458824200008 Publication Date 2019-02-13  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0031-9007 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor 8.462 Times cited 3 Open Access OpenAccess  
  Notes This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (WO.010.16N, G.0934.17N, G.0502.18N, G.0267.18N), and a grant to A. D. B. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement No. 312483— ESTEEM2 (Integrated Infrastructure Initiative-I3) and the UK EPSRC (Grant No. EP/M010708/1). Approved Most recent IF: 8.462  
  Call Number EMAT @ emat @UA @ admin @ c:irua:157175 Serial 5156  
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