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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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Thermally activated delayed fluorescence enhanced by macrocyclization

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Science China Chemistry 2025年

作者： Shuo Li Chenghao zhu Lijun Mao xin Zhang Zecong Ye Chunju Li Da Ma School of Pharmaceutical and Chemical Engineering & Institute for Advanced Studies Taizhou University School of Chemical Engineering and Light Industry Guangdong University of Technology Tianjin Key Laboratory of Structure and Performance for Functional Molecules Tianjin Normal University

Thermally activated delayed fluorescence (TADF) depends on reverse intersystem crossing (RISC) from the lowest triplet to the singlet excited state. Here, a macrocyclization strategy is developed to achieve TADF emission by promoting RISC. 5-(9Hcarbazol-9-yl) isophthalonitrile, a fluorescent molecule, is coupled with 1,4-dimethoxybenzene by methylene bridges to form a macrocycle with TADF emission. Experimental results and theoretical calculation indicate that the macrocyclization strategy contributes to RISC promotion and suppression of nonradiative decay, resulting in effective TADF emission transformed from prompt fluorescence. Three TADF luminophores are cyclized with the same strategy, and an enhanced TADF emission of up to3.8 folds is observed. The marriage of macrocycle chemistry and luminescent materials will provide new guidelines for designing efficient TADF materials.

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基于阅读推广的卫生类高职仁爱校园文化体系构建

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科技视界 2019年第24期 146-147,199页

作者：李静朱心琪宁波卫生职业技术学院图书信息中心

仁爱是中华文化最核心的价值理念。卫生类高职院校所含有的仁爱、健康、生命关怀等文化特质,决定了仁爱文化是主流校园文化。图书馆是校园文化建设的主阵地,其阅读推广必然聚焦仁爱文化,开展精准服务,构建基于阅读推广的卫生类高职仁爱... 详细信息

仁爱是中华文化最核心的价值理念。卫生类高职院校所含有的仁爱、健康、生命关怀等文化特质,决定了仁爱文化是主流校园文化。图书馆是校园文化建设的主阵地,其阅读推广必然聚焦仁爱文化,开展精准服务,构建基于阅读推广的卫生类高职仁爱校园文化体系。

关键词：仁爱文化阅读推广卫生类高职院校

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Maintaining moderate levels of hypochlorous acid promotes neural stem cell proliferation and differentiation in the recovery phase of stroke

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Neural Regeneration Research 2025年第3期20卷 845-857页

作者： Lin-Yan Huang Yi-De Zhang Jie Chen Hai-Di Fan Wan Wang Bin Wang Ju-Yun Ma Peng-Peng Li Hai-Wei Pu xin-Yian Guo Jian-Gang Shen Su-Hua qi School of Medical Technology Xuzhou Key Laboratory of Laboratory DiagnosticsXuzhou Medical UniversityXuzhouJiangsu ProvinceChina School of Pharmacy Xuzhou Medical UniversityXuzhouJiangsu ProvinceChina Department of Laboratory Medicine Branch Hospital of Huai’an First People’s HospitalHuai’anJiangsu ProvinceChina Department of Laboratory Medicine the Affiliated Hospital of Xuzhou Medical UniversityXuzhouJiangsu ProvinceChina School of Chinese Medicine The University of Hong KongHong Kong Special Administrative RegionChina

It has been shown clinically that continuous removal of ischemia/reperfusion-induced reactive oxygen species is not conducive to the recovery of late ***,previous studies have shown that excessive increases in hypochlorous acid after stroke can cause severe damage to brain *** previous studies have found that a small amount of hypochlorous acid still exists in the later stage of stroke,but its specific role and mechanism are currently *** simulate stroke in vivo,a middle cerebral artery occlusion rat model was established,with an oxygen-glucose deprivation/reoxygenation model established in vitro to mimic *** found that in the early stage(within 24 hours)of ischemic stroke,neutrophils produced a large amount of hypochlorous acid,while in the recovery phase(10 days after stroke),microglia were activated and produced a small amount of hypochlorous ***,in acute stroke in rats,hypochlorous acid production was prevented using a hypochlorous acid scavenger,taurine,or myeloperoxidase inhibitor,4-aminobenzoic acid *** results showed that high levels of hypochlorous acid(200μM)induced neuronal apoptosis after oxygen/glucose deprivation/***,in the recovery phase of the middle cerebral artery occlusion model,a moderate level of hypochlorous acid promoted the proliferation and differentiation of neural stem cells into neurons and *** suggests that hypochlorous acid plays different roles at different phases of cerebral ischemia/reperfusion *** levels of hypochlorous acid(5 and 100μM)promoted nuclear translocation ofβ-*** transfection of single-site mutation plasmids,we found that hypochlorous acid induced chlorination of theβ-catenin tyrosine 30 residue,which promoted nuclear ***,our study indicates that maintaining low levels of hypochlorous acid plays a key role in the recovery of neurological function.

关键词： cell differentiation cerebral ischemia/reperfusion injury chlorination hypochlorous acid microglia neural stem cell neurogenesis nuclear translocation stroke β-catenin

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重介分选密度智能控制系统在济二煤矿选煤厂的应用

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煤炭加工与综合利用 2024年第2期 1-6页

作者：朱绍文李新祥戴长官朱新奇徐鹏展兖矿能源济宁二号煤矿山东济宁272072 山东能源集团技术研究总院山东济南250000 华为技术有限公司广东深圳518116

阐述了济宁二号煤矿选煤厂针对重介分选密度控制问题,以数字化建设为基础,依托人工智能技术进行了智能化建设的探索。基于完善的生产传感器,采集原煤灰分、入洗煤量、磁性物含量、精煤灰分等生产数据入库保存,作为智能控制系统的数据基... 详细信息

阐述了济宁二号煤矿选煤厂针对重介分选密度控制问题,以数字化建设为基础,依托人工智能技术进行了智能化建设的探索。基于完善的生产传感器,采集原煤灰分、入洗煤量、磁性物含量、精煤灰分等生产数据入库保存,作为智能控制系统的数据基础。基于盘古大模型和优化求解技术构建重介分选密度设定值的智能推荐系统,并将推荐的分选密度自动下发到PLC系统执行,形成完整的生产闭环。生产实践表明,该系统控制得到的精煤产品灰分稳定性更高,精煤理论产率相比人工控制提升0.334%。

关键词：选煤厂重介质旋流器人工智能大模型分选密度控制

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Pharmacological targeting cGAS/STING/NF-κB axis by tryptanthrin induces microglia polarization toward M2 phenotype and promotes functional recovery in a mouse model of spinal cord injury

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Neural Regeneration Research 2025年第11期20卷 3287-3301页

作者： Ziwei Fan Mengxian Jia Jian Zhou Zhoule zhu Yumin Wu Xiaowu Lin Yiming qian Jiashu Lian xin Hua Jianhong Dong Zheyu Fang Yuqing Liu Sibing Chen Xiumin Xue Juanqing Yue Minyu zhu Ying Wang Zhihui Huang Honglin Teng Department of Orthopedics(Spine Surgery) the First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang ProvinceChina School of Pharmacy Hangzhou Normal UniversityHangzhouZhejiang ProvinceChina Department of Neurology The First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang ProvinceChina Department of Pathology Affiliated Hangzhou First People’s HospitalSchool of MedicineWestlake UniversityHangzhouZhejiang ProvinceChina Department of Clinical Research Center Affiliated Hangzhou First People’s HospitalSchool of MedicineWestlake UniversityHangzhouZhejiang ProvinceChina

The M1/M2 phenotypic shift of microglia after spinal cord injury plays an important role in the regulation of neuroinflammation during the secondary injury phase of spinal cord *** of shifting microglia polarization from M1(neurotoxic and proinflammatory type)to M2(neuroprotective and anti-inflammatory type)after spinal cord injury appears to be *** possesses an anti-inflammatory biological ***,its roles and the underlying molecular mechanisms in spinal cord injury remain *** this study,we found that tryptanthrin inhibited microglia-derived inflammation by promoting polarization to the M2 phenotype in *** promoted M2 polarization through inactivating the cGAS/STING/NF-κB ***,we found that targeting the cGAS/STING/NF-κB pathway with tryptanthrin shifted microglia from the M1 to M2 phenotype after spinal cord injury,inhibited neuronal loss,and promoted tissue repair and functional recovery in a mouse model of spinal cord ***,using a conditional co-culture system,we found that microglia treated with tryptanthrin suppressed endoplasmic reticulum stress-related neuronal *** together,these results suggest that by targeting the cGAS/STING/NF-κB axis,tryptanthrin attenuates microglia-derived neuroinflammation and promotes functional recovery after spinal cord injury through shifting microglia polarization to the M2 phenotype.

关键词： cGAS/STING functional recovery microglia neuroinflammation neuroprotection nuclear factor-κB polarization spinal cord injury tryptanthrin

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Detecting and assessing Spartina invasion in coastal region of China： A case study in the Xiangshan Bay

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Acta Oceanologica Sinica 2016年第4期35卷 35-43页

作者： zhu Changming ZHANG xin qi Jiaguo Department of Geography and Environment Jiangsu Normal University Xuzhou 221116 China Institute of Remote Sensing and Digital Earth Chinese Academy of Sciences Beijing 100101 China Center for Global Change and Earth Observations Michigan State University East Lansing MI 48864 USA

Spartina alterniflora is one of exotic plants along the coastal region in China. It was introduced as an important engineering approach to ecological restoration in the later 1970 s. However, owing to its good adaptability and strong reproductive capacity, the introduced species is explosively spreading along the coastal region quickly and resulting in a significant impact on the health and safety of coastal wetland ecosystems. It is imperative to quantify the spatial extent and the rate of S. alterniflora sprawl in order to assess its ecological damages and economic impacts. Remote sensing techniques have been used to address these challenges but large unsuccessful due to mixed spectral properties. In this study, a hybrid method was proposed for S. alterniflora detection using medium resolution remote sensing images by integrating both spatial and spectral features of S. alterniflora. The hybrid method consists of two phases：（1） delineation of intertidal zone as the potential area of S. alterniflora distribution and（2） extraction of S. alterniflora fraction distribution with a mixture pixel analysis. The proposed method was tested at the Xiangshan Bay on the east coastal region of Zhejiang Province, China, and mapped the spatial extent of S. alterniflora with Landsat datasets in the 2003, 2009 and 2014. The results showed that, the S. alterniflora has grown exponentially over past 10 years. In 2003, the total area of S. alterniflora was about 590 hm2, but quickly reached to 1 745 hm2 in 2009, and 5 715 hm2 in 2014. With a rate of approximately 10-folds growth within a decade, the invasive species almost occupied all muddy beaches to become the most dominant coastal salt vegetation in this region. It is believed that the strong biological reproductive capacity was the primary reason for such quick spread and at the same time human reclamation activities were also believed to have facilitated the environmental conditions for S. alterniflora sprawl.

关键词： Spartina alterniflora invasive species remote sensing Xiangshan Bay

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Bifunctional bridging capping layer enables 24.5% efficiency of perovskite solar cells with polymer-based hole transport materials

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Science China Chemistry 2025年第1期 350-359页

作者： Can zhu Yiyang Wang Lei Meng Beibei qiu Jing Li Shucheng qin Ke Hu xin Jiang Wenbin Lai Minchao Liu Zhe Liu Chenxing Lu Jinyuan Zhang Yongfang Li Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Organic Solids Institute of Chemistry Chinese Academy of Sciences School of Chemical Science University of Chinese Academy of Sciences Key Laboratory of Solid State Optoelectronic Devices of Zhejiang Province College of Physics and Electronic Information Engineering Zhejiang Normal University Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and ChemistryChinese Academy of Sciences Laboratory of Advanced Optoelectronic Materials College of Chemistry Chemical Engineering and Materials ScienceSoochow University

Developing a bridge capping layer between perovskite and hole transport layer materials（HTMs） in the n-i-p perovskite solar cells（pero-SCs） is an effective approach to modify the morphology of HTMs and passivate the perovskite ***, we select the quinoxaline-based bifunctional passivation agent, quinoxalin-6-yl-methylamine hydrochloride（Qx MACl）,as the bridging layer, and a D-A copolymer PBQ12 containing the same quinoxaline unit as an HTM for the n-i-p pero-SCs. Due to the π-π stacking among the common quinoxaline units in the bridge layer and HTM, Qx MACl induces the π-π stacking of the PBQ12 film and improves the film morphology of HTMs with better conductivity. Additionally, Qx MACl can effectively passivate the perovskite surface, and PBQ12 possesses appropriate energy levels and high hole mobility. The pero-SCs based on FAPbI3with PBQ12/Qx MACl treatment showed a higher power conversion efficiency（PCE） of 24.05% and outstanding stability, maintaining 95.4% and 92.1% of its initial PCE after 750 h of storage and after over 800 h of thermal annealing at 85 °C, respectively. To further enhance the PCE of the PBQ12/Qx MACl-based devices, we developed a non-metal ion dopant for the PBQ12 HTM. Through trace doping of PBQ12 HTM by the non-metal ion dopant, the PCE of the PBQ12/Qx MACl-based devices reached 25.24%（the calibrated PCE of 24.55% by the National Institute of Metrology, China）.

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Study of thermal decoherence of harmonic oscillators

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原子与分子物理学报 2025年第5期42卷 108-114页

作者： LI Jian ZHOU Gao-Liang YAN Zheng-xin LIU Wei WANG Zhao-qi College of Science Xi’an University of Science and TechnologyXi’an 710054China

The thermal decoherence of harmonic oscillators is investigated *** quantum system presented here is a one-dimensional oscillator with angular frequency,which is surrounded by a thermal bath of environmental *** are various environmental oscillators with different angular frequency(below an ultraviolet cutoff).At the beginning,the quantum system is a pure state and the environmental oscillators are in thermodynamic equilibrium with *** a period,the system-environment interactions inspire significant decoherence of the quantum *** decoherence is displayed by explicit calculations of the purity and von Neumann entropy of the quantum *** is worth noting that the decoherence could be significant even in the weak coupling and low temperature case due to the large amount of environmental degrees of *** the decoherence process is inspired between the quantum system and an ordinary thermal environment here,the thermal decoherence result is quite general.

关键词： Quantum decoherence Grand canonical ensemble Oscillators

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卵胎生硬骨鱼许氏平鲉繁殖生物学研究进展

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中山大学学报（自然科学版）（中英文） 2025年第1期64卷 106-115页

作者：齐鑫杨欣琳温海深中国海洋大学水产学院山东青岛266003

卵胎生作为卵生向胎生进化的中间状态,具有子代成活率高的特性。因此,卵胎生许氏平鲉成为我国重要的北方海水养殖对象之一。然而,大量养殖该物种又带来了一些繁殖过程中的实际问题。比如,网箱养殖的亲鱼出现明显的交配失败,导致其子代... 详细信息

卵胎生作为卵生向胎生进化的中间状态,具有子代成活率高的特性。因此,卵胎生许氏平鲉成为我国重要的北方海水养殖对象之一。然而,大量养殖该物种又带来了一些繁殖过程中的实际问题。比如,网箱养殖的亲鱼出现明显的交配失败,导致其子代出生率极低;妊娠期亲鱼母胎器官发育障碍,导致仔鱼胎死腹中;早产、难产导致的亲鱼、仔鱼大量死亡等。本综述将针对上述问题,分别探讨许氏平鲉交配发生、妊娠维持及分娩启动相关的内分泌调控机制,以期为后续研究提供潜在思路,最终实现水产养殖问题的解决。

关键词：卵胎生许氏平鲉繁殖生理

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