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

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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) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our 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 intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These 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 sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This 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

Performance Analysis and Improvement of Flat Torque Converters Using DOE Method

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Chinese Journal of Mechanical Engineering 2018年第4期31卷 101-109页

作者： Guang-Qiang Wu Jie Chen Wen-Jie Zhu school of Automotive studies Tongji University Institute of industrial Science The University of Tokyo

Automotive torque converters have recently been designed with an increasingly narrower profile for the purpose of achieving a smaller axial size and reducing weight. Design of experiment(DOE) and computational fluid dynamics(CFD) techniques are applied to improve the performance of a flat torque converter. Four torque converters with different flatness ratios(0.204, 0.186, 0.172, and 0.158) are designed and simulated first to investigate the effects of flatness ratio on their overall performance, including efficiency, torque ratio, and impeller torque factor. The simulation results show that the overall performance tends to deteriorate as the flatness ratio decreases. Then a parametric study covering six geometric parameters, namely, inlet and outlet angles of impeller, turbine, and stator is carried out. The results demonstrate that the inlet and outlet angles play an important role in determining the performance characteristics of a torque converter. Furthermore, the relative importance of the six design parameters is investigated using DOE method for each response(stall torque ratio and peak efficiency). The turbine outlet angle is found to exert the greatest influence on both responses. After DOE analysis, an optimized design for the flat torque converter geometry is obtained. Compared to the conventional product, the width of the optimized flat torque converter torus is reduced by about 20% while the values of stall torque ratio and peak efficiency are only decreased by 0.4% and 1.7%, *** proposed new optimization strategy based on DOE method together with desirability function approach can be used for performance enhancement in the design process of flat torque converters.

关键词： Torque converter Flatness ratio Computational fluid dynamics(CFD) Parametric study Design of experiment(DOE)

Creating the Conditions for Community Resilience: Aberdeen,Scotland——An Example of the Role of Community Planning Groups

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International Journal of Disaster Risk Science 2019年第2期10卷 244-260页

作者： Helen Baxter National Centre for Resilience School of Interdisciplinary Studies The University of Glasgow Dumfries Campus

Governments are increasingly trying to ensure that communities are resilient to the effects of climate change and encourage community empowerment and autonomy. Local resilience planning groups(LRPGs),which include stakeholders with an interest in a local area,are emerging as one potential approach to building community resilience. A conceptual framework has been developed to identify the common requirements for community resilience, building upon existing work in the wider community resilience literature. Aberdeen Resilient,Included and Supported Group, Scotland, UK is an example of a LRPG. In this study the data collected during a workshop with the Aberdeen LRPG were used with the conceptual framework to identify some of the challenges faced when building community resilience. The study examined whether the Aberdeen LRPG illustrates the challenges and constraints faced by LRPGs more widely,and how the membership influences the potential to develop the attributes of community resilience outlined in the conceptual framework. The thematic analysis of the workshop revealed Aberdeen LRPG’s six dominant challenges: engaging with individuals, culture, attitudes,assumptions, terminology, and timescale. These challenges impede the group in utilizing the skills, knowledge, and resources that its members possess to build community resilience. While the Aberdeen LRPG cannot change all factors that affect community resilience, framing specific problems experienced by the group within a conceptual framework applicable to any community contributes to understanding the practical challenges to developing community resilience.

关键词： Community planning Community resilience Natural hazards Scotland

Emerging properties of two-dimensional twisted bilayer materials

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Chinese Physics B 2019年第10期28卷 83-92页

作者： Yang Cheng Chen Huang Hao Hong Zixun Zhao Kaihui Liu State Key Laboratory for Mesoscopic Physics Academy for Advanced Interdisciplinary Studies School of Physics Peking University

Recent studies in van der Waals coupled two-dimensional(2D) bilayer materials have demonstrated a new freedom for material engineering by the formation of moiré pattern. By tuning the twist angle between two layers, one can modulate their electronic band structures and therefore the associated electrical transport and optical properties, which are distinct from the original ones of each individual layer. These new properties excite great passion in the exploration of new quantum states and possible applications of 2D bilayers. In this article, we will mainly review the prevailing fabrication methods and emerging physical properties of twisted bilayer materials and lastly give out a perspective of this topic.

关键词： two-dimensional materials twist angle moiré potential interlayer coupling

Vector meson's spin alignments in high energy reactions

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 5-20页

作者： Jin-Hui Chen Zuo-Tang Liang Yu-Gang Ma Xin-Li Sheng Qun Wang Key Laboratory of Nuclear Physics and Ion-beam Application (MoE) Institute of Modern PhysicsFudan University Institute of Frontier and interdisciplinary Science Key Laboratory of Particle Physics and Particle Irradiation (MOE)Shandong University INFN-Firenze Department of Modern Physics University of Science and Technology of China school of Mechanics and Physics Anhui University of Science and Technology

The global spin alignment of vector mesons has been observed by the STAR collaboration at the Relativistic Heavy Ion Collider （RHIC） at Brookhaven National Laboratory （BNL）.It provides a unique opportunity to probe the correlation between the polarized quark and antiquark in the strongly coupled quark-gluon plasma （sQGP） produced in relativistic heavy ion collisions,opening a new window to explore the properties of s *** addition,spin alignments of vector mesons have also been observed in other high-energy particle collisions such as e+e-annihilations at high energies where hadron production is dominated by quark fragmentation *** results obtained are quite different from those obtained in heavy ion collisions where quark coalescence/combination mechanism dominates suggesting strong dependence on hadronization *** comprehensive studies in different hadronization processes are *** this article,we present a brief review of theoretical and experimental advances in the study of vector meson’s spin alignments in a variety of high-energy particle collisions,with emphasis on hadronization mechanisms.

关键词： vector meson spin alignment global polarization relativistic heavy ion collisions fragmentation

BCCLR:A Skeleton-Based Action Recognition with Graph Convolutional Network Combining Behavior Dependence and Context Clues

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Computers, Materials & Continua 2024年第3期78卷 4489-4507页

作者： Yunhe Wang Yuxin Xia Shuai Liu College of Information Science and Engineering Institute of Interdisciplinary StudiesHunan Normal UniversityChangsha410081China school of Educational Sciences Institute of Interdisciplinary StudiesHunan Normal UniversityChangsha410081China

In recent years,skeleton-based action recognition has made great achievements in Computer Vision.A graph convolutional network(GCN)is effective for action recognition,modelling the human skeleton as a spatio-temporal *** GCNs define the graph topology by physical relations of the human ***,this predefined graph ignores the spatial relationship between non-adjacent joint pairs in special actions and the behavior dependence between joint pairs,resulting in a low recognition rate for specific actions with implicit correlation between joint *** addition,existing methods ignore the trend correlation between adjacent frames within an action and context clues,leading to erroneous action recognition with similar ***,this study proposes a learnable GCN based on behavior dependence,which considers implicit joint correlation by constructing a dynamic learnable graph with extraction of specific behavior dependence of joint *** using the weight relationship between the joint pairs,an adaptive model is *** also designs a self-attention module to obtain their inter-frame topological relationship for exploring the context of *** the shared topology and the multi-head self-attention map,the module obtains the context-based clue topology to update the dynamic graph convolution,achieving accurate recognition of different actions with similar *** experiments on public datasets demonstrate that the proposed method achieves better results and realizes higher quality representation of actions under various evaluation protocols compared to state-of-the-art methods.

关键词： Action recognition deep learning GCN behavior dependence context clue self-attention

Quark-antiquark scattering phase shift and meson spectral function in pion superfluid

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Chinese Physics C 2019年第5期43卷 47-56页

作者： Tao Xia Jin Hu Shijun Mao College of Advanced interdisciplinary studies National University of Defense Technology school of Science Xi'an Jiaotong University

We study the quark-antiquark scattering phase shift and meson spectral function in the pion superfluid described by the Nambu-Jona-Lasinio model. Meson mixing in the pion superfluid dramatically changes the full scatt... 详细信息

关键词： scattering phase shift meson spectral function pion superfluid

A data-driven model predictive control for lighting system based on historical occupancy in an office building: Methodology development

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Building Simulation 2021年第1期14卷 219-235页

作者： Yuan Jin Da Yan Xingxing Zhang Jingjing An Mengjie Han school of Architecture Tsinghua UniversityBeijing100084China school of industrial Technology and Business studies Dalarna UniversityFalun79188Sweden

The lighting system accounts for 8%of the total electricity consumption in commercial buildings in the United States and 12%of the total electricity consumption in public buildings *** consumption share can be effectively reduced using the demand-response *** traditional lighting system control method commonly depends on the real-time occupancy data collected using the passive infrared(PIR)***,the detection inaccuracy of the PIR sensor usually results in *** diminish the false-error frequency,the existing lighting system control simply deploys a delayed reaction period(e.g.,5 to 20 min),which is not sufficiently accurate for the demand-response ***,in this research,a novel data-driven model predictive control(MPC)method that is based on the temporal sequential-based artificial neural network(TS-ANN)is proposed to overcome this challenge using an updated historical occupancy *** an office as case study,the proposed model is also compared with the traditional lighting system control *** the proposed model,the occupancy data was trained to predict the occupancy pattern to improve the *** was found that the occupancy prediction mainly correlates with the historical occupancy ratio and the time sequential *** simulation results indicated that the proposed method achieved higher accuracy(97.4%)and fewer false-offs(from 79.5 with traditional time delay method to 0.6 times per day)are achieved by the MPC *** proposed TS-ANN-MPC method integrates the analysis of the occupant behavior routine into on-site control and has the potential to further enhance the control performance practice for maximum energy conservation.

关键词： lighting system occupant behavior data-driven model predictive control

Development status of high power fiber lasers and their coherent beam combination

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Science China(Information Sciences) 2019年第4期62卷 56-87页

作者： Zejin LIU Xiaoxi JIN Rongtao SU Pengfei MA Pu ZHOU College of Advanced interdisciplinary studies National University of Defense Technology

High-power fiber laser has been emerged great potential in a wide range of applications and becomes a robust candidate for high energy solid state laser system. To further increase the output brightness of single-channel fiber laser, high-brightness pump sources and high-power-handling passive components should be fabricated and utilized in the fiber laser systems, in addition to the advanced techniques for multiple nonlinear effects managements. The state-of-the-art high power fiber lasers are reviewed, in terms of narrow-linewidth fiber lasers, broadband fiber lasers and fiber lasers at 2 μm. Coherent beam combining is a promising technique to obtain higher output power while maintaining excellent beam quality simultaneously,which breaks through the bottlenecks of single-channel fiber laser. Based on a series of key techniques for coherent beam combining, high-power coherent beam combining of fiber lasers could be enabled with high combining efficiency. In this paper, we review the progress of high-power fiber lasers and their coherent beam combining in the recent decade, particularly the relevant work in our group. The future prospects of fiber lasers and coherent beam combining technique are also discussed.

关键词： fiber lasers and amplifiers nonlinear effects and mode instability coherent beam combining passive components 2 μm fiber lasers