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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

Analysis of existing agroforestry practices in Madhupur Sal forest: an assessment based on ecological and economic perspectives

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Journal of Forestry Research 2011年第4期22卷 533-542页

作者： Mohammad Golam Kibria Narayan Saha Department of Forestry and Environmental Science School of Agricul- ture and Mineral Sciences Shahjalal University of Science and Technol- ogy Sylhet-3114 Bangladesh

A study was conducted in Madhupur sal forest of Tangail, Bangladesh to identify the suitable agroforestry practices of the area. Considering the ecological aspects of different agroforestry practices 10 sample plots （10 m× 10 m） from each land uses were taken, including natural forest to get a comparative scenario. The study showed that among the different agroforestry practices, Margalef and Shannon- Weiner index values are the maximum for pineapple agroforestry and lower for banana agroforestry, and Evenness index value is the maximum for lemon agroforestry. Determination of tree biomass in different land uses revealed that it is highest （3 078.6 kg/100 m^2） in natural forest followed by pineapple agroforestry, lemon agroforestry and banana agroforestry. Soil pH, moisture content, organic matter, organic carbon, phosphorus and total nitrogen showed statistically significant variation while bulk density, particle density, sulphur and potassium did not show any statistically significant variation among the land uses. Soil fertility status showed that pineapple agroforestry is more fertile than rest of other land uses. The Net Present Value （NPV） indicated that banana agroforestry is financially more profitable than other two systems, while the Benefit- Cost ratio （BCR） is higher in pineapple agroforestry （4.21 in participatory agroforestry and 3.35 in privately managed land）. Even though banana agroforestry gives higher NPV, capital required for this practice is much higher. The findings suggest that pineapple agroforestry has a tendency towards becoming ecologically and economically more sound than other two practices as it has better ecological attributes and required comparatively low investment.

关键词： Bangladesh Sal forest agroforestry ecological attributes profitability

Silk damping in scalar-induced gravitational waves: a novel probe for new physics

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 79-85页

作者： Yan-Heng Yu Sai Wang Theoretical Physics Division Institute of High Energy Physics Chinese Academy of Sciences school of Physics University of Chinese Academy of Sciences

Silk damping is well known in the study of cosmic microwave background（CMB） and accounts for suppression of the angular power spectrum of CMB on large angular multipoles. In this article, we study the effect of Silk damping on the scalar-induced gravitational waves（SIGWs）. Resulting from the dissipation of cosmic fluid, the Silk damping notably suppresses the energydensity spectrum of SIGWs on scales comparable to a diffusion scale at the decoupling time of weakly-interacting particles. The effect offers a novel observable for probing the underlying particle interaction, especially for those mediated by heavy gauge bosons beyond the standard model of particles. We anticipate that pulsar timing arrays are sensitive to gauge bosons with mass ～10～3-10～4 GeV, while space-and ground-based interferometers to those with mass ～10～7-1012GeV, leading to essential complements to on-going and future experiments of high-energy physics.

关键词： scalar-induced gravitational waves Silk damping new physics

Regression analysis of squeezing-induced hybrid nanofluid flow in Darcy-Forchheimer porous medium

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Applied Mathematics and Mechanics(English Edition) 2025年第1期46卷 193-208页

作者： K.MUHAMMAD M.SARFRAZ Department of Humanities and sciences School of Electrical Engineering and Computer Science National University of Sciences and Technology Department of Mathematics Quaid-i-Azam University

This article presents a mathematical model addressing a scenario involving a hybrid nanofluid flow between two infinite parallel plates. One plate remains stationary, while the other moves downward at a squeezing velocity. The space between these plates contains a Darcy-Forchheimer porous medium. A mixture of water-based fluid with gold(Au) and silicon dioxide(Si O2) nanoparticles is formulated. In contrast to the conventional Fourier's heat flux equation, this study employs the Cattaneo-Christov heat flux equation. A uniform magnetic field is applied perpendicular to the flow direction, invoking magnetohydrodynamic(MHD) effects. Further, the model accounts for Joule heating, which is the heat generated when an electric current passes through the fluid. The problem is solved via NDSolve in MATHEMATICA. Numerical and statistical analyses are conducted to provide insights into the behavior of the nanomaterials between the parallel plates with respect to the flow, energy transport, and skin *** findings of this study have potential applications in enhancing cooling systems and optimizing thermal management strategies. It is observed that the squeezing motion generates additional pressure gradients within the fluid, which enhances the flow rate but reduces the frictional drag. Consequently, the fluid is pushed more vigorously between the plates, increasing the flow velocity. As the fluid experiences higher flow rates due to the increased squeezing effect, it spends less time in the region between the plates. The thermal relaxation, however, abruptly changes the temperature, leading to a decrease in the temperature fluctuations.

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In vivo direct neuronal conversion as a therapeutic strategy for ischemic stroke

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Neural Regeneration Research 2025年第8期20卷 2309-2310页

作者： Takashi Irie Taito Matsuda Department of Stem Cell Biology and Medicine Graduate School of Medical SciencesKyushu UniversityFukuokaJapan Department of Neurology Neurological InstituteGraduate School of Medical SciencesKyushu UniversityFukuokaJapan

Stroke causes neuronal loss,which ultimately results in persistent neurological ***,stroke was the third-leading cause of death and disability combined in all ages in 2019,after neonatal disorders and ischemic heart *** that year,there were 12.2 million incident strokes,101 million prevalent strokes,and 143 million disability-adjusted life-years due to stroke.

关键词： neonatal death therapeutic

Lipid droplets in the nervous system:involvement in cell metabolic homeostasis

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Neural Regeneration Research 2025年第3期20卷 740-750页

作者： Yuchen Zhang Yiqing Chen Cheng Zhuang Jingxuan Qi Robert Chunhua Zhao Jiao Wang school of Life sciences Shanghai UniversityShanghaiChina school of Medicine Shanghai UniversityShanghaiChina Institute of Basic Medical sciences Chinese Academy of Medical sciences School of Basic MedicinePeking Union Medical CollegeBeijingChina Center of Excellence in Tissue Engineering Chinese Academy of Medical SciencesBeijingChina Beijing Key Laboratory of New Drug Development and Clinical Trial of Stem Cell Therapy BeijingChina

Lipid droplets serve as primary storage organelles for neutral lipids in neurons,glial cells,and other cells in the nervous *** droplet formation begins with the synthesis of neutral lipids in the endoplasmic ***,lipid droplets were recognized for their role in maintaining lipid metabolism and energy homeostasis;however,recent research has shown that lipid droplets are highly adaptive organelles with diverse functions in the nervous *** addition to their role in regulating cell metabolism,lipid droplets play a protective role in various cellular stress ***,lipid droplets exhibit specific functions in neurons and glial *** of lipid droplet formation leads to cellular dysfunction,metabolic abnormalities,and nervous system *** review aims to provide an overview of the role of lipid droplets in the nervous system,covering topics such as biogenesis,cellular specificity,and ***,it will explore the association between lipid droplets and neurodegenerative *** the involvement of lipid droplets in cell metabolic homeostasis related to the nervous system is crucial to determine the underlying causes and in exploring potential therapeutic approaches for these diseases.

关键词： Alzheimer's disease lipid droplet biogenesis lipid droplets lipid metabolism nervous system neurodegenerative disorders oxidative stress Parkinson's disease

Harnessing therapeutic potential of induced pluripotent stem cell–derived endothelial cells for remyelination in the central nervous system

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Neural Regeneration Research 2025年第6期20卷 1715-1716页

作者： Dan Ma Nona Pop Aston Medical school College of Health and Life SciencesAston UniversityBirminghamUK

Myelin is the protective sheath surrounding nerve fibers, and its damage(demyelination) occurs in many central nervous system(CNS) diseases, including multiple sclerosis(MS), traumatic injury, neurodegenerative diseases such as Alzheimer's disease, and mental disorders such as schizophrenia(Barateiro et al., 2016). Repair of damaged myelin sheaths(remyelination) often fails in MS, leading to neuronal loss and irreversible functional deficits.

关键词： myelin protective diseases

Insights from a proteomic atlas of human Alzheimer's disease brain tissue

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Neural Regeneration Research 2025年第3期20卷 799-800页

作者： Tomas Kavanagh Eleanor Drummond Brain and Mind Centre and school of Medical sciences University of SydneyCamperdownNSWAustralia

There is an urgent need to identify new drug targets for Alzheimer's disease(AD). While new immunotherapies show promise, clinical benefit appears low, and side effects are high. A greater understanding of the disease mechanisms driving AD is an essential factor that will facilitate the identification of new, effective drug targets.

关键词： Alzheimer clinical driving

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