Daily Papers

The emerging area of computational pathology (CPath) is ripe ground for the application of deep learning (DL) methods to healthcare due to the sheer volume of raw pixel data in whole-slide images (WSIs) of cancerous tissue slides. However, it is imperative for the DL algorithms relying on nuclei-level details to be able to cope with data from `the clinical wild', which tends to be quite challenging. We study, and extend recently released PanNuke dataset consisting of ~200,000 nuclei categorized into 5 clinically important classes for the challenging tasks of segmenting and classifying nuclei in WSIs. Previous pan-cancer datasets consisted of only up to 9 different tissues and up to 21,000 unlabeled nuclei and just over 24,000 labeled nuclei with segmentation masks. PanNuke consists of 19 different tissue types that have been semi-automatically annotated and quality controlled by clinical pathologists, leading to a dataset with statistics similar to the clinical wild and with minimal selection bias. We study the performance of segmentation and classification models when applied to the proposed dataset and demonstrate the application of models trained on PanNuke to whole-slide images. We provide comprehensive statistics about the dataset and outline recommendations and research directions to address the limitations of existing DL tools when applied to real-world CPath applications.

This study developed a novel method for detecting hypernuclear events recorded in nuclear emulsion sheets using machine learning techniques. The artificial neural network-based object detection model was trained on surrogate images created through Monte Carlo simulations and image-style transformations using generative adversarial networks. The performance of the proposed model was evaluated using alpha-decay events obtained from the J-PARC E07 emulsion data. The model achieved approximately twice the detection efficiency of conventional image processing and reduced the time spent on manual visual inspection by approximately 1/17. The established method was successfully applied to the detection of hypernuclear events. This approach is a state-of-the-art tool for discovering rare events recorded in nuclear emulsion sheets without any real data for training.

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at github.com/windygoo/PromptNucSeg

Nuclear segmentation, classification and quantification within Haematoxylin & Eosin stained histology images enables the extraction of interpretable cell-based features that can be used in downstream explainable models in computational pathology (CPath). However, automatic recognition of different nuclei is faced with a major challenge in that there are several different types of nuclei, some of them exhibiting large intraclass variability. In this work, we propose an approach that combine Separable-HoverNet and Instance-YOLOv5 to indentify colon nuclei small and unbalanced. Our approach can achieve mPQ+ 0.389 on the Segmentation and Classification-Preliminary Test Dataset and r2 0.599 on the Cellular Composition-Preliminary Test Dataset on ISBI 2022 CoNIC Challenge.

Pre-trained on a large and diverse dataset, the segment anything model (SAM) is the first promptable foundation model in computer vision aiming at object segmentation tasks. In this work, we evaluate SAM for the task of nuclear instance segmentation performance with zero-shot learning and finetuning. We compare SAM with other representative methods in nuclear instance segmentation, especially in the context of model generalisability. To achieve automatic nuclear instance segmentation, we propose using a nuclei detection model to provide bounding boxes or central points of nu-clei as visual prompts for SAM in generating nuclear instance masks from histology images.

Nuclei detection and segmentation in hematoxylin and eosin-stained (H&E) tissue images are important clinical tasks and crucial for a wide range of applications. However, it is a challenging task due to nuclei variances in staining and size, overlapping boundaries, and nuclei clustering. While convolutional neural networks have been extensively used for this task, we explore the potential of Transformer-based networks in this domain. Therefore, we introduce a new method for automated instance segmentation of cell nuclei in digitized tissue samples using a deep learning architecture based on Vision Transformer called CellViT. CellViT is trained and evaluated on the PanNuke dataset, which is one of the most challenging nuclei instance segmentation datasets, consisting of nearly 200,000 annotated Nuclei into 5 clinically important classes in 19 tissue types. We demonstrate the superiority of large-scale in-domain and out-of-domain pre-trained Vision Transformers by leveraging the recently published Segment Anything Model and a ViT-encoder pre-trained on 104 million histological image patches - achieving state-of-the-art nuclei detection and instance segmentation performance on the PanNuke dataset with a mean panoptic quality of 0.50 and an F1-detection score of 0.83. The code is publicly available at https://github.com/TIO-IKIM/CellViT

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

We introduce an optical tweezer platform for assembling and individually manipulating a two-dimensional register of nuclear spin qubits. Each nuclear spin qubit is encoded in the ground ^{1}S_{0} manifold of ^{87}Sr and is individually manipulated by site-selective addressing beams. We observe that spin relaxation is negligible after 5 seconds, indicating that T_1gg5 s. Furthermore, utilizing simultaneous manipulation of subsets of qubits, we demonstrate significant phase coherence over the entire register, estimating T_2^star = left(21pm7right) s and measuring T_2^echo=left(42pm6right) s.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

In biological research, fluorescence staining is a key technique to reveal the locations and morphology of subcellular structures. However, it is slow, expensive, and harmful to cells. In this paper, we model it as a deep learning task termed subcellular structure prediction (SSP), aiming to predict the 3D fluorescent images of multiple subcellular structures from a 3D transmitted-light image. Unfortunately, due to the limitations of current biotechnology, each image is partially labeled in SSP. Besides, naturally, subcellular structures vary considerably in size, which causes the multi-scale issue of SSP. To overcome these challenges, we propose Re-parameterizing Mixture-of-Diverse-Experts (RepMode), a network that dynamically organizes its parameters with task-aware priors to handle specified single-label prediction tasks. In RepMode, the Mixture-of-Diverse-Experts (MoDE) block is designed to learn the generalized parameters for all tasks, and gating re-parameterization (GatRep) is performed to generate the specialized parameters for each task, by which RepMode can maintain a compact practical topology exactly like a plain network, and meanwhile achieves a powerful theoretical topology. Comprehensive experiments show that RepMode can achieve state-of-the-art overall performance in SSP.

We describe a new detector, called NuLat, to study electron anti-neutrinos a few meters from a nuclear reactor, and search for anomalous neutrino oscillations. Such oscillations could be caused by sterile neutrinos, and might explain the "Reactor Antineutrino Anomaly". NuLat, is made possible by a natural synergy between the miniTimeCube and mini-LENS programs described in this paper. It features a "Raghavan Optical Lattice" (ROL) consisting of 3375 boron or ^6Li loaded plastic scintillator cubical cells 6.3\,cm (2.500") on a side. Cell boundaries have a 0.127\,mm (0.005") air gap, resulting in total internal reflection guiding most of the light down the 3 cardinal directions. The ROL detector technology for NuLat gives excellent spatial and energy resolution and allows for in-depth event topology studies. These features allow us to discern inverse beta decay (IBD) signals and the putative oscillation pattern, even in the presence of other backgrounds. We discuss here test venues, efficiency, sensitivity and project status.

The study of high-speed rotating matter is a crucial research topic in physics due to the emergence of novel phenomena. In this paper, we combined cranking covariant density functional theory (CDFT) with a similar renormalization group approach to decompose the Hamiltonian from the cranking CDFT into different Hermit components, including the non-relativistic term, the dynamical term, the spin-orbit coupling, and the Darwin term. Especially, we obtained the rotational term, the term relating to Zeeman effect-like, and the spin-rotation coupling due to consideration of rotation and spatial component of vector potential. By exploring these operators, we aim to identify novel phenomena that may occur in rotating nuclei. Signature splitting, Zeeman effect-like, spin-rotation coupling, and spin current are among the potential novelties that may arise in rotating nuclei. Additionally, we investigated the observability of these phenomena and their dependence on various factors such as nuclear deformation, rotational angular velocity, and strength of magnetic field.

Every second greater than 10^{25} antineutrinos radiate to space from Earth, shining like a faint antineutrino star. Underground antineutrino detectors have revealed the rapidly decaying fission products inside nuclear reactors, verified the long-lived radioactivity inside our planet, and informed sensitive experiments for probing fundamental physics. Mapping the anisotropic antineutrino flux and energy spectrum advance geoscience by defining the amount and distribution of radioactive power within Earth while critically evaluating competing compositional models of the planet. We present the Antineutrino Global Map 2015 (AGM2015), an experimentally informed model of Earth's surface antineutrino flux over the 0 to 11 MeV energy spectrum, along with an assessment of systematic errors. The open source AGM2015 provides fundamental predictions for experiments, assists in strategic detector placement to determine neutrino mass hierarchy, and aids in identifying undeclared nuclear reactors. We use cosmochemically and seismologically informed models of the radiogenic lithosphere/mantle combined with the estimated antineutrino flux, as measured by KamLAND and Borexino, to determine the Earth's total antineutrino luminosity at 3.4^{+2.3}_{-2.2} times 10^{25} nu_e. We find a dominant flux of geo-neutrinos, predict sub-equal crust and mantle contributions, with sim1% of the total flux from man-made nuclear reactors.

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the observation of their conformational changes in real time. The innovative liquid-phase electron microscopy (liquid-phase EM) technique allows molecules to be placed in the native liquid environment, providing a unique opportunity to observe their dynamics. In this paper, we propose TEMPOR, a Temporal Electron MicroscoPy Object Reconstruction algorithm for liquid-phase EM that leverages an implicit neural representation (INR) and a dynamical variational auto-encoder (DVAE) to recover time series of molecular structures. We demonstrate its advantages in recovering different motion dynamics from two simulated datasets, 7bcq and Cas9. To our knowledge, our work is the first attempt to directly recover 3D structures of a temporally-varying particle from liquid-phase EM movies. It provides a promising new approach for studying molecules' 3D dynamics in structural biology.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

With the rapid development of computational pathology, many AI-assisted diagnostic tasks have emerged. Cellular nuclei segmentation can segment various types of cells for downstream analysis, but it relies on predefined categories and lacks flexibility. Moreover, pathology visual question answering can perform image-level understanding but lacks region-level detection capability. To address this, we propose a new benchmark called Pathology Visual Grounding (PathVG), which aims to detect regions based on expressions with different attributes. To evaluate PathVG, we create a new dataset named RefPath which contains 27,610 images with 33,500 language-grounded boxes. Compared to visual grounding in other domains, PathVG presents pathological images at multi-scale and contains expressions with pathological knowledge. In the experimental study, we found that the biggest challenge was the implicit information underlying the pathological expressions. Based on this, we proposed Pathology Knowledge-enhanced Network (PKNet) as the baseline model for PathVG. PKNet leverages the knowledge-enhancement capabilities of Large Language Models (LLMs) to convert pathological terms with implicit information into explicit visual features, and fuses knowledge features with expression features through the designed Knowledge Fusion Module (KFM). The proposed method achieves state-of-the-art performance on the PathVG benchmark.

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

This paper will discuss the microphysical simulation of interactions in liquid xenon, the active detector medium in many leading rare-event searches for new physics, and describe experimental observables useful for understanding detector performance. The scintillation and ionization yield distributions for signal and background will be presented using the Noble Element Simulation Technique (NEST), which is a toolkit based on experimental data and simple, empirical formulae, which mimic previous microphysics modeling, but are guided by data. The NEST models for light and charge production as a function of the particle type, energy, and electric field will be reviewed, as well as models for energy resolution and final pulse areas. NEST will be compared to other models or sets of models, and vetted against real data, with several specific examples pulled from XENON, ZEPLIN, LUX, LZ, PandaX, and table-top experiments used for calibrations.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Astrochemical models of interstellar clouds, the sites of stars, and planet formation require information about spin-state chemistry to allow quantitative comparison with spectroscopic observations. In particular, it is important to know if full scrambling or H abstraction (also known as proton hopping) takes place in ion-neutral reactions. The reaction of Cl+ and HCl+ with H2 and isotopologues has been studied at cryogenic temperatures between 20 and 180 K using a 22 pole radio frequency ion trap. Isotopic exchange processes are used to probe the reaction mechanism of the HCl+ + H2 reaction. The results are compared with previous measurements and theoretical predictions. The rate coefficients for the Cl+ + H2 and HCl+ + H2 reactions are found to be constant in the range of temperatures studied, except for the DCl+ + D2 reaction, where a weak negative temperature dependence is observed, and reactions with D2 are found to be significantly slower than the Langevin rate. No isotopic exchange reactions are observed to occur for the H2Cl+ ion. The analysis of the products of the HCl+ + H2 isotopic system clearly indicates that the reaction proceeds via simple hydrogen atom abstraction.

The measured neutron flux from the Moons south polar region shows evidence of locally enhanced hydrogen concentrations, likely in the form of water ice, within most permanently shadowed regions (PSR), poleward of 77 deg S latitude. Results are consistent with the original findings of Watson et al, 1961, which found that the PSRs cryogenic surfaces create exclusive conditions for the sequestration of water ice, due to their extremely low sublimation rates. Widespread PSR hydrogenation is demonstrated in several studies by showing that the contrasting PSR area distribution is being instrumentally blurred. The PSRs expected hydrogen observations are correlated by their area fraction of the fixed 30 km diameter footprint area of the Collimated Sensor for Epithermal Neutrons (CSETN), which is part of the Lunar Exploration Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter (LRO). The correlation indicates that the PSRs are similarly hydrogenated, with an expected concentration = 0.27 wt%, relative to that of the anhydrous reference terrain (lower bounds). Hydrogen concentrations are demonstrated to be correlated to maximum temperature distributions within the basins of Haworth, Shoemaker and Faustini PSRs. Cabeus-1 PSR shows an anomalously enhanced hydrogen concentration indicating a second process contributes to its hydrogen budget. Results are consistent with ongoing processes that introduce volatiles to the surface including outgassing, solar wind production with regolith silicates, and mixing from small scale meteor impacts and diurnal temperature variation. We validate the bandpass filter used to subtract CSETNs detection of uncollimated neutrons with profiles of several PSRs neutron suppression before and after processing. Keywords: Moon, Epithermal Neutron, Hydrogen, Water, Ice, Volatiles, LRO, LEND, Diviner, LOLA

Solar activity is one of the main drivers of variability in our solar system and the key source of space weather phenomena that affect Earth and near Earth space. The extensive record of high resolution extreme ultraviolet (EUV) observations from the Solar Dynamics Observatory (SDO) offers an unprecedented, very large dataset of solar images. In this work, we make use of this comprehensive dataset to investigate capabilities of current state-of-the-art generative models to accurately capture the data distribution behind the observed solar activity states. Starting from StyleGAN-based methods, we uncover severe deficits of this model family in handling fine-scale details of solar images when training on high resolution samples, contrary to training on natural face images. When switching to the diffusion based generative model family, we observe strong improvements of fine-scale detail generation. For the GAN family, we are able to achieve similar improvements in fine-scale generation when turning to ProjectedGANs, which uses multi-scale discriminators with a pre-trained frozen feature extractor. We conduct ablation studies to clarify mechanisms responsible for proper fine-scale handling. Using distributed training on supercomputers, we are able to train generative models for up to 1024x1024 resolution that produce high quality samples indistinguishable to human experts, as suggested by the evaluation we conduct. We make all code, models and workflows used in this study publicly available at https://github.com/SLAMPAI/generative-models-for-highres-solar-images.

Solar photospheric abundances and CI-chondrite compositions are reviewed and updated to obtain representative solar system abundances of the elements and their isotopes. The new photospheric abundances obtained here lead to higher solar metallicity. Full 3D NLTE photospheric analyses are only available for 11 elements. A quality index for analyses is introduced. For several elements, uncertainties remain large. Protosolar mass fractions are H (X = 0.7060), He (Y = 0.2753), and for metals Li to U (Z = 0.0187). The protosolar (C+N)/H agrees within 13% with the ratio for the solar core from the Borexino experiment. Elemental abundances in CI-chondrites were screened by analytical methods, sample sizes, and evaluated using concentration frequency distributions. Aqueously mobile elements (e.g., alkalis, alkaline earths, etc.) often deviate from normal distributions indicating mobilization and/or sequestration into carbonates, phosphates, and sulfates. Revised CI-chondrite abundances of non-volatile elements are similar to earlier estimates. The moderately volatile elements F and Sb are higher than before, as are C, Br and I, whereas the CI-abundances of Hg and N are now significantly lower. The solar system nuclide distribution curves of s-process elements agree within 4% with s-process predictions of Galactic chemical evolution models. P-process nuclide distributions are assessed. No obvious correlation of CI-chondritic to solar elemental abundance ratios with condensation temperatures is observed, nor is there one for ratios of CI-chondrites/solar wind abundances.

Ultracold gases of highly magnetic lanthanide atoms have enabled the realisation of dipolar quantum droplets and supersolids. However, future studies could be limited by the achievable atom numbers and hindered by high three-body loss rates. Here we study density-dependent atom loss in an ultracold gas of {}^{166}Er for magnetic fields below 4 G, identifying six previously unknown features which display both a strong temperature dependence and also sensitivity to the polarisation and intensity of the light used to optically trap the atoms. This detailed knowledge of the loss landscape allows us to optimise the production of dipolar BECs with more than 2 times 10^5 atoms and points towards optimal strategies for the study of large-atom-number dipolar gases in the droplet and supersolid regimes.

Since the last nuclear atmospheric test carried out by the People Republic of China in 1980 and since the Chernobyl accident in 1986, the plutonium hasn't been directly released into the atmosphere. However, nowadays, it is still present in the troposphere. This is due to plutonium-bearing soil particles physical resuspension processes. In this work, we study for the first time the temporal variation of plutonium isotopes, 239Pu and 240Pu, baseline concentrations on a monthly basis in surface air from Seville (Spain), and their correlation with some tracers of mineral dust, during 2001 and 2002. The Pu analyses were performed by low-energy Accelerator Mass Spectrometry (AMS). The 239Pu plus 240Pu (239+240Pu) activity levels achieved maximums during the summer period, characterized by the absence of rains, and minimums during the rainy seasons, laying in the range 1-20 nBq per cubic meter. The 240Pu/239Pu two-year average atomic ratio was 0.18(0.03), in agreement with the fallout plutonium. A good correlation with Pu and Al and Ti levels is observed. They are crustal components usually used as tracers of African dust over European countries. The hypothesis of the influence of the Saharan dust intrusions is supported as well through the study of Total Ozone Mass Spectrometer (TOMS) daily images.

Low-mass X-ray binaries with a neutron star as the primary object show a complex array of phenomenology during outbursts. The observed variability in X-ray emission primarily arises from changes in the innermost regions of the accretion disk, neutron star surface, and corona. In this work, we present the results of a comprehensive X-ray spectral and timing analysis of the neutron star transient MAXI J1807+132 during its 2023 outburst using data from the NICER observatory. The outburst is marked by a very rapid rise in the count rate by about a factor of 20 in a day. The source undergoes full state transitions and displays hysteresis effect in the hardness and rms intensity diagrams. Spectral analysis with a three-component model is consistent with disk truncation during the hard states and reaching the last stable orbit during the intermediate and soft states. We discuss the different values of the last stable radius in the context of possible distance of the source and magnetic field strength. The characteristic frequencies throughout the hard and intermediate states are found to be strongly correlated with the inner radius of the disk. Together with the spectral and fast variability properties, we attempt to trace the evolution of the size of the corona along the outburst. Following the main outburst, the source undergoes a high amplitude reflare wherein it shows a complex behavior with relatively high variability (10 %), but low hardness.

A dynamical model based on a phenomenological charm quark-nucleon(c-N) potential v_{cN} and the Pomeron-exchange mechanism is constructed to investigate the J/Psi photo-production on the nucleon from threshold to invariant mass W=300 GeV. The J/Psi-N potential,V_{J/Psi N}(r),is constructed by folding v_{cN} into the wavefunction Phi_{J/Psi}(cc) of J/Psi within a Constituent Quark Model(CQM) of Ref.[43]. A photo-production amplitude is also generated by v_{cN} by a cc-loop integration over the gammarightarrow cc vertex function and Phi_{J/Psi}(cc). No commonly used Vector Meson Dominance assumption is used to define this photo-production amplitude which is needed to describe the data near the threshold. The potential v_{cN}(r) is parameterized in a form such that the predicted V_{J/Psi N}(r) at large distances has the same Yukawa potential form extracted from a Lattice QCD(LQCD) calculation of Ref.[18]. The parameters of v_{cN} are determined by fitting the total cross section data of JLab by performing calculations that include J/Psi-N final state interactions(FSI). The resulting differential cross sections are found in good agreements with the data. It is shown that the FSI effects dominate the cross section in the very near threshold region, allowing for sensitive testing of the predicted J/Psi-N scattering amplitudes. By imposing the constraints of J/Psi-N potential extracted from the LQCD calculation, we have obtained three J/Psi-N potentials which fit the JLab data equally well. The resulting J/Psi-N scattering lengths are in the range of a=(-0.05 fm sim -0.25 fm). With the determined v_{cN}(r) and the wavefunctions generated from the same CQM, the constructed model is used to predict the cross sections of photo-production of eta_c(1S) and Psi(2S) mesons for future experimental tests.

An amplitude analysis of B^-rightarrow D^- D^0 K_S^0 decays is performed using proton-proton collision data, corresponding to an integrated luminosity of 9,fb^{-1}, collected with the LHCb detector at center-of-mass energies of 7, 8, and 13,Tekern -0.1em V. A resonant structure of spin-parity 0^+ is observed in the D^0 K_S^0 invariant-mass spectrum with a significance of 5.3,sigma. The mass and width of the state, modeled with a Breit-Wigner lineshape, are determined to be 2883pm11pm6,Mekern -0.1em V!/c^2 and 87_{-47}^{+22}pm6,Mekern -0.1em V respectively, where the first uncertainties are statistical and the second systematic. These properties and the quark content are consistent with those of the open-charm tetraquark state T_{cs 0}^{*}(2870)^0 observed previously in the D^+ K^- final state of the B^-rightarrow D^- D^+ K^- decay. This result confirms the existence of the T_{cs 0}^{*}(2870)^0 state in a new decay mode. The T_{cs1}^{*}(2900)^0 state, reported in the B^-rightarrow D^- D^+ K^- decay, is also searched for in the D^0 K_S^0 invariant-mass spectrum of the B^- rightarrow D^- D^0 K_S^0 decay, without finding evidence for it.

Computational pathology can lead to saving human lives, but models are annotation hungry and pathology images are notoriously expensive to annotate. Self-supervised learning has shown to be an effective method for utilizing unlabeled data, and its application to pathology could greatly benefit its downstream tasks. Yet, there are no principled studies that compare SSL methods and discuss how to adapt them for pathology. To address this need, we execute the largest-scale study of SSL pre-training on pathology image data, to date. Our study is conducted using 4 representative SSL methods on diverse downstream tasks. We establish that large-scale domain-aligned pre-training in pathology consistently out-performs ImageNet pre-training in standard SSL settings such as linear and fine-tuning evaluations, as well as in low-label regimes. Moreover, we propose a set of domain-specific techniques that we experimentally show leads to a performance boost. Lastly, for the first time, we apply SSL to the challenging task of nuclei instance segmentation and show large and consistent performance improvements under diverse settings.

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

The recent surge in performance for image analysis of digitised pathology slides can largely be attributed to the advances in deep learning. Deep models can be used to initially localise various structures in the tissue and hence facilitate the extraction of interpretable features for biomarker discovery. However, these models are typically trained for a single task and therefore scale poorly as we wish to adapt the model for an increasing number of different tasks. Also, supervised deep learning models are very data hungry and therefore rely on large amounts of training data to perform well. In this paper, we present a multi-task learning approach for segmentation and classification of nuclei, glands, lumina and different tissue regions that leverages data from multiple independent data sources. While ensuring that our tasks are aligned by the same tissue type and resolution, we enable meaningful simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve the performance of additional tasks via transfer learning, including nuclear classification and signet ring cell detection. As part of this work, we train our developed Cerberus model on a huge amount of data, consisting of over 600K objects for segmentation and 440K patches for classification. We use our approach to process 599 colorectal whole-slide images from TCGA, where we localise 377 million, 900K and 2.1 million nuclei, glands and lumina, respectively and make the results available to the community for downstream analysis.

The automatic extraction of materials and related properties from the scientific literature is gaining attention in data-driven materials science (Materials Informatics). In this paper, we discuss Grobid-superconductors, our solution for automatically extracting superconductor material names and respective properties from text. Built as a Grobid module, it combines machine learning and heuristic approaches in a multi-step architecture that supports input data as raw text or PDF documents. Using Grobid-superconductors, we built SuperCon2, a database of 40324 materials and properties records from 37700 papers. The material (or sample) information is represented by name, chemical formula, and material class, and is characterized by shape, doping, substitution variables for components, and substrate as adjoined information. The properties include the Tc superconducting critical temperature and, when available, applied pressure with the Tc measurement method.

We present new JWST-NIRSpec IFS data for the luminous infrared galaxy NGC7469: a nearby (70.6Mpc) active galaxy with a Sy 1.5 nucleus that drives a highly ionized gas outflow and a prominent nuclear star-forming ring. Using the superb sensitivity and high spatial resolution of the JWST instrument NIRSpec-IFS, we investigate the role of the Seyfert nucleus in the excitation and dynamics of the circumnuclear gas. Our analysis focuses on the [Fe ii], H2, and hydrogen recombination lines that trace the radiation/shocked-excited molecular and ionized ISM around the AGN. We investigate the gas excitation through H2/Br{\gamma} and [Fe ii]/Paeta emission line ratios and find that photoionization by the AGN dominates within the central 300 pc of the galaxy and together with a small region show ing signatures of shock-heated gas; these shock-heated regions are likely associated with a compact radio jet. In addition, the velocity field and velocity dispersion maps reveal complex gas kinematics. Rotation is the dominant feature, but we also identify non-circular motions consistent with gas inflows as traced by the velocity residuals and the spiral pattern in the Pa{\alpha} velocity dispersion map. The inflow is consistent with the mass outflow rate and two orders of magnitude higher than the AGN accretion rate. The compact nuclear radio jet has enough power to drive the highly ionized outflow. This scenario suggests that the inflow and outflow are in a self-regulating feeding-feedback process, with a contribution from the radio jet helping to drive the outflow.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Volatiles like H_2O are present as ice in solids in the outer cold regions of protoplanetary disks and as vapor in the warm inner regions within the water snow line. Icy pebbles drifting inwards from the outer disk sublimate after crossing the snow line, enriching the inner disk with solid mass and water vapor. Meanwhile, proto-planets forming within the disk open gaps in the disk gas, creating traps against the inward drift of pebbles and in turn reducing water enrichment in the inner disk. Recent disk observations from millimeter interferometry and infrared spectroscopy have supported this broad picture by finding a correlation between the outer radial distribution of pebbles and the properties of inner water vapor spectra. In this work, we aim at further informing previous and future observations by building on previous models to explore pebble drift in disks with multiple gaps. We systematically explore multiple gap locations and their depths (equivalent to specific masses of planets forming within), and different particle sizes to study their impact on inner disk water enrichment. We find that the presence of close-in deep gaps carved by a Jupiter-mass planet is likely crucial for blocking icy pebble delivery into the inner disk, while planets with lower masses only provide leaky traps. We also find that disks with multiple gaps show lower vapor enrichment in the inner disk. Altogether, these model results support the idea that inner disk water delivery and planet formation are regulated by the mass and location of the most massive planets.

We use deep, mu_{r} lesssim 28,mag,arcsec^{-2}, r-band imaging from the Dark Energy Camera Legacy Survey (DECaLS) to search for past, or ongoing, merger activity in a sample of 282 Low Excitation Radio Galaxies (LERGs) at z<0.07. Our principle aim is to assess the the role of mergers in the evolution of LERGs. Exploiting the imaging depth, we classify tidal remnants around galaxies as both minor and major morphological disturbances for our LERG sample and 1,622 control galaxies matched in redshift, stellar mass, and environment. In groups and in the field, the LERG minor merger fraction is consistent with the control population. In galaxy clusters, 8.8 pm 2.9, % of LERGs show evidence of recent minor mergers in contrast to 23.0pm 2.0, % of controls. This sim 4 sigma deficit of minor mergers in cluster LERGs suggests these events may inhibit this type of nuclear activity for galaxies within the cluster environment. We observe a > 4sigma excess of major mergers in the LERGs with M_{*} lesssim 10^{11},M_{odot}, with 10 pm 1.5, % of these AGN involved in such large-scale interactions compared to 3.2 pm 0.4,% of control galaxies. This excess of major mergers in LERGs decreases with increasing stellar mass, vanishing by M_{*} > 10^{11.3},M_{odot}. These observations show that minor mergers do not fuel LERGs, and are consistent with typical LERGs being powered by accretion of matter from their halo. Where LERGs are associated with major mergers, these objects may evolve into more efficiently accreting active galactic nuclei as the merger progresses and more gas falls on to the central engine.

Magnetohydrodynamic turbulence drives the central engine of post-merger remnants, potentially powering both a nucleosynthetically active disk wind and the relativistic jet behind a short gamma ray burst. We explore the impact of the magnetic field on this engine by simulating three post-merger black hole accretion disks using general relativistic magnetohydrodynamics with Monte Carlo neutrino transport, in each case varying the initial magnetic field strength. We find increasing ejecta masses associated with increasing magnetic field strength. We find that a fairly robust main r -process pattern is produced in all three cases, scaled by the ejected mass. Changing the initial magnetic field strength has a considerable effect on the geometry of the outflow and hints at complex central engine dynamics influencing lanthanide outflows. We find that actinide production is especially sensitive to magnetic field strength, with overall actinide mass fraction calculated at 1 Gyr post-merger increasing by more than a factor of six with a tenfold increase in magnetic field strength. This hints at a possible connection to the variability in actinide enhancements exhibited by metal poor, r -process-enhanced stars.

In this work, we explore two classes of density dependent relativistic mean-field models, their predictions of proton fractions at high densities and neutron star structure. We have used a metamodelling approach to these relativistic density functionals. We have generated a large ensemble of models with these classes and then applied constraints from theoretical and experimental nuclear physics and astrophysical observations. We find that both models produce similar equations of state and neutron star mass-radius sequences. But, their underlying compositions, denoted by the proton fraction in this case, are vastly different. This reinstates previous findings that information on composition gets masqueraded in beta-equilibrium. Additional observations of non-equilibrium phenomena are necessary to pin it down.

Along with binary neutron star mergers, the in-spiral and merger of a black hole and a neutron star is a predicted site of r-process nucleosynthesis and associated kilonovae. For the right mass ratio, very large amounts of neutron rich material may become unbound from the post-merger accretion disk. We simulate a suite of four post-merger disks with full-transport general relativistic neutrino radiation magnetohydrodynamics. We find that the outflows from these disks are very close to the threshold conditions for robust r-process nucleosynthesis. For these conditions, the detailed properties of the outflow determine whether a full r-process can or cannot occur, implying that a wide range of observable phenomena are possible. We show that on average the disk outflow lanthanide fraction is suppressed relative to the solar isotopic pattern. In combination with the dynamical ejecta, these outflows imply a kilonova with both blue and red components.

In this work, we show that, if axion-like particles (ALPs) from core-collapse supernovae (SNe) couple to protons, they would produce very characteristic signatures in neutrino water Cherenkov detectors through their scattering off free protons via a , p rightarrow p , gamma interactions. Specifically, sub-MeV ALPs would generate photons with energies sim 30 MeV, which could be observed by Super-Kamiokande and Hyper-Kamiokande as a delayed signal after a future detection of SN neutrinos. We apply this to a hypothetical neighbouring SN (at a maximum distance of 100 kpc) and demonstrate that the region in the parameter space with ALP masses between 10^{-4} MeV and 1 MeV and ALP-proton couplings in the range 3 times 10^{-6}-4 times 10^{-5} could be probed. We argue that this new signature, combined with the one expected at sim 7 MeV from oxygen de-excitation, would allow us to disentangle ALP-neutron and ALP-proton couplings.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Context. Low-mass bodies, such as comets, asteroids, planetesimals, and free-floating planets, are continuously injected into the intra-cluster environment after expulsion from their host planetary systems. These can be modeled as massless particles (MLPs, hereafter). The dynamics of large populations of MLPs, however, has yet received little attention in literature. Aims. We investigate the dynamical evolution of MLP populations in star clusters, and characterize their kinematics and ejection rates. Methods. We present NBODY6++GPU-MASSLESS, a modified version of the N-body simulation code NBODY6++GPU, that allows fast integration of star clusters that contain large numbers of massless particles (MLPs). NBODY6++GPU-MASSLESS contains routines specifically directed at the dynamical evolution of low-mass bodies, such as planets. Results. Unlike stars, MLPs do not participate in the mass segregation process. Instead, MLPs mostly follow the gravitational potential of the star cluster, which gradually decreases over time due to stellar ejections and stellar evolution. The dynamical evolution of MLPs is primarily affected by the evolution of the core of the star cluster. This is most apparent in the outer regions for clusters with higher initial densities. High escape rates of MLPs are observed before the core-collapse, after which escape rates remain stable. Denser star clusters undergo a more intense core collapse, but this does not impact the dynamical evolution of MLPs. The speeds of escaping stars are similar to those of escaping MLPs, when disregarding the high-velocity ejections of neutron stars during the first 50 Myr.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

Interior models of gas giants in the Solar System traditionally assume a fully convective molecular hydrogen envelope. However, recent observations from the Juno mission suggest a possible depletion of alkali metals in Jupiter's molecular hydrogen envelope, indicating that a stable radiative layer could exist at the kilobar level. Recent studies propose that deep stable layers help reconcile various Jupiter observations, including its atmospheric water and CO abundances and the depth of its zonal winds. However, opacity tables used to infer stable layers are often outdated and incomplete, leaving the precise molecular hydrogen envelope composition required for a deep radiative zone uncertain. In this paper, we determine atmospheric compositions that can lead to the formation of a radiative zone at the kilobar level in Jupiter and Saturn today. We computed radiative opacity tables covering pressures up to 10^5 bar, including the most abundant molecules present in the gas giants of the Solar System, as well as contributions from free electrons, metal hydrides, oxides, and atomic species, using the most up-to-date line lists published in the literature. These tables were used to calculate Rosseland-mean opacities for the molecular hydrogen envelopes of Jupiter and Saturn, which were then compared to the critical mean opacity required to maintain convection. We find that the presence of a radiative zone is controlled by the existence of K, Na, and NaH in the atmosphere of Jupiter and Saturn. For Jupiter, the elemental abundance of K and Na must be less than sim 10^{-3} times solar to form a radiative zone. In contrast, for Saturn, the required abundance for K and Na is below sim 10^{-4} times solar.

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.

We present developments and applications for the diagonalization of shell-model hamiltonians in a discrete non-orthogonal basis (DNO-SM). The method, and its actual numerical implementation CARINA, based on mean-field and beyond-mean field techniques has already been applied in previous studies and is focused on basis states selection optimization. The method is benchmarked against a full set of sd shell exact diagonalizations, and is applied for the first time to the heavy deformed ^{254}No nucleus.

Methods. We utilized the combined five SRG/eROSITA All-Sky Survey data (eRASS:5) to perform X-ray imaging and spectral analyses of the Centaurus cluster in various directions to large radii. Surface brightness (SB) profiles out to 2R_{200} were constructed. We acquired gas temperature, metallicity, and normalization per area profiles out to R_{200}. We compared our results with previous Centaurus studies, cluster outskirts measurements, and simulations. Comprehensive sky background analysis was done across the FoV, in particular, to assess the variation of the eROSITA Bubble emission that partially contaminates the field. Results. The processed X-ray images show the known sloshing-induced structures in the core. The core (rleq11~kpc) is better described with a 2T model than a 1T model. Here, we measured lower T from the cooler component (~1.0 keV) and higher Z (sim!1.6Z_odot), signifying an iron bias. In the intermediate radial range, we observed prominent SB and normalization per area excesses in the eastern sector (Cen 45 location), reaching out to R_{500}. Temperature enhancements near the location of Cen 45 imply that the gas is shock-heated due to the interaction with Cen 30, the significant excess behind Cen 45 center might be the tail/ram-pressure-stripped gas. We found good agreement between the outskirt temperatures with the profile from simulations and fit from Suzaku outskirts measurements. We detected significant SB emission to the sky background level out to R_{200} with a 3.5sigma and followed by 2.9sigma at 1.1R_{200}. The metallicity at R_{500}-R_{200} is low but within the ranges of other outskirts studies. Conclusions. We present the first measurement of ICM morphology and properties of Centaurus cluster sampling the whole azimuth beyond 30', increasing the probed volume by a factor of almost 30.

As host to two accreting planets, PDS 70 provides a unique opportunity to probe the chemical complexity of atmosphere-forming material. We present ALMA Band 6 observations of the PDS~70 disk and report the first chemical inventory of the system. With a spatial resolution of 0.4''-0.5'' (sim50 au), 12 species are detected, including CO isotopologues and formaldehyde, small hydrocarbons, HCN and HCO+ isotopologues, and S-bearing molecules. SO and CH3OH are not detected. All lines show a large cavity at the center of the disk, indicative of the deep gap carved by the massive planets. The radial profiles of the line emission are compared to the (sub-)mm continuum and infrared scattered light intensity profiles. Different molecular transitions peak at different radii, revealing the complex interplay between density, temperature and chemistry in setting molecular abundances. Column densities and optical depth profiles are derived for all detected molecules, and upper limits obtained for the non detections. Excitation temperature is obtained for H2CO. Deuteration and nitrogen fractionation profiles from the hydro-cyanide lines show radially increasing fractionation levels. Comparison of the disk chemical inventory to grids of chemical models from the literature strongly suggests a disk molecular layer hosting a carbon to oxygen ratio C/O>1, thus providing for the first time compelling evidence of planets actively accreting high C/O ratio gas at present time.

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

We present Monte Carlo (MC) simulation results from a study of a compact plastic-scintillator detector suitable for imaging fast neutrons in the 1 -- 10 MeV energy range: the miniTimeCube (mTC). Originally designed for antineutrino detection, the mTC consists of 24 MultiChannel Plate (MCP) photodetectors surrounding a 13 cm cube of boron-doped plastic scintillator. Our simulation results show that waveform digitization of 1536 optically sensitive channels surrounding the scintillator should allow for spatiotemporal determination of individual neutron-proton scatters in the detector volume to thicksim100 picoseconds and thicksim5 mm. A Bayesian estimation framework is presented for multiple-scatter reconstruction, and is used to estimate the incoming direction and energy of simulated individual neutrons. Finally, we show how populations of reconstructed neutrons can be used to estimate the direction and energy spectrum of nearby simulated neutron sources.

Metadata are general characteristics of the data in a well-curated and condensed format, and have been proven to be useful for decision making, knowledge discovery, and also heterogeneous data organization of biobank. Among all data types in the biobank, pathology is the key component of the biobank and also serves as the gold standard of diagnosis. To maximize the utility of biobank and allow the rapid progress of biomedical science, it is essential to organize the data with well-populated pathology metadata. However, manual annotation of such information is tedious and time-consuming. In the study, we develop a multimodal multitask learning framework to predict four major slide-level metadata of pathology images. The framework learns generalizable representations across tissue slides, pathology reports, and case-level structured data. We demonstrate improved performance across all four tasks with the proposed method compared to a single modal single task baseline on two test sets, one external test set from a distinct data source (TCGA) and one internal held-out test set (TTH). In the test sets, the performance improvements on the averaged area under receiver operating characteristic curve across the four tasks are 16.48% and 9.05% on TCGA and TTH, respectively. Such pathology metadata prediction system may be adopted to mitigate the effort of expert annotation and ultimately accelerate the data-driven research by better utilization of the pathology biobank.

Detailed detector simulation is the major consumer of CPU resources at LHCb, having used more than 90% of the total computing budget during Run 2 of the Large Hadron Collider at CERN. As data is collected by the upgraded LHCb detector during Run 3 of the LHC, larger requests for simulated data samples are necessary, and will far exceed the pledged resources of the experiment, even with existing fast simulation options. An evolution of technologies and techniques to produce simulated samples is mandatory to meet the upcoming needs of analysis to interpret signal versus background and measure efficiencies. In this context, we propose Lamarr, a Gaudi-based framework designed to offer the fastest solution for the simulation of the LHCb detector. Lamarr consists of a pipeline of modules parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Most of the parameterizations are made of Deep Generative Models and Gradient Boosted Decision Trees trained on simulated samples or alternatively, where possible, on real data. Embedding Lamarr in the general LHCb Gauss Simulation framework allows combining its execution with any of the available generators in a seamless way. Lamarr has been validated by comparing key reconstructed quantities with Detailed Simulation. Good agreement of the simulated distributions is obtained with two-order-of-magnitude speed-up of the simulation phase.

We use new interior models of cold planets to investigate the mass-radius relationships of solid exoplanets, considering planets made primarily of iron, silicates, water, and carbon compounds. We find that the mass-radius relationships for cold terrestrial-mass planets of all compositions we considered follow a generic functional form that is not a simple power law: log_{10} R_s = k_1 + 1/3 log_{10}(M_s) - k_2 M_s^{k_3} for up to M_p approx 20 M_{oplus}, where M_s and R_s are scaled mass and radius values. This functional form arises because the common building blocks of solid planets all have equations of state that are well approximated by a modified polytrope of the form rho = rho_0 + c P^n. We find that highly detailed planet interior models, including temperature structure and phase changes, are not necessary to derive solid exoplanet bulk composition from mass and radius measurements. For solid exoplanets with no substantial atmosphere we have also found that: with 5% fractional uncertainty in planet mass and radius it is possible to distinguish among planets composed predominantly of iron or silicates or water ice but not more detailed compositions; with sim~5% uncertainty water ice planets with gtrsim 25% water by mass may be identified; the minimum plausible planet size for a given mass is that of a pure iron planet; and carbon planet mass-radius relationships overlap with those of silicate and water planets due to similar zero-pressure densities and equations of state. We propose a definition of "super Earths'' based on the clear distinction in radii between planets with significant gas envelopes and those without.

Front-end electronics equipped with high-speed digitizers are being used and proposed for future nuclear detectors. Recent literature reveals that deep learning models, especially one-dimensional convolutional neural networks, are promising when dealing with digital signals from nuclear detectors. Simulations and experiments demonstrate the satisfactory accuracy and additional benefits of neural networks in this area. However, specific hardware accelerating such models for online operations still needs to be studied. In this work, we introduce PulseDL-II, a system-on-chip (SoC) specially designed for applications of event feature (time, energy, etc.) extraction from pulses with deep learning. Based on the previous version, PulseDL-II incorporates a RISC CPU into the system structure for better functional flexibility and integrity. The neural network accelerator in the SoC adopts a three-level (arithmetic unit, processing element, neural network) hierarchical architecture and facilitates parameter optimization of the digital design. Furthermore, we devise a quantization scheme compatible with deep learning frameworks (e.g., TensorFlow) within a selected subset of layer types. We validate the correct operations of PulseDL-II on field programmable gate arrays (FPGA) alone and with an experimental setup comprising a direct digital synthesis (DDS) and analog-to-digital converters (ADC). The proposed system achieved 60 ps time resolution and 0.40% energy resolution at signal to noise ratio (SNR) of 47.4 dB.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

The catalog of ringed galaxies was compiled through visual classification of synthetic images from the TNG50 simulation. Galaxies were selected based on specific criteria: a redshift range of 0.01 < z < 0.1, stellar mass M_star >10^9 M_odot, stellar half-mass radius r_{50} > 1 kpc, and specific star formation rate (sSFR), log(sSFR/yr^{-1}) > -13. Our classification allowed for differentiation between inner rings, outer rings, combinations of rings, and partial rings (pseudo-rings), including barred and non-barred ringed galaxies. We constructed a control sample of non-ringed galaxies with similar redshift, stellar mass, and environmental density distributions. We identified 807 ringed galaxies. Approximately 59% possess an inner ring, 22% a partial ring, 12% an outer ring, and 7% have i+o rings. Our statistical analysis reveals that 64% (507 galaxies) exhibit bars. Ringed galaxies exhibit lower efficiency for star formation, reduced gas fractions, redder colors, and higher metallicities compared to non-ringed disk objects. They also show greater variability in metallicity for a given stellar mass. From the analysis of radial profiles, galaxies with outer rings exhibit a r_{50} similar to or slightly larger than their control group, while those with inner or partial rings tend to have smaller sizes. A deeper exploration of radial density profiles revealed a pronounced central mass deficit preceding the ring structures, with inner and outer rings located at r_{50} and 1.5 , r_{50}, respectively. Galaxies with both i+o rings have inner rings that are more compact and massive. Additionally, galaxies with partial rings exhibit deeper mass profiles than their controls, particularly in central areas. These findings improve our understanding of galactic evolution and the complex interplay between mass distribution and morphology.

In this paper we introduce the concept of what we call "NUDAR" (NeUtrino Direction and Ranging), making the point that measurements of the observed energy and direction vectors can be employed to passively deduce the exact three-dimensional location and thermal power of geophysical and anthropogenic neutrino sources from even a single detector. We present the most precise background estimates to date, all handled in full three dimensions, as functions of depth and geographical location. For the present calculations, we consider a hypothetical 138 kiloton detector which can be transported to an ocean site and deployed to an operational depth. We present a Bayesian estimation framework to incorporate any a priori knowledge of the reactor that we are trying to detect, as well as the estimated uncertainty in the background and the oscillation parameters. Most importantly, we fully employ the knowledge of the reactor spectrum and the distance-dependent effects of neutrino oscillations on such spectra. The latter, in particular, makes possible determination of range from one location, given adequate signal statistics. Further, we explore the rich potential of improving detection with even modest improvements in individual neutrino direction determination. We conclude that a 300 MWth reactor can indeed be geolocated, and its operating power estimated with one or two detectors in the hundred kiloton class at ranges out to a few hundred kilometers. We note that such detectors would have natural and non-interfering utility for scientific studies of geo-neutrinos, neutrino oscillations, and astrophysical neutrinos. This motivates the development of cost effective methods of constructing and deploying such next generation detectors.