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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

Reconstructing forest and grassland cover changes in China over the past millennium

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Science China Earth Sciences 2025年第1期 94-110页

作者： fanneng HE fan YANG Yafei WANG Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Key Research Institute of Yellow River Civilization and Sustainable Development Henan University University of Chinese Academy of Sciences

Historical forest and grassland cover changes not only are critical indicators for quantifying ecological and environmental change processes but also serve as fundamental data for long-term climate change simulations and terrestrial ecosystem carbon emission assessments. However, because of limitations in historical data, quantitative estimations and spatially gridded reconstructions of these changes remain challenging, necessitating further methodological exploration. This study focused on China's present-day land area over the past millennium, objectively capturing the characteristics and drivers of forest and grassland cover changes. On this basis, using the forest transition theory and the space-for-time substitution method, we depicted the historical deforestation process as an inverted “S” curve and developed a model to reconstruct historical forest area changes based on the functional relationship between the forest area and population size dynamics. Subsequently, a gridded forest allocation model was established on the basis of deforestation tendencies. For the grassland cover, we implemented regionspecific methods, such as the cropland area deduction method and the habitat constraint method, to quantitatively reconstruct historical changes. Consequently, we obtained provincial forest and grassland area changes over the past millennium and mapped 10-km-resolution gridded data of forest and grassland cover. The results indicated the following.(1) The methods developed using population data as a proxy objectively reproduced the spatiotemporal evolution of forest and grassland cover in China over the past millennium. These feasible methods offer a novel pathway for the quantitative reconstruction of historical forest and grassland cover changes.(2) The data indicated that China's forest area generally decreased over the past millennium, characterized by a “decrease-then-increase” pattern. The forest area experienced three distinct phases: a slow decline(AD 1000

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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

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

基于IWOA-LSTM算法的预应力钢筋混凝土梁损伤识别

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江苏大学学报（自然科学版） 2025年第1期46卷 105-112,119页

作者：范旭红章立栋杨帆李青郁董凯江苏大学土木工程与力学学院江苏镇江212013 河南省公路工程局集团第二公路工程有限公司河南郑州450015 中国葛洲坝集团第二工程有限公司四川成都610091

为准确识别桥梁结构的损伤程度,制作了桥梁的关键构件——预应力钢筋混凝土梁,进行三点弯曲加载试验.收集了损伤破坏全过程的声发射(AE)信号,通过AE信号参数分析,将梁的损伤破坏过程划分为4个典型阶段.构建了长短时记忆神经网络(LSTM)模... 详细信息

为准确识别桥梁结构的损伤程度,制作了桥梁的关键构件——预应力钢筋混凝土梁,进行三点弯曲加载试验.收集了损伤破坏全过程的声发射(AE)信号,通过AE信号参数分析,将梁的损伤破坏过程划分为4个典型阶段.构建了长短时记忆神经网络(LSTM)模型,根据经验设置LSTM模型的超参数容易导致网络陷入局部最优而影响了分类结果,提出采用Sine混沌映射和自适应权重来改进鲸鱼优化算法(WOA),对LSTM进行超参数寻优.设计了IWOA-LSTM算法模型,训练识别试验梁各损伤阶段的AE信号特征参数.定型网络结构,并识别同种工况下其他梁的AE信号.结果表明:IWOA-LSTM算法模型识别准确率均超过或接近92%,相较于普通LSTM模型,IWOA-LSTM模型识别准确率提高了约7%.

关键词：预应力钢筋混凝土梁声发射损伤识别长短时记忆神经网络改进的鲸鱼优化算法

Identification of a dual functional betulinic acid analog for the treatment of osteoarthritis by phenotypic screening

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Science China Life Sciences 2025年第1期 300-302页

作者： Ze-Min Lin Mai Xiang Wen-Hui Wei Shu-Hui fan Li Chen Jie Wang Xiao-Qian Yang Chun-Hao Yang Shi-Jun He Jian-Ping Zuo Laboratory of Immunopharmacology State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of Sciences School of Pharmacy University of Chinese Academy of Sciences School of Pharmacy Nanjing University of Chinese Medicine State Key Laboratory of Drug Research Department of Medicinal ChemistryShanghai Institute of Materia MedicaChinese Academy of Sciences Innovation Research Institute of Traditional Chinese Medicine Shanghai University of Traditional Chinese Medicine Experiment Center for Science and Technology Shanghai University of Traditional Chinese Medicine

Dear Editor, Phenotypic drug discovery, which observes compound effects on physiology,has given way to targeting specific molecules, but has revived by using modern methods to find drugs based on therapeutic outcomes in disease models(Vincent et al., 2022). Osteoarthritis(OA) is a prevalent chronic joint disorder, primarily affecting knee joints, with osteoclast activation due to low-grade inflammation resulting in increased bone resorption and structural changes in the joint(Katz et al.,2021).

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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

Automatic and Rapid Throughflow-Based Optimal Design Method for Multi-Stage Axial-Flow Compressors

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Journal of Thermal Science 2025年第1期 77-91页

作者： LEI fan ZHANG Xiawen JU Yaping ZHANG Chuhua Department of Fluid Machinery and Engineering School of Energy and Power EngineeringXi'an Jiaotong University Production and Environmental Department China Huaneng Group.Co.Ltd. State Key Laboratory for Strength and Vibration of Mechanical Structures Xi'an Jiaotong University

Throughflow design has the advantages of less time consumption and large optimization space,and thus is the corner stone of advanced design system of multi-stage axial-flow *** majority of relevant studies were limited to the throughflow inverse designs,and quite few works have been till now devoted to the throughflow optimal *** this work,an automatic and rapid throughflow-based optimal design method is proposed for axial-flow compressors in which a throughflow inverse design solver is embedded in optimal genetic algorithm to improve the design efficiency of axial-flow *** types of design parameters in the throughflow inverse design of axial-flow compressors,i.e.,swirl and shroud curve,are simultaneously used to optimize both the blade shape and flow *** proposed method is validated by the redesign optimization of the benchmark axial-flow compressor NASA Stage 35,and the CFD predictions show that the throughflow-based optimization leads to 1.18% efficiency benefit at design *** proposed method is then utilized to the two-dimensional throughflow optimal design of a large-scale 6.5-stage axial-flow industrial *** optimal design results are confirmed by CFD predictions,indicating that the proposed method can effectively improve the design adiabatic efficiency of the compressors by 1.09% within a few minutes on desk-top *** throughflow design implications are also obtained for advanced axial-flow industrial *** work could enhance the capability of throughflow design method and has engineering application value to explore the throughflow optimization space of multi-stage axial-flow compressors.

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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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