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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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Surfing the nano-wave:Emerging trends in cancer diagnostics and therapy

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Nano Research 2025年第1期18卷 520-544页

作者： Genping Fu Yuting Weng Yunfan Li Carl Ho Yiyu Fu Wenxuan Wang Songbin Fu Wenjing Sun Jie Lin Xiaoyu fan Binbin Jia Mengdi Cai Linlin Li Laboratory of Medical Genetics Harbin Medical UniversityHarbin 150081China Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China(Harbin Medical University) Ministry of EducationHarbin 150081China Beijing Key Laboratory for Optical Materials and Photonic Devices Department of ChemistryCapital Normal UniversityBeijing 100048China College of Materials and Chemical Engineering Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion MaterialsChina Three Gorges UniversityYichang 443002China Washington University School of Medicine in St.Louis St.LouisMO 63110USA Ningbo Institute of Materials Technology and Engineering Chinese Academy of SciencesNingbo 315201China Aix-Marseille College Wuhan University of TechnologyWuhan 430070China

Facing the growing global challenge posed by cancer,the quest for more accurate and potent cancer diagnostic and therapeutic strategies continues to require a multidisciplinary integration *** review firstly summarizes various types of nanoparticles in cancer ***,it offers a comprehensive overview of signalenhancing techniques for visualizing in situ tumors,along with multimodal diagnostic methods for detecting *** for tumor therapy,cutting-edge drug delivery methods that can cross biological barriers and the pinpoint targeting of tumor lesions for precise medical intervention are *** the domain of therapeutic diagnostics,we elucidate the theoretical underpinnings and structural paradigms that underlie a spectrum of advanced diagnostic and therapeutic ***,we present a compendium of publications delineating the clinical applications of each nano-based theragnostic integration ***,this comprehensive review discusses the safety concerns pertaining to the clinical application of nanoparticles and proposes some strategic recommendations to enhance the precision and safety of theragnostic-guided,nanotechnology-based clinical practices.A deeper understanding of nanomaterials,together with intimate interdisciplinary collaborations,nano-wave will most probably guide human beings to win the battle against cancers.

关键词： nanoparticles drug delivery gastric cancer glioma glioblastoma

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Comparative analysis of volatile compounds in different muskmelon cultivars in Xinjiang based on HS-SPME-GC-MS and transcriptomics

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Food Innovation and Advances 2023年第3期2卷 217-224页

作者： Yingying fan Binxin Jia Xiaoqian Cao Jun Yang Xiaolong Li Weizhong He fengjuan Liu Cheng Wang Key Laboratory of Agro-products Quality and Safety of Xinjiang Laboratory of Quality and Safety Risk Assessment for Agri-products(Urumqi)Key Laboratory of Functional Nutrition and Health of Characteristic Agricultural Products in Desert Oasis Ecological Region(Co-construction by Ministry and Province)Ministry of Agriculture and Rural AffairsInstitute of Quality Standards&Testing Technology for Agri-productsXinjiang Academy of Agricultural SciencesUrumqi 830091XinjiangChina College of Food Science and Pharmaceutical Science Xinjiang Agricultural UniversityUrumqi 830052XinjiangChina Weinan Vocational&Technical College Weinan 714026ShaanxiChina Institute of Grape and Melon Fruit Xinjiang Uygur Autonomous RegionShanshan 838200XinjiangChina Information Center of Agriculture and Rural Affairs Department Xinjiang Uygur Autonomous RegionUrumqi 830000XinjiangChina

Volatile flavor has prompted a great amount of influence in acceptance and view points in fruit ***(Pyrus communis)is an aromadense fruit,thus,the evaluation of volatile flavor is crucial to *** volatile compounds present in nine varieties of Xinjiang muskmelons were identified and analyzed using the headspace solid-phase microextraction and gas chromatography-mass spectrometry *** addition,transcriptomics were used to discover the differential genes in fatty acid degradation *** was found that a total of 170 volatile substances,including 52 alcohols,41 esters,24 aldehydes,32 ketones,14 acids and seven phenols,were identified in the nine *** of PCA showed that 3-nonanol,2-nonanol,bis(2-ethylhexyl)adipate,and 2-methylpropanal contributed more to the flavor of *** was verified that high activities of acyl-coenzyme A cholesterol acyltransferase(AAT)promoted the conversion of alcohols to esters,so that the melons have a high content of *** genes of long-chain acyl-CoA synthetase were mainly responsible for the large difference in volatile *** practice may further undermine the primary rationale for the breeding and promotion in different cultivars of muskmelon.

关键词： volatile esters alcohols

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金属卤素钙钛矿CsPbBr3的电声耦合输运特性研究

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原子与分子物理学报 2025年第2期42卷 169-174页

作者：杨帆周贤中广东工业大学集成电路学院广州510006

金属卤素钙钛矿CsPbBr_(3)在发光方面(Light emitter)的优良表现吸引了许多人把它作为下一代发光、显示与量子信息的可选材料,但其关键的漂移迁移率会受到声子限制.本文将以第一性原理计算得到CsPbBr_(3)的包括极性光学声子(Polar optic... 详细信息

金属卤素钙钛矿CsPbBr_(3)在发光方面(Light emitter)的优良表现吸引了许多人把它作为下一代发光、显示与量子信息的可选材料,但其关键的漂移迁移率会受到声子限制.本文将以第一性原理计算得到CsPbBr_(3)的包括极性光学声子(Polar optical phonon)在内的电声耦合特性,然后使用线性玻尔兹曼方程给出在电场下的解,从而得出漂移迁移率.在论文详述中会给出CsPbBr_(3)的各向异性载流子输运特性的研究,为金属卤素钙钛矿的应用提供一些必要信息.

关键词：第一性原理计算电子-声子耦合漂移迁移率

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Impacts of Nutlin-3a and exercise on murine double minute 2-enriched glioma treatment

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Neural Regeneration Research 2025年第4期20卷 1135-1152页

作者： Yisheng Chen Zhongcheng fan Zhiwen Luo Xueran Kang Renwen Wan fangqi Li Weiwei Lin Zhihua Han Beijie Qi Jinrong Lin Yaying Sun Jiebin Huang Yuzhen Xu Shiyi Chen Department of Sport Medicine Huashan HospitalFudan UniversityShanghaiChina Department of Orthopedic Surgery Hainan Province Clinical Medical CenterHaikou Affiliated Hospital of Central South University Xiangya School of MedicineHaikouHainan ProvinceChina Department of Basic Medicine Shanghai Jiao Tong University School of MedicineShanghai Jiao Tong UniversityShanghaiChina Department of Neurosurgery Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouZhejiang ProvinceChina Department of Orthopedics Shanghai General HospitalSchool of Medicine Shanghai Jiao Tong UniversityShanghaiChina Department of Infectious Diseases Children’s Hospital of Fudan UniversityNational Children’s Medical CenterShanghaiChina Department of Rehabilitation The Second Affiliated Hospital of Shandong First Medical UniversityTaianShandong ProvinceChina

Recent research has demonstrated the impact of physical activity on the prognosis of glioma patients,with evidence suggesting exercise may reduce mortality risks and aid neural *** role of the small ubiquitin-like modifier(SUMO)protein,especially post-exercise,in cancer progression,is gaining attention,as are the potential anti-cancer effects of *** used machine learning to create the exercise and SUMO-related gene signature(ESLRS).This signature shows how physical activity might help improve the outlook for low-grade glioma and other *** demonstrated the prognostic and immunotherapeutic significance of ESLRS markers,specifically highlighting how murine double minute 2(MDM2),a component of the ESLRS,can be targeted by *** underscores the intricate relationship between natural compounds such as nutlin-3 and immune *** comprehensive CRISPR screening,we validated the effects of specific ESLRS genes on low-grade glioma *** also revealed insights into the effectiveness of Nutlin-3a as a potent MDM2 inhibitor through molecular docking and dynamic ***-3a inhibited glioma cell proliferation and activated the p53 *** efficacy decreased with MDM2 overexpression,and this was reversed by Nutlin-3a or *** using a low-grade glioma mouse model highlighted the effect of physical activity on oxidative stress and molecular pathway ***,both physical exercise and Nutlin-3a administration improved physical function in mice bearing tumors derived from MDM2-overexpressing *** results suggest the potential for Nutlin-3a,an MDM2 inhibitor,with physical exercise as a therapeutic approach for glioma *** research also supports the use of natural products for therapy and sheds light on the interaction of exercise,natural products,and immune regulation in cancer treatment.

关键词： exercise and SUMO-related gene signatures(ESLRS) glioblastoma management low-grade glioma natural bioactives neural regeneration physical exercise

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Flight dynamics modeling of a small ducted fan aerial vehicle based on parameter identifcation

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Chinese Journal of Aeronautics 2013年第6期26卷 1439-1448页

作者： Wang Zhengjie Liu Zhijun fan Ningjun Guo Meifang School of Mechatronical Engineering Beijing Institute of Technology North Institute for Science & Technical Information

This paper presents a simple and useful modeling method to acquire a dynamics model of an aerial vehicle containing unknown parameters using mechanism modeling,and then to design different identifcation experiments to identify the parameters based on the sources and features of its unknown *** on the mathematical model of the aerial vehicle acquired by modeling and identifcation,a design for the structural parameters of the attitude control system is carried out,and the results of the attitude control flaps are verifed by simulation experiments and flight tests of the aerial *** of the mathematical simulation and flight tests show that the mathematical model acquired using parameter identifcation is comparatively accurate and of clear mechanics,and can be used as the reference and basis for the structural design.

关键词： Aerodynamics Experimental aerodynamics Flight vehicle design Multidisciplinary design optimization Structural design

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Single-cell technologies: current and near future

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Science China Life Sciences 2025年第1期 1-4页

作者： Chenfei Wang Qi Liu Xiaohui fan Tieliu Shi Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics 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 Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University 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 Key Laboratory of Advanced Theory and Application in Statistics and Data Science (MOE) School of StatisticsEast China Normal University

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity, tissue organization, and overall organism function(Sun et al.,2024). In 2009, single-cell RNA sequencing(sc RNA-seq) was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology, single-cell approaches have expanded to encompass other omics, such as genomics, epigenomics, proteomics,and metabolomics.

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Light tuning CO/H_(2)composition on Ag:Unraveling CO_(2)mass transfer and electron-phonon coupling in plasmon-enhanced electrocatalysis

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Nano Research 2025年第1期18卷 173-185页

作者： Rui Lin Dong fan Luca MBerger Thomas Possmayer Yu Zhou Jiexin Zhu Xingbao Chen Wen Luo Lars Allmendinger Andreas Tittl Leonardo de Souza Menezes Guillaume Maurin Shihe Yang and Stefan AMaier Nanoinstitute Munich Faculty of PhysicsLudwig-Maximilians-Universität München80539 MunichGermany Institut Charles Gerhardt Montpellier UMR 5253 CNRS ENSCM UniversitéMontpellierPlace E.Bataillon34090 MontpellierFrance Guangdong Provincial Key Lab of Nano-Micro Material Research School of Advanced MaterialsPeking University Shenzhen Graduate SchoolShenzhen 518055China State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of TechnologyWuhan 430070China Faculty of Chemistry and Pharmacy Ludwig-Maximilians-Universität München81377 MunichGermany Departamento de Física Universidade Federal de Pernambuco50670-901 Recife-PEBrazil School of Physics and Astronomy Monash University Clayton CampusMelbourneVictoria 3800Australia Department of Physics Imperial College LondonSW72AZ LondonUK

Plasmon-enhanced electrocatalysis(PEEC)is an emerging approach to mitigate CO_(2)*** mechanisms behind CO_(2)adsorption and reduction at the catalyst-electrolyte interface in PEEC still need to be further ***,we employ a well-defined Ag nanostructure to elucidate these pivotal *** shining light with wavelengths of 625,525,405 nm on Ag,an adjustable CO/H_(2)ratio from 35 to 1 can be *** reaction pathway changing under plasmonic excitation does not originate from the lowered CO_(2)mass transfer in the vicinity of Ag,as the electrochemical quartz crystal microbalance results unravel that a slightly elevated temperature in bulk electrolyte caused by light irradiation cannot weaken the CO_(2)adsorption at the Ag catalyst-electrolyte *** calculations reveal that optical excitation towards shorter wavelengths leads to a progressive lowered energy barrier for H_(2)formation together with an enhanced energy barrier for^(*)COOH *** thermodynamically suppressed,CO_(2)reduction can still be improved kinetically by optimizing the excitation wavelength and intensity,being accompanied with the enhanced *** absorption spectroscopy results further correlate the higher photocurrent with a prolonged electron-phonon coupling time,verifying that the improvement of CO_(2)reduction kinetics in PEEC can be realized by hot electron harnessing.

关键词： plasmonic catalysis photoelectrochemical CO_(2)reduction CO/H_(2)ratio hot electron generation electronphonon coupling thermal effect

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基于Radix-4 Booth编码的并行乘法器设计

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郑州大学学报（工学版） 2025年第1期46卷 26-33页

作者：范文兵周健章郑州大学电气与信息工程学院河南郑州450001

速度和面积是评价乘法器单元性能优劣的两个基本指标。针对当前乘法器设计难以平衡版图面积和传输延时的问题,采用Radix-4 Booth算法,设计了一种新型的16位有符号定点乘法器。在部分积生成过程中,首先改进对乘数的取补码电路,然后优化... 详细信息

速度和面积是评价乘法器单元性能优劣的两个基本指标。针对当前乘法器设计难以平衡版图面积和传输延时的问题,采用Radix-4 Booth算法,设计了一种新型的16位有符号定点乘法器。在部分积生成过程中,首先改进对乘数的取补码电路,然后优化基数为4的改进Booth编码器和解码器,此结构采用较少的逻辑门资源,并且易对输入比特进行并行化处理。在Wallace压缩电路中,对符号扩展位进行预处理并设计新的压缩器结构,优化整个Wallace压缩模块。在第二级压缩过程中提前对高位使用纹波进位加法器结构计算,减小了多bit伪和的求和位数。在求和电路中,使用两级超前进位加法器结构,在缩短关键路径传输延时的同时避免增大芯片面积,提高了乘法器的运行速度。新型定点乘法器与已有的乘法器结构相比,减少了12.0%的面积,降低了20.5%的延时。

关键词： Radix-4 Booth编码面积传输延时编码器解码器 Wallace压缩

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高速公路对绿色经济效率的影响分析--基于产业结构优化视角

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生态经济 2025年第1期41卷 114-122页

作者：樊建强谢靖雯长安大学经济与管理学院陕西西安710064

当前中国高速公路建设布局日趋完善,探究如何发挥其对地区产业结构优化的有力支持,进而助力绿色经济发展转型具有重要意义。论文基于2006—2019年中原城市群27个城市的面板数据,运用超效率SBM模型测算其绿色经济效率,从产业结构优化的... 详细信息

当前中国高速公路建设布局日趋完善,探究如何发挥其对地区产业结构优化的有力支持,进而助力绿色经济发展转型具有重要意义。论文基于2006—2019年中原城市群27个城市的面板数据,运用超效率SBM模型测算其绿色经济效率,从产业结构优化的视角实证分析了高速公路对绿色经济效率的影响,并以产业结构优化为中介与门槛变量,进一步探讨产业结构优化对于高速公路影响绿色经济效率的门槛效应。研究结果表明:中原城市群高速公路与绿色经济效率间呈现先抑制后促进的“U”型关系;产业结构优化在高速公路和绿色经济效率间发挥部分中介作用;产业结构优化存在单一门槛效应,随着产业结构优化水平的提升,高速公路对绿色经济效率由抑制作用转为促进作用。

关键词：绿色经济效率高速公路产业结构优化超效率SBM 中原城市群

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