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Astronomical Knowledge Entity Extraction in Astrophysics Journal Articles via Large Language Models

Research in Astronomy and Astrophysics 2024年第6期24卷 140-155页

作者： Wujun Shao Rui Zhang Pengli Ji Dongwei Fan Yaohua Hu Xiaoran Yan Chenzhou Cui yihan tao Linying Mi Lang Chen National Astronomical Observatories Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China National Astronomical Data Center Beijing 100101China Research Institute of Artificial Intelligence Zhejiang LabHangzhou 311100China Guilin University Guangxi 541006China Xidian University Xi’an 710126China

Astronomical knowledge entities,such as celestial object identifiers,are crucial for literature retrieval and knowledge graph construction,and other research and applications in the field of *** methods of extracting knowledge entities from texts face numerous challenging obstacles that are difficult to ***,there is a pressing need for improved methods to efficiently extract *** study explores the potential of pre-trained Large Language Models(LLMs)to perform astronomical knowledge entity extraction(KEE)task from astrophysical journal articles using *** propose a prompting strategy called PromptKEE,which includes five prompt elements,and design eight combination prompts based on *** select four representative LLMs(Llama-2-70B,GPT-3.5,GPT-4,and Claude 2)and attempt to extract the most typical astronomical knowledge entities,celestial object identifiers and telescope names,from astronomical journal articles using these eight combination *** accommodate their token limitations,we construct two data sets:the full texts and paragraph collections of 30 *** the eight prompts,we test on full texts with GPT-4and Claude 2,on paragraph collections with all *** experimental results demonstrate that pre-trained LLMs show significant potential in performing KEE tasks,but their performance varies on the two data ***,we analyze some important factors that influence the performance of LLMs in entity extraction and provide insights for future KEE tasks in astrophysical articles using ***,compared to other methods of KEE,LLMs exhibit strong competitiveness in multiple aspects.

关键词： astronomical databases:miscellaneous virtual observatory tools methods:data analysis

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X-Ray Source Classification Using Machine Learning:A Study with EP-WXT Pathfinder LEIA

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Research in Astronomy and Astrophysics 2024年第8期24卷 175-195页

作者： Xiaoxiong Zuo yihan tao Yuan Liu Yunfei Xu Wenda Zhang Haiwu Pan Hui Sun Zhen Zhang Chenzhou Cui Weimin Yuan National Astronomical Observatories Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China National Astronomical Data Center Beijing 100101China

X-ray observations play a crucial role in time-domain *** Einstein Probe(EP),a recently launched X-ray astronomical satellite,emerges as a forefront player in the field of time-domain astronomy and high-energy *** a focus on systematic surveys in the soft X-ray band,EP aims to discover high-energy transients and monitor variable sources in the *** achieve these objectives,a quick and reliable classification of observed sources is *** this study,we developed a machine learning classifier for autonomous source classification using data from the EP-WXT Pathfinder—Lobster Eye Imager for Astronomy(LEIA)and EP-WXT *** proposed Random Forest classifier,built on selected features derived from light curves,energy spectra,and location information,achieves an accuracy of approximately 95%on EP simulation data and 98%on LEIA observational *** classifier is integrated into the LEIA data processing pipeline,serving as a tool for manual validation and rapid classification during *** paper presents an efficient method for the classification of X-ray sources based on single observations,along with implications of most effective features for the *** work facilitates rapid source classification for the EP mission and also provides valuable insights into feature selection and classification techniques for enhancing the efficiency and accuracy of X-ray source classification that can be adapted to other X-ray telescope data.

关键词： methods data analysis-X-rays binaries-stars variables general-X-rays bursts

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LettuceGDB:The community database for lettuce genetics and omics

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Plant Communications 2023年第1期4卷 87-99页

作者： Zhonglong Guo Bo Li Jianjun Du Fei Shen Yongxin Zhao Yang Deng Zheng Kuang yihan tao Miaomiao Wan Xianju Lu Dong Wang Ying Wang Yingyan Han Jianhua Wei Lei Li Xinyu Guo Chunjiang Zhao Xiaozeng Yang Beijing Academy of Agriculture and Forestry Sciences Beijing 100097P.R.China State Key Laboratory of Protein and Plant Gene Research Peking-Tsinghua Center for Life SciencesSchool of Life Sciences and School of Advanced Agricultural SciencesPeking UniversityBeijing 100871P.R.China Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology Beijing Agro-biotechnology Research CenterBeijing 100097P.R.China College of Biology and the Environment Nanjing Forestry UniversityNanjing 510275P.R.China Beijing Key Lab of Digital Plant Beijing Research Center for Information Technology in AgricultureBeijing 100097P.R.China WeiRan Biotech Beijing 100085P.R.China Beijing Key Laboratory of New Technology in Agricultural Application Beijing University of AgricultureBeijing 102206P.R.China

As a globally popular leafy vegetable and a representative plant of the Asteraceae family,lettuce has great economic and academic *** the last decade,high-throughput sequencing,phenotyping,and other multi-omics data in lettuce have accumulated on a large scale,thus increasing the demand for an integrative lettuce ***,we report the establishment of a comprehensive lettuce database,LettuceGDB(https://***/).As an omics data hub,the current LettuceGDB includes two reference genomes with detailed annotations;re-sequencing data from over 1000 lettuce varieties;a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies;re-analyses of 256 RNA sequencing datasets;a complete miRNAome;extensive metabolite information for representative varieties and wild relatives;epigenetic data on the genome-wide chromatin accessibility landscape;and various lettuce research papers published in the last *** hierarchically accessible functions(Genome,Genotype,Germplasm,Phenotype,and O-Omics)have been developed with a user-friendly interface to enable convenient data *** built-in tools(Assembly Converter,Search Gene,BLAST,JBrowse,Primer Design,Gene Annotation,Tissue Expression,Literature,and Data)are available for data downloading and browsing,functional gene exploration,and experimental practice.A community forum is also available for information sharing,and a summary of current research progress on different aspects of lettuce is *** believe that LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration,useful for both scientific research and lettuce breeding.

关键词： lettuce genome multi-omics germplasms breeding community

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Einstein Probe discovery of EP240408a: A peculiar X-ray transient with an intermediate timescale

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 222-240页

作者： Wenda Zhang Weimin Yuan Zhixing Ling Yong Chen Nanda Rea Arne Rau Zhiming Cai Huaqing Cheng Francesco Coti Zelati Lixin Dai Jingwei Hu Shumei Jia Chichuan Jin Dongyue Li Paul O’Brien Rongfeng Shen Xinwen Shu Shengli Sun Xiaojin Sun Xiaofeng Wang Lei Yang Bing Zhang Chen Zhang Shuang-Nan Zhang Yonghe Zhang Jie An David Buckley Alexis Coleiro Bertrand Cordier Liming Dou Rob Eyles-Ferris Zhou Fan Hua Feng Shaoyu Fu Johan P.U.Fynbo Lluis Galbany Saurabh W.Jha Shuaiqing Jiang Albert Kong Erik Kuulkers Weihua Lei Wenxiong Li Bifang Liu Mingjun Liu Xing Liu Yuan Liu Zhu Liu Chandreyee Maitra Alessio Marino Itumeleng Monageng Kirpal Nandra Jeremy Sanders Roberto Soria Lian tao Junfeng Wang Song Wang Tinggui Wang Zhongxiang Wang Qingwen Wu Xuefeng Wu Dong Xu Yanjun Xu Suijian Xue Yongquan Xue Zijian Zhang Zipei Zhu Hu Zou Congying Bao Fansheng Chen Houlei Chen Tianxiang Chen Wei Chen Yehai Chen Yifan Chen Chenzhou Cui Weiwei Cui Yanfeng Dai Dongwei Fan Ju Guan Dawei Han Dongjie Hou Haibo Hu Maohai Huang Jia Huo Zhenqing Jia Bowen Jiang Ge Jin Chengkui Li Junfei Li Longhui Li Maoshun Li Wei Li Zhengda Li Tianying Lian Congzhan Liu Heyang Liu Huaqiu Liu Fangjun Lu Laidan Luo Jia Ma Xuan Mao Haiwu Pan Xin Pan Liming Song Hui Sun Yunyin Tan Qingjun Tang yihan tao Hao Wang Juan Wang Lei Wang Wenxin Wang Yilong Wang Yusa Wang Qinyu Wu Haitao Xu Jingjing Xu Xinpeng Xu Yunfei Xu Zhao Xu Changbin Xue Yulong Xue Ailiang Yan Haonan Yang Xiongtao Yang Yanji Yang Juan Zhang Mo Zhang Wenjie Zhang Zhen Zhang Zhen Zhang Ziliang Zhang Donghua Zhao Haisheng Zhao Xiaofan Zhao Zijian Zhao Hongyan Zhou Yilin Zhou Yuxuan Zhu Zhencai Zhu National Astronomical Observatories Chinese Academy of Sciences School of Astronomy and Space Sciences University of Chinese Academy of Sciences Key Laboratory of Particle Astrophysics Institute of High Energy Physics Chinese Academy of Sciences Institute of Space Sciences (ICE) CSIC Institut d’Estudis Espacials de Catalunya (IEEC) Max Planck Institute for Extraterrestrial Physics Innovation Academy for Microsatellites Chinese Academy of Sciences Department of Physics University of Hong Kong School of Physics and Astronomy University of Leicester School of Physics and Astronomy Sun Yat-sen University Department of Physics Anhui Normal University Shanghai Institute of Technical Physics Chinese Academy of Sciences Physics Department Tsinghua University Nevada Center for Astrophysics University of Nevada Las Vegas Department of Physics and Astronomy University of Nevada Las Vegas South African Astronomical Observatory Department of Astronomy University of Cape Town Department of Physics University of the Free State Université Paris Cité CNRS Astroparticule et Cosmologie Université Paris Cité CEA Paris-Saclay IRFU/DAp-AIM Department of Astronomy Guangzhou University Cosmic Dawn Center (DAWN) Niels Bohr Institute University of Copenhagen Department of Physics and Astronomy Rutgers the State University of New Jersey Institute for Cosmic Ray Research The University of Tokyo ESA/ESTEC Department of Astronomy School of Physics Huazhong University of Science and Technology INAF-Osservatorio Astrofisico di Torino Sydney Institute for Astronomy School of Physics The University of Sydney Department of Astronomy Xiamen University Institute for Frontiers in Astronomy and Astrophysics Beijing Normal University Department of Astronomy University of Science and Technology School of Astronomy and Space Sciences University of Science and Technology of China Institute of Deep Space Sciences Deep Space Exploration Laboratory Department of Astronomy School of Physics and Astronomy Yunnan University Shanghai Astronomical Observatory Chi

We report the discovery of a peculiar X-ray transient,EP240408a,by Einstein Probe （EP） and follow-up studies made with EP,Swift,NICER,GROND,ATCA and other ground-based multiwavelength *** new transient was first detected with Wide-field X-ray Telescope （WXT） on board EP on April 8th,2024,manifested in an intense yet brief X-ray flare lasting for *** flare reached a peak flux of 3.9×10-9erg cm-2s-1in 0.5-4 ke V,～300 times brighter than the underlying X-ray emission detected throughout the *** and more precise follow-up observations by EP/FXT,Swift and NICER confirmed the finding of this new *** X-ray spectrum is non-thermal in 0.5-10 ke V,with a power-law photon index varying *** X-ray light curve shows a plateau lasting for ～4 d,followed by a steep decay till becoming undetectable ～10 d after the initial *** on its temporal property and constraints from previous EP observations,an unusual timescale in the range of 7-23 d is found for EP240408a,which is intermediate between the commonly found fast and long-term *** counterparts have been found in optical and near-infrared,with the earliest observation at 17 h after the initial X-ray detection,suggestive of intrinsically weak emission in these *** demonstrate that the remarkable properties of EP240408a are inconsistent with any of the transient types known so far,by comparison with,in particular,jetted tidal disruption events,gamma-ray bursts,X-ray binaries and fast blue optical *** nature of EP240408a thus remains an *** suggest that EP240408a may represent a new type of transients with intermediate timescales of the order of～10 *** detection and follow-ups of more of such objects are essential for revealing their origin.

关键词： X-ray transients ${\bm~{Einstein~~Probe}}$

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Complete biosynthesis of the phenylethanoid glycoside verbascoside

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Plant Communications 2023年第4期4卷 286-300页

作者： yihan Yang Daoyi Xi Yanan Wu tao Liu Key Laboratory of Engineering Biology for Low-Carbon Manufacturing Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308China National Center of Technology Innovation for Synthetic Biology Tianjin 300308China University of Chinese Academy of Sciences Beijing 100049China

Verbascoside,which was first discovered in 1963,is a well-known phenylethanoid glycoside(PhG)that exhibits antioxidant,anti-inflammatory,antimicrobial,and neuroprotective activities and contributes to the therapeutic effects of many medicinal ***,the biosynthetic pathway of verbascoside remains to be fully ***,we report the identification of two missing enzymes in the verbascoside biosynthesis pathway by transcriptome mining and in vitro enzymatic ***,a BAHD acyltransferase(hydroxycinnamoyl-CoA:salidroside hydroxycinnamoyltransferase[SHCT])was shown to catalyze the regioselective acylation of salidroside to form osmanthuside A,and a CYP98 hydroxylase(osmanthuside B 3,30-hydroxylase[OBH])was shown to catalyze meta-hydroxylations of the p-coumaroyl and tyrosol moieties of osmanthuside B to complete the biosynthesis of *** SHCTs and OBHs are found in many Lamiales species that produce verbascoside,this pathway may be *** findings from the study provide novel insights into the formation of caffeoyl and hydroxytyrosol moieties in natural product biosynthetic *** addition,with the newly acquired enzymes,we achieved heterologous production of osmanthuside B,verbascoside,and ligupurpuroside B in Escherichia coli;this work lays a foundation for sustainable production of verbascoside and other PhGs in micro-organisms.

关键词： acyltransferase cytochrome P450 microbial synthesis verbascoside acteoside phenylpropanoid

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Tracing the origin of large respiratory droplets by their deposition characteristics inside the respiratory tract during speech

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Building Simulation 2023年第5期16卷 781-794页

作者： yihan Wang Jianjian Wei Caroline X.Gao tao Jin Li Liu Institute of Refrigeration and Cryogenics Key Laboratory of Refrigeration and Cryogenic Technology of Zhejiang ProvinceZhejiang UniversityHangzhou 310000China Public Health and Preventive Medicine Monash UniversityMelbourneVIC3004Australia Department of Building Science Tsinghua UniversityBeijing 100084China

Origin of differently sized respiratory droplets is fundamental for clarifying their viral loads and the sequential transmission mechanism of SARS-CoV-2 in indoor *** talking activities characterized by low(0.2 L/s),medium(0.9 L/s),and high(1.6 L/s)airflow rates of monosyllabic and successive syllabic vocalizations were investigated by computational fluid dynamics(CFD)simulations based on a real human airway *** k-ωmodel was chosen to predict the airflow field,and the discrete phase model(DPM)was used to calculate the trajectories of droplets within the respiratory *** results showed that flow field in the respiratory tract during speech is characterized by a significant laryngeal jet,and bronchi,larynx,and pharynx-larynx junction were main deposition sites for droplets released from the lower respiratory tract or around the vocal cords,and among which,over 90%of droplets over 5μm released from vocal cords deposited at the larynx and pharynx-larynx ***,droplets’deposition fraction increased with their size,and the maximum size of droplets that were able to escape into external environment decreased with the airflow *** threshold size for droplets released from the vocal folds was 10-20μm,while that for droplets released from the bronchi was 5-20μm under various airflow ***,successive syllables pronounced at low airflow rates promoted the escape of small droplets,but do not significantly affect the droplet threshold *** study indicates that droplets larger than 20μm may entirely originate from the oral cavity,where viral loads are lower;it provides a reference for evaluating the relative importance of large-droplet spray and airborne transmission route of COVID-19 and other respiratory infections.

关键词： respiratory droplets deposition viral load airborne transmission COVID-19

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Numerical study on falling film flowing characteristics of R113 inside vertical tube under different structural conditions

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Chinese Journal of Chemical Engineering 2020年第1期28卷 23-32页

作者： Weishu Wang yihan Liao Youzhi Yan Bingchao Zhao tao Wang Shanshan Shangguan North China University of Water Resources and Electric Power Zhengzhou 450045China

To develop an appropriate falling film evaporation device for organic fluid cogeneration, a numerical study on the gas–liquid two-phase counter-current flow characteristics of R113 inside a vertical tube under different structural conditions was conducted using the Fluent software. The effects of the tube length, tube diameter, and annular gap on the falling film flow characteristics were determined, respectively. The results indicated that under a certain spray density, the falling film thickness in the region of the steady section was almost constant with different structural parameters for the tube diameter, tube length, and annular gap. In addition, a smaller tube diameter resulted in a steadier film flow. When the tube diameter decreased to a specific value, the film thickness showed a uniform distribution along the wall surface. This indicated that a best falling tube diameter exists. Meanwhile, the film fluctuation was enhanced with an increase in the tube length. When the tube length was greater than 1.2 m, the falling film splashed and could not completely wet the wall surface. The film fluctuation was enhanced by decreasing the annular gap, and the film could not be formed when the annular gap was smaller than 1.2 mm.

关键词： Falling film Numerical simulation R113

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^(137)Cs tracing of the spatial patterns in soil redistribution,organic carbon and total nitrogen in the southeastern Tibetan Plateau

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International Soil and Water Conservation Research 2023年第1期11卷 86-96页

作者： Zhengan Su Lijuan Wang yihan Liu Bin Fu Jjianhui Zhang Zuo Wu tao Zhou Junjie Wang Key Laboratory of Mountain Environment Evolution and Regulation Institute of Mountain Hazards and EnvironmentChinese Academy of SciencesChengdu610041PR China University of Chinese Academy of Science Beijing100049PR China College of Geography and Resources Science Sichuan Normal UniversityChengdu610101PR China College of Water Conservancy and Hydropower Engineering Sichuan Agricultural UniversityYa'an625014.PR China

The southeastern Tibetan Plateau,which profoundly affects East Asia by helping to maintain the stability of climate systems,biological diversity and clean water,is one of the regions most vulnerable to water erosion,wind erosion,tillage erosion,freeze-thaw erosion and overgrazing under global climate changes and intensive human *** variations in soil erosion in terraced farmland(TL),sloping farmland(SL)and grassland(GL)were determined by the^(137)Cs tracing method and compared with spatial variations in soil organic carbon(SOC)and total nitrogen(total N).The^(137)Cs concentration in the GL was higher in the 0-0.03 m soil layer than in the other soil layers due to weak migration and diffusion under low precipitation and temperature conditions,while the^(137)Cs concentration in the soil layer of the SL was generally uniform in the 0-0.18 m soil layer due to tillage-induced ***^(137)Cs inventories appeared at the summit and toe slope positions in the SL due to soil loss by tillage erosion and water erosion,respectively,while the highest^(137)Cs inventories appeared at the middle slope posi-tions due to soil accumulation under relatively flat landform *** the GL,the^(137)Cs data showed that higher soil erosion rates appeared at the summit due to freeze-thaw erosion and steep slope gradients and at the toe slope position due to wind erosion,gully erosion,freeze-thaw erosion and ***^(137)Cs inventory generally increased from upper to lower slope positions within each terrace(except the lowest terrace).The^(137)Cs data along the terrace toposequence showed abrupt changes in soil erosion rates between the lower part of the upper terrace and the upper part of the immediate terrace over a short distance and net deposition on the lower and toe ***,tillage erosion played an important role in the soil loss at the summit slope positions of each terrace,while water erosion dominantly transported soil from the upper terrace to

关键词： Southeastern Tibetanplateau ^(137)Cs SOC Total N Soil erosion

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FAST科学观测项目管理信息系统

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数据与计算发展前沿 2022年第1期4卷 20-29页

作者：韩军樊东卫陶一寒许允飞李珊珊米琳莹李长华崔辰州中国科学院国家天文台北京100101 国家天文科学数据中心北京100101

【应用背景】500米口径球面射电望远镜(FAST)是国家“十一五”重大科技基础设施建设项目。随着FAST的落成,如何对外提供观测服务,成为FAST必须要解决的关键需求。【方法】文章首先介绍了FAST对外开放的技术需求和面临的挑战,然后介绍信... 详细信息

【应用背景】500米口径球面射电望远镜(FAST)是国家“十一五”重大科技基础设施建设项目。随着FAST的落成,如何对外提供观测服务,成为FAST必须要解决的关键需求。【方法】文章首先介绍了FAST对外开放的技术需求和面临的挑战,然后介绍信息系统的框架结构及功能模块,主要包括用户管理、内容管理、观测申请评审、项目管理、数据中心五个核心模块及辅助模块。【结论】经过用户实际使用,FAST科学观测项目管理信息系统的应用效果符合预期,有效满足了FAST对外开放的功能需要,提升了观测运行效率。

关键词： 500米口径球面射电望远镜信息系统科学观测数据中心

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Serum metabolic effects of corn oligopeptides with 7-day supplementation on early post-surgery primary liver cancer patients: a double-blind randomized controlled trial

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Hepatobiliary Surgery and Nutrition 2022年第6期11卷 834-847页

作者： Weiqi Rong Hui Xia Kai Zhang yihan Zhang Changcheng tao Fan Wu Liming Wang Hong Zhang Guiju Sun Jianxiong Wu Department of Hepatobiliary Surgery National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences(CAMS)and Peking Union Medical College(PUMC)BeijingChina Key Laboratory of Environmental Medicine and Engineering of Ministry of Education Department of Nutrition and Food HygieneSchool of Public HealthSoutheast UniversityNanjingChina Department of Interventional Therapy Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin’s Clinical Research Center for CancerTianjinChina

Background:Liver cancer as the main leading cancer has caused heavy burdens *** prognosis of liver cancer is closely related with postoperative nutrition *** oligopeptides(COPs)are protein hydrolysates produced by enzymatic treatments,which have shown potential bioactivities,such as inhibiting angiotensin I-converting enzyme,resisting lipid peroxidation and ***,the correlation between COPs and liver cancer patients is still unknown and the potential mechanism of COPs on liver cancer is unclear as *** aim of this study was to assess effects of 7-day intervention of COPs after surgery on liver function and serum metabolic profiles of liver cancer ***:Patients were assigned into COPs intervention group(n=50)and control group(n=91)for 7 *** were scheduled at 1st day and 7th day after liver resection surgery respectively,mainly including anthropometric,biochemical indexes and liquid chromatography-mass spectrometry(LC/MS)***:Seven-day supplementation of COPs on early post-surgery liver cancer patients down-regulated levels of alanine aminotransferase,aspartate aminotransferase,total bilirubin,direct bilirubin and up-regulated prothrombin time activity and prealbumin ***/MS analysis revealed metabolic signatures including regulation of 16 metabolites,which was closely related with two metabolic pathways(nicotinate and nicotinamide metabolism,fatty acid metabolism).Conclusions:COPs supplementation has displayed the potentials on alleviating the injury of liver function and it may be due to regulation of fatty acid metabolism,nicotinate and nicotinamide metabolism,lipid peroxidation and anti-inflammatory *** researches are warranted in future to confirm the exact mechanisms.

关键词： Liver cancer corn oligopeptides supplementation metabolomics randomized controlled trial

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