检索结果-内蒙古大学图书馆

SSRN 2023年

作者： Luo, Le Pervaiz, Shazib Clement, Marie-Veronique Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore Singapore117596 Singapore Department of Physiology Yong Loo Lin School of Medicine National University of Singapore Singapore NUS Medicine Healthy Longevity Program National University of Singapore Singapore Integrated Science and Engineering Program NUS Graduate School National University of Singapore Singapore Yong Loo Lin School of Medicine National University of Singapore Singapore National University Cancer Institute National University Health System Singapore

Using S-phase synchronized RPE1-hTERT cells exposed to the DNA damaging agent, methyl methanesulfonate, we unravel the existence of a redox state associated with replication stress-induced senescence that we have coined senescence-associated redox state (SA-redox state). SA-redox state is characterized by its reactivity with superoxide-sensing fluorescent probes such as dihydroethidine, lucigenin and mitosox and peroxynitrite or hydroxyl radical sensing probe hydroxyphenyl fluorescein (HPF) but not the hydrogen peroxide (H2O2) reactive fluorescent probe DCFH-DA. Moreover, measurement of GSH and GSSH reveals that SA-redox state mitigates the level of total GSH rather than oxidizes GSH to GSSG. Further supporting the key role of superoxide (O2.-) in the generation of SA-redox state, we show that incubation of senescent RPE1-hTERT with the O2.- scavenger, Tiron, decreases the reactivity of SA-redox state with the oxidantś reactive probes lucigenin and HPF while the H2O2 antioxidant N-acetyl cysteine has no effect. Moreover, SA-redox state activates NF-κB, dictates the profile of the Senescence Associated Secretory Phenotype, increases the rate of TFEB protein synthesis, promotes geroconversion evidenced by increased phosphorylation of S6K and S6 proteins, and renders cells resistant to senolysis. However, SA-redox state does not prevent the loss of proliferative capacity, G2/M cell cycle arrest or the increase in SA-βGal activity. Furthermore, while p53 mitigates the establishment of SA-redox state, p21 is critical for the sustained reinforcement of the SA-redox state involved in geroconversion and resistance to senolysis. The latter is validated by the increased rate of p21 synthesis leading to p21 abundance upon the acquisition of SA-redox status, while maintaining low levels of p53 through an increase in the rate of p53 degradation despite buffering a decrease in p53 mRNA. © 2023, The Authors. All rights reserved.

关键词： Probes

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Interactive Ultrasound Prostate Cancer Segmentation using Deep Learning with Principal Curve-based Fine-tuning

Interactive Ultrasound Prostate Cancer Segmentation using De...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Tao Peng Hui Mao Caishan Wang Gongye Di Ting Hu Lei Zhang School of Future Science and Engineering Soochow University Suzhou China Department of Radiation Oncology UT Southwestern Medical Center Dallas TX USA Department of Dermatology Huangshi Central Hospital Hubei China Department of Ultrasound Second Affiliated Hospital of Soochow University Suzhou China Department of Ultrasonic Taizhou People’s Hospital Affiliated to Nanjing Medical University Taizhou China Department of Obstetrics and Gynaecology Ultrasonography The First Affiliated Hospital of Soochow University Suzhou China Graduate Program of Medical Physics and Data Science Research Center Duke Kunshan University Kunshan China

Segmentation of prostate cancer on ultrasound (US) images is challenging because of the low-intensity contrast around the region of interest (ROI) contour caused by the intestinal gas. To the best of our knowledge, our work is one of the extremely rare groups to segment prostate cancer on US images, which designs a coarse-to-refinement segmentation framework with four merits: 1) it fuses the advantages of the deep learning- and principal curve-based algorithms to locate the ROI and fit the data center automatically, respectively; 2) a principal curve-based polygon searching method is designed by newly adding some constraints so that the performance of our method could be enhanced; 3) the quantum characteristics are added into evolution network, while newly adding numerous- operator scheme and global optimum search schemes; 4) an interpretable mathematical mapping model is developed to denote the ROI contour. Segmentation results show that our network outperforms other medical image segmentation models.

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High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH

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Cell 2025年第12期188卷 3310-3328.e27页

作者： Zhu, Yanyu Balaji, Ashwin Han, Mengting Andronov, Leonid Roy, Anish R. Wei, Zheng Chen, Crystal Miles, Leanne Cai, Sa Gu, Zhengxi Tse, Ariana Yu, Betty Chentzu Uenaka, Takeshi Lin, Xueqiu Spakowitz, Andrew J. Moerner, W.E. Qi, Lei S. Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Chemistry Stanford University Stanford 94305 CA United States Biophysics PhD Program Stanford University Stanford 94305 CA United States Computational Biology Program Public Health Sciences Division and Translational Data Science IRC Fred Hutchinson Cancer Center Seattle 98109 WA United States Department of Chemical Engineering Stanford University Stanford 94305 CA United States Department of Materials Science and Engineering Stanford University Stanford 94305 CA United States Institute for Stem Cell Biology & Regenerative Medicine and Department of Pathology Stanford University School of Medicine Stanford 94305 CA United States Sarafan ChEM-H Stanford University Stanford 94305 CA United States Chan Zuckerberg Biohub San Francisco 94080 CA United States

Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease. © 2025 Elsevier Inc.

关键词： CRISPR imaging DNA communication dynamic tracking enhancer-promoter interaction high-resolution imaging live DNA imaging non-repetitive genome imaging Oligo-LiveFISH polymer modeling primary cell

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Stokesian Dynamics with odd viscosity

arXiv

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arXiv 2022年

作者： Yuan, Hang de la Cruz, Monica Olvera Applied Physics Graduate Program Northwestern University EvanstonIL60208 United States Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Department of Chemistry Northwestern University EvanstonIL60208 United States Department of Physics and Astronomy Northwestern University EvanstonIL60208 United States

Stokesian Dynamics is a well-established computational method for simulating dynamics of many particles suspended in a conventional passive fluid medium. Active fluids composed of self-propelling particles with broken time reversal symmetry permit the emergence of a so-called odd viscosity. In this work, we extended the conventional Stokesian Dynamics formalism to incorporate the additional hydrodynamic effects due to odd viscosity, which enables simulating collective behaviors of many particles suspended in an active fluid medium with both even viscosity and odd viscosity. © 2022, CC BY.

关键词： Viscosity

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Quantifying U-Net Uncertainty in Multi-Parametric MRI-based Glioma Segmentation by Spherical Image Projection

arXiv

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arXiv 2022年

作者： Yang, Zhenyu Lafata, Kyle Vaios, Eugene Hu, Zongsheng Mullikin, Trey Yin, Fang-Fang Wang, Chunhao Department of Radiation Oncology Duke University DurhamNC United States Medical Physics Graduate Program Duke Kunshan University Jiangsu Kunshan China Medical Physics Graduate Program Duke University DurhamNC United States Department of Radiology Duke University DurhamNC United States Department of Electrical and Computer Engineering Duke University DurhamNC United States Department of Radiation Physics The University of Texas MD Anderson Cancer Center HoustonTX United States The University of Texas MD Anderson Graduate School of Biomedical Science HoustonTX United States

Background: Uncertainty quantification in deep learning is an important research topic. For medical image segmentation, the uncertainty measurements are usually reported as the likelihood that each pixel belongs to the predicted segmentation region. In potential clinical applications, the uncertainty result reflects the algorithm's robustness and supports the confidence and trust of the segmentation result when the ground-truth result is absent. For commonly studied deep learning models, novel methods for quantifying segmentation uncertainty are in demand. Purpose: To develop a U-Net segmentation uncertainty quantification method based on spherical image projection of multi-parametric MRI (MP-MRI) in glioma segmentation. Methods: The projection of planar MRI data onto a spherical surface is equivalent to a nonlinear image transformation that retains global anatomical information. By incorporating this image transformation process in our proposed spherical projection-based U-Net (SPU-Net) segmentation model design, multiple independent segmentation predictions can be obtained from a single MRI. The final segmentation is the average of all available results, and the variation can be visualized as a pixel-wise uncertainty map. An uncertainty score was introduced to evaluate and compare the performance of uncertainty measurements. The proposed SPU-Net model was implemented on the basis of 369 glioma patients with MP-MRI scans (T1, T1-Ce, T2, and FLAIR). Three SPU-Net models were trained to segment enhancing tumor (ET), tumor core (TC), and whole tumor (WT), respectively. The SPU-Net model was compared with (1) the classic U-Net model with test-time augmentation (TTA) and (2) linear scaling-based U-Net (LSU-Net) segmentation models in terms of both segmentation accuracy (Dice coefficient, sensitivity, specificity, and accuracy) and segmentation uncertainty (uncertainty map and uncertainty score). Results: The developed SPU-Net model successfully achieved low uncertainty

关键词： Tumors

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Two-dimensional perovskites with maximum symmetry enable exciton diffusion length exceeding 2 micrometers

arXiv

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arXiv 2025年

作者： Hou, Jin Fletcher, Jared Hall, Siedah J. Zhang, Hao Zacharias, Marios Volonakis, George Welton, Claire Mandani, Faiz Metcalf, Isaac Sun, Shuo Zhang, Bo Guo, Yinsheng Reddy, G.N. Manjunatha Katan, Claudine Even, Jacky Sfeir, Matthew Y. Kanatzidis, Mercouri G. Mohite, Aditya D. Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States Department of Chemistry Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Photonics Initiative Advanced Science Research Center City University of New York New York10031 United States Department of Physics The Graduate Center City University of New York New York10016 United States Department of Chemical and Biomolecular Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley‐Curl Institute Rice University HoustonTX77005 United States Univ Rennes INSA Rennes CNRS Institut FOTON UMR 6082 Rennes35708 France UMR 6226 RennesF-35000 France University of Lille CNRS Centrale Lille Institute Univ. Artois UMR 8181−UCCS− Unité de Catalyse et Chimie du Solide LilleF-59000 France Department of Chemistry University of Nebraska-Lincoln LincolnNE68588 United States

Realizing semiconductors with high symmetry of their crystallographic structures has been a virtue of inorganic materials and has resulted in novel physical behaviors. In contrast, hybrid (organic and inorganic) crystals such as two-dimensional metal halide perovskites exhibit much lower crystal symmetry due to in-plane or out-of-plane octahedral distortions. Despite their amazing ability for photoinduced light emission at room temperature, the Achilles' heel of this attractive class of 2D materials for optoelectronics remains the poor control and lack of performance for charge carrier transport. Inspired by the tremendous charge carrier properties of the 3D cubic perovskite phase (α) of FAPbI3 and combining the use of the appropriate cage cation, the spacer molecule and the temperature and rate of crystallization, we report a new series of FA-based layered two-dimensional perovskites that exhibits the highest theoretically predicted symmetry with a tetragonal P4/mmm space group, resulting in no octahedral distortion in both in-plane and out-of-plane directions. These 2D perovskites present the shortest interlayer distances (4 Å), which results in systematically lower bandgaps (1.7 to 1.8 eV). Finally, the absence of octahedral distortions, results in an exciton diffusion length of 2.5 µm, and a diffusivity of 4.4 cm2s-1, both of which are an order of magnitude larger compared to previously reported 2D perovskites and on par with monolayer transition metal dichalcogenides. © 2025, CC BY.

关键词： Charge carriers

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Deep learning inter-atomic potential for thermal and phonon behaviour of silicon carbide with quantum accuracy

arXiv

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arXiv 2021年

作者： Fu, Baoqin Sun, Yandong Zhang, Linfeng Wang, Han Xu, Ben Key Laboratory of Radiation Physics and Technology of the Ministry of Education Institute of Nuclear Science and Technology Sichuan University Chengdu610064 China Graduate School China Academy of Engineering Physics Beijing100193 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing100088 China

Silicon carbide (SiC) is an essential material for next generation semiconductors and components for nuclear plants. It’s applications are strongly dependent on its thermal conductivity, which is highly sensitive to microstructures. Molecular dynamics (MD) simulation is the most used methods to address thermal transportation mechanisms in devices or microstructures of nano-meters. However, the implementation of MD is limited in SiC because of lacking accurate inter-atomic potentials. In this work, using the Deep Potential (DP) methodology, we developed two inter-atomic potentials (DP-*Corresponding author. IAPs) for SiC based on two adaptively generated datasets within the density functional approximations at the local density and the generalized gradient levels. These two DP-IAPs manifest their speed with quantum accuracy in lattice dynamics simulations as well as scattering rate analysis of phonon transportation. Combining with molecular dynamics simulations, the thermal transport and mechanical properties were systematically investigated. The presented methodology and the inter-atomic potentials pave the way for a systematic approach to model heat transport in SiC related devices using multiscale modelling. Copyright © 2021, The Authors. All rights reserved.

关键词： Silicon carbide

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Universal mechanical response of metallic glasses during strain-rate-dependent uniaxial compression

arXiv

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arXiv 2022年

作者： Jin, Weiwei Datye, Amit Schwarz, Udo D. Shattuck, Mark D. O'Hern, Corey S. Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Chemical and Environmental Engineering Yale University New HavenCT06520 United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY10031 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

Experimental data on the compressive strength σmax versus strain rate Ε eng for metallic glasses undergoing uniaxial compression shows significantly different behavior for different alloys. For some metallic glasses, σmax decreases with increasing Ε eng, for others, σmax increases with increasing Ε eng, and for others σmax versus Ε eng is nonmonotonic. Using numerical simulations of metallic glasses undergoing uniaxial compression at nonzero strain rate and temperature, we show that they obey a universal relation for the compressive strength versus temperature, which determines their mechanical response. At low Ε eng, increasing strain rate leads to increases in temperature and decreases in σmax∗, whereas at high Ε eng, increasing strain rate leads to decreases in temperature and increases in σmax∗. This non-monotonic behavior of σmax∗ versus temperature causes the nonmonotonic behavior of σmax∗ versus Ε eng. Variations in the internal dissipation change the characteristic strain rate at which the nonmonotonic behavior occurs. These results are general for a wide range of metallic glasses with different atomic interactions, damping coefficients, and chemical compositions. © 2022, CC BY.

关键词： Strain rate

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Inverse-Designed Optical Metagratings for Free-Space Integral Equations Solving

Inverse-Designed Optical Metagratings for Free-Space Integra...

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Conference on Lasers and Electro-Optics Europe (CLEO EUROPE)

作者： Andrea Cordaro Brian Edwards Vahid Nikkhah Andrea Alù Nader Engheta Albert Polman Institute of Physics University of Amsterdam Amsterdam The Netherlands Center for Nanophotonics NWO-Institute AMOLF Amsterdam The Netherlands Department of Electrical and Systems Engineering University of Pennsylvania Philadelphia USA Photonics Initiative Advanced Science Research Center City University of New York New York USA Physics Program Graduate Center City University of New York New York USA

ISBN: (纸本)9798350345995

The world's ever-growing need for efficient computing has been driving researchers from diverse research fields to explore alternatives to the current digital computing paradigm. In this context, the field of all-optical analog processing is gaining significant attention opening new possibilities to overcome the bottlenecks of standard microelectronics [1–5]. We present a Si-based optical metastructure that solves Fredholm integral equations of the second kind in a fully analog fashion at optical frequencies. We exploit the analogy between the integral equation solving and the behavior of an optimized periodic metagrating coupled to a feedback system. At the foundations of this mapping lies the possibility of designing the S-matrix of a periodic structure by setting its periodicity (i.e., the number of input/output modes and hence the dimension of the S-matrix) and optimizing its unit cell (i.e., optimizing the coupling of light into the defined diffraction modes in amplitude and phase), as shown in Fig. 1a. Next, we show how the designed metastructure effectively solves the problem of interest and compare the metasurface-based solution to the ideal solution. We show that electron beam lithography and reactive ion etching provide the spatial resolution required to create a hardware representation of a predefined Kernel, with relatively small deviations between experiments and simulations. We optically characterize the output for different input signals showing good agreement with the ideal simulated response and use the data to retrieve the solution experimentally provided by the metadevice (see Fig. 1b). Fig. 1 A. Schematic of the proposed structure. A silicon metasurface is patterned on top of a sapphire substrate. The superstrate consists of $\text{SiO}_{2}$ with a semi-transparent au mirror on top. Scale-bar 500 nm b. Estimate of the solution to the integral equation obtained by the fabricated metadevice.

关键词： Crosstalk Electron beam lithography Light diffraction Modes Phase Spatial resolution

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Mechanically reprogrammable Pancharatnam-Berry metasurface for microwaves

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Advanced Photonics 2022年第1期4卷 69-79页

作者： Quan Xu Xiaoqiang Su Xueqian Zhang Lijuan Dong Lifeng Liu Yunlong Shi Qiu Wang Ming Kang Andrea Alù Shuang Zhang Jiaguang Han Weili Zhang Tianjin University Center for Terahertz Waves and College of Precision Instrument and Optoelectronics EngineeringKey Laboratory of Optoelectronic Information Technology(Ministry of Education of China)TianjinChina Shanxi Datong University Institute of Solid State Physics and College of Physics and Electronic ScienceShanxi Province Key Laboratory of Microstructure Electromagnetic Functional MaterialsDatongChina Wuhan University of Technology School of Information EngineeringWuhanChina Tianjin Normal University College of Physics and Materials ScienceTianjinChina City University of New York Advanced Science Research CenterPhotonics InitiativeNew YorkUnited States City University of New York Graduate CenterPhysics ProgramNew YorkUnited States University of Hong Kong Faculty of ScienceDepartment of PhysicsHong KongChina University of Hong Kong Department of Electrical and Electronic EngineeringHong KongChina Guilin University of Electronic Technology Guangxi Key Laboratory of Optoelectronic Information ProcessingSchool of Optoelectronic EngineeringGuilinChina Oklahoma State University School of Electrical and Computer EngineeringStillwaterOklahomaUnited States

Metasurfaces have enabled the realization of several optical functionalities over an ultrathin platform,fostering the exciting field of flat *** metasurfaces are achieved by arranging a layout of static meta-atoms to imprint a desired operation on the impinging wavefront,but their functionality cannot be *** and programmability of metasurfaces are the next important step to broaden their impact,adding customized on-demand functionality in which each meta-atom can be individually *** demonstrate a mechanical metasurface platform with controllable rotation at the meta-atom level,which can implement continuous Pancharatnam–Berry phase control of circularly polarized *** the proof-of-concept experiments,we demonstrate metalensing,focused vortex beam generation,and holographic imaging in the same metasurface template,exhibiting versatility and superior *** dynamic control of electromagnetic waves using a single,low-cost metasurface paves an avenue towards practical applications,driving the field of reprogrammable intelligent metasurfaces for a variety of applications.

关键词： reprogrammable metasurfaces Pancharatnam-Berry phase mechanical metasurfaces microwaves

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