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arXiv 2024年

作者： Remedios, Lucas W. Bao, Shunxing Remedios, Samuel W. Lee, Ho Hin Cai, Leon Y. Li, Thomas Deng, Ruining Newlin, Nancy R. Saunders, Adam M. Cui, Can Li, Jia Liu, Qi Lau, Ken S. Roland, Joseph T. Washington, Mary K. Coburn, Lori A. Wilson, Keith T. Huo, Yuankai Landman, Bennett A. Vanderbilt University Department of Computer Science Nashville United States Vanderbilt University Department of Electrical and Computer Engineering Nashville United States Johns Hopkins University Department of Computer Science Baltimore United States National Institutes of Health Department of Radiology and Imaging Sciences Bethesda United States Vanderbilt University Department of Biomedical Engineering Nashville United States Vanderbilt University Medical Center Department of Biostatistics Nashville United States Vanderbilt University Medical Center Center for Quantitative Sciences Nashville United States Vanderbilt University Medical Center Epithelial Biology Center Nashville United States Vanderbilt University School of Medicine Department of Cell and Developmental Biology Nashville United States Vanderbilt University Medical Center Division of Gastroenterology Hepatology and Nutrition Department of Medicine Nashville United States Vanderbilt University Medical Center Vanderbilt Center for Mucosal Inflammation and Cancer Nashville United States Vanderbilt University School of Medicine Program in Cancer Biology Nashville United States Veterans Affairs Tennessee Valley Healthcare System NashvilleTN United States Vanderbilt University Medical Center Department of Pathology Microbiology and Immunology NashvilleTN United States

Purpose: Cells are building blocks for human physiology;consequently, understanding the way cells communicate, co-locate, and interrelate is essential to furthering our understanding of how the body functions in both health and disease. Hematoxylin and eosin (H&E) is the standard stain used in histological analysis of tissues. Microscope slides of H&E-stained tissues are widely available in both clinical and research settings. While H&E is ubiquitous and reveals tissue microanatomy, the classification and tracking of cell subtypes often requires expert knowledge and the use of specialized stains, such as immunofluorescence staining. To reduce both the manual annotation burden and reliance on specialized staining technologies, artificial intelligence has been proposed for the automatic classification of cell types on H&E slides. For example, the recent Colon Nucleus Identification and Classification (CoNIC) Challenge focused on labeling 6 cell types on imaging of H&E stains from the human colon. However, this is a very small fraction of the number of potential cell subtypes within the intestines. Specifically, the CoNIC Challenge was unable to classify epithelial subtypes (progenitor, enteroendocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), and connective subtypes (fibroblasts). To approach this problem, we propose to use inter-modality learning to label previously un-labelable cell types on H&E. Approach: We take advantage of the cell classification information inherent in whole slide images (WSIs) of multiplexed immunofluorescence (MxIF) histology to create cell level annotations for 14 subclasses. We performed style transfer on the same MxIF tissues to synthesize realistic virtual H&E which we paired with the MxIF-derived cell subclassification labels. We evaluated the efficacy of using a supervised learning scheme where the input was realistic-quality virtual H&E and the labels were MxIF-derived cell subclasses. We assessed our model on a testing

关键词： Tissue

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Layer-dependent optically induced spin polarization in InSe

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Physical Review B 2023年第11期107卷 115304-115304页

作者： Jovan Nelson Teodor K. Stanev Dmitry Lebedev Trevor LaMountain J. Tyler Gish Hongfei Zeng Hyeondeok Shin Olle Heinonen Kenji Watanabe Takashi Taniguchi Mark C. Hersam Nathaniel P. Stern Applied Physics Program Northwestern University Evanston Illinois 60208 USA Department of Physics and Astronomy Northwestern University Evanston Illinois 60208 USA Department of Material Science and Engineering Northwestern University Evanston Illinois 60208 USA Computational Science Division Argonne National Laboratory Lemont Illinois 60439 USA Material Science Division Argonne National Laboratory Lemont Illinois 60439 USA Research Center for Functional Materials National Institute for Materials Science 1-1 Namiki Tsukuba 305-0044 Japan International Center for Materials Nanoarchitectonics National Institute for Materials Science 1-1 Namiki Tsukuba 305-0044 Japan Department of Chemistry Northwestern University Evanston Illinois 60208 USA Department of Electrical Engineering and Computer Science Northwestern University Evanston Illinois 60208 USA

Optical control of spin in semiconductors has been pioneered using nanostructures of III-V and II-VI semiconductors, but the emergence of two-dimensional van der Waals materials offers an alternative low-dimensional platform for spintronic phenomena. Indium selenide (InSe), a group-III monochalcogenide van der Waals material, has shown promise for optoelectronics due to its high electron mobility, tunable direct band gap, and quantum transport. In addition to these confirmed properties, there are predictions of spin-dependent optical selection rules, suggesting the potential for all-optical excitation and control of spin in a two-dimensional layered material. Despite these predictions, layer-dependent optical spin phenomena in InSe have yet to be explored. Here, we present measurements of layer-dependent optical spin dynamics in few-layer and bulk InSe. Polarized photoluminescence reveals layer-dependent optical orientation of spin, thereby demonstrating the optical selection rules in few-layer InSe. Spin dynamics are also studied in many-layer InSe using time-resolved Kerr rotation spectroscopy. By applying out-of-plane and in-plane static magnetic fields for polarized emission measurements and Kerr measurements, respectively, the g factor for InSe was extracted. Further investigations are done by calculating precession values using a k·p model, which is supported by ab initio density functional theory. Comparison of predicted precession rates with experimental measurements highlights the importance of excitonic effects in InSe for understanding spin dynamics. Optical orientation of spin is an important prerequisite for optospintronic phenomena and devices, and these first demonstrations of layer-dependent optical excitation of spins in InSe lay the foundation for combining layer-dependent spin properties with advantageous electronic properties found in this material.

关键词： Magneto-optics Spin dynamics Chalcogenides Layered semiconductors Van der Waals systems Density functional theory Kerr effect Photoluminescence k dot p method

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Topological Metamaterials

arXiv

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arXiv 2022年

作者： Ni, Xiang Yves, Simon Krasnok, Alex Alu, Andrea Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Department of Electrical and Computer Engineering Florida International University MiamiFL33174 United States Department of Electrical Engineering City College The City University of New York 160 Convent Avenue New York10031 United States Physics Program The Graduate Center The City University of New York 365 Fifth Avenue New York10016 United States

Unlike geometrical features, such as shape or volume, the topological properties of an object do not change continuously, but only due to abrupt transitions associated with a change in the integer quantities that describe these properties - known as topological invariants. In turn, this resilience of topological features is associated with intrinsic robustness. For example, the topological invariant known as the Chern number, associated with the quantization of the Hall conductance in a two-dimensional electron gas, supports disorder-immune electron transport at the surface of topological insulators (TIs). One of the most significant breakthroughs in physics of the last decade has been the discovery that materials with non-trivial topological properties for electronic, electromagnetic, acoustic and mechanical responses can be designed and manufactured at our will through engineered metamaterials (MMs). Here, we review the foundation and the state-of-the-art advances of topological photonics, acoustics and mechanical MMs. We discuss how topological MMs enable nontrivial wave phenomena in physics, engineering, of great interest for a broad range of interdisciplinary science disciplines such as classical and quantum chemistry. We first introduce the foundations of topological materials and the main concepts behind their peculiar features, including the concepts of topological charge and geometric phase. We then discuss the topology of electronic band structures in natural topological materials, like topological insulators and gapless Dirac and Weyl semimetals. Based on these concepts, we review the concept, design and response of topologically nontrivial MMs in photonics and phononics, including topological phases in 2D MMs with and without time-reversal symmetry, Floquet TIs based on spatial and temporal modulation, topological phases in 3D MMs, higher-order topological phases in MMs, non-Hermitian and nonlinear topological MMs and the topological features of scatteri

关键词： Metamaterials

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Quantum simulation of an extended Dicke model with a magnetic solid

Communications Materials

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Communications Materials 2024年第1期5卷 1-9页

作者： Marquez Peraca, Nicolas Li, Xinwei Moya, Jaime M. Hayashida, Kenji Kim, Dasom Ma, Xiaoxuan Neubauer, Kelly J. Fallas Padilla, Diego Huang, Chien-Lung Dai, Pengcheng Nevidomskyy, Andriy H. Pu, Han Morosan, Emilia Cao, Shixun Bamba, Motoaki Kono, Junichiro Department of Physics and Astronomy Rice University HoustonTX United States Department of Physics California Institute of Technology PasadenaCA United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX United States Division of Applied Physics Graduate School of Engineering Hokkaido University Hokkaido Japan Department of Electrical and Computer Engineering Rice University HoustonTX United States Department of Physics International Center of Quantum and Molecular Structures and Materials Genome Institute Shanghai University Shanghai China Department of Physics and Center for Quantum Frontiers of Research and Technology National Cheng Kung University Tainan Taiwan Department of Chemistry Rice University HoustonTX United States Department of Physics I Kyoto University Kyoto Japan The Hakubi Center for Advanced Research Kyoto University Kyoto Japan PRESTO Japan Science and Technology Agency Saitama Japan Department of Physics Yokohama National University Yokohama Japan Department of Materials Science and NanoEngineering Rice University HoustonTX United States

The Dicke model describes the cooperative interaction of an ensemble of two-level atoms with a single-mode photonic field and exhibits a quantum phase transition as a function of light–matter coupling strength. Extending this model by incorporating short-range atom–atom interactions makes the problem intractable but is expected to produce new physical phenomena and phases. Here, we simulate such an extended Dicke model using a crystal of ErFeO3, where the role of atoms (photons) is played by Er3+ spins (Fe3+ magnons). Through terahertz spectroscopy and magnetocaloric effect measurements as a function of temperature and magnetic field, we demonstrated the existence of a novel atomically ordered phase in addition to the superradiant and normal phases that are expected from the standard Dicke model. Further, we elucidated the nature of the phase boundaries in the temperature–magnetic-field phase diagram, identifying both first-order and second-order phase transitions. These results lay the foundation for studying multiatomic quantum optics models using well-characterized many-body solid-state systems. © The Author(s) 2024.

关键词： Atoms

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Beyond Bounds on Light Scattering with Complex Frequency Excitations

arXiv

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arXiv 2022年

作者： Kim, Seunghwi Lepeshov, Sergey Krasnok, Alex Alù, Andrea Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States DTU Electro Department of Electrical and Photonics Engineering Technical University of Denmark Ørsteds Plads 343 Kgs. LyngbyDK-2800 Denmark Department of Electrical and Computer Engineering Florida International University MiamiFL33174 United States Physics Program Graduate Center City University of New York New YorkNY10016 United States

Light scattering is one of the most established wave phenomena in optics, lying at the heart of light-matter interactions and of crucial importance for nanophotonic applications. Passivity, causality and energy conservation imply strict bounds on the degree of control over scattering from small particles, with implications on the performance of many optical devices. Here, we demonstrate that these bounds can be surpassed by considering excitations at complex frequencies, yielding extreme scattering responses as tailored nanoparticles reach a quasi-steady-state regime. These mechanisms can be used to engineer light scattering of nanostructures beyond conventional limits for noninvasive sensing, imaging, and nanoscale light manipulation. Copyright © 2022, The Authors. All rights reserved.

关键词： Light scattering

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Aerogel from sustainably grown bacterial cellulose pellicle as thermally insulative film for building envelope

arXiv

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arXiv 2022年

作者： Fleury, Blaise Abraham, Eldho De La Cruz, Joshua A. Chandrasekar, Varun S. Senyuk, Bohdan Liu, Qingkun Cherpak, Vladyslav Park, Sungoh ten Hove, Jan Bart Smalyukh, Ivan I. Department of Physics University of Colorado Boulder CO80309 United States Materials Science and Engineering Program University of Colorado Boulder CO80309 United States Soft Materials Research Center and Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado Boulder CO80303 United States

Improving building energy performance requires the development of new highly insulative materials. An affordable retrofitting solution comprising a thin film could improve the resistance to heat flow in both residential and commercial buildings and reduce overall energy consumption. Here we propose cellulose aerogel films formed from pellicles produced by the bacteria Gluconacetobacter hansenii as insulation materials. We studied the impact of density and nanostructure on the aerogels' thermal properties. Thermal conductivity as low as 13 mW/(K·m) was measured for native pellicle-based aerogels dried as-is with minimal post-treatment. The use of waste from the beer brewing industry as a solution to grow the pellicle maintained the cellulose yield obtained with standard Hestrin-Schramm medium, making our product more affordable and sustainable. In the future, our work can be extended through further diversification of the sources of substrate among food wastes, facilitating larger potential production and applications. © 2022, CC BY-NC-ND.

关键词： Aerogels

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Multimodal imaging of the mouse eye using visible light photoacoustic ophthalmoscopy and near-infrared-II optical coherence tomography

arXiv

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arXiv 2023年

作者： Haindl, Richard Bellemo, Valentina Rajendran, Praveenbalaji Tan, Bingyao Liu, Mengyang Zhou, Qifa Leitgeb, Rainer A. Drexler, Wolfgang Schmetterer, Leopold Pramanik, Manojit School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University 62 Nanyang Drive Singapore Singapore Centre for Medical Physics and Biomedical Engineering Medical University of Vienna Währinger Gürtel 18-20/4L Vienna Austria Singapore Eye Research Institute Singapore National Eye Centre Singapore Singapore Program Nanyang Technological University Singapore Singapore Department of Radiation Oncology Stanford University StanfordCA94305 United States University of Southern California Department of Biomedical Engineering Los AngelesCA90033 United States Ophthalmology and Visual Sciences Academic Clinical Program Duke-NUS Medical School National University of Singapore Singapore Department of Clinical Pharmacology Medical University Vienna Vienna Austria Institute of Molecular and Clinical Ophthalmology Basel Switzerland Department of Electrical and Computer Engineering Iowa State University AmesIA50011 United States

Non-invasive imaging plays a crucial role in diagnosing and studying eye diseases. However, existing photoacoustic ophthalmoscopy (PAOM) techniques in mice have limitations due to handling restrictions, suboptimal optical properties, limited availability of light sources and permissible light fluence at the retina. This study introduces an innovative approach that utilizes Rose Bengal, a contrast agent, to enhance PAOM contrast. This enables visualization of deeper structures like the choroidal microvasculature and sclera in the mouse eye using visible light. The integration of near-infrared-II optical coherence tomography (NIR-II OCT) provides additional tissue contrast and insights into potential NIR-II PAOM capabilities. To optimize imaging, we developed a cost-effective 3D printable mouse eye phantom and a fully 3D printable tip/tilt mouse platform. This solution elevates PAOM to a user-friendly technology, which can be used to address pressing research questions concerning several ocular diseases such as myopia, glaucoma and/or age-related macular degeneration in the future. © 2023, CC BY.

关键词： Optical tomography

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Nucleus subtype classification using inter-modality learning

arXiv

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arXiv 2024年

作者： Remedios, Lucas W. Bao, Shunxing Remedios, Samuel W. Lee, Ho Hin Cai, Leon Y. Li, Thomas Deng, Ruining Cui, Can Li, Jia Liu, Qi Lau, Ken S. Roland, Joseph T. Washington, Mary K. Coburn, Lori A. Wilson, Keith T. Huo, Yuankai Landman, Bennett A. Vanderbilt University Department of Computer Science Nashville United States Vanderbilt University Department of Electrical and Computer Engineering Nashville United States Johns Hopkins University Department of Computer Science Baltimore United States National Institutes of Health Department of Radiology and Imaging Sciences Bethesda United States Vanderbilt University Department of Biomedical Engineering Nashville United States Vanderbilt University Medical Center Department of Biostatistics Nashville United States Vanderbilt University Medical Center Center for Quantitative Sciences Nashville United States Vanderbilt University Medical Center Epithelial Biology Center Nashville United States Vanderbilt University School of Medicine Department of Cell and Developmental Biology Nashville United States Vanderbilt University Medical Center Division of Gastroenterology Hepatology and Nutrition Department of Medicine Nashville United States Vanderbilt University Medical Center Vanderbilt Center for Mucosal Inflammation and Cancer Nashville United States Vanderbilt University School of Medicine Program in Cancer Biology Nashville United States Veterans Affairs Tennessee Valley Healthcare System NashvilleTN United States Vanderbilt University Medical Center Department of Pathology Microbiology and Immunology NashvilleTN United States

Understanding the way cells communicate, co-locate, and interrelate is essential to understanding human physiology. Hematoxylin and eosin (H&E) staining is ubiquitously available both for clinical studies and research. The Colon Nucleus Identification and Classification (CoNIC) Challenge has recently innovated on robust artificial intelligence labeling of six cell types on H&E stains of the colon. However, this is a very small fraction of the number of potential cell classification types. Specifically, the CoNIC Challenge is unable to classify epithelial subtypes (progenitor, endocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), or connective subtypes (fibroblasts, stromal). In this paper, we propose to use inter-modality learning to label previously un-labelable cell types on virtual H&E. We leveraged multiplexed immunofluorescence (MxIF) histology imaging to identify 14 subclasses of cell types. We performed style transfer to synthesize virtual H&E from MxIF and transferred the higher density labels from MxIF to these virtual H&E images. We then evaluated the efficacy of learning in this approach. We identified helper T and progenitor nuclei with positive predictive values of 0.34 ± 0.15 (prevalence 0.03 ± 0.01) and 0.47 ± 0.1 (prevalence 0.07 ± 0.02) respectively on virtual H&E. This approach represents a promising step towards automating annotation in digital pathology. © 2024, CC BY.

关键词： Cell culture

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Cellulose-Based Reflective Liquid Crystal Films as Optical Filters and Solar Gain Regulators

arXiv

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arXiv 2022年

作者： De La Cruz, Joshua A. Liu, Qingkun Senyuk, Bohdan Frazier, Allister W. Peddireddy, Karthik Smalyukh, Ivan I. Materials Science and Engineering Program University of Colorado Boulder CO80309 United States Department of Physics University of Colorado Boulder CO80309 United States Soft Materials Research Center Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado Boulder CO80303 United States

Many promising approaches for designing interactions of synthetic materials with light involve solid optical monocrystals and nanofabricated photonic crystal structures with spatially periodic variations of refractive index. Although their high costs limit current technological applications, remarkably, such photonic and optically anisotropic materials have also evolved throughout nature and enable narrow or broad-band spectral reflection of light. Here we use self-assembly of biomaterial cellulose nanocrystals to obtain three-layer films with helicoidal and nematic-like organization of the cellulose nanoparticles, which mimics naturally occurring polarization-insensitive reflectors found in the wings of Plusiotis resplendens beetles. These films were characterized with polarized optical microscopy and circular dichroism spectrometry, as well as scanning and transmission electron microscopies. These films exhibit high reflectivity tunable within the visible and near-infrared regions of the optical spectrum and may find applications ranging from color filters to smart cloth designs and in solar-gain-regulating building technologies. © 2022, CC BY-NC-ND.

关键词： Reflection

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Neural population dynamics in songbird RA and HVC during learned motor-vocal behavior

arXiv

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arXiv 2024年

作者： Tostado-Marcos, Pablo Arneodo, Ezequiel M. Ostrowski, Lauren Brown, Daril E. Perez, Xavier A. Kadwory, Adam Stanwicks, Lauren L. Alothman, Abdullah Gentner, Timothy Q. Gilja, Vikash Department of Bioengineering University of California San Diego 9500 Gilman Drive La Jolla CA92093 United States Department of Electrical and Computer Engineering University of California San Diego 9500 Gilman Drive La Jolla CA92093 United States Department of Psychology University of California San Diego 9500 Gilman Drive La Jolla CA92093 United States Department of Neurobiology University of California San Diego 9500 Gilman Drive La Jolla CA92093 United States Neurosciences Graduate Program University of California San Diego 9500 Gilman Drive La Jolla CA92093 United States

Complex, learned motor behaviors involve the coordination of large-scale neural activity across multiple brain regions, but our understanding of the population-level dynamics within different regions tied to the same behavior remains limited. Here, we investigate the neural population dynamics underlying learned vocal production in awake-singing songbirds. We use Neuropixels probes to record the simultaneous extracellular activity of populations of neurons in two regions of the vocal motor pathway. In line with observations made in non-human primates during limb-based motor tasks, we show that the population-level activity in both the premotor nucleus HVC and the motor nucleus RA is organized on low-dimensional neural manifolds upon which coordinated neural activity is well described by temporally structured trajectories during singing behavior. Both the HVC and RA latent trajectories provide relevant information to predict vocal sequence transitions between song syllables. However, the dynamics of these latent trajectories differ between regions. Our state-space models suggest a unique and continuous-over-time correspondence between the latent space of RA and vocal output, whereas the corresponding relationship for HVC exhibits a higher degree of neural variability. We then demonstrate that comparable high-fidelity reconstruction of continuous vocal outputs can be achieved from HVC and RA neural latents and spiking activity. Unlike those that use spiking activity, however, decoding models using neural latents generalize to novel sub-populations in each region, consistent with the existence of preserved manifolds that confine vocal-motor activity in HVC and RA. © 2024, CC BY.

关键词： Dynamics

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