|
Dabaghmanesh S (2017) Atomistic modeling of the structural and electronic properties of Cr-based oxides and their potential application as TCO materials. Antwerpen
Keywords: Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
|
|
|
“Controlling the bioreceptor spatial distribution at the nanoscale for single molecule counting in microwell arrays”. Daems D, Rutten I, Bath J, Decrop D, Van Gorp H, Pérez Ruiz E, De Feyter S, Turberfield AJ, Lammertyn J, ACS sensors 4, 2327 (2019). http://doi.org/10.1021/ACSSENSORS.9B00877
Abstract: The ability to detect low concentrations of protein biomarkers is crucial for the early-stage detection of many diseases and therefore indispensable for improving diagnostic devices for healthcare. Here, we demonstrate that by integrating DNA nanotechnologies like DNA origami and aptamers, we can design innovative biosensing concepts for reproducible and sensitive detection of specific targets. DNA origami structures decorated with aptamers were studied as a novel tool to structure the biosensor surface with nanoscale precision in a digital detection bioassay, enabling control of the density, orientation, and accessibility of the bioreceptor to optimize the interaction between target and aptamer. DNA origami was used to control the spatial distribution of an in-house-generated aptamer on superparamagnetic microparticles, resulting in an origami-linked digital aptamer bioassay to detect the main peanut antigen Ara h1 with 2-fold improved signal-to-noise ratio and 15-fold improved limit of detection compared to a digital bioassay without DNA origami. Moreover, the sensitivity achieved was 4 orders of magnitude higher than commercially available and literature-reported enzyme-linked immunosorbent assay techniques. In conclusion, this novel and innovative approach to engineer biosensing interfaces will be of major interest to scientists and clinicians looking for new molecular insights and ultrasensitive detection of a broad range of targets, and, for the next generation of diagnostics.
Keywords: A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1021/ACSSENSORS.9B00877
|
|
|
“Potentiometric detection in UPLC as an easy alternative to determine cocaine in biological samples”. Daems D, van Nuijs ALN, Covaci A, Hamidi-Asl E, Van Camp G, Nagels LJ, Biomedical chromatography 29, 1124 (2015). http://doi.org/10.1002/BMC.3400
Abstract: The analytical methods which are often used for the determination of cocaine in complex biological matrices are a prescreening immunoassay and confirmation by chromatography combined with mass spectrometry. We suggest an ultra-high-pressure liquid chromatography combined with a potentiometric detector, as a fast and practical method to detect and quantify cocaine in biological samples. An adsorption/desorption model was used to investigate the usefulness of the potentiometric detector to determine cocaine in complex matrices. Detection limits of 6.3ngmL(-1) were obtained in plasma and urine, which is below the maximum residue limit (MRL) of 25ngmL(-1). A set of seven plasma samples and 10 urine samples were classified identically by both methods as exceeding the MRL or being inferior to it. The results obtained with the UPLC/potentiometric detection method were compared with the results obtained with the UPLC/MS method for samples spiked with varying cocaine concentrations. The intraclass correlation coefficient was 0.997 for serum (n =7) and 0.977 for urine (n =8). As liquid chromatography is an established technique, and as potentiometry is very simple and cost-effective in terms of equipment, we believe that this method is potentially easy, inexpensive, fast and reliable. Copyright (c) 2014 John Wiley & Sons, Ltd.
Keywords: A1 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Toxicological Centre
DOI: 10.1002/BMC.3400
|
|
|
Daems E (2021) Shaping up oligonucleotides : aptamer-target recognition investigated by native mass spectrometry. 235 p
Abstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
|
|
|
Daems E, Bassini S, Marië,n L, Op de Beeck H, Stratulat A, Zwaenepoel K, Vandamme T, op de Beeck K, Koljenovic S, Peeters M, Van Camp G, De Wael K (2023) Singlet oxygen-based photoelectrochemical detection of single-point mutations in the KRAS oncogene. 115957–7
Abstract: Single nucleotide point mutations in the KRAS oncogene occur frequently in human cancers, rendering them intriguing targets for diagnosis, early detection and personalized treatment. Current detection methods are based on polymerase chain reaction, sometimes combined with next-generation sequencing, which can be expensive, complex and have limited availability. Here, we propose a novel singlet oxygen (1O2)-based photoelectrochemical detection methodology for single-point mutations, using KRAS mutations as a case study. This detection method combines the use of a sandwich assay, magnetic beads and robust chemical photosensitizers, that need only air and light to produce 1O2, to ensure high specificity and sensitivity. We demonstrate that hybridization of the sandwich hybrid at high temperatures enables discrimination between mutated and wild-type sequences with a detection rate of up to 93.9%. Additionally, the presence of background DNA sequences derived from human cell-line DNA, not containing the mutation of interest, did not result in a signal, highlighting the specificity of the methodology. A limit of detection as low as 112 pM (1.25 ng/mL) was achieved without employing any amplification techniques. The developed 1O2-based photoelectrochemical methodology exhibits unique features, including rapidity, ease of use, and affordability, highlighting its immense potential in the field of nucleic acid-based diagnostics.
Keywords: University Hospital Antwerp; A1 Journal article; Center for Oncological Research (CORE); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab); Medical Genetics (MEDGEN)
Impact Factor: 12.6
DOI: 10.1016/J.BIOS.2023.115957
|
|
|
“Aptamer-ligand recognition studied by native ion mobility-mass spectrometry”. Daems E, Dewaele D, Barylyuk K, De Wael K, Sobott F, Talanta 224, 121917 (2021). http://doi.org/10.1016/J.TALANTA.2020.121917
Abstract: The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 4.162
DOI: 10.1016/J.TALANTA.2020.121917
|
|
|
“Native mass spectrometry for the design and selection of protein bioreceptors for perfluorinated compounds”. Daems E, Moro G, Berghmans H, Moretto LM, Dewilde S, Angelini A, Sobott F, De Wael K, Analyst 146, 2065 (2021). http://doi.org/10.1039/D0AN02005B
Abstract: Biosensing platforms are answering the increasing demand for analytical tools for environmental monitoring of small molecules, such as per- and polyfluoroalkyl substances (PFAS). By transferring toxicological findings in bioreceptor design we can develop innovative pathways for biosensor design. Indeed, toxicological studies provide fundamental information about PFAS-biomolecule complexes that can help evaluate the applicability of the latter as bioreceptors. The toolbox of native mass spectrometry (MS) can support this evaluation, as shown by the two case studies reported in this work. The analysis of model proteins’ (i.e. albumin, haemoglobin, cytochrome c and neuroglobin) interactions with well-known PFAS, such as perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), demonstrated the potential of this native MS screening approach. In the first case study, untreated albumin and delipidated albumin were compared in the presence and absence of PFOA confirming that the delipidation step increases albumin affinity for PFOA without affecting protein stability. In the second case study, the applicability of our methodology to identify potential bioreceptors for PFOS/PFOA was extended to other proteins. Structurally related haemoglobin and neuroglobin revealed a 1 : 1 complex, whereas no binding was observed for cytochrome c. These studies have value as a proof-of-concept for a general application of native MS to identify bioreceptors for toxic compounds.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 3.885
DOI: 10.1039/D0AN02005B
|
|
|
“Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions”. Daems E, Moro G, Campos R, De Wael K, Trac-Trends In Analytical Chemistry 142, 116311 (2021). http://doi.org/10.1016/J.TRAC.2021.116311
Abstract: Aptamers are promising biorecognition elements with a wide applicability from therapeutics to bio-sensing. However, to successfully use these biomolecules, a complete characterisation of their bindingperformance in the presence of the target is crucial. Several multi-analytical approaches have been re-ported including techniques to describe kinetic and thermodynamic aspects of the aptamer-targetinteraction, and techniques which allow an in-depth understanding of the aptamer-target structures.Recent literature shows the need of a critical data interpretation, a combination of characterisationtechniques and suggests the key role of the characterisation protocol design. Indeed, thefinal applicationof the aptamer should be considered before choosing the characterisation method. All the limitations andcapabilities of the analytical tools in use for aptamer characterisation should be taken into account. Here,we present a critical overview of the current methods and multi-analytical approaches to study aptamer-target binding, aiming to provide researchers with guidelines for the design of characterisation protocols.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Impact Factor: 8.442
DOI: 10.1016/J.TRAC.2021.116311
|
|
|
“Radiation dose estimation and mass attenuation coefficients of cement samples used in Turkey”. Damla N, Čevik U, Kobya AI, Celik A, Celik N, Van Grieken R, Journal of hazardous materials 176, 644 (2010). http://doi.org/10.1016/J.JHAZMAT.2009.11.080
Abstract: Different cement samples commonly used in building construction in Turkey have been analyzed for natural radioactivity using gamma-ray spectrometry. The mean activity concentrations observed in the cement samples were 52, 40 and 324 Bq kg−1 for 226Ra, 232Th and 40K, respectively. The measured activity concentrations for these radionuclides were compared with the reported data of other countries and world average limits. The radiological hazard parameters such as radium equivalent activities (Raeq), gamma index (Iγ) and alpha index (Iα) indices as well as terrestrial absorbed dose and annual effective dose rate were calculated and compared with the international data. The Raeq values of cement are lower than the limit of 370 Bq kg−1, equivalent to a gamma dose of 1.5 mSv y−1. Moreover, the mass attenuation coefficients were determined experimentally and calculated theoretically using XCOM in some cement samples. Also, chemical compositions analyses of the cement samples were investigated.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/J.JHAZMAT.2009.11.080
|
|
|
“Characterization of gas concrete materials used in buildings of Turkey”. Damla N, Čevik U, Kobya AI, Celik A, Van Grieken R, Kobya Y, Journal of hazardous materials 168, 681 (2009). http://doi.org/10.1016/J.JHAZMAT.2009.02.092
Abstract: The activity concentration of 226Ra, 232Th and 40K in gas concrete samples collected from different suppliers and some provinces in Turkey were measured using gamma-ray spectrometry. Knowledge of radioactivity in gas concrete used in building materials enables one to assess any possible radiological risks to human health. The mean activity concentrations observed in the gas concrete samples were 82.0, 28.2 and 383.9 Bq kg−1 for 226Ra, 232Th and 40K, respectively. The radium equivalent activity, external and internal hazard indices as well as terrestrial absorbed dose and annual effective dose rate was calculated. The results indicate that the radium equivalent activity values of gas concrete samples are lower than the limit of 370 Bq kg−1, equivalent to a gamma-dose of 1.5 mSv y−1. Moreover, mass attenuation coefficients were measured in some gas concrete samples. It was found that the mass attenuation coefficients decreased with increasing photon energies. Also, chemical compositions and structural analysis (XRD and SEM) of the gas concrete samples were investigated.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/J.JHAZMAT.2009.02.092
|
|
|
“Precise gamma ray measurement of the radial distribution of a cracking catalyst at diluted concentrations in a glass riser”. Dantas CC, Dos Santos VA, Melo ACBA, Van Grieken R, Nuclear instruments and methods in physics research: B: beam interactions with materials and atoms 251, 201 (2006). http://doi.org/10.1016/J.NIMB.2006.05.009
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/J.NIMB.2006.05.009
|
|
|
“Composition of prehistoric rock-painting pigments from Egypt (Gilf Kébir area)”. Darchuk L, Gatto Rotondo G, Swaenen M, Worobiec A, Tsybrii Z, Makarovska Y, Van Grieken R, Spectrochimica acta: part A: molecular and biomolecular spectroscopy 83, 34 (2011). http://doi.org/10.1016/J.SAA.2011.06.054
Abstract: The composition of rock-painting pigments from Egypt (Gilf Kebia area) has been analyzed by means of molecular spectroscopy such as Fourier transform infrared and micro-Raman spectroscopy and scanning electron microscopy coupled to an energy dispersive X-ray spectrometer and X-ray fluorescence analysis. Red and yellow pigments were recognized as red and yellow ochre with additional rutile.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1016/J.SAA.2011.06.054
|
|
|
“Composition of pigments on human bones found in excavations in Argentina studied with micro-Raman spectrometry and scanning electron microscopy”. Darchuk L, Stefaniak EA, Vázquez C, Palacios OM, Worobiec A, Van Grieken R, e-Preservation Science 6, 112 (2009)
Abstract: Results on analysis of prehistoric pigments from excavations and pigments on coloured child bones from North Patagonia, Argentina, are reported. To analyze their composition we used two micro-analytical techniques: micro- Raman spectrometry (MRS) and scanning electron microscopy coupled with X-ray micro-analysis (SEM/EDX). Most investigated excavated pigments show red or yellow ochres consistent with reddish or yellow minerals, such as á- and ã-goethite, haematite, erdite, haapalaite and jarosite. Raman spectra show also evidence of calcium oxalate monohydrate and calcite indicating lichen activity. Pigments covering human bones were identified as hematite and magnetite. This study allows us to infer that pigments found in excavation were employed for burial ceremonies, even though distances between excavated pigment archaeological site and buried remains are quite far, more than 50 km in a straight line.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
|
|
|
“Argentinean prehistoric pigments' study by combined SEM/EDX and molecular spectroscopy”. Darchuk L, Tsybrii Z, Worobiec A, Vázquez C, Palacios OM, Stefaniak EA, Gatto Rotondo G, Sizov F, Van Grieken R, Spectrochimica acta: part A: molecular and biomolecular spectroscopy 75, 1398 (2010). http://doi.org/10.1016/J.SAA.2010.01.006
Abstract: Composition of the prehistoric pigments (from Carriqueo rock shelter, Rio Negro province, Argentina) has been analysed by means of molecular spectroscopy (Fourier transform infrared (FTIR) and micro-Raman) and scanning electron microscopy (SEM) coupled to an energy-dispersive X-ray spectrometer (EDS). Red and yellow pigments were recognized as red and yellow ochre. The matrix of the pigments is composed of one or more substances. According to the matrix composition yellow and red pigments were also divided into two groupsi.e. those containing kaolinite or sulphates. Green pigment was detected as green earth, made up of celadonite as a chromophore.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1016/J.SAA.2010.01.006
|
|
|
“Composition of aerosols from the shelter of the Chernobyl power plant”. Darchuk L, Worobiec A, Khan V, Krasnov V, Van Grieken R, AIP conference proceedings 1267, 512 (2010). http://doi.org/10.1063/1.3482646
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1063/1.3482646
|
|
|
“Infrared investigation of hard human teeth tissues exposed to various doses of ionizing radiation from the 1986 Chernobyl accident”. Darchuk LA, Zaverbna LV, Bebeshko VG, Worobiec A, Stefaniak EA, Van Grieken R, Spectroscopy 22, 105 (2008). http://doi.org/10.1155/2008/843612
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1155/2008/843612
|
|
|
“Molecular spectroscopy study of human tooth tissues affected by high dose of external ionizing radiation (caused by the nuclear catastrophe of the Chernobyl plant)”. Darchuk LA, Zaverbna LV, Worobiec A, Van Grieken R page 349 (2012).
Keywords: H1 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
|
|
|
“Structural features of human tooth tissues affected by high dose of external ionizing radiation after nuclear catastrophe of Chernobyl plant”. Darchuk LA, Zaverbna LV, Worobiec A, Van Grieken R, Microchemical journal 97, 282 (2011). http://doi.org/10.1016/J.MICROC.2010.09.016
Abstract: The application of micro-Raman spectroscopy is discussed for the analysis of structural features of human tooth tissues affected by high doses of external ionizing radiation (0.51.7 Gy) after the nuclear plant catastrophe in Chernobyl in 1986. The results have shown significant changes in the mineral matrix of dental enamel that lead to the decrease of tooth enamel hardness. Destruction of the collagen chain of the organic matrix has been observed for dentin and cementum.
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1016/J.MICROC.2010.09.016
|
|
|
“The elemental chemistry of sediments in the Nainital lake, Kumaun Himalaya, India”. Das BK, Singh M, Van Grieken R, The science of the total environment 168, 85 (1995). http://doi.org/10.1016/0048-9697(95)04242-S
Keywords: A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/0048-9697(95)04242-S
|
|
|
“Combined effects of blockage and yield stress on drag and heat transfer from an in-line array of three spheres”. Dasgupta N, Borah R, Mishra P, Gupta AK, Chhabra RP, Journal of dispersion science and technology 40, 855 (2019). http://doi.org/10.1080/01932691.2018.1485581
Abstract: This work reports results on the drag and heat transfer from an in-line array of three isothermal spheres falling in a cylindrical confinement filled with Bingham plastic fluids. The effects of dimensionless parameters, such as the Reynolds number (1 ≤ Re ≤ 100), Prandtl number (1 ≤ Pr ≤ 100), Bingham number (0 ≤ Bn ≤ 100), blockage ratio (2 ≤ β ≤ 4) and sphere-to-sphere distance (1.5 ≤ t ≤ 6) have been elucidated. The flow and heat transfer characteristics were analysed in terms of yielded/unyielded regions, streamline and isotherm contours, drag coefficient, pressure coefficient, and local and average Nusselt number. Broadly, the drag coefficient shows a positive dependence on Bn and sphere-to-sphere distance (t) while it exhibits an inverse dependence on Re and β. On the other hand, the Nusselt number shows a positive dependence on Re, Pr, Bn and β; and a complex dependence on t for each sphere. Simple predictive expressions for the average Nusselt number for each sphere are formulated, thereby enabling its prediction in a new application.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1080/01932691.2018.1485581
|
|
|
“Parabolic trigonometry”. Dattoli G, Di Palma E, Gielis J, Licciardi S, International journal of applied and computational mathematics 6, 37 (2020). http://doi.org/10.1007/S40819-020-0789-6
Keywords: A1 Journal article; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1007/S40819-020-0789-6
|
|
|
de Aquino BRCHT (2018) Carbon nanotubes and graphene based devices : from nanosensors to confined water. Antwerpen
Keywords: Doctoral thesis; Condensed Matter Theory (CMT)
|
|
|
de Aquino BRCHT (2018) Carbon nanotubes and graphene based devices : from nanosensors to confined water. 161 p
Keywords: Doctoral thesis; Condensed Matter Theory (CMT)
|
|
|
de Backer A (2015) Quantitative atomic resolution electron microscopy using advanced statistical techniques. Antwerpen
Keywords: Doctoral thesis; Electron microscopy for materials research (EMAT)
|
|
|
“Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting : what are the limits?”.de Backer A, De wael A, Gonnissen J, Martinez GT, Béché, A, MacArthur KE, Jones L, Nellist PD, Van Aert S, Journal of physics : conference series 644, 012034 (2015). http://doi.org/10.1088/1742-6596/644/012034
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 atomcounting diagnosed by combining a thorough statistical method and detailed image simulations.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
DOI: 10.1088/1742-6596/644/012034
|
|
|
De Backer J (2023) The versatile nature of cytoglobin, the Swiss army knife among globins, with a preference for oxidative stress. XVIII, 232 p
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.
Keywords: Doctoral thesis; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES)
|
|
|
“Functional imaging to predict treatment success of mandibular advancement devices in sleep-disordered breathing”. de Backer J, Vanderveken O, Vos W, Devolder A, Verhulst S, Verbraecken J Antwerpen, page 141 (2008).
Keywords: H3 Book chapter; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
|
|
|
“Benchmark study on algae harvesting with backwashable submerged flat panel membranes”. de Baerdemaeker T, Lemmens B, Dotremont C, Fret J, Roef L, Goiris K, Diels L, Bioresource technology 129, 582 (2013). http://doi.org/10.1016/J.BIORTECH.2012.10.153
Abstract: The feasibility of algae harvesting with submerged flat panel membranes was investigated as pre-concentration step prior to centrifugation. Polishing of the supernatant coming from the centrifuge was evaluated as well. The effect of membrane polymer (polyvinyl chloride [PVC], polyethersulfone polyvinyl-pyrollidone [PES-PVP], poly vinylidene fluoride [PVDF]), pore size (microfiltration [MF], ultrafiltration [UF]), algae cell concentrations and species were investigated at lab-scale. In addition, backwashing as fouling control was compared to standard relaxation. PVDF was the superior polymer, and UF showed better fouling resistance. Backwashing outperformed relaxation in fouling control. The backwashable membranes allowed up to 300% higher fluxes compared to commercial flat panel benchmark (PVC) membranes. Estimations on energy consumption for membrane filtration followed by centrifugation revealed relatively low values of 0.169 kW h/kg of dry weight of algae compared to 0.5 kW h/kg for algae harvesting via classical centrifuge alone. (C) 2012 Elsevier Ltd. All rights reserved.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.1016/J.BIORTECH.2012.10.153
|
|
|
“In situ study of the parameters quantifying the corrosion in ballast tanks and an evaluation of improving alternative”. de Baere K, Verstraelen H, Lemmens L, Lenaerts S, Potters G, (2011)
Abstract: An in situ study of more than 100 ballast tanks of merchant marine vessels looks to the corrosion process in these tanks from another perspective. The developed corrosion model shows major similarities with earlier studies based on laboratory experiments. The field work exposes the influence of ship construction parameters such as land of construction, coating type and the presence of sacrificial anodes on the corrosion process in the ballast tanks. Possible alternatives for vessels constructed with ordinary grade A steel and coated according to IMO PSPC standards are presented, even though further research is required to come to final conclusions.
Keywords: P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
|
|
|
“Noise barriers as a road traffic noise intervention in an urban environment”. de Barros AG, Hasheminejad N, Kampen JK, Vanlanduit S, Vuye C, , 1 (2021)
Abstract: Intending to tackle road traffic noise in urban environments, noise barriers have been proven to effectively reduce environmental noise levels, leading to positive effects on noise perception by the exposed population. This work assesses the impacts of replacing an obsolete noise barrier in a site near a highway. The effects of this change were monitored via a combination of field surveys, acoustic measurements and noise maps. The results have shown that even though the barrier replacement led to a 4.1 dB reduction in the LA,eq,(15 min.), the annoyance levels of the respondents increased. Possibly, the expectations regarding the improvement of the noise barrier were not met, after a history of complaints. Additionally, existing exposure-response relationships were not successful in predicting the annoyance levels in this particular case. In this dataset, noise annoyance presented a weak link with reported health problems, while a strong correlation was found with the comfort level to perform activities outdoors. Questions regarding the COVID-19 pandemic showed that even though the respondents were spending more time at home, they were less annoyed due to road traffic noise in the period when circulation restrictions were in place.
Keywords: P1 Proceeding; Engineering sciences. Technology; Engineering Management (ENM); Condensed Matter Theory (CMT); Energy and Materials in Infrastructure and Buildings (EMIB); Social Epidemiology & Health Policy (SEHPO)
|
|