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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

Error field penetration in j-TEXT tokamak based on two-fluid drift-MHD model

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Chinese Physics B 2024年第4期33卷 545-551页

作者：王文徐涛张仪 the j-TEXT team State Key Laboratory of Advanced Electromagnetic Technology International Joint Research Laboratory of Magnetic Confinement Fusion and Plasma PhysicsSchool of Electrical and Electronic EngineeringHuazhong University of Science and TechnologyWuhan 430074China

An externally generated resonant magnetic perturbation can induce complex non-ideal MHD responses in their resonant *** have studied the plasma responses using Fitzpatrick's improved two-fluid model and program *** calculated the error field penetration threshold for *** addition,we find that the island width increases slightly as the error field amplitude increases when the error field amplitude is below the critical penetration ***,the island width suddenly jumps to a large value because the shielding effect of the plasma against the error field disappears after the *** scanning the natural mode frequency,we find that the shielding effect of the plasma decreases as the natural mode frequency ***,we obtain the m/n=2/1 penetration threshold scaling on density and temperature.

关键词： plasma responses drift-MHD model error field penetration

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恰克·伯乐 “电影伯乐”的电影节

东方电影 2015年第7期 36-39页

作者： toby

＂Aloha,Aloha＂（你好,夏威夷土语）,他笑呵呵地向参与此次采访的工作人员一边打招呼,一边分发名片。名片上赫然用中文写着＂伯乐＂二字,这是他的中文名,也极其符合他的职业和身份。他是恰克·伯乐（Chuck Boller）,法学博士（j.D.）,... 详细信息

＂Aloha,Aloha＂（你好,夏威夷土语）,他笑呵呵地向参与此次采访的工作人员一边打招呼,一边分发名片。名片上赫然用中文写着＂伯乐＂二字,这是他的中文名,也极其符合他的职业和身份。他是恰克·伯乐（Chuck Boller）,法学博士（j.D.）,常驻檀香山的纽约客,夏威夷国际电影节董事会主席,他自己最中意的中文称呼是＂电影伯乐＂。

关键词：上海国际电影节高清演播室法学博士二字董事会主席合作拍摄梅雨季节柏林电影节贾樟柯东方文化

The nature of the companion of PSR j1719-1438: a white dwarf or an exotic object?

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Research in Astronomy and Astrophysics 2012年第7期12卷 813-816页

作者： j. E. Horvath Instituto de Astronomia Geofísica e Ciências Atmosfricas - Universidade de So Paulo

We raise the possibility that the very dense, compact companion of PSR j1719-1438, which has a jupiter-like mass, is an exotic quark object rather than a light helium or carbon white dwarf. The exotic hypothesis naturally explains some of the observed features, and provides quite strong predictions for this system, to be confirmed or refuted in feasible future studies.

关键词： binary pulsars -- exotic matter-- pulsars: individual (PSR j1719-1438)

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NT和Unix DNS服务器的混合使用

电子与电脑 1998年第10期5卷 57-58页

作者： toby j.Velte 郭志坚 Velte Systems网络咨询公司

为什么要用Windows NT DNS 来取代Unix DNS 呢？NT 和Unix混合使用会有什么后果呢？使用的方法又是什么呢？看过本文后你就会知道的。

关键词： UNIX Windows-NT 计算机网络服务器

Helicity Amplitude Analysis of Z_c(3900)~± in e^+e^- →π^+π^-j/ψ

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Chinese Physics Letters 2016年第6期33卷 9-11页

作者：平荣刚 j.G.Messchendorp 苑长征 Institute of High Energy Physics Chinese Academy of Sciences KVI-CART University of Groningen

It is crucial to determine the spin and parity （jR） of Zc（3900）＋ for understanding its structure. We perform a helicity amplitude analysis on Zc（3900）＋ in the process e＋e- →π＋π-j/φ＊ with the hypotheses jP = 0-, 1＋, 1-, 2＋ and 2-. To estimate the significance of jP = 1＋ over other hypotheses, we perform a Monte Carlo simulation study, and we also discuss the prospect of measuring the spin parity in the future experiment with a large data sample.

关键词： of on is Helicity Amplitude Analysis of Z_c in e for that

Inflammasome links traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease

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Neural Regeneration Research 2025年第6期20卷 1644-1664页

作者： Gabriela Seplovich Yazan Bouchi juan Pablo de Rivero Vaccari jennifer C.Munoz Pareja Andrew Reisner Laura Blackwell Yehia Mechref Kevin K.Wang j.Adrian Tyndall Binu Tharakan Firas Kobeissy Department of Surgery Morehouse School of MedicineAtlantaGAUSA Department of Neurobiology Center for NeurotraumaMultiomics&Biomarkers(CNMB)Neuroscience InstituteMorehouse School of MedicineAtlantaGAUSA Department of Neurological Surgery and the Miami Project to Cure Paralysis University of Miami Miller School of MedicineMiamiFLUSA Division of Pediatric Critical Care Department of PediatricsUniversity of Miami Miller School of MedicineMiamiFLUSA Department of Pediatrics Emory UniversityAtlantaGAUSA Department of Neurosurgery Children’s Healthcare of AtlantaAtlantaGAUSA Department of Chemistry and Biochemistry Texas Tech UniversityLubbockTXUSA Morehouse School of Medicine AtlantaGAUSA

Traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease are three distinct neurological disorders that share common pathophysiological mechanisms involving neuroinflammation. One sequela of neuroinflammation includes the pathologic hyperphosphorylation of tau protein, an endogenous microtubule-associated protein that protects the integrity of neuronal cytoskeletons. Tau hyperphosphorylation results in protein misfolding and subsequent accumulation of tau tangles forming neurotoxic aggregates. These misfolded proteins are characteristic of traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease and can lead to downstream neuroinflammatory processes, including assembly and activation of the inflammasome complex. Inflammasomes refer to a family of multimeric protein units that, upon activation, release a cascade of signaling molecules resulting in caspase-induced cell death and inflammation mediated by the release of interleukin-1β cytokine. One specific inflammasome, the NOD-like receptor protein 3, has been proposed to be a key regulator of tau phosphorylation where it has been shown that prolonged NOD-like receptor protein 3 activation acts as a causal factor in pathological tau accumulation and spreading. This review begins by describing the epidemiology and pathophysiology of traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease. Next, we highlight neuroinflammation as an overriding theme and discuss the role of the NOD-like receptor protein 3 inflammasome in the formation of tau deposits and how such tauopathic entities spread throughout the brain. We then propose a novel framework linking traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease as inflammasomedependent pathologies that exist along a temporal continuum. Finally, we discuss potential therapeutic targets that may intercept this pathway and ultimately minimize long-term neurological decline.

关键词： Alzheimer's disease caspase-1 chronic traumatic encephalopathy inflammasomes neurodegeneration neuroinflammation NLRP1 NLRP3 pyroptosis tauopathy traumatic brain injury

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中国芝麻资源核心收集品研究

中国农业科学 1998年第3期31卷 49-55页

作者：张秀荣郭庆元赵应忠冯祥运周明德ＴｏｂｙＨｏｄｇｋｉｎ中国农业科学院油料作物研究所中国农业科学院ＩＰＧＲＩ东亚办事处

对中国收集编目的４２５１份芝麻种质资源材料，依据来源、品种类别、生态类型３层分成１４个组。应用计算机系统对随机小样本的１４个性状数据进行聚类分析，选择确定了离差平方和法是芝麻资源聚类的适宜方法。通过组内聚类分析并结合... 详细信息

对中国收集编目的４２５１份芝麻种质资源材料，依据来源、品种类别、生态类型３层分成１４个组。应用计算机系统对随机小样本的１４个性状数据进行聚类分析，选择确定了离差平方和法是芝麻资源聚类的适宜方法。通过组内聚类分析并结合随机选取和预选比例２０％的原则，预选出核心收集品材料８８４份，对其１４个性状的６个特征值的初步研究结果表明，基本代表了总收集品的遗传变异范围。对预选核心收集品在中国３个生态试验点两年的农艺性状鉴定表明：６个质量性状的５３０４性状次与原评价资料之间完全一致的为９７．８５％，３个数量性状呈良好的显著正相关。对决选的核心收集品代表性测验表明，１４个性状的平均值符合率达９７％以上，标准差符合率在９０％以上，表明核心收集品良好地代表了预选核心收集品。

关键词：芝麻资源预选核心收集品聚类分析

The supernova remnant CTB 37B and its associated magnetar CXOU j171405.7-381031:evidence for a magnetar-driven remnant

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Research in Astronomy and Astrophysics 2011年第6期11卷 625-630页

作者： j.E.Horvath M.P.Allen Instituto de Astronomia Geofísica e Ciências Atmosféricas-Universidade de So PauloRua do Mato122605508-900 Cidade Universitria So Paulo SPBrazil CEFET So Paulo Rua Pedro Vicente 62501109-010Caninde'So Paulo SPBrazil

We discuss the association between the candidate magnetar CXOU j171405.7-381031 and the supernova remnant CTB *** recent detection of the period derivative of the object allowed an estimation of a young characteristic age of only ～ *** value is too small to be compatible even with the minimum radius of the remnant being ≥ 10 pc,the value corresponding to the lower limit of the estimated distance of 10.2 ± 3.5 kpc,unless the true distance happens to be even smaller than the lower *** argue that a consistent scenario for the remnant＇s origin,in which the latter is powered by the energy injected by a young magnetar,is indeed more accurate to explain the young age,and demonstrates its non-standard（***-driven） nature.

关键词： stars:supernova — stars:neutron