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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

Endoplasmic reticulum stress and autophagy in cerebral ischemia/reperfusion injury:PERK as a potential target for intervention

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Neural Regeneration Research 2025年第5期20卷 1455-1466页

作者： Ju Zheng Yixin Li Ting Zhang Yanlin Fu Peiyan Long xiao Gao Zhengwei wang Zhizhong Guan xiaolan qi Wei hong Yan xiao Key Laboratory of Endemic and Ethnic Diseases Ministry of Education&Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyangGuizhou ProvinceChina Guizhou Center for Disease Control and Prevention GuiyangGuizhou ProvinceChina Department of Histology and Embryology Guizhou Medical UniversityGuiyangGuizhou ProvinceChina Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry GuiyangGuizhou ProvinceChina

Several studies have shown that activation of unfolded protein response and endoplasmic reticulum(ER)stress plays a crucial role in severe cerebral ischemia/reperfusion *** occurs within hours after cerebral ischemia,but the relationship between ER stress and autophagy remains *** this study,we established experimental models using oxygen-glucose deprivation/reoxygenation in PC12 cells and primary neurons to simulate cerebral ischemia/reperfusion *** found that prolongation of oxygen-glucose deprivation activated the ER stress pathway protein kinase-like endoplasmic reticulum kinase(PERK)/eukaryotic translation initiation factor 2 subunit alpha(e IF2α)-activating transcription factor 4(ATF4)-C/EBP homologous protein(CHOP),increased neuronal apoptosis,and induced ***,inhibition of ER stress using inhibitors or by si RNA knockdown of the PERK gene significantly attenuated excessive autophagy and neuronal apoptosis,indicating an interaction between autophagy and ER stress and suggesting PERK as an essential target for regulating *** autophagy with chloroquine exacerbated ER stress-induced apoptosis,indicating that normal levels of autophagy play a protective role in neuronal injury following cerebral ischemia/reperfusion *** from this study indicate that cerebral ischemia/reperfusion injury can trigger neuronal ER stress and promote autophagy,and suggest that PERK is a possible target for inhibiting excessive autophagy in cerebral ischemia/reperfusion injury.

关键词： apoptosis ATF4 autophagy C/EBP homologous protein cerebral ischemia/reperfusion injury eIF2α endoplasmic reticulum stress PERK

Tumor inflammation-specific self-amplifying fluorescent molecular probes induce an anti-tumor immune response

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Science China Chemistry 2025年第1期 273-287页

作者： Shuguang Yang Lijun Hu hong xiao Zecong xiao Xintao Shuai PCFM Lab of Ministry of Education School of Materials Science and Engineering Sun Yat-sen University Department of Ultrasound The Fifth Affiliated Hospital Sun Yat-sen University Department of Medical Ultrasound The Third Affiliated Hospital of Sun Yat-sen University Nanomedicine Research Center The Third Affiliated Hospital of Sun Yat-sen University

Enhancing the concentration of exogenous molecular drugs within the tumor microenvironment through enzyme-catalyzed polymerization presents a novel strategy for cancer therapy. Nonetheless, the optimization of the catalytic efficiency is often impeded by the inefficient expression of enzymes. Herein, we reported a self-amplifying fluorescent molecular probe, Bis-HTPICG, for photodynamic therapy(PDT) and subsequent PDT-induced immunoreaction. The Bis-HTP-ICG probe possesses a noticeable enzyme-catalyzed polymerization facilitated by myeloperoxidase(MPO), a crucial enzyme secreted by neutrophils at inflammation sites. Upon exposure to laser irradiation, Bis-HTP-ICG showed a high PDT efficacy, inducing an acute inflammatory response that stimulates further recruitment of neutrophils and then elevated MPO secretion. The heightened level of MPO enhances the accumulation of the Bis-HTP-ICG via self-polymerization or binding with intratumoral proteins following MPO enzyme catalysis, instigating a self-amplifying chain reaction cycle involving Bis-HTP-ICG, neutrophils and ***, PDT efficiently incites immunogenic cell death(ICD) in tumor cells, initiating an anti-tumor immune response including dendritic cells(DCs) maturation, T cell proliferation and reprogramming of tumor-associated neutrophils(TANs). This work portrays a promising strategy for self-amplification of fluorescent molecular probes through adjustable enzyme levels,potentially offering a unique avenue to enhance the tumor accumulation of molecular drugs for improved tumor therapy.

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Enhanced post-combustion CO2 capture and direct air capture by plasma surface functionalization of graphene adsorbent

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Journal of Energy Chemistry 2025年第1期100卷 653-664页

作者： Rahul Navik Eryu wang xiao Ding Huang Yunyi Yiyu Liu Jia Li Guangdong-hong Kong Joint Laboratory for Carbon Neutrality Jiangmen Laboratory of Carbon and Science and Technology Guangzhou HKUST Fok Ying Tung Research Institute The hong Kong University of Science and Technology (Guangzhou) Carbon Neutrality and Climate Change Thrust Society Hub The Hong Kong University of Science and Technology (Guangzhou) Stoddart Institute of Molecular Science Department of Chemistry Zhejiang University

Graphene has enormous potential to capture CO2due to its unique properties and ***,graphene-based adsorbents have drawbacks of lower CO2adsorption capacity and poor *** work demonstrates a one-step rapid and sustainable N2/H2plasma treatment process to prepare graphene-based sorbent material with enhanced CO2adsorption *** treatment directly enriches amine species,increases surface area,and improves textural *** CO2adsorption capacity increases from 1.6 to 3.3 mmol/g for capturing flue gas,and from 0.14 to 1.3 mmol/g for direct air capture （DAC）.Importantly,the electrothermal property of the plasma-modified aerogels has been significantly improved,resulting in faster heating rates and significantly reducing energy consumption compared to conventional external heating for regeneration of *** aerogels display improved selectivity of 42 and 87 after plasma modification for 5 and 10 min,*** plasma-treated aerogels display minimal loss between 17%and 19% in capacity after 40 adsorption/desorption cycles,rendering excellent *** N2/H2plasma treatment of adsorbent materials would lower energy expenses and prevent negative effects on the global economy caused by climate change.

关键词： Carbon neutrality CO 2 capture Climate change Plasma treatment Graphene aerogel

Metal nanoparticles decorated CoFe-(oxy)hydroxysulfides nanosheets fabricated by a general strategy for electrocatalytic water splitting

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Journal of Energy Chemistry 2025年第1期100卷 26-38页

作者： xiaodong Yang Haochen Shen xiaoming xiao Zhichao Li qi Zhou Wei Yang Bin Jiang Yongli Sun Luhong Zhang Zhenhua Yan School of Chemical Engineering and Technology Tianjin University Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education) Nankai University

This study presents a novel method to fabricate metal-decorated,sulfur-doped layered double hydroxides （M/SLDH） through spontaneous redox and sulfurization *** developed Ag/SLDH and Pt/SLDH catalysts with abundant heterogeneous interfaces and hierarchical nanostructures demonstrated outstanding oxygen evolution reaction （OER） and hydrogen evolution reaction （HER） performance,achieving low overpotentials of 212 and 35 mV at 10 mA cm-2in 1 M KOH,*** both anode and cathode in water splitting,they required only 1.47 V to reach 10 mA cm-2and exhibited high structural robustness,maintaining stability at 1000 mA cm-2for 300 ***-situ Raman analysis revealed that the synergistic effects of metal nanoparticles and S doping significantly promote the transformation into the S-Co1-xFexOOH layer,which serves as the active phase for water ***,ultraviolet photoelectron spectroscopy （UPS） and density functional theory （DFT） analyses indicated that incorporating metal nanoparticles and S doping increase electron density near the Fermi level and reduce reaction energy barriers,thus enhancing intrinsic OER and HER *** study provides a scalable strategy for synthesizing high-performance electrocatalysts for water splitting,with promising potential for broader applications.

关键词： LDH Spontaneous reaction Metal nanoparticles Water splitting

Improvement of 3-D FEM Coupled Model on Strip Crown in Hot Rolling

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Journal of Iron and Steel Research International 2012年第3期19卷 14-19页

作者： wang tao, xiao hong, ZHAO Tie-yong, qi xiang-dong (College of Mechanical and Engineering, Yanshan University, qinhuangdao 066004, Hebei, China) College of Mechanical and Engineering Yanshan University Qinhuangdao 066004 Hebei China

In order to simulate and analyze hot strip crown and flatness accurately and efficiently, the 3-D （three-di- mensional） coupled model involved in RPFEM （rigid-plastic finite element method） is improved based on the analyti- cal model of forecasting rolling force distribution. In the analytical model, variational method is employed to solve the lateral flow of metal and influential function method is employed to calculate roll deflection, the lateral distribution of rolling force can be obtained rapidly by iterative strategy. Then the 3-D coupled model uses the result as initial distri- bution of rolling force to calculate roll deflection and makes the initial on-load roll gap profile close to the final value, so as to reduce iterations and increase efficiency. Compared with previous algorithms, the improved model can reduce the iterations by about 50% and shorten the computing time by about 60% on the basis of the calculation accuracy.

关键词： rolling force analytical model RPFEM coupled model efficiency

Modi cation of Roll Flattening Analytical Model Based on the Plane Assumption

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Chinese Journal of Mechanical Engineering 2018年第3期31卷 69-75页

作者： tao wang qing-Xue Huang hong xiao xiang-dong qi College of Mechanical Engineering Taiyuan University of Technology National Engineering Research Center of Cold Strip Rolling Equipment and Technology Yanshan University

Roll flattening is an important component in the roll stack elastic deformation,which has important influence on controlling of the strip crown and flatness. Foppl formula and semi?infinite body model are the most popular analyti?cal models in the roll flattening calculation. However,the roll flattening calculated by traditional flattening models has a great deviation from actual situation,especially near the barrel edges. Therefore,in order to improve the accuracy of roll flattening,a new model is proposed based on the elastic half plane theory. The calculation formulas of roll flatten?ing are deduced respectively under the assumptions of plane strain and plane stress. Then,the two assumptions are combined through the method of introducing an transition coe cient,and the distribution rules of roll flattening for di erent rolling force,flattening width,roll length and roll diameter are analyzed by using the FEM analysis software Marc. Regarding the ratio of the length to roll end and the roll diameter as variable to fit the transition coe cient,the new model of roll flattening is established based on the elastic half plane theory. Finally,the transition coe cient is fitted to establish the model. Compared with the traditional models,the new model can e ectively improve the cal?culation deviation in the roll end,which has important significance for accurate simulation of plate shape,especially for the distribution of rolling force between rolls.

关键词： Roll flattening Plane strain Plane stress Transition coe cient FEM

Individualized Pixel Synthesis and Characterization of Combinatorial Materials Chips

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Engineering 2015年第2期1卷 225-233页

作者： xiao-dong xiang Gang wang xiaokun Zhang Yong xiang hong wang State Key Laboratory of Green Building Materials China Building Materials Academy Intematix Corporation State Key Laboratory of Electronic Thin Films & Integrated Devices School of Energy Science and Engineering University of Electronic Science and Technology of China

Conventionally, an experimentally determined phase diagram requires studies of phase formation at a range of temperatures for each composition, which takes years of effort from multiple research groups. Combinatorial materials chip technology, featuring high-throughput synthesis and characterization, is able to determine the phase diagram of an entire composition spread of a binary or ternary system at a single temperature on one materials library, which, though significantly increasing efficiency, still requires many libraries processed at a series of temperatures in order to complete a phase diagram. In this paper, we propose a "one-chip method" to construct a complete phase diagram by individually synthesizing each pixel step by step with a progressive pulse of energy to heat at different temperatures while monitoring the phase evolution on the pixel in situ in real time. Repeating this process pixel by pixel throughout the whole chip allows the entire binary or ternary phase diagram to be mapped on one chip in a single experiment. The feasibility of this methodology is demonstrated in a study of a Ge-Sb-Te ternary alloy system, on which the amorphouscrystalline phase boundary is determined.

关键词： combinatorial materials chip phase diagram pixel synthesis in-situ characterization phase-boundary determination

Multilevel analysis of the central-peripheral-target organ pathway:contributing to recovery after peripheral nerve injury

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Neural Regeneration Research 2025年第10期20卷 2807-2822页

作者： Xizi Song Ruixin Li xiaolei Chu qi Li Ruihua Li qingwen Li Kai-Yu Tong xiaosong Gu dong Ming Academy of Medical Engineering and Translational Medicine Tianjin UniversityTianjinChina Haihe Laboratory of Brain-Machine Interface and Human-Machine Fusion TianjinChina Department of Rehabilitation Tianjin University Tianjin HospitalTianjinChina Department of Hand Microsurgery Tianjin University Tianjin HospitalTianjinChina School of Exercise and Health Tianjin University of SportTianjinChina Department of Biomedical Engineering the Chinese University of Hong KongHong Kong Special Administrative RegionChina

Peripheral nerve injury is a common neurological condition that often leads to severe functional limitations and *** on the pathogenesis of peripheral nerve injury has focused on pathological changes at individual injury sites,neglecting multilevel pathological analysis of the overall nervous system and target *** has led to restrictions on current therapeutic *** this paper,we first summarize the potential mechanisms of peripheral nerve injury from a holistic perspective,covering the central nervous system,peripheral nervous system,and target *** peripheral nerve injury,the cortical plasticity of the brain is altered due to damage to and regeneration of peripheral nerves;changes such as neuronal apoptosis and axonal demyelination occur in the spinal *** nerve will undergo axonal regeneration,activation of Schwann cells,inflammatory response,and vascular system regeneration at the injury *** damage to target organs can occur,including skeletal muscle atrophy and sensory receptor *** then provide a brief review of the research advances in therapeutic approaches to peripheral nerve *** main current treatments are conducted passively and include physical factor rehabilitation,pharmacological treatments,cell-based therapies,and physical ***,most treatments only partially address the problem and cannot complete the systematic recovery of the entire central nervous system-peripheral nervous system-target organ ***,we should further explore multilevel treatment options that produce effective,long-lasting results,perhaps requiring a combination of passive(traditional)and active(novel)treatment methods to stimulate rehabilitation at the central-peripheral-target organ levels to achieve better functional recovery.

关键词： central nervous system central peripheral target organ multilevel pathological analysis nerve regeneration peripheral nerve injury peripheral nervous system target organs therapeutic approach