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Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy

Virologica Sinica 2024年第4期39卷 655-666页

作者： Zerui Yang Jingyan Zeng Yueyue Chen Mengchun Wang Hongchun luo Ai-Long Huang Haijun Deng yuan Hu Key Laboratory of Molecular Biology on Infectious Diseases Ministry of EducationChongqing Medical UniversityChongqing400016China Department of Infectious Diseases The First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China

The landscape of hepatitis B virus(HBV)integration in the plasma cell-free DNA(cfDNA)of HBV-infected patients with different stages of liver diseases[chronic hepatitis B(CHB),liver cirrhosis(LC),and hepatocellular carcinoma(HCC)]remains *** this study,we developed an improved strategy for detecting HBV DNA integration in plasma cfDNA,based on DNA probe capture and next-generation *** this optimized strategy,we successfully detected HBV integration events in chimeric artificial DNA samples and HBV-infected HepG2-NTCP cells at day one post infection,with high sensitivity and *** characteristics of HBV integration events in the HBV-infected HepG2-NTCP cells and plasma cfDNA from HBV-infected individuals(CHB,LC,and HCC)were further investigated.A total of 112 and 333 integration breakpoints were detected in the HepG2-NTCP cells and 22 out of 25(88%)clinical HBV-infected samples,*** vivo analysis showed that the normalized number of support unique sequences(nnsus)in HCC was significantly higher than in CHB or LC patients(P values<0.05).All integration breakpoints are randomly distributed on human chromosomes and are enriched in the HBV genome around nt *** majority of integration breakpoints(61.86%)are located in the gene-coding *** non-homologous end-joining(NHEJ)and microhomology-mediated end-joining(MMEJ)interactions occurred during HBV integration across the three different stages of liver *** study provides evidence that HBV DNA integration can be detected in the plasma cfDNA of HBV-infected patients,including those with CHB,LC,or HCC,using this optimized strategy.

关键词： Hepatitis B virus(HBV) DNA integration Cell-free DNA(cfDNA) DNA capture

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Design and Application of an S-band Fast Radio Bursts Search Pipeline for the Nanshan 26 m Radio Telescope

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Research in Astronomy and Astrophysics 2024年第7期24卷 111-117页

作者： Yan-Ling Liu Mao-Zheng Chen jian Li jian-Ping yuan Rai Yuen Zhi-Yong Liu Hao Yan Wen-Long Du Nan-Nan Zhai Xinjiang Astronomical Observatory Chinese Academy of SciencesUrumqi 830011China Xinjiang Key Laboratory of Microwave Technology Urumqi 830011China University of Chinese Academy of Sciences Beijing 100049China

Fast radio bursts(FRBs)are among the most studied radio transients in astrophysics,but their origin and radiation mechanism are still *** is a challenge to search for FRB events in a huge amount of observational data with high speed and high *** the rapid advancement of the FRB research process,FRB searching has changed from archive data mining to either long-term monitoring of the repeating FRBs or all-sky surveys with specialized ***,establishing a highly efficient and high quality FRB search pipeline is the primary task in FRB *** learning techniques provide new ideas for FRB search *** have detected radio bursts from FRB 20201124A in the L-band observational data of the Nanshan 26 m radio telescope(NSRT-26m)using the constructed deep learning based search pipeline named dispersed dynamic spectra search(DDSS).Afterwards,we further retrained the deep learning model and applied the DDSS framework to S-band *** this paper,we present the FRB observation system and search pipeline using the S-band *** carried out search experiments,and successfully detected the radio bursts from the magnetar SGR J1935+2145and FRB *** experimental results show that the search pipeline can complete the search efficiently and output the search results with high accuracy.

关键词： radio continuum general-methods data analysis-methods observational

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Multi-genome evolutionary study of the ABC1 gene family and identification of the pleiotropic effects of OsABC1-13 in rice development

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The Crop Journal 2024年第4期12卷 1022-1030页

作者： Fuying Ma Mingyu Liu Peiwen Yan Shicong He jian Hu Xinwei Zhang Fuan Niu Jinhao Cui Xinyu yuan Xiaoyun Xin Liming Cao Jinshui Yang Ying Wang Xiaojin luo State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology(Ministry of Education) School of Life SciencesFudan UniversityShanghai 200433China Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering Department of Ecology and Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Institute of Crop Breeding and Cultivation Shanghai Academy of Agricultural SciencesShanghai 200241China Ministry of Education Key Laboratory of Crop PhysiologyEcology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045JiangxiChina

In four rice genomes,85 ABC1-family genes were identified by comparative genomics,evolution,genetics,and ***,OsABC1-13,was shown by knockdown and knockout experiments to affect plant height,grain size,and photosynthet... 详细信息

关键词： Multi-genome analysis Activity of bc1 complex gene Photosynthesis Biomass Osabc1-13 Haplotype

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Combined intestinal microbiota and transcriptomic analysis to investigate the effect of different stocking densities on the ability of Pacific fi c white shrimp ( Litopenaeus vannamei) ) to utilize Chlorella sorokiniana

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ANIMAL NUTRITION 2024年第3期18卷 203-219页

作者： yuan, Hang Xie, Minghua Chen, jian Hu, Naijie Wang, Honming Tan, Beiping Shi, Lili Zhang, Shuang Guangdong Ocean Univ Coll Fisheries Zhanjiang Peoples R China Chinese Acad Trop Agr Sci Zhanjiang Expt Stn Zhanjiang Peoples R China Dalian Ocean Univ Coll Fisheries & Life Sci Dalian Peoples R China

Aiming to investigate the impact of different stocking densities on the ability of Pacific white shrimp (Litopenaeus vannamei) to utilize Chlorella sorokiniana (CHL), a 3 x 2 factorial design stocking experiment was used in this study. Specifically, shrimp was fed with two dietary protein sources (fishmeal [FM] and CHL) at low (LSD; 100 per m(3)), medium (MSD; 200 per m3) and high (HSD; 300 per m3) stocking densities for 8 weeks. The growth performance and resistance to Vibrio parahaemolyticus (1.0 x 107 CFU/ mL) of shrimp decreased with the increase of stocking density, but dietary CHL improved this result. Differences between the CHL and FM groups for V. parahaemolyticus resistance were significant only under high-density conditions (P < 0.05). Significant interactions between stocking density and protein source were found on the activities of catalase (CAT), superoxide dismutase (SOD) and phenol oxidase (PO), and the contents of malondialdehyde (MDA) in the hepatopancreas and the activities of intestinal amylase, most of which were significantly different between CHL and FM groups only at high stocking density (P < 0.05). Analysis of 16S rDNA sequencing showed that dietary CHL increased the alpha diversity of intestinal microbiota, inhibited the colonization of pathogenic bacteria and enhanced the abundance of beneficial bacteria. Transcriptomic results showed that at high stocking densities, differentially expressed genes (DEGs) in the FM vs CHL group were mostly upregulated and primarily enriched in immune and metabolic related pathways including Toll, immune deficiency (Imd) and glycolysis -gluconeogenesis pathways. Pearson correlation analysis revealed significant correlation between the top ten intestinal bacteria at the genus level and markedly enriched DEGs, also more were detected under high density situations. In conclusion, CHL has great potential as a novel protein source in the intensive farming of shrimp. (c) 2024 The Authors. Publishing services by

关键词： Chlorella sorokiniana Stocking density Microbiota structure Transcriptomic profile Litopenaeus vannamei CLARIAS-GARIEPINUS BURCHELL GROWTH-PERFORMANCE BODY-COMPOSITION RAINBOW-TROUT SPIRULINA-PLATENSIS ENZYME-ACTIVITIES MEAL REPLACEMENT FEED-UTILIZATION PROTEIN-SOURCES IMMUNE

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Dynamic mechanical characteristics of deep Jinping marble in complex stress environments

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第2期16卷 630-644页

作者： Chendi Lou Heping Xie Ru Zhang Hai Ren Hao luo Kun Xiao yuan Peng Qiang Tan Li Ren Institute for Disaster Management and Reconstruction Sichuan UniversityChengdu610207China College of Water Resource&Hydropower Sichuan UniversityChengdu610065China MOE Key Laboratory of Deep Earth Science&Engineering Sichuan UniversityChengdu610065China Yalong River Hydropower Development Company Ltd.Chengdu610051China (Chongqing)International Engineering Technology Company Ltd.Chongqing401121China

To reveal the dynamic mechanical characteristics of deep rocks,a series of impact tests under triaxial static stress states corresponding to depths of 300-2400 m were *** results showed that both the strain rates and the stress environments in depth significantly affect the mechanical characteristics of *** sensitivity of strain rate to the dynamic strength and deformation modulus shows a negative correlation with depth,indicating that producing penetrative cracks in deep environments is more difficult when damage *** dynamic strength shows a tendency to decrease and then increase slightly,but decreases sharply *** demonstrates a similar trend as that of strength,whereas reflectivity indicates the opposite ***,two critical depths with high dynamically induced hazard possibilities based on the China Jinping Underground Laboratory(CJPL)were proposed for deep *** first critical depth is 600-900 m,beyond which the sensitivity of rock dynamic characteristics to the strain rate and restraint of circumferential stress decrease,causing instability of surrounding rocks under axial stress *** second one lies at 1500-1800 m,where the wave impedance and dynamic strength of deep surrounding rocks drop sharply,and the dissipation energy presents a negative *** suggests that the dynamic instability of deep surrounding rocks can be divided into dynamic load dominant and dynamic load induced types,depending on the second critical depth.

关键词： Rock mechanics Split-Hopkinson pressure bar Coupled static‒dynamic loading Different depths Holmquist-Johnson-Cook(HJC)model

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Strong Antiferromagnetic Exchange-Coupling Observed in Hydride-Bridged Dimeric Dysprosium(Ⅲ)Single-Molecule Magnet

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Chinese Journal of Chemistry 2024年第4期42卷 391-396页

作者： Qian-Cheng luo Ke-Xin Yu Peng-Bo Jin Ye-Ye Liu yuan-Qi Zhai Yan-Zhen Zheng Frontier Institute of Science and Technology State Key Laboratory of Electrical Insulation and Power EquipmentXi'an Key Laboratory of Electronic Devices and Materials ChemistrySchool of Chemistry and School of PhysicsXi'an Jiaotong University99 Yanxiang RoadXi'anShaanxi710054 China

One dihydride-bridged dimeric Dy(Ⅲ)guanidinate complex,formulated as[{(Me_(3)Si)_(2)NC(NiPr)_(2)}_(2)Dy(μ-H)]_(2)(1Dy),was successfully isolated and the introduction of hydride bridges significantly reduces the intramolecular Dy(Ⅲ)…Dy(Ⅲ)distance to only 3.688(1)Å.To investigate the effect of such a short Dy(Ⅲ)…Dy(Ⅲ)distance on magnetism,we also prepared its dibromide-bridged analogue[{(Me_(3)Si)_(2)NC(NiPr)_(2)}_(2)Dy(μ-Br)]_(2)(2Dy),which has a much longer Dy(Ⅲ)…Dy(Ⅲ)distance of 4.605(4)Å.Surprisingly,2Dy demonstrates much larger effective energy barrier for magnetization reversal(U_(eff))and higher blocking temperature(T_(B)).The worse performance of 1Dy is attributed to the concerted effect of strong antiferromagnetic interactions between Dy(Ⅲ)ions(J_(total)=–2.683 cm^(–1))and the unparallel arrangement of magnetic principle axes of the Dy(Ⅲ)ions for 1Dy.

关键词： Single-molecule magnets Lanthanides Guanidinate ligand Hydride bridge Magnetic properties Ab initio calculations

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Identification of differentially expressed mRNAs as novel predictive biomarkers for gastric cancer diagnosis and prognosis

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World Journal of Gastrointestinal Oncology 2024年第5期16卷 1947-1964页

作者： jian-Wei Zhou Yi-Bing Zhang Zhi-Yang Huang Yu-Ping yuan Jie Jin Department of Gastroenterology Wenzhou Central HospitalDingli Clinical College of Wenzhou Medical UniversityThe Second Affiliated Hospital of Shanghai UniversityWenzhou 325000Zhejiang ProvinceChina

BACKGROUND Gastric cancer(GC)has a high mortality rate *** significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains *** To identify important candidate genes related to the development of GC and iden-tify potential pathogenic mechanisms through comprehensive bioinformatics *** The Gene Expression Omnibus database was used to obtain the GSE183136 dataset,which includes a total of 135 GC *** limma package in R software was employed to identify differentially expressed genes(DEGs).Thereafter,enrichment analyses of Gene Ontology(GO)terms and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed for the gene modules using the clusterProfile package in R *** protein-protein interaction(PPI)networks of target genes were constructed using STRING and visualized by Cytoscape *** common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn *** expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier ***,real-time quantitative polymerase chain reaction(RT-qPCR)and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase(GPT)in GC and normal immortalized cell *** addition,cell viability,cell cycle distribution,migration and invasion were evaluated by cell counting kit-8,flow cytometry and transwell ***,we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital,Dingli Clinical College of Wenzhou Medical University,The Second Affiliated Hospital of Shanghai University between January 2017 to December *** tumor and adjacent normal samples were collected from the patients to determine the

关键词： Gastric cancer Differentially expressed genes Bioinformatics Hub genes Prognosis

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A highly sensitive fluorescent probe RN-NA reveals peroxynitrite as a novel biomarker for primary open angle glaucoma

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International Journal of Ophthalmology(English edition) 2024年第2期17卷 219-227页

作者： Bo Qin yuan Lei luo Bao You-Jia Zhang Ke-Yin Liu Yu-Hong Chen Department of Ophthalmology&Visual Science Eye&ENT HospitalShanghai Medical CollegeFudan UniversityShanghai 200031China Key Laboratory of Myopia NHFPC(Fudan University)Shanghai Key Laboratory of Visual Impairment and Restoration(Fudan University)Shanghai 200031China State Key Laboratory of Biobased Material and Green Papermaking Key Laboratory of Pulp&Paper Science and Technology of Shandong Province/Ministry of EducationQilu University of TechnologyShandong Academy of SciencesJinan 250353Shandong ProvinceChina

AIM:To directly quantify peroxynitrite(ONOO-)using a highly sensitive fluorescence resonance energy transfer probe RN-NA,investigate the association between ONOOand primary open angle glaucoma(POAG),and clarify whether RN-NA could be used as a potential tool for POAG ***:Plasma and aqueous humor(AH)samples were collected from POAG patients(n=100,age:59.70±6.87y)and age-related cataract(ARC)patients(n=100,age:61.15±4.60y)admitted to our ***,RN-NA was used to detect ONOO-in plasma and AH samples,and the relationship between ONOO-level and POAG was analyzed using binary logistic ***,Pearson correlation analysis was applied to characterize the correlation of the levels of ONOO-with the patients’age,intraocular pressure(IOP),and mean deviation of visual field *** ONOO-scavenger MnTMPyP was employed to treat the 3-morpholinosyndnomine(SIN-1)-induced ocular hypertension in mice(n=7,6-8wk).Finally,the IOP and ONOO-in both eyes were measured 30min after the last drug ***:ONOO-levels of AH and plasma were significantly higher in the POAG group than in the ARC group(P<0.01).Additionally,ONOO-levels were closely correlated with POAG in a binary logistic regression analysis[odds ratio(OR)=1.008,95%confidence interval(CI):1.002-1.013,P<0.01 for AH;OR=1.004,95%CI:1.002-1.006,P<0.001 for plasma].Pearson correlation analysis showed that ONOO-levels in AH or plasma were positively associated with visual field defects(R=0.51,P<0.01 for AH;R=0.45,P<0.001 for plasma),and ONOO-levels in plasma and AH were correlated in the POAG group(R=0.69,P<0.001).However,administering MnTMPyP to mouse eyes reversed the elevated IOP caused by SIN-1(P<0.05).CONCLUSION:ONOO-levels in AH and plasma,detected by RN-NA,are significantly related to POAG and positively correlated with visual field defects in POAG ***,ONOO-is a potential biomarker of POAG,especially advanced ***,anti-nitration compounds may be novel ocular hypotens

关键词： peroxynitrite fluorescent probe RN-NA primary open angle glaucoma 3-morpholinosyndnomine

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(Benzimidazolium)_(2)GeI_(4):A layered two-dimensional perovskite with dielectric switching and broadband near-infrared photoluminescence

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Chinese Journal of Structural Chemistry 2024年第6期43卷 45-49页

作者： Xuan Zhu Lin Zhou Xiao-Yun Huang Yan-Ling luo Xin Deng Xin Yan Yan-Juan Wang Yan Qin yuan-yuan Tang Ordered Matter Science Research Center Nanchang UniversityNanchang330031People's Republic of China

Two-dimensional(2D)lead halide perovskites have attracted tremendous attention due to their outstanding physical ***,the presence of toxic lead is a major problem for large-scale ***,we report the synthesis,phase transition,dielectric and photoluminescence(PL)properties of a lead-free 2D Ge-based perovskite(BIM)_(2)GeI_(4)(BIM=benzimidazolium)which experiences a phase transition at 405 K accompanied by an order-disorder change of organic ***,the step-like dielectric transition near the phase transition temperature makes it suitable for dielectric ***,(BIM)_(2)GeI_(4)has a direct bandgap of 2.23 eV and broadband emission from 550 to 1000 nm,implying its unique optical property for potential near-infrared lighting and *** work provides a fresh example for the development of lead-free 2D Ge-based perovskite with potential applications in the fields of optoelectronics and high temperature dielectric switching.

关键词： Dielectric switching Photoluminescence Two-dimensional perovskite Lead-free perovskite

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Highly Aromatic Norditerpenoid Heterodimers and Monomers from Trigonostemon fragilis

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Engineering 2024年第7期38卷 144-154页

作者： Jun-Su Zhou Long Cheng yuan Gao Zhan-Peng Ge Bin Zhou Jing-Ya Li Jin-Xin Zhao jian-Min Yue State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China Shandong Laboratory of Yantai Drug Discovery Bohai Rim Advanced Research Institute for Drug DiscoveryYantai 264117China

Four new norditerpenoid heterodimers with different dimerization patterns-namely,trigofragiloids A-C(denoted as compounds 1-3)and(+)-and(-)-trigofragiloid D(compound 4)-and three new phenanthrenone norditerpenoids-namely,trigofragiloids E-G(compounds 5-7)-were isolated from Trigonostemon *** 1 and 2 feature a novel heterodimeric carbon skeleton formed by the conjugation of a tetra-norditerpenoid and an ennea-norditerpenoid;they have been identified as class 2 atropisomers by means of quantum chemical *** 3 is an unprecedented phenylpropanoid-norditerpenoid adduct with a new dimerization ***(+)-and(-)-4 are the first example of S-shaped 1,4-dioxane-fused norditerpenoid *** by the structure elucidation of compound 4,two co-occurring analogues,actephilol A and epiactephilol A,were structurally revised as a pair of geometrical isomers and were identified as two pairs of enantiomers,(+)-and(-)-8 and(+)-and(-)-9,*** structures were characterized using a combined ***,compound 7 exhibits remarkable adenosine triphosphate-citrate lyase(ACLY)inhibition with a halfmaximal inhibition concentration(IC50)value of(0.46±0.11)lmol·L^(-1),as active as the positive control BMS-303141,and a molecular docking study offers deep insight into the interaction between compound 7 and ACLY.

关键词： Norditerpenoid heterodimer Trigonostemon fragilis Euphorbiaceae Trigofragiloid Structural revision Adenosine triphosphate-citrate lyase(ACLY) inhibitory activity

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