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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

Ab initio Molecular Dynamics Study of Local Atomic Structure Evolution of U–zr Alloy Melts upon Solidification

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Acta Metallurgica Sinica(English Letters) 2023年第9期36卷 1549-1558页

作者： Mingfeng liu Jiantao Wang Yongpeng Shi Heyu Zhu Yan Sun Peitao liu Xing-Qiu Chen Shenyang National Laboratory for Materials Sciences Institute of Metal ResearchChinese Academy of SciencesShenyang110016China School of Materials Science and Engineering University of Science and Technology of ChinaShenyang110016China

We study the local atomic structure evolution of Uzr and Uzr_(2) alloy melts upon solidification through ab initio molecular dynamics *** is achieved by analyzing in detail the temperature dependence of structure factors,pair correlation functions,the bond angle distributions,Honeycutt-Anderson index and Voronoi tessellation analysis as well as local bond orientation order *** observe that as the temperature decreases the pair correlation functions and structure factors become more structured with clear distinctions at the liquid–solid phase transition *** Honeycutt-Anderson indices and Voronoi tessellation analysis indicate that the liquid phase is predominantly comprised of the icosahedra-like local structures,whose fraction increases with decreasing temperature up to the transition temperature and then abruptly drops at the transition temperature,whereas the bcc-like local atomic structures dominate during the solidification ***,the bond orientation order analyses with\({\overline{w}}_{6}\)–\({\overline{q}}_{6}\)correlation map and bond angle distribution imply that the local structures mainly consist of the bcc-type during the solidification below the transition *** the analyses are consistent with each other,showing a first-order liquid to solid phase transition for both Uzr and Uzr_(2) solid solutions,which only differ in different predicted transition *** work provides a comprehensive insight into the detailed local structure evolution during the solidification of the U–zr alloy melts at the atomic *** strategies used here can be extended to studying the liquid–solid phase transition in other alloy systems.

关键词： Local atomic structure Molecular dynamics Solidification U-zr alloy melts

Effects of cerium salts on corrosion behaviors of Si–zr hybrid sol–gel coatings

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Chinese Journal of Aeronautics 2015年第2期28卷 600-608页

作者： Yu Mei liu Yuxing liu Jianhua Li Songmei Xue Bing Zhang You Yin Xiaolin School of Materials Science and Engineering Beihang University

The present work examines the effects of cerium salts on corrosion behaviors of Si-zr hybrid sol-gel coatings. The Si-zr hybrid sol-gel coatings on a 2A l2 aluminum substrate were pre- pared through hydrolysis and condensation of glycidoxypropyl-trimethoxy-silane （GTMS） and zirconium（IV） n-propoxide （TPOZ）. Used as inhibitors for corrosion, three types of cerium salts （Co（NO3）3, CeCl3, and Ce（CH3COO）3） were doped into the sol-gel coatings. Fourier transform infrared （FTIR） and scanning electron microscopy （SEM） were employed to investigate the structures and morphologies of various coatings, and the corrosion resistances of the coatings were evaluated by electrochemical methods and neutral salt spray tests. Experimental results indicate that the addition of cerium salts can hinder the process of corrosion due to their self-healing abili- ties. Furthermore, the sol-gel coating doped with Ce（CH3COO）3 has the best corrosion resistance because of the promotions of hydrolysis and condensation provided by CH3COO-.

关键词： Cerium salts Corrosion resistance Hybrid coating Inhibitor

High toughness and CMAS resistance of REAlO_(3)/RE_(2)zr_(2)O_(7)(RE=La,Nd,Sm,Eu,Gd,and Dy)composites with eutectic composition for thermal barrier coatings

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Journal of Advanced Ceramics 2024年第6期13卷 800-809页

作者： Zijian Zhang Jian Sun Guanghua liu Yi Han Wei liu Yi Li Wei Wang Xiangyang liu Peng Zhang Wei Pan Chunlei Wan State Key Laboratory of New Ceramics and Fine Processing School of Materials Science and EngineeringTsinghua UniversityBeijing 100084China China United Gas Turbine Technology Co. Ltd.Beijing 100015China College of Mathematics and Physics Beijing University of Chemical TechnologyBeijing 100029China College of Materials Science and Engineering Beijing University of TechnologyBeijing 100124China

Although rare earth zirconates(RE_(2)zr_(2)O_(7))have garnered attention as viable candidates for thermal barrier coatings(TBCs),they suffer from low fracture toughness and accelerated calcium–magnesium–alumina–silicate(CMAS)melt corrosion at high service temperatures,which impedes their practical *** this work,we developed a series of REAlO_(3)/RE_(2)zr_(2)O_(7)(RE=La,Nd,Sm,Eu,Gd,and Dy)composites with a eutectic composition that not only significantly enhanced the fracture toughness by more than 40%relative to that of RE_(2)zr_(2)O_(7)but also exhibited improved resistance to CMAS *** increase in toughness arises from multiple mechanisms,such as ferroelastic toughening,fine-grain strengthening,and residual stress toughening,all of which trigger more crack defects and energy ***,the CMAS penetration depth of the REAlO_(3)/RE_(2)zr_(2)O_(7)composites is approximately 36%lower than that of RE_(2)zr_(2)O_(7).Al–O constituents in composites can capture CaO,SiO_(2),and MgO in CMAS melts and increase their viscosity,resulting in enhanced CMAS corrosion *** thermophysical properties of the REAlO_(3)/RE_(2)zr_(2)O_(7)composites were also investigated,and their coefficient of thermal expansion and thermal conductivity are comparable to those of 7–8 wt%Y_(2)O_(3)partially stabilized zrO2(YSZ),indicating their potential as TBC materials.

关键词： fracture toughness thermal property calcium-magnesium-alumina-silicate(CMAS)corrosion REAlO_(3)/RE_(2)zr_(2)O_(7) eutectic composition

On the structure of isomeric state in neutron-rich 108zr: A projected shell model analysis

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Science China(Physics,Mechanics & Astronomy) 2015年第11期58卷 92-98页

作者： liu YanXin YU ShaoYing SUN Yang School of Science Huzhou University Department of Physics and Astronomy Shanghai Jiao Tong University IFSA Collaborative Innovation Center Shanghai Jiao Tong University State Key Laboratory of Theoretical Physics Institute of Theoretical Physics Chinese Academy of Sciences

Inspired by the recent experimental identification of the new isomer with a half-life of （620±150） ns in the very neutron-rich nucleus 180Szr, we apply the projected shell model with axially-deformed bases to discuss possible shapes near the ground state and the nature of the isomer. The structure of the new isomer is investigated by restricting the calculation to prolate and oblate shapes. It is shown that the isomer can be understood as a K-isomer. Meanwhile, the calculation predicts more low-lying high-K configurations, which may be confirmed by future experiments,

关键词： K isomer shape isomer prolate shape oblate shape projected shell model

Performance of Nb_(0.8)zr_(0.2) Layer-Modified AISI430 Stainless Steel as Bipolar Plates for Direct Formic Acid Fuel Cells

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Acta Metallurgica Sinica(English Letters) 2021年第1期34卷 77-84页

作者： Yuanyuan liu Zhongmin Lang Jinlong Cui Shengli An Inner Mongolia Key Laboratory of Coal Chemical Engineering and Comprehensive Utilization School of Chemistry and Chemical EngineeringInner Mongolia University of Science and TechnologyBaotou 014010China School of Materials and Metallurgy Inner Mongolia University of Science and TechnologyBaotou 014010China

To improve the interfacial conductivity and corrosion resistance of AISI430 stainless steel(430 SS)as bipolar plates for direct formic acid fuel cells(DFAFCs),a Nb_(0.8)zr_(0.2) layer has been successfully synthesized via the pulsed laser deposition(PLD)technique on the surface of 430 *** Nb_(0.8)zr_(0.2) layer is smooth,uniform,and comparatively compact without any surface flaw and *** under the simulated anodic environment of DFAFCs(0.05 M H_(2)SO_(4)+2 ppm HF+10 M HCOOH at 70℃)shows that the corrosion resistance of 430 SS is obviously ameliorated after the PLD *** addition,the interfacial contact resistance of Nb_(0.8)zr_(0.2)-430 SS(6.0 mΩcm^(2))is much smaller than that of bare 430 SS(151.3 mΩcm^(2))at the clamping force of 140 N cm^(-2).Besides,diff erent from the highly increased interfacial contact resistance of bare 430 SS,the Nb_(0.8)zr_(0.2)-430 SS shows a minor increase resistance after potentiostatic tests in simulated anodic environment of DFAFCs.

关键词： Corrosion resistance Nb_(0.8)zr_(0.2) layer Direct formic acid fuel cell Interfacial contact resistance Bipolar plates

Effect of Sc and zr additions on microstructures and corrosion behavior of Al-Cu-Mg-Sc-zr alloys

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Journal of Materials Science & Technology 2017年第9期33卷 1015-1022页

作者： Fangfang Sun Guiru liu Nash Qunying Li Enzuo liu Chunnain He Chunsheng Shi Naiqin Zhao School of Materials Science and Engineering Tianjin University Department of Mechanical Materials and Aerospace EngineeringIllinois Institute of Technology Tianjin Key Laboratory of Composite and Functional Materials

The effects of adding the alloy element Sc to Al alloys on strengthening, recrystallization and modification of the grain microstructure have been investigated. The combination of Sc and zr alloying not only produces a remarkable synergistic effect of inhibition of recrystallization and refinement of grain size but also substantially reduce the amount of high-cost additional Sc. In this work, the microstructures and corrosion behavior of a new type of Al-Cu-Mg-Sc-zr alloy with Sc/zr ratio of 1/2 were *** experimental results showed that the Sc and zr additions to Al-Cu-Mg alloy could strongly inhibit recrystallization, refine grain size, impede the segregation of Cu element along the grain boundary and increase the spacing of grain boundary precipitates. In addition, adding Sc and zr to Al-Cu-Mg alloy effectively restricts the corrosion mechanism conversion associated with Al2 Cu Mg particles, which resulted in the change of the cross-section morphology of inter-granular corrosion from an undercutting to an elliptical shape. The susceptibility to inter-granular corrosion was significantly decreased with increasing Sc and zr additions to the Al-Cu-Mg alloy. The relationships between microstructures evolution and inter-granular corrosion mechanism of Al-Cu-Mg-Sc-zr alloys were also discussed.

关键词： Aluminum alloy Microstructure Scandium Inter-granular corrosion

Hot deformation behavior of 51.1zr–40.2Ti–4.5Al–4.2V alloy in the single β phase field

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Progress in Natural Science:Materials International 2015年第1期25卷 34-41页

作者： Jingli Duan Yuanbiao Tan Liyuan Ji Wenchang liu Jingwu Zhang Riping liu Key Laboratory of Metastable Materials Science and Technology College of Materials Science and Engineering Yanshan University

The hot deformation behavior of a newly developed 51.1zr–40.2Ti–4.5Al–4.2 V alloy was investigated by compression tests in the deformation temperature range from 800 to 1050 ℃ and strain rate range from 10-3to 100 s-1. At low temperatures and high strain rates, the flow curves exhibited a pronounced stress drop at the very beginning of deformation, followed by a slow decrease in flow stress with increasing strain. The magnitude of the stress drop increased with decreasing deformation temperature and increasing strain rate. At high temperatures and low strain rates, the flow curves exhibited typical characteristics of dynamic recrystallization. A hyperbolic-sine Arrhenius-type equation was used to characterize the dependences of the flow stress on deformation temperature and strain rate. The activation energy for hot deformation decreased slightly with increasing strain and then tended to be a constant value. A microstructural mechanism map was presented to help visualize the microstructure of this alloy under different deformation conditions.

关键词： 51.1zr–40.2Ti–4.5Al–4.2V alloy Hot deformation Microstructure Dynamic recovery Dynamic recrystallization

Oxidation behavior of the Fe-36Al-0.09C-0.09B-0.04zr alloy at 1250℃

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International Journal of Minerals,Metallurgy and Materials 2010年第4期17卷 441-447页

作者： Jun-you liu Feng Li Jie liu Yi Zhang Jin-cheng Jiang Dun-xu Zou School of Materials Science and Engineering University of Science and Technology Beijing Beijing 100083 China Beijing BKDR Metallurgy Engineering ＆ Technology Co. Ltd. Beijing 100083 China China Iron ＆ Steel Research Institute Group Beijing 100081 China

To explore and study the Fe-A1 system alloy presenting exceptional oxidation resistance at high temperature, the Fe-36Al-0.09C-0.09B-0.04zr alloy was designed and developed. The microstructure and hardness of the backing at 1250℃were analyzed and measured. Thermodynamics and kinetics of the oxidation behavior were also analyzed by X-ray diffraction, scanning electron micros- copy, and energy-dispersive X-ray spectroscopy techniques. The results show that the microstructttre of the Fe-36Al-0.09C-0.09B-0.04zr alloy is FeAl phase at ambient temperature and is stable at 1250℃. It displays the excellent property of oxidation resistance because the oxide film has only the Al2O3 layer, and its oxidation kinetics curve obeys the parabolic law at 1250℃. The oxidation mechanism at 1250℃ is presumed that in the early oxidation period, the alloy oxidizes to form a large number of Al2O3 and a little Fe2O3, then, the enrichment of Al caused by Fe oxidization combines with O to form Al2O3.

关键词： Fe-alloy oxidation behavior oxide film oxidation thermodynamics oxidation kinetics