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Single-cell omics: experimental workflow, data analyses and applications

Science China(Life Sciences) 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University(The Second People’s Hospital of Wuhu City)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** exploration of how the genomes orchestrate the formation and maintenance of each cell,and control the cellular phenotypes of various organismsis,is both captivating and *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** technologies have expanded horizontally to include single-cell genome,epigenome,proteome,and metabolome,while vertically,they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Research on the Current State of Privacy Risks in Children's Mobile applications 4

Research on the Current State of Privacy Risks in Children's...

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4th International Symposium on Computer Technology and Information Science, ISCTIS 2024

作者： Geng, Xinrui Liu, Tao Shang, Chong Chen, Jianxiang Lu, Yueran Zhang, Yan Wang, Lifeng Xi'an Jiaotong-Liverpool University School of AI and Advanced Computing Suzhou China MIIT Key Laboratory of Mobile Application Innovation and Governance Technology Beijing China Chinese Academy of Sciences Institute of Information Engineering Beijing China Shanxi Agricultural University School of Agricultural Engineering China Tianjin Normal University School of Software Engineering Tianjin China University of Chinese Academy of Sciences Institute of Information Engineering Chinese Academy of Sciences School of Cyber Security Beijing China Shandong Yeda Smart City Operation Technology Co. Ltd. Shandong China

ISBN: (纸本)9798350354560

In the digital age, children increasingly access a vast world of information through mobile applications. Despite global regulations and protective measures by app stores, privacy breaches in these apps persist. This study investigates privacy issues and threats in children's mobile applications by comparing APKs and legal provisions across different countries. It examines 70 representative children's apps from China, Europe, the U.S., and Japan through static code analysis and dynamic runtime testing. Using a mixed-methods approach, the research identifies integrated third-party services, data transmission protocols, permission requests, and conducts code audits to assess privacy compliance. It also simulates real usage scenarios to track data flow and detect unauthorized data collection and sharing practices. Furthermore, the study compares national privacy laws, focusing on data minimization, parental consent mechanisms, data encryption, and storage duration regulations. The goal is to provide empirical evidence and recommendations for optimizing global children's online privacy protection policies. © 2024 IEEE.

关键词： Differential privacy

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Effects of Minor CE Doping on the Microstructure and Mechanical Performances of a Eh47 Grade Hsla Steel for Ship and Ocean Engineering

SSRN

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SSRN 2023年

作者： Xiao, Jiuhan Yan, Ling Zhang, Peng Li, Guanglong Li, Boyong Zhao, Tan Wang, Hua Chen, Lijia Wang, Dong State Key Laboratory of Metal Material for Marine Equipment and Application Anshan114021 China Anshan Iron and Steel Group Company Limited Anshan114021 China School of Materials Science and Engineering Shenyang University of Technology Shenyang110870 China Shi-changxu Innovation Center for Advanced Materials Institute of Metal Research Chinese Academy of Sciences Shenyang110016 China

The influence of minor Ce doping on the evolution mechanisms of microstructure and mechanical performances of EH47 grade HSLA steel for marine engineering was investigated by microstructure observation and analysis. In the present work, the chemical composition of steels with different Ce contents was designed, and the TMCP hot-rolling process was applied to obtain a portion of bainitic microstructure for the purpose of achieve the performance indicators. The microstructures, precipitates, and inclusions of Ce-free and Ce-containing steels were observed and analyzed by using scanning electron microscopy (SEM) equipped with electron backscatter diffraction (EBSD) detector and transmission electron microscope (TEM) equipped with energy dispersive X-ray spectrometers (EDS). The strength, plasticity, and impact toughness of the experimental steels was measured and evaluated. According to the results, after adding rare earth Ce, the microstructures including grains, M-A constituents, and inclusions of steel were refined and optimized significantly. Then, the influencing mechanisms of Ce doping on precipitates and inclusions formation were further discussed in detail. Simultaneously, a clear variation tendency of mechanical properties was presented by Ce addition. The strength and hardness enhanced significantly, and the total elongation declined slightly. Moreover, the impact absorbed energy enhanced from 56 J to 152 J. © 2023, The Authors. All rights reserved.

关键词： Scanning electron microscopy

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Research on Intelligent Joint Detection Technology for application Privacy Behavior Compliance

Research on Intelligent Joint Detection Technology for Appli...

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

作者： Ruoding Zhang Tao Liu Qifeng Shi Yan Zhang Xiaoyi Song Xinrui Geng Institute of Information Engineering Chinese Academy of Sciences Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Key Laboratory of Mobile Application Innovation and Governance Technology MIIT Chinese Academy of Information and Communications Technologys Beijing China School of AI and Advanced Computing Xi’an Jiaotong-Liverpool University Suzhou China

ISBN: (数字)9798331506209

ISBN: (纸本)9798331506216

The surge in mobile applications has introduced substantial challenges in protecting user privacy. Despite the global enactment of privacy protection laws, ensuring compliance in mobile applications remains complex. We propose a deep learning-based detection technique that focuses on detecting the compliance of mobile applications at the level of privacy policy statements and code behaviors. We have developed a hierarchical classification system that sorts privacy statements into primary and secondary categories, aligning them with relevant privacy regulations and associated code actions. Our research introduces an automated dual-detection system that utilizes the BERT pre-trained model alongside convolutional neural networks to execute multilabel classification of privacy statements, thus pinpointing the privacy management actions they describe. By employing static analysis, the study decomposes Android application package files to scrutinize their behavior and assess the alignment between code actions and privacy statements. The results of our experiments indicate that the proposed dual-detection system effectively identifies compliance issues in mobile applications, providing an innovative technical solution to enhance user privacy protection.

关键词： Privacy Codes Surge protection Static analysis Multi label classification Regulation Mobile applications Convolutional neural networks Protection Surges

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Simultaneous q-Space Sampling Optimization and Reconstruction for Fast and High-fidelity Diffusion Magnetic Resonance Imaging

arXiv

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arXiv 2024年

作者： Yang, Jing Cheng, Jian Li, Cheng Fan, Wenxin Zou, Juan Wu, Ruoyou Wang, Shanshan Paul C. Lauterbur Research Center for Biomedical Imaging Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Guangdong Shenzhen China University of Chinese Academy of Sciences Beijing China State Key Laboratory of Software Development Environment Beihang University Beijing China Peng Cheng Laboratory Guangdong Shenzhen China Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application Guangdong China Key Laboratory of Data Science and Intelligent Computing Institute of International Innovation Beihang University Yuhang District Hangzhou China

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation *** experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise. Copyright © 2024, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Galvanic Corrosion Behavior of Cu-Fe-Zn Trimetallic Couple in Acidic Media

SSRN

引用

SSRN 2022年

作者： Chen, Lei Daniel, Enobong Felix Wang, Changgang Liu, Chen Li, Chao Ma, Chaojiang Wu, Liping Bian, Guixue Chen, Shaofeng Ma, Rongyao Dong, Junhua Chen, Yiqing School of Materials Science and Engineering University of Science and Technology of China Shenyang110016 China Shenyang National Laboratory for Materials Science Institute of Metal Research Chinese Academy of Sciences Shenyang110016 China Naval Aviation University Qingdao Campus Qingdao266041 China Shi-changxu Innovation Center for Advanced Materials Institute of Metal Research Chinese Academy of Sciences Shenyang110016 China State Key Laboratory of Metal Material for Marine Equipment and Application Anshan114009 China

The galvanic corrosion behavior of Cu-Fe-Zn trimetallic couple and its factors were investigated in acidic chloride solution using electrochemical and numerical methods. Results demonstrated that the potential difference of galvanic couple reflects only the thermodynamic tendency of galvanic corrosion, while the cathodic kinetic process controls the galvanic corrosion rate. It is found that the galvanic effect between Cu and Zn is much less than that between Zn and Fe when ohmically coupled. This is opposite to the theory of galvanic series. Despite possessing the maximum corrosion potential difference as the driving force, the galvanic current of Zn-Cu couple was less than that of Zn-Fe couple with equal area ratio. This drove the intermediate metal (Fe) to act as the main cathode in Cu-Fe-Zn trimetallic couple. Furthermore, it is found that Fe can be transformed into the anode due to the area change of Cu. The electrochemical experimental results are in good agreement with the FEM, suggesting that this method can accurately predict the galvanic corrosion behavior of multielectrode systems. © 2022, The Authors. All rights reserved.

关键词： Galvanic corrosion

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Self-Supervised Rotation Learning for 3D Segmentation on Nasopharyngeal Carcinoma MRI Images

Self-Supervised Rotation Learning for 3D Segmentation on Nas...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Changtai Li Ruohui Jiang Shihua Yin Jinzhu Yang Xiaojuan Ban Beijing Advanced Innovation Center for Materials Genome Engineering School of Intelligence Science and Technology University of Science and Technology Beijing Beijing China School of Intelligence Science and Technology University of Science and Technology Beijing Beijing China Second Affiliated Hospital of Guangxi Medical University Nanning China Key Laboratory of Intelligent Computing in Medical Image Ministry of Education Northeastern University Shenyang China

Segmenting the tumors of nasopharyngeal carcinoma (NPC) in Magnetic Resonance Imaging (MRI) images is critical for its diagnosis and treatment. In medical image segmentation, it is vital to exploit the rich information contained in 3D sliced images. However, the precise identification and location of lesion regions often require plenty of labels. To alleviate this situation, in this article, we propose 3DRotNPC, a framework based on a tailored Self-Supervised Learning (SSL) strategy, to accurately segment tumor regions for NPC under the circumstance of label limitation. To learn the rich 3D spatial and geometric nature of MRI images in a Self-Supervised way, the proxy task of randomly selecting and rotating images in consecutively sliced data is designed. After the SSL pre-training stage, the learned parameters of the Convolutional Neural Networks (CNNs) based model are transferred to adapt the downstream segmentation task. We verify the capability of 3DRotNPC on the NPC tumor dataset which is collected and curated from the clinical treatment in the representative hospital. Extensive experiments demonstrate that our approach delivers considerable gains in downstream 3D voxel segmentation, especially with a 10% to 50% number of labels.

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Anomalous Contribution to the Nematic Electronic States from the Structural Transition in FeSe Revealed by Time- and Angle-Resolved Photoemission Spectroscopy

引用

Physical Review Letters 2022年第24期128卷 246401-246401页

作者： Yuanyuan Yang Qisi Wang Shaofeng Duan Hongliang Wo Chaozhi Huang Shichong Wang Lingxiao Gu Dao Xiang Dong Qian Jun Zhao Wentao Zhang Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education) Shenyang National Laboratory for Materials Science School of Physics and Astronomy Shanghai Jiao Tong University Shanghai 200240 China State Key Laboratory of Surface Physics and Department of Physics Fudan University Shanghai 200433 China Key Laboratory for Laser Plasmas (Ministry of Education) School of Physics and Astronomy Shanghai Jiao Tong University Shanghai 200240 China Tsung-Dao Lee Institute Shanghai Jiao Tong University Shanghai 200240 China Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjing 210093 China Institute of Nanoelectronics and Quantum Computing Fudan University Shanghai 200433 China

High-resolution time- and angle-resolved photoemission measurements were made on FeSe superconductors. With ultrafast photoexcitation, two critical excitation fluences that correspond to two ultrafast electronic phase transitions were found only in the dyz-orbit-derived band near the Brillouin-zone center within our time and energy resolution. Upon comparison to the detailed temperature dependent measurements, we conclude that there are two equilibrium electronic phase transitions (at approximately 90 and 120 K) above the superconducting transition temperature, and an anomalous contribution on the scale of 10 meV to the nematic states from the structural transition is experimentally determined. Our observations strongly suggest that the electronic phase transition at 120 K must be taken into account in the energy band development of FeSe, and, furthermore, the contribution of the structural transition plays an important role in the nematic phase of iron-based high-temperature superconductors.

关键词： Electronic structure Iron-based superconductors Strongly correlated systems Time & angle resolved photoemission spectroscopy

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Research on the Current State of Privacy Risks in Children’s Mobile applications

Research on the Current State of Privacy Risks in Children’...

引用

Computer Technology and Information Science (ISCTIS), International Symposium on

作者： Xinrui Geng Tao Liu Chong Shang Jianxiang Chen Yueran Lu Yan Zhang Lifeng Wang School of AI and Advanced Computing Xi’an Jiaotong-Liverpool University Suzhou China Key Laboratory of Mobile Application Innovation and Governance Technology MIIT Beijing China Institute of Information Engineering Chinese Academy of Sciences Beijing China School of Agricultural Engineering Shanxi Agricultural University China School of Software Engineering Tianjin Normal University Tianjin China Institute of Information Engineering Chinese Academy of Sciences School of Cyber Security University of Chinese Academy of Sciences Beijing China Shandong Yeda Smart City Operation Technology Co. Ltd. Shandong China

ISBN: (数字)9798350354560

ISBN: (纸本)9798350354577

In the digital age, children increasingly access a vast world of information through mobile applications. Despite global regulations and protective measures by app stores, privacy breaches in these apps persist. This study investigates privacy issues and threats in children’s mobile applications by comparing APKs and legal provisions across different countries. It examines 70 representative children’s apps from China, Europe, the U.S., and Japan through static code analysis and dynamic runtime testing. Using a mixed-methods approach, the research identifies integrated third-party services, data transmission protocols, permission requests, and conducts code audits to assess privacy compliance. It also simulates real usage scenarios to track data flow and detect unauthorized data collection and sharing practices. Furthermore, the study compares national privacy laws, focusing on data minimization, parental consent mechanisms, data encryption, and storage duration regulations. The goal is to provide empirical evidence and recommendations for optimizing global children’s online privacy protection policies.

关键词： Pediatrics Data privacy Codes Law Europe Privacy breach Regulation Mobile applications Protection Testing

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Anomalous contribution to the nematic electronic states from the structural transition in FeSe revealed by time- and angle-resolved photoemission spectroscopy

arXiv

引用

arXiv 2022年

作者： Yang, Yuanyuan Wang, Qisi Duan, Shaofeng Wo, Hongliang Huang, Chaozhi Wang, Shichong Gu, Lingxiao Xiang, Dao Qian, Dong Zhao, Jun Zhang, Wentao Shenyang National Laboratory for Materials Science School of Physics and Astronomy Shanghai Jiao Tong University Shanghai200240 China State Key Laboratory of Surface Physics Department of Physics Fudan University Shanghai200433 China School of Physics and Astronomy Shanghai Jiao Tong University Shanghai200240 China Tsung-Dao Lee Institute Shanghai Jiao Tong University Shanghai200240 China Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjing210093 China Institute of Nanoelectronics and Quantum Computing Fudan University Shanghai200433 China

关键词： Selenium compounds

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