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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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Deciphering the molecular mechanisms of Simiaowan in the treatment of hyperuricemia: in vivo and in silico approaches

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Traditional Medicine Research 2025年第2期10卷 37-54页

作者： Yong-Chang Zeng jun-Hong wu Dan-Dan Xu Kang He Chang-Qing Liu Li-Fei Song Zheng-Zhi wu Qian-Qian Jiang Shao-Yu Liang Department of Neurology The First Affiliated Hospital of Shenzhen UniversityShenzhen 518020China Pharmaceutical Department The Affiliated TCM Hospital of Guangzhou Medical UniversityGuangzhou 510000China School of Pharmacy Guizhou University of Traditional Chinese MedicineGuiyang 550025China Guangzhou Zeli Medical Technology Co. Ltd.Guangzhou 510700China

Background:Simiaowan(SMW),a well-known traditional Chinese medicine,has been employed to treat hyperuricemia(HUA)and gout for ***,the bioactive components and underlying mechanisms have not been *** objective of this study was to identify the active components and potential mechanisms of SMW by integrating pharmacological experimentation,serum pharmacochemistry,network pharmacology and molecular ***:HUA rats modelling by high-fat/high-sugar diet and potassium oxonate/adenine oral administration were used to evaluate the pharmacodynamic effects of ***-Q-Exactive-MS/MS was employed to detect the bioactive components present in SMW-containing *** pharmacology and molecular docking were utilized to elucidate the potential targets and underlying ***:SMW effectively ameliorated HUA rats via the inhibition of uric acid(UA)production,promotion of UA excretion,improvement of lipid and glucose metabolic abnormalities,antioxidant,anti-inflammatory and anti-insulin resistance effects.A total of 73 compounds detected in SMW-containing serum were identified as potential active components,with alkaloids,flavonoids,organic acids,and terpenoids emerging as the primary active *** 203 corresponding targets were obtained as SMW anti-HUA/gout targets,which mainly participated in apoptosis,insulin resistance,TNF,PI3K-Akt,HIF-1,NF-κB,MAPK,IL-17 and TLR signaling *** docking indicated that active compounds(***,phellodendrine,quercetin,formononetin,ferulic acid)had superior binding abilities to the key targets(*** carrier family 22 member 12(URAT1),solute carrier family 22 member 6(OAT1),ATP-binding cassette sub-family G member 2(ABCG2),solute carrier family 2,facilitated glucose transporter member 9(GLUT9),xanthine dehydrogenase/oxidase(XDH),transcription factor p65(RELA),toll-like receptor 4(TLR4),prostaglandin G/H synthase 2(PTGS2),caspase-3(CASP3),insulin(INS)).Conclusion:S

关键词： hyperuricemia network pharmacology serum pharmacochemistry Simiaowan UPLC-Q-Exactive-MS/MS

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Broadband absorption enhancement with ultrathin MoS2 film in the visible regime

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Chinese Physics B 2021年第2期30卷 319-323页

作者： jun wu College of Electrical Engineering Anhui Polytechnic UniversityWuhu 241000China Department of Physics Zhejiang University of Science and TechnologyHangzhou 310023China

The broadband absorption enhancement effect in ultrathin molybdenum disulfide(Mo S2)films is *** is achieved by inserting the Mo S2 film between a dielectric film and a one-dimensional silver grating backed with a silver *** broadband absorption enhancement in the visible region is achieved,which exhibits large integrated absorption and short-circuit current density for solar energy under normal *** optical properties of the proposed absorber are found to be superior to those of a reference planar structure,which makes the proposed structure advantageous for practical photovoltaic ***,the integrated absorption and short-circuit current density can be maintained high for a wide range of incident angles.A qualitative understanding of such broadband absorption enhancement effect is examined by illustrating the electromagnetic field distribution at some selected *** results pave the way for developing high-performance optoelectronic devices,such as solar cells,photodetectors,and modulators.

关键词： two-dimensional(2D)materials transition-metal dichalcogenide plasmonics absorption enhancement

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Effect of gastric fluid on adsorption and desorption of endocrine disrupting chemicals on microplastics

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Frontiers of Environmental Science & Engineering 2022年第8期16卷 193-205页

作者： Jie wu Jian Lu jun wu CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation Yantai Institute of Coastal Zone Research(YIC)Chinese Academy of Sciences(CAS)Shandong Key Laboratory of Coastal Environmental ProcessesYICCASYantai 264003China University of Chinese Academy of Sciences Beijing 100049China Yantai Research Institute Harbin Engineering UniversityYantai 264006China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao 266071China

Microplastics and endocrine disrupting chemicals are emerging pollutants in the marine environment because of their potential *** effect of gastric fluid on the adsorption and desorption of 17β-estradiol(E2)and 17α-ethynylestradiol(EE2)to microplastics was *** adsorption and desorption isotherms of E2/EE2 on microplastics could be well fitted by the Freundlich model while the Gibbs free energy of these processes were negative,proving that the reaction occurred spontaneously on the heterogeneous surface of the *** ratios of EE2(55%–59%)on PVC were larger than that of E2(49%–55%)to indicate that EE2 was less stable in gastric fluid,which could be explained by the fact that the hydrophobicity of EE2 was greater than E2.E2/EE2 were more easily desorbed from PVC in the gastric fluid and the desorption amount(5.25–12.91/7.19–17.86μg/g)increased by 2.51 times in comparison with that in saline solution(2.22–7.81/2.87–10.80μg/g).The decrease of pH and the increase of ionic strength in gastric fluid could further strengthen desorption of E2/EE2 from *** promotion of gastric juice on desorption of PVC was achieved by reducing the hydrophobicity of the PVC *** desorption rate of E2/EE2 at 18°C and 38°C was respectively 44%–47%/46%–50%and 49%–55%/56%–59%,indicating that PVC loaded with E2/EE2 had a relatively greater risk of releasing pollutants in the gastric fluid of constant temperature marine organisms while higher temperatures exposed higher hazards for variable temperature *** interaction between microplastics and pollutants might be mainly hydrophobic interaction.

关键词： Microplastics Gastric fluid Endocrine-disrupting chemicals Adsorption Desorption

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Residual index for measurement configuration optimization in robot kinematic calibration

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Science China(Technological Sciences) 2023年第7期66卷 1899-1915页

作者： YE Hao wu jun State Key Laboratory of Tribology in Advanced Equipment and Institute of Manufacturing Engineering Department of Mechanical EngineeringTsinghua UniversityBeijing 100084China Beijing Key Lab of Precision/Ultra-precision Manufacturing Equipment and Control Beijing 100084China

To improve the efficiency and accuracy of kinematic calibration,the selection of measurement configurations is an important *** previous research,optimal measurement configurations mainly are selected by maximizing observability ***,the traditional observability indices only focus on the identification efficiency of the error parameters,while the purpose of robot kinematic calibration is to improve *** solve the inconsistency of the purpose between the observability index and calibration,the concept of the residual index to represent the residual distribution of the end effector after robot kinematic calibration with the measurement noise is *** on the quadratic form minimization of residuals,this article defines a specific residual index,O^(r),which is dimensionless and strictly better with the increase of measurement *** indices are used to select measurement configurations in the kinematic calibration of a 5-DOF 2UPU/SP-RR hybrid robot,and the calibration results show that the proposed residual index is better than the traditional indices in the accuracy and stability of the end effector residual.

关键词： residual index observability index kinematic calibration measurement configuration optimization

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Adsorption and desorption of steroid hormones on saline soil

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Frontiers of Environmental Science & Engineering 2022年第11期16卷 177-190页

作者： Jie wu Jian Lu jun wu CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation Yantai Institute of Coastal Zone ResearchChinese Academy of SciencesYantai 264003China Shandong Key Laboratory of Coastal Environmental Processes Yantai 264003China University of Chinese Academy of Sciences Beijing 100049China Yantai Research Institute Harbin Engineering UniversityYantai 264006China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao 266071China

Soil organic matter content was the main driving factor affecting adsorption and desorption process of 17β-estradiol(E2)and 17α-ethynylestradiol(EE2)on saline *** adsorption and desorption of E2 and EE2 on three saline soils showed the similar behavior that soil with the highest organic content possessed the highest adsorption capacity and the lowest desorption capacity for E2 and *** adsorption capacity of untreated soil samples(with organic matter)was larger than that of soil samples without organic *** soil with the largest adsorption capacity,adsorption capacity of E2/EE2 on the untreated soil and soil colloid(with organic matter)respectively reached 0.15/0.30μg/g and 0.16/0.33μg/g while the soil and soil colloid without organic matter hardly adsorbed *** adsorption capacity of E2/EE2 at the initial concentration of 100μg/L was 25/15 times higher than that at the initial concentration of 5μg/L.E2 and EE2 had the same adsorption sites on saline soil while EE2 possessed higher competition intensity for adsorption sites than ***-first-order model(R^(2)=0.995–0.986)and Langmuir model(R^(2)=0.989–0.999)could better fit the adsorption process of E2 or *** thermodynamic study further showed that the adsorption of E2/EE2 on saline soil was a spontaneous exothermic *** desorption capacity of EE2/E2 accounted for 40%/78%of the total adsorption capacity to possibly exert potential risk to the *** variation of the salinity led to the variation of soil organic carbon which subsequently changed the adsorption and desorption behaviors of endocrine disrupting chemicals in coastal saline *** study provides a new insight on the interfacial behavior of endocrine disrupting chemicals on saline soil.

关键词： Saline soil Steroid hormones Adsorption Desorption Soil organic matter

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Controlling the probability density of quantum systems

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Journal of Systems Engineering and Electronics 2011年第6期22卷 975-981页

作者： Yifan Xing jun wu Institute of Cyber-Systems and Control Zhejiang University Hangzhou 310027 P. R. China

A new method to design a quantum controller which directly controls the probability density function（PDF） of quantum systems is *** on the quantum model from the PDF perspective,two specific control algorithms are proposed with uniform and non-uniform fields,*** a detailed control algorithm with convergence analysis is given for the small error *** appropriately estimating the selected Lyapunov function,more accurate control effect is *** proposed scheme provides a constructive method to find appropriate parameters for controller design.

关键词： quantum control probability density control stochastic distribution control.

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A New Simulation Model for Recoil Analysis of Deep-Water Drilling Risers After Emergency Disconnection

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China Ocean Engineering 2023年第4期37卷 637-644页

作者： wu jun-kang MENG Shuai State Key Laboratory of Ocean Engineering Shanghai Jiao Tong UniversityShanghai 200240China

The recoil response of a deep-water drilling riser following an ED(Emergency Disconnection)scenario is a transient and sensitive *** recoiling displacement of the riser is the resultant of recoil motion and axial ***-ever,it is typically represented by one variable in recoil *** axial deformation is quite small compared with axial motion in the recoil process,it inevitably introduces numerical errors(i.e.,a large number annihilating a small number).Thus,it is hard to perform a quantitative analysis of axial deformation,although a consensus initial deformation is essential for recoil ***,the triggered axial natural modes have never been examined *** this study,the recoil response is decomposed into two parts:recoil motion and axial deformation,and a novel model is developed by Galerkin *** has demonstrated that the initial stretch has a significant effect at the initial stage in *** existing models underestimate the effects of axial *** new model can capture information of triggered natural modes and figure out the modes undergoing dynamic *** study can be beneficial to overpull setting,determination of ED time and anti-recoil control optimization.

关键词： recoil analysis drilling riser emergency disconnection axial deformation Galerkin method

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Facile and One-step Direct Synthesis of Poly(valine)as a Robust Drug Nanocarrier for Enhanced Breast Cancer Therapy

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Chinese Journal of Polymer Science 2022年第9期40卷 1016-1027页

作者： Ya-Bin Meng jun wu School of Biomedical Engineering Sun Yat-sen UniversityShenzhen 518107China

Synthetic poly(amino acid)s with good biodegradable and biocompatible properties have attracted increased attention as carriers in biomedical applications in recent years,their synthesis and purification procedures are usually complicated and some by-products would occur *** this,polypeptide with good biodegradable and biocompatible properties is prepared and optimized by one-step and direct synthesis strategy and poly(valine)(PVal)is selected here as a model polypeptide in this *** newly generated PVal can self-assemble into poly(valine)nanoparticles(PVal-NPs)with a high drug-loading capacity(>20 wt%)of doxorubicin(DOX)and shows strong cytotoxicity against 4T1 *** cellular internalization,the release of DOX could be accelerated by the endosomal acidic environment which leads to enhanced anticancer *** results in vivo show that DOX@PVal-NPs have a long blood circulation time,high cancer accumulation and penetration,and good therapeutic performance in 4T1 tumor-bearing mice without causing obvious adverse effect on main *** these combined advantages,these PVal-based nanoplatform would provide an effective drug delivery tool for clinical breast cancer therapy.

关键词： Poly(amino acid) Nanoparticle Drug carrier Doxorubicin Breast cancer

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The Average Value Inequality in Sequential Effect Algebras

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Acta Mathematica Sinica,English Series 2010年第5期26卷 831-836页

作者： jun SHEN jun De wu Department of Mathematics Zhejiang University Hangzhou 310027 P. R. China Department of Mathematics Anhui Normal University Wuhu 241003 P. R. China

A sequential effect algebra （E, 0, 1, ,o） is an effect algebra on which a sequential product o with certain physics properties is defined; in particular, sequential effect algebra is an important model for studying quantum measurement theory. In 2005, Gudder asked the following problem： If a, b E （E, 0, 1, , o） and a⊥b and a o b⊥a o b, is it the case that 2（a o b） ≤ a2 b2 ？ In this paper, we construct an example to answer the problem negatively.

关键词： effect algebras sequential effect algebras average value inequality

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