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Construction of CDKN2A-related competitive endogenous RNA network and identification of GAS5 as a prognostic indicator for hepatocellular carcinoma

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World Journal of Gastrointestinal Oncology 2024年第4期16卷 1514-1531页

作者： Yong Pan Yi-Ru Zhang ling-Yun wang li-Na wu Ying-Qiu Ma Zhou Fang shi-Bo li Department of Infectious Disease Zhoushan HospitalWenzhou Medical UniversityZhoushan 316021Zhejiang ProvinceChina State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital of Zhejiang UniversityHangzhou 310003Zhejiang ProvinceChina Department of Infectious Disease The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325035Zhejiang ProvinceChina

BACKGROUND Competitive endogenous RNA(ceRNA)is an innovative way of gene expression modulation,which plays a crucial part in ***,the intricacy and behavioral characteristics of the ceRNA network in hepatocellular carcinoma(HCC)remain *** To establish a cyclin dependent kinase inhibitor 2A(CDKN2A)-related ceRNA network and recognize potential prognostic indicators for *** The mutation landscape of CDKN2A in HCC was first explored using the cBioPortal *** expression analysis was implemented between CDKN2Ahigh and CDKN2Alow expression HCC *** targeted microRNAs were predicted by lncBasev3.0,and the targeted mRNAs were predicted by miRDB,and Targetscan *** univariate and multivariate analysis were utilized to identify independent prognostic *** CDKN2A was frequently mutated and deleted in *** single-cell RNA-sequencing analysis revealed that CDKN2A participated in cell cycle *** CDKN2A-related ceRNA network-growth arrest specific 5(GAS5)/miR-25-3p/SRY-box transcription factor 11(SOX11)was successfully ***5 was recognized as an independent prognostic biomarker,whose overexpression was correlated with a poor prognosis in HCC *** association between GAS5 expression and methylation,immune infilt-ration was ***,traditional Chinese medicine effective components targeting GAS5 were *** This CDKN2A-related ceRNA network provides innovative insights into the molecular mechanism of HCC formation and ***,GAS5 might be a significant prognostic biomarker and therapeutic target in HCC.

关键词： Hepatocellular carcinoma Competitive endogenous RNA Molecular mechanism Prognosis Biomarker

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Edge modes in finite-size systems with different edge terminals

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Chinese Physics B 2024年第10期33卷 381-387页

作者： Huiping wang li ren Xiuli Zhang liguo Qin School of Mathematics Physics and StatisticsShanghai University of Engineering ScienceShanghai 201620China

We investigate the behavior of edge modes in the presence of different edge terminations and long-range(LR)***,we mainly focus on such model crystals with two different types of structures(type I:“…-P-Q-P-Q-…”and type II:“…=P-Q=P-Q=…”),where P and Q represent crystal lines(CLs),while the symbols“-”and“=”denote the distance between the nearest neighbor(NN)*** on the lattice model Hamiltonian with LR hopping,the existence of edge modes is determined analytically by using the transfer matrix method(TMM)when different edge terminals are taken into *** findings are consistent with the numerical results obtained by the exact diagonalization *** also notice that edge modes can exhibit different behaviors under different edge *** result is helpful in solving novel edge modes in honeycomb crystalline graphene and transition metal dichalcogenides with different edge terminals.

关键词： edge modes long-range hopping different edge terminals

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Urban growth scenario projection using heuristic cellular automata in arid areas considering the drought impact

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Journal of Arid Land 2024年第4期16卷 580-601页

作者： TANG Xiaoyan FENG yongjiu LEI Zhenkun CHEN Shurui wang Jiafeng wang Rong TANG Panli wang Mian JIN Yanmin TONG Xiaohua College of Surveying&Geo-Informatics Tongji UniversityShanghai 200092China Shanghai Key Laboratory of Space Mapping and Remote Sensing for Planetary Exploration Tongji UniversityShanghai 200092China

Arid areas with low precipitation and sparse vegetation typically yield compact urban pattern,and drought directly impacts urban site selection,growth processes,and future *** simulation and projection based on cellular automata(CA)models is important to achieve sustainable urban development in arid *** developed a new CA model using bat algorithm(BA)named bat algorithm-probability-of-occurrence-cellular automata(BA-POO-CA)model by considering drought constraint to accurately delineate urban growth patterns and project future scenarios of Urumqi City and its surrounding areas,located in Xinjiang Uygur Autonomous Region,*** calibrated the BA-POO-CA model for the drought-prone study area with 2000 and 2010 data and validated the model with 2010 and 2020 data,and finally projected its urban scenarios in *** results showed that BA-POO-CA model yielded overall accuracy of 97.70%and figure-of-merits(FOMs)of 35.50%in 2010,and 97.70%and 26.70%in 2020,*** inclusion of drought intensity factor improved the performance of BA-POO-CA model in terms of FOMs,with increases of 5.50%in 2010 and 7.90%in 2020 than the model excluding drought intensity *** suggested that the urban growth of Urumqi City was affected by drought,and therefore taking drought intensity factor into account would contribute to simulation *** BA-POO-CA model including drought intensity factor was used to project two possible scenarios(i.e.,business-as-usual(BAU)scenario and ecological scenario)in *** the BAU scenario,the urban growth dominated mainly in urban fringe areas,especially in the northern part of Toutunhe District,Xinshi District,and Midong *** exceptional and extreme drought areas as a spatial constraint,the urban growth was mainly concentrated in the"main urban areas-Changji-Hutubi"corridor urban pattern in the ecological *** results of this research can help to adjust urban planning and development *** mode

关键词： bat algorithm cellular automata(CA) probability-of-occurrence drought intensity algorithm-probability-of-occurrence-cellular automata(BA-POO-CA)model arid areas

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link Prediction Method Fusion with Local Structural Entropy for Directed Network

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Chinese Journal of Electronics 2024年第1期33卷 204-216页

作者： Shuxin liU Hongchang CHEN Lan wu Kai wang Xing li People’s liberation Army Strategic Support Force Information Engineering University

link prediction utilizes accessible network information to complement or predict the network *** is an important prerequisite for link prediction which means links more likely occurs between two similar nodes. Existing methods utilize the similarity of nodes but neglect of network structure. However the link direction leads to a far more complex structure and contains more information useful than the undirected networks. Most classic methods are difficult to depict the distribution of the network structure with incidental direction so the similarity characteristics of the network structure itself are lost. In this respect, a new method of local structure entropy is proposed to depict the directed structural distribution characteristics, which can be used to evaluate the degree of local structural similarity of nodes and then applied to link prediction methods. Experimental results on 8 real directed networks show that this method is effective for both area under the receiver operating characteristic curve(AUC)and ranking-score measures, and improved predictive capacity of the baseline methodology.

关键词： Correlation Current measurement Area measurement Prediction methods Receivers Benchmark testing Entropy

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Genome-wide association study of grain micronutrient concentrations in bread wheat

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Journal of Integrative Agriculture 2024年第5期23卷 1468-1480页

作者： Yongchao Hao Fanmei Kong lili wang Yu Zhao Mengyao li Naixiu Che Shuang li Min wang Ming Hao Xiaocun Zhang Yan Zhao State Key Laboratory of Crop Biology/College of Agronomy Shandong Agricultural UniversityTai'an 271018China College of Resources and Environment Shandong Agricultural UniversityTai'an 271018China Jining liangshan Ecological Environment Affairs Center Jining 272100China College of Forestry Shandong Agricultural UniversityTai'an 271018China

Bread wheat(Triticum aestivum)is a staple food crop *** genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world's growing ***,45,298 single-nucleotide polymorphisms(SNPs)from 55K chip arrays were used to genotype a panel of 768 wheat cultivars,and a total of 154 quantitative trait loci(QTLs)were detected for eight traits under three environments by genome-wide association study(GWAS).Three QTLs(qMn-3B.1,qFe-3B.4,and qSe-3B.1/qFe-3B.6)detected repeatedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant *** SNPs in the three QTL regions formed six haplotypes for qMn-3B.1,three haplotypes for qFe-3B.4,and three haplotypes for qSe-3B.1/*** analysis revealed significant differences among *** results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern *** on the QTL regions,we identified 15 high-confidence genes,eight of which were stably expressed in different tissues and/or developmental ***3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology(GO)***3B02G199000,which belongs to qSe-3B.1/qFe-3B.6,was determined to be a member of the WRKY gene ***,this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain,and this information will facilitate the breeding of wheat cultivars with improved grain properties.

关键词： bread wheat nutritional element GWAS domestication haplotype

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A credibility-aware swarm-federated deep learning framework in internet of vehicles

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Digital Communications and Networks 2024年第1期10卷 150-157页

作者： Zhe wang Xinhang li Tianhao wu Chen Xu lin Zhang School of Artificial Intelligence Beijing University of Posts and TelecommunicationsBeijing100876China

Although Federated Deep Learning(FDL)enables distributed machine learning in the Internet of Vehicles(IoV),it requires multiple clients to upload model parameters,thus still existing unavoidable communication overhead and data privacy *** recently proposed Swarm Learning(SL)provides a decentralized machine learning approach for unit edge computing and blockchain-based coordination.A Swarm-Federated Deep Learning framework in the IoV system(IoV-SFDL)that integrates SL into the FDL framework is proposed in this *** IoV-SFDL organizes vehicles to generate local SL models with adjacent vehicles based on the blockchain empowered SL,then aggregates the global FDL model among different SL groups with a credibility weights prediction *** experimental results show that compared with the baseline frameworks,the proposed IoV-SFDL framework reduces the overhead of client-to-server communication by 16.72%,while the model performance improves by about 5.02%for the same training iterations.

关键词： Swarm learning Federated deep learning Internet of vehicles Privacy Efficiency

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Inhibiting the phase transition of WO_(3)for highly stable aqueous electrochromic battery

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Journal of Energy Chemistry 2024年第8期95卷 86-95,I0003页

作者： Zhisheng wu Zhendong lian Ting Ding Jielei li Jincheng Xu Jinxiao wang liangxing Zhang Bo wang shi Chen Peng Xiao Hua Xu Shuang-Peng wang Kar Wei Ng Joint Key Laboratory of the Ministry of Education Institute of Applied Physics and Materials EngineeringUniversity of MacaoAvenida da UniversidadeMacao 999078China School of Applied Physics and Materials Wuyi UniversityJiangmen 529020GuangdongChina Guangdong-Hong Kong-Macao Joint Laboratory for Intelligent Micro-Nano Optoelectronic Technology School of Physics and Optoelectronic EngineeringFoshan UniversityFoshan 528225GuangdongChina Guangzhou New Vision Optoelectronic Technology Co. Ltd.Guangzhou 510530GuangdongChina

Aqueous electrochromic battery(ECB)has shown intense potential for achieving energy storage and saving *** tungsten oxide(WO_(3))is the most promising EC material for commercialization,the cycling stability of WO_(3)-based aqueous ECBs is currently unsatisfactory due to the repeated phase transition during the redox process and the corrosion by acidic ***,we present a titanium-tungsten oxide alloy(Ti-WO_(3))with controllable morphology and crystal phase synthesized by a facile hot injection method to overcome the *** contrast to conventional monoclinic WO_(3),the Ti-WO_(3)nanorods can stably maintain their cubic crystal phase during the redox reaction in an acidic electrolyte,thus leading to dramatically enhanced response speed and cycling stability,Specifically,when working in a well-matched hybrid Al^(3+)/Zn^(2+)aqueous electrolyte,our phasetransition-free cubic Ti-WO_(3)exhibits an ultra-high cycling stability(>20000 cycles),fast response speed(3,95 s/4,65 s for bleaching/coloring),as well as excellent discharge areal capacity of 214.5 mA h m^(-2),We further fabricate a fully complementa ry aqueous electrochromic device,for the first time,using a Ti-WO_(3)/Prussian blue device ***,the complementary ECB shows>10000 stable operation cycles,attesting to the feasibility of our Ti-WO_(3)for practical *** work validates the significance of inhibiting the phase transitions of WO_(3)during the electrochromic process for realizing highly cyclable aqueous ECB,which can possibly provide a generalized design guidance for other high-quality metallic oxides for electrochemical applications.

关键词： Aqueous electrochromic battery Ti-WO_(3) Phase transition Long-term stability

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Diverse nucleotide substitutions in rice base editing mediated by novel TadA variants

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Plant Communications 2024年第8期5卷 104-112页

作者： Man Yu Yongjie Kuang Chenyang wang Xuemei wu Shaofang li Dawei Zhang Wenxian Sun Xueping Zhou Bin ren Huanbin Zhou State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Department of Plant Pathology China Agricultural UniversityBeijing 100193China Scientific Observing and Experimental Station of Crop Pests in Guilin Ministry of Agriculture and Rural AffairsGuilin 541399China Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment College of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610064China State Key Laboratory of Vegetable Biobreeding National Engineering Research Center for VegetablesBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijing 100097China State Key Laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Key Laboratory of Gene Editing Technologies(Hainan) Ministry of Agricultural and Rural AffairsSanya 572024China

CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution for the rapid genetic improvement of *** editing capabilities of base editors strictly rely on the performance of various nucleotide modification *** with the welldeveloped adenine base editors(ABEs),cytosine base editors(CBEs)and dual base editors suffer from unstable editing efficiency and patterns at different genomic loci in rice,significantly limiting their ***,we comprehensively examined the base editing activities of multiple evolved TadA8e variants in *** found that both TadA-CDd and TadA-E27R/N46L achieved more robust C-to-T editing than previously reported hyperactive hAID*D,and TadA-CDd outperformed TadA-E27R/N46L.A C-to-G base editor(CGBE)engineered with TadA-CDd and OsUNG performed highly efficient C-to-G editing in rice compared with that of *** addition,a dual base editor constructed with a single protein,TadDE,enabled simultaneous,highly efficient C-to-T and A-to-G editing in ***,our results demonstrate that TadA8e derivatives improve both CBEs and dual base editors in rice,providing a powerful way to induce diverse nucleotide substitutions for plant genome editing.

关键词： CRISPR TadA variants cytosine base editing dual base editor rice

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Sludge composition and characteristics shaped microbial community and further determined process performance: A study on full-scale thermal hydrolysis-anaerobic digestion processes

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Journal of Environmental Sciences 2024年第3期137卷 96-107页

作者： Wei liu Chenxiang Sun Wei li Tianle li Zhan Chen Jiawei wang Zhengran ren Xianghua Wen School of Environment Tsinghua UniversityBeijing 100084China Jinneng Holding Group DatongShanxi 037000China Research and Development Center Beijing Drainage Group Co.Ltd.Beijing 100124China Beijing Dabeinong Science and Technology Group Co. Ltd.Beijing 100080China

Anaerobic digestion (AD) with thermal hydrolysis (TH) pretreatment is a promising process for excess sludge treatment,while there lacks of the knowledge from full-scale process about the impact of sludge composition and characteristics on microbial community and *** sludge physiochemical indices,microbial community and performance data of four full-scale TH-AD plants were characterized,and their relationships was *** four plants were operated under almost similar total organic loading rate (OLR)but their methanogenesis performance differentiate into two groups,namely superior group(SupG) and the inferior group (Inf G).In both groups,TH effectively solubilized particulate organic compounds,meanwhile raised the ammonia nitrogen (NH_(4)^(+)-N) and volatile fatty acid (VFA) *** with the Sup G,thermal hydrolyzed sludge of Inf G had higher level of VFAs,NH_(4)^(+)-N and total chemical oxygen demand (t COD),which showed higher inhibition effect on microbes,leading to a community with lower diversity,lower abundance of carbohydrate degrading functional guild,higher protein degrading one,and methanogens that adapted to limited substrates,and further declined the methane production ***,it was recommended that OLR alone was not sufficient for controlling the system in design and operation,the concentration of VFAs,NH_(4)^(+)-N and t COD should be equally *** higher concentration,together with the higher abundance of Defluviitoga and Proteiniphilum were recommended as indicators for inferior running *** results proposed that microbial communities played a role of bridge between environmental factors and performance,provided implications for engineering ecology and operational regulation for full-scale sludge TH-AD process.

关键词： Thermal hydrolysis Anaerobic digestion Microbial community Full-scale

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Synergistic silver-mediated and palladium-catalyzed nondirected olefination of aryl C–H bond: quick access to multi-substituted aryl olefins

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Science China Chemistry 2024年第3期67卷 882-889页

作者： Jian Yao lili Shao Xiaohong Huo Xiaoming wang Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Frontiers Science Center for Transformative MoleculesSchool of Chemistry and Chemical EngineeringShanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Organometallic Chemistry Center for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 20032China School of Chemistry and Materials Science Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China

Transition metal-catalyzed olefination of aryl C-H bond is a powerful tool for the synthesis of alkenes. While the Pd-catalyzed oxidative C-H olefination of arenes, also known as Fujiwara-Moritani reaction, has been established as one of the most efficient methods, the substrates are largely limited to terminal olefins with electron-withdrawing group(s). Herein, we report a synergistic silver-mediated and palladium-catalyzed non-directed C-H olefination of arenes with vinyl(pseudo)halides, which offers a complementary strategy to the typical Fujiwara-Moritani reaction. The reactions proceeded well for a variety of halogenated arenes, heteroarenes, and olefin substrates, providing an efficient access to various multi-substituted aryl olefins, including trisubstituted/tetrasubstituted olefins and several complex olefins derived from medicines or natural products. Mechanistic studies indicated a bimetallic Pd/Ag cooperation is operative in the catalysis, i.e., the reaction is initiated by aryl C-H bond cleavage via ligation with phosphine/Ag species, followed by transferring of the aryl moiety to a vinyl palladium intermediate,which is in turn formed by oxidative addition of vinyl(pseudo)halide to a Pd complex. This method enables the synthesis of a wide range of challenging multi-substituted vinyl products from simple arenes(directing-group free) in a streamlined and controllable fashion.

关键词： direct C–H olefination multi-substituted aryl alkenes bimetallic Pd/Ag cooperation C–H functionalization

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