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| 1 | TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data显示文摘The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine('JIGplot')developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at http://gffzz188fe103f8f1460asb96wffcxbo0v650c.ffgz.tsg.suse.edu.cn/CJ-Chen/TBtools/releases. | Chengjie Chen Hao Chen Yi Zhang Hannah R.Thomas Margaret H.Frank Yehua He Rui Xia | 2020 | Molecular Plant2020，13，8： | 805 |
| 2 | Small RNAs, emerging regulators critical for the development of horticultural traits显示文摘Small RNAs(sRNAs)have been recently recognized as key genetic and epigenetic regulators in various organisms,ranging from the modification of DNA and histone methylations to the modulation of the abundance of coding or non-coding RNAs.In plants,major regulatory sRNAs are classified as respective microRNA(miRNA)and small interfering RNA(siRNA)species,with the former primarily engaging in posttranscriptional regulation while the latter in transcriptional one.Many of these characterized sRNAs are involved in regulation of diverse biological programs,processes,and pathways in response to developmental cues,environmental signals/stresses,pathogen infection,and pest attacks.Recently,sRNAs-mediated regulations have also been extensively investigated in horticultural plants,with many novel mechanisms unveiled,which display far more mechanistic complexity and unique regulatory features compared to those studied in model species.Here,we review the recent progress of sRNA research in horticultural plants,with emphasis on mechanistic aspects as well as their relevance to trait regulation.Given that major and pioneered sRNA research has been carried out in the model and other plants,we also discuss ongoing sRNA research on these plants.Because miRNAs and phased siRNAs(phasiRNAs)are the most studied sRNA regulators,this review focuses on their biogenesis,conservation,function,and targeted genes and traits as well as the mechanistic relation between them,aiming at providing readers comprehensive information instrumental for future sRNA research in horticulture crops. | Chengjie Chen Zaohai Zeng Zongrang Liu Rui Xia | 2018 | Horticulture Research2018，5，1： | 12 |
| 3 | sRNAanno-a database repository of uniformly annotated small RNAs in plants显示文摘Small RNAs(sRNAs)are essential regulatory molecules,and there are three major sRNA classes in plants:microRNAs(miRNAs),phased small interfering RNAs(phased siRNAs or phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).Excluding miRNAs,the other two classes are not well annotated or available in public databases for most sequenced plant genomes.We performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly available.The results are available via an online repository called sRNAanno(www.plantsRNAs.org).Compared with other public plant sRNA databases,we obtained was much more miRNA annotations,which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA annotations.sRNAanno also provides free access to genomic information for>22,721 PHAS loci and>22 million hc-siRNA loci annotated from these 143 plant species.Both miRNA and PHAS loci can be easily browsed to view their main features,and a collection of archetypal trans-acting siRNA 3(TAS3)genes were annotated separately for quick access.To facilitate the ease of sRNA annotation,sRNAanno provides free service for sRNA annotations to the community.In summary,the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs. | Chengjie Chen Jiawei Li Junting Feng Bo Liu Lei Feng Xiaoling Yu Guanliang Li Jixian Zhai Blake C.Meyers Rui Xia | 2021 | Horticulture Research2021，8，1： | 1 |
| 4 | Mathematical Model and Machining Method for Spiral Flute Rake Faces of Hourglass Worm Gear Hob显示文摘To improve the cutting performance of an hourglass worm gear hob and the accuracy of the resulting worm gear,the rake angles of the teeth on the pitch circle should be reduced.A method of forming the spiral flutes by using a variable transmission ratio was developed.This method ensures that the rake angles on the indexing torus of each tooth are approximately 0°.Based on the gear meshing theory and the hourglass worm forming method,the discretization mathematical model of the rake face of a planar double enveloping worm gear hob was established by using cylindrical generating surface,and the feed parameters for machining the rake face for a variable transmission ratio were obtained.The spiral flute was simulated and the hob was machined on a four axis CNC milling machine.A contourgraph was used to measure the rake angle.The measurement results showed that the proposed method can reduce the absolute value of the rake angle on both sides of the cutting teeth,which can be used for machining the spiral flute rake face of an hourglass worm gear hob. | YANG Jie LI Haitao RUI Chengjie HUANG Yi ZHANG Xiaodi | 2019 | Transactions of Nanjing University of Aeronautics and Astronautics2019，36，3： | 1 |
| 5 | Species-specific regulatory pathways of small RNAs play sophisticated roles in flower development in Dimocarpus longan Lour.显示文摘Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house protocols.Our results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive development.Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and miRN15.miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from D14.These small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway. | Bo Liu Guanliang Li Chengjie Chen Zaohai Zeng Jing Xu Jisen Zhang Rui Xia Yuanlong Liu | 2023 | Horticultural Plant Journal2023，9，2： | 1 |
| 6 | Liquid metal-based paper electronics:Materials,methods,and applications显示文摘The liquid metals exhibit both the properties of liquids and metals and have a low melting point near room temperature.As a lowcost and easy-to-obtain flexible substrate,paper has significant advantages for large-area and multilayer flexible circuit fabrication.This has led to a growing interest in liquid metal-based paper electronics among both scientists and industry.In order to promote the development and application of liquid metal-based paper electronics,this review will summarize and analyze the progress from three perspectives,including liquid metal inks,printing methods,and their applications.A variety of liquid metalbased electronic inks are introduced,and their advantages and disadvantages are discussed.Then,a comparison of typical fabrication methods has been presented,including chemical interaction-based selective adhesion and surface roughness-based transfer printing.A number of emerging applications used and expected to be applied to liquid metal-based paper electronics have been demonstrated.Finally,paper electronics based on liquid metals are discussed along with their challenges and opportunities for the further development.In the future,further investigations and applications of paper electronics based on liquid metals are expected. | JIANG ChengJie GUO Rui | 2023 | Science China(Technological Sciences)2023，66，6： | 1 |
| 7 | Jack of Many Trades: The Multifaceted Role of miR528 in Monocots显示文摘MicroRNAs (miRNAs) are essential regulators,involved in almost all aspects of plant growth and development.In plants,miRNAs prese nt in all an giosperms are regarded as con served miRNAs;in contrast,miRNAs restricted to certain lineages (lessconserved) or a single species (species-specific) constitute the non-conserved miRNAs (Cuperus et al.,2011).Different members of a miRNA family usually target similar target genes from a gene family among different species.For in stance,in most analyzed plants,the well-known miR156 family,usually consist!ng of a number of members in a given species,collectively target SQUAMOSA-PROMOTER BINDING PROTEINLIKE (SPL) genes.Gen erally,con served miRNAs target genes encoding transcript factors which function in diverse biological processes.This functional diversity of miRNAs is mainly achieved by the plasticity of their target genes from the same family,such as miR156-targeted SPLs and miR167-targeted ARF (AUXIN RESPONSIVE FACTOR) genes,on regulating distinct downstream gen es. | Chengjie Chen Yuanlong Liu Rui Xia | 2019 | Molecular Plant2019，12，8： | 1 |
| 8 | Driving Forces Analysis for Residential Housing Price in Beijing显示文摘 | Chengjie He Zhen Wang Huaicheng Guo Hu Sheng Rui Zhou Yonghui Yang | 2010 | Procedia Environmental Sciences Volume 22010，，： | 1 |
| 9 | TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining显示文摘Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era. | Chengjie Chen Ya Wu Jiawei Li Xiao Wang Zaohai Zeng Jing Xu Yuanlong Liu Junting Feng Hao Chen Yehua He Rui Xia | 2023 | Molecular Plant2023，16，11： | 0 |
| 10 | Wireless Communication Based on Microwave Photon-Level Detection with Superconducting Devices:Achievable Rate Prediction显示文摘Future wireless communication systemembraces physical-layer signal detection with highsensitivity, especially in the microwave photon level.Currently, the receiver primarily adopts the signal detection based on semi-conductor devices for signal detection, while this paper introduces high-sensitivityphoton-level microwave detection based on superconducting structure. We first overview existing works onthe photon-level communication in the optical spectrum as well as the microwave photon-level sensingbased on superconducting structure in both theoreticaland experimental perspectives, including microwavedetection circuit model based on Josephson junction,microwave photon counter based on Josephson junction, and two reconstruction approaches under background noise. In addition, we characterize channelmodeling based on two different microwave photondetection approaches, including the absorption barrierand the dual-path Handury Brown-Twiss (HBT) experiments, and predict the corresponding achievablerates. According to the performance prediction, it isseen that the microwave photon-level signal detectioncan increase the receiver sensitivity compared withthe state-of-the-art standardized communication system with waveform signal reception, with gain over 10dB. | Junyu Zhang Chen Gong Shangbin Li Rui Ni Chengjie Zuo Jinkang Zhu Ming Zhao Zhengyuan Xu | 2022 | China Communications2022，19，12： | 0 |
| 11 | Expression and possible role of Smad3 in postnecrotizing enterocolitis stricture显示文摘Objective To investigate the expression of Smad3(mothers against decapentaplegic homolog 3)protein in postnecrotizing enterocolitis stricture and its possible mechanism of action.Methods We used immunohistochemistry to detect the expression characteristics of Smad3 and nuclear factor kappa B(NF-κB)proteins in human postnecrotizing enterocolitis stricture.We cultured IEC-6(crypt epithelial cells of rat small intestine)in vitro and inhibited the expression of Smad3 using siRNA technique.Quantitative PCR,western blotting,and ELISA were used to detect the changes in transforming growth factor-β1(TGF-β1),NF-κB,tumor necrosis factor-α(TNF-α),vascular endothelial growth factor(VEGF),and zonula occludens-1(ZO-1)messenger RNA(mRNA)and protein expressions in IEC-6 cells.CCK8 kit and Transwell cellular migration were used to detect cell proliferation and migration.Changes in epithelial-mesenchymal transition(EMT)markers(E-cadherin and vimentin)in IEC-6 cells were detected by immunofluorescence technique.Results The results showed that Smad3 protein and NF-κB protein were overexpressed in narrow intestinal tissues and that Smad3 protein expression was positively correlated with NF-κB protein expression.After inhibiting the expression of Smad3 in IEC-6 cells,the mRNA expressions of NF-κB,TGF-β1,ZO-1,and VEGF decreased,whereas the mRNA expression of TNF-αdid not significantly change.TGF-β1,NF-κB,and TNF-αprotein expressions in IEC-6 cells decreased,whereas ZO-1 and intracellular VEGF protein expressions increased.IEC-6 cell proliferation and migration capacity decreased.There was no significant change in protein expression levels of EMT markers E-cadherin and vimentin and also extracellular VEGF protein expression.Conclusions We suspect that the high expression of Smad3 protein in postnecrotizing enterocolitis stricture may promote the occurrence and development of secondary intestinal stenosis.The mechanism may be related to the regulation of TGF-β1,NF-κB,TNF-α,ZO-1,and VEGF mRNA and protein expression.This may also be related to the ability of Smad3 to promote epithelial cell proliferation and migration. | Rui Chen Chengjie Lv Xiaoxia Zhao Dong Ma Dengming Lai Yun Zhao Luyin Zhang Jinfa Tou | 2022 | World Journal of Pediatric Surgery2022，5，1： | 0 |
| 12 | Microwave Communication Under Weak Intensity to Quantumized Level:Recent Progress and Future Challenges显示文摘We provide an overview of the recent progresses on the system architecture design and performance prediction for microwave signal detection under weak signal intensity regime,up to quantumized level.The technique roadmap includes two perspectives,the opto-electro-mechanical(OEM)and superconducting devices.For the former one,we first overview the concept of OEM,and then introduce the signal detection based on capacitive-opto-electro-mechanical systems and piezoopto-electro-mechanical systems.For the latter one,we first overview the concept and architecture of Josephson junction,and then introduce the signal detection based on superconducting Hanbury Brown-Twiss(HBT)experiments andΛenergy-level splitting system.Besides,we review the microwave detection based on Rydberg atom system.We believe that this overview can provide a guidance for future transmission limit,signal processing,detection device fabrication and real experiments. | Chen Gong Shanchi Wu Chengjie Zuo Kai Yang Shangbin Li Junyu Zhang Zhongbin Dai Ming Huang Ming Zhao Rui Ni Zhengyuan Xu Jinkang Zhu | 2021 | Journal of Communications and Information Networks2021，6，1： | 0 |
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