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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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Design and testing research of LiDAR for detecting atmospheric turbulence

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Optoelectronics Letters 2025年第3期21卷 172-176页

作者： QIU Duoyang LI Xianyang YANG Hao ZHU Xiaomeng FANG Zhiyuan XU Xiang School of Advanced Manufacturing Engineering Hefei University Anhui Provincial Engineering Technology Research Center of Intelligent Vehicle Control and Integrated Design Technology Hefei University Science Island Branch of Graduate School University of Science and Technology of China School of Mechanical and Energy Engineering Ningbo Tech University Key Laboratory of Atmospheric Optics Anhui Institute of Optics and Fine Mechanics Chinese Academy of Sciences

Atmospheric turbulence is an important parameter affecting laser atmospheric transmission. This paper reports on a self-developed atmospheric turbulence detection Li DAR system (scanning differential image motion Li DAR(DIM-Li DAR) system). By designing and simulating the optical system of atmospheric turbulence detection Li DAR,the basic optical imaging accuracy has been determined.

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基于双向交互结构的多意图识别与槽位填充联合模型

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Wuhan University Journal of Natural Sciences 2025年

作者：王昌晶曾翔辉王钰鑫孙钰昕左正康江西师范大学数字产业学院江西师范大学计算机信息工程学院

意图识别与槽位填充是自然语言理解的两个重要组成部分,由于两者的相关性,所以常进行联合训练提高性能。现有研究多是采用单向交互的多意图识别与槽位填充联合模型,通过在槽位填充部分融合意图信息提高了模型整体性能。为了进一步利用... 详细信息

意图识别与槽位填充是自然语言理解的两个重要组成部分,由于两者的相关性,所以常进行联合训练提高性能。现有研究多是采用单向交互的多意图识别与槽位填充联合模型,通过在槽位填充部分融合意图信息提高了模型整体性能。为了进一步利用两者的相关性提高模型整体性能,本文提出了基于双向交互结构的多意图识别与槽位填充联合模型,在槽位填充编码部分融合了意图编码信息,在意图识别解码部分融合了槽位解码信息。在MixATIS和MixSNIPS两个公共多意图联合训练数据集上的实验结果表明,该双向交互结构能有效提高联合模型的性能。此外,为了验证意图与槽位双向交互结构的泛化性,在本文模型的基础上提出了针对单意图场景的联合模型,在CAIS和SNIPS两个公共单意图联合训练数据集上也取得了优异的性能。

关键词：自然语言理解多意图识别槽位填充双向交互结构联合训练

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Study on two-dimensional analytical models for symmetrical gate stack dual gate strained silicon MOSFETs

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Chinese Physics B 2010年第10期19卷 492-498页

作者：李劲刘红侠李斌曹磊袁博 Key Laboratory for Wide Bandgap Semiconductor Devices Ministry of Education School of Microelectronics Xidian University

Based on the exact resultant solution of two-dimensional Poisson＇s equation, the novel two-dimensional models, which include surface potential, threshold voltage, subthreshold current and subthreshold swing, have been developed for gate stack symmetrical double-gate strained-Si MOSFETs. The models are verified by numerical simulation. Besides offering the physical insight into device physics, the model provides the basic designing guidance of further immunity of short channel effect of complementary metal-oxide-semiconductor （CMOS）-based device in a nanoscale regime.

关键词： strained-Si gate stack double-gate MOSFETs short channel effect the drain-inducedbarrier-lowering

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Measuring Stress Distributions of Orthotropic Composite Material in Plane Stress State by the Lock-in Infrared Thermography Technique

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Chinese Physics Letters 2011年第6期28卷 179-182页

作者： LI Xu-Dong WANG Wei-Bo LI Yong-Sheng WU Dong-Liu China Aero-Polytechnology Establishment Beijing 100028 China Ship Scientific Research Center Wuxi 214082

Feasibility of measuring stress distributions of orthotropic composite materials and structures in plane stress state by the lock-in infrared thermography technique is analyzed and stress distributions of a lap joint structure made of a kind of glass reinforced plastic composite lamination plates under tensile loadings are obtained by the lock-in infrared thermography *** and credibility of using this technique to measure stress distributions of orthotropic composite materials and structures in plane stress state are proved by comparing the results with the data given by the digital speckle correlation method.

关键词： technique method orthotropic

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Quick preparation and thermal transport properties of nanostructured β-FeSi_2 bulk material

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Chinese Physics B 2009年第1期18卷 287-292页

作者：李涵唐新峰曹卫强张清杰 State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of Technology

This paper reports that the nanostructured β-FeSi2 bulk materials are prepared by a new synthesis process by combining melt spinning （MS） and subsequent spark plasma sintering （SPS）. It investigates the influence of linear speed of the rolling copper wheel, injection pressure and SPS regime on microstructure and phase composition of the rapidly solidified ribbons after MS and bulk production respectively, and discusses the effects of the microstructure on thermal transport properties. There are two crystalline phases （α-Fe2Si5 and ε-FeSi） in the rapidly solidified ribbons; the crystal grains become smaller when the cooling rate increases （the 20 nm minimum crystal of ε-FeSi is obtained）. Having been sintered for 1 min above 1123K and annealed for 5min at 923K, the single-phase nanostructured β- FeSi2 bulk materials with 200-500 nm grain size and 98% relative density are obtained. The microstructure of β-FeSi2 has great effect on thermal transport properties. With decreasing sintering temperature, the grain size decreases, the thermal conductivity of β-FeSi2 is reduced remarkably. The thermal conductivity of β-FeSi2 decreases notably （reduced 72% at room temperature） in comparison with the β-FeSi2 prepared by traditional casting method.

关键词： thermoelectric materials nanostructure thermal conductivity

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Theoretical study on tetrazole and its derivatives (3) MP2 and thermodynamic calculations of amino derivatives of tetrazole

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Chinese Journal of Chemistry 1999年第2期17卷 114-124页

作者：陈兆旭肖鹤鸣高宝华 Department of Chemistry Nanjing university of Science and Technology Nanjing Jiangsu 210094 China

Fully optimized geometries and electronic structures of amino derivatives of tetrazole are obtained at MP2/6-31G* level. The tetrazole rings are planar and aromatic for all the amino derivatives of tetrazole. The amino group is not co-planar with the ring and its conformation is mainly determined by the lone pair electronic repulsion between the substituents and the ring. N(4) atom is more negatively charged and is the most probable coordination site. The energy gaps between LUMOs and HOMOs of 2H-aminotetrazoles and C-aminotetrazole neutrals are smaller than those of the corresponding 1H-isomers and N-aminotetrazole neutrals respectively. The IR frequencies, thermodynamic properties and temperature-dependent functions for heat capacities in the fom (a + bT + cT2) in the 300–1000K range are reported.

关键词： Tetrazole derivatives ab initio method molecular geometry IR spectra thermodynamic property

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First-principles investigation on structural and electrochemical properties of NaCoO_2 for rechargeable Na-ion batteries

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Journal of Central South University 2015年第6期22卷 2036-2042页

作者：粟劲苍周广裴勇杨振华王先友 Key Laboratory of Environmentally Friendly Chemistry and Applications of Minister of Education (School of Chemistry Xiangtan University) School of Materials Science and Engineering Central South University Faculty of Materials Optoelectronics and Physics Key Laboratory of Low Dimensional Materials & Application Technology of Ministry of Education Xiangtan University

NaxCoO2 is a commonly used cathode material for sodium ion batteries because of its easy synthesis, high reversible capacity and good cyclability. The structural and electrochemical properties of NaxCoO2 during sodium ion insertion/extraction process are studied based on first principles calculations. The calculation results of crystal structure parameters and average intercalation voltage are in good agreement with experiment data. Through calculation of the geometric structure and charge transfer in charging and discharging processes of NaxCoO2, it is found that the oxygen atom surrounding Co of the CoO6 octahedral screens the coulomb potential produced by sodium vacancy in NaxCoO2, and the charge is removed from the entire Co-O layer instead of the Co atom adjacent to sodium vacancy when sodium ions are extracted from the Na CoO2 lattice. Thus, during the insertion/extraction of sodium ion from Na CoO2, the CoO6 octahedral structure undergoes small lattice distortion, which makes the local structure quite stable and is beneficial to the cycling stability of the material for the application of sodium ion batteries.

关键词： sodium ion batteries first principles calculation cathode material electronic structure

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Laser-Ionization TOF Mass Spectrometer Characterization of Benzene Destruction in Atmospheric Pressure Pulsed Discharge

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Plasma Science and Technology 2009年第2期11卷 171-176页

作者：刘佳宏肖青梅王丽萍姚志丁洪斌 School of Physics and Optical Electronic Technology Dalian University of Technology School of Applied Mathematics and Physics Dalian Nationalities University Department of Physics Baicheng Normal University

Benzene is a major industrial air pollutant and can cause serious human health disorders. In this paper an investigation on benzene destruction, in an atmospheric-pressure fast-flow pulsed DC-discharge by means of laser ionization combined with time-of-flight （TOF） mass spectrometry, is reported. Most by-products including transient reactive species from the benzene discharge were characterized by molecular beam sampling combined with TOF mass spectrometry. It is showed that, with a gas mixture of 0.5% C6H6 in Ar, benzene can be effectively destroyed by discharge plasma. The intermediate species consisted of small fragments of CnHm （n=3-5, m = 1-11）, cycle-chain species of CnHm （n =6-9, m = 7-10） and polycyclic species CnHm （n ≥9, m = 8-12）. The alternation of mass peaks （intensity） with even/odd electrons was observed in the measured mass spectra. The results indicated that the alternation is mainly due to the different ionization potentials of the open shell and close shell species. Based on the examination of the features of the species＇ composition, the primary reaction pathways are proposed and discussed.

关键词： laser-ionization TOF mass spectrometer benzene plasma VOCs

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Influence of depositional environment on coalbed methane accumulation in the Carboniferous-Permian coal of the Qinshui Basin, northern China

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Frontiers of Earth Science 2019年第3期13卷 535-550页

作者： Haihai HOU Longyi SHAO Shuai WANG Zhenghui XIAO Xuetian WANG Zhen LI College of Geoscience and Surveying Engineering China University of Mining and TechnologyBeijing 100083China College of Mining Liaoning Technical UniversityFuxin 123000China School of Civil Engineering Hunan University of Science and TechnologyXiangtan 411201China

Based on analyses of the lithofacies palaeo-geography of the Taiyuan and the Shanxi Formations in the Qinshui Basin, the spatial variations of the coal seam thickness, coal maceral composition, coal quality, and gas content, together with the lithofacies of the surrounding rocks in each palaeogeographic unit were investigated. The results show that the thick coals of the Taiyuan Formation are mainly distributed in delta and barrier island depositional units in the Yangquan area in the northern part of the basin and the Zhangzi area in the southeastern part of the basin. The thick coals of the Shanxi Formation are located within transitional areas between delta plain and delta front depositional units in the central southern part of the basin. The Taiyuan Formation generally includes mudstone in its lower part, thick, continuous coal seams and limestones in its middle part, and thin, discontinuous coal seams and limestone and sand-mud interbeds in its top part. The Shanxi Formation consists of thick, continuous sandstones in its lower part, thick coal seams in its middle part, and thin coal seams, sandstone, and thick mudstone in its upper part. From the perspective of coal-bearing sedimentology and coalbed methane (CBM) geology, the lithology and thickness of the surrounding rocks of coal seams play more significant roles in controlling gas content variation than other factors such as coal thickness, coal macerals, and coal quality. Furthermore, it is found that the key factors influencing the gas content variation are the thicknesses of mudstone and limestone overlying a coal seam. At similar burial depths, the gas content of the Taiyuan coal seams decreases gradually in the lower delta plain, barrier-lagoon,delta front, barrier-tidal flat, and carbonate platform depositional units. The CBM enrichment areas tend to be located in zones of poorly developed limestone and well-developed mudstone. In addition, the gas content of the Shanxi Formation is higher in the coa

关键词： depositional environment coalbed methane enrichment condition gas content Taiyuan Formation Shanxi Formation

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