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| 1 | A three level linearized compact difference scheme for the Cahn-Hilliard equation显示文摘This article is devoted to the study of high order accuracy difference methods for the Cahn-Hilliard equation.A three level linearized compact difference scheme is derived.The unique solvability and unconditional convergence of the difference solution are proved.The convergence order is O(τ 2 + h 4 ) in the maximum norm.The mass conservation and the non-increase of the total energy are also verified.Some numerical examples are given to demonstrate the theoretical results. | LI Juan 1,2 ,SUN ZhiZhong 1,& ZHAO Xuan 1 1 Department of Mathematics,Southeast University,Nanjing 210096,China 2 Yingtian College,Nanjing 210046,China | 2012 | Science China Mathematics2012，55，4： | 22 |
| 2 | PepperHub, an Informatics Hub for the Chili Pepper Research Community显示文摘 | Feng Liu Huiyang Vu Yingtian Deng Jingyuan Zheng Minglei Liu Lijun Ou Bozhi Yang Xiongze Dai Yanqing Ma Shengyu Feng Shuang He Xuefeng Li Zhuqing Zhang Wenchao Chen Shudong Zhou Rong Chen Minmin Liu Sha Yang Ruimin Wei Huadong Li Feng Li Bo Ouyang Xuexiao Zou | 2017 | Molecular Plant2017，10，8： | 13 |
| 3 | microRNA-mediated R gene regulation: molecular scabbards for double-edged swords显示文摘Plant resistance(R) proteins are immune receptors that recognize pathogen effectors and trigger rapid defense responses, namely effector-triggered immunity. R protein-mediated pathogen resistance is usually race specific. During plant-pathogen coevolution,plant genomes accumulated large numbers of R genes. Even though plant R genes provide important natural resources for breeding disease-resistant crops, their presence in the plant genome comes at a cost. Misregulation of R genes leads to developmental defects, such as stunted growth and reduced fertility. In the past decade, many microRNAs(miRNAs) have been identified to target various R genes in plant genomes. miRNAs reduce R gene levels under normal conditions and allow induction of R gene expression under various stresses. For these reasons, we consider R genes to be double-edged 'swords' and miRNAs as molecular 'scabbards'. In the present review, we summarize the contributions and potential problems of these 'swords' and discuss the features and production of the 'scabbards', as well as the mechanisms used to pull the 'sword' from the 'scabbard'when needed. | Yingtian Deng Minglei Liu Xiaofei Li Feng Li | 2018 | Science China(Life Sciences)2018，61，2： | 9 |
| 4 | Principles and methods for stiffness modulation in soft robot design and development显示文摘 | Yang Yang Yingtian Li Yonghua Chen | 2018 | Bio-Design and Manufacturing2018，1，1： | 5 |
| 5 | Formal Analysis and Verification of Oauth 2.0 Protocol Improved by Key Cryptosystems显示文摘The reasons which take huge losses to enterprises and users are:Open authorization(OAuth)2.0protocol is excessively dependent on Hyper text transfer protocol over secure socket layer(HTTPS)to transmit data and ignores per-message encryption,and the transmission efficiency of HTTPS is too low to work well under poor network.The improved OAuth 2.0 modified by Hyper text transfer protocol(HTTP),public key system and private key signature is proposed.With verifying the security of OAuth 2.0 by model checking technology,an improved protocol of higher security is acquired.Comparing different protocol modeling optimized by three combination optimization strategies which involve technologies such as type checking,static analysis and syntactic reordering,an optimal security verification model of the improved protocol is obtained.Program enumeration is presented to compute the repository of attacker.The modeling method of attacker above can effectively reduce the complexity of attacker modeling,consequently those methods can be applied to analyze and validate multi-principal protocols. | XIAO Meihua CHENG Daolei LI Wei LI Ya'nan LIU Xinqian MEI Yingtian | 2017 | Chinese Journal of Electronics2017，26，3： | 2 |
| 6 | Activation of notch‐1 enhances epithelial–mesenchymal transition in gefitinib‐acquired resistant lung cancer cells显示文摘 | MianXie LiZhang Chao‐shengHe FeiXu Jun‐lingLiu Zhi‐huangHu Li‐pingZhao YingTian | 2012 | J. Cell. Biochem2012，，5： | 1 |
| 7 | Transcriptomic and proteomic analyses of far-red light effects in inducing shoot elongation in the presence or absence of paclobutrazol in Chinese pine显示文摘In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation. | Yingtian Guo Shihui Niu Yousry A.El-Kassaby Wei Li | 2022 | Journal of Forestry Research2022，33，3： | 0 |
| 8 | CoBRA: Containerized Bioinformatics Workflow for Reproducible Ch IP/ATAC-seq Analysis显示文摘Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility.However,there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples,correction of copy number variations,and integration of new downstream analysis tools.Here we present Containerized Bioinformatics workflow for Reproducible Ch IP/ATAC-seq Analysis(Co BRA),a modularized computational workflow which quantifies Ch IP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses.Co BRA provides a comprehensive state-of-the-art Ch IP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience.This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering,differential peak calling,motif enrichment,comparison of sites to a reference database,and pathway analysis.Co BRA is publicly available online at https://bitbucket.org/cfce/cobra. | Xintao Qiu Avery S.Feit Ariel Feiglin Yingtian Xie Nikolas Kesten Len Taing Joseph Perkins Shengqing Gu Yihao Li Paloma Cejas Ningxuan Zhou Rinath Jeselsohn Myles Brown XShirley Liu Henry W.Long | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 0 |
| 9 | The link between genetic variation and variability in vaccine responses:a narrative review显示文摘Vaccines are one of the biggest successes in modern history and are particularly important in light of the multiple ongoing epidemics.Recently,vaccines have protected peoples’health and lives around the world during the coronavirus disease 2019 pandemic.Different types of vaccines have their own characteristics and advantages and are used in the context of different epidemics.Responses to vaccination are also different,and can include adverse reactions and absent responses.These individual differences are thought to be influenced by host genes.In this review,we first discuss vaccine types and characteristics.Second,we discuss different responses to vaccination,primarily focusing on the association between genetic variation and inter-individual differences. | Yingtian Zhang Mingzhe Zhao Wei Zhou Luan Chen Mo Li Bixuan Jiang Xianglong Zhao Hao Wu Lu Shen Na Zhang Hengwei Qin Yuhao Tang Chenhan Jiad Lin He Shengying Qin | 2022 | Journal of Bio-X Research2022，5，2： | 0 |
| 10 | Boosting Fischer-Tropsch Synthesis via Tuning of N Dopants in TiO_(2)@CN-Supported Ru Catalysts显示文摘Nitrogen(N)-doped carbon materials as metal catalyst supports have attracted signifi cant attention,but the eff ect of N dopants on catalytic performance remains unclear,especially for complex reaction processes such as Fischer-Tropsch synthesis(FTS).Herein,we engineered ruthenium(Ru)FTS catalysts supported on N-doped carbon overlayers on TiO_(2)nanoparticles.By regulating the carbonization temperatures,we successfully controlled the types and contents of N dopants to identify their impacts on metal-support interactions(MSI).Our fi ndings revealed that N dopants establish a favorable surface environment for electron transfer from the support to the Ru species.Moreover,pyridinic N demonstrates the highest electron-donating ability,followed by pyrrolic N and graphitic N.In addition to realizing excellent catalytic stability,strengthening the interaction between Ru sites and N dopants increases the Ru^(0)/Ru^(δ+)ratios to enlarge the active site numbers and surface electron density of Ru species to enhance the strength of adsorbed CO.Consequently,it improves the catalyst’s overall performance,encompassing intrinsic and apparent activities,as well as its ability for carbon chain growth.Accordingly,the as-synthesized Ru/TiO_(2)@CN-700 catalyst with abundant pyridine N dopants exhibits a superhigh C_(5+)time yield of 219.4 mol CO/(mol Ru·h)and C_(5+)selectivity of 85.5%. | Xincheng Li Yunhao Liu Dejian Zhao Shuaishuai Lyu Jingwei Ye Xiaoshen Li Peipei Wu Ye Tian Yingtian Zhang Tong Ding Song Song Qingpeng Cheng Xingang Li | 2024 | Transactions of Tianjin University2024，30，1： | 0 |
| 11 | Pepper(Capsicum annuum)xylogen-like arabinogalactan protein(XYLP)1 and XYLP2 promote synthesis of lignin during stem development to cope with stresses显示文摘Pepper stems exhibit a high level of strength and lignin deposition to support plant growth,which direct the cultivation style without binding sticks or scaffolding.However,regulation of lignin synthesis and accumulation in pepper stem has not been extensively studied.Herein,we first investigated the pepper stem developmental process and confirmed that increasing lignin accumulation occurs during stem growth.We then performed genome-wide identification and characterization of xylogen-like arabinogalactan protein(XYLP)family members and obtained 10,22,and 19 XYLPs in pepper,tomato,and potato respectively.Evaluation of the phylogenetic relationship among the identified XYLPs suggested that these proteins are conserved in Solanaceae.Thereafter,we analyzed the 10 CanXYLP genes and observed that these genes exhibit differential expressing patterns at different stages of pepper stem development.Among these genes,two XYLPs,namely CanXYLP1 and CanXYLP2,exhibited an increased expression pattern and a strong correlation with lignin accumulation in pepper stem.We further found that CanXYLP1 and CanXYLP2 play a role in pepper stem lignification by positively regulating the lignin synthesis pathway genes in pepper,and the CanXYLP1/2-silenced plants displayed a blocked lignification phenotype.Finally,we confirmed that CanXYLP1/2 expression is upregulated in response to some abiotic and biotic signals,suggesting that these two genes enhance the tolerance of pepper stem to unfavorable conditions.These results contribute to our understanding of the molecular mechanism controlling pepper stem lignification,and the relationship between the lignin content of pepper stem and XYLPs. | Min Zhang Qianwen Zhang Long Cheng Qianying Li Xinyue He Kaixuan Wang Jianan Liu Feng Li Yingtian Deng | 2022 | Vegetable Research2022，2，1： | 0 |
| 12 | High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals显示文摘Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research.However,genomic studies of these species have lagged.Here we report the chromosome-level reference genome assemblies for N.benthamiana and N.tabacum with an estimated 99.5%and 99.8%completeness,respec-tively.Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N.tabacum.Comparative analyses revealed evidence for the parental origins and chromosome structural changes,leading to hybrid genome formation of each species.Interestingly,theantiviral silencinggenesRDR1,RDR6,DCL2,DCL3,andAGO2were lost from one or both subgenomes in N.benthamiana,while both homeologs were kept in N.tabacum.Furthermore,the N.benthamiana genome encodes fewer immune receptors and signaling components than that of N.tabacum.These find-ings uncover possible reasons underlying the hypersusceptible nature of N.benthamiana.We developed the user-friendly Nicomics(http:/lifenglab.hzau.edu.cn/Nicomics/)web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses. | Jubin Wang Qingling Zhang Jeffrey Tung Xi Zhang Dan Liu Yingtian Deng Zhendong Tian Huilan Chen Taotao Wang Weixiao Yin Bo Lij Zhibing Lai Savithramma P.Dinesh-Kumar Barbara Baker Feng Li | 2024 | Molecular Plant2024，17，3： | 0 |
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