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eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses

National science Review 2019年第5期6卷 867-869页

作者： Dalang Yu Lili Dong Fangqi Yan Hailong Mu Bixia Tang Xiao Yang Tao Zeng Qing Zhou Feng Gao Zhonghuang Wang Ziqian Hao Hongen Kang Yi Zheng Hongwei Huang Yuzhang Wei Wei Pan Yaochen Xu Junwei Zhu Shilei Zhao Ciran Wang Pengyu Wang Long Dai Mushan Li Li Lan Yiwei Wang Hua Chen Yi-Xue Li Yun-Xin Fu Zhen Shao Yiming Bao Fangqing Zhao Luo-Nan Chen Guo-Qing Zhang Wenming Zhao Haipeng Li CAS Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational Biology Shanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of Sciences Chinese Academy of Sciences University of Chinese Academy of Sciences BIG Data Center Beijing Institute of GenomicsChinese Academy of Sciences Shanghai Center for Bioinformation Technology Key Laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences CAS Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Department of Biostatistics and Data Science School of Public Health University of Texas Health Science Center at Houston Computational Genomics Lab Beijing Institutes of Life Science Chinese Academy of Sciences Shanghai Research Center for Brain Science and Brain-Inspired Intelligence

It has become increasingly challenging for researchers to analyze the exponentially expanding amount of multi-omic ***, we describe multi-functional software named evolutionary GenotypePhenotype Systems (eGPS) that en... 详细信息

关键词： GPS eGPS 1.0 comprehensive software for multi-omic and evolutionary analyses

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Extending Registration and Authentication Processes of FIDO2 External Authenticator with QR Codes

Extending Registration and Authentication Processes of FIDO2...

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IEEE International Conference on Trust, Security and Privacy in Computing and Communications (TrustCom)

作者： Chengqian Guo Quanwei Cai Qiongxiao Wang Jingqiang Lin State Key Laboratory of Information Security Institute of Information Engineering CAS Data Assurance and Communication Security Research Center CAS School of Cyber Security University of Chinese Academy of Sciences School of Cyber Security University of Science and Technology of China

ISBN: (数字)9781665403924

ISBN: (纸本)9781665403931

FIDO2, the newest set of FIDO specifications, enables the user to leverage an external authenticator for the authentication in both mobile and desktop environments (referred to as user agent). For the secure registration and authentication, FIDO2 requires the external authenticator and user agent to establish a confidential and mutually authenticated data transport channel through either USB interfaces, Near Field Communication (NFC) or Bluetooth. However, the external authenticator and host may not be equipped with one of the above physical media simultaneously, for example, a desktop may only have USB interfaces while an external authenticator (e.g., a smartphone) may have no USB inferfaces. This affects the wide adoption of FIDO2. In this paper, we extend the registration and authentication processes of FIDO2 external authenticator with QR code, which enables the external authenticator being equipped with a camera to be used for the authentication at any user agent. During the registration process, our scheme requires the user to provide the original credential and a one-time password displayed on the authenticator, and therefore ensures the correct user will only be bound with the expected authenticator. The security of our scheme has been formally analyzed based on the Dolev-Yao style model, a widely adopted model for the analysis of web systems. We have implemented the prototype, and the performance evaluation demonstrated the efficiency of our scheme, which needs 373 ms for registration and 141 ms for authentication in our environment.

关键词： Analytical models Privacy Authentication Prototypes Near field communication Universal Serial Bus Security

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Back Cover: PD-L1 Aptamer-Functionalized Metal–Organic Framework Nanoparticles for Robust Photo-Immunotherapy against Cancer with Enhanced Safety (Angew. Chem. Int. Ed. 5/2023)

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Angewandte Chemie International Edition 2023年第5期62卷

作者： Dr. Jingfang Zhang Dr. Wenzhe Li Dr. Yafei Qi Dr. Guorong Wang Prof. Lele Li Prof. Zhengyu Jin Prof. Jie Tian Prof. Yang Du Beijing Key Laboratory for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering University of Science and Technology Beijing Beijing 100083 China CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University Beijing 100191 China CAS Key Laboratory of Molecular Imaging Beijing Key Laboratory of Molecular Imaging the State Key Laboratory of Management and Control for Complex Systems Institute of Automation Chinese Academy of Sciences Beijing 100190 China Department of Radiology Peking Union Medical College Hospital Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730 China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine School of Medicine Beihang University Beijing 100191 China

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Rücktitelbild: PD-L1 Aptamer-Functionalized Metal–Organic Framework Nanoparticles for Robust Photo-Immunotherapy against Cancer with Enhanced Safety (Angew. Chem. 5/2023)

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Angewandte Chemie 2023年第5期135卷

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Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging (vol 42, 112593, 2023)

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CELL REPORTS 2023年第11期42卷 113396页

作者： Zhang, Hui Li, Jiaming Yu, Yang Ren, Jie Liu, Qiang Bao, Zhaoshi Sun, Shuhui Liu, Xiaoqian Ma, Shuai Liu, Zunpeng Yan, Kaowen Wu, Zeming Fan, Yanling Sun, Xiaoyan Zhang, Yixin Ji, Qianzhao Cheng, Fang Wei, Peng-Hu Ma, Xibo Zhang, Shiqiang Xie, Zhengwei Niu, Yuyu Wang, Yan-Jiang Han, Jing-Dong J. Jiang, Tao Zhao, Guoguang Ji, Weizhi Belmonte, Juan Carlos Izpisua Wang, Si Qu, Jing Zhang, Weiqi Liu, Guang-Hui State Key Laboratory of Membrane Biology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics Chinese Academy of Sciences and China National Center for Bioinformation Beijing 100101 China Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction Ministry of Education Center of Reproductive Medicine Department of Obstetrics and Gynecology Peking University Third Hospital Beijing China Clinical Stem Cell Research Center Peking University Third Hospital Beijing China Institute for Stem Cell and Regeneration CAS Beijing 100101 China Department of Neurology Tianjin Medical University General Hospital Tianjin 300052 China Department of Neurosurgery Beijing Tiantan Hospital Capital Medical University Beijing 100070 China Chinese Glioma Genome Atlas Network & Asian Glioma Genome Atlas Network Beijing 100070 China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101 China State Key Laboratory of Stem Cell and Reproductive Biology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China National Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China Beijing Municipal Geriatric Medical Research Center Beijing 100053 China MAIS State Key Laboratory of Multimodal Artificial Intelligence Systems Institute of Automation Chinese Academy of Sciences Beijing 100190 China School of Artificial Intelligence University of Chinese Academy of Sciences Beijing 100049 China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Center for Quantitative Biology (CQB) Peking University Beijing 100871 China Peking University International Cancer Institute Peking University Health Science Cen

The primate frontal lobe (FL) is sensitive to aging-related neurocognitive decline. However, the aging-associated molecular mechanisms remain unclear. Here, using physiologically aged non-human primates (NHPs), we depicted a comprehensive landscape of FL aging with multidimensional profiling encompassing bulk and single-nucleus transcriptomes, quantitative proteome, and DNA methylome. Conjoint analysis across these molecular and neuropathological layers underscores nuclear lamina and heterochromatin erosion, resurrection of endogenous retroviruses (ERVs), activated pro-inflammatory cyclic GMP-AMP synthase (cGAS) signaling, and cellular senescence in post-mitotic neurons of aged NHP and human FL. Using human embryonic stem-cell-derived neurons recapitulating cellular aging in vitro, we verified the loss of B-type lamins inducing resurrection of ERVs as an initiating event of the aging-bound cascade in post-mitotic neurons. Of significance, these aging-related cellular and molecular changes can be alleviated by abacavir, a nucleoside reverse transcriptase inhibitor, either through direct treatment of senescent human neurons in vitro or oral administration to aged mice.

关键词： nuclear lamina endogenous retroviruses brain aging inflammation

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Weakly supervised learning for textbook question answering

TechRxiv

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TechRxiv 2021年

作者： Ma, Jie Chai, Qi Huang, Jingyue Liu, Jun You, Yang Zheng, Qinghua National Engineering Lab for Big Data Analytics School of Computer Science and Technology Xi’an Jiaotong University Shaanxi Xi’an710049 China Shaanxi Province Key Laboratory of Satellite and Terrestrial Network Tech. R&D School of Computer Science and Technology Xi’an Jiaotong University Shaanxi Xi’an710049 China The High Performance Computing for Artificial intelligence Lab Department of Computer Science National University of Singapore 117417 Singapore

Textbook Question Answering (TQA) is the task of answering diagram and non-diagram questions given large multimodal contexts consisting of abundant text and diagrams. Deep text understandings and effective learning of diagram semantics are important for this task due to its specificity. In this paper, we propose a Weakly Supervised learning method for TQA (WSTQ), which regards the incompletely accurate results of essential intermediate procedures for this task as supervision to develop Text Matching (TM) and Relation Detection (RD) tasks and then employs the tasks to motivate itself to learn strong text comprehension and excellent diagram semantics respectively. Specifically, we apply the result of text retrieval to build positive as well as negative text pairs. In order to learn deep text understandings, we first pre-train the text understanding module of WSTQ on TM and then fine-tune it on TQA. We build positive as well as negative relation pairs by checking whether there is any overlap between the items/regions detected from diagrams using object detection. The RD task forces our method to learn the relationships between regions, which are crucial to express the diagram semantics. We train WSTQ on RD and TQA simultaneously, i.e., multitask learning, to obtain effective diagram semantics and then improve the TQA performance. Extensive experiments are carried out on CK12-QA and AI2D to verify the effectiveness of WSTQ. Experimental results show that our method achieves significant accuracy improvements of 5.02% and 4.12% on test splits of the above datasets respectively than the current state-of-the-art baseline. We have released our code on https://***/dr-majie/WSTQ. © 2021, CC BY.

关键词： Semantics

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There are finitely many 5-vertex-critical (P6, bull)-free graphs

arXiv

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arXiv 2025年

作者： Ju, Yiao Jooken, Jorik Goedgebeur, Jan Huang, Shenwei College of Computer Science Nankai University Tianjin300071 China Tianjin Key Laboratory of Network and Data Security Technology Nankai University Tianjin300071 China Department of Computer Science KU Leuven Campus Kulak-Kortrijk Kortrijk8500 Belgium Department of Applied Mathematics Computer Science and Statistics Ghent University Ghent9000 Belgium School of Mathematical Sciences and LPMC Nankai University Tianjin300071 China

In this paper, we are interested in 4-colouring algorithms for graphs that do not contain an induced path on 6 vertices nor an induced bull, i.e., the graph with vertex set {v1, v2, v3, v4, v5} and edge set {v1v2, v2v3, v3v4, v2v5, v3v5}. Such graphs are referred to as (P6, bull)-free graphs. A graph G is k-vertex-critical if χ(G) = k, and every proper induced subgraph H of G has χ(H) 6, bull)-free graphs and show that there are only finitely many such graphs, thereby answering a question of Maffray and Pastor. A direct corollary of this is that there exists a polynomial-time algorithm to decide if a (P6, bull)-free graph is 4-colourable such that this algorithm can also provide a certificate that can be verified in polynomial time and serves as a proof of 4-colourability or non-4-colourability. © 2025, CC BY.

关键词： Polynomial approximation

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Research of Association Rules Mining based on Fuzzy Alarm Extraction

Research of Association Rules Mining based on Fuzzy Alarm Ex...

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作者： Li tongyan Lei dong Qin Zhiguang Chengdu University of Information Technology Dept.of Communication Engineering Network and Data Security Key Laboratory of Sichuan Province University of Electronic Science and Technology of China Chengdu University of Information Technology Dept.of Communication Engineering

In communication alarm correlation analysis, original alarm data often have problems about information redundancy, data incompleteness, time synchronization and "sharp boundary". This paper proposed a novel alarm extraction algorithm in order to resolve above problems. We first fuzzy the original alarms to avoid "sharp boundary" during the alarm preprocessing process, and then we proposed a novel double constraint based sliding time window method to improve the efficiency on extracting data. Performance tests of the algorithm indicate that this method has higher extracting efficiency than traditional methods, which is suitable for alarm data in telecommunication networks.

关键词： Alarm correlation analysis fuzzy alarm sharp boundary

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An infinite class of Neumaier graphs and non-existence results

arXiv

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arXiv 2021年

作者： Abiad, Aida castryck, Wouter de Boeck, Maarten Koolen, Jack H. Zeijlemaker, Sjanne Department of Mathematics and Computer Science Eindhoven University of Technology Netherlands Department of Mathematics: Analysis Logic and Discrete Mathematics Ghent University Flanders Belgium Department of Mathematics and Data Science Vrije Universiteit Brussel Belgium Imec-COSIC Department of Electrical Engineering KU Leuven Belgium Department of Mathematics: Algebra and Geometry Ghent University Flanders Belgium School of Mathematical Sciences University of Science and Technology of China Hefei China CAS Wu Wen-Tsun Key Laboratory of Mathematics University of Science and Technology of China Hefei China

A Neumaier graph is a non-complete edge-regular graph containing a regular clique. A Neumaier graph that is not strongly regular is called a strictly Neumaier graph. In this work we present a new construction of strictly Neumaier graphs, and using Jacobi sums, we show that our construction produces infinitely many instances. Moreover, we prove some necessary conditions for the existence of (strictly) Neumaier graphs that allow us to show that several parameter sets are not admissible. Copyright © 2021, The Authors. All rights reserved.

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Match2: A Matching over Matching Model for Similar Question Identification

arXiv

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arXiv 2020年

作者： Wang, Zizhen Fan, Yixing Guo, Jiafeng Yang, Liu Zhang, Ruqing Lan, Yanyan Cheng, Xueqi Jiang, Hui Wang, Xiaozhao University of Chinese Academy of Sciences Beijing China CAS Key Lab of Network Data Science and Technology Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Massachusetts Amherst MA United States Alibaba Group Beijing China

Community Question Answering (CQA) has become a primary means for people to acquire knowledge, where people are free to ask questions or submit answers. To enhance the efficiency of the service, similar question identification becomes a core task in CQA which aims to find a similar question from the archived repository whenever a new question is asked. However, it has long been a challenge to properly measure the similarity between two questions due to the inherent variation of natural language, i.e., there could be different ways to ask a same question or different questions sharing similar expressions. To alleviate this problem, it is natural to involve the existing answers for the enrichment of the archived questions. Traditional methods typically take a one-side usage, which leverages the answer as some expanded representation of the corresponding question. Unfortunately, this may introduce unexpected noises into the similarity computation since answers are often long and diverse, leading to inferior performance. In this work, we propose a two-side usage, which leverages the answer as a bridge of the two questions. The key idea is based on our observation that similar questions could be addressed by similar parts of the answer while different questions may not. In other words, we can compare the matching patterns of the two questions over the same answer to measure their similarity. In this way, we propose a novel matching over matching model, namely Match2, which compares the matching patterns between two question-answer pairs for similar question identification. Empirical experiments on two benchmark datasets demonstrate that our model can significantly outperform previous state-of-the-art methods on the similar question identification *** CONCEPTS •Information systems → Question answering;Copyright © 2020, The Authors. All rights reserved.

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