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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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Constraints on holographic QCD phase transitions from PTA observations

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 71-78页

作者： Song He Li Li Sai Wang Shao-Jiang Wang Center for Theoretical Physics and College of Physics Jilin University School of Physical Science and Technology Ningbo University Max Planck institute for Gravitational Physics (Albert Einstein institute) CAS Key Laboratory of Theoretical Physics Institute of Theoretical Physics Chinese Academy of Sciences School of Fundamental Physics and Mathematical sciences Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of Sciences (UCAS) School of Physical sciences University of Chinese Academy of Sciences (UCAS) Theoretical Physics Division Institute of High Energy Physics Chinese Academy of Sciences

The underlying physics of QCD phase transition in the early Universe remains largely unknown due to its strong-coupling nature during the quark-gluon plasma/hadron gas transition, yet a holographic model has been proposed to quantitatively fit the lattice QCD data while with its duration of the first-order phase transition(FoPT) left undetermined. At specific baryon chemical potential, the first-order QCD phase transition agrees with the observational constraint of baryon asymmetry. It, therefore, provides a scenario for phase transition gravitational waves(GWs) within the standard model of particle physics. If these background GWs could contribute dominantly to the recently claimed common-spectrum red noise from pulsar timing array(PTA) observations, the duration of this FoPT can be well constrained, and the associated primordial black holes are still allowed by current observations.

关键词： pulsar timing array QCD phase transition gravitational waves primordial black holes

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Highly conductive and stable iodine doped argyrodite electrolyte for all-solid-state lithium batteries

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Journal of Energy Chemistry 2025年第1期100卷 50-58页

作者： Gaozhan Liu Jing Zhang Jing Yang Jinghui Chen Xingyue Xiao Xiayin Yao Ningbo institute of Materials Technology and Engineering Chinese Academy of Sciences Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of Sciences

Lithium argyrodites with high ionic conductivity and low cost are considered as one of the most prospective solid electrolytes for all-solid-state lithium ***,the poor chemical stability and compatibility with lithium metal limit their ***,Li5.4PS4.4Cl1.4I0.2solid electrolyte with high ionic conductivity of 11.49 m S cm-1and improved chemical stability is synthesized by iodine *** ultra-thin Li5.4PS4.4Cl1.4I0.2membrane with thickness of 10μm can be obtained by wet coating process,exhibiting a high ionic conductivity of 2.09 mS cm-1and low areal resistance of 1.17Ω***,iodine doping could in-situ form LiI at the lithium/electrolyte interface and improve the critical current density of Li5.4PS4.4Cl1.6from 0.8 to 1.35 mA *** resultant LiCoO2/Li5.4PS4.4Cl1.4I0.2/Li battery shows excellent cycling stability at 1 C,with a reversible specific capacity of 110.1 mA h g-1and a retention of 80.5% after 1000 *** addition,the assembled LiCoO2/Li5.4PS4.4Cl1.4I0.2membrane/Li pouch cell delivers an initial discharge capacity of 110.4 mA h g-1and 80.5% capacity retention after 100 cycles.

关键词： Argyrodite electrolytes Iodine doping Ionic conductivity Stability All-solid-state lithium battery

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Tuning beneficial calcineurin phosphatase activation to counterα-synuclein toxicity in a yeast model of Parkinson’s disease

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Neural Regeneration Research 2025年第1期20卷 199-200页

作者： Srishti Chawla Mikael Molin Thomas Nystrom institute for Biomedicine Sahlgrenska AcademyCentre for Ageing and Health-AgeCapUniversity of GothenburgGothenburgSweden Department of life sciences Chalmers University of TechnologyGothenburgSweden

Calcineurin(CN)is a calcium-and calmodulindependent serine/threonine that has been studied in many model organisms including yeast,filamentous fungi,plants,and *** biological functions range from ion homeostasis and virulence in lower eukaryotes to T-cell activation in humans by human nuclear factors of activated *** is a heterodimeric protein consisting of a catalytic subunit,calcineurin A(Cna1p),which contains an active site with a dinuclear metal center,and a regulatory Ca^(2+) binding subunit called calcineurin B(Cnb1p)required to activate *** calcineurin B subunit has been highly conserved through evolution:For example,the mammalian calcineurin B shows 54%identity with calcineurin B from Saccharomyces cerevisiae.

关键词： activation dinuclear conserved

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Increased excitatory amino acid transporter 2 levels in basolateral amygdala astrocytes mediate chronic stress–induced anxiety-like behavior

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Neural Regeneration Research 2025年第6期20卷 1721-1734页

作者： Xirong Xu Shoumin Xuan Shuai Chen Dan Liu Qian Xiao Jie Tu Shenzhen Key Laboratory of Neuroimmunomodulation for Neurological Diseases Shenzhen-Hong Kong Institute of Brain ScienceShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong ProvinceChina CAS Key Laboratory of Brain Connectome and Manipulation Brain Cognition and Brain Disease Institute(BCBDI)Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong ProvinceChina Guangdong Provincial Key Laboratory of Brain Connectome and Behavior the Brain Cognition and Brain Disease Institute(BCBDI)Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong ProvinceChina University of Chinese of Academy of sciences BeijingChina Faculty of life and Health sciences Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong ProvinceChina

The conventional perception of astrocytes as mere supportive cells within the brain has recently been called into question by empirical evidence, which has revealed their active involvement in regulating brain function and encoding behaviors associated with ***, astrocytes in the basolateral amygdala have been found to play a role in the modulation of anxiety-like behaviors triggered by chronic stress. Nevertheless, the precise molecular mechanisms by which basolateral amygdala astrocytes regulate chronic stress–induced anxiety-like behaviors remain to be fully elucidated. In this study, we found that in a mouse model of anxiety triggered by unpredictable chronic mild stress, the expression of excitatory amino acid transporter 2 was upregulated in the basolateral amygdala. Interestingly, our findings indicate that the targeted knockdown of excitatory amino acid transporter 2 specifically within the basolateral amygdala astrocytes was able to rescue the anxiety-like behavior in mice subjected to stress. Furthermore, we found that the overexpression of excitatory amino acid transporter 2 in the basolateral amygdala, whether achieved through intracranial administration of excitatory amino acid transporter 2agonists or through injection of excitatory amino acid transporter 2-overexpressing viruses with GfaABC1D promoters, evoked anxiety-like behavior in mice. Our single-nucleus RNA sequencing analysis further confirmed that chronic stress induced an upregulation of excitatory amino acid transporter 2 specifically in astrocytes in the basolateral amygdala. Moreover, through in vivo calcium signal recordings, we found that the frequency of calcium activity in the basolateral amygdala of mice subjected to chronic stress was higher compared with normal *** knocking down the expression of excitatory amino acid transporter 2 in the basolateral amygdala, the frequency of calcium activity was not significantly increased, and anxiety-like behavior was ob

关键词： anxiety astrocytes basolateral amygdala behavior dihydrokainic acid excitatory amino acid transporter 2 fiber photometry glutamate LDN-212320 transporter

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Anomalous quality factor evolution of induced transparency in a virtualized coupled-oscillator system

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 148-155页

作者： Yunhan Yang Han Jia Tuo Liu Yuzhen Yang Jun Yang Key Laboratory of Noise and Vibration Research Institute of Acoustics Chinese Academy of Sciences University of Chinese Academy of sciences State Key Laboratory of Acoustics Institute of Acoustics Chinese Academy of Sciences

The phenomenon of induced transparency, characterized by a high quality(Q) factor, holds significant importance in the fields of high-precision sensing, energy storage and wave manipulation. Conventional transparency systems are often constrained by the limited experimentally accessible parameter space and the lack of independent control over intrinsic parameters, thereby hindering advanced research on high-Q effects. Here we propose a virtualized coupled-oscillator system that enables reconfigurable induced transparency in the reflection spectrum. By virtually incorporating a pair of coupled oscillators into an individual acoustic meta-atom, we achieve the manipulation of induced transparency in a decoupled, wide-ranging, and elaborate manner. Exploiting the diverse evolutions across the intrinsic parameter space, we show experimentally a counter-intuitive increase in the Q-factor of the transparency window, which is attributed to the enhanced dissipation of the bright ***, a constant group delay at the center frequency is observed accompanying this evolution. Our work demonstrates an intriguing platform as well as a novel strategy to engineer high-Q induced transparency phenomenon, and paves the way towards applications in programmable acoustic sensors, filters and slow-wave devices.

关键词： induced transparency acoustic meta-atom high quality-factor scattering programmable intrinsic parameter

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Sky location of massive black hole binaries in the foreground of Galactic white dwarf binaries

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 97-108页

作者： Pan Guo Hong-Bo Jin Cong-Feng Qiao Yue-Liang Wu The International Centre for Theoretical Physics Asia-Pacific University of Chinese Academy of Sciences The School of Physical sciences University of Chinese Academy of Sciences institute for Frontiers in Astronomy and Astrophysics Beijing Normal University National Astronomical Observatories Chinese Academy of Sciences institute of Theoretical Physics Chinese Academy of Sciences

For space-based gravitational wave （GW） detection,the main noise source for massive black hole binaries （MBHBs） is attributed to approximately 10～7double white dwarf binaries in the *** a GW source,the amplitude of the detector response,recorded by a space-based gravitational wave detector,exhibits a modulation effect with a year period when observing the source from various orbital *** the adverse conditions mentioned above,where there is a strong foreground noise and annual modulation in the signals,we employed the wavelet transform and the strong-amplitude relevant orbital position search methods,which allows the weak MBHB sources to achieve higher locating *** detail,for two MBHB sources of lower intensity,the precision of luminosity distance,represented by the ratio ?DL/DLat the 95%confidence level,is enhanced by factors of ～*** angular resolutions,denoted by??s,are enhanced by a factor of ～*** improvements increase the number of detectable GW sources,facilitate multi-messenger follow-up observations and provide constraints on the cosmological constant.

关键词： space-based gravitational wave detection gravitational waves massive black hole binaries

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Secretome of polarized macrophages:potential for targeting inflammatory dynamics in spinal cord injury

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Neural Regeneration Research 2025年第11期20卷 3231-3232页

作者： Andreia Monteiro Susana Monteiro Nuno A.Silva life and Health sciences Research institute(ICVS) School of MedicineUniversity of MinhoBragaPortugal ICVS/3B’s Associate Lab PT Government Associated LabBraga/GuimaraesPortugal

Spinal cord injury(SCI)involves an initial traumatic phase,followed by secondary events such as ischemia,increased blood-spinal cord barrier permeability,ionic disruption,glutamate excitotoxicity,and metabolic alterations.A pe rsistent and exagge rated inflammato ry response within the spinal cord accompanies these events(Lima et al.,2022).The complexity and interplay of these mechanisms exacerbate the initial injury,leading to a degenerative process at the injury *** the initial trauma is unavoidable,the secondary injury begins within minutes and can last for months,creating an optimal window for therapeutic intervention.

关键词： alterations injury companies

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The interaction between KIF21A and KANK1 regulates dendritic morphology and synapse plasticity in neurons

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Neural Regeneration Research 2025年第1期20卷 209-223页

作者： Shi-Yan Sun Lingyun Nie Jing Zhang Xue Fang Hongmei Luo Chuanhai Fu Zhiyi Wei Ai-Hui Tang Hefei National Research Center for Physical sciences at the Microscale CAS Key Laboratory of Brain Function and DiseaseMinistry of Education Key Laboratory for Membrane-less Organelles and Cellular DynamicsDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina institute of Artificial Intelligence Hefei Comprehensive National Science CenterHefeiAnhui ProvinceChina CAS Center for Excellence in Molecular Cell sciences Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina Department of Neurobiology School of Life SciencesSouthern University of Science and TechnologyShenzhenGuangdong ProvinceChina Brain Research Center Southern University of Science and TechnologyShenzhenGuangdong ProvinceChina

Morphological alterations in dendritic spines have been linked to changes in functional communication between neurons that affect learning and ***-4 KIF21A helps organize the microtubule-actin network at the cell cortex by interacting with KANK1;however,whether KIF21A modulates dendritic structure and function in neurons remains *** this study,we found that KIF21A was distributed in a subset of dendritic spines,and that these KIF21A-positive spines were larger and more structurally plastic than KIF21A-negative ***,the interaction between KIF21A and KANK1 was found to be critical for dendritic spine morphogenesis and synaptic *** of either KIF21A or KANK1 inhibited dendritic spine morphogenesis and dendritic branching,and these deficits were fully rescued by coexpressing full-length KIF21A or KANK1,but not by proteins with mutations disrupting direct binding between KIF21A and KANK1 or binding between KANK1 and *** down KIF21A in the hippocampus of rats inhibited the amplitudes of long-term potentiation induced by high-frequency stimulation and negatively impacted the animals’cognitive *** together,our findings demonstrate the function of KIF21A in modulating spine morphology and provide insight into its role in synaptic function.

关键词： actin cytoskeleton dendrite KANK1 KIF21A microtubule spine morphology spine synaptic plasticity talin1

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Limnological instrumentation in the middle of the 19^(th) century:the first temperature and density profiles measured in the Dead Sea

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Chinese Journal of Oceanology and Limnology 2015年第6期33卷 1496-1504页

作者： Aharon OREN Department of Plant and Environmental sciences Alexander Silberman Institute of Life SciencesHebrew University of Jerusalem

The first modem survey of the Dead Sea was performed by the Geological Survey of Israel in 1959-1960, and the report published remains the baseline study for our understanding of the physical and chemical properties of the lake. At the time the Dead Sea was a meromictic lake with a strong salinity gradient separating the deep waters （〉40 m depth） from the less saline surface waters. A few results of analyses of deeper water samples collected in the 1930s were reported, but overall we have very little information about the structure of the lake＇s water column before the 1959-1960 survey. However, it is little known that data on the physical and the chemical structure of the Dead Sea water column were obtained already in the middle of the 19~ century, and the information collected then is highly relevant for the reconstruction of the limnological properties of the lake in earlier times. The expedition of Lieutenant William Lynch （U.S. Navy） in 1848 reported the presence of a temperature minimum at a depth of-18 m, and also retrieved a water sample collected close to the bottom for chemical analysis. In 1864, the French Dead Sea exploration by the Duc de Luynes and his crew yielded detailed density and salinity profiles for a number of sampling stations. The results of these pioneering studies are discussed here, as well as the sampling equipment and measuring instruments used by the 1848 and the 1864 expeditions.

关键词： Dead Sea stratification research history sampling equipment self-registering thermometer

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