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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
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Debie Y, van Audenaerde JRM, Vandamme T, Croes L, Teuwen L-A, Verbruggen L, Vanhoutte G, Marcq E, Verheggen L, Le Blon D, Peeters B, Goossens M, Pannus P, Arië,n KK, Anguille S, Janssens A, Prenen H, Smits ELJ, Vulsteke C, Lion E, Peeters M, Van Dam PA (2023) Humoral and cellular immune responses against SARS-CoV-2 after third dose BNT162b2 following double-dose vaccination with BNT162b2 versus ChAdOx1 in patients with cancer. 635–646
Abstract: Purpose: Patients with cancer display reduced humoral responses after double-dose COVID-19 vaccination, whereas their cellular response is more comparable with that in healthy individuals. Recent studies demonstrated that a third vaccination dose boosts these immune responses, both in healthy people and patients with cancer. Because of the availability of many different COVID-19 vaccines, many people have been boosted with a different vaccine fromthe one used for double-dose vaccination. Data on such alternative vaccination schedules are scarce. This prospective study compares a third dose of BNT162b2 after double-dose BNT162b2 (homologous) versus ChAdOx1 (heterologous) vaccination in patients with cancer. Experimental Design: A total of 442 subjects (315 patients and 127 healthy) received a third dose of BNT162b2 (230 homologous vs. 212 heterologous). Vaccine-induced adverse events (AE) were captured up to 7 days after vaccination. Humoral immunity was assessed by SARS-CoV-2 anti-S1 IgG antibody levels and SARSCoV- 2 50% neutralization titers (NT50) against Wuhan and BA.1 Omicron strains. Cellular immunity was examined by analyzing CD4þ and CD8þ T-cell responses against SARS-CoV-2–specific S1 and S2 peptides. Results: Local AEs were more common after heterologous boosting. SARS-CoV-2 anti-S1 IgG antibody levels did not differ significantly between homologous and heterologous boosted subjects [GMT 1,755.90 BAU/mL (95% CI, 1,276.95–2,414.48) vs. 1,495.82 BAU/mL (95% CI, 1,131.48–1,977.46)]. However, homologous- boosted subjects show significantly higher NT50 values against BA.1 Omicron. Subjects receiving heterologous boosting demonstrated increased spike-specific CD8þ T cells, including higher IFNg and TNFa levels. Conclusions: In patients with cancer who received double-dose ChAdOx1, a third heterologous dose of BNT162b2 was able to close the gap in antibody response.
Keywords: University Hospital Antwerp; A1 Journal article; Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
Impact Factor: 11.5
DOI: 10.1158/1078-0432.CCR-22-2185
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Gielis J (2023) Fred Van Oystaeyen : Time hybrids: a new generic theory of reality. 347–351
Keywords: Review; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.26830/SYMMETRY_2023_3_357
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“Noise-resistant correlation-based alignment of head-related transfer functions for high-fidelity spherical harmonics representation”. Reijniers J, Partoens B, Peremans H, (2023)
Abstract: It is standard practice in virtual reality applications to synthesize binaural audio based on a discrete set of directionally-dependent head-related impulse responses (HRIRs). This set of HRIRs is often time-aligned in a pre-processing step, to allow for high-fidelity interpolation between HRIRs corresponding with neighbouring directions. The fidelity of this operation depends on the similarity of neighbouring aligned HRIRs. The pairwise quality of similarity makes it a difficult criterion to optimize globally and consequently one often resorts to alignment methods based on a specific feature that can be extracted for each HRIR separately, e.g., the first-onset of the peak or the group delay. However, such proxies for similarity are very sensitive to noise and therefore require a high signal-to-noise ratio, which makes them less suitable for processing HRIRs acquired outside an anechoic room. In this paper, we advance a novel alignment method, which maximizes the similarity – defined as the correlation between the full-length HRIRs – between neighbouring aligned HRIRs for all directions at once. We show that this correlation-based alignment procedure outperforms the first-onset alignment with regards to the fidelity of the spherical harmonics representation of both the spectral and interaural time difference (ITD) information, when tested on the KEMAR HRIR and six human HRIRs. Finally, we show that the correlation-based alignment is more robust to noise.
Keywords: P3 Proceeding; Engineering sciences. Technology; Engineering Management (ENM); Condensed Matter Theory (CMT)
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“Ultrascaled graphene-capped interconnects : a quantum mechanical study”. Reyntjens P, Van de Put M, Vandenberghe WG, Sorée B, Proceedings of the IEEE ... International Interconnect Technology Conference
T2 –, IEEE International Interconnect Technology Conference (IITC) / IEEE, Materials for Advanced Metallization Conference (MAM), MAY 22-25, 2023, Dresden, Germany , 1 (2023). http://doi.org/10.1109/IITC/MAM57687.2023.10154656
Abstract: In this theoretical study, we assess the impact of a graphene capping layer on the resistivity of defective, extremely scaled interconnects. We investigate the effect of graphene capping on the electronic transport in ultrascaled interconnects, in the presence of grain boundary defects in the metal layer. We compare the results obtained using our quantum mechanical model to a simple parallel-conductor model and find that the parallel-conductor model does not capture the effect of the graphene cap correctly. At 0.5 nm metal thickness, the parallel-conductor model underestimates the conductivity by 3.0% to 4.0% for single-sided and double sided graphene capping, respectively.
Keywords: P1 Proceeding; Condensed Matter Theory (CMT)
DOI: 10.1109/IITC/MAM57687.2023.10154656
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“Advanced particle swarm optimization methods for electromagnetics”. Mescia L, Bia P, Gielis J, Caratelli D, , 109 (2023). http://doi.org/10.55060/s.atmps.231115.010
Abstract: Electromagnetic design problems involve optimizing multiple parameters that are nonlinearly related to objective functions. Traditional optimization techniques require significant computational resources that grow exponentially as the problem size increases. Therefore, a method that can produce good results with moderate memory and computational resources is desirable. Bioinspired optimization methods, such as particle swarm optimization (PSO), are known for their computational efficiency and are commonly used in various scientific and technological fields. In this article we explore the potential of advanced PSO-based algorithms to tackle challenging electromagnetic design and analysis problems faced in real-life applications. It provides a detailed comparison between conventional PSO and its quantum-inspired version regarding accuracy and computational costs. Additionally, theoretical insights on convergence issues and sensitivity analysis on parameters influencing the stochastic process are reported. The utilization of a novel quantum PSO-based algorithm in advanced scenarios, such as reconfigurable and shaped lens antenna synthesis, is illustrated. The hybrid modeling approach, based on the unified geometrical description enabled by the Gielis Transformation, is applied in combination with a suitable quantum PSO-based algorithm, along with a geometrical tube tracing and physical optics technique for solving the inverse problem aimed at identifying the geometrical parameters that yield optimal antenna performance.
Keywords: P1 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.55060/s.atmps.231115.010
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“Conquering Mount Improbable”. Gielis J, , 153 (2023). http://doi.org/10.55060/s.atmps.231115.013
Abstract: Our scientific and technological worldviews are largely dominated by the concepts of entropy and complexity. Originating in 19th-century thermodynamics, the concept of entropy merged with information in the last century, leading to definitions of entropy and complexity by Kolmogorov, Shannon and others. In its simplest form, this worldview is an application of the normal rules of arithmetic. In this worldview, when tossing a coin, a million heads or tails in a row is theoretically possible, but impossible in practice and in real life. On this basis, the impossible (in the binary case, the outermost entries of Pascal's triangle xn and yn for large values of n) can be safely neglected, and one can concentrate fully on what is common and what conforms to the law of large numbers, in fields ranging from physics to sociology and everything in between. However, in recent decades it has been shown that what is most improbable tends to be the rule in nature. Indeed, if one combines the outermost entries xn and yn with the normal rules of arithmetic, either addition or multiplication, one obtains Lamé curves and power laws respectively. In this article, some of these correspondences are highlighted, leading to a double conclusion. First, Gabriel Lamé's geometric footprint in mathematics and the sciences is enormous. Second, conic sections are at the core once more. Whereas mathematics so far has been exclusively the language of patterns in the sciences, the door is opened for mathematics to also become the language of the individual. The probabilistic worldview and Lamé's footprint can be seen as dual methods. In this context, it is to be expected that the notions of information, complexity, simplicity and redundancy benefit from this different viewpoint.
Keywords: P1 Proceeding; Economics; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.55060/s.atmps.231115.013
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“An extensive multisensor hyperspectral benchmark datasets of intimate mixtures of mineral powders”. Koirala B, Rasti B, Bnoulkacem Z, De Lima Ribeiro A, Madriz Y, Herrmann E, Gestels A, De Kerf T, Janssens K, Steenackers G, Gloaguen R, Scheunders P, IEEE International Geoscience and Remote Sensing Symposium proceedings
T2 –, IGARSS 2023 –, 2023 IEEE International Geoscience and Remote Sensing Symposium, 16-21 July 2023, Pasadena, CA, USA , 5890 (2023). http://doi.org/10.1109/IGARSS52108.2023.10281467
Abstract: Since many materials behave as heterogeneous intimate mixtures with which each photon interacts differently, the relationship between spectral reflectance and material composition is very complex. Quantitative validation of spectral unmixing algorithms requires high-quality ground truth fractional abundance data, which are very difficult to obtain.In this work, we generated a comprehensive hyperspectral dataset of intimate mineral powder mixtures by homogeneously mixing five different clay powders (Kaolin, Roof clay, Red clay, mixed clay, and Calcium hydroxide). In total 325 samples were prepared. Among the 325 samples, 60 mixtures were binary, 150 were ternary, 100 were quaternary, and 15 were quinary. For each mixture (and pure clay powder), reflectance spectra are acquired by 13 different sensors, with a broad wavelength range between the visible and the long-wavelength infrared regions (i.e., between 350 nm and 15385 nm) and with a large variation in sensor types, platforms, and acquisition conditions. We will make this dataset public, to be used by the community for the validation of nonlinear unmixing methodologies (https://github.com/VisionlabUA/Multisensor_datasets)
Keywords: P1 Proceeding; Economics; Vision lab; Antwerp X-ray Imaging and Spectroscopy (AXIS)
DOI: 10.1109/IGARSS52108.2023.10281467
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“A note on Generalized Möbius-Listing Bodies”. Gielis J, Tavkhelidze I, , 31 (2023). http://doi.org/10.55060/s.atmps.231115.003
Abstract: Generalized Möbius-Listing surfaces and bodies generalize Möbius bands, and this research was motivated originally by solutions of boundary value problems. Analogous to cutting of the original Möbius band, for this class of surfaces and bodies, results have been obtained when cutting such bodies or surfaces. In general, cutting leads to interlinked and intertwined different surfaces or bodies, resulting in very complex systems. However, under certain conditions, the result of cutting can be a single surface or body, which reduces complexity considerably. These conditions are based on congruence and rotational symmetry of the resulting cross sections after cutting, and on the knife cutting the origin
Keywords: P1 Proceeding; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.55060/s.atmps.231115.003
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“Quantum transport study of contact resistance of edge- and top-contacted two-dimensional materials”. Deylgat E, Chen E, Sorée B, Vandenberghe WG, International Conference on Simulation of Semiconductor Processes and Devices : [proceedings]
T2 –, International Conference on Simulation of Semiconductor Processes and, Devices (SISPAD), SEP 27-29, 2023, Kobe, Japan , 45 (2023). http://doi.org/10.23919/SISPAD57422.2023.10319537
Abstract: We calculate the contact resistance for an edge- and top-contacted 2D semiconductor. The contact region consists of a metal contacting a monolayer of MoS2 which is otherwise surrounded by SiO2. We use the quantum transmitting boundary method to compute the contact resistance as a function of the 2D semiconductor doping concentration. An effective mass Hamiltonian is used to describe the properties of the various materials. The electrostatic potentials are obtained by solving the Poisson equation numerically. We incorporate the effects of the image-force barrier lowering on the Schottky barrier and examine the impact on the contact resistance. At low doping concentrations, the contact resistance of the top contact is lower compared to edge contact, while at high doping concentrations, the edge contact exhibits lower resistance.
Keywords: P1 Proceeding; Condensed Matter Theory (CMT)
DOI: 10.23919/SISPAD57422.2023.10319537
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Verbruggen S, Van Acker M, Furlan C, Mercelis S, Durt A (2023) ATLANTES : the mATeriaL spAtial dimeNsion of wasTE flowS: visualising waste streams in the Province of Antwerp
Keywords: Minutes and reports; Economics; Engineering sciences. Technology; Internet Data Lab (IDLab); Research Group for Urban Development; Henry van de Velde
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“Leaf functional traits : ecological and evolutionary implications”. Shi P, Gielis J, Niklas KJ, Niinemets Ü, Schrader J page 185 p. (2023).
Keywords: ME3 Book as editor; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.3389/978-2-83252-086-4
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“Plant morphology and function, geometric morphometrics, and modelling : decoding the mathematical secrets of plants”. Gao J, Huang W, Gielis J, Shi P page 224 p. (2023).
Abstract: Delve into the diverse aspects of plant morphology, their responses to global climate change, and the spatiotemporal dynamics of forest productivity. Join us on a journey through the intricate web of plant characteristics and their impact on the environment.
Keywords: ME3 Book as editor; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.3390/BOOKS978-3-0365-9423-1
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“Proceedings of the 1st International Symposium on Square Bamboos and the Geometree (ISSBG 2022)”. Gielis J, Brasili S page xi, 175 p. (2023).
Keywords: ME3 Book as editor; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.55060/s.atmps.231115.000
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Labey E, Fonteyn F, Wilmot A, El Amouri S, Gjurova A, De Cock W, De Wael F (2023) Shaping utopia through law: how the law does (not) provide an answer to societal challenges. 210 p
Keywords: ME2 Book as editor or co-editor; Law; Government and Law
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“Ruimte en gezondheidsongelijkheid aanpakken : een kwestie van sociale rechtvaardigheid”. Vervoort P, Grymonprez H, Bouckaert N, Derijcke D, De Wael W (2023).
Abstract: De bijdrage gaat dieper in op de relatie tussen ruimte en gezondheidsongelijkheid, bespreekt gezondheidsongelijkheid vanuit een rechtenperspectief en illustreert een aantal praktijken waarin de aandacht voor ruimte en gezondheidsongelijkheid samenkomen.
Keywords: H2 Book chapter; Sociology; Law; Centre for Research on Environmental and Social Change
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“Foodborne outbreaks : sources and mode of transmission of foodborne pathogenic microorganisms”. Kollarahithlu SC, Sathiyamoorthy S, Thiruvottriyur Shanmugam S, De Wael K, Das J, Veluswamy P page 93 (2023).
Abstract: The foodborne pathogens and microorganisms have played a prevalent role in the ebb and flow of the economy worldwide. The increasing population has strained the food processing industry to produce food in large quantity, which in turn has affected the quality of food. To curb this issue, there is immense pressure to produce and maintain quality food within a short time frame. Hence, high throughput technology is used to determine and timely assess the safety and hygiene of food. Further, the revolution of the food industry has also seen an upsurge of new pathogens and microorganisms, thereby increasing the risk of exposure towards rarest diseases to a larger population. This chapter sheds light on the different types of foodborne pathogens affecting the food industry and its social impact. It further emphasizes the safety measures to be taken on the prevention of the disease from the farm to the processing industries and in turn to the household.
Keywords: H1 Book chapter; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
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“Editorial: leaf functional traits : ecological and evolutionary implications”. Niklas KJ, Shi P, Gielis J, Schrader J, Niinemets U, Frontiers in plant science 14, 1169558 (2023). http://doi.org/10.3389/FPLS.2023.1169558
Keywords: Editorial; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 5.6
DOI: 10.3389/FPLS.2023.1169558
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“Editorial hydrogen production storage and use”. Perreault P, Preuster P, Current opinion in green and sustainable chemistry 44, 100861 (2023). http://doi.org/10.1016/J.COGSC.2023.100861
Abstract: In the pursuit of clean and sustainable energy sources, hydrogen has emerged as a key contender, offering high energy density and the potential to serve as a carbon-neutral fuel. However, one of the major challenges associated with hydrogen is efficient and safe storage and transportation. In this Special Edition, we delve into the exciting developments in the upcoming hydrogen economy, from its sustainable production to chemical hydrogen storage. Some of our reviews focus on particular technologies namely on liquid organic hydrogen carriers (LOHCs) and the utilization of ammonia as a hydrogen carrier.
Keywords: Editorial; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 9.3
DOI: 10.1016/J.COGSC.2023.100861
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“Editorial overview : photocatalysis 2022 shining light on a diversity of research opportunities”. Verbruggen SW, Mul G, Current opinion in green and sustainable chemistry 42, 100838 (2023). http://doi.org/10.1016/J.COGSC.2023.100838
Keywords: Editorial; Engineering sciences. Technology
Impact Factor: 9.3
DOI: 10.1016/J.COGSC.2023.100838
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“EXRS2022 : the 2022 edition of the European X-ray Spectrometry conference, held in Bruges, Belgium”. Janssens K, X-ray spectrometry 52, 276 (2023). http://doi.org/10.1002/XRS.3386
Keywords: Editorial; Antwerp X-ray Imaging and Spectroscopy (AXIS)
Impact Factor: 1.2
DOI: 10.1002/XRS.3386
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“International Conference on “Strongly Coupled Coulomb Systems&rdquo, (July 24-29, 2022, Görlitz, Germany)”. Cangi A, Moldabekov ZA, Neilson D, Contributions to plasma physics 63, e202300110 (2023). http://doi.org/10.1002/CTPP.202300110
Keywords: Editorial; Condensed Matter Theory (CMT)
Impact Factor: 1.6
DOI: 10.1002/CTPP.202300110
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“Plant morphology and function, geometric morphometrics, and modelling : decoding the mathematical secrets of plants”. Gao J, Huang W, Gielis J, Shi P, Plants 12, 3724 (2023). http://doi.org/10.3390/PLANTS12213724
Keywords: Editorial; Sustainable Energy, Air and Water Technology (DuEL)
DOI: 10.3390/PLANTS12213724
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“Simple systems, complicated physics : an interview with Nir Navon”. Jorissen B, Fernandes L, Belgian journal of physics 1, 4 (2023)
Abstract: The EPS Antwerp Young Minds (AYM) invited Prof. Nir Navon (Yale University) to hold a colloquium for the physics department. For an audience of students and researchers, Prof. Navon presented recent advances in ultracold quantum matter and research from his own lab. His experimental work paves the way to make toy models used by theorists a reality. We sat down afterwards to discuss ultracold physics, box traps and setting up a lab from scratch.
Keywords: Editorial; Theory of quantum systems and complex systems; Condensed Matter Theory (CMT)
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Van Alphen S (2023) Modelling plasma reactors for sustainable CO2 conversion and N2 fixation. 202 p
Abstract: 200 years ago, humanity started the industrial revolution by discovering fossil fuels, which lead to unprecedented technological advancements. However it has become alarmingly clear that the major environmental concerns associated with fossil fuels require a short-term transition from a carbon-based energy economy to a sustainable one based on green electricity. A key step concerning this transition exists in developing electricity-driven alternatives for chemical processes that rely on fossil fuels as a raw material. A technology that is gaining increasing interest to achieve this, is plasma technology. Using plasmas to induce chemical reactions by selectively heating electrons in a gas has already delivered promising results for gas conversion applications like CO2 conversion and N2 fixation, but plasma reactors still require optimization to be considered industrially competitive to existing fossil fuel-based processes and emerging other electricity-based technologies. In this thesis I develop computational models to describe plasma reactors and identify key mechanisms in three different plasma reactors for three different gas conversion applications, i.e. N2 fixation, combined CO2-CH4 conversion and CO2 splitting. I first developed models to describe a new rotating gliding arc (GA) reactor operating in two arc modes, which, as revealed by my model, are characterized by distinct plasma chemistry pathways. Subsequently, my colleague and I study the quenching effect of an effusion nozzle to this rotating GA reactor, reaching the best results to date for N2 fixation into NOx at atmospheric pressure, i.e., NOx concentrations up to 5.9%, at an energy cost down to 2.1 MJ/mol. Afterwards, I investigate the possible improvement of N2 admixtures in plasma-based CO2 and CH4 conversion, as significant amounts of N2 are often found in industrial CO2 waste streams, and gas separations are financially costly. Through combining my models with the experiment from a fellow PhD student, we reveal that moderate amounts of N2 (i.e. around 20%) increase both the electron density and the gas temperature to yield an overall energy cost reduction of 21%. Finally, I model quenching nozzles for plasma-based CO2 conversion in a microwave reactor, to explain the enhancements in CO2 conversion that were demonstrated in experiments. Through computational modelling I reveal that the nozzle introduces fast gas quenching resulting in the suppression of recombination reactions, which have more impact at low flow rates, where recombination is the most limiting factor in the conversion process.
Keywords: Doctoral thesis; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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Ková,cs A (2023) A structured methodology for natural deep eutectic solvent selection and formulation for enzymatic reactions. viii, 216 p
Abstract: Natural deep eutectic solvents (NADES) show great promise as media for enzymatic reactions in areas where (bio)compatibility with natural or medicinal products is a must. While in theory they can be tailored to the intended reaction to ensure optimized yields, the knowledge to date is predominantly empirical, with some mechanistic reports providing a fragmented view at best. Therefore, it is not easy to explain experimental observations, let alone make predictions. The aim of this study was to develop a structured, holistic understanding of the effects of NADES media on enzymatic reactions, distinguishing between effects on solubility, solvation, viscosity, inhibition and denaturation. Experimental and computational chemistry methods were combined to separately study the interactions between enzyme, substrate, and NADES as reaction media. The initial enzyme activity and the final conversion of vinyl laurate transesterification by immobilized Candida antarctica lipase were studied experimentally. The direct effect of NADES on the same enzyme was modeled by molecular dynamics simulation. The effect of solubility was studied by both experimental and computational methods. To predict the solubility and viscosity of NADES, data-driven models were developed by combining group contribution and machine learning methods, based on the accumulated experimental knowledge on NADES found in the literature. Finally, the composed relationships and prediction models were applied to the practical example of deacetylation of mannosylerythritol lipids (MELs). The experimental findings show that the chosen NADES system has a significant effect on both the apparent initial activity and the final conversion. However, in the simulations, the enzyme retains its original structure; moreover, NADES has an additional stabilizing effect on the enzyme. In addition, changes in the molar ratio of the compounds in NADES do not show a significant effect on the stability of the enzyme. These results indicate that the main effect of NADES on the reaction is mainly related to the substrate-solvent interactions (solvation energy) and the viscosity of the system. On the other hand, the experimental results only confirmed the significance of solvation, viscosity did not show a clear correlation with the studied reaction parameters. The machine learning models built for solubility and viscosity gave quantitative predictions of these properties. The accumulated knowledge was used to optimize the yield in the deacetylation reaction of MELs. The combination of these methods provides fundamental knowledge about the effect of NADES on biocatalysis, but the results are also applicable to other uses of NADES.
Keywords: Doctoral thesis; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS)
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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)
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Khan SU (2023) Singlet oxygen-based photoelectrocatalysis : from photosensitizer structures to plasmonic enhancement. 182 p
Abstract: Singlet molecular oxygen (1O2) has continuously attracted researchers' interest because of its involvement in various processes, such as in photodynamic reactions in biological and chemical systems. 1O2 is an effective electrophile and potent oxidizing agent and can be easily generated by photosensitization via the illumination of organic dyes with visible light. As described in Chapter 1, 1O2 has gained prominence in various applications such as wastewater treatment, photodynamic therapy of cancer, organic synthesis, and recently developed 1O2-based photoelectrochemical (PEC) sensing of phenolic compounds. Phenolic compounds are a potential source of contaminants that originates from industrial effluents and waste products of chemical and pharmaceutical industries. These phenolic compounds pose severe threats to humans and aquatic life after reaching the environment. Therefore, it is imperative to develop photoactive materials that efficiently generate 1O2 and oxidize phenolic compounds and antibiotics. The existing 1O2 generating photosensitizers (PSs) include porphyrins, phthalocyanines (Pcs), subphthalocyanines (SubPcs), and other dyes such as derivatives of xanthene (e.g., Rose Bengal (RB)), and fluorinated boron-dipyrromethene (BODIPYs), and phenothiazinium dyes (e. g. Methylene Blue (MB)) which display long-lived triplet excited state and can be used in 1O2-based applications. This thesis focuses on preparing efficient hybrid materials based on newly synthesized Pcs, different surface area titanium dioxide (TiO2) and plasmonic gold nanoparticles (AuNPs) for their use in the PEC detection of phenolic compounds. The first focus was on developing a fast amperometric method to test the photo-electrocatalytic activity of 1O2 producing PSs dissolved in MeOH based on the redox cycling of an electroactive phenolic compound, hydroquinone (HQ) (Chapter 2). This method of testing PSs does not require the accumulation of a reaction product since the amperometric signal develops near instantly when the light is on, which enables dynamic monitoring of a PSs activity at varying conditions in a single experiment. This method was crucial to measure high 1O2 quantum yield and low yield in the same experimental conditions. Moreover, the obtained results revealed a range of working parameters affecting the PEC activity of PSs. The next goal was to immobilize tert-butyl substituted aluminum Pc (t-BuPcAlCl) on the solid support, which showed a high 1O2 quantum yield. However, before immobilizing Pc on a solid support such as TiO2, it is essential to know the electronic energy level of Pcs for the possible electron transfers from Pcs to TiO2. Therefore, Chapter 3 explored the (spectro)electrochemical properties of t-BuPcAlCl Pc. Next, in Chapter 4, t-BuPcAlCl Pc and other tert-butyl substituted Pcs with Zn central metal, t-BuPcZn, and its metal-free derivative t-BuPcH2 were immobilized on different surface area TiO2. The PEC activity of immobilized Pcs on TiO2 toward different phenols and antibiotics was studied, and the action mechanism was revealed and compared with sterically hindered fluorinated Pc F64PcZn. In the final part of this thesis plasmonic AuNPs were introduced combined with trimethylsilane-protected acetylene functionalized ZnPc (TMSZnPc) to study the synergistic effect that boosts the overall activity toward the detection of phenols under visible light illumination (Chapter 5) . The TMSZnPc was coupled with AuNPs via a click chemistry approach. The 1O2 quantum yield of TMSZnPc improved significantly after conjugating with AuNPs, and, subsequently, the PEC activity for detecting HQ. The theoretical and experimental investigation demonstrated that the plasmonic enhancement of TMSZnPc is driven by the near-field mechanism. This shows the importance of plasmonic AuNPs with other photoactive species for their use in 1O2-based applications. The fundamental knowledge obtained in this doctoral study will ultimately deepen the understanding of developing 1O2-based PEC sensors for detecting phenolic compounds and pharmaceuticals in the wastewater stream, helping to choose efficient materials and, in the last instance, a more sustainable future especially access to clean water for everyone.
Keywords: Doctoral thesis; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
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Yang T (2023) Characterization of Laves phase structural evolution and regulation of its precipitation behavior in Al-Zn-Mg based alloys. ii, 106 p
Abstract: Al-Zn-Mg-based high strength alloys are widely used in aerospace applications due to their low density and excellent mechanical properties. A systematic study of the structural evolution of the nano-precipitation phase and its growth mechanism is an important guide for the design of new high-strength alloys. In this work, the Laves structure precipitates in Al-Zn-Mg(-Cu/Y) alloy was systematically characterized. Based on the structure evolution, the structure of submicron Laves particles and quasicrystalline particles in the alloy at microscale, as well as the regulation of the precipitation behavior after adding Y at nanoscale were further investigated. The main innovative results are summarized as follows: (1) Investigation on coexistence of defect structures in Laves structural nanoprecipitates. Three types of Laves structures can coexist within the η-MgZn2 precipitates: C14, C15 and C36, and the Laves structure transition sequence of C14→C36→C15 in this system was determined. Meanwhile, it was found that there are diverse defect structures in the MgZn2 phase, including stacking faults, planar defects and five-fold domain structures, which have significant effects on relieving the internal stress/strain of the precipitates. (2) Investigation on multiple phase transition of Laves structural nanoprecipitates from C14 to C36 and from C14 to quasicrystal clusters. It is found that C14 precipitates can be completely transformed into the C36 precipitates. And it is also found that the C14 Laves phase structure can also transform into quasicrystalline clusters. These investigations on various phase transition mechanisms among Laves phases provide theoretical support for the microstructural characterization of materials containing multi-scale Laves phases. (3) Characterization of Laves and quasicrystal structural particles in submicron scale. Submicron-scale quasicrystal particles were obtained in conventional casting Al-Zn-Mg-Cu alloys for the first time. Industrial impurity elements Fe and Ni can induce the formation of quasicrystalline particles. When there is no Fe/Ni enriched in particles, the structure is characterized as C15-Laves phase. When Fe/Ni is as quasicrystalline core, a stable core-shell quasicrystalline structure with Al-Fe-Ni nucleus and Mg-Cu-Zn shell can be formed. (4) Investigation on the regulation of nanoscale Laves precipitates’ growth. To regulate the defect structure of the precipitates, rare earth element Y was added in Al-Zn-Mg alloys and its influence on the precipitation behavior was investigated. The addition of Y element can dynamically combine with different alloying elements during aging process, which can refine the size of precipitate and further improve the nucleation rate and precipitation rate of the precipitates.
Keywords: Doctoral thesis; Electron microscopy for materials research (EMAT)
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Voordeckers D (2023) Design to breathe : understanding and altering wind patterns in street canyons to reduce human exposure to air pollution. xxii, 303 p
Abstract: Air pollution is proclaimed by the World Health Organiaation (WHO) as the biggest environmental threat to human health. Street canyons, or urban roads flanked by a continuous row of high buildings on both sides, are perceived as typical bottleneck areas for air quality due to their lack of natural ventilation. This doctoral thesis aims to integrate expert knowledge on in-canyon flow fields and pollution dispersion in street canyons from the specialized field of (bio)engineering into the field of urban planning and vice versa. In Chapter 1, a Geospatial Information System (GIS) method was developed to detect exposure zones and hotspot street canyons. A critical combination between aspect ratio (AR > 0.65) and traffic volume (TVmax > 300) was detected and subsequently used to detect hotspot street canyons in three major European cities (Antwerp, London and Paris). Chapter 2 focusses on acquiring in-depth knowledge on flow and concentration fields in street canyons by conducting an extensive literature review on over 200 studies and translates this knowledge into nineteen guidelines and eleven spatial tools, comprised in a toolbox for urban planning. Subsequently, computational fluid dynamics (CFD) was used into a research trough design process (Chapter 4) to illustrate how the design tools can be applied to a specific case study (Belgiëlei, Antwerp). Alternations to traffic lanes (traffic lane reduction and lateral displacement) combined with low boundary walls (LBWs), were found to reduce NO2 levels in the entire pedestrian area up to – 3.6 % and peak pollutions were reduced by -8 %. A maximum NO2 reduction was reached by combining a traffic lane displacement with hedges, adjustments to the tree planting pattern and an increased ground-level permeability, leading to reductions up to – 4.5 % in the pedestrian areas. In conclusion, urban design was found to be a valuable tool to enhance the effect of emission reduction strategies and draw in-canyon concentrations closer to the value of the background concentration. However, the background concentration seemed to dominate the efficiency of the urban design interventions and therefore, additional measures should be taken to reduce background pollution levels. This dissertation aims to contribute to the awareness of air pollution in street canyons, as well as support local governments in taking action by delivering spatial tools and guidelines applicable for urban planning and represents a framework for the dissemination of expert information on air quality in street canyons to the field of urban planning.
Keywords: Doctoral thesis; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL); Research Group for Urban Development; Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS)
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