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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)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** 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 *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** 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 scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** 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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From single to combinatorial therapies in spinal cord injuries for structural and functional restoration

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Neural Regeneration Research 2025年第3期20卷 660-670页

作者： Ernesto Doncel-Pérez Gabriel guízar-Sahagún Israel Grijalva-Otero Hospital Nacional de Parapléjicos de Toledo Servicio de Salud de Castilla La Mancha(SESCAM)ToledoSpain Medical Research Unit for Neurological Diseases UMAE Hospital de EspecialidadesCentro Médico Nacional Siglo XXIIMSSCiudad de MéxicoMéxico

Spinal cord injury results in paralysis, sensory disturbances, sphincter dysfunction, and multiple systemic secondary conditions, most arising from autonomic dysregulation. All this produces profound negative psychosocial implications for affected people, their families, and their communities;the financial costs can be challenging for their families and health institutions. Treatments aimed at restoring the spinal cord after spinal cord injury, which have been tested in animal models or clinical trials, generally seek to counteract one or more of the secondary mechanisms of injury to limit the extent of the initial damage. Most published works on structural/functional restoration in acute and chronic spinal cord injury stages use a single type of treatment: a drug or trophic factor, transplant of a cell type, and implantation of a biomaterial. Despite the significant benefits reported in animal models, when translating these successful therapeutic strategies to humans, the result in clinical trials has been considered of little relevance because the improvement, when present, is usually insufficient. Until now, most studies designed to promote neuroprotection or regeneration at different stages after spinal cord injury have used single treatments. Considering the occurrence of various secondary mechanisms of injury in the acute and sub-acute phases of spinal cord injury, it is reasonable to speculate that more than one therapeutic agent could be required to promote structural and functional restoration of the damaged spinal cord. Treatments that combine several therapeutic agents, targeting different mechanisms of injury, which, when used as a single therapy, have shown some benefits, allow us to assume that they will have synergistic beneficial effects. Thus, this narrative review article aims to summarize current trends in the use of strategies that combine therapeutic agents administered simultaneously or sequentially, seeking structural and functional restoratio

关键词： neural regeneration neuroprotection spinal cord injury repair spinal cord injury treatments structural restoration of spinal cord injury

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Emission characteristics,environmental impacts and health risk assessment of volatile organic compounds from the typical chemical industry in China

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Journal of Environmental Sciences 2025年第3期149卷 113-125页

作者： kaitao Chen Xin gu Min Cai Weicheng Zhao Boxuan Wang Haoran Yang Xingang Liu Xingru Li Analysis and Testing Center Department of ChemistryCapital Normal UniversityBeijing 100048China College of Resources Environment and Tourism Capital Normal UniversityBeijing 100048China State Key Laboratory of Water Environment Simulation School of EnvironmentBeijing Normal UniversityBeijing 100875China

To study the volatile organic compounds(VOCs)emission characteristics of industrial enterprises in China,6 typical chemical industries in Yuncheng City were selected as research objects,including the modern coal chemical industry(MCC),pharmaceutical industry(PM),pesticide industry(PE),coking industry(CO)and organic chemical industry(OC).The chemical composition of 91 VOCs was quantitatively *** results showed that the emission concentration of VOCs in the chemical industry ranged from 1.16 to 155.59 mg/m^(3).Alkanes were the main emission components of MCC(62.0%),PE(55.1%),and OC(58.5%).Alkenes(46.5%)were important components of PM,followed by alkanes(23.8%)and oxygenated volatile organic compounds(OVOCs)(21.2%).Halocarbons(8.6%-71.1%),OVOCs(9.7%-37.6%)and alkanes(11.2%-27.0%)were characteristic components of *** largest contributor to OFP was alkenes(0.6%-81.7%),followed by alkanes(9.3%-45.9%),and the lowest onewas alkyne(0%-0.5%).Aromatics(66.9%-85.4%)were the largest contributing components to SOA generation,followed by alkanes(2.6%-28.5%),and the lowest one was alkenes(0%-4.1%).Ethylene and BTEX were the key active species in various chemical *** human health risk assessment showed workers long-term exposed to the air in the chemical industrial zone had a high cancer and non-cancer risk during work,and BTEX and dichloromethane were the largest contributors.

关键词： Industrial enterprise VOCs spectrum Reactivity Health risk

Accumulation characteristics and fate modeling of phthalic acid esters in surface water from the Three Gorges Reservoir area,China

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Journal of Environmental Sciences 2025年第3期149卷 46-56页

作者： Shuai Sun Bing Zhang Junjie Hu Wen gu ZhenWang Deling Fan Feng Ge Lili Shi LeiWang Nanjing Institute of Environmental Science Ministry of Ecology and Environment of the People’s Republic of ChinaNanjing 210042China Key Laboratory of Pesticide Environmental Assessment and Pollution Control Ministry of Ecology and Environment of the People’s Republic of ChinaNanjing 210042China Solid Waste and Chemicals Management Center Ministry of Ecology and Environment of the People’s Republic of ChinaBeijing 100029China

Phthalic acid esters(PAEs)are a group of compounds widespread in the *** investigate the occurrence and accumulation characteristics of PAEs,surface water samples were collected from the Three Gorges Reservoir area,*** total concentrations of∑_(11)analyzed PAEs(11PAEs)in the collected water samples ranging from 197.7 to 1,409.3 ng/L(mean±IQR:583.1±308.4 ng/L).While DEHP was the most frequently detected PAE,DnBP and DnNP were the most predominant PAEs in the analyzed water samples with a mean contribution of 63.3%of the∑_(11)*** concentrations of the∑_(11)PAEs in the water samples from the upper reaches of the Yangtze River were significantly higher than those from themiddle *** better understand the transport and fate of the PAEs,seven detected PAEs were modeled by Quantitative Water Air Sediment Interaction(QWASI).The simulated and measured values were close for most PAEs,and differences are within one order of magnitude even for the worst *** all simulated PAEs,water and particle inflow were main sources in the reservoir,whereas water outflow and degradation in water were important removal *** contribution ratios of different sources/losses varied fromPAEs,depending on their *** calculated risk quotients of DnNP in the Three Gorges Reservoir area whether based onmonitoring or simulating results were all far exceeded the safety threshold value,implying the occurrence of this PAE compound may cause potential adverse effects for the aquatic ecology of the Three Gorges Reservoir area.

关键词： Phthalic esters Surface water Transport and fate Three Gorges Reservoir area Risk assessment

液相色谱串联质谱法测定人血浆中比伐卢定的浓度

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中国临床药理学杂志 2012年第6期28卷 453-455页

作者：张冬梅顾景凯赵侠王梓凝崔一民北京大学第一医院药剂科吉林大学药物代谢研究中心

目的建立测定人血浆中比伐卢定浓度的液相色谱串联质谱方法。方法用Zorbax 300SB-C18色谱柱;流动相为甲醇-水-甲酸(55∶45∶0.45);流速为0.8 ***-1;柱温为35℃;正离子电离、多离子反应监测进行定量分析。结果比伐卢定线性范围为15～1000... 详细信息

目的建立测定人血浆中比伐卢定浓度的液相色谱串联质谱方法。方法用Zorbax 300SB-C18色谱柱;流动相为甲醇-水-甲酸(55∶45∶0.45);流速为0.8 ***-1;柱温为35℃;正离子电离、多离子反应监测进行定量分析。结果比伐卢定线性范围为15～10000 ***-1;批内、批间精密度均98%。结论本方法专属、灵敏、准确、快速、简便,可用于比伐卢定的临床开发研究及上市后临床应用中的浓度测定。

关键词：液相色谱串联质谱比伐卢定血浆浓度

GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling

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Science China(Information Sciences) 2025年第1期68卷 145-158页

作者： Wei JU Yiyang gu Zhengyang MAO Ziyue QIAO Yifang QIN Xiao LUO Hui XIONG Ming ZHANG School of Computer Science National Key Laboratory for Multimedia Information ProcessingPeking University Artificial Intelligence Thrust The Hong Kong University of Science and Technology Department of Computer Science University of California

Self-supervised graph representation learning has recently shown considerable promise in a range of fields, including bioinformatics and social networks. A large number of graph contrastive learning approaches have shown promising performance for representation learning on graphs, which train models by maximizing agreement between original graphs and their augmented views(i.e., positive views). Unfortunately, these methods usually involve pre-defined augmentation strategies based on the knowledge of human experts. Moreover, these strategies may fail to generate challenging positive views to provide sufficient supervision signals. In this paper, we present a novel approach named graph pooling contrast(GPS) to address these *** by the fact that graph pooling can adaptively coarsen the graph with the removal of redundancy, we rethink graph pooling and leverage it to automatically generate multi-scale positive views with varying emphasis on providing challenging positives and preserving semantics, i.e., strongly-augmented view and weakly-augmented view. Then, we incorporate both views into a joint contrastive learning framework with similarity learning and consistency learning, where our pooling module is adversarially trained with respect to the encoder for adversarial robustness. Experiments on twelve datasets on both graph classification and transfer learning tasks verify the superiority of the proposed method over its counterparts.

关键词： graph representation learning graph neural networks graph contrastive learning graph augmentations graph pooling

Visual electrophysiological assessment of children with poor response to treatment for functional amblyopia

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International Journal of Ophthalmology(English edition) 2025年第2期18卷 315-322页

作者： Dong-Qing Yuan Wei-Wei Zhang Liu-Wei gu Qing-Huai Liu Department of Ophthalmology Jiangsu Province Hospitalthe First Affiliated Hospital of Nanjing Medical UniversityJiangsu Women and Children Health HospitalNanjing 210029Jiangsu ProvinceChina

AIM:To assess the visual electrophysiological outcomes in children with functional amblyopia who exhibited poor response to conventional ***:Twenty-one children with functional amblyopia,aged 5.7±2.1y(range:4-10y),underwent comprehensive ophthalmic and refractive *** domain-optical coherence tomography(SD-OCT)and multifocal electroretinography(mfERG)were conducted to analyze the macular retinal thickness and the first-order response P1 ring of the mfERG in the amblyopic eye(AE)compared to the fellow good eye(GE).RESULTS:Initially,visual acuity in the AE ranged from 20/800 to 20/40,while the GE exhibited a range of 20/25 to 20/20(P<0.01).After 6mo of treatment,17 patients demonstrated improved visual acuity in the AE to 20/50 or better,while 4 children showed no ***-OCT revealed comparable macular and optic disc structures between the AE and *** to treatment,the mfERG P1 ring amplitude was significantly reduced in the AE compared to GE(P<0.05).The AE/GE ratio of P1 ring amplitude showed significant improvement ***,a smaller AE/GE ratio before treatment was associated with poorer improvement ***:In the management of functional amblyopia,a thorough assessment of amblyopic eye examinations is *** 20%of amblyopic eyes may not achieve significant improvement in visual acuity,despite the absence of detectable organic retinal *** may reveal underlying *** mfERG into initial assessments or treatment follow-ups can aid in identifying potential hidden retinal defects and predicting the prognosis of the amblyopic eye.

关键词： functional amblyopia poor response optical coherence tomography multifocal electroretinography retinal defects

Molecular Mechanism Behind the Capture of Fluorinated Gases by Metal–Organic Frameworks

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Nano-Micro Letters 2025年第5期17卷 407-462页

作者： Qian Wang Yong Hu Yifan gu College of Environmental Science and Engineering State Key Laboratory of Pollution Control and Resource ReuseTongji UniversitySiping Rd 1239Shanghai 200092People’s Republic of China Department of Polymeric Materials School of Materials Science and EngineeringTongji UniversityCaoan Road 4800Shanghai 201804People’s Republic of China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092People’s Republic of China Key Laboratory of Cities’Mitigation and Adaptation to Climate Change China Meteorological Administration(CMA)Tongji UniversityShanghai 200092People’s Republic of China

Fluorinated gases(F-gases)play a vital role in the chemical industry and in the fields of air conditioning,refrigeration,health care,and organic ***,the direct emission of waste gases containing F-gases into the atmosphere contributes to greenhouse effects and generates toxic *** porous materials for the energy-efficient capture,separation,and recovery of F-gases is highly ***,as a highly designable porous adsorbents,metal–organic frameworks(MOFs)exhibit excellent selective sorption performance toward F-gases,especially for the recognition and separation of different F-gases with highly similar properties,showing their great potential in F-gases control and *** this review,we discuss the capture and separation of F-gases and their azeotropic,near-azeotropic,and isomeric mixtures in various application scenarios by MOFs,specifically classify and analyze molecular interaction between F-gases and MOFs,and interpret the mechanisms underlying their high performance regarding both adsorption capacity and selectivity,providing a repertoire for future materials *** faced in the transformation research roadmap of MOFs adsorbent separation technologies toward F-gases are also discussed,and areas for future research endeavors are highlighted.

关键词： Fluorinated gas Metal–organic framework Adsorption Separation Molecular interaction

Clinical pharmacokinetic analysis method of Baicalein and its four main metabolites in human plasma,urine,feces

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Clinical pharmacokinetic analysis method of Baicalein and it...