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Dear-DIA^(XMBD): Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics

Research 2024年第1期6卷 707-720页

作者： Qingzu He Chuan-Qi Zhong Xiang Li Huan Guo Yiming Li Mingxuan Gao Rongshan Yu Xianming Liu Fangfei Zhang Donghui Guo Fangfu Ye Tiannan Guo Jianwei Shuai Jiahuai Han Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials ResearchXiamen UniversityXiamen 361005China oujiang laboratory(zhejiang Lab for regenerative medicine Vision and Brain Health)and Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang 325001China School of Life Sciences Xiamen UniversityXiamen 361102China State Key laboratory of Cellular Stress Biology Innovation Center for Cell Signaling NetworkXiamen 361102China Department of Computer Science Xiamen UniversityXiamen 361005China National Institute for Data Science in Health and medicine School of MedicineXiamen UniversityXiamen 361102China Bruker(Beijing)Scientific Technology Co.Ltd. BeijingChina Westlake laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake University18 Shilongshan RoadHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced Study18 Shilongshan RoadHangzhou 310024China Westlake Omics Ltd. Yunmeng Road 1HangzhouChina Department of Electronic Engineering Xiamen UniversityXiamen 361005China

Data-independent acquisition(DIA)technology for protein identification from mass spectrometry and related algorithms is developing *** spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising *** this paper,we proposed an untargeted analysis method,Dear-DIA^(XMBD),for direct analysis of DIA ***-DIA^(XMBD) first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms,then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes,and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and *** show that Dear-DIA^(XMBD) performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms.

关键词： Deep Auto Independent

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Generic Interpretable Reaction Condition Predictions with Open Reaction Condition Datasets and Unsupervised Learning of Reaction Center

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Research 2024年第2期2023卷 773-794页

作者： Xiaorui Wang Chang-Yu Hsieh Xiaodan Yin Jike Wang Yuquan Li Yafeng Deng Dejun Jiang Zhenxing Wu Hongyan Du Hongming Chen Yun Li Huanxiang Liu Yuwei Wang Pei Luo Tingjun Hou Xiaojun Yao Dr.Neher's Biophysics laboratory for lnnovative Drug Discovery State Key Laboratory of Quality Research in Chinese MedicineMacao Institute for Applied Research in Medicine and HealthMacao University of Science and TechnologyMacao999078China innovation Institute for Artificial Intelligence in medicine of zhejiang University College of Pharmaceutical SciencesZhejiang UniversityHangzhou310058China Faculty of Applied Sciences Macao Polytechnic UniversityMacao999078China College of Chemistry and Chemical Engineering Lanzhou UniversityLanzhou730000China Carbon Silicon AI Technology Co. LtdHangzhouZhejiang 310018China Center of Chemistry and Chemical Biology Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhou 510530China College of Pharmacy Shaanxi University of Chinese MedicineXianyangShaanxi712044China

Effective synthesis planning powered by deep learning(DL)can significantly accelerate the discovery of new drugs and ***,most DL-assisted synthesis planning methods offer either none or very limited capability to recommend suitable reaction conditions(RCs)for their reaction ***,the prediction of RCs with a DL framework is hindered by several factors,including:(a)lack of a standardized dataset for benchmarking,(b)lack of a general prediction model with powerful representation,and(c)lack of *** address these issues,we first created 2 standardized RC datasets covering a broad range of reaction classes and then proposed a powerful and interpretable Transformer-based RC predictor named *** careful design of the model architecture,pretraining method,and training strategy,Parrot improved the overall top-3 prediction accuracy on catalysis,solvents,and other reagents by as much as 13.44%,compared to the best previous model on a newly curated ***,the mean absolute error of the predicted temperatures was reduced by about 4℃.Furthermore,Parrot manifests strong generalization capacity with superior cross-chemical-space prediction *** analysis indicates that Parrot effectively captures crucial chemical information and exhibits a high level of interpretability in the prediction of *** proposed model Parrot exemplifies how modern neural network architecture when appropriately pretrained can be versatile in making reliable,generalizable,and interpretable recommendation for RCs even when the underlying training dataset may still be limited in diversity.

关键词： versatile absolute generalization

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Generation and characterization of nanobodies targeting GPCR

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Biophysics Reports 2024年第1期10卷 22-30页

作者： Shenglan Zhang Zhiran Fan Jianfeng Liu Bioland laboratory (Guangzhou regenerative medicine and Health Guangdong laboratory) Cellular Signaling laboratory International Research Center for Sensory Biology and Technology of MOST Key Laboratory of Molecular Biophysics of MOE College of Life Science and Technology Huazhong University of Science and Technology

G protein-coupled receptors(GPCRs) are a large family of cell membrane proteins that are important targets for drug discovery. Nanobodies, also known as VHH(variable domains of heavy chain-only antibodies, HcAbs) antibodies, are small antibody fragments derived from camelids that have gained significant attention as potential therapeutics for targeting GPCRs due to their advantages over conventional antibodies. However, there are challenges in developing nanobodies targeting GPCRs, among which epitope accessibility is the most significant because the cell membrane partially shields the GPCR surface. We developed a universal protocol for making nanobodies targeting GPCRs using the cell membrane extract of GPCR-overexpressing HEK293 cells as the llama/alpaca immunization antigen. We constructed an immune VHH library and identified nanobodies by phage display bio-panning. The monoclonal nanobodies were recombinantly expressed in Escherichia coli(E. coli) and purified to characterize their binding potency.

关键词： Nanobody Single domain antibody Heavy chain-only antibody GPCR G protein-coupled receptor

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De novo design of highly efficient type-Ⅰphotosensitizer based onπ-conjugated oligomer for photodynamic eradication of multidrug-resistant bacterial infections

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Chinese Chemical Letters 2024年第3期35卷 389-393页

作者： Qi Zhao Guangchao Qing Jie Yu Ying Liu Jianliang Shen Yang Luo Xingjie Zan Shengliang Li State Key laboratory of Ophthalmology Optometry and Vision ScienceSchool of Ophthalmology and OptometrySchool of Biomedical EngineeringWenzhou Medical UniversityWenzhou InstituteUniversity of Chinese Academy of SciencesOujiang Laboratory(Zhejiang Lab for Regenerative MedicineVision and Brain Health)Wenzhou 325001China College of Pharmaceutical Sciences Soochow UniversitySuzhou 215123China Center of Smart laboratory and Molecular medicine School of MedicineChongqing UniversityChongqing 400044China College of Life Science and laboratory medicine Kunming Medical UniversityKunming 650050China

Traditional photosensitizers show limited singlet oxygen generation in hypoxic infection lesions,which greatly suppress their performance in antibacterial ***,there still is lack of feasible design strategy for developing hypoxia-overcoming photosensitizers ***,radical generation ofπ-conjugated small molecules is efficiently manipulated by an individual selenium(Se)*** this strategy,the first proof-of-concept study of a Se-anchored oligo(thienyl ethynylene)(OT-Se)with high-performance superoxide radical(O_(2)^(·-))and hydroxyl radical(·OH)generation capability is present,and achieves efficient antibacterial activities towards the clinically extracted multidrug-resistant bacteria methicillin-resistant ***(MRSA)and carbapenem-resistant ***(CREC)at sub-micromolar concentration under a low white light irradiation(30 mW/cm^(2)).The water-dispersible OT-Se shows a good bacteria-anchoring capability,biocompatibility,and complete elimination of multidrug-resistant bacteria wound infection in *** work offers a strategy to boost type-I photodynamic therapy(PDT)performance for efficient antibacterial treatments,advancing the development of antibacterial agents.

关键词： Photodynamic therapy Antibacterial Type-Ⅰphotosensitizers Multidrug-resistant bacteria Conjugated oligomers

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Corrigendum to"A novel FGFR1 inhibitor CYY292 suppresses tumor progression,invasion,and metastasis of glioblastoma by inhibiting the Akt/GSK3β/snail signaling axis"[Genes&Diseases 11(2024)479-494]

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Genes & Diseases 2024年第3期11卷 485-490页

作者： Yanran Bi Ruiling Zheng Jiahao Hu Ruiqing Shi Junfeng Shi Yutao Wang Peng Wang Wenyi Jiang Gyudong Kim Zhiguo Liu Xiaokun Li Li Lin School of Pharmaceutical Science Wenzhou Medical UniversityWenzhou 325035China College of Pharmacy and Research Institute of Drug Development Chonnam National UniversityGwangju 61186Republic of Korea Department of Dermatology Wenzhou Hospital of Integrated Traditional Chinese and Western MedicineWenzhou 325000China zhejiang Lab for regenerative medicine Oujiang LaboratoryWenzhou 325035China

The authors regret that in Figure 3C,the Western Blot(WB)image representing GAPDH levels was mistakenly chosen as the same image for ERK(indicated by the red dotted-line rectangle).We have attached the original WB strip for GAPDH to demonstrate that this was an unintentional error in image ***,we noticed that the Transwell images in the two upper panels of the right column in Figure 4J are misleading due to errors in image *** have attached the original data to show that this was also an unintentional *** assure you that these two corrections do not alter the scientificconclusionof thearticle.

关键词： GSK3β invasion metastasis

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FUBP3 mediates the amyloid-β-induced neuronal NLRP3 expression

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Neural Regeneration Research 2025年第7期20卷 2068-2083页

作者： Jing Yao Yuan Li Xi Liu Wenping Liang Yu Li Liyong Wu Zhe Wang Weihong Song The National Clinical Research Center for Geriatric Disease Xuanwu HospitalCapital Medical UniversityBeijingChina Department of Neurology The First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina Department of Neurosurgery Xuanwu HospitalCapital Medical UniversityBeijingChina Department of Pediatrics The Second Affiliated Hospital and Yuying Children’s HospitalKey Laboratory of Alzheimer’s Disease of Zhejiang ProvinceInstitute of AgingWenzhou Medical UniversityWenzhouZhejiang ProvinceChina oujiang laboratory(zhejiang laboratory for regenerative medicine Visionand Brain Health)WenzhouZhejiang ProvinceChina

Alzheimer's disease is characterized by deposition of amyloid-β,which forms extracellular neuritic plaques,and accumulation of hyperphosphorylated tau,which aggregates to form intraneuronal neurofibrillary tangles,in the *** NLRP3 inflammasome may play a role in the transition from amyloid-βdeposition to tau phosphorylation and *** NLRP3 is primarily found in brain microglia,and tau is predominantly located in neurons,it has been suggested that NLRP3 expressed by microglia indirectly triggers tau phosphorylation by upregulating the expression of pro-inflammatory ***,we found that neurons also express NLRP3 in vitro and in vivo,and that neuronal NLRP3 regulates tau *** biochemical methods,we mapped the minimal NLRP3 promoter and identified FUBP3 as a transcription factor regulating NLRP3 expression in *** primary neurons and the neuroblastoma cell line Neuro2A,FUBP3 is required for endogenous NLRP3 expression and tau phosphorylation only when amyloid-βis *** the brains of aged wild-type mice and a mouse model of Alzheimer's disease,FUBP3 expression was markedly increased in cortical *** analysis suggested that FUBP3 plays a role in neuron-mediated immune *** also found that FUBP3 trimmed the 5′end of DNA fragments that it bound,implying that FUBP3 functions in stress-induced *** findings suggest that neuronal NLRP3 may be more directly involved in the amyloid-β-to–phospho-tau transition than microglial NLRP3,and that amyloid-βfundamentally alters the regulatory mechanism of NLRP3 expression in *** that FUBP3 was only expressed at low levels in young wild-type mice and was strongly upregulated in the brains of aged mice and Alzheimer's disease mice,FUBP3 could be a safe therapeutic target for preventing Alzheimer's disease progression.

关键词： 5′end trimming Alzheimer's disease amyloid-beta amyloid-β-dependent transcription FUBP3 inflammasome inflammation neuron NLRP3 tau transcription factor

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Mechanically strong porous bioceramic tubes facilitate large segmental bone defect repair by providing long-term structurally stability and promoting osteogenesis

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Engineered Regeneration 2024年第1期5卷 1-10页

作者： Lijun Xie Jiahao Zhang Hangxiang Sun Zehao Chen Wangsiyuan Teng Xupeng Chai Cong Wang Xianyan Yang Yifan Li Sanzhong Xu Zhongru Gou Zhaoming Ye Department of Orthopedic Surgery the Second Affiliated HospitalZhejiang University School of MedicineHangzhou 310000PR China Orthopedics Research Institute of zhejiang University Hangzhou 310000PR China Key laboratory of Motor System Disease Research and Precision Therapy of zhejiang Province Hangzhou 310000PR China Bio-nanomaterials and regenerative medicine Research Division Zhejiang-California International Nanosystem InstituteZhejiang UniversityHangzhou 310058PR China Department of Orthopedics the First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003PR China

Mechanically strong magnesium-doped Ca-silicate bioceramic scaffolds have many advantages in repairing large segmental bone *** we combine β-TCP with 6 mol%magnesium-doped calcium silicate(Mg6)at three different ratios(TCP,TCP+15%Mg6,TCP+85%Mg6)to find an appropriate ratio which can exert considerable influence on bone *** this study,the bioceramic scaffolds were assessed for mechanical strength,bioactive ion release,biocompatibility,and osteogenic capacity through in vitro ***,the potential for promoting bone regeneration was investigated through in vivo implantation of porous tube-like *** results showed that the compressive strength increased with the augmentation of Mg6 *** the compressive strength of the TCP+85%Mg6 group reached 38.1±3.8 MPa,three times that of the other two ***,extensive in vivo investigations revealed that the TCP+85%Mg6 bioceramic scaffolds were particularly beneficial for the osteogenic capacity of critical-sized femoral defects(20 mm in length).Altogether,magnesium doping in bioceramic implants is a promising strategy to provide stronger mechanical support and enhance osteogenesis to accelerate the repair of large defects.

关键词： Bioceramic tubes Mg-doped calcium silicate Porous structural stability Large segmental bone defects Digital light processing

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Mesenchymal stem cell-derived extracellular vesicles in skin wound healing:roles,opportunities and challenges

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Military Medical Research 2024年第3期11卷 400-429页

作者： Jia-Yi Ding Min-Jiang Chen Ling-Feng Wu Gao-Feng Shu Shi-Ji Fang Zhao-Yu Li Xu-Ran Chu Xiao-Kun Li Zhou-Guang Wang Jian-Song Ji Key laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research Institute of Imaging Diagnosis and Minimally Invasive Intervention Researchthe Fifth Affiliated Hospital of Wenzhou Medical UniversityZhejiangLishui 323000China oujiang laboratory(zhejiang Lab for regenerative medicine Vision and Brain Health)School of Pharmaceutical ScienceWenzhou Medical UniversityWenzhou 325035ZhejiangChina Clinical College of the Affiliated Central Hospital School of MedicineLishui UniversityLishui 323000ZhejiangChina Department of Overseas Education College Jimei UniversityXiamen 361021FujianChina Department of medicine Ⅱ Internal MedicineCardio-Pulmonary Institute(CPI)Universities of Giessen and Marburg Lung Center(UGMLC)Member of the German Center for Lung Research(DZL)Justus-Liebig University Giessen35392 GiessenGermany Pulmonary and Critical Care Department of Medicine VInternal MedicineInfectious Diseases and Infection ControlUniversities of Giessen and Marburg Lung Center(UGMLC)Member of the German Center for Lung Research(DZL)Justus-Liebig University Giessen35392 GiessenGermany

Skin wounds are characterized by injury to the skin due to trauma,tearing,cuts,or *** such injuries are common to all human groups,they may at times represent a serious socioeconomic ***,increasing numbers of studies have focused on the role of mesenchymal stem cell(MSC)-derived extracellular vesicles(EVs)in skin wound *** a cell-free therapy,MSC-derived EVs have shown significant application potential in the field of wound repair as a more stable and safer option than conventional cell *** based on MSC-derived EVs can significantly promote the repair of damaged substructures,including the regeneration of vessels,nerves,and hair *** addition,MSC-derived EVs can inhibit scar formation by affecting angiogenesis-related and antifibrotic pathways in promoting macrophage polarization,wound angiogenesis,cell proliferation,and cell migration,and by inhibiting excessive extracellular matrix ***,these structures can serve as a scaffold for components used in wound repair,and they can be developed into bioengineered EVs to support trauma *** the formulation of standardized culture,isolation,purification,and drug delivery strategies,exploration of the detailed mechanism of EVs will allow them to be used as clinical treatments for wound *** conclusion,MSCderived EV-based therapies have important application prospects in wound *** we provide a comprehensive overview of their current status,application potential,and associated drawbacks.

关键词： Mesenchymal stem cell(MSC) Extracellular vesicles(EVs) Wound repair Engineered nanoparticles

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Brain circuits for retching-like behavior

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National Science Review 2024年第1期11卷 145-160页

作者： Lifang Huo Zhimin Ye Meiling Liu Ziqing He Meizhu Huang Dapeng Li Qian Wu Qian Wang Xiaoqun Wang Peng Cao Ji Dong Congping Shang School of Basic Medical Sciences Guangzhou National Laboratory The Fifth Afflliated Hospital Guangzhou Medical University Bioland laboratory (Guangzhou regenerative medicine and Health Guangdong laboratory) Department of Neurobiology School of Basic Medical Sciences Beijing Key Laboratory of Neural Regeneration and Repair Advanced Innovation Center for Human Brain Protection Capital Medical University State Key laboratory of Cognitive Neuroscience and Learning IDG/McGovern Institute for Brain Research Beijing Normal University Changping Life Science laboratory National Institute of Biological Sciences

Nausea and vomiting are important defensive responses to cope with pathogens and toxins that invade the body. The nucleus of the solitary tract(NTS) is important for initiating these responses. However, the molecular heterogeneities and cellular diversities of the NTS occlude a better understanding of these defensive responses. Here, we constructed the single-nucleus transcriptomic atlas of NTS cells and found multiple populations of NTS neurons that may be involved in these defensive responses. Among these, we identified Calbindin1-positive(Calb1+) NTS neurons that are molecularly distinct from Tac1+*** Calb1+neurons are critical for nausea and retching induced by cereulide; an emetic toxin secreted by Bacillus Cereus. Strikingly, we found that cereulide can directly modulate vagal sensory neurons that innervate Calb1+NTS neurons, a novel mechanism distinct from that for nausea and retching induced by Staphylococcal enterotoxin A. Together, our transcriptomic atlas of NTS neurons and the functional analyses revealed the neural mechanism for cereulide-induced retching-like behavior. These results demonstrate the molecular and cellular complexities in the brain that underlie defensive responses to the diversities of pathogens and toxins.

关键词： vomiting nausea nucleus of the solitary tract Calbindin1 neural circuits

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The cooperative migration dynamics of particles correlates to the nature of hexatic-isotropic phase transition in 2D systems of corner-rounded hexagons

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Fundamental Research 2024年第2期4卷 284-290页

作者： Zhanglin Hou Mingwei Liu Yiwu Zong Fangfu Ye Kun Zhao Wenzhou Institute University of Chinese Academy of SciencesWenzhouZhejiang 325001China Frontiers Science Center for Synthetic Biology and Key laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin 300072China School of Physical Science University of Chinese Academy of SciencesBeijing 100049China Beijing National laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China oujiang laboratory(zhejiang Lab for regenerative medicine Vision and Brain Health)WenzhouZhejiang 325001China Sichuan Provincial People’s Hospital University of Electronic Science and Technology of ChinaChengduSichuan 610054China Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengduSichuan 610054China

In the two-dimensional(2D)melting transition of colloidal systems,the hexatic-isotropic(H-I)transition can be either first-order or ***,how particle dynamics differs at the single-particle level during these two different melting transitions remains to be *** this work,by Brownian dynamics(BD)simulations,we have systematically studied the dynamic behavior of corner-rounded hexagons during the H-I transition,for a range of corner-roundness𝜁=0.40 to 0.99 that covers the crossover from the continuous to first-order nature of H-I *** results show that hexagons with𝜁≤0.5 display a continuous H-I transition,whereas those with𝜁≥0.6 demonstrate a first-order H-I *** analysis shows different evolution pathways of the dominant cluster formed by migrating particles,which results in a droplet-like cluster structure for𝜁=0.40 hexagons and a tree-like cluster structure for𝜁=0.99 *** investigations on the hopping activities of particles suggest a cooperative origin of migrating *** work provides a new aspect to understand the dependence of the nature of H-I transition on the roundness of hexagons through particle dynamic behavior.

关键词： Melting transition Colloids Hexatic phase Cooperative migration Hexagons

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