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Si-Wu-Tang attenuates liver fibrosis via regulating lncRNA H19-dependent pathways involving cytoskeleton remodeling and ECM deposition

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Chinese Journal of Natural Medicines 2024年第1期22卷 31-46页

作者： QU Jiaorong XUE Xiaoyong WANG Zhixing MA Zhi JIA Kexin LI Fanghong ZHANG Yinhao WU Ruiyu ZHOU Fei ZHAO Piwen LI Xiaojiaoyang School of Life Sciences Beijing University of Chinese MedicineBeijing 100029China School of Chinese Materia Medica Beijing University of Chinese MedicineBeijing 100029China State Key Laboratory of Medical Molecular biology Department of Molecular Biology and BiochemistryInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100005China

Liver fibrosis is a dynamic wound-healing response characterized by the agglutination of the extracellular matrix(ECM).Si-Wu-Tang(SWT),a traditional Chinese medicine(TCM)formula,is known for treating gynecological diseases and liver *** previous studies demonstrated that long non-coding RNA H19(H19)was markedly upregulated in fibrotic livers while its deficiency markedly reversed ***,the mechanisms by which SWT influences H19 remain ***,we established a bile duct ligation(BDL)-induced liver fibrosis model to evaluate the hepatoprotective effects of SWT on various cells in the *** results showed that SWT markedly improved ECM deposition and bile duct reactions in the ***,SWT relieved liver fibrosis by regulating the transcription of genes involved in the cytoskeleton remodeling,primarily in hepatic stellate cells(HSCs),and influencing cytoskeleton-related angiogenesis and hepatocellular *** modulation collectively led to reduced ECM *** extensive bioinformatics analyses,we determined that H19 acted as a miRNA sponge and mainly inhibited miR-200,miR-211,and let7b,thereby regulating the above cellular regulatory ***,SWT reversed H19-related miRNAs and signaling pathways,diminishing ECM deposition and liver ***,these protective effects of SWT were diminished with the overexpression of H19 in *** conclusion,our study elucidates the underlying mechanisms of SWT from the perspective of H19-related signal networks and proposes a potential SWT-based therapeutic strategy for the treatment of liver fibrosis.

关键词： Liver fibrosis LncRNA H19 Si-Wu-Tang miRNAs Cytoskeleton ECM deposition

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Sarve:synthetic data and local differential privacy for private frequency estimation

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Cybersecurity 2022年第4期5卷 97-116页

作者： Gatha Varmal Ritu Chauhan Dhananjay Singh Amity Institute of Information Technology Amity UniversityNoidaIndia Center for computational biology and bioinformatics Amity UniversityNoidaIndia Department of Electronics Engineering HUFSSeoulKorea

The collection of user attributes by service providers is a double-edged *** are instrumental in driving statistical analysis to train more accurate predictive models like *** analysis of the collected user data includes frequency estimation for categorical ***,the users deserve privacy guarantees against inadvertent identity *** algorithms called frequency oracles were developed to randomize or perturb user attributes and estimate the frequencies of their *** propose Sarve,a frequency oracle that used Randomized Aggregatable Privacy-Preserving Ordinal Response(RAPPOR)and Hadamard Response(HR)for randomization in combination with fake *** design of a service-oriented architecture must consider two types of complexities,namely computational and *** functions of such systems aim to minimize the two complexities and therefore,the choice of privacy-enhancing methods must be a calculated *** variant of RAPPOR we had used was realized through bloom flters.A bloom filter is a memory-efficient data structure that offers time complexity of O(1).On the other hand,HR has been proven to give the best communication costs of the order of log(b)for b-bits ***,Sarve is a step towards frequency oracles that exhibit how privacy provisions of existing methods can be combined with those of fake data to achieve statistical results comparable to the original *** also implemented an adaptive solution enhanced from the work of Arcolezi et *** use of RAPPOR was found to provide better privacy-utility tradeoffs for specific privacy budgets in both high and general privacyregimes.

关键词： Synthetic data Differential privacy Frequency estimation Frequency oracle Privacy

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Convergent Usage of Amino Acids in Human Cancers as A Reversed Process of Tissue Development

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Genomics, Proteomics & bioinformatics 2022年第1期20卷 147-162页

作者： Yikai Luo Han Liang Graduate Program in Quantitative and computational Biosciences Baylor College of MedicineHoustonTX 77030USA Department of bioinformatics and computational biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA Department of Systems biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA

Genome-and transcriptome-wide amino acid usage preference across different species is a well-studied phenomenon in molecular evolution,but its characteristics and implication in cancer evolution and therapy remain largely ***,we analyzed large-scale transcriptome/proteome profiles,such as The Cancer Genome Atlas(TCGA),the Genotype-Tissue Expression(GTEx),and the Clinical Proteomic Tumor Analysis Consortium(CPTAC),and found that compared to normal tissues,different cancer types showed a convergent pattern toward using biosynthetically low-cost amino *** a pattern can be accurately captured by a single index based on the average biosynthetic energy cost of amino acids,termed energy cost per amino acid(ECPA).With this index,we further compared the trends of amino acid usage and the contributing genes in cancer and tissue development,and revealed their reversed ***,focusing on the liver,a tissue with a dramatic increase in ECPA during development,we found that ECPA represents a powerful biomarker that could distinguish liver tumors from normal liver samples consistently across 11 independent patient cohorts and outperforms any index based on single *** study reveals an important principle underlying cancer evolution and suggests the global amino acid usage as a system-level biomarker for cancer diagnosis.

关键词： Amino acid usage Tissue development Biosynthetic energy Diagnostic biomarker

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生物信息学资源助力蛋白质磷酸化的系统层次理解

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Science Bulletin 2024年第8期69卷 989-992页

作者：彭迪贾大夏宏光张珞颖黄鹏宇薛宇 Department of bioinformatics and Systems biology MOE Key Laboratory of Molecular BiophysicsHubei Bioinformatics and Molecular Imaging Key LaboratoryCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Key Laboratory of Birth Defects and Related Diseases of Women and Children Department of PaediatricsWest China Second University HospitalState Key Laboratory of BiotherapySichuan UniversityChengdu 610041China Department of Biochemistry&Research Center of Clinical Pharmacy of The First Affiliated Hospital Zhejiang University School of MedicineHangzhou 310058China Institute of Biomedical Engineering Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjin 300192China Nanjing University Institute of Artificial Intelligence Biomedicine Nanjing 210031China

Protein phosphorylation,catalyzed by protein kinases(PKs),is one of the most prevalent post-translational modifications(PTMs)in *** occurring at different positions in a protein sequence can possess distinct functional impacts,and sitespecific phosphorylation may drastically alter a protein’s conformation,activity,and ***,biologists usually focused on studying regulatory mechanisms of phosphorylation in a limited number of proteins,mainly due to a lack of highthroughput *** the past two decades,advances in liquid chromatography coupled with tandem mass spectrometry(LC-MS/MC)have boomed a revolutionary technology named phosphoproteomics,which can simultaneously quantify thousands of phosphorylation sites(p-sites),and provide a great opportunity for a systems-level understanding of *** LCMS/MC,other approaches such as immunohistochemistry(IHC)and immune-detection by sequencing(ID-seq)have also emerged.

关键词： positions catalyzed translational

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Plant virology in the 21st century in China:Recent advances and future directions

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Journal of Integrative Plant biology 2024年第3期66卷 579-622页

作者： Jianguo Wu Yongliang Zhang Fangfang Li Xiaoming Zhang Jian Ye Taiyun Wei Zhenghe Li Xiaorong Tao Feng Cui Xianbing Wang Lili Zhang Fei Yan Shifang Li Yule Liu Dawei Li Xueping Zhou Yi Li State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops Vector-borne Virus Research CenterCollege of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou 350002China State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology College of Biological SciencesChina Agricultural UniversityBeijing 100193China State Key Laboratory for biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Plant Genomics Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Rice biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Department of Plant Pathology The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjing 210095China State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Institute of Plant VirologyNingbo UniversityNingbo 315211China MOE Key Laboratory of bioinformatics Center for Plant BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China

Plant viruses are a group of intracellular pathogens that persistently threaten global food *** advances in plant virology have been achieved by Chinese scientists over the last 20 years,including basic research and technologies for preventing and controlling plant viral ***,we review these milestones and advances,including the identification of new crop-infecting viruses,dissection of pathogenic mechanisms of multiple viruses,examination of multilayered interactions among viruses,their host plants,and virus-transmitting arthropod vectors,and in-depth interrogation of plantencoded resistance and susceptibility ***,various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in *** also recommend future plant virology studies in China.

关键词： China emerging plant viruses plant virology plant resistance/susceptibility to viral infection plant-virus transmission vector interactions plant virus-based vectors viral pathogenesis

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Molecular bases of morphologically diffused tumors across multiple cancer types

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National Science Review 2022年第11期9卷 65-67页

作者： Dingyun Liu Feiyang Xing Yueying Wang Jun Xiao Zheng An Ying Xu College of Computer Science and Technology Jilin University Center for Cancer Systems biology China-Japan Union Hospital of Jilin University School of Life Sciences Jilin University China computational Systems biology Lab Department of Biochemistry and Molecular Biology and Institute of BioinformaticsUniversity of Georgia

Diffuse gastric cancer (DGC) and intestinal gastric cancer (IGC) are the two main gastric cancer subtypes [1]. Morphologically, DGC consists of numerous disjoint tiny tumors while IGC forms one or a few solid tumors (Supplementary Supplementary Fig. S1)[1,2]. In-depth studies have discovered that DGCs generally have an ill-defined or missing glandular structure and reduced cell–cell adhesion,

关键词： identification enantioselective semisynthesis (−)-anisomelic acid oral agent anti-SARS-CoV-2

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Gut microbial metabolite targets HDAC3-FOXK1-interferon axis in fibroblast-like synoviocytes to ameliorate rheumatoid arthritis

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Bone Research 2024年第2期12卷 421-437页

作者： Hongzhen Chen Xuekun Fu Xiaohao Wu Junyi Zhao Fang Qiu Zhenghong Wang Zhuqian Wang Xinxin Chen Duoli Xie Jie Huang Junyu Fan Xu Yang Yi Song Jie Li Dongyi He Guozhi Xiao Aiping Lu Chao Liang Department of Systems biology School of Life SciencesSouthern University of Science and TechnologyGuangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchShenzhen Key Laboratory of Cell MicroenvironmentShenzhen 518055China Institute of Integrated Bioinfomedicine and Translational Science(IBTS) School of Chinese MedicineHong Kong Baptist UniversityHong Kong SAR 999077China Department of Biochemistry School of MedicineSouthern University of Science and TechnologyGuangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchShenzhen Key Laboratory of Cell MicroenvironmentShenzhen 518055China Division of Immunology and Rheumatology Stanford UniversityStanfordCA 94305USA VA Palo Alto Health Care System Palo AltoCA 94304USA Institute of Plant and Food Science Department of BiologySouthern University of Science and TechnologyShenzhen 518055China Department of Rheumatology Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai University of Traditional Chinese MedicineShanghaiChina Department of computational biology St.Jude Children’s Research HospitalMemphisTNUSA Department of Laboratory Medicine Peking University Shenzhen HospitalShenzhenChina Guangdong-Hong Kong-Macao Joint Lab on Chinese Medicine and Immune Disease Research Guangzhou 510006China Shanghai University of Traditional Chinese Medicine Shanghai 200032China State Key Laboratory of Proteomics National Center for Protein Sciences(Beijing)Beijing Institute of Lifeomics100850 BeijingChina

Rheumatoid arthritis(RA)is an autoimmune *** studies hold an opinion that gut microbiota is environmentally acquired and associated with RA ***,accumulating evidence demonstrates that genetics also shape the gut *** is known that some strains of inbred laboratory mice are highly susceptible to collagen-induced arthritis(CIA),while the others are resistant to ***,we show that transplantation of fecal microbiota of CIA-resistant C57BL/6J mice to CIA-susceptible DBA/1J mice confer CIA resistance in DBA/1J mice.C57BL/6J mice and healthy human individuals have enriched *** than DBA/1J mice and RA *** of *** prevents CIA in DBA/1J *** identify that *** mainly produces propionate and C57BL/6J mice and healthy human individuals have higher level of ***-like synoviocytes(FLSs)in RA are activated to undergo tumor-like *** disrupts HDAC3-FOXK1 interaction to increase acetylation of FOXK1,resulting in reduced FOXK1 stability,blocked interferon signaling and deactivation of *** treat CIA mice with propionate and show that propionate attenuates ***,a combination of propionate with anti-TNF etanercept synergistically relieves *** results suggest that *** or propionate could be an alternative or complementary approach to the current therapies.

关键词： HDAC3 cytes interferon

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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt Dirk Jan van Dijk State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint Lab of Vegetable Genomics Beijing 100081China bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands Plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

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Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu Michael H Perlin David Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale Paweł Łabaj Nicolás Rascovan Nur Hazlin Hazrin-Chong Soojin Jang Haruo Suzuki Marina Nieto-Caballero Bharath Prithiviraj Patrick K H Lee Agnieszka Chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher E Mason Tieliu Shi Center for bioinformatics and computational biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Performance and Cloud Computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen Research Center Bogotá110311Colombia Applied Environmental Metagenomics and Infectious Diseases Research(AEMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska Centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of Environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of Energy and Environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban *** address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based *** findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical *** also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel *** study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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A computational model to identify fertility-related proteins using sequence information

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Frontiers of Computer Science 2024年第1期18卷 229-237页

作者： Yan LIN Jiashu WANG Xiaowei LIU Xueqin XIE De WU Junjie ZHANG Hui DING Key Laboratory for Animal Disease-Resistance Nutrition of the Ministry of Agriculture Animal Nutrition InstituteSichuan Agricultural UniversityChengdu 611130China School of Life Science and Technology and Center for Informational biology University of Electronic Science and Technology of ChinaChengdu 610054China

Fertility is the most crucial step in the development process,which is controlled by many fertility-related proteins,including spermatogenesis-,oogenesis-and embryogenesis-related *** identification of fertility-related proteins can provide important clues for studying the role of these proteins in ***,in this study,we constructed a two-layer classifier to identify fertility-related *** this classifier,we first used the composition of amino acids(AA)and their physical and chemical properties to code these three fertility-related ***,the feature set is optimized by analysis of variance(ANOVA)and incremental feature selection(IFS)to obtain the optimal feature *** five-fold cross-validation(CV)and independent data tests,the performance of models constructed by different machine learning(ML)methods is evaluated and ***,based on support vector machine(SVM),we obtained a two-layer model to classify three fertility-related *** the independent test data set,the accuracy(ACC)and the area under the receiver operating characteristic curve(AUC)of the first layer classifier are 81.95%and 0.89,respectively,and them of the second layer classifier are 84.74%and 0.90,*** results show that the proposed model has stable performance and satisfactory prediction accuracy,and can become a powerful model to identify more fertility related proteins.

关键词： sfertility-related proteins machine1 learning sequence information feature selection

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