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Frontiers of Computer Science 2024年第3期18卷 143-153页

作者： Zhe yuan Zhewei WEI Fangrui LV Ji-Rong WEN The Country and Area Studies Academy Beijing Foreign Studies UniversityBeijing 100089China Gaoling School of Artificial Intelligence Renmin University of ChinaBeijing 100872China

Motif-based graph local clustering(MGLC)is a popular method for graph mining tasks due to its various ***,the traditional two-phase approach of precomputing motif weights before performing local clustering loses locality and is impractical for large *** some attempts have been made to address the efficiency bottleneck,there is still no applicable algorithm for large scale graphs with billions of *** this paper,we propose a purely local and index-free method called Index-free Triangle-based Graph Local Clustering(TGLC^(*))to solve the MGLC problem w.r.t.a ***^(*)directly estimates the Personalized PageRank(PPR)vector using random walks with the desired triangleweighted distribution and proposes the clustering result using a standard sweep *** demonstrate TGLC^(*)’s scalability through theoretical analysis and its practical benefits through a novel visualization ***^(*)is the first algorithm to solve the MGLC problem without precomputing the motif *** experiments on seven real-world large-scale datasets show that TGLC^(*)is applicable and scalable for large graphs.

关键词： graph local clustering triangle motif index-free sampling method visualization

Recent Advances in Deciphering the Mechanisms and Biological Functions of DNA Demethylation

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Chinese Journal of Chemistry 2024年第6期42卷 645-651页

作者： Yang Feng Sheng-Jun Chen Bi-Feng yuan Key Laboratory of Aquatic Product Processing Ministry of Agriculture and Rural AffairsNational R&D Center for Aquatic Product ProcessingSouth China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouGuangdong510300 China School of Public Health Research Center of Public HealthRenmin Hospital of Wuhan UniversityWuhan UniversityWuhanHubei430071 China

5-Methylcytosine (5mC) is a dynamic and reversible epigenetic modification in genomic DNA of higher *** has been well-established that the demethylation of 5mC occurs through the ten-eleven translocation (TET)-mediated oxidation of 5mC followed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER).Recent findings also have identified an alternative pathway of DNA *** this pathway,TET enzymes directly oxidize 5mC to form 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC).These modified bases can undergo direct deformylation or decarboxylation,***,DNA demethylation can also occur through the deamination of 5mC and 5hmC,resulting in the production of thymine and 5-hydroxymethyluracil (5hmU),*** DNA demethylation pathways possess critical functional implications and roles in biological *** Recent Advances article will focus on the studies of mechanisms and biological functions of DNA demethylation,shedding light on the reversible nature of the epigenetic modification of 5mC.

关键词： Epigenetics DNA DNA methylation 5-Methylcytosine Demethylation Mechanisms Biological functions C—C bond cleavage Mass spectrometry

A Survey of Social Nutrition Status of the Elderly in theUrban Area of Chengdu, Sichuan Province

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Biomedical and Environmental Sciences 1998年第3期11卷 277-285页

作者： HUANG CHENG-YU WANG RUI-SHU GU HUA-QIANG CHEN HAI AND yuan HONG-JIANG (CMB on gerontology, West china university of the ical Sciences,Chengdu 610041, china) CMB on gerontology West China University of Medical Sciences Chengdu China

The social nutrition status was investigated among 246 subjects aged 60-90 living at three urban communities in Chengdu of Sichuan Province. The questionnaire was designed to evaluate socirydeweraphic background, the subjects' nutrition knowledge, and the support systerns for geriatric nutrition. Fasting venous blcod was colected for the analysis of biochemical parameters. Blood pressure, bene mineral contents (BMC), body weight (BW) and they height (BH) were measured at the same time. Only 49. 7% of the subjects correctly an swered four basic questions on nutrition. Food patterns for the elder1y were simple and modest. Several nutrition-related disorders for the elderly were including high systolic bbo pressure (44. 6 % ), hyPertriglyceridemia (25. 9 % ), high diasto1ic blood pressure (25. 1% ),obesity (24. 5% ), high PBG (20. 6% ), emaciation (19. 9%), high FBG (17.9%) and osteoporosis (16. 8%). These data indicate that the support systems for the geriatric nutrition will have to be improved.

关键词： A Survey of Social Nutrition Status of the Elderly in theUrban Area of Chengdu Sichuan Province PBG

Mitochondrial dysfunction: A promising therapeutic target for liver diseases

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Genes & Diseases 2024年第3期11卷 324-337页

作者： Ping Chen Lichao Yao Mengqin yuan Zheng Wang Qiuling Zhang Yingan Jiang Lanjuan Li Department of Infectious Diseases Renmin Hospital of Wuhan UniversityWuhanHubei 430060China State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouZhejiang 310003China

The liver is an important metabolic and detoxification organ and hence demands a large amount of energy,which is mainly produced by the *** tissues of pa-tients with alcohol-related or non-alcohol-related liver diseases contain ultrastructural mito-chondrial lesions,mitochondrial DNA damage,disturbed mitochondrial dynamics,and compromised ATP *** of mitochondrial reactive oxygen species in-duces oxidative damage to mitochondrial proteins and mitochondrial DNA,decreases mito-chondrial membrane potential,triggers hepatocyte inflammation,and promotes programmed cell death,all of which impair liver *** DNA may be a poten-tial novel non-invasive biomarker of the risk of progression to liver cirrhosis and hepatocellular carcinoma in patients infected with the hepatitis B *** herein present a review of the mechanisms of mitochondrial dysfunction in the development of acute liver injury and chronic liver diseases,such as hepatocellular carcinoma,viral hepatitis,drug-induced liver injury,alcoholic liver disease,and non-alcoholic fatty liver *** review also discusses mito-chondrion-centric therapies for treating liver diseases.

关键词： Chronic diseases Liverdamage Mesenchymalstem cell Mitochondrial dysfunction Oxidativestress

Applying dynamic light scattering to investigate the self-assembly process of DNA nanostructures

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Chinese Chemical Letters 2024年第3期35卷 316-320页

作者： Wei yuan Gui-Zhi Dong Hui Ning Xiang-Xiang Guan Jia-Feng Cheng Zi-Wei Shi Xiu-Ji Du Si-Wen Meng Dong-Sheng Liu yuan-Chen Dong CAS Key Laboratory of Colloid Interface and Chemical ThermodynamicsInstitute of ChemistryChinese Academy of SciencesBeijing 100190China university of Chinese Academy of Sciences Beijing 100049China Dandong Bettersize Instruments Ltd. Dandong 118000China Key Laboratory of Organic Optoelectronics&Molecular Engineering of the Ministry of Education Department of ChemistryTsinghua UniversityBeijing 100084China Department of Chemistry Renmin University of ChinaBeijing 100872China

Understanding the dynamic assembly process of DNA nanostructures is important for developing novel strategy to design and construct functional *** this work,temperature-controlled dynamic light scattering(DLS)strategy has been applied to study the global assembly process of DNA origami and DNA *** the temperature dependent size and intensity profiles,the self-assembly process of various DNA nanostructures with different morphologies have been well-studied and the temperature transition ranges could be *** advantage of the DLS information,rapid preparation of the DNA origami and the brick assembly has been realized through a constant temperature *** results demonstrate that the DLS-based strategy provides a convenient and robust tool to study the dynamic process of forming hieratical DNA structures,which will benefit understanding the mechanism of self-assembly of DNA nanostructures.

关键词： Dynamic light scattering Self-assembly process DNA nanostructures Temperature transition ranges Rapid preparation

Chronic sleep deprivation induces alterations in DNA and RNA modifications by liquid chromatography-mass spectrometry analysis

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Chinese Chemical Letters 2024年第8期35卷 413-417页

作者： Tian Feng Yun-Ling Gao Di Hu Ke-Yu yuan Shu-Yi Gu Yao-Hua Gu Si-Yu Yu Jun Xiong Yu-Qi Feng Jie Wang Bi-Feng yuan School of Public Health Research Center of Public HealthRenmin Hospital of Wuhan UniversityWuhan UniversityWuhan 430071China Department of Radiation and Medical Oncology Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan 430071China Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular PhysicsNational Center for Magnetic Resonance in WuhanWuhan Institute of Physics and MathematicsInnovation Academy for Precision Measurement Science and TechnologyChinese Academy of Sciences-Wuhan National Laboratory for OptoelectronicsWuhan 430071China university of Chinese Academy of Sciences Beijing 101408China Institute of Neuroscience and Brain Diseases Xiangyang Central HospitalAffiliated Hospital of Hubei University of Arts and ScienceXiangyang 441000China Phase I Clinical Trial Laboratory Zhongnan Hospital of Wuhan UniversityWuhan 430071China

Sleep deprivation(SD)is a widespread issue that disrupts the lives of millions of *** effects ini-tiate as changes within neurons,specifically at the DNA and RNA level,leading to disruptions in neuronal plasticity and the dysregulation of various cognitive functions,such as learning and *** acid epigenetic modifications that could regulate gene expression have been reported to play crucial roles in this ***,there is a lack of comprehensive research on the correlation of SD with nucleic acid epigenetic *** the current study,we aimed to systematically investigate the landscape of modifications in DNA as well as in small RNA molecules across multiple tissues,including the heart,liver,kidney,lung,hippocampus,and spleen,in response to chronic sleep deprivation(CSD).Using liquid chromatography-tandem mass spectrometry(LC-MS/MS)analysis,we characterized the dynamic changes in DNA and RNA modification profiles in different tissues of mice under CSD ***,we ob-served a significant decrease in the level of 5-methylcytosine(5mC)and a significant increase in the level of 5-hydroxymethylcytosine(5hmC)in the kidney in CSD *** RNA modifications,we observed an overall increased trend for most of these significantly changed modifications across six tis-sues in CSD *** study sheds light on the significance of DNA and RNA modifications as crucial epigenetic markers in the context of CSD-induced stress.

关键词： Sleep deprivation Epigenetics Mass spectrometry DNA modification RNA modification Small RNA

A Non-canonical Excitatory PV RGC–PV SC Visual Pathway for Mediating the Looming-evoked Innate Defensive Response

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Neuroscience Bulletin 2024年第3期40卷 310-324页

作者： Man yuan Sen Jin Gao Tan Siyuan Song Yizong Liu Huadong Wang Yin Shen Eye Center Renmin Hospital of Wuhan UniversityWuhan UniversityWuhan430060China The Brain Cognition and Brain Disease Institute Shenzhen Key Laboratory of Viral Vectors for BiomedicineShenzhen Institute of Advanced TechnologyChinese Academy of Sciences(CAS)Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research InstitutionsNational Medical Products Administration Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal ProductsShenzhen Key Laboratory of Quality Control Technology for Virus-Based TherapeuticsGuangdong Provincial Medical Products AdministrationShenzhen518055China Jan and Dan Duncan Neurological Research Institute Baylor College of MedicineHouston77030USA State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Key Laboratory of Magnetic Resonance in Biological SystemsWuhan Center for Magnetic ResonanceInnovation Academy for Precision Measurement Science and TechnologyCASWuhan430071China Frontier Science Center of Immunology and Metabolism Medical Research InstituteWuhan UniversityWuhan430071China

Parvalbumin-positive retinal ganglion cells(PV+RGCs)are an essential subset of RGCs found in various ***,their role in transmitting visual information remains ***,we characterized PV+RGCs in the retina and explored the functions of the PV+RGC-mediated visual *** applying multiple viral tracing strategies,we investigated the downstream of PV+RGCs across the whole ***,we found that the PV+RGCs provided direct monosynaptic input to PV+excitatory neurons in the superficial layers of the superior colliculus(SC).Ablation or suppression of SC-projecting PV+RGCs abolished or severely impaired the flight response to looming visual stimuli in mice without affecting visual ***,using transcriptome expression profiling of individual cells and immunofluorescence colocalization for RGCs,we found that PV+RGCs are predominant glutamatergic ***,our findings indicate the critical role of PV+RGCs in an innate defensive response and suggest a non-canonical subcortical visual pathway from excitatory PV+RGCs to PV+SC neurons that regulates looming visual *** results provide a potential target for intervening and treating diseases related to this circuit,such as schizophrenia and autism.

关键词： Parvalbumin-positive retinal ganglion cell Innate fear Superior colliculus Excitatory-excitatory neuronal connection Looming-evoked defensive response Subcortical pathway

Tetramethylpyrazine and paeoniflorin combination(TMP-PF)alleviates atherosclerosis progress by reducing hyperlipemia and inhibiting plaque angiogenesis via the NR4A1/VEGFR2 pathway

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Food Science and Human Wellness 2024年第5期13卷 2642-2652页

作者： Rong yuan Qiqi Xin Weili Shi Yu Miao Zhengchuan Zhu Yahui yuan Ying Chen Xiaoning Chen Sean Xiao Leng Keji Chen Weihong Cong Cardiovascular Diseases Laboratory Xiyuan HospitalChina Academy of Chinese Medical SciencesBeijing 100091China National Clinical Research Center for Chinese Medicine Cardiology Xiyuan HospitalChina Academy of Chinese Medical SciencesBeijing 100091China School of Health Economics and Management Nanjing University of Chinese MedicineNanjing 210023China Department of Otolaryngology Jiangsu Province Hospital of Chinese MedicineNanjing 210029China Division of Geriatric Medicine and gerontology Department of MedicineJohns Hopkins University School of MedicineBaltimore 21224United States

Atherosclerosis remains a great threat to human health *** studies found that tetramethylpyrazine(TMP)and paeonifl orin(PF)combination(TMP-PF)exerts anti-atherosclerotic effects in ***,whether TMP-PF improves atherosclerosis in vivo needs further *** present study aims to assess the anti-atherosclerotic properties of TMP-PF in ApoE^(-/-)mice and explore the related molecule *** showed that TMP and high-dose TMP-PF decreased serum triglyceride and low-density lipoprotein cholesterol levels,suppressed vascular endothelial growth factor receptor 2(VEGFR2)and nuclear receptor subfamily 4 group A member 1(NR4A1)expression in aortic tissues,inhibited plaque angiogenesis,reduced plaque areas,and alleviated atherosclerosis in ApoE^(-/-)***,TMP-PF exhibited a better modulation effect than TMP or PF ***,NR4A1 agonist abolished the anti-atherosclerotic effects of *** conclusion,TMP-PF was first found to alleviate atherosclerosis progression by reducing hyperlipemia and inhibiting plaque angiogenesis via the NR4A1/VEGFR2 pathway,indicating that TMP-PF had a positive effect on reducing hyperlipemia and attenuating atherosclerosis development.

关键词： Atherosclerosis Hyperlipemia Angiogenesis Plaque stability Chinese medicine Tetramethylpyrazine Paeoniflorin

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Pathogen-induced methylglyoxal negatively regulates rice bacterial blight resistance by inhibiting OsCDR1 protease activity

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Molecular Plant 2024年第2期17卷 325-341页

作者： Zheng-Wei Fu Jian-Hui Li Xiang Gao Shi-Jia Wang Ting-Ting yuan Ying-Tang Lu State Key Laboratory of Hybrid Rice College of Life SciencesRenmin Hospital of Wuhan UniversityWuhan UniversityWuhan 430072China Key Laboratory of Biology and Genetic Improvement of OilCrops Ministry of Agriculture and Rural AffairsOilCrops Research Institute of the Chinese Academy of Agricultural SciencesWuhan 430062China

Xanthomonas oryzae ***(Xoo)causes bacterial blight(BB),a globally devastating disease of rice(Oryza sativa)that is responsible for significant crop *** and sugar metabolites are important for pathogen infection,providing energy and regulating events associated with defense responses;howev-er,the mechanisms by which they regulate such events in BB are *** an inevitable sugar metabolite,methylglyoxal(MG)is involved in plant growth and responses to various abiotic stresses,but the underlying mechanisms remain *** and how MG functions in plant biotic stress responses is almost completely ***,we report that the Xoo strain PXO99 induces OsWRKY62.1 to repress transcrip-tion of OsGLY Il genes by directly binding to their promoters,resulting in overaccumulation of *** negatively regulates rice resistance against Pxo99:osglyll2 mutants with higher MG levels are more sus-ceptible to the pathogen,whereas OsGLYIl2-overexpressing plants with lower MG content show greater resistance than the wild *** of OsGLYll2 to prevent excessive MG accumulation confers broad-spectrum resistance against the biotrophic bacterial pathogens Xoo and Xanthomonas oryzae *** and the necrotrophic fungal pathogen Rhizoctonia solani,which causes rice sheath *** evidence shows that MG reduces rice resistance against PXO99 through CONSTITUTIVE DISEASE RESISTANCE 1(OsCDR1).MGmodifies the Arg97 residue of OsCDR1to inhibit its aspartic protease activ-ity,which is essential for OsCDR1-enhanced *** together,these findings illustrate how Xoo promotes infection by hijacking a sugar metabolite in the host plant.

关键词： Oryza sativa bacterial blight OsWRKY62.1 methylglyoxal OsCDR1