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MP3RNA-seq:Massively parallel 3’end RNA sequencing for high-throughput gene expression profiling and genotyping

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Journal of Integrative Plant Biology 2021年第7期63卷 1227-1239页

作者： jian Chen Xiangbo Zhang fei Yi Xiang gao Weibin Song Haiming Zhao Jinsheng Lai State Key Laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China

Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression ***,its application tolarge‐scale experiments remains limited by costand labor *** we describe amassively parallel 3′end RNA‐seq(MP3RNA‐seq)method that introduces unique samplebarcodes during reverse transcription to permitsample pooling immediately following this ***3RNA‐seq allows for handling of hun-dreds of samples in a single experiment,at acost of about$6 per sample for libraryconstruction and ***3RNA‐seq iseffective for not only high‐throughput geneexpression profiling,but also *** its utility,we applied MP3RNA‐seqto 477 double haploid lines of *** iden-tified 19,429 genes expressed in at least 50%ofthe lines and 35,836 high‐quality singlenucleotide polymorphisms for *** with these data,we performedexpression and agronomic trait quantitativetrait locus(QTL)mapping and identified 25,797expression QTLs for 15,335 genes and 21 QTLsfor plant height,ear height,and relative *** conclude that MP3RNA‐seq is highlyreproducible,accurate,and sensitive forhigh‐throughput gene expression profiling andgenotyping,and should be generally applicableto most eukaryotic species.

关键词： gene expression profiling genotyping maize MP3RNA‐seq quantitative trait loci

Dynamical brane creation and annihilation via a background flux

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Science China(Physics,Mechanics & Astronomy) 2022年第2期65卷 24-29页

作者： Yi-fei Chen jian-Xin Lu Interdisciplinary Center for Theoretical Study University of Science and Technology of ChinaPeng Huanwu Center for Fundamental TheoryHefei 230026China

We study the dynamical Myers effect by allowing the fuzzy(or the dynamical dielectric brane)coordinates to be time *** find three novel kinds of the dynamical spherical dielectric branes depending on their respective excess *** first represents a dynamical spherical brane carrying a negative excess energy(having a lower bound)with its radius oscillating periodically between two given non-zero *** second is the one with zero excess energy and whose time dependence can be expressed in terms of a simple *** particular dynamical spherical configuration represents the dielectric brane creation and/or annihilation like a photon in the presence of a background creating an electron-position pair and then annihilating back to a *** third is the one carrying positive excess energy and the radius can also oscillate periodically between two non-zero values but,unlike the first kind,it passes zero twice for each *** of the above can also be interpreted as the time evolution of a semi-spherical D-brane–anti semi-spherical D-brane system.

关键词： dynamical Myers effect D-branes string/M-theory

Diversity and abundance of resistome in rhizosphere soil

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Science China(Life Sciences) 2020年第12期63卷 1946-1949页

作者： jian Cao fei Liu Baoli Zhu Yi Shi George Fu gao CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Savaid Medical School University of Chinese Academy of SciencesBeijing 100049China National Institute for Communicable Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing 102206China

Dear Editor,Antibiotic resistance genes(ARGs) have posed a huge threat to public health, causing great economic cost worldwide(Nathan and Cars, 2014). Soil microbiota represents an important reservoir of diverse and ancient ARGs(Bahram et al.,2018). The horizontal gene transfer(HGT) including conjugation and transformation can lead to the exchange of resistance genes between soil microbes and clinical pathogens(Forsberg et al., 2012). However, the transfer of ARGs between genomes and habitats are rarely observed in *** composition significantly correlates with the underlying structure of bacterial communities both across and within soil types, suggesting bacterial phylogeny structures resistomes in soil across habitats(Forsberg et al., 2014).

关键词： soil rhizosphere habitat

Crystal Structure of Lithium Yttrium Borate LiY_6O_5(BO_3)_3

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Chinese Journal of Structural Chemistry 2006年第10期25卷 1175-1178页

作者： gao jian-Hua Beijing Center for Crystal Research and Development Technical Institute of Physics and Chemistry The Chinese Academy of Sciences Beijing 100080 China

Single crystals of LiY6O5（BO3）3 were obtained by the flux method and its structure was determined by a four-circle automatic diffractometer with a MoKα radiation. It crystallizes in monoclinic, space group P21/n with a = 8.330（3）, b = 15.444（4）, c = 8.780（3）°A,β = 91.85（3）°, V = 1129.0（6）°A^3, Z = 4, Mr= 796.83, F（000） = 1456, μ = 30.567 mm^-1, Dc= 4.688 g/cm^3, the final R = 0.0722 and wR = 0.1304. It exhibits a three-dimensional fiamework of yttrium-oxygen polyhedra interconnected by common edges and corners. B and Li atoms are located in the planes and cavities formed by oxygen atoms, respectively.

关键词： borate lithium yttrium borate single-crystal structure VUV luminescent materials

Overexpression of AMPD2 indicates poor prognosis in colorectal cancer patients via the Notch3 signaling pathway

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World Journal of Clinical Cases 2020年第15期8卷 3197-3208页

作者： Qi-Zhong gao Yan Qin Wei-Jia Wang Bo-jian fei Wei-Feng Han jian-Qiang Jin Xiang gao Department of Gastrocolorectal Surgery Affiliated Hospital of Jiangnan UniversityWuxi 214100Jiangsu ProvinceChina Department of Pathology Affiliated Hospital of Jiangnan UniversityWuxi 214000Jiangsu ProvinceChina Department of Oncology Affiliated Hospital of Jiangnan UniversityWuxi 214062Jiangsu ProvinceChina

BACKGROUND AMPD2 is a critical enzyme catalyzing smooth muscle energy supply and metabolism;however,its cellular biological function and clinical implication in colorectal cancer(CRC)are largely *** To clarify the role of AMPD2 in CRC and study the pathway and prognostic value of its *** AMPD2 expression was analyzed by integrated bioinformatics analysis based on TCGA data sets and immunohistochemistry in tissue microarrays,and the correlation between AMPD2 expression and clinicopathological parameters,Notch3 expression,and prognostic features was *** Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were then performed to investigate the regulatory pathway *** effects of AMPD2 expression on CRC cells and Notch3 protein expression were investigated by downregulation and overexpression of *** AMPD2 mRNA was significantly overexpressed in tumor tissue when compared with normal tissue in a cohort of the TCGA-COAD data *** function enrichment analysis indicated that the Notch pathway strongly correlated with AMPD2 expression,and that the expression of Notch3 and JAG2 mRNA was positively associated with AMPD2 in CRC *** vitro,AMPD2 overexpression markedly reduced Notch3 protein expression in CRC cells,while knockdown of AMPD2 showed the opposite *** addition,protein expression was significantly up-regulated in our CRC cohort as indicated by tissue microarray *** expression of AMPD2 protein correlated with advanced depth of tumor and poor ***,high AMPD2 expression in CRC tissues was an indicator of poor outcome for CRC *** AMPD2 is commonly overexpressed in CRC,and acts as a metabolism oncogene to induce CRC progression through the Notch signaling ***,AMPD2 may be a novel prognostic biomarker for CRC.

关键词： Colorectal cancer AMPD2 Notch3 Tumor metabolism Poor prognosis Biomarkers

Homomorphic Error-Control Codes for Linear Network Coding in Packet Networks

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China Communications 2017年第9期14卷 178-189页

作者： Xiaodong Han fei gao Department of Information and Electronic Engineering Beijing Institute of Technology

In this work, the homomorphism of the classic linear block code in linear network coding for the case of binary field and its extensions is studied. It is proved that the classic linear error-control block code is homomorphic network error-control code in network coding. That is, if the source packets at the source node for a linear network coding are precoded using a linear block code, then every packet flowing in the network regarding to the source satisfies the same constraints as the source. As a consequence, error detection and correction can be performed at every intermediate nodes of multicast flow, rather than only at the destination node in the conventional way, which can help to identify and correct errors timely at the error-corrupted link and save the cost of forwarding error-corrupted data to the destination node when the intermediate nodes are ignorant of the errors. In addition, three examples are demonstrated which show that homomorphic linear code can be combined with homomorphic signature, McEliece public-key cryptosystem and unequal error protection respectively and thus have a great potential of practical utility.

关键词： network coding network errorcorrection homomorphic linear code multi-cast

DISSIPATION-BASED CONSISTENT RATE-DEPENDENT MODEL FOR CONCRETE

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Acta Mechanica Solida Sinica 2010年第2期23卷 147-155页

作者： fei Leng gao Lin Earthquake Engineering Research Division Dalian University of Technology Dalian 116085 China College of Civil and Transportation Engineering Hohai University Nanjing 210098 China

An energy-dissipation based viscoplastic consistency model is presented to describe the performance of concrete under dynamic loading. The development of plasticity is started with the thermodynamic hypotheses in order that the model may have a sound theoretical background. Independent hardening and softening and the rate dependence of concrete are described separately for tension and compression. A modified implicit backward Euler integration scheme is adopted for the numerical computation. Static and dynamic behavior of the material is illustrated with certain numerical examples at material point level and structural level, and compared with existing experimental data. Results validate the effectiveness of the model.

关键词： constitutive model viscoplasticity consistency model energy dissipation rate dependency concrete backward Euler scheme

FLOW REGIMES BELOW AERATORS FOR DISCHARGE TUNNELS

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Journal of Hydrodynamics 2012年第3期24卷 378-382页

作者： MA fei WU jian-hua College of Water Conservancy and Hydropower Engineering Hohai University Nanjing 210098 China

The flow regimes below an aerator influence directly the air entrainment and the cavitation damage control. Based on the theoretical considerations, the experiments of the aerator for a discharge tunnel were conducted, and the relationships between the flow regime and hydraulic and geometric parameters were investigated. The results showed that, there are two kinds of threshold values for the flow regime conversions. One is Fr1-2 standing for the conversion from the fully filled cavity to the partially filled cavity, and the other is Fr2-3 which shows the change from the partially filled cavity to the net air cavity. Two empirical expressions were obtained for the conversions of the flow regimes, which can be used in the designs of the aerators.

关键词： aerator discharge tunnel flow regime filling water jet length

Data-driven fault diagnosis method for analog circuits based on robust competitive agglomeration

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Journal of Systems Engineering and Electronics 2013年第4期24卷 706-712页

作者： Rongling Lang Zheping Xu fei gao School of Electronic and Information Engineering Beihang University

The data-driven fault diagnosis methods can improve the reliability of analog circuits by using the data generated from it. The data have some characteristics, such as randomness and incompleteness, which lead to the diagnostic results being sensitive to the specific values and random noise. This paper presents a data-driven fault diagnosis method for analog circuits based on the robust competitive agglomeration （RCA）, which can alleviate the incompleteness of the data by clustering with the competing process. And the robustness of the diagnostic results is enhanced by using the approach of robust statistics in RCA. A series of experiments are provided to demonstrate that RCA can classify the incomplete data with a high accuracy. The experimental results show that RCA is robust for the data needed to be classified as well as the parameters needed to be adjusted. The effectiveness of RCA in practical use is demonstrated by two analog circuits.

关键词： data-driven fault diagnosis analog circuit robust competitive agglomeration (RCA).