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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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A comprehensive investigation on nonlinear vibration and bending characteristics of bio-inspired helicoidal laminated composite structures

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Applied Mathematics and Mechanics(English Edition) 2025年第1期46卷 81-100页

作者： S.SAURABH R.KIRAN D.SINGH R.VAISH V.S.CHAUHAN school of Mechanical and Materials engineering Indian Institute of Technology Mandi

Bio-inspired helicoidal composite laminates, inspired by the intricate helical structures found in nature, present a promising frontier for enhancing the mechanical properties of structural designs. Hence, this study provides a comprehensive investigation into the nonlinear free vibration and nonlinear bending behavior of bio-inspired composite plates. The inverse hyperbolic shear deformation theory(IHSDT) of plates is employed to characterize the displacement field, with the incorporation of Green-Lagrange nonlinearity. The problem is modeled using the C0finite element method(FEM), and an in-house code is developed in the MATLAB environment to solve it numerically. Various helicoidal layup configurations including helicoidal recursive(HR), helicoidal exponential(HE), helicoidal semi-circular(HS), linear helicoidal(LH), and Fibonacci helicoidal(FH)with different layup sequences and quasi-isotropic configurations are studied. The model is validated, and parametric studies are conducted. These studies investigate the effects of layup configurations, side-to-thickness ratio, modulus ratios, boundary conditions, and loading conditions at different load amplitudes on the nonlinear vibration and nonlinear bending behaviors of bio-inspired composite plates. The results show that the laminate sequence exerts a substantial impact on both nonlinear natural frequencies and nonlinear bending behaviors. Moreover, this influence varies across different side-to-thickness ratios and boundary conditions of the bio-inspired composite plate.

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Photoinduced radical sulfur dioxide insertion with asymmetric cyclization of alkenes: accessing β-chiral sulfones bearing S-stereocentric cyclic sulfinamides

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Science China Chemistry 2025年第1期 257-263页

作者： Jiapian Huang Chenxin Wang Xu Wang Xiaoyu Zhou Wei Xiao Jie Wu school of pharmaceutical and Chemical engineering & institute for advanced studies Taizhou University State Key Laboratory of Organometallic Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences school of Chemistry and Chemical engineering Henan Normal University

The generation of various β-chiral sulfones bearing chiral cyclic sulfinamides through photoredox-catalyzed sulfur dioxide insertion with asymmetric radical cyclization is described. This method features a broad substrate scope and excellent stereospecificity. Computational studies reveal that the dispersion interaction between sulfinyl group and CH2SO2Ph group plays a crucial role in the stereoselectivity control.

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Context-dependent role of sirtuin 2 in inflammation

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Neural Regeneration Research 2025年第3期20卷 682-694页

作者： NoemíSola-Sevilla Maider Garmendia-Berges MCarmen Mera-Delgado Elena Puerta Department of pharmaceutical Sciences Division of PharmacologySchool of Pharmacy and NutritionUniversity of NavarraPamplonaSpain Navarra institute for Health Research(IdiSNA) PamplonaSpain

Sirtuin 2 is a member of the sirtuin family nicotinamide adenine dinucleotide(NAD~+)-dependent deacetylases, known for its regulatory role in different processes, including inflammation. In this context, sirtuin 2 has been involved in the modulation of key inflammatory signaling pathways and transcription factors by deacetylating specific targets, such as nuclear factor κB and nucleotide-binding oligomerization domain-leucine-rich-repeat and pyrin domain-containing protein 3(NLRP3). However, whether sirtuin 2-mediated pathways induce a pro-or an anti-inflammatory response remains controversial. Sirtuin 2 has been implicated in promoting inflammation in conditions such as asthma and neurodegenerative diseases, suggesting that its inhibition in these conditions could be a potential therapeutic strategy. Conversely, arthritis and type 2 diabetes mellitus studies suggest that sirtuin 2 is essential at the peripheral level and, thus, its inhibition in these pathologies would not be recommended. Overall, the precise role of sirtuin 2 in inflammation appears to be context-dependent, and further investigation is needed to determine the specific molecular mechanisms and downstream targets through which sirtuin 2 influences inflammatory processes in various tissues and pathological conditions. The present review explores the involvement of sirtuin 2 in the inflammation associated with different pathologies to elucidate whether its pharmacological modulation could serve as an effective strategy for treating this prevalent symptom across various diseases.

关键词： interferon inflammation lipopolysaccharide neuroinflammation NLRP3 nuclear factorκB sirtuin 2

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Bandgap characteristics analysis and graded design of a novel metamaterial for flexural wave suppression

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Applied Mathematics and Mechanics(English Edition) 2025年第1期46卷 1-24页

作者： Fan YANG Zhaoyang MA Xingming GUO Shanghai Key Laboratory of Mechanics in Energy engineering Shanghai Institute of Applied Mathematics and Mechanics School of Mechanics and Engineering ScienceShanghai University Shanghai institute of Aircraft Mechanics and Control

A novel elastic metamaterial is proposed with the aim of achieving lowfrequency broad bandgaps and bandgap regulation. The band structure of the proposed metamaterial is calculated based on the Floquet-Bloch theorem, and the boundary modes of each bandgap are analyzed to understand the effects of each component of the unit cell on the bandgap formation. It is found that the metamaterials with a low elastic modulus of ligaments can generate flexural wave bandgaps below 300 Hz. Multi-frequency vibrations can be suppressed through the selective manipulation of bandgaps. The dual-graded design of metamaterials that can significantly improve the bandgap width is proposed based on parametric studies. A new way that can regulate the bandgap is revealed by studying the graded elastic modulus in the substrate. The results demonstrate that the nonlinear gradient of the elastic modulus in the substrate offers better bandgap performance. Based on these analyses, the proposed elastic metamaterials can pave the way for multi-frequency vibration control, low-frequency bandgap broadening, and bandgap tuning.

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Recent advances for the photoinduced C—C bond cleavage of cycloketone oximes

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Chinese Chemical Letters 2020年第12期31卷 3083-3094页

作者： Wei Xiao Jie Wu school of pharmaceutical and Materials engineering&institute for advanced studies Taizhou UniversityTaizhou 318000China State Key Laboratory of Organometallic Chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 200032China

Nitriles are widely existed in many bioactive compounds,and they can be easily transformed into other functional ***,the synthesis of nitriles under cyanide-free conditions is of significant *** advances for the synthesis of nitriles through photoinduced C—C bond cleavage of cycloketone oximes classified by the type of C—X bond forming are *** compounds possessing nitriles can be efficiently accessed via this method.

关键词： Nitriles C—C bond cleavage Cycloketone oximes Radical Photocatalysis

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Assembly of 3-sulfonated 2H-pyrrol-2-ones through the insertion of sulfur dioxide with allenoic amides

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Chinese Chemical Letters 2020年第12期31卷 2996-2998页

作者： Kaida Zhou Jianqiang Chen Jie Wu school of pharmaceutical and Materials engineering&institute for advanced studies Taizhou UniversityTaizhou 318000China State Key Laboratory of Organometallic Chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 200032China

Generation of 3-sulfonated 2 H-pyrrol-2-ones through a three-component reaction of allenoic amides,sulfur dioxide,and aryldiazonium tetrafluoroborates under metal-free conditions is *** transformation proceeds under mild conditions without the addition of catalysts or additives,giving rise to 3-sulfonated 2 H-pyrrol-2-ones in moderate to good *** functional group compatibility is observed.A plausible mechanism is proposed,which is initiated by aryl radicals formed in situ from aryldiazonium tetrafluoroborates and DABCO·(SO2)***,excellent chemoselectivity and regioselectivity are presented in this transformation.

关键词： Allenoic amide Aryldiazonium tetrafluoroborate 3-Sulfonated 2H-pyrrol-2-one Sulfur dioxide Metal-free

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Pathogenesis, diagnosis, and treatment of epilepsy: electromagnetic stimulation-mediated neuromodulation therapy and new technologies

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Neural Regeneration Research 2025年第4期20卷 917-935页

作者： Dian Jiao Lai Xu Zhen Gu Hua Yan Dingding Shen Xiaosong Gu Academy of Medical engineering and Translational Medicine Tianjin UniversityTianjinChina Key Laboratory of advanced Drug Delivery Systems of Zhejiang Province College of Pharmaceutical SciencesZhejiang UniversityHangzhouZhejiang ProvinceChina Affiliated Hospital of Nantong University NantongJiangsu ProvinceChina

Epilepsy is a severe,relapsing,and multifactorial neurological *** regarding the accurate diagnosis,prognosis,and in-depth pathogenesis are crucial for the precise and effective treatment of *** pathogenesis of epilepsy is complex and involves alterations in variables such as gene expression,protein expression,ion channel activity,energy metabolites,and gut microbiota *** results are lacking for conventional treatments for *** resection of lesions,drug therapy,and non-drug interventions are mainly used in clinical practice to treat pain associated with ***-pharmacological treatments,such as a ketogenic diet,gene therapy for nerve regeneration,and neural regulation,are currently areas of research *** review provides a comprehensive overview of the pathogenesis,diagnostic methods,and treatments of *** also elaborates on the theoretical basis,treatment modes,and effects of invasive nerve stimulation in neurotherapy,including percutaneous vagus nerve stimulation,deep brain electrical stimulation,repetitive nerve electrical stimulation,in addition to non-invasive transcranial magnetic stimulation and transcranial direct current *** studies have shown that electromagnetic stimulation-mediated neuromodulation therapy can markedly improve neurological function and reduce the frequency of epileptic ***,many new technologies for the diagnosis and treatment of epilepsy are being ***,current research is mainly focused on analyzing patients’clinical manifestations and exploring relevant diagnostic and treatment methods to study the pathogenesis at a molecular level,which has led to a lack of consensus regarding the mechanisms related to the disease.

关键词： diagnosis drug treatment electroencephalography epilepsy monitoring epilepsy nerve regeneration neurostimulation non-drug interventions pathogenesis prediction

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Brain region-specific roles of brain-derived neurotrophic factor in social stress-induced depressive-like behavior

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Neural Regeneration Research 2025年第1期20卷 159-173页

作者： Man Han Deyang Zeng Wei Tan Xingxing Chen Shuyuan Bai Qiong Wu Yushan Chen Zhen Wei Yufei Mei Yan Zeng Brain Science and advanced Technology institute Wuhan University of Science and TechnologyWuhanHubei ProvinceChina Geriatric Hospital Affiliated to Wuhan University of Science and Technology WuhanHubei ProvinceChina school of Public Health Wuhan University of Science and TechnologyWuhanHubei ProvinceChina

Brain-derived neurotrophic factor is a key factor in stress adaptation and avoidance of a social stress behavioral *** studies have shown that brain-derived neurotrophic factor expression in stressed mice is brain region–specific,particularly involving the corticolimbic system,including the ventral tegmental area,nucleus accumbens,prefrontal cortex,amygdala,and *** how brain-derived neurotrophic factor participates in stress processing in different brain regions will deepen our understanding of social stress *** this review,we discuss the expression and regulation of brain-derived neurotrophic factor in stress-sensitive brain regions closely related to the pathophysiology of *** focused on associated molecular pathways and neural circuits,with special attention to the brain-derived neurotrophic factor–tropomyosin receptor kinase B signaling pathway and the ventral tegmental area–nucleus accumbens dopamine *** determined that stress-induced alterations in brain-derived neurotrophic factor levels are likely related to the nature,severity,and duration of stress,especially in the above-mentioned brain regions of the corticolimbic ***,BDNF might be a biological indicator regulating stress-related processes in various brain regions.

关键词： amygdala chronic mild stress chronic social defeat stress corticolimbic system depression hippocampus medial prefrontal cortex nucleus accumbens social stress models ventral tegmental area

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Benzothiadiazole-based water-soluble macrocycle:Synthesis,aggregation-induced emission and selective detection of spermine

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Chinese Chemical Letters 2024年第11期35卷 314-317页

作者： Shuo Li Qianfa Liu Lijun Mao Xin Zhang Chunju Li Da Ma school of pharmaceutical engineering&institute for advanced studies Taizhou UniversityTaizhou 318000China Tianjin Key Laboratory of Structure and Performance for Functional Molecules College of ChemistryTianjin Normal UniversityTianjin 300387China

Reported here is the synthesis of a new macrocycle bearing anionic carboxylate groups with water-soluble aggregation-induced emission(AIE).The water-soluble macrocycle without typical AIE luminogens is constructed based on the building block of *** exhibits a remarkable AIE *** watersoluble macrocycle can selectively bind different types of biogenic amines in aqueous media with the tightest binding towards *** fluorescence enhancement induced by supramolecular encapsulation is used to detect spermine.

关键词： Macrocycle Water-soluble Aggregation-induced emission Biogenic amines Host-guest interaction

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