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Cancer subtyping is one of the most challenging tasks in digital pathology, where Multiple Instance Learning (MIL) by processing gigapixel whole slide images (WSIs) has been in the spotlight of recent research. However, MIL approaches do not take advantage of inter- and intra-magnification information contained in WSIs. In this work, we present GRASP, a novel graph-structured multi-magnification framework for processing WSIs in digital pathology. Our approach is designed to dynamically emulate the pathologist's behavior in handling WSIs and benefits from the hierarchical structure of WSIs. GRASP, which introduces a convergence-based node aggregation instead of traditional pooling mechanisms, outperforms state-of-the-art methods over two distinct cancer datasets by a margin of up to 10% balanced accuracy, while being 7 times smaller than the closest-performing state-of-the-art model in terms of the number of parameters. Our results show that GRASP is dynamic in finding and consulting with different magnifications for subtyping cancers and is reliable and stable across different hyperparameters. The model's behavior has been evaluated by two expert pathologists confirming the interpretability of the model's dynamic. We also provide a theoretical foundation, along with empirical evidence, for our work, explaining how GRASP interacts with different magnifications and nodes in the graph to make predictions. We believe that the strong characteristics yet simple structure of GRASP will encourage the development of interpretable, structure-based designs for WSI representation in digital pathology. Furthermore, we publish two large graph datasets of rare Ovarian and Bladder cancers to contribute to the field., Comment: Early version: To be updated

We investigate the topological phases that appear in an orbital version of the Benalcazar-Bernevig-Hughes (BBH) model in the presence of conventional spin-singlet $s$-wave superconductivity and with the possibility of tuning an in-plane magnetic field. We chart out the phase diagram by considering different boundary conditions, with the topology of the individual phases further examined by considering both the Wannier and entanglement spectra, as well as the Majorana polarization. For weak to moderate values of magnetic field and superconducting pairing amplitude, we find a second-order topological superconductor phase with eight zero-energy corner modes. Further increasing field or pairing, half of the corner states can be turned into zero-energy edge-localized modes, thus forming a type of hybrid-order phase. Then, we find two different putative first-order topological phases, a nodal and a nodeless phase, both with zero-energy flat bands localized along mirror-symmetric open edges. For the nodal phase, the flat bands are localized between the nodes in reciprocal space, while in the nodeless phase, with its a full bulk gap, the zero-energy boundary flat band spans the whole Brillouin zone., Comment: 14+3 pages, 14 figures

Through spectral unmixing, hyperspectral imaging (HSI) in fluorescence-guided brain tumor surgery has enabled detection and classification of tumor regions invisible to the human eye. Prior unmixing work has focused on determining a minimal set of viable fluorophore spectra known to be present in the brain and effectively reconstructing human data without overfitting. With these endmembers, non-negative least squares regression (NNLS) was used to compute the abundances. However, HSI images are heterogeneous, so one small set of endmember spectra may not fit all pixels well. Additionally, NNLS is the maximum likelihood estimator only if the measurement is normally distributed, and it does not enforce sparsity, which leads to overfitting and unphysical results. Here, we analyzed 555666 HSI fluorescence spectra from 891 ex vivo measurements of patients with brain tumors to show that a Poisson distribution models the measured data 82% better than a Gaussian in terms of the Kullback-Leibler divergence and that the endmember abundance vectors are sparse. With this knowledge, we introduce (1) a library of 9 endmember spectra, (2) a sparse, non-negative Poisson regression algorithm to perform physics-informed unmixing with this library without overfitting, and (3) a highly realistic spectral measurement simulation with known endmember abundances. The new unmixing method was then tested on the human and simulated data and compared to four other candidate methods. It outperforms previous methods with 25% lower error in the computed abundances on the simulated data than NNLS, lower reconstruction error on human data, beUer sparsity, and 31 times faster runtime than state-of-the-art Poisson regression. This method and library of endmember spectra can enable more accurate spectral unmixing to beUer aid the surgeon during brain tumor resection., Comment: 17 pages, 4 tables, 6 figures; Under review

We study interaction-mediated magnetism on the surface of ABC-multilayer graphene driven by its zero-energy topological flat bands. Using the random-phase approximation we treat onsite Hubbard repulsion and find multiple competing magnetic states, due to both intra- and inter-valley scattering, with the latter causing an enlarged magnetic unit cell. At half-filling and when the Hubbard repulsion is weak, we observe two different ferromagnetic orders. Once the Hubbard repulsion becomes more realistic, new ferrimagnetic orders arise with distinct incommensurate intra- or inter-valley scattering vectors depending on interaction strength and doping, leading to a multitude of competing magnetic states., Comment: Main text: 7 pages and 4 figures, Supplementary Material: 11 pages and 8 figures

Recent advances in generative modeling have led to promising progress on synthesizing 3D human motion from text, with methods that can generate character animations from short prompts and specified durations. However, using a single text prompt as input lacks the fine-grained control needed by animators, such as composing multiple actions and defining precise durations for parts of the motion. To address this, we introduce the new problem of timeline control for text-driven motion synthesis, which provides an intuitive, yet fine-grained, input interface for users. Instead of a single prompt, users can specify a multi-track timeline of multiple prompts organized in temporal intervals that may overlap. This enables specifying the exact timings of each action and composing multiple actions in sequence or at overlapping intervals. To generate composite animations from a multi-track timeline, we propose a new test-time denoising method. This method can be integrated with any pre-trained motion diffusion model to synthesize realistic motions that accurately reflect the timeline. At every step of denoising, our method processes each timeline interval (text prompt) individually, subsequently aggregating the predictions with consideration for the specific body parts engaged in each action. Experimental comparisons and ablations validate that our method produces realistic motions that respect the semantics and timing of given text prompts. Our code and models are publicly available at https://mathis.petrovich.fr/stmc., Comment: CVPR 2024, HuMoGen Workshop

Vitamin K is emerging as a multi-function vitamin that plays a role in bone, brain and vascular health. Vitamin K composition data remain limited globally and Australia has lacked nationally representative data for vitamin K1 (phylloquinone, PK) in horticultural commodities. Primary samples (n = 927) of 90 different Australian-grown fruit, vegetable and nut commodities were purchased in three Australian cities. We measured PK in duplicate in 95 composite samples using liquid chromatography with electrospray ionisation-tandem mass spectrometry. The greatest mean concentrations of PK were found in kale (565 ug/100 g), baby spinach (255 ug/100 g) and Brussels sprouts (195 ug/100 g). The data contribute to the global collection of vitamin K food composition data. They add to the evidence that PK concentrations vary markedly between geographic regions, supporting development of region-specific datasets for national food composition databases that do not yet contain data for vitamin K., Comment: 22 pages, 2 tables

Recent progress in manufacturing high-electron-mobility transistors and optoelectronic devices highlights the necessity of understanding the charge dynamics and its impact on the optical properties inside heterostructures. Herein, we study the optical properties of GaN/AlGaN/GaN heterostructures using cathodoluminescence and photoluminescence spectroscopy. We explore the influence of generated secondary carriers after electron illumination and their penetration depth on the luminescence spectra. Our findings indicate that a higher laser power intensifies the photoluminescence response and establishes Fabry-Perot-like resonances. Furthermore, the intensity of the cathodoluminescence response shows a linear behavior versus the acceleration voltage and the current of electron beams for the yellow luminescence peak. A near-infrared cathodoluminescence peak (740 nm) is observed only when illuminating the sample with high currents that is attributed to the trapping of the secondary electrons within the Schottky barrier and the manipulation of the two-dimensional electron gas and the quantum-confined states within the barrier. Self-consistent Poisson-Schr\"odinger simulations verify this aspect. This research unveils the intricate charge dynamics associated with the interaction of electron beams with heterostructure systems, paving the way for innovative optoelectronic applications in semiconductor devices.

We explore the application of the reference map technique, originally developed for the Eulerian simulation of solid mechanics, in Lagrangian kinematics of fluid flows. Unlike traditional methods based on explicit particle tracking, the reference map facilitates the calculation of flow maps and gradients without the need for particles. This is achieved through an Eulerian update of the reference map, which records the take-off positions of fluid particles. Using the reference map, measures of Lagrangian fluid-element deformation can be computed solely from Eulerian data, such as displacement, deformation gradient, Cauchy-Green tensor, and Finite-Time Lyapunov Exponent (FTLE) fields. We first demonstrate the accuracy of FTLE calculations based on the reference map against the standard particle-based approach in a 2D Taylor-Green vortex. Then, we apply it to turbulent channel flow at $Re_\tau=180$ where Lagrangian coherent structures identified as ridges of the backward-time FTLE are found to bound vortical regions of flow, consistent with Eulerian coherent structures from the Q-criterion. The reference map also proves suitable for material surface tracking despite not explicitly tracking particles. This capability can provide valuable insights into the Lagrangian landscape of turbulent momentum transport, complementing Eulerian velocity-field analysis. The evolution of initially wall-normal material surfaces in the viscous sublayer, buffer layer, and log layer sheds light on the Reynolds stress-generating events from a Lagrangian perspective. Eliminating the need for tracking numerous particles, the reference map approach offers a convenient and promising avenue for future investigations into Lagrangian kinematics and dynamics of fluid flows.

The Latent Block Model (LBM) is a prominent model-based co-clustering method, returning parametric representations of each block cluster and allowing the use of well-grounded model selection methods. The LBM, while adapted in literature to handle different feature types, cannot be applied to datasets consisting of multiple disjoint sets of features, termed views, for a common set of observations. In this work, we introduce the multi-view LBM, extending the LBM method to multi-view data, where each view marginally follows an LBM. In the case of two views, the dependence between them is captured by a cluster membership matrix, and we aim to learn the structure of this matrix. We develop a likelihood-based approach in which parameter estimation uses a stochastic EM algorithm integrating a Gibbs sampler, and an ICL criterion is derived to determine the number of row and column clusters in each view. To motivate the application of multi-view methods, we extend recent work developing hypothesis tests for the null hypothesis that clusters of observations in each view are independent of each other. The testing procedure is integrated into the model estimation strategy. Furthermore, we introduce a penalty scheme to generate sparse row clusterings. We verify the performance of the developed algorithm using synthetic datasets, and provide guidance for optimal parameter selection. Finally, the multi-view co-clustering method is applied to a complex genomics dataset, and is shown to provide new insights for high-dimension multi-view problems.

Forty years ago it was proposed that gas phase organic chemistry in the interstellar medium was initiated by the methyl cation CH3+, but hitherto it has not been observed outside the Solar System. Alternative routes involving processes on grain surfaces have been invoked. Here we report JWST observations of CH3+ in a protoplanetary disk in the Orion star forming region. We find that gas-phase organic chemistry is activated by UV irradiation., Comment: Published in Nature

The percentage of children with certain allergic conditions has increased over previous decades. Seasonal allergies, which includes hay fever, allergic rhinitis, and allergic conjunctivitis, causes sneezing, cough, runny nose, and itchy eyes. Eczema, also known as atopic dermatitis, causes itchy, bumpy rashes and thickened skin that can appear anywhere on the body. Food allergies can cause hives, vomiting, trouble breathing, or throat tightening. Children with allergic conditions may have increased healthcare use and decreased quality of life. Food allergies can be life threatening. This report describes the percentage of children who had diagnosed seasonal allergy, eczema, or food allergy by sex, age, and race and Hispanic origin from the 2021 National Health Interview Survey (NHIS).