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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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Sequence-activated chemiluminescence probes: programmable illumination for high-contrast in vivo sensing and imaging

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science China Chemistry 2025年第01期 26-34页

作者： Yutao Zhang Juan Li Wei-Hong Zhu Zhiqian Guo shanghai Key Laboratory of Functional Materials Chemistry Joint International Research Laboratory of Precision Chemistry and Molecular Engineering Institute of Fine Chemicals School of Chemistry and Molecular Engineering East China University of Science and Technology State Key Laboratory of Bioreactor Engineering Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell MetabolismEast China University of Science & Technology

Sequence-activated chemiluminescence(CL) technique offers a unique approach to detecting specific biomolecules or cellular events with high sensitivity and spatial resolution. The fundamental principle behind sequence-activated CL probes involves tailoring highly-controllable CL signals in response to specific sequences or events of interest, thus enabling high-contrast signals under complex physiological conditions. This sequential activation could be triggered by enzymes, reactive oxygen species(ROS), biothiols or changes in the microenvironment. These unique sequence-activated CL probes bestow several advantages, including minimal background, deep-tissue penetration, and the ability of non-invasive or minimally invasive detection. The sequence-activated CL techniques represent a significant advancement in molecular imaging and diagnostics. In this mini-review, we focus on the latest developments in sequential CL probes, addressing the technical challenges and discussing the future trajectory by harnessing CL signaling and molecular recognition.

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Antithetical impacts of deleterious LRP1B mutations in non-squamous and squamous NSCLCs on predicting benefits from immune checkpoint inhibitor alone or with chemotherapy over chemotherapy alone: retrospective analyses of the POPLAR/OAK and CHOICE-01 trial

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science China Life sciences 2025年第1期 249-262页

作者： Jinliang Wang Wenyong Zhou Yu Xu Jianchun Duan Qiaoxia Zhou Guoqiang Wang Leo Li Chunwei Xu Wenxian Wang Shangli Cai Zhijie Wang Jie Wang Department of Oncology The Fifth Medical Center of Chinese PLA General Hospital Department of Thoracic Surgery Shanghai Chest HospitalSchool of MedicineShanghai Jiao Tong University Burning Rock Biotech CAMS Key Laboratory of Translational Research on Lung Cancer State Key Laboratory of Molecular OncologyDepartment of Medical OncologyNational Cancer Center/National Clinical Research Center for ancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical College Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences Department of Clinical Trial The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)

In non-small cell lung cancers,the non-squamous and squamous subtypes（nsqNSCLC and sqNSCLC） exhibit disparities in pathophysiology,tumor immunology,and potential genomic correlates affecting responses to immune checkpoint inhibitor（ICI）-based *** our inhouse training cohort（n=85）,the presence of the LRP1B deleterious mutation（LRP1B-del） was associated with longer and shorter progression-free survival（PFS） on ICIs alone in nsqNSCLCs and sqNSCLCs,respectively(Pinteraction=0.008).These results were validated using a larger public ICI cohort(n=208,Pinteraction<0.001).Multiplex immunofluorescence staining revealed an association between LRP1B-del and increased and decreased numbers of tumor-infiltrating CD8+T cells in nsqNSCLCs（P=0.040） and sqNSCLCs（P=0.014）,*** the POPLAR/OAK cohort,nsqNSCLCs with LRP1B-del demonstrated improved PFS benefits from atezolizumab over docetaxel(hazard ratio（HR）=0.70,P=0.046),whereas this benefit was negligible in those without LRP1B-del（HR=1.05,P=0.64）.Conversely,sqNSCLCs without LRP1B-del benefited more from atezolizumab（HR=0.60,P=0.002） than those with LRP1B-del（HR=1.30,P=0.31）.Consistent results were observed in the in-house CHOICE-01 cohort,in which nsqNSCLCs with LRP1B-del and sqNSCLCs without LRP1B-del benefited more from toripalimab plus chemotherapy than from chemotherapy alone(Pinteraction=0.008).This multi-cohort study delineates the antithetical impacts of LRP1B-del in nsqNSCLCs and sqNSCLCs on predicting the benefits from ICI alone or with chemotherapy over chemotherapy *** findings highlight the distinct clinical utility of LRP1B-del in guiding treatment choices for nsqNSCLCs and sqNSCLCs,emphasizing the necessity for a detailed analysis based on pathological subtypes when investigating biomarkers for cancer therapeutics.

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3D fracture modelling and limit state analysis of prestressed composite concrete pipes

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Frontiers of Structural and Civil Engineering 2019年第1期13卷 165-175页

作者： Pengfei HE Yang SHEN Yun GU Pangyong SHEN School of Aerospace Engineering and Applied Mechanics Tongji UniversityShanghai 200092China shanghai SMI Engineering Project Management Co. Ltd.Shanghai 201103China

In this manuscript,we study fracture of prestressed cylindrical concrete *** concrete pipes play a major role in tunneling and underground *** structure is modelled fully in 3D using three-dimensional continuum elements for the concrete structure which beam elements are employed to model the *** allows the method to capture important phenomena compared to a pure shell model of concrete.A continuous approach to fracture is chosen when concrete is subjected to compressive loading while a combined continuous-discrete fracture method is employed in *** model is validated through comparisons with experimental data.

关键词： cylindrical concrete structures limit state analysis 3D fracture modelling prestressed composite pipes reinforced concrete three-point bending test

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Cascade degradation and electrocatalytic upcycling of waste poly(ethylene terephthalate)to valued products

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Nano Research 2025年第1期18卷 76-93页

作者： Xin Li Zirui Jiang Zongkui Kou John Wang Shiyou Zheng School of Materials and Chemistry University of Shanghai for Science and TechnologyShanghai 200093China School of Materials science and Engineering Wuhan University of TechnologyWuhan 430070China Department of Materials science and Engineering National University of SingaporeSingapore 117574Singapore

The global annual production of poly(ethylene terephthalate)(PET)has reached 82 million tons,yet only a small fraction(less than 20%)is *** ultra-slow degradation rate of PET results in the accumulation of PET waste in the environment,causing serious plastic pollution and posing severe challenges to *** response,great efforts have been directed toward developing a cascade degradation and electrocatalytic upcycling strategy,which serves as a“waste-towealth”*** strategy involves electro-reforming PEThydrolyzed intermediates or using PET pyrolyzed products as electrocatalysts to generate high-value *** review provides an overview of the state-of-the-art strategies for the“degradation-electrocatalytic upcycling(De-eUp)”of PET ***,an introduction to the strategy is provided,categorizing it into two main frameworks:“pyrolysis-electrocatalytic upcycling”and“hydrolysis-electrocatalytic upcycling”.The section on“pyrolysis-electrocatalytic upcycling”delves into the degradation methods for designing derived carbon nanomaterials and their utilization as high-performance ***“hydrolysis-electrocatalytic upcycling”section discusses recent advancements in electro-reforming of PET hydrolyzed intermediates for the production of C_(1) and C_(2) *** review concludes by examining the challenges and future prospects in developing an efficient and economical PET upcycling *** is anticipated that this review will stimulate further progress in plastic waste valorization.

关键词： poly(ethylene terephthalate)waste electrocatalytic upcycling pyrolysis hydrolysis ethylene glycol oxidation reaction

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DEVELOPMENT OF THE ENERGY MANAGEMENT STRATEGY FOR PARALLEL HYBRID ELECTRIC URBAN BUSES

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Chinese Journal of Mechanical Engineering 2008年第4期21卷 44-50页

作者： HUANG Yuanjun YIN Chengliang ZHANG Jianwu Institute of Automotive Engineering School of Mechanical Engineering Shanghai Jiaotong University Shanghai 200240 China

A novel parallel hybrid electrical urban bus （PHEUB） configuration consisting of an extra one-way clutch and an automatic mechanical transmission （AMT） is taken as the study subject. An energy management strategy combining a logic threshold approach and an instantaneous optimization algorithm is proposed for the investigated PHEUB. The objective of the energy management strategy is to achieve acceptable vehicle performance and drivability requirements while simultaneously maximizing the engine fuel consumption and maintaining the battery state of charge in its operation range at all times. Under the environment of Matlab/Simulink, a computer simulation model for the PHEUB is constructed by using the model building method combining theoretical analysis and bench test data. Simulation and experiment results for China Typical Bus Driving Schedule at Urban District （CTBDS_UD） are obtained, and the results indicate that the proposed control strategy not only controls the hybrid system efficiently but also improves the fuel economy significantly.

关键词： Parallel hybrid electric urban bus (PHEUB) Energy management strategy (EMS) Instantaneous optimization

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Speculation of fluid dynamics equations based on Liutex theory and constitutive relation of symmetric shearing deformation

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Journal of Hydrodynamics 2023年第4期35卷 607-629页

作者： Shuai-chen Zhu Duo Wang Yang Liu Hongyi Xu Department of Aeronautics and Astronautics Fudan UniversityShanghai200433China

The fluid kinematics of Liutex decomposes a velocity gradient tensor(VGT)of∇v into four components,including rotation(R),stretching/compressing(SC),anti-symmetric shear(Santi-sym)and symmetric shear(Ssym),as oppose to the traditional Cauchy-Stokes decomposition where a VGT was decomposed into the strain rate and vorticity *** current study limpidly clarified the physical meanings of these deformations in the newly-proposed decomposition from the perspectives of both fluid kinematics and *** in-depth understanding the physical connotations of these deformations,the present study further suggests that the Ssym be the only deformation appropriately correlated to the stress tensor,leading to the establishment of a new constitutive relation for Newtonian fluids with the modified model assumptions originated from Stokes in ***,the present research finds that the“principal decomposition”proposed by Liu is not mathematically unique when a VGT has three real eigenvalues(TR).Within the context,a new decomposition method is introduced to avoid the non-uniqueness issue arising from using the principal decomposition to establish fluid dynamics *** on the modified Stokes assumptions and the novel VGT decomposition method,a set of new fluid dynamics momentum equations are obtained for Newtonian *** added stress tensor of Fadd is identified as the key difference between the newly-derived governing equations and the conventional Navier-Stokes(N-S)equations,which is caused by excluding the SC correlation to the stress tensor in the new constitutive ***,a preliminary analysis of Fadd is conducted using the existing channel turbulence direct numerical simulations(DNS)data based on the traditional N-S *** Fadd is found widely existing in turbulence and is of the same order of magnitude with the other force ***,the Fadd is expected to have some nonnegligible effects on altering the current DNS data based on

关键词： Constitutive relation Liutex principal decomposition Newtonian fluid Navier-Stokes equations fluid kinematics fluid dynamics

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Polybenzoxazine/organosilicon composites with low dielectric constant and dielectric loss

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Chinese Journal of Chemical Engineering 2023年第12期64卷 241-249页

作者： Manlin Yuan Xin Lu Xiaoyun Ma Hao Lin Angui Lu Liyan Shao Zhong Xin State Key Laboratory of Chemical Engineering School of Chemical EngineeringEast China University of Science and TechnologyShanghai 200237China

The evolution of electronic communication technology raises higher requirements for low dielectric constant(low-k)*** this,a benzoxazine functional organosilicon(HP-aptes)with dense Si—O—Si crosslinking networks and large sterically hindered tert-butyl groups was prepared by the sol–gel ***,a series of polybenzoxazine composites(PPHP)were prepared from intrinsically low dielectric constant bis-functional benzoxazine monomer(P-aptmds)and *** double crosslinking networks of polybenzoxazine and organosilicon further increased the crosslinking density and decreased the dipole density of composites,which endowed the composites with enhanced low-k *** the content of HP-aptes is 30%(mass),the crosslinking density was 2.05×10^(-3)mol·cm^(-3),while that of PP-aptmds was 3.31×10^(-3)mol·cm^(-3).In addition,the dielectric constant and dielectric loss of PPHP composite at 1 MHz could reach 2.61 and 0.0056,respectively.

关键词： Polybenzoxazine Organosilicon Composite Dielectric constant

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Tracking and localization for omni-directional mobile industrial robot using reflectors

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Advances in Manufacturing 2018年第1期6卷 118-125页

作者： Shuai Guo Ting-Ting Fang Tao Song Feng-Feng Xi Bang-Guo Wei shanghai Key Laboratory of Intelligent Manufacturing andRobotics Shanghai University Shanghai 200444 People'sRepublic of China Department of Aerospace Engineering Ryerson UniversityToronto Canada

In this paper, an improved tracking and local-ization algorithm of an omni-directional mobile industrialrobot is proposed to meet the high positional accuracyrequirement, improve the robot＇s repeatability positioningprecision in the traditional trilateral algorithm, and solvethe problem of pose lost in the moving process. Lasersensors are used to identify the reflectors, and by associ-ating the reflectors identified at a particular time with thereflectors at a previous time, an optimal triangular posi-tioning method is applied to realize the positioning andtracking of the robot. The experimental results show thatpositioning accuracy can be satisfied, and the repeatabilityand anti-jamming ability of the omni-directional mobileindustrial robot will be greatly improved via this algorithm.

关键词： Mobile industrial robot Tracking and positioning Matching

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晶格畸变增强卤化锑晶体团簇的自陷激子发射（英文）

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science China Materials 2025年第1期 132-140页

作者：刘达何敬敬孙玉婷刘心翊彭玉李庆杨化桂牛强杨双侯宇 Key Laboratory for Ultrafine Materials of Ministry of Education Shanghai Engineering Research Center of Hierarchical Nanomaterials School of Materials Science and Engineering East China University of Science and Technology China National Enterprise technology Center Inner Mongolia Erdos Electric Power and Metallurgy Group Company Limited

零维钙钛矿材料以自陷激子引起的宽带发射为特征,是一种很有前途的刺激响应和光加密材料.然而,现有的研究主要集中在结构相变对光物理性质的影响上,对自陷激子的发射机制缺乏深入了解.本文证明了零维卤化锑单晶中的脱水反应,在不诱导结...

零维钙钛矿材料以自陷激子引起的宽带发射为特征,是一种很有前途的刺激响应和光加密材料.然而,现有的研究主要集中在结构相变对光物理性质的影响上,对自陷激子的发射机制缺乏深入了解.本文证明了零维卤化锑单晶中的脱水反应,在不诱导结构相变的基础上显著增强了自陷激子的发射,导致光致发光量子产率从3.5%大幅提高到91.4%.利用原位X射线衍射和光致发光技术揭示了晶体结构和光致发光强度之间的定性关系,证明了在脱水过程中引入了丰富的晶格畸变.温度依赖的荧光光谱和瞬态吸收光谱表明,晶格畸变导致中等的电子-声子耦合强度和更高的激子结合能,加速了自陷激子从非辐射复合单重态弛豫到辐射复合三重态,进而表现出增强的光致发光.作为概念验证,在防伪、可重写发光纸和湿度传感等多重场景中实现了应用.这一发现阐明了自陷激子的发射机制,并为设计可切换发光材料提供了一条新途径.

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