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| 1 | Fine-Tuning of MiR528 Accumulation Modulates Flowering Time in Rice显示文摘In plants,microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored.However,the mechanisms regulating the accumulation of miRNAs remain poorly under.stood.Here,we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA,rice (Oryza sativa) miR528.At the transcriptional level,miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves;at the post-transcriptional level,aging also modulated miR528 levels by enhancing pri-miR528 alter.native splicing.We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE2 (OsRFI2).Moreover,natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties,which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528.Taken together,our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants. | Rongxin Yang Pingchuan Li Hailiang Mei Dong Wang Jing Sun Chao Yang Lili Hao Shouyun Cao Chengcai Chu Songnian Hu Xianwei Song Xiaofeng Cao | 2019 | Molecular Plant2019，12，8： | 12 |
| 2 | Cybersecurity Named Entity Recognition Using Bidirectional Long Short-Term Memory with Conditional Random Fields显示文摘Network texts have become important carriers of cybersecurity information on the Internet.These texts include the latest security events such as vulnerability exploitations,attack discoveries,advanced persistent threats,and so on.Extracting cybersecurity entities from these unstructured texts is a critical and fundamental task in many cybersecurity applications.However,most Named Entity Recognition(NER)models are suitable only for general fields,and there has been little research focusing on cybersecurity entity extraction in the security domain.To this end,in this paper,we propose a novel cybersecurity entity identification model based on Bidirectional Long Short-Term Memory with Conditional Random Fields(Bi-LSTM with CRF)to extract security-related concepts and entities from unstructured text.This model,which we have named XBi LSTM-CRF,consists of a word-embedding layer,a bidirectional LSTM layer,and a CRF layer,and concatenates X input with bidirectional LSTM output.Via extensive experiments on an open-source dataset containing an office security bulletin,security blogs,and the Common Vulnerabilities and Exposures list,we demonstrate that XBi LSTM-CRF achieves better cybersecurity entity extraction than state-of-the-art models. | Pingchuan Ma Bo Jiang Zhigang Lu Ning Li Zhengwei Jiang | 2021 | Tsinghua Science and Technology2021，26，3： | 9 |
| 3 | Conservation analysis of long non-coding RNAs in plants显示文摘Long non-coding RNAs(lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. In this study, we performed an analysis of lncRNAs in five monocot and five dicot species. Our results showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes. The numbers of lncRNAs were positively correlated with the numbers of protein-coding genes in different plant species, despite a high range of variation. Sequence conservation analysis showed that the majority of lncRNAs had high sequence conservation at the intra-species and sub-species levels, reminiscent of protein-coding genes. At the inter-species level, a subset of lncRNAs were highly diverged at the nucleotide level, but conserved by position.Interestingly, we found that plant lncRNAs have identical splicing signals, and those which can form precursors or targets of miRNAs have a conservative identity in different species. We also revealed that most of the lowly expressed lncRNAs were tissue-specific, while those highly conserved were constitutively transcribed. Meanwhile, we characterized a subset of rice lncRNAs that were co-expressed with their adjacent protein-coding genes, suggesting they may play cis-regulatory roles. These results will contribute to understanding the biological significance and evolution of lncRNAs in plants. | Pingchuan Deng Shu Liu Xiaojun Nie Song Weining Liang Wu | 2018 | Science China(Life Sciences)2018，61，2： | 4 |
| 4 | Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)显示文摘MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice. | Ming ZHOU Lianfeng GU Pingchuan LI Xianwei SONG Liya WEI Zhiyu CHEN Xiaofeng CAO | 2010 | Frontiers in Biology2010，5，1： | 3 |
| 5 | A Genetic-Algorithm-based Neural Network Approach for Radioactive Activity Prediction显示文摘In this paper,a genetic-algorithm-based artificial neural network(GAANN)model radioactivity prediction is proposed,which is verified by measuring results from Long Range Alpha Detector(LRAD).GAANN can integrate capabilities of approximation of Artificial Neural Networks(ANN)and of global optimization of Genetic Algorithms(GA)so that the hybrid model can enhance capability of generalization and prediction accuracy,theoretically.With this model,both the number of hidden nodes and connection weights matrix in ANN are optimized using genetic operation.The real data sets are applied to the introduced method and the results are discussed and compared with the traditional Back Propagation(BP)neural network,showing the feasibility and validity of the proposed approach. | WANG Lei TUO Xianguo YAN Yucheng LIU Mingzhe CHENG Yi LI Pingchuan | 2013 | Nuclear Science and Techniques2013，24，6： | 2 |
| 6 | An Integrated Workflow for DNA Methylation Analysis显示文摘The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our 'Next-Gen Sequence' websites(http://gffzz6bc3b4d9dcb04306hwf60vu5fcvfn6n0p.ffgz.tsg.suse.edu.cn),along with small RNA,RNA-seq and other data types. | Pingchuan Li Feray Demirci Gayathri Mahalingam Caghan Demirci Mayumi Nakano Blake C.Meyers | 2013 | Journal of Genetics and Genomics2013，40，5： | 2 |
| 7 | Nuclear translocation of OsMFT1 that is impeded by OsFTIP1 promotes drought toleranee in rice显示文摘Drought is the leading environmental threat affecting crop productivity,and plants have evolved a series of mechanisms to adapt to drought stress.The FT-interacting proteins(FTIPs)and phosphatidylethanola mine.binding proteins(PEBPs)play key roles in developmental processes,whereas their roles in the regulation of stress response are still largely unknown.Here,we report that OsFTIP1 negatively regulates drought response in rice.We showed that OsFTIP1 interacts with rice MOTHER OF FT AND TFL1(OsMFT1),a PEBP that promotes rice tolerance to drought treatment.Further studies discovered that OsMFT1 interacts with two key drought-related transcription factors,OsbZIP66 and OsMYB26,regulating their binding capacity on drought-related genes and thereby enhancing drought toleranee in rice.Interestingly,we found that OsFTIP1 impedes the nucleocytoplasmic translocation of OsMFT1,implying that dynamic modulation of drought-responsive genes by the OsMFT1-OsMYB26 and OsMFT1-OsbZIP66 complexes is integral to OsFTIP1-modulated nuclear accumulation of OsMFT1.Our findings also suggest that OsMFT1 might act as a hitherto unknown nucleocytoplasmic trafficking signal that regulates drought tolerance in rice in response to environmental signals. | Ying Chen Jun Shen Liang Zhangi Haoyue Qi Lijia Yang Huanyu Wang Jiaxuan Wang Yuexing Wang Hao Du Zeng Tao Ting Zhao Pingchuan Deng Qingyao Shu Qian Qian Hao Yu Shiyong Song | 2021 | Molecular Plant2021，14，8： | 2 |
| 8 | Hierarchically porous Fe/N/S/C nanospheres with high-content of Fe-Nx for enhanced ORR and Zn-air battery performance显示文摘Heteroatom-doped carbon-based transition-metal single-atom catalysts(SACs) are promising electrocatalysts for oxygen reduction reaction(ORR). Herein, with the aid of hierarchically porous silica as hard template, a facile and general melting perfusion and mesopore-confined pyrolysis method was reported to prepare single-atomic Fe/N–S-doped carbon catalyst(FeNx/NC-S) with hierarchically porous structure and well-defined morphology. The FeNx/NC-S exhibited excellent ORR activity with a half-wave potential(E_(1/2)) of 0.92 V, and a lower overpotential of 320 mV at a current density of 10 mA cm^(-2)for OER under alkaline condition. The remarkable electrocatalysis performance can be attributed to the hierarchically porous carbon nanospheres with S doping and high content of Fe-Nx sites(up to 3.7 wt% of Fe), resulting from the nano-confinement effect of the hierarchically porous silica spheres(NKM-5) during the pyrolysis process. The rechargeable Zn-air battery with FeNx/NC-S as a cathode catalyst demonstrated a superior power density of 194.5 mW cm-2charge–discharge stability. This work highlights a new avenue to design advanced SACs for efficient sustainable energy storage and conversion. | Luming Wu Ruge Zhao Guo Du Huan Wang Machuan Hou Wei Zhang Pingchuan Sun Tiehong Chen | 2023 | Green Energy & Environment2023，8，6： | 1 |
| 9 | Simulated annealing study of diblock copolymer thin films confined between two homogeneous surfaces 显示文摘 | Yin Yuhua Sun Pingchuan Chen Tiehong | 2004 | ChemPhysChem2004，，5： | 1 |
| 10 | Simulated annealing study of morphological transitions of diblock copolymers in solution显示文摘 | Sun Pingchuan Yin Yuhua Li Baohui | 2005 | J Chem Phys2005，122，： | 1 |
| 11 | Rotated neighbor learning-based auto-configured evolutionary algorithm显示文摘More and more evolutionary operators have been integrated and manually configured together to solve a wider range of problems. Considering the very limited progress made on the automatic configuration of evolutionary algorithms(EAs), a rotated neighbor learning-based auto-configured evolutionary algorithm(RNLACEA) is presented. In this framework, multiple EAs are combined as candidates and automatically screened for different scenarios with a rotated neighbor structure. According to a ranking record and a group of constraints,the algorithms can be better scheduled to improve the searching efficiency and accelerate the searching pace.Experimental studies based on 14 classical EAs and 22 typical benchmark problems demonstrate that RNLACEA outperforms other six representative auto-adaptive EAs and has high scalability and robustness in solving different kinds of numerical optimization problems. | Yuanjun LAILI Lin ZHANG Fei TAO Pingchuan MA | 2016 | Science China(Information Sciences)2016，59，5： | 1 |
| 12 | A collagen-chitosan hydrogel for endothelial differentiation and angiogenesis显示文摘 | Deng Chao Zhang Pingchuan Vulesevic B | 2010 | Tissue Engingeering2010，16，10： | 1 |
| 13 | Evaluation of linkage of markers on chromosome 6p with schizophrenia in taiwanesefamilies显示文摘 | HWU Haigwo LIN Mingwei LEE Pingchuan | 2000 | Am J Med Genet ( Neuropsychiatric Genet)2000，96，： | 1 |
| 14 | Confinement-induced novel morphologies of block copolymers显示文摘 | Yu Bin Sun Pingchuan Chen Tiehong | 2006 | Physical Review Letters2006，96，13： | 1 |
| 15 | Oceanic crustal structure and tectonic origin of the southern Kyushu-Palau Ridge in the Philippine Sea显示文摘A new high-resolution velocity model of the southern Kyushu-Palau Ridge(KPR) was derived from an activesource wide-angle seismic reflection/refraction profile. The result shows that the KPR crust can be divided into the upper crust with the P-wave velocity less than 6.1 m/s, and lower crust with P-wave velocity between 6.1 km/s and 7.2 km/s. The crustal thickness of the KPR reaches 12.0 km in the center, which gradually decreases to 5.0–6.0 km at sides. The velocity structure of the KPR is similar to the structures of the adjacent West Philippine Basin and Parece Vela Basin(PVB), indicating a typical oceanic crust. Isostatic analysis shows that some regional compensation occurs during the loading of the KPR, which implies that the KPR was built mainly by magmatism during the splitting of the Izu-Bonin-Mariana arc and the following back-arc seafloor spreading of the PVB during30–28 Ma BP. The absence of the thick middle crust(6.0–6.5 km/s) and high velocity lower-crustal layers(7.2–7.6 km/s) suggest that arc magmatism plays a less important role in the KPR formation. | Xiongwei Niu Pingchuan Tan Weiwei Ding Wei Wang Yao Wei Xiaodong Wei Aiguo Ruan Jie Zhang Chunyang Wang Yong Tang Jiabiao Li | 2022 | Acta Oceanologica Sinica2022，41，1： | 1 |
| 16 | The Intemet of Things Brings New Wave of the Information Industry 显示文摘 | LEI Yingying MA Pingchuan ZHAO Lili | 2011 | International Jour- nal of Computer Science and Network Security2011，11，5： | 1 |
| 17 | Synthesis and characterization of thermo- and pH- sensitive hydrogels based on Chitosan-grafted N-isopropylacrylamide via γ-radiation 显示文摘 | Cai Hong Zhang Zhengpu Sun Pingchuan | 2005 | Radiation Phys Chem2005，74，1： | 1 |
| 18 | Influence of polymerization temperature on the molecular recognition of imprinted polymers显示文摘 | Yan Lu Chenxi Li Xudong Wang Pingchuan Sun Xianghua Xing | 2003 | Journal of Chromatography B2003，，1： | 1 |
| 19 | A study on the templating ability of diquaternary cations for the zeolite synthesis in terms of energetics 显示文摘 | Sun Pingchuan Jin Qinghua Wang Lijun | 2003 | J Porous Materials2003，10，： | 1 |
| 20 | Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family显示文摘 | Xiaojun Nie Pingchuan Deng Kewei Feng Peixun Liu Xianghong Du Frank M You Song Weining | 2014 | Plant Molecular Biology Reporter2014，，： | 1 |
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