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arXiv 2022年

作者： Chen, Yu-Hsueh Hsu, Ke Tu, Wei-Lin Lee, Hyun-Yong Kao, Ying-Jer Center for Theoretical Physics Department of Physics National Taiwan University Taipei10607 Taiwan Division of Display and Semiconductor Physics Korea University Sejong30019 Korea Republic of Department of Applied Physics Graduate School Korea University Sejong30019 Korea Republic of Interdisciplinary Program in E·ICT-Culture-Sports Convergence Korea University Sejong30019 Korea Republic of Center for Quantum Science and Technology National Taiwan University Taipei10607 Taiwan

We propose a simple and generic construction of the variational tensor network operators to study the quantum spin systems by the synergy of ideas from the imaginary-time evolution and variational optimization of trial wave functions. By applying these operators to simple initial states, accurate variational ground state wave functions with extremely few parameters can be obtained. Furthermore, the framework can be applied to study spontaneously symmetry breaking, symmetry protected topological, and intrinsic topologically ordered phases, and we show that symmetries of the local tensors associated with these phases can emerge directly after the optimization without any gauge fixing. This provides a universal way to identify quantum phase transitions without prior knowledge of the system. Copyright © 2022, The Authors. All rights reserved.

关键词： Tensors

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Quantifying Outdoor Cooling Effects of Vertical Green System on Mean Radiant Temperature

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SSRN 2023年

作者： Kim, Eun Sub Yun, Seok Hwan Lee, Dong Kun Kim, Na Youn Piao, Zheng Gang Kim, Sang Hyuck Park, Seunghwan Interdisciplinary Program in Landscape Architecture Seoul National University Seoul08826 Korea Republic of Integrated Major in Smart City Global Convergence Program Seoul National University Seoul08826 Korea Republic of Specialized Graduate School of Intelligent Eco-Science 4 Dept. of Landscape Architecture Seoul National University Seoul08826 Korea Republic of Department of Landscape Architecture and Rural System Engineering Seoul National University Seoul08826 Korea Republic of Department of Building Energy Research Korea Institute of Civil Engineering and Building Technology Goyang10223 Korea Republic of

Vertical green systems (VGS) are expected to mitigate outdoor heat stress through a transpiration cooling effect. There is a lack of knowledge on how VGS influence outdoor thermal comfort, particularly focusing on energy flux. This study quantifies the outdoor cooling effects of VGS, and distinguishes the energy flux between them and outdoor urban spaces. In addition, we discuss their cooling efficiency. Outdoor experiments were conducted during the hot summer period on building facades in city. Our study on VGS focused on the measurement of climatic variables, surface temperatures of plant leaves (Fatsia japonica), net radiation, and estimating transpiration and evaporation. The surface temperature of VGS were up to 4.3 °C higher than those of high albedo walls, while the reflected radiations (short and long-wave radiation) were 120 w/m2 lower than albedo walls during the day. The mean radiant temperature (MRT) of VGS was 3.02 °C lower than the high albedo wall during daytime, except in the case of shaded areas (0.45 °C). We confirmed that the cooling efficiency of transpiration was 7.38 times more effective than evaporation from soil without plants. Therefore, VGS is efficient in terms of long-term heat reduction and can be an effective strategy to mitigate outdoor heat stress. © 2023, The Authors. All rights reserved.

关键词： Transpiration

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Cubic ferromagnet and emergent U(1) symmetry on its phase boundary

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Physical Review B 2023年第22期107卷 224406-224406页

作者： Wei-Lin Tu Xinliang Lyu S. R. Ghazanfari Huan-Kuang Wu Hyun-Yong Lee Naoki Kawashima Division of Display and Semiconductor Physics Korea University Sejong 30019 Korea Faculty of Science and Technology Keio University 3-14-1 Hiyoshi Kohoku-ku Yokohama 223-8522 Japan Institute for Solid State Physics University of Tokyo Kashiwa Chiba 277-8581 Japan Department of Physics Condensed Matter Theory Center and Joint Quantum Institute University of Maryland College Park Maryland 20742 USA Department of Applied Physics Graduate School Korea University Sejong 30019 Korea Interdisciplinary Program in E.ICT-Culture-Sports Convergence Korea University Sejong 30019 Korea Trans-scale Quantum Science Institute The University of Tokyo Bunkyo Tokyo 113-0033 Japan

We study the simplest quantum lattice spin model for the two-dimensional (2D) cubic ferromagnet by means of mean-field analysis and tensor network calculation. While both methods give rise to similar results in detecting related phases, the 2D infinite projected entangled-pair state (iPEPS) calculation provides more accurate values of transition points. Near the phase boundary, moreover, our iPEPS results indicate that it is more difficult to pin down the orientation of magnetic easy axes, and we interpret it as the easy-axis softening. This phenomenon implies an emergence of continuous U(1) symmetry, which is indicated by the low-energy effective model and has been analytically shown by the field theory. Our model and study provide a concrete example for utilizing iPEPS near the critical region, showing that the emergent phenomenon living on the critical points can already be captured by iPEPS with a rather small bond dimension.

关键词： Magnetic anisotropy Magnetism Quantum criticality Projected entangled pair states Tensor network methods

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Structure-Based Optimization of Tead Inhibitors: Exploring a Novel Subpocket Near Glu347 for the Treatment of Nf2-Mutant Cancer

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SSRN 2024年

作者： Kim, Jin Kwan Kim, Jinhyuk Kim, Hadong Jin, Haiyan Yoo, Youngki Fei, Xiang Maeng, Han-Joo Seo, Seung-Yong Han, Gyoonhee No, Kyoung Tai Baobab AiBIO Co. Ltd. Incheon21983 Korea Republic of Gachon Institute of Pharmaceutical Sciences College of Pharmacy Gachon University Incheon21936 Korea Republic of Department of Integrative Biotechnology Yonsei University Incheon21983 Korea Republic of Incheon21983 Korea Republic of Department of Pharmacy College of Pharmacy Yonsei University Incheon21983 Korea Republic of Institute of Convergence Science and Technology Yonsei University Incheon21983 Korea Republic of Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine Korea Republic of

The Hippo pathway is a signaling pathway implicated in various diseases, including cancer, that regulates the levels of yes-associated protein (YAP) and PDZ-binding motif (TAZ) proteins. These proteins bind to transcriptional enhanced associate domain (TEAD) proteins and function as transcription factors in the nucleus, producing oncogenic target genes such as CTGF and CYR61. TEAD proteins require palmitoylation via a covalent bond with cysteine in the central pocket to bind YAP/TAZ. Therefore, competitive inhibition that prevents palmitoylation could serve as an effective anticancer strategy. In this study, we analyzed the crystal structures of known inhibitors to identify new binding spots that were previously unexplored, with the aim of discovering more potent compounds using structure-based drug design. Consequently, we identified a novel hydrogen-bonding site and discovered Compound 2, which effectively binds to this site, as confirmed by X-ray crystallography. Furthermore, Compound 2 exhibited stable pharmacokinetic properties and demonstrated impressive efficacy in a mouse xenograft model. © 2024, The Authors. All rights reserved.

关键词： Transcription

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Caco-2 Cell-Derived Biomimetic Electrochemical Biosensor for Cholera Toxin Detection

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SSRN 2022年

作者： Kim, Yonghwan Lee, Dongtak Seo, Youngjun Jung, Hyo Gi Jang, Jae Won Park, Dongsung Kim, Insu Lee, Gyudo Hwang, Kyo Seon Kim, Seung-Hyun Lee, Sang Won Lee, Jeong Hoon Yoon, Dae Sung School of Biomedical Engineering Korea University Seoul02841 Korea Republic of Interdisciplinary Program in Precision Public Health Korea University Seoul02841 Korea Republic of Department of Clinical Pharmacology and Therapeutics College of Medicine Kyung Hee University Seoul02447 Korea Republic of Department of Biotechnology and Bioinformatics Korea University Sejong30019 Korea Republic of Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology Korea University Sejong30019 Korea Republic of School of Engineering Brown University ProvidenceRI02912 United States Department of Electrical Engineering and Computer Science University of California IrvineCA92697 United States Department of Electrical Engineering Kwangwoon University Seoul01897 Korea Republic of Astrion Inc Seoul02841 Korea Republic of

Cholera is a highly contagious and lethal waterborne disease induced by an infection with Vibrio cholerae (V. cholerae) secreting cholera toxin (CTx). Cholera toxin subunit B (CTxB) from the CTx specifically binds with monosialo-tetra-hexosyl-ganglioside (GM1) found on the exterior cell membrane of an enterocyte. Owing to the pathological process of CTx, a biomimetic electrochemical biosensor (CCB) was developed by applying GM1-expressing Caco-2 cell membrane (CCM) on the electrode surface of the biosensor for CTx detection. Briefly, the electrode surface was functionalized with CCM using the vesicle fusion method. The specific binding between GM1 and CTxB on the electrode surface was verified using confocal laser scanning microscopy and atomic force microscopy. The CTxB detection performances of the CCB, including sensitivity, selectivity, and long-term stability, were determined using electrochemical impedance spectroscopy (EIS). Based on the results, the CCB had an excellent limit of detection of ~11.46 nM and a detection range spanning 100 ng/mL - 1 mg/mL. Further, the CCB had high selectivity for the CTxB compared to different interfering molecules, which are abundant constituents of intestinal fluid and fecal matter in the human body. The long-term stability of the CCBs was also verified for 3 weeks using EIS. Overall, the CCB was found to have an excellent potential for application to point-of-care and cost-effective testing for CTxB detection in developing countries. © 2022, The Authors. All rights reserved.

关键词： Electrochemical impedance spectroscopy

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Correction to: Role of NADPH oxidase and its therapeutic intervention in TGF-β-mediated EMT progression: an in vitro analysis on HeLa cervical cancer cells

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Applied Biological Chemistry 2021年第1期64卷 1-1页

作者： Muthuramalingam, Karthika Cho, Moonjae Kim, Youngmee Department of Biochemistry School of Medicine Jeju National University Jeju Republic of Korea Institute of Medical Science Jeju National University Jeju Republic of Korea Interdisciplinary Graduate Program in Advanced Convergence Technology & Science Jeju National University Jeju Republic of Korea

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SU-E-T-30: Absorbed Doses Determined by Texture Analysis of Gafchromic EBT3 Films Using Scanning Electron Microscopy: A Feasibility Study

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Medical Physics 2014年第6PART11期41卷 228-228页

作者： S Park H Kim S Ye Interdisciplinary Program in Radiation Applied Life Science Seoul National University College of Medicine Seoul Korea Department of Radiation Oncology Seoul National University Hospital Seoul Korea Program in Biomedical Radiation Sciences Department of Transdisciplinary Studies Graduate School of Convergence Science and Technology Seoul National University Suwon Korea

Purpose: The texture analysis method is useful to estimate structural features of images as color, size, and shape. The study aims to determine a dose-response curve by texture analysis of Gafchromic EBT3 film images using scanning electron microscopy (SEM). Methods: The uncoated Gafchromic EBT3 films were prepared to directly scan over the active surface layer of EBT3 film using SEM. The EBT3 films were exposed at a dose range of 0 to 10 Gy using a 6 MV photon beam. The exposed film samples were SEM-scanned at 100X, 1000X, and 3000X magnifications. The four texture features (Homogeneity, Correlation, Contrast, and Energy) were calculated based on the gray level co-occurrence matrix (GLCM) derived from the SEM images at each dose. To validate a correlation between delivered doses and texture features, an R-squared value in linear regression was tested. Results: The results showed that the Correlation index was more suitable as dose indices than the other three texture features due to higher linearity and sensitivity of the dose response curves. Further the Correlation index of 3000X magnified SEM images with 9 pixel offsets had an R-squared value of 0.964. The differences between the delivered doses and the doses measured by this method were 0.9, 1.2, 0.2, and 0.2 Gy at 5, 10, 15, and 20 Gy, respectively. Conclusion: It seems to be feasible to convert micro-scale structural features of χ t χχχ he EBT3 films to absorbed doses using the texture analysis method.

关键词： Scanning electron microscopy Thin film structure Image color analysis Photons Rough surfaces Linear regression

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SU-E-E-04: Automated Analysis of Quality Assurance Phantom Scan Image in Functional Lung CT Study by Using Simulated CT Imaging Technique

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Medical Physics 2013年第6PART4期40卷 118-118页

作者： C Heo Z Yang J Kim Interdisciplinary Program of Radiation Applied Life Science College of Medicine Seoul National University Seoul Rep. Korea Department of Intelligent Convergence Systems Graduate School of Convergence Science and Technology Seoul National University Suwon Rep. Korea Department of Radiology College of Medicine Seoul National University Seoul Rep. Korea

Purpose: Quality assurance is of crucial importance in functional lung studies and yet requires time consuming manual measurements on phantom scan images. We present an automated method for analyzing CT scan images of quality assurance phantom. Methods: COPDgene™ quality assurance phantom was scanned in 4 commercial scanners (Discovery750, GE, Sensation16, Siemens, Ingenuity, Philips, Aquillion One, Toshiba) with 45 different combinations of mAs, reconstruction kernels and display FOV. In addition, simulated CT images were generated by using geometric and attenuation properties of design sheet of phantom and applying projection and filtered backprojection algorithms. In order to mimic real CT images, filter kernels were derived from measured MTFs of the CT scanners. Rigid image registration technique was used to find best matching translation and rotation parameters between simulated and real CT scan images, followed by measurements of FWHM and ROI statistic for the known positions and sizes of artificial airways and simulated lung foam materials. Results: Image registration was performed successfully in all CT scan images, yielding rotation and translation parameters within accuracy range less than 0.8 mm. FWHM measurements were extracted for 14 holes and 6 tubes ranging 2mm ∼ 10mm in diameter. Discrepancies between measured FWHM and ground truth value ranged from 0.02 ∼ 1.5mm. Conclusion: Proposed method could successfully recognize locations and types of objects in the quality assurance phantom, and thereby carrying out measurements required for the quality assurance procedure. This technique has the potential to improve quality of functional lung CT studies.

关键词： Computed tomography Medical imaging Quality assurance Medical image quality Lungs Image analysis Image registration Time measurement Germanium Image scanners

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Volume entropy and generalized Markov system for modelling information flow in a brain graph

arXiv

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arXiv 2018年

作者： Lee, Hyekyoung Kim, Eunkyung Kang, Hyejin Huh, Youngmin Lee, Youngjo Lim, Seonhee Lee, Dong Soo Biomedical Research Institute Seoul National University Hospital Seoul National University Department of Nuclear Medicine Seoul National University Department of Rehabilitation Medicine Seoul National University College of Medicine Seoul National University Data Science for Knowledge Creation Research Center Seoul National University Interdisciplinary Program in Cognitive Science Seoul National University Department of Statistics College of Natural Sciences Seoul National University Department of Molecular Medicine and Biopharmaceutical Sciences College of Medicine or College of Pharmacy Seoul National University Graduate School of Convergence Science and Technology Department of Mathematical Sciences Seoul National University Seoul Korea Republic of Korea Brain Research Institute Daegu Korea Republic of

Entropy is a classical measure to quantify the amount of information or complexity of a system. Various entropy-based measures such as functional and spectral entropies have been proposed in brain network analysis. However, they are less widely used than traditional graph theoretic measures such as global and local efficiencies because either they are not well-defined on a graph or difficult to interpret its biological meaning. In this paper, we propose a new entropy-based graph invariant, called volume entropy. It measures the exponential growth rate of the number of paths in a graph, which is a relevant measure if information flows through the graph forever. We model the information propagation on a graph by the generalized Markov system associated to the weighted edge-transition matrix. We estimate the volume entropy using the stationary equation of the generalized Markov system. A prominent advantage of using the stationary equation is that it assigns certain distribution of weights on the edges of the brain graph, which we call the stationary distribution. The stationary distribution shows the information capacity of edges and the direction of information flow on a brain graph. The simulation results show that the volume entropy distinguishes the underlying graph topology and geometry better than the existing graph measures. In brain imaging data application, the volume entropy of brain graphs was significantly related to healthy normal aging from 20s to 60s. In addition, the stationary distribution of information propagation gives a new insight into the information flow of functional brain graph. Copyright © 2018, The Authors. All rights reserved.

关键词： Entropy

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SU-G-JeP4-14: Assessment of Inter- and Intra-Fractional Motion for Extremity Soft Tissue Sarcoma Patients by Using In-House Real-Time Optical Image-Based Monitoring System

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Medical Physics 2016年第6PART28期43卷 3684-3684页

作者： H Kim I Kim S Ye Interdisciplinary Program in Radiation Applied Life Science College of Medicine Seoul National University Seoul Republic of Korea Dept. of Radiation Oncology Seoul National University Hospital Seoul Republic of Korea Program in Biomedical Radiation Sciences Graduate School of Convergence Science and Technology Seoul National University Seoul Republic of Korea

Purpose: This study aimed to assess inter- and intra-fractional motion for extremity Soft Tissue Sarcoma (STS) patients, by using in-house real-time optical image-based monitoring system (ROIMS) with infra-red (IR) external markers. Methods: Inter- and intra-fractional motions for five extremity (1 upper, 4 lower) STS patients received postoperative 3D conformal radiotherapy (3D-CRT) were measured by registering the image acquired by ROIMS with the planning CT image (REG_ROIMS). To compare with the X-ray image-based monitoring, pre- and post-treatment cone beam computed tomography (CBCT) scans were performed once per week and registered with planning CT image as well (REG_CBCT). If the CBCT scan is not feasible due to the large couch shift, AP and LR on-board imager (OBI) images were acquired. The comparison was done by calculating mutual information (MI) of those registered images. Results: The standard deviation (SD) of the inter-fractional motion was 2.6 mm LR, 2.8 mm SI, and 2.0 mm AP, and the SD of the intra-fractional motion was 1.4 mm, 2.1 mm, and 1.3 mm in each axis, respectively. The SD of rotational inter-fractional motion was 0.6° pitch, 0.9° yaw, and 0.8° roll and the SD of rotational intra-fractional motion was 0.4° pitch, 0.9° yaw, and 0.7° roll. The derived averaged MI values were 0.83, 0.92 for REG_CBCT without rotation and REG_ROIMS with rotation, respectively. Conclusion: The in-house real-time optical image-based monitoring system was implemented clinically and confirmed the feasibility to assess inter- and intra-fractional motion for extremity STS patients while the daily basis and real-time CBCT scan is not feasible in clinic.

关键词： Medical X-ray imaging Cone beam computed tomography Optical devices Three dimensional image processing Tissues Image registration Cancer Radiation therapy

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