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: Nitrification is well-suited for urine stabilization. No base dosage is required if the pH is controlled within an appropriate operating range by urine feeding, producing an ammonium-nitrate fertilizer. However, the process is highly dependent on the selected pH set-points and is susceptible to process failures such as nitrite accumulation or the growth of acid-tolerant ammonia-oxidizing bacteria. To address the need for a robust and reliable process in decentralized applications, two different strategies were tested: operating a two-position pH controller (inflow on/off) with a narrow pH control band at 6.20/6.25 (∆pH = 0.05, narrow-pH) vs. a wider pH control band at 6.00/6.50 (∆pH = 0.50, wide-pH). These variations in pH also cause variations in the chemical speciation of ammonia and nitrite and, as shown, the microbial production of nitrite. It was hypothesized that the higher fluctuations would result in greater microbial diversity and, thus, a more robust process. The diversity of nitrifiers was higher in the wide-pH reactor, while the diversity of the entire microbiome was similar in both systems. However, the wide-pH reactor was more susceptible to tested process disturbances caused by increasing pH or temperature, decreasing dissolved oxygen, or an influent stop. In addition, with an emission factor of 0.47%, the nitrous oxide (N2O) emissions from the wide-pH reactor were twice as high as the N2O emissions from the narrow-pH reactor, most likely due to the nitrite fluctuations. Based on these results, a narrow control band is recommended for pH control in urine nitrification.

Abstract: Single-shot structured light profilometry (SLP) aims at reconstructing the 3D height map of an object from a single deformed fringe pattern and has long been the ultimate goal in fringe projection profilometry. Recently, deep learning was introduced into SLP setups to replace the task-specific algorithm of fringe demodulation with a dedicated neural network. Research on deep learning-based profilometry has made considerable progress in a short amount of time due to the rapid development of general neural network strategies and to the transferrable nature of deep learning techniques to a wide array of application fields. The selection of the employed loss function has received very little to no attention in the recently reported deep learning-based SLP setups. In this paper, we demonstrate the significant impact of loss function selection on height map prediction accuracy, we evaluate the performance of a range of commonly used loss functions and we propose a new mixed gradient loss function that yields a higher 3D surface reconstruction accuracy than any previously used loss functions.

Abstract: Switching induced by spin-orbit torque (SOT) is being vigorously explored, as it allows the control of magnetization using an in-plane current, which enables a three-terminal magnetic-tunnel-junction geometry with isolated read and write paths. This significantly improves the device endurance and the read stability, and allows reliable subnanosecond switching. Tungsten in the beta phase, beta-W, has the largest reported antidamping SOT charge-to-spin conversion ratio (theta(AD) approximate to -60%) for heavy metals. However, beta-W has a limitation when one is aiming for reliable technology integration: the beta phase is limited to a thickness of a few nanometers and enters the alpha phase above 4 nm in our samples when industry-relevant deposition tools are used. Here, we report our approach to extending the range of beta-W, while simultaneously improving the SOT efficiency by introducing N and O doping of W. Resistivity and XRD measurements confirm the extension of the beta phase from 4 nm to more than 10 nm, and transport characterization shows an effective SOT efficiency larger than -44.4% (reaching approximately -60% for the bulk contribution). In addition, we demonstrate the possibility of controlling and enhancing the perpendicular magnetic anisotropy of a storage layer (Co-Fe-B). Further, we integrate the optimized W(O, N) into SOT magnetic random-access memory (SOT-MRAM) devices and project that, for the same thickness of SOT material, the switching current decreases by 25% in optimized W(O, N) compared with our standard W. Our results open the path to using and further optimizing W for integration of SOT-MRAM technology.

Abstract: Having a strong electromagnetic absorption, MXene multilayers are readily envisaged for applications in electromagnetic shields and related prospective technology. However, an ab initio characterization of the optical properties of MXenes is still lacking, due in part to major difficulties with the treatment of metallicity in the first-principles approaches. Here we addressed the latter challenge, after a careful treatment of intraband transitions, to present a thorough analysis of the electronic and optical properties of a selected set of metallic MXene layers based on density functional theory (DFT) and many-body perturbation theory calculations. Our results reveal that the GW corrections are particularly important in regions of the band structure where d and p states hybridize. For some systems, we show that GW corrections open a gap between occupied states, resulting in a band structure that closely resembles that of an intrinsic transparent conductor, thereby opening an additional line of prospective applications for the MXenes family. Nevertheless, GW and Bethe-Salpeter corrections have a minimal influence on the absorption spectra, in contrast to what is typically observed in semiconductor layers. Our present results suggest that calculations within the independent particle approximation (IPA) calculations are sufficiently accurate for assessing the optical characteristics of bulk-layered MXene materials. Finally, our calculated dielectric properties and absorption spectra, in agreement with existing experimental data, confirm the potential of MXenes as effective infrared emitters.

Abstract: Purple non-sulfur bacteria (PNSB) show potential for microbial protein production on wastewater as animal feed. They offer good selectivity (i.e., low microbial diversity and high abundance of one species) when grown anaerobically in the light. However, the cost of closed anaerobic photobioreactors is prohibitive for protein production. Although open raceway reactors are cheaper, their feasibility to selectively grow PNSB is thus far unexplored. This study developed operational strategies to boost PNSB abundance in the biomass of a raceway reactor fed with volatile fatty acids. For a flask reactor run at a 2 day sludge retention time (SRT), matching the chemical oxygen demand (COD) loading rate to the removal rate in the light period prevented substrate availability during the dark period and increased the PNSB abundance from 50-67 to 88-94%. A raceway reactor run at a 2 day SRT showed an increased PNSB abundance from 14 to 56% when oxygen supply was reduced (no stirring at night). The best performance was achieved at the highest surface-to-volume ratio (10 m(2) m(-3) increased light availability) showing productivities up to 0.2 g protein L-1 day(-1) and a PNSB abundance of 78%. This study pioneered in PNSB-based microbial protein production in raceway reactors, yielding high selectivity while avoiding the combined availability of oxygen, COD, and darkness.

Abstract: Recent observations made by the authors revealed the activation of stress induced amorphization and sliding at grain boundary in olivine [1], a mechanism which is expected to play a pivotal role in the viscosity drop at the lithosphere-asthenosphere boundary and the brittle -ductile transition in the lithospheric mantle. However, there is a lack of information in the literature regarding the intrinsic mechanical properties and the elementary deformation mechanisms of this material, especially at time scales relevant for geodynamics. In the present work, amorphous olivine films were obtained by pulsed laser deposition (PLD). The mechanical response including the rate dependent behavior are investigated using a tension -on -chip (TOC) method developed at UCLouvain allowing to perform creep/relaxation tests on thin films at extremely low strain rates. In the present work, strain rate down to 10-12 s- 1 was reached which is unique. High strain rate sensitivity of 0.054 is observed together with the activation of relaxation at the very early stage of deformation. Furthermore, digital image correlation (DIC), used for the first time on films deformed by TOC, reveals local strain heterogeneities. The relationship between such heterogeneities, the high strain rate sensitivity and the effect of the electron beam in the scanning electron microscope is discussed and compared to the literature.

Abstract: There is a type of filament that forms dosed contours encircling regions of one polarity of magnetic field, while the surrounding region has the opposite polarity One distribution of ring-filaments has sizes 2R = 40,000 to 160,000 km with the maximum around 100,000 km; the other distribution (with filaments and filament channels) has bigger sizes, with a maximum around 300,000 km. At low and mid latitudes the radial component B-rs (radial for the Sun) in the region outlined by filaments varies from 50 to 100 gauss, while the longitudinal component B-phi varies from 10 to 30 gauss. The total current inside the filament is 10(10) – 10(11) A, the ratio R/a approximate to 5 to 10, the magnetic flux crossing the surface is approximate to 10(21) – 10(22) MX; th, magnetic energy is approximate to 10(29) – 10(31) erg. Polar ring-filaments at latitudes 60 degrees-80 degrees are related to the polar magnetic field reversal and the quasi-flare processes at the poles during the field reversal. Correlation between B-rs and B-phi for the polar filament bands cannot be satisfactorily explained. A theoretical model using the conservation laws is used to study the relations between the various fields, currents, etc, of shrinking polar ring-filaments and their evolution. According to this theory ring-filaments should rise higher above the photosphere when shrinking. However, observations show that the height lowers. Presumably the discrepancy is due to the lack of dissipation in the model.