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| 1 | Beneficial effects of Houttuynia cordata polysaccharides on “two-hit” acute lung injury and endotoxic fever in rats associated with anti-complementary activities显示文摘Houttuynia cordata Thunb. is a traditional herb used for clearing heat and eliminating toxins,and has also been used for the treatment of severe acute respiratory syndrome(SARS). In vitro, the crude H. cordata polysaccharides(CHCP) exhibited potent anti-complementary activity through both the classical and alternative pathways by acting on components C3 and C4 of the complement system without interfering with the coagulation system. This study was to investigate the preventive effects of CHCP on acute lung injury(ALI) induced by hemorrhagic shock plus lipopolysaccharide(LPS) instillation(two-hit)and LPS-induced fever in rats. CHCP significantly attenuated pulmonary injury in the 'two-hit' ALI model by reducing pulmonary edema and protein exudation in bronchoalveolar lavage fluid(BALF). In addition, it reduced the deposit of complement activation products in the lung and improved oxidantantioxidant imbalance. Moreover, CHCP administration inhibited fever in rats, reduced the number of leukocytes and restored serum complement levels. The inhibition on the inappropriate activation of complement system by CHCP may play an important role in its beneficial effects on inflammatory diseases. The anti-complementary polysaccharides are likely to be among the key substances for the heatclearing function of H. cordata. | Yan Lu Yun Jiang Lijun Ling Yunyi Zhang Hong Li Daofeng Chen | 2018 | Acta Pharmaceutica Sinica B2018，8，2： | 18 |
| 2 | The deep-lake deposit in the Upper Triassic Yanchang Formation in Ordos Basin, China and its significance for oil-gas accumulation显示文摘The deep-lake facies of the Yanchang Formation represents a large outflowing lake basin in the Ordos area. Its deposition can be divided into four stages: lake genetic and expanding stage, peak stage, inversion stage and dying stage. All the stages are obviously consistent with the evolution of depositional environment and the paleoclimate in the region. The study indicates that the lake basin has evolution fluctuations from highstand to lowstand for four times in its evolution history, and the deposition center of the lake has not obviously moved, staying along the Huachi-Yijun belt. The deep lake sedimentary system mainly consists of deep water deltas and turbidite fans during the entire evolution course of the lake basin in the Late Triassic. The former mainly developed on the slope of steep shore of the delta in the early period of the deep-water expansion and gradually experienced a big shift from deep-water deltas to shallow-water platform delta. And the latter appeared almost in all the above stages and had two types of turbidite fans, slope-moving turbidite fans and slump turbidite fans. The slope-moving turbidite fans have relatively complete facies belts overlapping one another vertically and consist of the slope channel of inter fans, the turbidite channel, inter turbidite channel and turbidite channel front of middle fans and outer fans (or lakebottom plain). However, the slide-moving turbidity fans are formed in the deep lake with their microfacies difficult to be distinguished, and only the center microfacies and edge microfacies can be determined. The two types of the turbidity fans are similarly distributing in the near-root-slope and far-root-slope regions. The deep-lake deposition governs the distribution of the hydrocarbon and reservoir, while the slope-moving turbidite fans are excellent reservoirs for oil-gas exploration due to their great thickness, widespread distribution and accumulation properties. | CHEN QuanHong LI WenHou GAO YongXiang GUO YanQin FENG JuanPing ZHANG DaoFeng CAO HongXia LIANG JiWei | 2007 | Science China Earth Sciences2007，50，z2： | 12 |
| 3 | A draft sequence of the rice (Oryza sativa ssp. indica) genome显示文摘The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a 'whole genome shotgun' approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package | YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing Genomics Institute/Center of Genomics & Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China National Hybrid Rice R & D Center, Changsha 410125, China Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Peking University, Beijing 100871, China Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1Q0080, China Digital China Ltd., Beijing 100080, China Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China Medical College, Xi’an Jiaotong University, Xi’an 710061, ChinaThese authors contributed equally to this work.Corresponding author.Corresponden | 2001 | Chinese Science Bulletin2001，46，23： | 6 |
| 4 | Genome architecture and tetrasomic inheritance of autotetraploid potato显示文摘Potato(Solanum tuberosum)is the most consumed non-cereal food crop.Most commercial potato cultivars are autotetraploids with highly heterozygous genomes,severely hampering genetic analyses and improvement.By leveraging the state-of-the-art sequencing technologies and polyploid graph binning,we achieved a chromosome-scale,haplotype-resolved genome assembly of a cultivated potato,Cooperation-88(C88).lntra-haplotype comparative analyses revealed extensive sequence and expression differences in this tetraploid genome.We identified haplotype-specific pericentromeres on chromosomes,suggesting a distinct evolutionary trajectory of potato homologous centromeres.Furthermore,we detected double reduction events that are unevenly distributed on haplotypes in 1021 of 1034 selfing progeny,a feature of autopolyploid inheritance.By distinguishing maternal and paternal haplotype sets in C88,we simulated the origin of heterosis in cultivated tetraploid with a survey of 3110 tetra-allelic loci with deleterious mutations,which were masked in the heterozygous condition bytwo parents.This study provides insights into the genomic architecture of autopolyploids and will guide their breeding. | Zhigui Bao Canhui Li Guangcun Li Pei Wang Zhen Peng Lin Cheng Hongbo Li Zhiyang Zhang Yuying Li Wu Huang Mingwang Ye Daofeng Dong Zhukuan Cheng Peter VanderZaag Evert Jacobsen Christian W.B.Bachem Suomeng Dong Chunzhi Zhang Sanwen Huang Qian Zhou | 2022 | Molecular Plant2022，15，7： | 4 |
| 5 | The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions显示文摘Dear Editor,Potato is a vital food security crop and is ranked as the world’s third most important food crop after rice and wheat.In 2011,the first genome assembly of a doubled monoploid potato DM1-3516 R44(DM)was released(Potato Genome Sequencing Consortium,2011),which has been widely used as one of the most popular reference genomes in the last decade and served as a valuable resource in plant genomics and potato genetics community(Leisner et al.,2018;Yang et al.,2020;Zheng et al.,2020). | Xiaohui Yang Lingkui Zhang Xiao Guo Jianfei Xu Kang Zhang Yinqing Yang Yu Yang Yinqiao Jian Daofeng Dong Sanwen Huang Feng Cheng Guangcun Li | 2023 | Molecular Plant2023，16，2： | 2 |
| 6 | Development of a C3c-based ELISA method for the determination of anti-complementary potency of Bupleurum polysaccharides显示文摘Traditionally, determination of inhibitory potency of complement inhibitors is performed by the hemolytic assay. However, this assay is not applicable to the lectin pathway, thus impeding the understanding of complement inhibitors against the overall function of the complement system. The main objective of our study was to develop a specific enzyme-linked immunosorbent assay(ELISA) as an alternative method to assess the anti-complement activity, particularly against the lectin pathway. By using respective coating substrates against different activation pathways, followed by capturing the stable C3c fragments, our ELISA method can be used to screen complement inhibitors against the classical pathway and the lectin pathway. The inhibitory effect of suramin on the classical pathway, as measured by our hemolytic assay is consistent with previous reports. Further assessment of suramin and Bupleurum polysaccharides against the lectin pathway showed a good reproducibility of the method. Comparison of the lectin pathway IC50 between Bupleurum smithii var. parvifolium polysaccharides(1.055 mg/mL) and Bupleurum chinense polysaccharides(0.98 mg/mL) showed that, similar to the classical and alterative pathway, these two Bupleurum polysaccharides had comparable anti-complementary properties against the lectin pathway. The results demonstrate that the described ELISA assay can compensate for the shortcomings of the hemolytic assay in lectin pathway. | Mulu Wu Hong Li Yunyi Zhang Daofeng Chen | 2015 | Acta Pharmaceutica Sinica B2015，5，4： | 1 |
| 7 | Benthic algae of the Xiangxi River, China显示文摘 | TAHG Tao QU Xiaodong LI Daofeng | 2004 | Journal of Freshwater Ecology2004，19，4： | 1 |
| 8 | Diel vertical migration of Peridiniopsis niei, Liu et al., a new species of dinoflagellates in an eutrophic bay of Three-Gorge Reservoir, China显示文摘 | Yaoyang Xu Qinghua Cai Lan Wang Linghui Kong Daofeng Li | 2010 | Aquatic Ecology2010，，2： | 1 |
| 9 | A novel Sm–Co polymeric complex formed via metal-mediated oxidation–hydrolysis of orotic acid in a hydrothermal reaction显示文摘 | Xing Li Rong Cao Daofeng Sun Qian Shi Wenhua Bi Maochun Hong | 2003 | Inorganic Chemistry Communications2003，，7： | 1 |
| 10 | Assembling ionic liquid into porous molecular filler of mixed matrix membrane to trigger high gas permeability,selectivity,and stability for CO_(2)/CH_(4) separation显示文摘As an emerging zero-dimensional nano crystalline porous material,porous organic cages(POCs)with soluble properties in organic solvents,are promising candidates as molecular fillers in mixed matrix membranes(MMMs).The pore structure of POCs should be adjusted to trigger efficient gas separation performance,and the interaction between filler and matrix should be optimized.In this work,ionic liquid(IL)was introduced into the molecular fillers of CC3,to construct the IL@CC3/PIM-1 membrane to effectively separate CO_(2) from CH_(4).The advantages of doping IL include:(1)narrowing the cavity size of POCs from 4.4 to 3.9Åto enhance the diffusion selectivity,(2)strengthening the CO_(2) solubility to heighten the gas permeability,and(3)improving the compatibility between filler and matrix to upgrade membrane stability.After the optimization of the membrane composite,the IL@CC3/PIM-1-10%membrane possesses the CO_(2) permeability of 7868 Barrer and the CO_(2)/CH_(4) selectivity of 73.4,which compared to the CC3/PIM-1-10%membrane,improved by 15.9%and 106.2%,respectively.Furthermore,the membrane has maintained a stable separation performance at varied temperatures and pressures during the long-term test.The proposed method offers an efficient way to improve the performance of POCs-based MMMs in gas separation. | Liting Yu Liqin Hao Yang Feng Jia Pang Mengwei Guo Liangjun Li Weidong Fan Lili Fan Rongming Wang Zixi Kang Daofeng Sun | 2024 | Nano Research2024，17，5： | 0 |
| 11 | Phosphorus-doped iron-nitrogen-carbon catalyst with pentacoordinated single atom sites for efficient oxygen reduction显示文摘Single-atomic Fe-N4 is the well-acknowledged active site in iron-nitrogen-carbon(Fe-N-C)material for oxygen reduction reaction(ORR).The adjusting of the electronic distribution of Fe-N4 is promising for further enhancing the performance of the Fe-N-C catalyst.Herein,a phosphorus(P)-doped Fe-N-C catalyst with penta-coordinated single atom sites(FeNPC)is reported for efficient oxygen reduction.Fe K-edge X-ray absorption spectroscopy(XAS)verifies the coordination environment of single Fe atom,while density functional theory(DFT)calculations reveal that the penta-coordination and neighboring doped P atoms can simultaneously change the electronic distribution of Fe-N_(4)and its adsorption strength of key intermediates,reducing the reactionfree energy of the potential-limiting step.Electrochemical tests validate the remarkable intrinsic ORR activity of FeNPC in alkaline media(a half-wave potential(E_(1/2))of 0.904 V vs.reversible hydrogen electrode(RHE)and limited current density(JL)of 6.23 mA·cm^(−2))and an enhanced ORR performance in neutral(E_(1/2)=0.751 V,J_(L)=5.27 mA·cm^(−2))and acidic media(E_(1/2)=0.735 V,JL=5.82 mA·cm^(−2))with excellent stability,highlighting the benefits of optimizing the local environment of singleatomic Fe-N4. | Lili Fan Xiaofei Wei Xuting Li Zhanning Liu Mengfei Li Shuo Liu Zixi Kang Fangna Dai Xiaoqing Lu Daofeng Sun | 2023 | Nano Research2023，16，2： | 0 |
| 12 | Expanding the dimensionality of proton conduction enables ultrahigh anhydrous proton conductivity of phosphoric acid-doped covalent-organic frameworks显示文摘It is of great significance to develop high-temperature anhydrous proton conducting materials.Herein,we report a new strategy to significantly enhance the proton conductivity of covalent organic frameworks(COFs)through expanding the dimensionality of proton conduction.Three COF-based composites,COF-1@PA,COF-2@PA,and COF-3@PA(PA:phosphoric acid),are prepared by PA doping of three COFs with similar pore sizes but different amounts of hydrophilic groups.With the increase of hydrophilic groups,COFs can load more PA because of the enhanced hydrogen–bonding interactions between PA and the frameworks.powder X-ray diffraction(PXRD),scanning electron microscopy(SEM),and two-dimensional(2D)solid-state nuclear magnetic resonance(NMR)analyses show that PA can not only enter the channels of COF-3,but also insert into its 2D interlayers.This expands the proton conduction pathways from one-dimensional(1D)to three-dimensional(3D),which greatly improves the proton conductivity of COF-3.Meanwhile,the confinement effect of 1D channels and 2D layers of COF-3 also makes the hydrogen-bonded networks more orderly in COF-3@PA-30(30μL of PA loaded on COF-3).At 150℃,COF-3@PA-30 exhibits an ultrahigh anhydrous proton conductivity of 1.4 S·cm−1,which is a record of anhydrous proton conductivity reported to date.This work develops a new strategy for increasing the proton conductivity of 2D COF materials. | Qianqian Yang Xinyu Li Changsong Xie Ning Liu Jianjian Yang Zhihui Kong Zixi Kang Rongming Wang Xiyou Li Daofeng Sun | 2023 | Nano Research2023，16，8： | 0 |
| 13 | AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis显示文摘Assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are critical to ensure accurate analysis.Several tools have been developed for assessing sequencing quality and insertion size distribution for ATAC-seq data;however, key quality control(QC) metrics have not yet been established to accurately determine the quality of ATAC-seq data. Here, we optimized the analysis strategy for ATAC-seq and defined a series of QC metrics for ATAC-seq data,including reads under peak ratio(RUPr), background(BG), promoter enrichment(Pro En), subsampling enrichment(Sub En), and other measurements. We incorporated these QC tests into our recently developed ATAC-seq Integrative Analysis Package(AIAP) to provide a complete ATAC-seq analysis system, including quality assurance, improved peak calling, and downstream differential analysis. We demonstrated a significant improvement of sensitivity(20%–60%) in both peak calling and differential analysis by processing paired-end ATAC-seq datasets using AIAP. AIAP is compiled into Docker/Singularity, and it can be executed by one command line to generate a comprehensive QC report. We used ENCODE ATAC-seq data to benchmark and generate QC recommendations, and developed q ATACViewer for the userfriendly interaction with the QC report. The software, source code, and documentation of AIAP are freely available at http://gffzz188fe103f8f1460askcbc9cwp6nob6bno.ffgz.tsg.suse.edu.cn/Zhang-lab/ATAC-seq_QC_analysis. | Shaopeng Liu Daofeng Li Cheng Lyu Paul MGontarz Benpeng Miao Pamela A.F.Madden Ting Wang Bo Zhang | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 0 |
| 14 | Ultrahigh Hydrogen Uptake in an Interpenetrated Zn_(4)O-Based Metal–Organic Framework显示文摘As a highly promising candidate for hydrogen storage,crucial to vehicles powered by fuel cells,metal–organic frameworks(MOFs)have attracted the attention of chemists in recent decades.H_(2) uptake in an MOF is influenced by many factors such as pore size,ligand functionalization,and open metal sites.The synergistic effect of these factors can significantly enhance the H_(2) uptake in an MOF.Herein,we report a twofold interpenetrated MOF(UPC-501)based on a Zn_(4)O(COO)_(6)secondary building unit with the H_(2) uptake of 14.8 mmol g^(−1)(2.96 wt%)at 77 K and 0.1 MPa.This uptake is the highest among all the reported porous Zn-based MOF materials.Both experimental and theoretical results confirm that the reduced pore size derived from twofold interpenetration and the imidazole-functionalized ligand are responsible for the extremely high H_(2) uptake of UPC-501. | Fu-Gang Li Caiping Liu Daqiang Yuan Fangna Dai Rongming Wang Zhikun Wang Xiaoqing Lu Daofeng Sun | 2022 | CCS Chemistry2022，4，3： | 0 |
| 15 | Provably Secure APK Redevelopment Authorization Scheme in the Standard Model显示文摘The secure issues of APK are very important in Android applications.In order to solve potential secure problems and copyrights issues in redevelopment of APK files,in this paper we propose a new APK redevelopment mechanism(APK-SAN).By exploring sanitizable signature technology,APK-SAN allows the original developer to authorize specified modifier who can redevelop the designated source code of APK files.Our scheme does not require interactions between the developer and modifiers.It can reduce the communication overhead and computational overhead for developers.Especially,the signature of redeveloped APK files is valid and maintains the copyrights.The proposed APK-SAN signature can effectively protect the security of the redeveloped APK files and copyrights of the developer and modifier. | Daofeng Li Mingxing Luo Bowen Zhao Xiangdong Che | 2018 | Computers, Materials & Continua2018，，9： | 0 |
| 16 | Exogenously applied methyl Jasmonate induces early defense related genes in response to Phytophthora infestans infection in potato plants显示文摘In order to elucidate the contributions of JA in orchestrating disease resistance in potato plants,the potato genotype‘SD20’,which exhibits strong resistance against the highly virulent Phytophthora infestans isolate CN152,while infected by the super virulent isolate 2013-18-306,was treated with exogenous JA and then challenged by inoculation with 2013-18-306.The results showed that exogenously applied JA significantly delayed the onset and alleviated the symptoms of late blight,indicating exogenous JA could induce resistance to P.infestans in the early biotrophic stage of infection in‘SD20’plants.To further clarify the role of JA in the early defense response and identify key genes involved in JA signal transduction,gene expression profiling via RNA sequencing(RNA-seq)in‘SD20’plants treated with exogenously applied JA was performed.A total of 2927 differentially expressed genes were specifically induced,the majority encoded transcription factors,protein kinases,secondary metabolites,defense enzymes and disease resistance related proteins.GO functional annotation and KEGG metabolic pathway analysis showed that exogenously applied JA rapidly induced the expression of genes related to immune response regulation,pathogen defense,and other biological processes,and stimulated endogenous JA synthesis and signal transduction,and the overall early pathogen defense response in‘SD20’.These results provide useful information in understanding the JA’s function involved in pathogen defense responses and a theoretical basis for the application of JA in potato production. | Yu Yang Xiaohui Yang Xiao Guo Xinxi Hu Daofeng Dong Guangcun Li Xingyao Xiong | 2022 | Horticultural Plant Journal2022，8，4： | 0 |
| 17 | Mating system and progeny genetic diversity of Camellia oleifera ‘Ruan Zhi’显示文摘Camellia oleifera Abel.is an important economic tree species of southern China.In this study,we evaluated the mating system and genetic diversity of a series of cultivars of C.oleifera‘Ruan Zhi’.A total of 159 individuals from the progenies of four cultivars were tested by simple sequence repeat molecular markers.Results reveal that 11 pairs of primers showed polymorphism and their polymorphism information content value was greater than 0.73,suggesting that these primers could be used to identify the genetic diversity of open-pollinated populations.The average number of effective alleles(Ne=4.88)was significantly different from the average number of alleles(Na=12.18),and their distribution in the sample population was not uniform.The average observed heterozygosity(Ho=0.96)was greater than the average expected heterozygosity(He=0.79),and the population heterozygote was excessive.Shannon index was 1.84 and populations showed high genetic diversity.As regards to the mating system,the multilocus outcrossing rate was 0.996,and the single locus 0.866.These results indicate a high degree of outcrossing by C.oleifera‘Ruan Zhi’.We recommend selecting individuals for high genetic gain from the progenies of cultivars because of outcrossing characteristics and genetic diversity for application to germplasm conservation and promotion. | Zijie Zhang Jingxiang Meng Daofeng Pan Ci Yang Yue Li | 2019 | Journal of Forestry Research2019，30，5： | 0 |
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