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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://gffzz188fe103f8f1460asokx9wc9cvcu06u59.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 | Identification and characterization of putative CIPK genes in maize显示文摘当在细胞内部的发信号的第二个送信人由发展、环境的暗示得到了,钙(Ca ) 起一个关键作用。Calcineurin 象 B 一样蛋白质(CBL ) 和他们的目标蛋白质,交往 CBL 蛋白质 kinases (CIPK ) 在植物响应压力作为一个关键调停 Ca2+ 的发信号网络出现了。生物信息的分析被用来识别 43 通常认为的 ZmCIPK (Zea mays CIPK ) 在玉米的染色体的基因生来的线 B73。基于基因结构,这些 ZmCIPKs 被划分成 intron 富有、 intron 差的组。种系发生的分析显示 ZmCIPK 家庭与 30 个成员的米饭 CIPK 家庭一起有一种高进化的关系。Microarray 数据和 RT-PCR 试金显示出基因 transcriptionally 回答了到不能生活的压力,和基因是的那 24, 31, 20 和 19 ZmCIPK 的那 ZmCIPK 由盐,干旱,热和冷压力起来调整分别地。在冷应力下面有在寒冷容忍的生来的线 B73 和寒冷敏感的生来的线 Mo17 之间的 ZmCIPKs 的不同表示模式。我们的调查结果将在玉米帮助 CIPK 的生物功能的进一步分子的解剖,并且提供新卓见进在植物表明网络的 CBLCIPK。 | Xifeng Chen Zhimin Gu Dedong Xin Liang Hao Chengjie Liu Ji Huang Bojun Ma Hongsheng Zhang | 2011 | Journal of Genetics and Genomics2011，38，2： | 40 |
| 3 | Collagen type Ⅱ suppresses articular chondrocyte hypertrophy and osteoarthritis progression by promoting integrin β1-SMAD1 interaction显示文摘Hypertrophic differentiation is not only the terminal process of endochondral ossification in the growth plate but is also an important pathological change in osteoarthritic cartilage.Collagen type II(COL2A1)was previously considered to be only a structural component of the cartilage matrix,but recently,it has been revealed to be an extracellular signaling molecule that can significantly suppress chondrocyte hypertrophy.However,the mechanisms by which COL2A1 regulates hypertrophic differentiation remain unclear.In our study,a Col2a1 p.Gly1170Ser mutant mouse model was constructed,and Col2a1 loss was demonstrated in homozygotes.Loss of Col2a1 was found to accelerate chondrocyte hypertrophy through the bone morphogenetic protein(BMP)-SMAD1 pathway.Upon interacting with COL2A1,integrinβ1(ITGB1),the major receptor for COL2A1,competed with BMP receptors for binding to SMAD1 and then inhibited SMAD1 activation and nuclear import.COL2A1 could also activate ITGB1-induced ERK1/2 phosphorylation and,through ERK1/2-SMAD1 interaction,it further repressed SMAD1 activation,thus inhibiting BMP-SMAD1-mediated chondrocyte hypertrophy.Moreover,COL2A1 expression was downregulated,while chondrocyte hypertrophic markers and BMP-SMAD1 signaling activity were upregulated in degenerative human articular cartilage.Our study reveals novel mechanisms for the inhibition of chondrocyte hypertrophy by COL2A1 and suggests that the degradation and decrease in COL2A1 might initiate and promote osteoarthritis progression. | Chengjie Lian Xudong Wang Xianjian Qiu Zizhao Wu Bo Gao Lei Liu Guoyan Liang Hang Zhou Xiaoming Yang Yan Peng Anjing Liang Caixia Xu Dongsheng Huang Peiqiang Su | 2019 | Bone Research2019，7，1： | 17 |
| 4 | 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 |
| 5 | Research progress in high intensity cyclotron technology显示文摘This paper briefly introduces several major application fields of high intensity proton accelerators and compares the developing status of various types of proton accelerators currently available at home and abroad. Technical parameters of typical accelerators are specified. The technical features of high intensity cyclotrons are summarized and a general introduction is given to the 3 major phases of research and development on high intensity cyclotrons at CIAE. In the end, emphasis is laid on the recent research of critical technology of high intensity cyclotrons as well as its developing progress. | ZHANG TianJue FAN MingWu LI ZhenGuo CHU ChengJie | 2009 | Chinese Science Bulletin2009，54，21： | 10 |
| 6 | Underdetermined Blind Source Separation of Adjacent Satellite Interference Based on Sparseness显示文摘The problem of underdetermined blind source separation of adjacent satellite interference is proposed in this paper. Density Clustering algorithm(DC-algorithm) presented in this article is different from traditional methods. Sparseness representation has been applied in underdetermined blind signal source separation. However, some difficulties have not been considered, such as the number of sources is unknown or the mixed matrix is ill-conditioned. In order to find out the number of the mixed signals, Short Time Fourier Transform(STFT) is employed to segment received mixtures. Then, we formulate the blind source signal as cluster problem. Furthermore, we construct Cost Function Pair and Decision Coordinate System by using density clustering. At the end of this paper, we discuss the performance of the proposed method and verify the novel method based on several simulations. We verify the proposed method on numerical experiments with real signal transmission, which demonstrates the validity of the proposed method. | Chengjie Li Lidong Zhu Zhongqiang Luo | 2017 | China Communications2017，14，4： | 10 |
| 7 | Benefit allocation model of distributed photovoltaic power generation vehicle shed and energy storage charging pile based on integrated weighting-Shapley method显示文摘In this study,to develop a benefit-allocation model,in-depth analysis of a distributed photovoltaic-powergeneration carport and energy-storage charging-pile project was performed;the model was developed using Shapley integrated-empowerment benefit-distribution method.First,through literature survey and expert interview to identify the risk factors at various stages of the project,a dynamic risk-factor indicator system is developed.Second,to obtain a more meaningful risk-calculation result,the subjective and objective weights are combined,the weights of the risk factors at each stage are determined by the expert scoring method and entropy weight method,and the interest distribution model based on multi-dimensional risk factors is established.Finally,an example is used to verify the rationality of the method for the benefit distribution of the charging-pile project.The results of the example indicate that the limitations of the Shapley method can be reasonably avoided,and the applicability of the model for the benefit distribution of the charging-pile project is verified. | Qingkun Tan Peng Wu Wei Tang Chang Cao Chengjie Wang Yu Zhang | 2020 | Global Energy Interconnection2020，3，4： | 8 |
| 8 | Association between glucose transporter 1 rs841853 polymorphism and type 2 diabetes mellitus risk may be population specific (葡萄糖转移酶1的rs841853基因多态性与2型糖尿发生风险的关系可能具有人群特异性)显示文摘 | Bing Du Shengmao Liu Chengji Cui Songyan Wang Wenpeng Cui | 2013 | Journal of Diabetes2013，，3： | 6 |
| 9 | Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers显示文摘Plant biosynthesis involves numerous specialized metabolites with diverse chemical natures and biological activities.The biosynthesis of metabolites often exclusively occurs in response to tissue-specific combinatorial developmental cues that are controlled at the transcriptional level.Capsaicinoids are a group of specialized metabolites that confer a pungent flavor to pepper fruits.Capsaicinoid biosynthesis occurs in the fruit placenta and combines its developmental cues.Although the capsaicinoid biosynthetic pathway has been largely characterized,the regulatory mechanisms that control capsaicinoid metabolism have not been fully elucidated.In this study,we combined fruit placenta transcriptome data with weighted gene coexpression network analysis(WGCNA)to generate coexpression networks.A capsaicinoid-related gene module was identified in which the MYB transcription factor CaMYB48 plays a critical role in regulating capsaicinoid in pepper.Capsaicinoid biosynthetic gene(CBG)and CaMYB48 expression primarily occurs in the placenta and is consistent with capsaicinoid biosynthesis.CaMYB48 encodes a nucleus-localized protein that primarily functions as a transcriptional activator through its C-terminal activation motif.CaMYB48 regulates capsaicinoid biosynthesis by directly regulating the expression of CBGs,including AT3a and KasIa.Taken together,the results of this study indicate ways to generate robust networks optimized for the mining of CBG-related regulators,establishing a foundation for future research elucidating capsaicinoid regulation. | Binmei Sun Xin Zhou Changming Chen Chengjie Chen Kunhao Chen Muxi Chen Shaoqun Liu Guoju Chen Bihao Cao Fanrong Cao Jianjun Lei Zhangsheng Zhu | 2020 | Horticulture Research2020，7，1： | 5 |
| 10 | Tetrahymena Gene Expression Database (TGED):A resource of microarray data and co-expression analyses for Tetrahymena显示文摘Tetrahymena thermophila is a model eukaryotic organism. Functional genomic analyses in Tetrahymena present rich opportunities to address fundamental questions of cell and molecular biology. The Tetrahymena Gene Expression Database (TGED; available at http://gffzz5d146715fb2e495ehokx9wc9cvcu06u59.ffgz.tsg.suse.edu.cn) is the first expression database of a ciliated protozoan. It covers three major physiological and developmental states: growth, starvation, and conjugation, and can be accessed through a user-friendly web interface. The gene expression profiles and candidate co-expressed genes for each gene can be retrieved using Gene ID or Gene description searches. Descriptions of standardized methods of sample preparation and the opportunity to add new Tetrahymena microarray data will be of great interest to the Tetrahymena research community. TGED is intended to be a resource for all members of the scientific research community who are interested in Tetrahymena and other ciliates. | XIONG Jie LU XingYi LU YuMing ZENG HongHui YUAN DongXia FENG LiFang CHANG Yue Josephine BOWEN Martin GOROVSKY FU ChengJie MIAO Wei | 2011 | Science China(Life Sciences)2011，54，1： | 5 |
| 11 | Responses of plant community to the linkages in plant-soil C:N:P stoichiometry during secondary succession of abandoned farmlands,China显示文摘Succession is one of the central themes of ecology;however,the relationship between aboveground plant communities and underground soils during secondary succession remains unclear.In this study,we investigated the composition of plant community,plant-soil C:N:P stoichiometry and their relationships during secondary succession after the abandonment of farmlands for 0,10,20,30,40 and 50 a in China,2016.Results showed that the composition of plant communities was most diverse in the farmlands after secondary succession for 20 and 50 a.Soil organic carbon and total nitrogen contents slightly decreased after secondary succession for 30 a,but both were significantly higher than those of control farmland(31.21%-139.10%and 24.24%-121.21%,respectively).Moreover,C:N ratios of soil and microbe greatly contributed to the changes in plant community composition during secondary succession of abandoned farmlands,explaining 35.70%of the total variation.Particularly,soil C:N ratio was significantly and positively related with the Shannon-Wiener index.This study provides the evidence of synchronous evolution between plant community and soil during secondary succession and C:N ratio is an important linkage between them. | LIU Weichao FU Shuyue YAN Shengji REN Chengjie WU Shaojun DENG Jian LI Boyong HAN Xinhui YANG Gaihe | 2020 | Journal of Arid Land2020，12，2： | 5 |
| 12 | Slag-Resistance of MgAlON Spinel显示文摘The slag-resistance and microstructural changes after the slag tests of MgAlON spinel containing different amount of nitrogenwere studied by means of crucible slag-resistant experiment, SEM and EDS in the work. The results show that the slag-resistance ofMgAlON is dependent on the nitrogen content, and the optimum amount is 2.88%. The strUcture is not changed although the grains havebeen permeated by some silicon, calcium and iron. A glass phase which contained nitrogen formed in the metaInorphic layeL The glasscan driprove the ability of the slag-resistance of MgAlON because of its higher viscosity. | Chengji Deng Yanruo Hong Xiangchong Zhong Jialin Sun(State Laboratory on Solid Electrolytes and Metallurgical Testing Techniques, University of Science and Technology Beijing, Bejing100083, China) | 2000 | International Journal of Minerals,Metallurgy and Materials2000，14，2： | 4 |
| 13 | Simultaneous measurement of particle velocity and size based on gray difference and autocorrelation显示文摘The gray of two images of a same particle taken by a digital camera with different exposure times is different too. Based on the gray difference of particle images in a double-exposed photo and autocorrelation processing of digital images,this paper proposes a method for measuring particle velocities and sizes simultaneously. This paper also introduces the theoretical foundation of this method,the process of particle imaging and image processing,and the simultaneous measurement of velocity and size of a low speed flow field with 35 μm and 75 μm standard particles. The graphical measurement results can really reflect the flow characteristics of the flow field. In addition,although the measured velocity and size histograms of these two kinds of standard particles are slightly wider than the theoretical ones,they are all still similar to the normal distribution,and the peak velocities and diameters of the histograms are consistent with the default values. Therefore,this measurement method is capable of providing moderate measurement accuracy,and it can be further developed for high-speed flow field measurements. | Huang ChengJie Wu ZhiJun Li ZhiLong Li LiGuang | 2010 | Science China(Technological Sciences)2010，53，10： | 4 |
| 14 | Influence of co-solvent hydroxyl group number on properties of water-based conductive carbon pastes显示文摘 | Chengjie Hua Xiaoming Li Lijuan Shen Hong Lei Xiaoqian Guo Zhuo Liu Qingqiang Kong Lijing Xie cheng-Meng Chen | 2017 | Particuology2017，15，4： | 3 |
| 15 | Ecological Offsetting in China's Coastal Wetlands: Existing Challenges and Strategies for Future Improvement显示文摘Land-use changes in coastal wetlands have led to a worldwide degradation of marine coastal ecosystems and a loss of the ecological services they provide. Ecological offsetting is a popular strategy and an effective mitigation measure for ecosystems that have been degraded, damaged, or destroyed and is critical for habitats where natural recovery is hindered. However, the current understanding of the theory and practice of ecological offsetting for coastal wetlands is extremely limited in many developing countries. We conducted a review of ecological offsetting for coastal wetlands projects and studies in China in 1979–2017 to explore the application and limitations of ecological offsetting theory. It was found that China's coastal ecological offsetting regime has recently entered a rapidly developing stage, with an increasing number of different types of offsetting projects conducted, but theoretical research lags behind practical applications. Considerable governmental, social, technological and ethical challenges remain to resolve. Coastal ecological offsetting schemes have been inconsistent in meeting conservation objectives or preventing net losses because of the challenges of ensuring they are fully consistent in practice(mainly in-kind offsets) and theory(mainly out-of-kind offsets). Ecological offsetting projects were primarily implemented by government, developers, and non-profit organizations. The available funding of coastal ecological offsetting projects is insufficient, which makes ecological offsetting a risky operation. Therefore, we propose strategies for improvement that integrate the consideration of theoretical and practical challenges in the offsetting process, while providing a scientific basis and directional guidance for the future practice of biodiversity conservation and environmental management. | YU Shuling CUI Baoshan XIE Chengjie MA Xu MAN Ying NING Zhonghua | 2019 | Chinese Geographical Science2019，29，2： | 3 |
| 16 | Influence of Temperature on the Protectiveness and Morphological Characteristics of Calcareous Deposits Polarized by Galvanostatic Mode显示文摘The influence of temperature on calcareous deposits formed under galvanostatic polarization mode was studied.The deposition was monitored by electrochemical impedance spectrum,and a supplementary loop in Nyquist diagram at high frequency was found to be an indicator of deposits precipitation with sufficient protection at above 20 ℃.An exponential increase of protectiveness with temperature was observed,which was quantified by linear polarization resistance technique.Observation by scanning electron microscope and X-ray diffraction analyses demonstrated that the critical temperature of calcium carbonate crystal form transition ranged from 15 to 20 ℃.Calcite formed below 15 ℃,while aragonite precipitated at above 20 ℃. | Chengjie Li Min Du Jing Qiu Jing Zhang Congjie Gao | 2014 | Acta Metallurgica Sinica(English Letters)2014，27，1： | 3 |
| 17 | Independent Component Analysis Based Blind Adaptive Interference Reduction and Symbol Recovery for OFDM Systems显示文摘To overcome the inter-carrier interference(ICI) of orthogonal frequency division multiplexing(OFDM) systems subject to unknown carrier frequency offset(CFO) and multipath, this paper develops a blind adaptive interference suppression scheme based on independent component analysis(ICA). Taking into account statistical independence of subcarriers' signals of OFDM, the signal recovery mechanism is investigated to achieve the goal of blind equalization. The received OFDM signals can be considered as the mixed observation signals. The effect of CFO and multipath corresponds to the mixing matrix in the problem of blind source separation(BSS) framework. In this paper, the ICAbased OFDM system model is built, and the proposed ICA-based detector is exploited to extract source signals from the observation of a received mixture based on the assumption of statistical independence between the sources. The blind separation technique can increase spectral efficiency and provide robustness performance against erroneous parameter estimation problem. Theoretical analysis and simulation results show that compared with the conventional pilot-based scheme, the improved performance of OFDM systems is obtained by the proposed ICA-based detection | LUO Zhongqiang ZHU Lidong LI Chengjie | 2016 | China Communications2016，13，2： | 3 |
| 18 | Comprehensive test stand for high-intensity cyclotron development显示文摘A comprehensive test stand for high-intensity cyclotron development,a 10 MeV 430 μA cyclotron,has been successfully constructed at China Institute of Atomic Energy (CIAE) for the experimental verification of the viability of a 100 MeV high-intensity cyclotron (CYCIAE-100) being constructed at CIAE.The verification includes the overall design technology,detail design and engineering technology for the crucial parts of the machine,e.g.main magnet and beam diagnostics.It will also pave the way for future enhancement of the beam intensity.The test stand consists of a H-ion source,axial injection system,central region,main magnet and coil,RF resonator,stripping extraction,and auxiliary systems,which include the RF power amplifier,high voltage and DC power supplies,electric apparatus,beam diagnostics,control,vacuum,water cooling,pneumatic system,and safety interlock.This paper presents the work regarding the design and sub-system development of the test sand,and the results of the beam commissioning of the machine. | ZHANG TianJue LI ZhenGuo CHU ChengJie XING JianSheng GUAN FengPing ZHONG JunQing JI Bin GE Tao YIN ZhiGuo HOU ShiGang PAN GaoFeng YAO HongJuan LU YinLong WANG ZhenHui WU LongCheng LIN Jun JIA XianLu WEI SuMin WEN LiPeng WANG Feng XIA Le CAI HongRu XIE HuaiDong CHEN RongFan ZHANG Yan ZHANG SuPing LIU GengShou ZOU Jian AN ShiZhong YANG JianJun BI YuanJie YANG Fang | 2011 | Chinese Science Bulletin2011，56，3： | 3 |
| 19 | Chemotherapeutic nanomaterials in tumor boundary delineation:Prospects for effective tumor treatment显示文摘Accurately delineating tumor boundaries is key to predicting survival rates of cancer patients and assessing response of tumor microenvironment to various therapeutic techniques such as chemotherapy and radiotherapy.This review discusses various strategies that have been deployed to accurately delineate tumor boundaries with particular emphasis on the potential of chemotherapeutic nanomaterials in tumor boundary delineation.It also compiles the types of tumors that have been successfully delineated by currently available strategies.Finally,the challenges that still abound in accurate tumor boundary delineation are presented alongside possible perspective strategies to either ameliorate or solve the problems.It is expected that the information communicated herein will form the first compendious baseline information on tumor boundary delineation with chemotherapeutic nanomaterials and provide useful insights into future possible paths to advancing current available tumor boundary delineation approaches to achieve efficacious tumor therapy. | Ozioma Udochukwu Akakuru Zhoujing Zhang M.Zubair Iqbal Chengjie Zhu Yewei Zhang Aiguo Wu | 2022 | Acta Pharmaceutica Sinica B2022，12，6： | 2 |
| 20 | Experimental study on multi-point autoignition characteristics and influence factors of diesel spray in a controllable active thermo-atmosphere显示文摘Auto-ignition characteristics of high-pressure diesel spray in the controllable active thermo-atmos-phere (CATA) were studied with a high-speed camera video system. Multi-point autoignition phe-nomenon of diesel spray in the CATA was observed and the influence factors of the autoignition were analyzed. The stabilization mechanisms of the spray flame in different coflow temperatures were also discussed. The stabilization of the flames was controlled by different factors: autoignition phenomenon in low coflow temperature and flame spread in high coflow temperature. The test results also show that the autoignition delay depends strongly on the coflow temperature and has nonlinear relationship with the temperature. Autoignition delay decreases by almost 10 ms from 16.9 to 7.1 ms when the coflow temperature increases from 996 to 1048 K and only 4 ms from 1048 to 1101 K. The injection parameters in terms of nozzle diameter, injection pressure and pump speed, have some effects on autoignition delay while these effects depend on the coflow temperature. The significant effect lies in low coflow temperature. The injection parameters influence the autoignition delay because it can shorten the physical delay by improving the spray quality and enlarging the spray angle or penetration rate to im-prove mixture quality. | DENG Jun WU ZhiJun HUANG ChengJie FENG Wei LI LiGuang | 2007 | Chinese Science Bulletin2007，52，2： | 2 |
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