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: Advances in multi-spectral detectors are causing a paradigm shift in x-ray computed tomography (CT). Spectral information acquired from these detectors can be used to extract volumetric material composition maps of the object of interest. If the materials and their spectral responses are known a priori, the image reconstruction step is rather straightforward. If they are not known, however, the maps as well as the responses need to be estimated jointly. A conventional workflow in spectral CT involves performing volume reconstruction followed by material decomposition, or vice versa. However, these methods inherently suffer from the ill-posedness of the joint reconstruction problem. To resolve this issue, we propose 'A Dictionary-based Joint reconstruction and Unmixing method for Spectral Tomography' (ADJUST). Our formulation relies on forming a dictionary of spectral signatures of materials common in CT and prior knowledge of the number of materials present in an object. In particular, we decompose the spectral volume linearly in terms of spatial material maps, a spectral dictionary, and the indicator of materials for the dictionary elements. We propose a memory-efficient accelerated alternating proximal gradient method to find an approximate solution to the resulting bi-convex problem. From numerical demonstrations on several synthetic phantoms, we observe that ADJUST performs exceedingly well compared to other state-of-the-art methods. Additionally, we address the robustness of ADJUST against limited and noisy measurement patterns. The demonstration of the proposed approach on a spectral micro-CT dataset shows its potential for real-world applications. Code is available at https://github.com/mzeegers/ADJUST.

Abstract: Using a particle-based model, we examine the collective dynamics of skyrmions interacting with a funnel potential under dc driving as the skyrmion density and relative strength of the Magnus and damping terms are varied. For driving in the easy direction, we find that increasing the skyrmion density reduces the average skyrmion velocity due to jamming of skyrmions near the funnel opening, while the Magnus force causes skyrmions to accumulate on one side of the funnel array. For driving in the hard direction, there is a critical skyrmion density below which the skyrmions become trapped. Above this critical value, a clogging effect appears with multiple depinning and repinning states where the skyrmions can rearrange into different clogged configurations, while at higher drives, the velocity-force curves become continuous. When skyrmions pile up near the funnel opening, the effective size of the opening is reduced and the passage of other skyrmions is blocked by the repulsive skyrmion-skyrmion interactions. We observe a strong diode effect in which the critical depinning force is higher and the velocity response is smaller for hard direction driving. As the ratio of Magnus force to dissipative term is varied, the skyrmion velocity varies in a non-linear and non-monotonic way due to the pile up of skyrmions on one side of the funnels. At high Magnus forces, the clogging effect for hard direction driving is diminished.

Abstract: Bamboo is an important component in subtropical and tropical forest communities. The plant has characteristic long lanceolate leaves with parallel venation. Prior studies have shown that the leaf shapes of this plant group can be well described by a simplified version (referred to as SGE-1) of the Gielis equation, a polar coordinate equation extended from the superellipse equation. SGE-1 with only two model parameters is less complex than the original Gielis equation with six parameters. Previous studies have seldom tested whether other simplified versions of the Gielis equation are superior to SGE-1 in fitting empirical leaf shape data. In the present study, we compared a three-parameter Gielis equation (referred to as SGE-2) with the two-parameter SGE-1 using the leaf boundary coordinate data of six bamboo species within the same genus that have representative long lanceolate leaves, with >300 leaves for each species. We sampled 2000 data points at approximately equidistant locations on the boundary of each leaf, and estimated the parameters for the two models. The root–mean–square error (RMSE) between the observed and predicted radii from the polar point to data points on the boundary of each leaf was used as a measure of the model goodness of fit, and the mean percent error between the RMSEs from fitting SGE-1 and SGE-2 was used to examine whether the introduction of an additional parameter in SGE-1 remarkably improves the model’s fitting. We found that the RMSE value of SGE-2 was always smaller than that of SGE-1. The mean percent errors among the two models ranged from 7.5% to 20% across the six species. These results indicate that SGE-2 is superior to SGE-1 and should be used in fitting leaf shapes. We argue that the results of the current study can be potentially extended to other lanceolate leaf shapes.

Abstract: We investigated the valley Zeeman splitting of excitonic peaks in the microphotoluminescence (mu PL) spectra of high-quality hBN/WS2/MoSe2/hBN heterostructures under perpendicular magnetic fields up to 20 T. We identify two neutral exciton peaks in the mu PL spectra; the lower-energy peak exhibits a reduced g-factor relative to that of the higher energy peak and much lower than the recently reported values for interlayer excitons in other van der Waals (vdW) heterostructures. We provide evidence that such a discernible g-factor stems from the spatial confinement of the exciton in the potential landscape created by the moire pattern due to lattice mismatch or interlayer twist in heterobilayers. This renders magneto-mu PL an important tool to reach a deeper understanding of the effect of moire patterns on excitonic confinement in vdW heterostructures.

Abstract: The Lamé curve is an extension of an ellipse, the latter being a special case. Dr. Johan Gielis further extended the Lamé curve in the polar coordinate system by introducing additional parameters (n1, n2, n3; m): rφ=1Acosm4φn2+1Bsinm4φn3−1/n1, which can be applied to model natural geometries. Here, r is the polar radius corresponding to the polar angle φ; A, B, n1, n2 and n3 are parameters to be estimated; m is the positive real number that determines the number of angles of the Gielis curve. Most prior studies on the Gielis equation focused mainly on its applications. However, the Gielis equation can also generate a large number of shapes that are rotationally symmetric and axisymmetric when A = B and n2 = n3, interrelated with the parameter m, with the parameters n1 and n2 determining the shapes of the curves. In this paper, we prove the relationship between m and the rotational symmetry and axial symmetry of the Gielis curve from a theoretical point of view with the condition A = B, n2 = n3. We also set n1 and n2 to take negative real numbers rather than only taking positive real numbers, then classify the curves based on extremal properties of r(φ) at φ = 0, π/m when n1 and n2 are in different intervals, and analyze how n1, n2 precisely affect the shapes of Gielis curves.

Abstract: A Raman scattering study covering the entire substitution range of the FeSe1-xSx solid solution is presented. Data were taken as a function of sulfur concentration x for 0 <= x <= 1, of temperature and of scattering symmetry. All types of excitations including phonons, spins, and charges are analyzed in detail. It is observed that the energy and width of the iron-related B-1g phonon mode vary continuously across the entire range of sulfur substitution. The A(1g) chalcogenide mode disappears above x = 0.23 and reappears at a much higher energy for x = 0.69. In a similar way the spectral features appearing at finite doping in A(1g) symmetry vary discontinuously. The magnetic excitation centered at approximately 500 cm(-1) disappears above x = 0.23 where the A(1g) lattice excitations exhibit a discontinuous change in energy. The low-energy mode associated with fluctuations displays maximal intensity at the nematostructural transition and thus tracks the phase boundary.

Abstract: A strong superconducting diode effect (SDE) is revealed in a thin superconducting film periodically nanostructured with magnetic dots. The SDE is caused by the current-activated dissipation mitigated by vortex-antivortex pairs (VAPs), which periodically nucleate under the dots, move and annihilate in the superconductor-eventually driving the system to the high-resistive state. Inversing the polarity of the applied current destimulates the nucleation of VAPs, the system remains superconducting up to far larger currents, leading to the pronounced diodic response. Our dissipative Ginzburg-Landau simulations detail the involved processes, and provide reliable geometric and parametric ranges for the experimental realiza-tion of such a nonvolatile superconducting diode, which operates in the absence of any applied magnetic field while being fluxonic by design.

Abstract: Vanadium dioxide (VO2) is a popular candidate for electronic and optical switching applications due to its well-known semiconductor-metal transition. Its study is notoriously challenging due to the interplay of long- and short-range elastic distortions, as well as the symmetry change and the electronic structure changes. The inherent coupling of lattice and electronic degrees of freedom opens the avenue toward mechanical actuation of single domains. In this work, we show that we can manipulate and monitor the reversible semiconductor-to-metal transition of VO2 while applying a controlled amount of mechanical pressure by a nanosized metallic probe using an atomic force microscope. At a critical pressure, we can reversibly actuate the phase transition with a large modulation of the conductivity. Direct tunneling through the VO2-metal contact is observed as the main charge carrier injection mechanism before and after the phase transition of VO2. The tunneling barrier is formed by a very thin but persistently insulating surface layer of the VO2. The necessary pressure to induce the transition decreases with temperature. In addition, we measured the phase coexistence line in a hitherto unexplored regime. Our study provides valuable information on pressure-induced electronic modifications of the VO2 properties, as well as on nanoscale metal-oxide contacts, which can help in the future design of oxide electronics.

Abstract: Multimodal contrast agents, which take advantage of different imaging modalities, have emerged as an interesting approach to overcome the technical limitations of individual techniques. We developed hybrid nanoparticles comprising an iron oxide core and an outer gold spiky layer, stabilized by a biocompatible polymeric shell. The combined magnetic and optical properties of the different components provide the required functionalities for magnetic resonance imaging (MRI), surface-enhanced Raman scattering (SERS), and fluorescence imaging. The fabrication of such hybrid nanoprobes comprised the adsorption of small gold nanoparticles onto premade iron oxide cores, followed by controlled growth of spiky gold shells. The gold layer thickness and branching degree (tip sharpness) can be controlled by modifying both the density of Au nanoparticle seeds on the iron oxide cores and the subsequent nanostar growth conditions. We additionally demonstrated the performance of these hybrid multifunctional nanoparticles as multimodal contrast agents for correlative imaging of in vitro cell models and ex vivo tissues.

Abstract: We investigate a Josephson junction in an electron-hole superfluid in a double-layer transition metal dichalco-genide heterostructure. The observation of a critical tunneling current is a clear signature of superfluidity. In addition, we find the BCS-BEC crossover physics in the narrow barrier region controls the critical current across the entire system. The corresponding critical velocity, which is measurable in this system, has a maximum when the excitations pass from bosonic to fermionic. Remarkably, this occurs for the density at the boundary of the BEC to BCS-BEC crossover regime determined from the condensate fraction. This provides, in a semiconductor system, an experimental way to determine the position of this boundary.

Abstract: Irradiation assisted stress corrosion cracking (IASCC) is an intergranular cracking effect which can occur in heavily irradiated internal structural components of nuclear reactor cores. It is a complex phenomenon which is not yet fully understood because it occurs through an interplay of several material degradation processes. The factors that influence IASCC susceptibility include irradiation damage (neutrons and other irradiation particles stemming from the nuclear fission reaction), the operating temperature of the nuclear reactor, water corrosion, operating stresses, and the composition of materials susceptible to IASCC. Such materials are typically fabricated from austenitic stainless steels because of their relatively high strength, ductility, and fracture toughness. However, besides excellent metallurgical and corrosion resistant qualities, the operating conditions may still cause severe material degradation and component failure, which is extremely important for nuclear power plant safety and lifetime managements. Despite much accumulated data in the literature, both crack initiation and crack propagation mechanisms still need to be further elucidated. To that end, a probabilistic fracture model entitled the subcritical crack propagation (SCP) was recently developed, which assumes that the oxidized part of stainless steel in front of the crack plays an essential role in the crack initiation and crack propagation in sample failures. Still, despite a very good agreement with experimental observations, the SCP model but also other contemporary models favoured within the literature, require further experimental verification to what concerns the investigation of (IA)SCC. To that end, the main objective of this doctorate was to utilize experimental instrumentations like SEM, FIB-SEM and (S)TEM to conduct the investigation of the crack initiation and propagation processes in both tested and industrial specimens. Some of the investigated materials were retrieved within a nuclear reactor and are thus considered as unique test material to investigate the material degradation processes relevant for cracking. Other specimens were tailor-made to simulate the cracking processes of irradiated materials in otherwise un-irradiated materials. The newly acquired experimental results in this doctorate help rationalize existing models and methodologies used in the literature to analyse the IASCC failures of structural materials of reactor components. These results also facilitate in the development of predictive methodologies and mitigation strategies towards IASCC cracking and provide more information on IASCC from a microstructural perspective.

Abstract: Bimetallic electrocatalysts have emerged as a viable strategy to tune the electrocatalytic CO2 reduction reaction (eCO2RR) for the selective production of valuable base chemicals and fuels. However, obtaining high product selectivity and catalyst stability remain challenging, which hinders the practical application of eCO2RR. In this work, it was found that a small doping concentration of tin (Sn) in copper oxide (CuO) has profound influence on the catalytic performance, boosting the Faradaic efficiency (FE) up to 98% for carbon monoxide (CO) at -0.75 V versus RHE, with prolonged stable performance (FE > 90%) for up to 15 h. Through a combination of ex situ and in situ characterization techniques, the in situ activation and reaction mechanism of the electrocatalyst at work was elucidated. In situ Raman spectroscopy measurements revealed that the binding energy of the crucial adsorbed *CO intermediate was lowered through Sn doping, thereby favoring gaseous CO desorption. This observation was confirmed by density functional theory, which further indicated that hydrogen adsorption and subsequent hydrogen evolution were hampered on the Sn-doped electrocatalysts, resulting in boosted CO formation. It was found that the pristine electrocatalysts consisted of CuO nanoparticles decorated with SnO2 domains, as characterized by ex situ high-resolution scanning transmission electron microscopy and X-ray photoelectron spectroscopy measurements. These pristine nanoparticles were subsequently in situ converted into a catalytically active bimetallic Sn-doped Cu phase. Our work sheds light on the intimate relationship between the bimetallic structure and catalytic behavior, resulting in stable and selective oxide-derived Sn-doped Cu electrocatalysts.

Abstract: All-inorganic lead-free halide double perovskites offer a promising avenue toward non-toxic, stable optoelec-tronic materials, properties that are missing in their prominent lead-containing counterparts. Their large ther-mopowers and high carrier mobilities also make them promising for thermoelectric applications. Here, we present a first-principles study of the lattice vibrations and thermal transport behaviors of Cs2SnI6 and gamma-CsSnI3, two prototypical compounds in this materials class. We show that conventional static zero temperature density functional theory (DFT) calculations severely underestimate the lattice thermal conductivities (kappa l) of these compounds, indicating the importance of dynamical effects. By calculating anharmonic renormalized phonon dispersions, we show that some optic phonons significantly harden with increasing temperature (T), which reduces the scattering of heat carrying phonons and enhances calculated kappa l values when compared with standard zero temperature DFT. Furthermore, we demonstrate that coherence contributions to kappa l, arising from wave like phonon tunneling, are important in both compounds. Overall, calculated kappa l with temperature-dependent inter-atomic force constants, built from particle and coherence contributions, are in good agreement with available measured data, for both magnitude and temperature dependence. Large anharmonicity combined with low phonon group velocities yield ultralow kappa l values, with room temperature values of 0.26 W/m-K and 0.72 W/m-K predicted for Cs2SnI6 and gamma-CsSnI3, respectively. We further show that the lattice dynamics of these compounds are highly anharmonic, largely mediated by rotation of the SnI6 octahedra and localized modes originating from Cs rattling motion. These thermal characteristics combined with their previously computed excellent electronic properties make these perovskites promising candidates for optoelectronic and room temperature thermoelectric applications.

Abstract: Chemically synthesized metal nanoparticles with morphological chiral features are known to exhibit strong circular dichroism. However, we still lack understanding of the correlation between morphological and chiroptical features of plasmonic nanoparticles. To shed light on that question, single nanoparticle experiments are required. We performed photothermal circular dichroism measurements of single chiral and achiral gold nanoparticles and correlated the chiroptical response to the 3D morphology of the same nanoparticles retrieved by electron tomography. In contrast to an ensemble measurement, we show that individual particles within the ensemble display a broad distribution of strength and handedness of circular dichroism signals. Whereas obvious structural chiral features, such as helical wrinkles, translate into chiroptical ones, nanoparticles with less obvious chiral morphological features can also display strong circular dichroism signals. Interestingly, we find that even seemingly achiral nanoparticles can display large g-factors. The origin of this circular dichroism signal is discussed in terms of plasmonics and other potentially relevant factors.