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Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptomesequencing

null

《医学前沿（英文）》 2016年 第10卷 第1期   页码 61-75 doi: 10.1007/s11684-016-0436-0

摘要：

The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through real-time PCR. We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.

关键词： Epstein-Barr virus     paired-end transcriptome sequencing     latency genes     lytic genes     nasopharyngeal carcinoma    

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TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

《医学前沿（英文）》 2015年 第9卷 第3期   页码 322-330 doi: 10.1007/s11684-015-0408-9

摘要：

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词： TCGA     whole-transcriptome sequencing     HCC     liver cancer    

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Exploring the cancer genome in the era of next-generation sequencing

null

《医学前沿（英文）》 2012年 第6卷 第1期   页码 48-55 doi: 10.1007/s11684-012-0182-x

摘要：

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

关键词： next-generation sequencing     cancer genome     whole genome sequencing     exome     transcriptome    

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Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

《农业科学与工程前沿（英文）》 2014年 第1卷 第1期   页码 77-84 doi: 10.15302/J-FASE-2014010

摘要： While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of , a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of .

关键词： Larix     transcriptome     age     wood formation     somatic embryogenesis     molecular marker    

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Topology-independent end-to-end learning model for improving the voltage profile in microgrids-integrated

《能源前沿（英文）》 2023年 第17卷 第2期   页码 211-227 doi: 10.1007/s11708-022-0847-3

摘要： With multiple microgrids (MGs) integrated into power distribution networks in a distributed manner, the penetration of renewable energy like photovoltaic (PV) power generation surges. However, the operation of power distribution networks is challenged by the issues of multiple power flow directions and voltage security. Accordingly, an efficient voltage control strategy is needed to ensure voltage security against ever-changing operating conditions, especially when the network topology information is absent or inaccurate. In this paper, we propose a novel data-driven voltage profile improvement model, denoted as system-wide composite adaptive network (SCAN), which depends on operational data instead of network topology details in the context of power distribution networks integrated with multiple MGs. Unlike existing studies that realize topology identification and decision-making optimization in sequence, the proposed end-to-end model determines the optimal voltage control decisions in one shot. More specifically, the proposed model consists of four modules, Pre-training Network and modified interior point methods with adversarial networks (Modified IPMAN) as core modules, and discriminator generative adversarial network (Dis-GAN) and Volt convolutional neural network (Volt-CNN) as ancillary modules. In particular, the generator in SCAN is trained by the core modules in sequence so as to form an end-to-end mode from data to decision. Numerical experiments based on IEEE 33-bus and 123-bus systems have validated the effectiveness and efficiency of the proposed method.

关键词： end-to-end learning     microgrids     voltage profile improvement     generative adversarial network    

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clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome

《医学前沿（英文）》 doi: 10.1007/s11684-023-1029-3

摘要： Microbiome subsets determine tumor prognosis and molecular characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome data

关键词： tumor prognosis molecular     Microbiome subsets determine     center analysis microbiome     transcriptome data    

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METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

 

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Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

《农业科学与工程前沿（英文）》 2018年 第5卷 第2期   页码 214-225 doi: 10.15302/J-FASE-2018219

摘要： Sweet potato, , is a globally important food crop. The purple-fleshed sweet potato, rich in anthocyanins, has great potential for both nutritional and pharmaceutical uses. In this study, we characterized the root transcriptomes of the purple-fleshed sweet potato cv. Jingshu 6 and its mutant JS6-5 with high anthocyanin content by high-throughput RNA sequencing. A total of 22873364 and 27955097 high quality reads were obtained from Jingshu 6 and JS6-5, respectively, and assembled into 35592 unigenes. In all, we obtained 1566 differentially expressed genes (DEGs). Among them, 994 were upregulated and 572 were downregulated in JS6-5 compared to the expression in Jingshu 6. A total of 1436 DEGs were annotated, in which 847 DEGs had gene ontology (GO) terms and 329 DEGs were assigned to 84 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most importantly, 23 differentially expressed genes and 24 transcription factors were identified as candidate genes involved in anthocyanin biosynthesis. In addition, 2349 SSRs were detected. This study not only provides the candidate genes but also provides insights into the molecular mechanism of anthocyanin biosynthesis in sweet potato.

关键词： anthocyanin     gene expression     mutant     purple-fleshed sweet potato     transcriptome    

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Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

《医学前沿（英文）》 2014年 第8卷 第1期   页码 42-57 doi: 10.1007/s11684-014-0303-9

摘要：

The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.

关键词： genetics     whole-exome sequencing     Mendelian disease     disease gene    

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单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞 Article

张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟

《工程（英文）》 2022年 第17卷 第10期   页码 161-169 doi: 10.1016/j.eng.2021.05.009

摘要：

了解重症新型冠状病毒肺炎（COVID-19）患者单核细胞的免疫学特征（包括与纤维化相关的特征）对了解疾病的重症化机制和阻止疾病恶化至关重要。本研究共纳入7名COVID-19患者（包括3名重症/危重症患者和4名普通型患者）和6名健康对照者。采集7名COVID-19患者不同疾病时期外周血样本，包括重症/危重症时期血样3例，轻症时期血样4例，康复期血样7例。将以上血样和6例健康对照者血样进行单细胞转录组测序分析。本研究发现在COVID-19重症/危重症时期，单核细胞发生显著变化。单核细胞在外周血单个核细胞中占比增加，多样性却显著降低。同时本研究发现两个新的COVID-19重症疾病特异性单核细胞亚群：Mono 0和Mono 5。这两个亚群表达amphiregulin（AREG）、epiregulin（EREG）和细胞因子基因IL-18，KEGG分析显示富集的ErbB信号通路，这两个亚群可能具有促纤维化和促炎的特征。进一步分析发现Mono 0和Mono 5发生代谢改变，包括糖酵解/糖异生的增加和HIF-1信号通路的增加。本研究同时发现一个疾病重症前期取得的样本显示出与重症/危重症时期样本相似的单核细胞UMAP图谱。本研究发现了两种新的COVID-19重症疾病特异性单核细胞亚群，可作为重症COVID-19的潜在预测因子和治疗靶点。

关键词： COVID-19     重症感染     危重症     单核细胞     纤维化    

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一种端到端语音合成中的高效解码自注意力网络 Research Article

赵伟1,2,许力1,2

《信息与电子工程前沿（英文）》 2022年 第23卷 第7期   页码 1127-1138 doi: 10.1631/FITEE.2100501

摘要： 自注意力网络由于其并行结构和强大的序列建模能力，被广泛应用于语音合成（TTS）领域。然而，当使用自回归解码方法进行端到端语音合成时，由于序列长度的二次复杂性，其推理速度相对较慢。当部署设备未配备图形处理器（GPU）时，该效率问题更加严重。为解决该问题，提出一种高效解码自注意力网络（EDSA）作为替代。通过一个动态规划解码过程，有效加速TTS模型推理，使其具有线性计算复杂度。基于普通话和英文数据集的实验结果表明，所提EDSA模型在中央处理器（CPU）和GPU上的推理速度分别提高720%和50%，而性能几乎相同。因此，在GPU资源有限的情况下，该方法可使此类模型的部署更加容易。此外，所提模型在域外语言处理上可能比基线Transformer TTS性能更好。

关键词： 高效解码；端到端；自注意力网络；语音合成    

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Accurate quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing

《医学前沿（英文）》 2022年 第16卷 第2期   页码 240-250 doi: 10.1007/s11684-021-0909-7

摘要： The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3′-terminal nucleotides via 2′-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2′-O-methylation at the RNA 3′-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3′-terminal 2′-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3′-terminal 2′-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3′-terminal 2′-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3′-terminal 2′-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.

关键词： small RNAs     2′-O-methylation     sequencing     RT-qPCR    

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Comparison on End-of-Life strategies of WEEE in China based on LCA

Bin Lu, Xiaolong Song, Jianxin Yang, Dong Yang

《环境科学与工程前沿（英文）》 2017年 第11卷 第5期 doi: 10.1007/s11783-017-0994-7

摘要： As the Electrical and Electronic Equipment (EEE) are upgraded more frequently in China, a large quantity of Waste Electrical and Electronic Equipment (WEEE) was and will be generated. It becomes an urgent issue to develop and adopt an effective End-of-Life (EoL) strategy for EEE in order to balance the resource recovery and environmental impacts. In an EoL strategy hierarchy for EEE, reuse strategy is usually deemed to be prior to materials recovery and other strategies. But in practice, the advantages and disadvantages of different strategies are always context-dependent. Therefore, main EoL strategies for EEE in China need to be evaluated in environment and resources aspects from the life cycle perspective. In this study, the obsolete refrigerator and Power Supply Unit (PSU) of desktop PC are both taken as the target products. Life Cycle Assessment (LCA) is applied to assess the environmental impacts of different EoL scenarios in China: Unit Reuse Scenario (URS), Component Reuse Scenario (CRS) and Materials Recovery Scenario (MRS). The LCA results show that the EoL strategies hierarchy is reasonable for the part of computer, but not necessarily suitable for obsolete refrigerators. When the policy makers promote or demote one EoL strategy especially reuse, it is necessary to take subsequent impacts into consideration.

关键词： End-of-Life     Waste electrical and electronic equipment     Life cycle assessment     Reuse    

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Development and application of high-end aerospace MEMS

Weizheng YUAN

《机械工程前沿（英文）》 2017年 第12卷 第4期   页码 567-573 doi: 10.1007/s11465-017-0424-3

摘要：

This paper introduces the design and manufacturing technology of aerospace microelectromechanical systems (MEMS) characterized by high performance, multi-variety, and small batch. Moreover, several kinds of special MEMS devices with high precision, high reliability, and environmental adaptability, as well as their typical applications in the fields of aeronautics and aerospace, are presented.

关键词： MEMS     design and manufacture technology     aeronautic and aerospace    

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End-to-end delay analysis for networked systems

Jie SHEN,Wen-bo HE,Xue LIU,Zhi-bo WANG,Zhi WANG,Jian-guo YAO

《信息与电子工程前沿（英文）》 2015年 第16卷 第9期   页码 732-743 doi: 10.1631/FITEE.1400414

摘要： End-to-end delay measurement has been an essential element in the deployment of real-time services in networked systems. Traditional methods of delay measurement based on time domain analysis, however, are not efficient as the network scale and the complexity increase. We propose a novel theoretical framework to analyze the end-to-end delay distributions of networked systems from the frequency domain. We use a signal flow graph to model the delay distribution of a networked system and prove that the end-to-end delay distribution is indeed the inverse Laplace transform of the transfer function of the signal flow graph. Two efficient methods, Cramer’s rule-based method and the Mason gain rule-based method, are adopted to obtain the transfer function. By analyzing the time responses of the transfer function, we obtain the end-to-end delay distribution. Based on our framework, we propose an efficient method using the dominant poles of the transfer function to work out the bottleneck links of the network. Moreover, we use the framework to study the network protocol performance. Theoretical analysis and extensive evaluations show the effectiveness of the proposed approach.

关键词： Networked system     End-to-end     Delay distribution    

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标题 作者 时间 类型 操作

Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptomesequencing

null

期刊论文

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

期刊论文

Exploring the cancer genome in the era of next-generation sequencing

null

期刊论文

Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

期刊论文

Topology-independent end-to-end learning model for improving the voltage profile in microgrids-integrated

期刊论文

clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome

期刊论文

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

期刊论文

Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

期刊论文

Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

期刊论文

单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞

张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟

期刊论文

一种端到端语音合成中的高效解码自注意力网络

赵伟1,2,许力1,2

期刊论文

Accurate quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing

期刊论文

Comparison on End-of-Life strategies of WEEE in China based on LCA

Bin Lu, Xiaolong Song, Jianxin Yang, Dong Yang

期刊论文

Development and application of high-end aerospace MEMS

Weizheng YUAN

期刊论文

End-to-end delay analysis for networked systems

Jie SHEN,Wen-bo HE,Xue LIU,Zhi-bo WANG,Zhi WANG,Jian-guo YAO

期刊论文