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: Dynamics of electron wave-packets is studied using the continuum Dirac model in a graphene geometric diode where the propagation of the wave packet is favored in certain direction due to the presence of geometric constraints. Clear rectification is obtained in the THz frequency range with the maximum rectification level of 3.25, which is in good agreement with recent experiments on graphene ballistic diodes. The rectification levels are considerably higher for systems with narrower channels. In this case, the wave packet transmission probabilities and rectification rate also strongly depend on the energy of the incident wave packet, as a result of the quantum nature of energy levels along such channels. These findings can be useful for fundamental understanding of the charge carrier dynamics in graphene geometry diodes.

Abstract: The recent advantages of the fabrication of artificial nanochannels enabled new research on the molecular transport, permeance, and selectivity of various gases and molecules. However, the physisorption/chemisorption of the unwanted molecules (usually hydrocarbons) inside nanochannels results in the alteration of the functionality of the nanochannels. We investigated contamination due to hydrocarbon molecules, nanochannels made of graphene, hexagonal boron nitride, BC2N, and molybdenum disulfide using molecular dynamics simulations. We found that for a certain size of nanochannel (i.e., h = 0.7 nm), as a result of the anomalous hydrophilic nature of nanochannels made of graphene, the hydrocarbons are fully adsorbed in the nanochannel, giving rise to full uptake. An increasing temperature plays an important role in unclogging, while pressure does not have a significant role. The results of our pioneering work contribute to a better understanding and highlight the important factors in alleviating the contamination and unclogging of nanochannels, which are in good agreement with the results of recent experiments.

Abstract: Owing to its inherent non-trivial geometry, the unique structural motif of the recently discovered kagome topological superconductor AV(3)Sb(5) (A = K, Rb, Cs) is an ideal host of diverse topologically non-trivial phenomena, including giant anomalous Hall conductivity, topological charge order, charge density wave (CDW), and unconventional superconductivity. Despite possessing a normal-state CDW order in the form of topological chiral charge order and diverse superconducting gaps structures, it remains unclear how fundamental atomic-level properties and many-body effects including Fermi surface nesting, electron-phonon coupling, and orbital hybridization contribute to these symmetry-breaking phenomena. Here, the direct participation of the V3d-Sb5p orbital hybridization in mediating the CDW phase transition in CsV3Sb5 is reported. The combination of temperature-dependent X-ray absorption and first-principles studies clearly indicates the inverse Star-of-David structure as the preferred reconstruction in the low-temperature CDW phase. The results highlight the critical role that Sb orbitals play and establish orbital hybridization as the direct mediator of the CDW states and structural transition dynamics in kagome unconventional superconductors. This is a significant step toward the fundamental understanding and control of the emerging correlated phases from the kagome lattice through the orbital interactions and provides promising approaches to novel regimes in unconventional orders and topology.

Abstract: We report a high-throughput first-principles characterization of the structural, mechanical, electronic, and vibrational properties of tetragonal single-layer transition metal Xenes (t-TMXs). Our calculations revealed 22 dynamically, mechanically and chemically stable structures among the 96 possible free-standing layers present in the t-TMX family. As a fingerprint for their structural identification, we identified four characteristic Raman active phonon modes, namely three in-plane and one out-of-plane optical branches, with various intensities and frequencies depending on the material in question. Spin-polarized electronic calculations demonstrated that anti-ferromagnetic (AFM) metals, ferromagnetic (FM) metals, AFM semiconductors, and non-magnetic semiconductor materials exist within this family, evidencing the potential of t-TMXs for further use in multifunctional heterostructures.

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: Transforming CO2 into value-added chemicals is crucial to realizing a carbon–neutral economy, and plasma-based conversion, a Power-2-X technology, offers a promising route to realizing an efficient and scalable process. This paper investigates the effects of post-plasma placement of a converging–diverging nozzle in a vortex-stabilized 2.45 GHz CO2 microwave plasma reactor to increase energy efficiency and conversion. The CDN leads to a 21 % relative increase in energy efficiency (31 %) and CO2 conversion (13 %) at high flow rates and near-atmospheric conditions. The most significant performance improvement was seen at low flow rates and sub-atmospheric pressure (300 mbar), where energy efficiency was 23 % and conversion was 28 %, a 71 % relative increase over conditions without the CDN. Using CFD simulations, we found that the CDN produces a change in the flow geometry, leading to a confined temperature profile at the height of the plasma, and forced extraction of CO to the post-CDN region.

Abstract: The introduction of Na+ is considered as an effective way to improve the performance of Ni-rich cathode materials. However, the direct structure-property correlation for Na+ doped NCM-based cathode materials remain unclear, due to the difficulty of local and accurate structural characterization for light elements such as Li and Na. Moreover, there is the complexity of the modeling for the whole Li ion battery (LIB) system. To tackle the above-mentioned issues, we prepared Na+-doped LiNi0.6Co0.2Mn0.2O2 (Na-NCM622) material. The crystal structure change and the lattice distortion with picometers precision of the Na+-doped material is revealed by Cs-corrected scanning transmission electron microscopy (STEM). Density functional theory (DFT) and the recently proposed electrochemical model, i.e., modified Planck-Nernst-Poisson coupled Frumkin-Butler-Volmer (MPNP-FBV), has been applied to reveal correlations between the activation energy and the charge transfer resistance at multiscale. It is shown that Na+ doping can reduce the activation energy barrier from. G = 1.10 eV to 1.05 eV, resulting in a reduction of the interfacial resistance from 297 O to 134 Omega. Consequently, the Na-NCM622 cathode delivers a superior capacity retention of 90.8 % (159 mAh.g(-1)) after 100 cycles compared to the pristine NCM622 (67.5 %, 108 mAh.g(-1)). Our results demonstrate that the kinetics of Li+ diffusion and the electrochemical reaction can be enhanced by Na+ doping the cathode material.

Abstract: Recently, an extremely low lattice thermal conductivity value has been reported for the alkali-based telluride material BaIn2Te4. The value is comparable with low-thermal conductivity metal chalcogenides, and the glass limit is highly intriguing. Therefore, to shed light on this issue, we performed first-principles phonon thermal transport calculations. We predicted highly anisotropic lattice thermal conductivity along different directions via the solution of the linearized phonon Boltzmann transport equation. More importantly, we determined several different factors as the main sources of the predicted ultralow lattice thermal conductivity of this crystal, such as the strong interactions between low-frequency optical phonons and acoustic phonons, small phonon group velocities, and lattice anharmonicity indicated by large negative mode Gruneisen parameters. Along with thermal transport calculations, we also investigated the electronic transport properties by accurately calculating the scattering mechanisms, namely the acoustic deformation potential, ionized impurity, and polar optical scatterings. The inclusion of spin-orbit coupling (SOC) for electronic structure is found to strongly affect the p-type Seebeck coefficients. Finally, we calculated the thermoelectric properties accurately, and the optimal ZT value of p-type doping, which originated from high Seebeck coefficients, was predicted to exceed unity after 700 K and have a direction averaged value of 1.63 (1.76 in the y-direction) at 1000 K around 2 x 1020 cm-3 hole concentration. For n-type doping, a ZT around 3.2 x 1019 cm-3 concentration was predicted to be a direction-averaged value of 1.40 (1.76 in the z-direction) at 1000 K, mostly originating from its high electron mobility. With the experimental evidence of high thermal stability, we showed that the BaIn2Te4 compound has the potential to be a promising mid- to high-temperature thermoelectric material for both p-type and n-type systems with appropriate doping.

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: Chiroptically active, hierarchically structured materials are difficult to accurately characterize due to linear anisotropic contributions (i.e., linear dichroism (LD) and linear birefringence (LB)) and parasitic ellipticities that produce artifactual circular dichroism (CD) signals, in addition to chiral analyte contributions ranging from molecular-scale clusters to micron-sized assemblies. Recently, we have shown that CdS magic-sized clusters (MSC) can self-assemble into ordered films that have a hierarchical structure spanning seven orders of length-scale. These films have a strong CD response, but the chiral origins are obfuscated by the hierarchical architecture and LDLB contributions. Here, we derive and demonstrate a method for extracting the “pure” CD signal (CD generated by structural dissymmetry) from hierarchical MSC films and identified the chiral origin. The theory behind the method is derived using Mueller matrix and Stokes vector conventions and verified experimentally before being applied to hierarchical MSC and nanoparticle films with varying macroscopic orderings. Each film's extracted “true CD” shares a bisignate profile aligned with the exciton peak, indicating the assemblies adopt a chiral arrangement and form an exciton coupled system. Interestingly, the linearly aligned MSC film possesses one of the highest g-factors (0.05) among semiconducting nanostructures reported. Additionally, we find that films with similar electronic transition dipole alignment can possess greatly different g-factors, indicating chirality change rather than anisotropy is the cause of the difference in the CD signal. The difference in g-factor is controllable via film evaporation geometry. This study provides a simple means to measure “true” CD and presents an example of experimentally understanding chiroptic interactions in hierarchical nanostructures.

Abstract: This study hypothesizes that the application of low-dose nonthermal biocompatible dielectric barrier discharge plasma (DBD-NBP) to human gingival fibroblasts (HGFs) will inhibit colony formation but not cell death and induce matrix metalloproteinase (MMP) expression, extracellular matrix (ECM) degradation, and subsequent cell migration, which can result in enhanced wound healing. HGFs treated with plasma for 3 min migrate to each other across the gap faster than those in the control and 5-min treatment groups on days 1 and 3. The plasma-treated HGFs show significantly high expression levels of the cell cycle arrest-related p21 gene and enhanced MMP activity. Focal adhesion kinase (FAK) mediated attenuation of wound healing or actin cytoskeleton rearrangement, and plasma-mediated reversal of this attenuation support the migratory effect of DBD-NBP. Further, this work performs computer simulations to investigate the effect of oxidation on the stability and conformation of the catalytic kinase domain (KD) of FAK. It is found that the oxidation of highly reactive amino acids (AAs) Cys427, Met442, Cys559, Met571, Met617, and Met643 changes the conformation and increases the structural flexibility of the FAK protein and thus modulates its function and activity. Low-dose DBD-NBP-induces host cell cycle arrest, ECM breakdown, and subsequent migration, thus contributing to the enhanced wound healing process.

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: 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.

Abstract: The WHO estimates that 8–10% of couples are facing fertility problems, often due to inaccuracy in predicting the female's ovulation period controlled by four key hormones. The quantification and monitoring of such key hormones are crucial for the early identification of infertility, but also in improving therapeutic management associated with hormonal imbalance. In this review, we extensively summarize and discuss: i) drawbacks of laboratory methods for fertility testing (costly, invasive, complex) and commercially available point-of-care tests (measuring only one/two of the four key hormones), ii) the understanding of different biosensors for fertility monitoring, and iii) an in-depth classification and overview of aptamer-based sensing of the hormones of interest. This review provides insights on hormone detection strategies for fertility, with a focus on the classification of the current ‘aptasensing’ strategies, aiming to assist as a basic guide for the development of accurate fertility window monitoring tools based on aptamers.