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Single-cell omics: experimental workflow, data analyses and applications

中国动物学会兽类学分会第六届会员代表大会暨学术讨论会

作者： wang jin-xing zhao xiao-fan deng yi qi hong-ying (School of Life Sciences, Shandong University, jinan 250100, China)

Niviventer confucianus (Milne-Edwards, 1871) as one of the harmful rodents in the woods, is widely distributed in China. wang and Zheng (1981) divided it into 6 subspecies. Different cytogenetic techniques were used to analyze the chromosomes of white-bellied rat, Niviventer confucianus from Mt. Tai and jinan, Shandong Province and Ningshan,

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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

Gd-EOB-DTPA-enhanced magnetic resonance imaging for bile duct intraductal papillary mucinous neoplasms

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World Journal of Gastroenterology 2015年第25期21卷 7824-7833页

作者： Shi-hong ying xiao-Dong Teng zhao-Ming wang qi-Dong wang yi-Lei zhao Feng Chen Wen-Bo xiao Department of Radiology The First Affiliated Hospital College of Medicine Zhejiang University Department of Pathology The First Affiliated Hospital College of Medicine Zhejiang University

AIM: To investigate gadolinium-ethoxybenzyldiethylenetriamine-pentaacetic acid(Gd-EOB-DTPA)-enhanced magnetic resonance imaging(MRI) of intraductal papillary mucinous neoplasms of the bile duct(IPMN-B). METHODS: The imaging findings of five cases of IPMN-B which were pathologically confirmed at our hospital between March 2012 and May 2013 were retrospectively analyzed. Three of these cases were diagnosed by duodenal endoscopy and biopsy pathology, and two cases were diagnosed by surgical pathology. All five patients underwent enhanced and non-enhanced computed tomography(CT), magnetic resonance cholangiopancreatography, and Gd-EOB-DTPA-enhanced MRI; one case underwent both Gd-EOB-DTPA-enhanced MRI and positron emission tomography-CT. The clinical data and imaging results for these cases were compared and are ***: Conventional imaging showed diffusedilatation of bile ducts and multiple intraductal polypoid and papillary neoplasms or serrated changes along the bile ducts. In two cases, Gd-EOB-DTPA-enhanced MRI revealed dilated biliary ducts and intraductal tumors, as well as filling defects caused by mucin in the dilated bile ducts in the hepatobiliary phase. GdEOB-DTPA-enhanced MRI in one case clearly showed a low-signal tumor in the hepatobiliary phase, similar to what was seen by positron emission tomographyCT. In two patients, routine inspection was unable to discern whether the lesions were inflammation or tumors. However, Gd-EOB-DTPA-enhanced MRI revealed a pattern of gradual enhancement during the hepatobiliary phase, and the signal intensity of the lesions was lower than the surrounding liver parenchyma, suggesting tissue inflammation in both cases, which were confirmed by surgical pathology. CONCLUSION: Gd-EOB-DTPA-enhanced MRI reveals the intraductal mucin component of IPMN-B in some cases and the extent of tumor infiltration beyond the bile ducts in invasive cases.

关键词： Gadolinium-ethoxybenzyl-diethylenetriaminepentaacetic acid Magnetic resonance imaging Magneticresonance cholangiopancreatography Multidetectorcomputed tomography Bile duct neoplasms

Ice Crystal Growth Mechanism and Structure-activity Relationships of Graphene Oxide/Poly(vinyl alcohol)Aerogels

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Chinese Journal of Polymer Science 2022年第7期40卷 772-780页

作者： xiao-Tian Xi xing-qi Luo Yu Xia Long-Fei yi yi wang Da-Yu Song Yong-Jiao Song jin-Rong Wu Li-Juan zhao College of Chemistry and Materials Science Sichuan Normal UniversityChengdu610068China State Key Laboratory of Polymer Materials Engineering College of Polymer Science and EngineeringSichuan UniversityChengdu610065China

Aerogels are special porous materials with low thermal conductivity,light weight,high energy absorption rate and large surface area,which have been applied in many ***,controlling the aerogel microstructure remains an academic ***,by employing graphene oxide(GO)as the aerogel skeleton and utilizing poly(vinyl alcohol)(PVA)to regulate the ice crystal growth,we elucidate the relationships between the physicochemical properties of GO/PVA aerogel precursors and the nucleation and growth of ice crystals by using an ice-templating *** demonstrate that due to the hydrogen bond formed between PVA and water molecules,resulting in the initial crystallization temperature being reduced from-12.60℃(GO/PVA-0.01)to-16.21℃(GO/PVA-0.1).Meanwhile,the strong hydrogen bond between PVA and GO limits the diffusion of water molecules,thereby inhibiting the growth of ice crystals,decreasing the pore size of the GO/PVA aerogel from 9.96 nm(GO/PVA-0.01)to 7.19 nm(GO/PVA-0.3),and thus the compressive strength of the aerogel increases from 0.045 MPa to ***,the finding of this study can be extended to other aerogel precursors,and exhibit important scientific value and practical significance for the preparation of aerogel materials with highly controllable structures and performances.

关键词： Aerogel GO/PVA Ice crystal growth Structure-activity relationships

Heterogeneity and Secondary Structure Analysis of 3' Untranslated Region in Classical Swine Fever Viruses

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Agricultural Sciences in China 2011年第1期10卷 142-148页

作者： fan Yun-feng zhao qi-zu zhao Yun ZOU xing-qi ZHANG Zhong-qiu wang qin NING yi-bao China Institute of Veterinary Drug Control Beijing 100081 P R.China China Animal Disease Control Center Beijing 100125 P.R.China

The attenuated vaccine strains of CSFV have a 12-nucleotides （nt） insertion in the 3＇-UTR of genome as compared to that of CSFV virulent strains. In this study, we found a distinct heterogeneity in the 3＇-UTR of attenuated Thiverval and HCLV strains. The longest 3＇-UTR of Thiverval strain was 259 base pairs （bp） with a 32-nt insertion, the shortest 3＇-UTR had only 233 bp with a 6-nt insertion. The longest 3＇-UTR of HCLV strain was 244 bp with a 17-nt insertion and the shortest 3＇ UTR was 235 bp with a 8-nt insertion. Compared with the published sequences of 3＇-UTR of vaccine and virulent strains, the 3＇-UTR of CSFV vaccine strains have two variable regions where insertion among the different vaccine strains were frequently found. The first is located between the second conservative TALk codon and the start of T-rich region where we found the variable length insertion in the same vaccine strain Thiveral or HCLV and the second is located between the end of T-rich region and the front of GAA eodon, however, a 4-nt deletion was found in this region in the virulent Shimen strain. These two regions may represent the ＂hot spot＂ for mutation. Modeling the secondary structures of the 3＇-UTR suggests that the T-rich insertion could result in the change of structure and free energy, thus affecting the stability of the 3＇-UTR structure. These findings will help to understand the mechanism of attenuated vaccines and improve vaccine safety, stability, and efficacy.

关键词： classical swine fever virus 3'-UTR heterogeneity RNA secondary structure

Single Zn atoms anchored on hollow carbon nanofiber network for dendrite-free lithium metal anode of flexible Li–S full cell

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Rare Metals 2023年第11期42卷 3705-3717页

作者： Zhi-Feng wang hong-ying wang xiao-Li Liu Yan-Xu Chen Yan zhao Yong-Guang Zhang qi-qi Han Chun-Ling qin Zhumabay Bakenov yi-Chao wang Xin wang School of Materials Science and Engineering Hebei University of TechnologyTianjin300401China School of Materials Science and Engineering Hebei University of Science and TechnologyShijiazhuang050018China South China Academy of Advanced Optoelectronics and International Academy of Optoelectronics at zhaoqing South China Normal UniversityGuangzhou510006China Shanxi Supercomputing Center Lvliang033000China Department of Chemical and Materials Engineering National Laboratory AstanaNazarbayev University010000Nur-SultanKazakhstan School of Life and Environmental Sciences Deakin UniversityWaurn PondsGeelongVIC3216Australia

The attractive energy density of lithium-sulfur(Li-S)batteries makes them desirable energy storage systems;however,the slow reaction kinetics and formation of lithium dendrites prevent them from reaching full *** address this issue,hierarchical porous carbon nanofibers network containing Zn single atoms(ZnSA@HPCNF)is synthesized by electrospinning and *** structure serves as the main anode body,providing excellent chemical anchoring and *** uniform distribution of Zn single atoms and N4coordination supports uniform deposition and continuous plating/stripping of *** results show that the Li|Li/ZnSA@HPCNF symmetrical battery presents stable and low overpotential during 700-and 900-h iterative plating/stripping process at1 and 5 mA·cm^(-2),***,the S/CNT||Li/ZnSA@HPCNF full cell shows good flexibility,reversible capacity and cycling *** work provides a lithium host strategy based on single-atom dispersed hierarchical porous carbon network,enabling the design of rational lithium metal anodes for use in flexible Li-S full cells.

关键词： Single atom Lithium metal anode Lithium deposition Lithium-sulfur battery

Direct preparation of semi-solid billets by the semi-solid isothermal heat treatment for commercial cold-rolled ZL104 aluminum alloy

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International Journal of Minerals,Metallurgy and Materials 2021年第7期28卷 1164-1173页

作者： Yong-fei wang yi Guo Sheng-dun zhao xiao-guang fan School of Mechanical Engineering Xi’an Jiaotong UniversityXi’an 710049China State Key Laboratory of Fluid Power and Mechatronic Systems Zhejiang UniversityHangzhou310027China School of Energy and Power Engineering Xi’an Jiaotong UniversityXi’an 710049China State Key Laboratory of Solidification Processing Northwestern Polytechnical UniversityXi’an 710072China

Semi-solid isothermal heat treatment was proposed to directly process cold-rolled ZL104 aluminum alloys and obtain semi-solid *** effects of two process parameters,namely,temperature and processing time,on the microstructure and hardness of the resulting bil-lets were also experimentally *** grain size(AGS)increased and the shape factor(SF)of the grain improved as the process temperature *** SF of the grain also increased with increasing processing time,and the AGS was augmented when the processing time was prolonged from 5 to 20 min at 570℃.The hardness of the aluminum alloy decreased because of the increase in AGS with increasing temperature and processing *** optimal temperature and time for the preparation of semi-solid ZL104 aluminum alloys were 570℃and 5 min,*** optimal process parameters,the AGS,SF,and hardness of the resulting alloy were 35.88μm,0.81,and 55.24 MPa,*** Lifshitz-Slyozov-Wagner relationship was analyzed to determine the coarsening rate constant at 570℃,and a rate constant of 1357.2μm3/s was obtained.

关键词： semi-solid aluminum alloy microstructure hardness semi-solid isothermal heat treatment

Understanding systemic risk induced by climate change

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Advances in Climate Change Research 2021年第3期12卷 384-394页

作者： LI Hui-Min wang Xue-Chun zhao xiao-fan qi Ye Beijing Climate Change Response Research and Education Center Beijing University of Civil Engineering and ArchitectureBeijing100044China School of Public Policy and Management Tsinghua UniversityBeijing100084China Division of Public Policy The Hong Kong University of Science and TechnologyHong KongChina Institute for Public Policy The Hong Kong University of Science and Technology(Guangzhou)GuangzhouChina

The systemic risk induced by climate change represents one of the most prominent threats facing humanity and has attracted increasing attention since the outbreak of the COVID-19 pandemic at the end of *** existing literature highlights the importance of systemic risk induced by climate change,but there are still deficiencies in understanding its dynamics and assessing the *** to bridge this gap,this study develops a theoretical framework and employs two cases to illustrate the concept,origin,occurrence,propagation,evolution,and assessment framework of systemic risk induced by climate *** key findings include:1)systemic risk induced by climate change derives from the rapid growth of greenhouse gas,emissions,increasingly complex connections among different socioeconomic systems,and continuous changes in exposure and vulnerability;2)systemic risk induced by climate change is a holistic risk generated by the interconnection,interaction,and dynamic evolution of different types of single risks,and its fundamental,defining feature is cascading *** extent of risk propagation and its duration depend on the characteristics of the various discrete risks that are connected to make up the systemic risk;3)impact domains,severity of impact,and probability of occurrences are three core indicators in systemic risk assessment,and the impact domains should include the economy,society,homeland security,human health,and living *** propose to deepen systemic risk research from three aspects:to develop theories to understand the mechanism of systemic risk;to conduct empirical research to assess future risks;and to develop countermeasures to mitigate the risk.

关键词： Systemic risk Climate change Disaster Risk assessment

Characterization of vortex structures with self-excited oscillations based on Liutex-Omega vortex identification method

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Journal of Hydrodynamics 2023年第1期35卷 95-111页

作者： Dong-dong wang zhao-hui wang yi-wei fan xiao Sun Quan-jie Gao Key Laboratory of Metallurgical Equipment and Control Technology of Ministry of Education Wuhan University of Science and TechnologyWuhan430081China Hubei Key Laboratory of Mechanical Transmission and Manufacturing Engineering Wuhan University of Science and TechnologyWuhan430081China

The self-excited oscillation effect produces a continuous periodic pulsation without an external excitation *** is widely used in fluid heat and mass transfer,cavitation and resistance reduction,and other related *** self-excited oscillation effect is significantly influenced by the vortex structure created by the jet passing through the specially designed *** flow field in a self-excited oscillation cavity is simulated in this paper using the large eddy simulation(LES)*** Liutex-Omega([Math Processing Error])method is used to analyze the vortex structure’s evolution inside the cavity and is contrasted with the Q-criterion,the λ_(2)-criterion,and the Omega(Ω)*** studies indicate that the[Math Processing Error]method is less sensitive to threshold selection compared with other methods,while it is more capable of identifying weak *** change in cavity vortex structure can be devided into the four stages of vortex ring priming,growth and development,wall touch separation,and *** turbulent energy generated by shear effect can promote the growth and development of the vortex ring structure and has an important influence on the formation of the vortex ring *** vortex strength reveals the interaction mechanism between the shear effect and vortex *** vortex core area illustrates that the small-scale vortices are mainly distributed inside the collision walls of the cavity and the downstream flow *** Liutex-omega method has unique advantages in analyzing the cavity flow field and revealing the mechanism of self-excited oscillations.

关键词： Vortex identification Liutex-Omega([Math Processing Error]) self-excited oscillation large eddy simulation(LES)

Accuracy of segmented measurement of axial length in ultra-high myopia filled with silicone oil using immersion B-scan ultrasonography

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International Journal of Ophthalmology(English edition) 2022年第5期15卷 793-799页

作者： qing-Hua Yang hong-Tao Zhang xiao-qi Li Bing Chen zhao-Hui Li yi-Fei Huang Xin jin ying Zhang Li-qiang wang Senior Department of Ophthalmology the Third Medical Center of PLA General HospitalBeijingChina

AIM:To evaluate the accuracy of segmented measurement of axial length(AL)in high myopia filled with silicone oil by immersion B-scan ultrasonography(immersion B-scan).METHODS:From June 2016 to June 2020,a total of 67 ultra-high myopia inpatients(67 eyes)who underwent silicone oil removal combined with cataract extraction and intraocular lens(IOL)implantation were retrospectively *** preoperative axial length(AL)of 31 patients with severe cataract were segmented measured using immersion B-scan(B-scan group)and another 36 patients with mild or moderate cataract were measured using IOLMaster 500(IOLMaster group).The post-operative ALs in two groups were both measured using IOLMaster *** IOL power was calculated with Haigis *** differences in ALs between pre-and post-surgery,as well as the postoperative refractive spherical equivalent,absolute refractive error,the prediction deviation of postoperative refraction and best corrected visual acuity(BCVA)were ***:The pre-and post-operative ALs were 30.46±1.63 mm(range 28.09-33.51 mm)and 30.42±1.70 mm(range 28.03-33.90 mm)in B-scan group(t=0.644,P=0.542)and 30.51±1.21 mm(range 28.03-33.90 mm)and 30.43±1.27 mm(range 28.54-33.50 mm)in IOLMaster group(t=1.843,P=0.074),*** months after surgery,BCVA were 0.45±0.13(range 0.3-0.9)and 0.44±0.20(range 0.2-1.0)in B-scan and IOLMaster group respectively(t=0.086,P=0.932).There was no significant difference of the postoperative spherical equivalent(-3.11±0.65 D vs-3.21±0.51 D,t=0.671,P=0.505)and the absolute refractive error(0.589±0.340 vs 0.470±0.245 D,t=1.615,P=0.112)between two *** B-scan group,absolute refractive error within±0.50 D was found in 18 eyes(58.1%),within±1.00 D in 26 eyes(83.9%),and within±1.50 D in 31 eyes(100%).In IOLMaster group,absolute refractive error within±0.50 D was found in 23 eyes(63.9%),within±1.00 D in 34 eyes(94.4%),and within±1.50 D in 36 eyes(Z=0.757,P=0.449).CONCLUSION:The segmented measurement of ALs

关键词： high myopia axial length immersion B-ultrasound IOLMaster silicone oil cataract