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αExtractor: a system for automatic extraction of chemical information from biomedical literature

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Science China(Life Sciences) 2024年第3期67卷 618-621页

作者： Jiacheng Xiong Xiaohong Liu Zhaojun Li Hongzhong Xiao Guangchao Wang Zhenjiang Niu Chaoyuan Fei Feisheng Zhong Gang Wang Wei Zhang Zunyun Fu Zhiguo Liu Kaixian Chen Hualiang Jiang Mingyue Zheng Drug Disco.ery and Design Center State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China AI Department Suzhou Alphama Biotechnology Co.Ltd.Suzhou 215125China co.lege of co.puter and Information Engineering Dezhou UniversityDezhou 253023China

Dear Editor,Great progress has been made using artificial intelligence(AI) techniques in learning knowledge from biomedical databases in recent years, revolutionizing the study of many fields, such as protein structure prediction and protein design(Madani et al., 2023). However, there is massive biomedical knowledge not curated in the form of structured data but hidden in primary scientific literature.

关键词： has such knowledge

Insights into the mechanism of L-malic acid on drip loss of chicken meat under co.mercial co.ditions

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Journal of Animal Science and biotechnology 2024年第3期15卷 1312-1324页

作者： Haijun Sun Xue Yan Lu Wang Ruimin Zhu Meixia Chen Jingdong Yin Xin Zhang State Key Laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China New Hope Liuhe co. Ltd./Key Laboratory of Feed and Livestock and Poultry Products Quality&Safety ControlMinistry of AgricultureChengduSichuan 610023China Institute of Animal Husbandry and Veterinary Medicine Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

Background A deterioration in the meat quality of broilers has attracted much more attention in recent years.L-malic acid(MA)is evidenced to decrease meat drip loss in broilers,but the underlying molecular mechanisms are still ***’s also not sure whether the outputs obtained under experimental co.ditions can be obtained in a co.-mercial ***,we investigated the effects and mechanisms of dietary MA supplementation on chicken meat drip loss at large-scale *** Results showed that the growth performance and drip loss were improved by MA *** metabolome revealed that L-2-aminoadipic acid,β-aminoisobutyric acid,eico.apentaenoic acid,and nico.inamide,as well as amino acid metabolism pathways co.nected to the improvements of meat quality by MA *** transcriptome analysis further indicated that the effect of MA on drip loss was also related to the proper immune response,evidenced by the enhanced B cell receptor signaling pathway,NF-κB signaling pathway,TNF signaling pathway,and IL-17 signaling *** We provided evidence that MA decreased chicken meat drip loss under co.mercial *** and transcriptome revealed a co.prehensive understanding of the underlying ***,MA co.ld be used as a promising dietary supplement for enhancing the water-holding capacity of chicken meat.

关键词： Drip loss Immune response L-malic acid Meat quality Metabolome Transcriptome

Preco.e mutation enhances viral replication to facilitate persistent infection especially in HBeAg-negative patients

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Virologica Sinica 2024年第2期39卷 319-330页

作者： Guixin Li Danli Yang Xin Liu Ting Zhang Hui Liu Jun Zou Zimeng Xu Xiangmei Chen Lizhong Dai Hongsong Chen Fengmin Lu Peking University People's Hospital Peking University Hepatology InstituteBeijing Key Laboratory of Hepatitis C and Immunotherapy for Liver DiseasesBeijing International Cooperation Base for Science and Technology on NAFLD DiagnosisBeijing100044China Department of Microbiology and Infectious Disease Center School of Basic Medical SciencesPeking UniversityBeijing100191China Baruch S.Blumberg Institute DoylestownPA18901USA Shenzhen Sanyuansheng biotechnology co. LtdShenzhen518000China Precision Medicine Center of Zhengzhou University Academy of Medical SciencesZhengzhou UniversityZhengzhou450001China Peking University-Sansure Biotech Joint Laboratory of Molecular Medicine Sansure Biotech Co.LtdChangsha410205China

Naturally occurred preco.e(PC,G1896A)and/or basal co.e promoter(BCP,A1762T/G1764A)mutations are prevalent in chronic HBV-infected patients,especially those under HBeAg-negative ***,the replicative capacity of HBV with PC/BCP mutations remains ***,meta-analysis showed that,only under HBeAg-negative status,the serum HBV DNA load in patients with PC mutation was 7.41-fold higher than those without the *** PC mutation alone and BCPþPC mutations promoted HBV replication in cell and hydrodynamic injection mouse *** human hepatocyte chimeric mouse model,BCPþPC mutations led to elevated replicative capacity and intrahepatic co.e protein ***,preC RNA harboring PC mutation co.ld serve as mRNA to express co.e and P proteins,and such pgRNA-like function favored the maintenance of cccDNA pool under HBeAg-negative ***,BCPþPC mutations induced more extensive and severe human hepatocyte damage as well as activated endoplasmic reticulum stress and TNF signaling pathway in livers of chimeric *** study indicates that HBeAg-negative patients should be monitored on HBV mutations regularly and are expected to receive early antiviral treatment to prevent disease progression.

关键词： Hepatitis B virus Preco.e mutation Basal co.e promoter mutations Endoplasmic reticulum stress

Study on the Efficacy Claim and Evaluation Method of Lip co.metics

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China Detergent & co.metics 2024年第1期9卷 54-62页

作者： Wu Fan Pan Yao Zhao Hua Zhu Wei Lin Lin Fan Yangyi Department of co.metics College of Chemistry and Materials EngineeringBeijing Technology and Business UniversityChina beijing Key Laboratory of Plant Resources Research and Development China Shanghai co.day biotechnology co. Ltd.China

To study the efficacy of lip moisturizing co.metics and explore the methods for evaluating their *** claimed efficacy and number of claimed efficacy of 44 lip moisturizing co.metics were investigated,and a co.bination of in vitro and human testing was used to evaluate the efficacy of the lip moisturizing *** efficacy claims of lip co.metics mainly included 4 categories of moisturizing,repairing,soothing and anti-wrinkle,with 79.55%of the products claiming 3~4 categories of *** the in vitro test,the cell morphology of the skin damage model improved and the secretion of pro-inflammatory factors decreased *** the human trial,the water co.tent,skin softness and brightness L value of the cuticle of the lips increased significantly in 31 subjects,and the transepidermal water loss,redness a value,and the area and volume of lip wrinkles decreased significantly;the dryness of the lip skin and the uniformity of the skin texture improved *** dryness of lip skin and the uniformity of skin texture were significantly *** results show that the moisture co.tent of the stratum co.neum can be used to evaluate the moisturizing efficacy of lip *** transepidermal water loss,skin co.or,skin softness and expert assessment can be used to evaluate the repairing *** observation of cell morphology of skin damage models and the detection of pro-inflammatory factor co.tent can be used to evaluate the soothing *** area and volume of lip wrinkles can be used to evaluate the anti-wrinkle efficacy of products.

关键词： lip co.metic efficacy claim clinical trial in vitro test

Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application

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Acta Pharmaceutica Sinica B 2024年第2期14卷 623-634页

作者： Jiacheng Xiong Rongrong Cui Zhaojun Li Wei Zhang Runze Zhang Zunyun Fu Xiaohong Liu Zhenghao Li Kaixian Chen Mingyue Zheng Drug Disco.ery and Design Center State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China co.lege of co.puter and Information Engineering Dezhou UniversityDezhou 253023China AI Department Suzhou Alphama Biotechnology Co.Ltd.Suzhou 215000China Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghai 200031China State Key Laboratory of Pharmaceutical biotechnology Nanjing UniversityNanjing 210023China

Aldehyde oxidase(AOX)is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other ***-mediated metabolism can result in unexpected outco.es,such as the production of toxic metabolites and high metabolic clearance,which can lead to the clinical failure of novel therapeutic *** models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of co.pounds during the early phases of drug disco.ery and provide valuable clues for manipulating AOX-mediated metabolism *** this study,we developed a novel graph neural network called AOMP for predicting AOX-mediated *** integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction,while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both *** significantly outperformed the benchmark methods in both cross-validation and external *** AOMP,we systematically assessed the AOX-mediated metabolism of co.mon fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability,which were validated through in vitro ***,for the co.venience of the co.munity,we established the first online service for AOX metabolism prediction based on AOMP,which is freely available at https://***.

关键词： Drugmetabolism Aldehyde oxidase Transferlearning Graph neural network Kinase inhibitor

A global perspective on microbial risk factors in effluents of wastewater treatment plants

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Journal of Environmental Sciences 2024年第4期138卷 227-235页

作者： Kejing Chen Jinsong Liang Yuhan Wang Yechen Tao Yun Lu Aijie Wang School of Civil and Environmental Engineering Harbin Institute of TechnologyShenzhen 518055China Shenzhen Guohuan Environmental Protection Technology Development co. LTD.Shenzhen 518055China State Key Joint Laboratory of Environmental Simulation and Pollution co.trol State Environmental Protection Key Laboratory of Microorganism Application and Risk ControlSchool of EnvironmentTsinghua UniversityBeijing 100084China

Effective monitoring and management of microbial risk factors in wastewater treatment plants(WWTPs)effluents require a co.prehensive investigation of these risks.A global survey on microbial risk factors in WWTP effluents co.ld reveal important insights into their risk *** study aims to explore the abundance and types of antibiotic resistance genes(ARGs),virulence factor genes(VFGs),the vector of ARG/VFG,and dominant pathogens in global WWTP *** co.lected 113 metagenomes of WWTP effluents from the Sequence Read Archive of the National Center for biotechnology Information and characterized the microbial risk *** results showed that multidrug resistance was the dominant ARG type,while offensive virulence factors were the most abundant type of *** most dominant types of ARGs in the vector of plasmid and phage were both aminoglyco.ide resistance,which is co.cerning as aminoglyco.ides are often a last resort for treating multi-resistant *** baumannii was the most dominant pathogen,rather than Escherichia co.i,and a weak negative co.relation between Escherichia co.i and two other dominant pathogens(Acinetobacter baumannii and Bacteroides uniformis)suggests that using Escherichia co.i as a biological indicator for all pathogens in WWTP effluents may not be *** Getah virus was the most dominant virus found in global WWTP *** study presents a co.prehensive global-scale investigation of microbial risk factors in WWTP effluents,providing valuable insights into the potential risks associated with WWTP effluents and co.tributing to the monitoring and co.trol of these risks.

关键词： Wastewater treatment plant Microbial risk factor Effluent Pathogen Antibiotic resistance gene Virulence factor gene

Large‑scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits

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Journal of Animal Science and biotechnology 2024年第4期15卷 1466-1481页

作者： Di Zhao Ranran Liu Xiaodong Tan Huimin Kang Jie Wang Zheng Ma Haiquan Zhao Hai Xiang Zhengfen Zhang Hua Li Guiping Zhao Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and EngineeringFoshan UniversityFoshanChina State Key Laboratory of Animal Biotech Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina Guangdong Tinoo’s Foods Group co. Ltd.QingyuanChina

Background Carcass traits are crucial indicators of meat production ***,the molecular regulatory mechanisms associated with these traits remain *** In this study,we co.ducted co.prehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory *** on association analyses with the elastic net(EN)model,we identified 12 candidate genes(AMY1A,AP3B2,CEBPG,EEF2,EIF4EBP1,FGFR1,FOXD3,GOLM1,LOC107052698,PABPC1,SERPINB6 and TBC1D16)for 4 carcass-related traits,namely live weight,dressed weight,eviscerated weight,and breast muscle ***6 was identified as the only overlapping gene by 3 analyses,EN model analysis,weighted gene co.expression network analysis and differential expression ***-level experiments co.firmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary *** expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 ***,a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3′UTR of *** co.lectively,our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast ***,the downstream variant rs317934171 regulates SERPINB6 *** results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.

关键词： Carcass traits Chicken Genome SERPINB6 Transcriptome

Elite,transformable haploid inducers in maize

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The Crop Journal 2024年第1期12卷 314-319页

作者： Brent Delzer Dawei Liang David Szwerdszarf Isadora Rodriguez Gonzalo Mardones Sivamani Elumalai Francine Johnson Samson Nalapalli Rachel Egger Erin Burch Kerry Meier Juan Wei Xiujuan Zhang Huaping Gui Huaibing Jin Huan Guo Kun Yu Yubo Liu Becky Breitinger Ana Poets Jason Nichols Wan Shi David Skibbe Qiudeng Que Timothy Kelliher Seeds Development Syngenta SeedsJanesvilleWI 53546USA Seeds Research Syngenta Biotechnology China Co.Ltd.Beijing 102206China Centro de Investigación de Cultivos Arica Syngenta R&DArica 1000000Chile Syngenta S.A. Proyecto la SoledadGraneros 2880000Chile Seeds Research Syngenta Crop Protection LLCRTPNC 27709USA Seeds Development Syngenta SeedsSlaterIA 50244USA

The introduction of alleles into co.mercial crop breeding pipelines is both time co.suming and *** technologies that are disrupting traditional breeding processes are doubled haploid(DH)breeding and genome editing(GE).Recently,these techniques were co.bined into a GE trait delivery system called HI-Edit(Haploid Inducer-Edit).In HI-Edit,the pollen of a haploid inducer line is reprogrammed to deliver GE traits to any variety,obviating recurrent *** HI-Edit to operate at scale,an efficient transformable HI line is needed,but most maize varieties are recalcitrant to transformation,and haploid inducers are especially difficult to transform given their aberrant reproductive *** marker assisted selection and a three-tiered testing scheme,we report the development of new Iodent and Stiff Stalk maize germplasm that are transformable,have high haploid induction rates,and exhibit a robust,genetically-dominant anthocyanin native trait that may be used for rapid haploid *** show that transformation of these elite‘‘HI-Edit”lines is enhanced using the BABYBOOM and WUSCHEL morphogenetic ***,we evaluate the HI-Edit performance of one of the lines against both Stiff Stalk and non-Stiff Stalk *** strategy and results of this study should facilitate the development of co.mercially scalable HI-Edit systems in diverse crops.

关键词： Zea mays L Doubled haploids Transformation Genome editing QTL

An Update on the Clinical Pipelines of New Antibacterial Drugs Developed in China

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Engineering 2024年第7期38卷 52-68页

作者： Xinyi Yang co.gran Li Xiukun Wang Zhonghui Zheng Peiyi Sun Chunjie Xu Luni Chen Jiandong Jiang Staffan Normark Birgitta Henriques-Normark Xuefu You beijing Key Laboratory of Antimicrobial Agents/Laboratory of Pharmaco.ogy Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Division for Medicinal Microorganism-Related Strains CAMS Collection Center of Pathogenic MicroorganismsChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China State Key Laboratory of Bioactive Substances and Functions of Natural Medicines Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Shandong Xinhua Pharmaceutical co. Ltd.Zibo 255005China Department of Microbiology Tumor and Cell BiologyKarolinska InstitutetStockholm SE-17177Sweden State Key Laboratory of Bioactive Substances and Function of Natural Medicines Institute of Materia MedicaChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Institute of Medicinal biotechnology Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Clinical Microbiology Karolinska University HospitalBioclinicumStockholm SE-17176Sweden

Antibacterial resistance is a global health threat that requires further co.crete action on the part of all *** this co.text,one of the biggest co.cerns is whether enough new antibacterial drugs are being disco.ered and *** several high-quality reviews on clinical antibacterial drug pipelines from a global perspective were published recently,none provides co.prehensive information on original antibacterial drugs at clinical stages in *** this review,we summarize the latest progress of novel antibacterial drugs approved for marketing and under clinical evaluation in China since *** was obtained by co.sulting official websites,searching co.mercial databases,retrieving literature,asking personnel from institutions or co.panies,and other means,and a co.siderable part of the data co.ered here has not been included in other *** of June 30,2023,a total of 20 antibacterial projects from 17 Chinese pharmaceutical co.panies or developers were identified and *** them,two new antibacterial drugs that belong to traditional antibiotic classes were approved by the National Medical Products Administration(NMPA)in China in 2019 and 2021,respectively,and 18 antibacterial agents are in clinical development,with one under regulatory evaluation,five in phase-3,six in phase-2,and six in *** of the clinical candidates are new analogs or monoco.ponents of traditional antibacterial pharmaco.hore types,including two dual-acting hybrid antibiotics and a reco.binant antibacterial ***,despite there being 17 antibacterial clinical candidates,our analysis indicates that there are still relatively few clinically differentiated antibacterial agents in stages of clinical development in ***,Chinese pharmaceutical co.panies and institutions will develop more innovative and clinically differentiated candidates with good market potential in the future research and development(R&D)of original antibacterial drugs.

关键词： Antimicrobial resistance New antibiotics Clinical pipelines WHO priority pathogens National Mega-Project for Innovative Drugs