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The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Cell 2025年

作者： Pekar, Jonathan E. Lytras, Spyros Ghafari, Mahan Magee, Andrew F. Parker, Edyth Wang, Yu Ji, Xiang Havens, Jennifer L. Katzourakis, Aris Vasylyeva, Tetyana I. Suchard, Marc A. Hughes, Alice C. Hughes, Joseph Rambaut, Andrew Robertson, David L. Dellicour, Simon Worobey, Michael Wertheim, Joel O. Lemey, Philippe Institute of Ecology and Evolution University of Edinburgh Edinburgh United Kingdom Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla 92093 CA United States Department of Biomedical Informatics University of California San Diego La Jolla 92093 CA United States Department of Medicine University of California San Diego La Jolla 92093 CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Medical Research Council University of Glasgow Centre for Virus Research Glasgow United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States Department of Immunology and Microbiology The Scripps Research Institute La Jolla 92037 CA United States Institute of Genomics and Global Health Redeemer's University Osun State Ede Nigeria Department of Computer Science and Engineering University of California San Diego La Jolla 92093 CA United States Department of Mathematics School of Science and Engineering Tulane University New Orleans LA United States Department of Population Health and Disease Prevention University of California Irvine Irvine 92617 CA United States Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles 90095 CA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States School of Biological Sciences University of Hong Kong Hong Kong Hong Kong China Biodiversity Green Development Foundation Beijing China Spatial Epidemiology Lab (SpELL) Université Libre de Bruxelles CP160/12 50 av. FD Roosevelt Bruxelles 1050 Belgium Department of Microbiology Immunology and Transplantation Rega Institute

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses. © 2025 The Authors

关键词： molecular epidemiology phylogeography sarbecoviruses virus evolution

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A BCLC Staging System for Hepatocellular Carcinoma using Swin Transformer and CT Imaging

A BCLC Staging System for Hepatocellular Carcinoma using Swi...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Shun-Cheng Chang Pochuang Wang Weichung Wang Tung-Hung Su Jia-Horng Kao Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taipei Taiwan Department of Computer Science and Information Engineering NTU Taipei Taiwan NTU Institute of Applied Mathematical Sciences Taipei Taiwan Department of Internal Medicine Division of Gastroenterology and Hepatology National Taiwan University Hospital Taipei Taiwan Department of Electrical Engineering NTU Taipei Taiwan NTU Center for Advanced Computing and Imaging in Biomedicine Taipei Taiwan NTU Smart Medicine and Health Informatics Program Taipei Taiwan

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

The Barcelona Clinic Liver Cancer (BCLC) staging system plays a crucial role in clinical planning, offering valuable insights for effectively managing hepatocellular carcinoma. Accurate prediction of BCLC stages can significantly ease the workload on radiologists. However, few datasets are explicitly designed for discerning BCLC stages. Despite the common practice of appending BCLC labels to clinical data within datasets, the inherent imbalance in BCLC distribution is further amplified by the diverse purposes for which datasets are curated. In this study, we aim to develop a BCLC staging system using the advanced Swin Transformer model. Additionally, we explore the integration of two datasets, each originally intended for separate objectives, highlighting the critical challenge of preserving class distribution in practical study designs. This exploration is pivotal for ensuring the applicability of our developed staging system in the designed clinical settings. Our resulting BCLC staging system demonstrates an accuracy of 55.81% (±7.8%), contributing to advancing medical image-based research for predicting BCLC stages.

关键词： Liver cancer Accuracy Computed tomography Biological system modeling Transformers Planning Biomedical imaging

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Exploring Tourist Feedback on Riau Attractions Through Indonesian Language YouTube Opinion Using Naïve Bayes Algorithm

Exploring Tourist Feedback on Riau Attractions Through Indon...

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IEEE International Conference on Industry 4.0, Artificial Intelligence, and Communications Technology (IAICT)

作者： Rahmad Kurniawan Iwan Iskandar Fitra Lestari Habibi Al Rasyid Harpizon Ilyas Husti Department of Computer Science Faculty of Mathematics and Natural Sciences Universitas Riau Pekanbaru Indonesia Department of Informatics Engineering Universitas Islam Negeri Sultan Syarif Kasim Riau Pekanbaru Indonesia Department of Industrial Engineering Universitas Islam Negeri Sultan Syarif Kasim Riau Pekanbaru Indonesia Faculty of Information Science and Technology Universiti Kebangsaan Malaysia Bangi Selangor Malaysia Graduate Program Universitas Islam Negeri Sultan Syarif Kasim Riau Pekanbaru Indonesia

YouTube is a widely-used platform in Indonesia, with 93.8% of its users. As such, it presents a valuable opportunity for marketing tourist destinations, particularly in Riau province, which aims to become Indonesia’s top Halal travel destination. Tourism is a vital contributor to the economic growth of regions, and each province in Indonesia competes to promote its tourist attractions to attract more visitors every year. However, the large volume of data can challenge the manual analysis of feedback from YouTube’s features, such as likes, dislikes, and comments. A literature review suggests that the Naive Bayes algorithm, which uses machine learning, is helpful for sentiment analysis. Therefore, this study aims to analyze public sentiment toward tourist destinations in Riau province by analyzing YouTube comments using the Naïve Bayes algorithm. The study used 1680 opinions collected from 10 YouTube videos showcasing tourist destinations in Riau. The Naive Bayes algorithm classified 60% of the comments as positive, 32% as neutral, and 8% as negative. The experimental results indicated an accuracy and precision of 73%, a recall of 94%, and an F-1 Score of 82%. The study used the word frequency technique to reveal that Riau could become a popular halal tourist destination based on several frequently occurring words in the comments.

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Learning Vector Quantized Shape Code for Amodal Blastomere Instance Segmentation

Learning Vector Quantized Shape Code for Amodal Blastomere I...

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IEEE International Symposium on Biomedical Imaging

作者： Won-Dong Jang Donglai Wei Xingxuan Zhang Brian Leahy Helen Yang James Tompkin Dalit Ben-Yosef Daniel Needleman Hanspeter Pfister School of Engineering and Applied Sciences Harvard University MA USA Boston College MA USA Department of Molecular and Cellular Biology Harvard University MA USA Harvard Graduate Program in Biophysics Harvard University MA USA Department of Computer Science Brown University RI USA Tel Aviv Sourasky Medical Center Fertility & IVF Institute Israel Dept. of Cell and Developmental Biology Sagol School of Neuroscience Tel Aviv University Israel

Blastomere instance segmentation is important for analyzing embryos’ abnormality. To measure the accurate shapes and sizes of blastomeres, their amodal segmentation is necessary. Amodal instance segmentation aims to recover an object’s complete silhouette even when the object is not fully visible. For each detected object, previous methods directly regress the target mask from input features. However, images of an object under different amounts of occlusion should have the same amodal mask output, making it harder to train the regression model. To alleviate the problem, we propose to classify input features into intermediate shape codes and recover complete object shapes. First, we pre-train the Vector Quantized Variational Autoencoder (VQ-VAE) model to learn these discrete shape codes from ground truth amodal masks. Then, we incorporate the VQ-VAE model into the amodal instance segmentation pipeline with an additional refinement module. We also detect an occlusion map to integrate occlusion information with a backbone feature. As such, our network faithfully detects bounding boxes of amodal objects. On an internal embryo cell image benchmark, the proposed method outperforms previous state-of-the-art methods. To show generalizability, we show segmentation results on the public KINS natural image benchmark. Our method would enable accurate measurement of blastomeres in In Vitro Fertilization (IVF) clinics, potentially increasing the IVF success rate.

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Predicting online item-choice behavior: A shape-restricted regression approach

arXiv

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arXiv 2020年

作者： Nishimura, Naoki Sukegawa, Noriyoshi Takano, Yuichi Iwanaga, Jiro Graduate School of Systems and Information Engineering University of Tsukuba Ibaraki305-8577 Japan Recruit Lifestyle Co. Ltd. Tokyo100-6640 Japan Department of Information and Computer Technology Tokyo University of Science Tokyo125-8585 Faculty of Engineering Information and Systems University of Tsukuba Ibaraki305-8577 Doctoral Program in Policy and Planning Sciences University of Tsukuba Ibaraki305-8577 Erdos Inc. Kanagawa222-0033

This paper examines the relationship between user pageview (PV) histories and their item-choice behavior on an e-commerce website. We focus on PV sequences, which represent time series of the number of PVs for each user-item pair. We propose a shape-restricted optimization model that accurately estimates item-choice probabilities for all possible PV sequences. This model imposes monotonicity constraints on item-choice probabilities by exploiting partial orders for PV sequences, according to the recency and frequency of a user's previous PVs. To improve the computational efficiency of our optimization model, we devise efficient algorithms for eliminating all redundant constraints according to the transitivity of the partial orders. Experimental results using real-world clickstream data demonstrate that our method achieves higher prediction performance than that of a state-of-the-art optimization model and common machine learning methods. Copyright © 2020, The Authors. All rights reserved.

关键词： Graph theory

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ReViT: A Hybrid Approach for BCLC Staging of Hepatocellular Carcinoma Using 3D CT with Multiple Instance Learning

ReViT: A Hybrid Approach for BCLC Staging of Hepatocellular ...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Shun-Cheng Chang Hsin-Pei Yu Yi-Hsien Hsieh Pochuang Wang Weichung Wang Tung-Hung Su Jia-Horng Kao Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taipei Taiwan Department of Computer Science and Information Engineering NTU Taipei Taiwan Institute of Applied Mathematical Sciences NTU Taipei Taiwan Department of Internal Medicine Division of Gastroenterology and Hepatology National Taiwan University Hospital Taipei Taiwan Department of Electrical Engineering NTU Taipei Taiwan Center for Advanced Computing and Imaging in Biomedicine NTU Taipei Taiwan Smart Medicine and Health Informatics Program NTU Taipei Taiwan

ISBN: (数字)9798350351552

ISBN: (纸本)9798350351569

Deep learning has revolutionized medical imaging, offering advanced methods for accurate diagnosis and treatment planning. The BCLC staging system is crucial for staging Hepatocellular Carcinoma (HCC), a high-mortality cancer. An automated BCLC staging system could significantly enhance diagnosis and treatment planning efficiency. However, we found that BCLC staging, which is directly related to the size and number of liver tumors, aligns well with the principles of the Multiple Instance Learning (MIL) framework. To effectively achieve this, we proposed a new preprocessing technique called Masked Cropping and Padding(MCP), which addresses the variability in liver volumes and ensures consistent input sizes. This technique preserves the structural integrity of the liver, facilitating more effective learning. Furthermore, we introduced Re ViT, a novel hybrid model that integrates the local feature extraction capabilities of Convolutional Neural Networks (CNNs) with the global context modeling of Vision Transformers (ViTs). Re ViT leverages the strengths of both architectures within the MIL framework, enabling a robust and accurate approach for BCLC staging. We will further explore the trade-off between performance and interpretability by employing TopK Pooling strategies, as our model focuses on the most informative instances within each bag.

关键词： Visualization Accuracy Three-dimensional displays Liver Transformers Planning Convolutional neural networks Context modeling Biomedical imaging Tumors

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3-3 Multimedia information hiding

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Journal of the National Institute of Information and Communications Technology 2011年第1-2期58卷 183-194页

作者： Takizawa, Osamu Sonoda, Kotaro Yoshioka, Katsunari Suzuki, Jouji Disaster Management and Mitigation Group Japan Security Fundamentals Group Information Security Research Center Japan Computer and Information Science Program Faculty of Engineering Nagasaki University Japan Disaster Management and Mitigation Group Information Security Research Center Japan Interdisciplinary Research Center Yokohama National University Japan Network Security Incident Response Group Information Security Research Center Japan Technology Transfer Promotion Office Outcome Promotion Department Japan Graduate School Research Institute of Environment and Information Sciences Yokohama National University Japan

We research the multimedia information hiding (MIH) which is a technology to overlay digital information on multimedia contents such as picture, sound, document, etc. As application to disaster management of MIH, we have developed a new technology called "PAIH" (Public Address Information Hiding) which is a technology to overlay information such as position or destination on siren sound of urgent vehicles. Siren sound is allowed to degrade of sound quality, but PAIH is required to decode correct information from siren sound with pitch shift (Doppler effect) or under noisy environment.

关键词： Disasters

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5th International Conference on Variable Neighborhood Search (ICVNS'17)

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Electronic Notes in Discrete Mathematics 2018年 66卷 1-5页

作者： Vitor Nazário Coelho Haroldo Gambini Santos Igor Machado Coelho Puca Huachi Vaz Penna Thays A. Oliveira Marcone Jamilson Freitas Souza Angelo Sifaleras Institute of Computer Science Universidade Federal Fluminense Niterói Brazil Grupo da Causa Humana Ouro Preto Brazil Department of Computing Universidade Federal de Ouro Preto Ouro Preto Brazil Institute of Mathematics Statitics Universidade Estadual do Rio de Janeiro Rio de Janeiro Brazil Graduate Program of the Department of Engineering and Information and Communication Technologies Universitat Pompeu Fabra Barcelona Spain Department of Applied Informatics School of Information Sciences University of Macedonia 156 Egnatia Str. Thessaloniki 54636 Greece

This volume presents selected, peer-reviewed, short papers that were accepted for presentation in the 5th International Conference on Variable Neighborhood Search (ICVNS'17) which was held in Ouro Preto, Brazil, d... 详细信息

关键词： Metaheuristics Variable Neighborhood Search Discrete Optimization Nonlinear optimization

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Nanoslot-Induced Ultrastrong Phonon-Photon and Phonon-Phonon Coupling in Hybrid Organic-Inorganic Perovskites 16

Nanoslot-Induced Ultrastrong Phonon-Photon and Phonon-Phonon...

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16th Pacific Rim Conference on Lasers and Electro-Optics, CLEO-PR 2024

作者： Kim, Dasom Hou, Jin Lee, Geon Agrawal, Ayush Kim, Sunghwan Zhang, Hao Bao, Di Baydin, Andrey Wu, Wenjing Tay, Fuyang Huang, Shengxi Hagenmüller, Daivd Chia, Elbert E. M. Kim, Dai-Sik Seo, Minah Mohite, Aditya D. Kono, Junichiro Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States Sensor System Research Center Korea Institute of Science and Technology Seoul02792 Korea Republic of Department of Physics and Astronomy Seoul National University Seoul08826 Korea Republic of Department of Chemical and Biomolecular Engineering Rice University HoustonTX77005 United States Ulsan44919 Korea Republic of Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University 637371 Singapore Smalley-Curl Institute Rice University HoustonTX77005 United States Université de Strasbourg Cnrs Strasbourg67000 France KU-KIST Graduate School of Converging Science and Technology Korea University Seoul02841 Korea Republic of Department of Physics and Astronomy Rice University HoustonTX77005 United States

Methods for harnessing vibrational states are desired for phonon-based technologies. We realized ultrastrong coupling of two phonon modes in perovskite materials induced by ultrastrong coupling with a common photonic ... 详细信息

ISBN: (纸本)9798350372076

关键词： Organic-inorganic materials

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Superconductivity and frozen electronic states at the (111) LaAlO3/SrTiO3 interface

arXiv

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arXiv 2017年

作者： Davis, S. Huang, Z. Han, K. Ariando Venkatesan, T. Chandrasekhar, V. Graduate Program in Applied Physics Department of Physics and Astronomy Northwestern University 2145 Sheridan Road EvanstonIL60208 United States NUSNNI-Nanocore National University of Singapore 117411 Singapore Department of Physics National University of Singapore 117551 Singapore NUS Graduate School for Integrative Sciences & Engineering National University of Singapore 117456 Singapore NUSNNI-NanoCore National University of Singapore 117411 Singapore Department of Physics National University of Singapore 117542 Singapore Department of Electrical and Computer Engineering National University of Singapore 117576 Singapore Department of Material Science and Engineering National University of Singapore 117575 Singapore

In spite of Anderson’s theorem1, disorder is known to affect superconductivity in conventional s-wave superconductors2–11. In most superconductors, the degree of disorder is fixed during sample preparation. Here we report measurements of the superconducting properties of the two-dimensional gas that forms at the interface between LaAlO3 (LAO) and SrTiO3 (STO) in the (111) crystal orientation, a system that permits in situ tuning of carrier density and disorder by means of a back gate voltage Vg. Like the (001) oriented LAO/STO interface12–15, superconductivity at the (111) LAO/STO interface can be tuned by Vg. In contrast to the (001) interface, superconductivity in these (111) samples is anisotropic, being different along different interface crystal directions, consistent with the strong anisotropy already observed other transport properties at the (111) LAO/STO interface16,17. In addition, we find that the (111) interface samples "remember" the backgate voltage VF at which they are cooled at temperatures near the superconducting transition temperature Tc, even if Vg is subsequently changed at lower temperatures. The low energy scale and other characteristics of this memory effect ( Copyright © 2017, The Authors. All rights reserved.

关键词： Aluminum compounds

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