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Making topological protein links using enzymatic reactions

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National Science Review 2024年第03期11卷 50-51页

作者： Roger Castells-Graells Todd O.Yeates Department of Chemistry and biochemistry University of California UCLA-DOE Institute for Genomics and Proteomics

Proteins are exceedingly complex molecules though, at their heart, they are essentially linear polymers. Pull at their ends and one obtains an extended backbone. While that is true in most cases, some natural proteins... 详细信息

关键词： DESIGN

Defining two subpopulations of marginal zone B cells

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Cellular & Molecular Immunology 2024年第4期21卷 412-413页

作者： Xiaojing Liu Fei-Long Meng Key laboratory of RNA Science and Engineering Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China

Marginal zone(MZ)B cells,which are composed of heterogeneous subpopulations,are participate in the rapid response to *** et *** that MZ B cells can be divided into two distinct subpopulations based on CD80 *** two sub... 详细信息

关键词： expression. subpopulations al.

Revealing Tissue Heterogeneity and Spatial Dark Genes from Spatially Resolved Transcriptomics by Multiview Graph Networks

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Research 2024年第2期6卷 629-645页

作者： Ying Li Yuejing Lu Chen Kang Peiluan Li Luonan Chen School of Mathematics and Statistics Henan University of Science and TechnologyLuoyang471023China Longmen laboratory LuoyangHenan471003China Key laboratory of Systems Biology Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai201100China Key laboratory of Systems Health Science of Zhejang Province Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310000China School of Life Science and Technology ShanghaiTech UniversityShanghai201100.China

Spatially resolved transcriptomics(SRT)is capable of comprehensively characterizing gene expression patterns and providing an unbiased image of spatial *** fully understand the organizational complexity and tumor immune escape mechanism,we propose stMGATF,a multiview graph attention fusion model that integrates gene expression,histological images,spatial location,and gene *** better extract information,stMGATF exploits SimCLRv2 for visual feature exaction and employs edge feature enhanced graph attention networks for the learning potential embedding of each view.A global attention mechanism is used to adaptively integrate 3 views to obtain low-dimensional *** to diverse SRT datasets,stMGATF is robust and outperforms other methods in detecting spatial domains and denoising data even with different resolutions and *** particular,stMGATF contributes to the elucidation of tissue heterogeneity and extraction of 3-dimensional expression ***,considering the associations between genes in tumors,stMGATF can identify the spatial dark genes ignored by traditional methods,which can be used to predict tumor-driving transcription factors and reveal tumor immune escape mechanisms,providing theoretical evidence for the development of new immunotherapeutic strategies.

关键词： Spatial integrate driving

The Role of E3 Ligases in Macrophage-mediated Inflammation

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生物化学与生物物理进展 2024年第9期51卷 2037-2060页

作者： JIN Jia-Bei GE Yi-Dong JIN Xiao-Feng Zhejiang Key laboratory of Pathophysiology Department of Biochemistry and Molecular BiologyHealth Science CenterNingbo UniversityNingbo 315211China

Macrophages,existed in almost all organs of the body,are responsible for detecting tissue injury,pathogens,playing a key role in host defense against a variety of invading pathogens triggering inflammatory *** evidence suggests that macrophage-mediated immune responses are efficiently regulated by the ubiquitination modification,which is responsible for normal immune ***,numerous studies indicates that the aberrant activation or inhibition of macrophage-mediated immune responses occurs in inflammation,mainly caused by dysregulated ubiquitination modification due to E3 ubiquitin ligases mutations or abnormal ***,E3 ubiquitin ligases,responsible for recognizing the substrates,are key enzymes in the ubiquitin proteasome system(UPS)composed of ubiquitin(Ub),ubiquitin-activating E1 enzymes,ubiquitin-conjugating E2 enzymes,E3 ubiquitin ligases,26S proteasome,and deubiquitinating ***,several E3 ubiquitin ligases are involved in the regulation of some common signal pathways in macrophage-mediated inflammation,including Toll-like receptors(TLRs),nucleotide-binding oligomerization domain(NOD)-like receptors(NLRs),RIG-I-like receptors(RLRs),C-type lectin receptors(CLRs)and the receptor for advanced glycation end products(RAGE).Herein,we summarized the physiological and pathological roles of E3 ligases in macrophage-mediated inflammation,as well as the inhibitors and agonists targeting E3 ligases in macrophage mediated inflammation,providing the new ideas for targeted therapies in macrophage-mediated inflammation caused aberrant function of E3 ligases.

关键词： E3 ligases macrophage NLRs/RLRs/TLRs targeted therapies

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The role of singlet oxygen and hydroxyl radical in the photobleaching of meso-substituted cationic pyridyl porphyrins in the presence of folic acid

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Journal of Innovative Optical Health Sciences 2024年第5期17卷 67-80页

作者： Lusine Mkrtchyan Torgom Seferyan Marina Parkhats Sergei Lepeshkevich Boris Dzhagarov Gagik Shmavonyan Elena Tuchina Valery Tuchin Grigor Gyulkhandanyan laboratory of Bioengineering Institute of Biochemistry After H.Buniatyan of the NAS of Armenia 5/1 Paruyr Sevak StreetYerevan 0014Armenia laboratory of Biomedical Research Institute of Biochemistry after H.Buniatyan of the NAS of Armenia 5/1 Paruyr Sevak StreetYerevan 0014Armenia B.I.Stepanov Institute of Physics NAS of Belarus 68-2 Nezavisimosti Avenue Minsk 220072Belarus National Polytechnic University of Armenia 105 Teryan Street Yerevan 0009Armenia Science Medical Centre Saratov State University 83 Astrakhanskaya StreetSaratov 410012Russia

Using a photosensitizer(PS),light,and oxygen,photodynamic therapy creates cytotoxic reactive oxygen species,such as singlet oxygen(1O2),that kill cancer *** cancer cell lines have up to 300 times more folic acid receptors than healthy ***,folic acid is often used to improve selectivity of *** poses a disadvantage for *** this paper,we have studied the photoinduced changes of meso-substituted cationic pyridyl porphyrins in the presence of folic acid using uorescence and absorption *** this work,it was demonstrated that L-histidine,which is a 1O2 quencher,and D-mannitol,which is a hydroxyl radical quencher,can reduce photobleaching of cationic porphyrins and their interaction products with *** implies both singlet oxygen and hydroxyl radicals are involved in ***,our study revealed certain important features of the photobleaching of cationic porphyrins in the presence of folic acid.

关键词： Photodynamic therapy cancer quenchers histidine mannitol

The emerging roles of lysine-specific demethylase 4A in cancer:Implications in tumorigenesis and therapeutic opportunities

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Genes & Diseases 2024年第2期11卷 645-663页

作者： Guanjun Yang Changyun Li Fan Tao Yanjun Liu Minghui Zhu Yu Du Chenjie Fei Qiusheng She Jiong Chen State Key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Ningbo UniversityNingboZhejiang 315211China School of Life Science and Engineering Henan University of Urban ConstructionPingdingshanHenan 467044China laboratory of biochemistry and Molecular Biology School of Marine SciencesNingbo UniversityNingboZhejiang 315211China Key laboratory of Aquacultural Biotechnology Ministry of Education Ningbo UniversityNingboZhejiang 315211China

Lysine-specific demethylase 4 A(KDM4A,also named JMJD2A,KIA0677,or JHDM3A)is a demethylase that can remove methyl groups from histones H3K9me2/3,H3K36me2/3,and H1.4K26me2/*** evidence suggests that KDM4A is not only involved in body homeostasis(such as cell proliferation,migration and differentiation,and tissue development)but also associated with multiple human diseases,especially ***,an increasing number of studies have shown that pharmacological inhibition of KDM4A significantly attenuates tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid *** there are several reviews on the roles of the KDM4 subfamily in cancer development and therapy,all of them only briefly introduce the roles of KDM4A in cancer without systematically summarizing the specific mechanisms of KDM4A in various physiological and pathological processes,especially in tumorigenesis,which greatly limits advances in the understanding of the roles of KDM4A in a variety of cancers,discovering targeted selective KDM4A inhibitors,and exploring the adaptive profiles of KDM4A ***,we present the structure and functions of KDM4A,simply outline the functions of KDM4A in homeostasis and non-cancer diseases,summarize the role of KDM4A and its distinct target genes in the development of a variety of cancers,systematically classify KDM4A inhibitors,summarize the difficulties encountered in the research of KDM4A and the discovery of related drugs,and provide the corresponding solutions,which would contribute to understanding the recent research trends on KDM4A and advancing the progression of KDM4A as a drug target in cancer therapy.

关键词： Cancer therapy Drug resistance Histone demethylation JmjC domain KDM4A

A multi-platform analysis of human gingival crevicular fluid reveals ferroptosis as a relevant regulated cell death mechanism during the clinical progression of periodontitis

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International Journal of Oral Science 2024年第2期16卷 265-279页

作者： Alfredo Torres M.Angélica Michea Ákos Végvári Marion Arce Valentina Pérez Marcela Alcota Alicia Morales Rolando Vernal Mauricio Budini Roman A.Zubarev Fermín E.González laboratory of Experimental Immunology&Cancer Faculty of DentistryUniversity of ChileSantiagoChile Department of Conservative Dentistry Faculty of DentistryUniversity of ChileSantiagoChile Division of Chemistry I Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden Periodontal Biology laboratory Faculty of DentistryUniversidad de ChileSantiagoChile laboratory of Cellular and Molecular Pathology Institute for Research in Dental SciencesFaculty of DentistryUniversity of ChileSantiagoChile

Ferroptosis is implicated in the pathogenesis of numerous chronic-inflammatory diseases,yet its association with progressive periodontitis remains *** investigate the involvement and significance of ferroptosis in periodontitis progression,we assessed sixteen periodontitis-diagnosed *** progression was clinically monitored over twelve weeks via weekly clinical evaluations and gingival crevicular fluid(GCF)collection was performed for further *** metrics,proteomic data,in silico methods,and bioinformatics tools were combined to identify protein profiles linked to periodontitis progression and to explore their potential connection with *** western blot analyses validated key ***,a single-cell RNA sequencing(scRNA-seq)dataset(GSE164241)for gingival tissues was analyzed to elucidate cellular dynamics during periodontitis *** progression was identified as occurring at a faster rate than traditionally *** samples from progressing and non-progressing periodontal sites showed quantitative and qualitatively distinct proteomic *** addition,specific biological processes and molecular functions during progressive periodontitis were revealed and a set of hub proteins,including SNCA,CA1,HBB,SLC4A1,and ANK1 was strongly associated with the clinical progression status of ***,we found specific proteins-drivers or suppressors-associated with ferroptosis(SNCA,FTH1,HSPB1,CD44,and GCLC),revealing the co-occurrence of this specific type of regulated cell death during the clinical progression of ***,the integration of quantitative proteomic data with scRNA-seq analysis suggested the susceptibility of fibroblasts to *** analyses reveal proteins and processes linked to ferroptosis for the first time in periodontal patients,which offer new insights into the molecular mechanisms of progressive periodontal *** findings may le

关键词： finding progression faster

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Conversion of a single-layer ANN to photonic SNN for pattern recognition

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Science China(Information Sciences) 2024年第1期67卷 261-270页

作者： Yanan HAN Shuiying XIANG Tianrui ZHANG Yahui ZHANG Xingxing GUO Yuechun SHI State Key laboratory of Integrated Service Networks State Key Discipline Laboratory of Wide Bandgap Semiconductor TechnologyXidian University Yongjiang laboratory

This work presents a complete conversion scheme for photonic spiking neural networks(SNNs).We verified that the output of an artificial neural network(ANN) trained with the simulated optical activation function can be directly converted into the spike rate of a photonic spiking neuron *** reveal the feasibility of hardware implementation,we considered the effects of different bit precisions of data and weight,noise level,and bias current mismatch on the converted *** proposed scheme was evaluated using the Deterding vowel,IRIS,TIDIGITS,and MNIST datasets for pattern recognition,and achieved mean accuracies of 95.80%,98.67%,96.19%,and 92.33%,*** proposed scheme can convert an ANN into a photonic SNN with almost no precision loss,and the performance was comparable to that of an ANN trained with the rectified linear unit *** proposed scheme can enable the high-performance implementation of photonic SNNs.

关键词： photonic SNN conversion optical computing pattern recognition artificial neural network

Macroscopic model and statistical model to characterize electromagnetic information of a digital coding metasurface

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National Science Review 2024年第03期11卷 159-171页

作者： Rui Wen Shao Jun Wei Wu Zheng Xing Wang Hui Xu Han Qing Yang Qiang Cheng Tie Jun Cui Institute of Electromagnetic Space Southeast University State Key laboratory of Millimeter Waves Southeast University Peng Cheng laboratory Pazhou laboratory(Huangpu)

A digital coding metasurface is a platform connecting the digital space and electromagnetic wave space, and has therefore gained much attention due to its intriguing value in reshaping wireless channels and realizing new communication architectures. Correspondingly, there is an urgent need for electromagnetic information theory that reveals the upper limit of communication capacity and supports the accurate design of metasurface-based communication systems. To this end, we propose a macroscopic model and a statistical model of the digital coding metasurface. The macroscopic model uniformly accommodates both digital and electromagnetic aspects of the meta-atoms and predicts all possible scattered fields of the digital coding metasurface based on a small number of simulations or measurements. Full-wave simulations and experimental results show that the macroscopic model is feasible and accurate. A statistical model is further proposed to correlate the mutual coupling between meta-atoms with covariance and to calculate the entropy of the equivalent currents of digital coding metasurface. These two models can help reconfigurable intelligent surfaces achieve more accurate beamforming and channel estimation, and thus improve signal power and coverage. Moreover, the models will encourage the creation of a precoding codebook in metasurface-based direct digital modulation systems, with the aim of approaching the upper limit of channel capacity. With these two models, the concepts of current space and current entropy, as well as the analysis of information loss from the coding space to wave space, is established for the first time, helping to bridge the gap between the digital world and the physical world, and advancing developments of electromagnetic information theory and new-architecture wireless systems.

关键词： electromagnetic information theory current entropy current space digital coding metasurface macroscopic model statistical model