Abstract: Background Patient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications. Methods Here, we developed a high-throughput compatible and automated live-cell image analysis software that allows for kinetic monitoring of organoids, named Organoid Brightfield Identification-based Therapy Screening (OrBITS), by combining computer vision with a convolutional network machine learning approach. The OrBITS deep learning analysis approach was validated against current standard assays for kinetic imaging and automated analysis of organoids. A drug screen of standard-of-care lung and pancreatic cancer treatments was also performed with the OrBITS platform and compared to the gold standard, CellTiter-Glo 3D assay. Finally, the optimal parameters and drug response metrics were identified to improve patient stratification. Results OrBITS allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D (R)-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. The obtained organoid Count, Mean Area, and Total Area had a strong correlation with the nuclear staining, Hoechst, following pairwise comparison over a broad range of sizes. By incorporating a fluorescent cell death marker, infra-well normalization for organoid death could be achieved, which was tested with a 10-point titration of cisplatin and validated against the current gold standard ATP-assay, CellTiter-Glo 3D. Using this approach with OrBITS, screening of chemotherapeutics and targeted therapies revealed further insight into the mechanistic action of the drugs, a feature not achievable with the CellTiter-Glo 3D assay. Finally, we advise the use of the growth rate-based normalised drug response metric to improve accuracy and consistency of organoid drug response quantification. Conclusion Our findings validate that OrBITS, as a scalable, automated live-cell image analysis software, would facilitate the use of patient-derived organoids for drug development and therapy screening. The developed wet-lab workflow and software also has broad application potential, from providing a launching point for further brightfield-based assay development to be used for fundamental research, to guiding clinical decisions for personalized medicine.

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.

Abstract: More and more countries and organisations emphasise the value of harm reduction measures in the context of illicit drug use and abuse. One of these measures is drug checking, a preventive action that can represent a quick win by tailored consultation on the risks of substance use upon analytical screening of a submitted sample. Unlike drop-in centres that operate within a fixed setting, enabling drug checking in a harm reduction context at events requires portable, easy to use analytical approaches, operated by personnel with limited knowledge of analytical chemistry. In this case study, four different approaches were compared for the characterisation of 3,4-methylenedioxymethamphetamine samples and this in the way the approaches would be applied today in an event context. The four approaches are mid-infrared (MIR), near-infrared, and Raman spectroscopy, which are today used in drug checking context in Belgium, as well as an electrochemical sensor approach initially developed in the context of law enforcement at ports. The MIR and the electrochemical approach came out best, with the latter allowing for a direct straightforward analysis of the percentage 3,4-methylenedioxymethamphetamine (as base equivalent) in the samples. However, MIR has the advantage that, in a broader drug checking context, it allows to screen for several molecules and so is able to identify unexpected active components or at least the group to which such components belong. The latter is also an important advantage in the context of the growing emergence of new psychotropic substances. MIR, NIR, Raman spectroscopy, and an electrochemical sensor (Narcoreader (R)) for MDMA analysis were compared in a realistic harm reduction context. NIR and Raman failed in simple library approaches. MIR and Narcoreader (R) were preferred. MIR came out as first choice. MIR and Narcoreader (R) have complementary (dis)advantages and could be used in a two-step approach: MIR for screening and Narcoreader (R) for dosage/risk evaluation of MDMA samples.image

Abstract: Human urine contains a high concentration of nitrogen and is therefore an interesting source for nutrient recovery. Ureolysis is a key requirement in many processes aiming at nitrogen recovery from urine. Although ureolytic activity is widespread in terrestrial and aquatic environments, very little is known about the urease activity and regulation in specific bacteria other than human pathogens. Given the relatively high salt concentration of urine, marine bacteria would be particularly well suited for biotechnological applications involving nitrogen recovery from urine, and therefore, in this study, we investigated ureolytic activity and its regulation in marine vibrios. Thirteen out of 14 strains showed ureolytic activity. The urease activity was induced by urea, since complete and very rapid hydrolysis, up to 4 g L-1 of urea, was observed in synthetic human urine when the bacteria were pretreated with 10 g L-1 urea, whereas slow hydrolysis occurred when they were pretreated with 1 g L-1 urea (14-35% hydrolysis after 2 days). There was no correlation between biofilm formation and "motility on one hand, and ureolysis on the other hand, and biofilm and motility inhibitors did not affect ureolysis. Together, our data demonstrate for the first time the potential of marine vibrios as fast urea hydrolyzers for biotechnological applications aiming at nutrient recovery from human urine.

Abstract: The principal aim of this work is to study the effect of the processes of sintering and Pd doping of SnO2 gas sensor materials on the conversion of CO to CO2. For this purpose, the gas phase above screen printed sensor material is investigated using FTIR spectroscopy, while surface area, porosity and particle size measurements are performed on the SnO2 powders. During sintering, larger agglomerates of primary particles are formed, which results in a larger conversion degree of CO. The effect of Pd doping of the tin dioxide film on the CO conversion is more pronounced. The transformation of CO starts at a lower temperature and the conversion degree increases remarkably.

Abstract: Two-dimensional Transition Metal Dichalcogenides (TMDs) possessing extraordinary physical properties at reduced dimensionality have attracted interest due to their promise in electronic and optical device applications. However, TMD monolayers can show a broad range of different properties depending on their crystal phase; for example, H phases are usually semiconductors, while the T phases are metallic. Thus, controlling phase transitions has become critical for device applications. In this study, the energetically low-lying crystal structures of pristine and Janus TMDs are investigated by using ab initio Nudged Elastic Band and molecular dynamics simulations to provide a general explanation for their phase stability and transition properties. Across all materials investigated, the T phase is found to be the least stable and the H phase is the most stable except for WTe2, while the T' and T '' phases change places according to the TMD material. The transition energy barriers are found to be large enough to hint that even the higher energy phases are unlikely to undergo a phase transition to a more stable phase if they can be achieved except for the least stable T phase, which has zero barrier towards the T ' phase. Indeed, in molecular dynamics simulations the thermodynamically least stable T phase transformed into the T ' phase spontaneously while in general no other phase transition was observed up to 2100 K for the other three phases. Thus, the examined T ', T '' and H phases were shown to be mostly stable and do not readily transform into another phase. Furthermore, so-called mixed phase calculations considered in our study explain the experimentally observed lateral hybrid structures and point out that the coexistence of different phases is strongly stable against phase transitions. Indeed, stable complex structures such as metal-semiconductor-metal architectures, which have immense potential to be used in future device applications, are also possible based on our investigation.

Abstract: Thermal expansion behavior of two-dimensional (2D) nitrides and graphene were studied by ab initio molecular dynamics (MD) simulations as well as quasiharmonic approximation (QHA). Anharmonicity of the acoustic phonon modes are related to the unusual negative thermal expansion (NTE) behavior of the nitrides. Our results also hint that direct ab initio MD simulations are a more elaborate method to investigate thermal expansion behavior of 2D materials than the QHA. Nevertheless, giant NTE coefficients are found for h-GaN and h-AlN within the covered temperature range 100-600 K regardless of the chosen computational method. This unusual NTE of 2D nitrides is reasoned with the out-of-plane oscillations related to the rippling behavior of the monolayers.