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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) 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

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不同轻骨料混凝土高温后劣化性能研究

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河南城建学院学报 2018年第4期27卷 85-92页

作者：田琦刘宗辉秦文博河南理工大学土木工程学院河南焦作454000 中建七局安装工程有限公司河南郑州450045

为改善轻骨料混凝土高温后的劣化性能以及抗爆裂性能,将玄武岩、聚丙烯纤维以单掺和混掺的形式掺入到轻骨料混凝土基体中进行试验。结果表明,聚丙烯纤维有利于轻骨料混凝土的高温抗爆裂性能,而玄武岩纤维仅可推迟而不能阻止其高温爆裂... 详细信息

为改善轻骨料混凝土高温后的劣化性能以及抗爆裂性能,将玄武岩、聚丙烯纤维以单掺和混掺的形式掺入到轻骨料混凝土基体中进行试验。结果表明,聚丙烯纤维有利于轻骨料混凝土的高温抗爆裂性能,而玄武岩纤维仅可推迟而不能阻止其高温爆裂。随着温度升高,不同轻骨料混凝土的色泽和表观变化规律大致相同;其立方体抗压强度在200℃以内略有升高,但随后一直下降;而轴心抗压强度、劈裂抗拉强度和弹性模量则呈直线下降趋势,但是掺入纤维后其残余力学性能指标均大于素全轻混凝土;高温后,应力-应变曲线上的峰值应力和峰值应变明显下降右移,这些特征变化反映了随着温度的增高,混凝土内部损伤加大及逐渐劣化。

关键词：轻骨料混凝土高温劣化性能应力-应变曲线

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Cloud Det ection Using Super Pixel Classification and Semantic Segmentation

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Journal of Computer Science & Technology 2019年第3期34卷 622-633页

作者： Han liu Hang Du Dan Zeng qi tian Key Laboratorij of Specialty Fiber Optics and Optical Access Networks Shanghai UniversityShanghai 200444China Shanghai Institute of Advanced Communication and Data Science Shanghai UniversityShanghai 200444China Department of Computer Science The University of Texas at San AntonioSan AntonioU.S.A.

Cloud detection plays a very significant role in remote sensing image *** paper introduces a cloud detection method based on super pixel level classification and semantic ***,remote sensing images are segmented into super *** super pixels compose a super pixel level remote sensing image *** cloud detection is essentially a binary classification task,our database is labeled into four categories to improve the generalization ability:thick cloud,cirrus cloud,building,and other ***,the super pixel level database is used to train our cloud detection models based on convolution neural network(CNN)and deep *** fusion CNN is proposed considering super pixel level images contain less semantic information than normal *** full advantage of low-level features like color and texture information,it is more applicable for super pixel level ***,a distance metric is proposed to refine ambiguous super ***,an end-to-end cloud detection model based on semantic segmentation is *** model has no restrictions on the input size,and takes less *** results show that compared with other cloud detection *** proj)osed method acliieves better performance.

关键词： cloud detection convolution neural network deep forest semantic segmentation

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循环水流速对换热器壁面CaCO_3水垢晶体的影响

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内蒙古师范大学学报（自然科学汉文版） 2016年第5期45卷 639-644页

作者：刘智安王雨萌夏添刘启旺赵巨东邵晓珏杨星贾建军内蒙古工业大学能源与动力工程学院内蒙古呼和浩特010051 吉林化工学院吉林吉林132002 内蒙古工业大学理学院内蒙古呼和浩特010051

模拟火电厂循环冷却水系统的运行工况,采用强制对流换热方式,在不同的水流速度下,分别对换热管壁面析出的CaCO_3附着垢及游离于水中的脱除垢进行多晶X射线衍射分析.结果表明,水垢中方解石和文石的晶粒尺寸均随水流速度的增加而增大,其... 详细信息

模拟火电厂循环冷却水系统的运行工况,采用强制对流换热方式,在不同的水流速度下,分别对换热管壁面析出的CaCO_3附着垢及游离于水中的脱除垢进行多晶X射线衍射分析.结果表明,水垢中方解石和文石的晶粒尺寸均随水流速度的增加而增大,其中附着垢中方解石和文石的晶粒尺寸变化较大,脱除垢中方解石和文石的晶粒尺寸变化较小;水流速度的增大会影响方解石和文石的晶面间距,附着垢中方解石和文石的最强衍射峰的晶面间距d_(104)和d_(111)均比脱除垢中的有所减小.从循环冷却水流速、剪切力变化和成垢离子有序稳定密堆积方面,对实验现象进行了解释.

关键词：循环水流速换热器附着垢脱除垢晶粒尺寸晶面间距

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An integrated approach to evaluating the coupling coordination degree between low-carbon development and air quality in Chinese cities

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Advances in Climate Change Research 2021年第5期12卷 710-722页

作者： liu tian-Le SONG qi-Jiao Jiaqi LU qi Ye Division of Public Policy Hong Kong University of Science and TechnologyHong KongChina Institute for Public Policy Hong Kong University of Science and TechnologyHong KongChina School of Humanities and Social Sciences North China Electric Power UniversityBeijing102206China Nelson Institute for Environmental Studies University of Wisconsin–MadisonMadison53706USA Department of Political Science University of Wisconsin–MadisonMadison53706USA School of Public Policy and Management Tsinghua UniversityBeijing100084China

Collaborative governance between ecological environment and climate change is a novel signature in China's policy agenda. However, such coordination remains understudied, especially at the local level. Using the principal component analysis, entropy evaluation methods, and the Coupling Coordination Degree Model (CCDM), we evaluated the level of coordination between carbon and air quality mitigation from 34 low-carbon pilot cities in China. We also illustrated the mechanism and policy formation that leads to different coupling patterns at the local level using three case studies. We found that most pilot cities perform a medium level of coupling coordination between low carbon development and air quality. The result reveals that most low-carbon pilot cities score relatively well in low-carbon development. Further, there is a significant cleavage in air quality between cities in the North and those in the South, indicating pilot cities in the South coordinate better than those in the North. In particular, pilot programs in the Southwest and Southeast coastal region perform well in collaborative governance, while the Beijing−tianjin−Hebei region is rated poorly because of the gap between air quality and low carbon development. Also, we found that the same low-carbon policy might have heterogeneous effects on different air pollutants and across different regions. The local government should adopt low-carbon development policies that address local level specific environmental and economic conditions to maximize their air pollution mitigation benefits.

关键词： Low-carbon development Air quality Coupling coordination degree model Low carbon pilot city

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Microstructure and mechanical properties of Nb–Mo–ZrB_2 composites prepared by hot-pressing sintering

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International Journal of Minerals,Metallurgy and Materials 2018年第7期25卷 824-831页

作者： Yuan Gao Zong-de liu qi Wang Yong-tian Wang Key Laboratory of Condition Monitoring and Control for Power Plant Equipment of Ministry of Education North China Electric Power UniversityBeijing 102206China

Nb-Mo-ZrB2 composites （V（Nb）/V（Mo） = 1） with 15v01% or 30v01% of ZrB2 were fabricated by hot-pressing sintering at 2000~C The phases, microstxucture, and mechamcal properties were then investigated. The composites contain Nb-Mo solid solution （denoted as （Nb, Mo）ss hereafter）, ZrB, MoB, and NbB phases. Compressive strength test results suggest that the strength of Nb-Mo-ZrB2 composites increases with increasing ZrB2 content; Nb-Mo-30vol%ZrB2 had the highest compressive strength （1905.1 MPa）. The improvement in the compressive strength of the Nb-Mo-ZrB2 composites is mainly attributed to the secondary phase strengthening oftke stiffer ZrB phase, sol- id-solution strengthening oftke （Nb, Mo）ss matrix as well as fme-grain strengtkening. The fracture toughness decreases with increasing ZrB2 content. Finally, the fracture modes oftke Nb-Mo-ZrB2 composites axe also discussed in detail.

关键词： metal-matrix composites microstJ-ucture mechaNcal properties sintering

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Design of piezoelectric energy harvesting devices subjected to broadband random vibrations by applying topology optimization

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Acta Mechanica Sinica 2011年第5期27卷 730-737页

作者： Zhe-qi Lin Hae Chang Gea Shu-tian liu Department of Engineering Mechanics Dalian University of Technology116024 Dalian China Department of Mechanical and Aerospace Engineering Rutgers The State University of New JerseyPiscataway NJ 08854 USA

Converting ambient vibration energy into electrical energy by using piezoelectric energy harvester has attracted a lot of interest in the past few *** this paper,a topology optimization based method is applied to simultaneously determine the optimal layout of the piezoelectric energy harvesting devices and the optimal position of the mass *** objective function is to maximize the energy harvesting performance over a range of vibration *** excitation method （PEM） is adopted to analyze structural stationary random responses,and sensitivity analysis is then performed by using the adjoint *** examples are presented to demonstrate the validity of the proposed approach.

关键词： Topology optimization · Energy harvesting · Piezoelectric material ··

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Non-Targeted Metabolomics Reveals the Metabolic Alterations in Response to Artificial Selective Breeding in the Fast-Growing Strains of Pacific Oyster

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Journal of Ocean University of China 2024年第2期23卷 518-528页

作者： HU Boyang tian Yuan liu Shikai LI qi Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China Laboratory for Marine Fisheries Science and Food Production Processes Laoshan LaboratoryQingdao 266237China

Pacific oyster(Crassostrea gigas)is one of the most important mollusks cultured all around the *** breeding programs of Pacific oysters in China is initiated since 2006 and developed the genetically improved strain with fast-growing ***,little is known about the metabolic signatures of the fast-growing *** the present study,the non-targeted metabolomics was performed to analyze the metabolic signatures of adductor muscle tissue in one-year old Pacific oysters from fast-growing strain and the wild population.A total of 7767 and 10174 valid peaks were extracted and quantified in ESI^(+)and ESI^(−)modes,resulting in 399 and 381 annotated metabolites,*** and OPLS-DA revealed that considerable separation among samples from fastgrowing strain and wild population,suggesting the differences in metabolic ***,81 significantly different metabolites(SDMs)were identified in the comparisons between fast-growing strain and wild population,based on the strict *** was found that there were highly correlation and conserved coordination among these *** enrichment analysis indicated that the SDMs were tightly related to pantothenate and CoA biosynthesis,steroid hormone biosynthesis,riboflavin metabolism,and arginine and proline *** them,the CoA biosynthesis and metabolism,affected by pantetheine and pantothenic acid,might be important for the growth of Pacific oysters under artificial selective *** study provides the comprehensive views of metabolic signatures in response to artificially selective breeding,and is helpful to better understand the molecular mechanism of fastgrowing traits in Pacific oysters.

关键词： metabolic signature Pacific oyster artificial selection fast-growing trait

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POLY(MALEIC ANHYDRIDE-CO-ACRYLIC ACID)/POLY(ETHYLENE GLYCOL)HYDROGELS WITH pH- AND IONIC-STRENGTH-RESPONSES

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Chinese Journal of Polymer Science 2010年第6期28卷 951-959页

作者： Meng Yang Bo-tian liu Ge Gao Xiao-li liu Feng-qi liu College of Chemistry and Macdiarmid Laboratory Jilin University Changchun 130012 China

Poly（maleic anhydride-coacrylic acid）,P（MA-AA）,was synthesized by the free-radical copolymerization of maleic anhydride with acrylic acid,and fast responsive pH-sensitive poly（maleic anhydride-co-acrylic acid）/polyethylene glycol,P（MA-AA）/PEG,hydrogels were prepared using PEG as macromolecular cross-linking ***-IR and ~1H-NMR spectrometry were applied to characterize the structure of P（MA-AA）.The influences of pH and ionic strength on the swelling behavior of P（MA-AA）/PEG hydrogels and the swelling-deswelling changes along with the repeated changes between acid and alkali conditions were *** results showed that there was a hundredfold difference in the swelling ratios between the conditions of acid and alkali,and the swelling capability could not be weakened after multiple swelling-deswelling *** results of swelling kinetics demonstrated that the response rate of P（MA-AA）/PEG hydrogels was very fast,because the swelling transition points always occurred at 10 *** pH-responsive hydrogels reported here might be a smart material for potentially applications in many areas,including biosensors,drug-delivery devices and tissue engineering.

关键词： pH-response P(MA-AA) Macromolecular cross-linking agent External cross-linking

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Shape optimization design of a heaving buoy of wave energy converter based on fully parametric modeling and CFD method

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Journal of Hydrodynamics 2022年第6期34卷 1081-1094页

作者： Shuo Huang Wei-qi liu Kai Wang Tie-cheng Wu tian-hui liu School of Ocean Engineering and Technology Sun Yat-sen University&Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)Zhuhai519000China

The hydrodynamic shape of the heaving buoy is an important factor of the motion response in waves and thus concerns the energy conversion efficiency for the point absorbers(PAs).The current experience-based designs are time consuming and not very efficient,hence,faster and smarter methods are *** automated optimization method based on a fully parametric modeling method and computational fluid dynamics(CFD),is proposed in this *** this method,a benchmark buoy is screen designed and then optimized by maximizing the heave motion *** geometry is described parametrically and deformed by means of the free-form deformation(FFD)*** the optimization process,the expansion factor of control points is the basis for the variations.A combination of the Sobol and the non-dominated sorting genetic algorithm II(NSGA-II)is used to search for the *** several iterations,the heaving buoy shape with optimal heave motion response is *** analyses show that the heave motion response has increased 55.3%after *** developed methodology is valid and seems to be a promising way to design a novel buoy that can significantly improve the wave energy conversion efficiency of the PAs in future.

关键词： Wave energy converter geometric shape optimization fully parametric modeling method computational fluid dynamics(CFD)

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