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Prediction of cell-cell communication patierns of dorsal root ganglion cells: single-cell RNA sequencing data analysis

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Neural Regeneration Research 2024年第6期19卷 1367-1374页

作者： Yanna Lian Cheng Wu Li Liu Xiangyao Li National Health Commission and Chinese Academy of Medical Sciences Key Laboratory of Medical Neurobiology Ministry of Education Frontier Science Center for Brain Research and Brain-Machine Integration School of Brain Science and Brain Medicine Zhejiang University International institutes of Medicine the Fourth Affiliated Hospital of Zhejiang University School of Medicine zhejiang university-university of edinburgh institute Zhejiang University School of Medicine Zhejiang University 4. Biomedical Sciences College of Medicine and Veterinary Medicine The University of Edinburgh Core Facilities of the School of Medicine Zhejiang University

Dorsal root ganglion neurons transmit peripheral somatic information to the central nervous system, and dorsal root ganglion neuron excitability affects pain perception. Dorsal root ganglion stimulation is a new approach for managing pain sensation. Knowledge of the cell-cell communication among dorsal root ganglion cells may help in the development of new pain and itch management strategies. Here, we used the single-cell RNA-sequencing(scRNA-seq) database to investigate intercellular communication networks among dorsal root ganglion cells. We collected scRNA-seq data from six samples from three studies, yielding data on a total of 17,766 cells. Based on genetic profiles, we identified satellite glial cells, Schwann cells, neurons, vascular endothelial cells, immune cells, fibroblasts, and vascular smooth muscle cells. Further analysis revealed that eight types of dorsal root ganglion neurons mediated proprioceptive, itch, touch, mechanical, heat, and cold sensations. Moreover, we predicted several distinct forms of intercellular communication among dorsal root ganglion cells, including cell-cell contact, secreted signals, extracellular matrix, and neurotransmitter-mediated signals. The data mining predicted that Mrgpra3-positive neurons robustly express the genes encoding the adenosine Adora2b(A2B) receptor and glial cell line-derived neurotrophic factor family receptor alpha 1(GFRα-1). Our immunohistochemistry results confirmed the coexpression of the A2B receptor and GFRα-1. Intrathecal injection of the A2B receptor antagonist PSB-603 effectively prevented histamine-induced scratching behaviour in a dose-dependent manner. Our results demonstrate the involvement of the A2B receptor in the modulation of itch sensation. Furthermore, our findings provide insight into dorsal root ganglion cell-cell communication patterns and mechanisms. Our results should contribute to the development of new strategies for the regulation of dorsal root ganglion excitability.

关键词： cell-cell communications CellChat dorsal root ganglion scRNA-Seq database

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Relation of tea ingestion to salivary redox and flow rate in healthy subjects

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Food Science and Human Wellness 2023年第6期12卷 2336-2343页

作者： Pik Han Chong Qiaojuan He Suyun Zhang Jianwu Zhou Pingfan Rao Min Zhang Lijing Ke zhejiang Gongshang university joint Centre for Food and Nutrition Sciences Zhejiang Gongshang UniversityHangzhou 310018China institute of Food Science Jishou UniversityJishou 416000China

The biochemistry of human saliva can be altered by food intake.The benefits of tea drinking were extensively studied but the influence of tea ingestion on human saliva has not been revealed.The work aimed to investigate the immediate and delayed effect of vine tea,oolong tea and black tea intake on certain salivary biochemistry and flow rate.The saliva samples of healthy subjects were collected before,after and 30 min after tea ingestion.The chemical compositions and antioxidant capacity of tea samples were analyzed to correlate with salivary parameters.Principal component analysis indicated that the effects of vine tea consumption were dominated by increasing salivary flow rate(SFR),production rate of total protein(TPC),thiol(SH),malondialdehyde,catalase activity and antioxidant capacity(FRAP)in saliva.The antioxidant profile of studied tea samples(FRAP,polyphenols,flavonoids)was positively correlated with salivary SFR,TPC,SH and FRAP but negatively correlated with salivary uric acid concentration in saliva.

关键词： Black tea Flow rate Oolong tea Salivary redox status Vine tea

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Visual knowledge guided intelligent generation of Chinese seal carving

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Frontiers of Information Technology & Electronic Engineering 2022年第10期23卷 1479-1493页

作者： Kejun ZHANG Rui ZHANG Yehang YIN Yifei LI Wenqi WU Lingyun SUN Fei WU Huanghuang DENG Yunhe PAN College of Computer Science and Technology Zhejiang UniversityHangzhou 310027China Alibaba-zhejiang university joint institute of Frontier Technologies Hangzhou 310027China School of Software Technology Zhejiang UniversityHangzhou 310027China

We digitally reproduce the process of resource collaboration,design creation,and visual presentation of Chinese seal-carving art.We develop an intelligent seal-carving art-generation system(zhejiang university Intelligent Seal-Carving System,http://***/seal/;the website of the seal-carving search and layout system is http://***/seal/search_app/)to deal with the difficulty in using a visual knowledge guided computational art approach.The knowledge base in this study is the Qiushi Seal-Carving Database,which consists of open datasets of images of seal characters and seal stamps.We propose a seal character generation method based on visual knowledge,guided by the database and expertise.Furthermore,to create the layout of the seal,we propose a deformation algorithm to adjust the seal characters and calculate layout parameters from the database and knowledge to achieve an intelligent structure.Experimental results show that this method and system can effectively deal with the difficulties in the generation of seal carving.Our work provides theoretical and applied references for the rebirth and innovation of seal-carving art.

关键词： Seal-carving Intelligent generation Deep learning Parametric modeling Computational art

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Iron metabolism,ferroptosis,and lncRNA in cancer: knowns and unknowns

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Journal of zhejiang university-Science B(Biomedicine & Biotechnology) 2022年第10期23卷 844-862页

作者： Lei QU Xinyu HE Qian TANG Xiao FAN Jian LIU Aifu LIN MOE Laboratory of Biosystem Homeostasis and Protection College of Life SciencesZhejiang UniversityHangzhou 310058China Cancer Center Zhejiang UniversityHangzhou 310058China Key Laboratory for Cell and Gene Engineering of zhejiang Province Hangzhou 310058China zhejiang university-university of edinburgh institute(ZJU-UoE institute) Zhejiang University School of MedicineZhejiang UniversityHaining 314400China Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of zhejiang Province Affiliated Hangzhou First People’s HospitalCancer CenterZhejiang University School of MedicineHangzhou 310006China College of Medicine and Veterinary Medicine the University of EdinburghEdinburgh EH164SBUK Biomedical and Health Translational Research Center of zhejiang Province Haining 314400China Breast Center of the First Affiliated Hospital Zhejiang University School of MedicineHangzhou 310003China International School of Medicine International Institutes of Medicinethe Fourth Affiliated HospitalZhejiang University School of MedicineYiwu 322000China ZJU-QILU joint Research institute Hangzhou 310058China

Cancer cells undergo substantial metabolic alterations to sustain increased energy supply and uncontrolled proliferation.As an essential trace element,iron is vital for many biological processes.Evidence has revealed that cancer cells deploy various mechanisms to elevate the cellular iron concentration to accelerate proliferation.Ferroptosis,a form of cell death caused by iron-catalyzed excessive peroxidation of polyunsaturated fatty acids(PUFAs),is a promising therapeutic target for therapyresistant cancers.Previous studies have reported that long noncoding RNA(lncRNA)is a group of critical regulators involved in modulating cell metabolism,proliferation,apoptosis,and ferroptosis.In this review,we summarize the associations among iron metabolism,ferroptosis,and ferroptosis-related lncRNA in tumorigenesis.This information will help deepen understanding of the role of lncRNA in iron metabolism and raise the possibility of targeting lncRNA and ferroptosis in cancer combination therapy.

关键词： Iron metabolism Ferroptosis Long noncoding RNA(lncRNA) Tumorigenesis

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UI layers merger: merging UI layers via visual learning and boundary prior

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Frontiers of Information Technology & Electronic Engineering 2023年第3期24卷 373-387页

作者： Yunnong CHEN Yankun ZHEN Chuning SHI Jiazhi LI Liuqing CHEN Zejian LI Lingyun SUN Tingting ZHOU Yanfang CHANG School of Software Technology Zhejiang UniversityHangzhou 310027China College of Computer Science and Technology Zhejiang UniversityHangzhou 310027China Alibaba-zhejiang university joint Research institute of Frontier Technologies Hangzhou 310027China Alibaba Group Hangzhou 311121China zhejiang-Singapore Innovation and AI joint Research Lab Hangzhou 310027China

With the fast-growing graphical user interface(GUI)development workload in the Internet industry,some work attempted to generate maintainable front-end code from GUI screenshots.It can be more suitable for using user interface(UI)design drafts that contain UI metadata.However,fragmented layers inevitably appear in the UI design drafts,which greatly reduces the quality of the generated code.None of the existing automated GUI techniques detects and merges the fragmented layers to improve the accessibility of generated code.In this paper,we propose UI layers merger(UILM),a vision-based method that can automatically detect and merge fragmented layers into UI components.Our UILM contains the merging area detector(MAD)and a layer merging algorithm.The MAD incorporates the boundary prior knowledge to accurately detect the boundaries of UI components.Then,the layer merging algorithm can search for the associated layers within the components’boundaries and merge them into a whole.We present a dynamic data augmentation approach to boost the performance of MAD.We also construct a large-scale UI dataset for training the MAD and testing the performance of UILM.Experimental results show that the proposed method outperforms the best baseline regarding merging area detection and achieves decent layer merging accuracy.A user study on a real application also confirms the effectiveness of our UILM.

关键词： User interface(UI)to code UI design lint UI layer merging Object detection

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Relation between Airy beams and triple-cusp beams

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Chinese Physics B 2014年第8期23卷 333-339页

作者：任志君李晓东金洪震陈晨吴疆苗 institute of Information Optics Zhejiang Normal University joint Research Laboratory of Optics of zhejiang Normal university and zhejiang university

Airy beams and triple-cusp beams are two kinds of accelerating beams. The propagation characteristics and internal topological structures of accelerating Airy beams are well understood because of the developed mathematical theory about Airy function. However, limited information is available about the optical characteristics of accelerating triple-cusp beams. In this work, the relationship between Airy beams and triple-cusp beams is examined theoretically and experimentally. Results reveal some important optical characteristics of triple-cusp beams based on the optical characteristics of Airy beams. These findings are expected to provide a foundation for future applications of triple-cusp beams.

关键词： Airy beams triple-cusp beams beam characteristics

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Hetero-trans-β-Glucanase Produces Cellulose-Xyloglucan Covalent Bonds in the Cell Walls of Structural Plant Tissues and Is Stimulated by Expansin

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Molecular Plant 2020年第7期13卷 1047-1062页

作者： Klaus Herburger Lenka Frankova Martina Picmanova Jia Wooi Loh Marcos Valenzuela-Ortega Frank Meulewaeter Andrew D.Hudson Christopher E.French Stephen C.Fry The edinburgh Cell Wall Group Institute of Molecular Plant SciencesSchool of Biological SciencesThe University of EdinburghEdinburgh EH93BFUnited Kingdom institute of Quantitative Biology Biochemistry and BiotechnologySchool of Biological SciencesThe University of EdinburghEdinburgh EH93BFUnited Kingdom BASF BBCC Innovation Center Gent-Trait Research9052 Gent(Zwijnaarde)Belgium zhejiang university-university of edinburgh joint Research Centre for Engineering Biology Zhejiang UniversityHainingZhejiang 314400China Present address:Section for Plant Glycobiology Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg 1871Denmark

Current cell-wall models assume no covalent bonding between cellulose and hemicelluloses such as xyloglu-can or mixed-linkageβ-D-glucan(MLG).However,Equisetum hetero-trans-β-glucanase(HTG)grafts cellu-lose onto xyloglucan oligosaccharides(XGOs)-and,we now show,xyloglucan polysaccharide-in vitro,thus exhibiting CXE(cellulose:xyloglucan endotransglucosylase)activity.In addition,HTG also catalyzes MLG-to-XGO bonding(MXE activity).In this study,we explored the CXE action of HTG in native plant cell walls and tested whether expansin exposes cellulose to HTG by disrupting hydrogen bonds.To quantify and visu-alize CXE and MXE action,we assayed the sequential release of HTG products from cell walls pre-labeled with substrate mimics.We demonstrated covalent cellulose--xyloglucan bonding in plant cell walls and showed that CXE and MXE action was up to 15%and 60%of total transglucanase action,respectively,and peaked in aging,strengthening tissues:CXE in xylem and cells bordering intercellular canals and MXE in scleren-chyma.Recombinant bacterial expansin(EXLX1)strongly augmented CXE activity in vitro.CXE and MXE ac-tion in living Equisetum structural tissues potentially strengthens stems,while expansin might augment the HTG-catalyzed CXE reaction,thereby allowing efficient CXE action in muro.Our methods will enable surveys for comparable reactions throughout the plant kingdom.Furthermore,engineering similar hetero-polymer formation into angiosperm crop plants may improve certain agronomic traits such as lodging tolerance.

关键词： cell wall cellulose hemicelluloses hetero-trans-p-glucanase hetero-transglycosylation xyloglucan

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Unsupervised feature selection via joint local learning and group sparse regression

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Frontiers of Information Technology & Electronic Engineering 2019年第4期20卷 538-553页

作者： Yue WU Can WANG Yue-qing ZHANG Jia-jun BU zhejiang Provincial Key Laboratory of Service Robot College of Computer Science and Technology Zhejiang University Alibaba-zhejiang university joint institute of Frontier Technologies

Feature selection has attracted a great deal of interest over the past decades. By selecting meaningful feature subsets, the performance of learning algorithms can be effectively improved. Because label information is expensive to obtain, unsupervised feature selection methods are more widely used than the supervised ones. The key to unsupervised feature selection is to find features that effectively reflect the underlying data distribution. However,due to the inevitable redundancies and noise in a dataset, the intrinsic data distribution is not best revealed when using all features. To address this issue, we propose a novel unsupervised feature selection algorithm via joint local learning and group sparse regression(JLLGSR). JLLGSR incorporates local learning based clustering with group sparsity regularized regression in a single formulation, and seeks features that respect both the manifold structure and group sparse structure in the data space. An iterative optimization method is developed in which the weights finally converge on the important features and the selected features are able to improve the clustering results. Experiments on multiple real-world datasets(images, voices, and web pages) demonstrate the effectiveness of JLLGSR.

关键词： Unsupervised Local learning Group sparse regression Feature selection

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Non-linear Radical Additions-Coupling Polymerization of Monovinyl Monomers towards Polymer Networks: Theory, Tunability and Heritable Architecture

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Chinese Journal of Polymer Science 2022年第12期40卷 1623-1630,I0008页

作者： Li-Mei Ren Cheng-Lin Li Qi Wang MOE Key Laboratory of Macromolecular Synthesis and Functionalization Department of Polymer Science&Engineering Zhejiang UniversityHangzhou 310027China Current address:zhejiang university-university of edinburgh institute Zhejiang University School of Medicineand Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou 310027China

Exploring new polymerization strategy for current available monomers is a big challenge in polymer science. Here we re-investigate radical polymerization of monovinyl monomer(MVM) initiated by uniform branched polyfunctional initiator(PFI), which is termed non-linear radical additions-coupling polymerization(NLRAs CP). In NLRAs CP, both addition and coupling reactions of radical contribute to the construction of the polymer chains, which leads to continuous growth of branch topology. Theoretical analysis of NLRAs CP predicts that the gelation is determined by the functionality of PFI(a), the extent of initiation of the PFI(q) and the termination factor of radical(φ). NLRAs CPs of styrene and methyl methacrylate promoted by Cu(0)/MeTREN or Mn_(2)(CO)_(10)/visible light were conducted. After the cleavage of incorporated PFI fragment or junctions in the network, the network was transformed to linear chains having almost the same structure as segmental chains in the precursor network. This allows the reverse deducing the network structure from its cleaved products. It has been proven that NLRAs CP includes stepwise initiation of PFI, chain-growth of segmental chains and successive endlinking of macroradicals derived from PFI. The three parameters related to the gelation process, a, q and φ, were adjusted via binary PFI, the feed ratio of [Mn_(2)(CO)_(10)]/[PFI] and addition of non-homopolymerizable comonomer respectively. The minimum values of a and q, and the minimum amount of comonomer required for gelation were determined,which can be applied to estimate φ of various macroradicals. NLRAs CP opens a general and facile strategy for synthesis of a variety of polymer networks with heritable architecture by one-pot polymerization of various MVMs.

关键词： Non-linear radical additions-coupling polymerization Monovinyl monomer Polyfunctional initiator Polymer network Theory

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A rapid method for extraction,purification and structure analysis of chondroitin sulfate from six marine tissues

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Food Quality and Safety 2023年第1期7卷 20-29页

作者： Yuying Wang Shokouh Ahmadi Chengxiao Yu Laiming Zhang Xinxin Hu Xingqian Ye Shiguo Chen College of Biosystems Engineering and Food Science National-Local Joint Engineering Laboratory of Intelligent Food Technology and EquipmentZhejiang Key Laboratory for Agro-Food ProcessingZhejiang Engineering Laboratory of Food Technology and EquipmentZhejiang UniversityHangzhouChina zhejiang university Zhongyuan institute ZhengzhouChina Shandong(Linyi)institute of Modern Agriculture Zhejiang UniversityLinliChina Fuli institute of Food Science Zhejiang UniversityHangzhouChina Ningbo Research institute Zhejiang UniversityHangzhouChina

This study was designed to establish a strategy for the extraction,purification,and structure analysis of chondroitin sulfate(cs)in milligram amounts.Crude acidic polysaccharides were extracted from six kinds of marine animals by enzymatic hydrolysis and hexadecylpyridinium chloride precipitation and purified by Q Sepharose Fast Flow strong anion exchange column.The purification of each crude polysaccharide was completed within 1 h.The structure of the polysaccharides,i.***.their chemical characterization,functional group,molecular weight and monosaccharide composition,were analyzed by colorimetry,nuclear magnetic resonace and high-performance liquid chromatogrpahy,respectively.All polysaccharides were identified as Cs.The oligosaccharide profile produced by enzyme hydrolysis of polysaccharides was determined by strong anion-exchange high-performance liquid chromatorgraphy.This method can be widely applied to the extraction and characterization of chondroitin sulfate from unknown raw materials,screening high-quality sources of functional polysaccharides,and laying a good foundation for thefollowing studyof the structure-function relationshipof polysaccharides.

关键词： Chondroitin sulfate marinepolysaccharide disaccharide analysis

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