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Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle

Science China(Life Sciences) 2014年第3期57卷 340-355页

作者： ZHOU YuanYuan GONG Wei XIAO JingFa WU JiaYan PAN LinLin LI XiaoNuan WANG XuMin WANG WeiWei hu songnian YU Jun Beijing Key Laboratory of Genome and Precision Medicine Technologies CAS Key Laboratory of Genome Sciences and InformationBeijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences Division of Gastroenterology Department of MedicineUniversity of Alberta

An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancy-lactation-involution cycle （PL cycle） during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy （day 12 of pregnancy）, lactation （day 14 of lactation）, and involution （day 7 of involution）. The pregnancy-, lacta- tion- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs （ncRNAs）, respectively. Differentially expressed genes （DEGs） were defined in the three samples, which comprised 4843 DEGs （749 up-regulated and 4094 down-regulated） from pregnancy to lactation and 4926 DEGs （4706 up-regulated and 220 down-regulated） from lactation to involution. Besides the obvious and substantive up- and down-regulation of the DEGs, we observe that lysosomal enzymes were highly expressed and that their expression coin- cided with milk secretion. Further analysis of transcription factors such as Trpsl, Gtf2i, Tcf712, Nuprl, Vdr, Rbl, and Aebpl, and ncRNAs such as mir-125b, Let7, mir-146a, and mir-15 has enabled us to identify key regulators in mammary gland de- velopment and the PL cycle.

关键词： mouse mammary gland mammogenesis transcriptome rmRNA-seq miRNAs transcription factors

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Exploring spatiotemporal patterns of geosocial media data for urban functional zone identification

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International Journal of Digital Earth 2022年第1期15卷 1305-1325页

作者： Aleta Mawuenyegah songnian Li Shishuo Xu Department of Civil Engineering Toronto Metropolitan UniversityTorontoCanada School of Geomatics and Urban Spatial Informatics Beijing University of Civil Engineering and ArchitectureBeijingPeople’s Republic of China Key Laboratory of Urban Spatial Informatics Ministry of Natural Resources of the People’s Republic of ChinaBeijingPeople’s Republic of China

Urban Functional Zones(UFZs)can be identified by measuring the spatiotemporal patterns of activities that occur within *** media data possesses abundant spatial and temporal information for activity *** UFZs from geosocial media data aids urban planning,infrastructure,resource allocation,and transportation modernization in the complex urban *** this work,we proposed an integrated approach by combining the spatiotemporal clustering method with a machine learning *** spatiotemporal clustering method was used to mine the spatiotemporal patterns of activities,of which the distinctive features were extracted as inputs into a machine learning classifier for UFZ *** results show that more than 80%of the UFZs can be correctly identified by our proposed *** reveals that this work serves as a functional groundwork for future studies,facilitating the understanding of urban systems as well as promoting sustainable urban development.

关键词： Urban functional zones geosocial media twitter spatiotemporal clustering random forest

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Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products

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GENOMICS PROTEOMICS & BIOINFORMATICS 2023年第2期22卷 qzad006页

作者： Yu, Tao Luo, Yingfeng Tan, Xinyu Zhao, Dahe Bi, Xiaochun Li, Chenji Zheng, Yanning Xiang, hua hu, songnian Chinese Acad Sci Inst Microbiol State Key Lab Microbial Resources Beijing 100101 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

关键词： Global marine cold seep Metagenome Prokaryotic microbiome Metabolic function Natural product ALIGNMENT ALGORITHM GENOMES GENES TOOL

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Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans

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Genomics, Proteomics & Bioinformatics 2010年第2期8卷 92-102页

作者： Kaifu Chen Lei Wang Meng Yang Jiucheng Liu Chengqi Xin songnian hu Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China.

Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found that the 10.5-nt periodicity, the sequence signature of DNA double helix, may not be sufficient for cross-nucleosome positioning but provides essential guiding rails to facilitate positioning. We further dissected nucleosome-protected sequences and identified a strong positive purine （AG） gradient from the 5＇-end to the 3＂-end, and also learnt that the nucleosome-enriched regions are GC-rich as compared to the nucleosome-free sequences as purine content is positively correlated with GC content. Sequence characterization allowed us to develop a hidden Markov model （HMM） algorithm for decoding nucleosome positioning computationally, and based on a set of training data from the fifth chromosome of C. elegans, our algorithm predicted 60%-70% of the well-positioned nucleosomes, which is 15%-20% higher than random positioning. We concluded that nucleosomes are not randomly positioned on DNA sequences and yet bind to different genome regions with variable stability, well-positioned nucleosomes leave sequence signatures on DNA, and statistical positioning of nucleosomes across genome can be decoded computationally based on these sequence signatures.

关键词： nucleosome positioning sequence signature periodicity HMM

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Diffusion welding of SiCp/2014Al composites using Ni as interlayer

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Journal of University of Science and Technology Beijing 2006年第3期13卷 267-271页

作者： Tao Feng Xizhang Chen Luhai Wu songnian Lou School of Material Science and Engineering Shanghai Jiaotong University Shanghai 200030 China School of Material Science and Engineering Jiangsu University Zhenjiang 212013 China

SiCp/2014Al composites were bonded with the vacuum diffusion welding technique using Ni as the interlayer metal. Ni and Al were interdiffused and there were intermetallic compounds formed in the inter transition layer, which was composed of Ni3Al//NiAl//NiAl3. The relation between the diffusion distance and the element concentration was calculated according to Fick＇s second law. The relations of the diffusion concentration and the diffusion welding technique parameters were calculated.

关键词： aluminum matrix composite diffusion bonding interface diffusion vacuum diffusion welding

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Discovery,Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae

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Genomics, Proteomics & Bioinformatics 2010年第4期8卷 229-237页

作者： Wanfei Liu Dawei huang Kan Liu songnian hu Jun Yu Gang Gao Shuhui Song Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China 3College of Life Sciences Shanxi Normal University Linfen 041004 China College of Life Sciences Shanxi Normal University Linfen 041004 China

Plant non-specific lipid transfer proteins （nsLtps） have been reported to be involved in plant defense activity against bacterial and fungal pathogens. In this study, we identified 135 （122 putative and 13 previously identified） Solanaceae nsLtps, which are clustered into 8 different groups. By comparing with Boutrot’s nsLtp classification, we classified these eight groups into five types （I, II, IV, IX and X）. We compared Solanaceae nsLtps with Arabidopsis and Gramineae nsLtps and found that （1） Types I, II and IV are shared by Solanaceae, Gramineae and Arabidopsis; （2） Types III, V, VI and VIII are shared by Gramineae and Arabidopsis but not detected in Solanaceae so far; （3） Type VII is only found in Gramineae whereas type IX is present only in Arabidopsis and Solanaceae; （4） Type X is a new type that accounts for 52.59% Solanaceae nsLtps in our data, and has not been reported in any other plant so far. We further built and compared the three-dimensional structures of the eight groups, and found that the major functional diversification within the nsLtp family could be predated to the monocot/dicot divergence, and many gene duplications and sequence variations had happened in the nsLtp family after the monocot/dicot divergence, especially in Solanaceae.

关键词： nsLtp family Solanaceae phylogenetic analysis three-dimensional structure

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Overfitting effect of artificial neural network based nonlinear equalizer: from mathematical origin to transmission evolution

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Science China(Information Sciences) 2020年第6期63卷 67-79页

作者： Zheng YANG Fan GAO songnian FU Ming TANG Deming LIU Wuhan National Laboratory for Optoelectronics School of Optical and Electronic InformationHuazhong University of Science and Technology Alibaba Infrastructure Service Alibaba Group

Overfitting effect of artificial neural network(ANN) based nonlinear equalizer(NLE) leads to a trap of bit error ratio(BER) overestimation in optical fiber communication system, especially when the performance is evaluated by the commonly-used pseudo-random binary sequence(PRBS). First, we mathematically investigate the PRBS generation and Gray code mapping rules, in comparison with the use of Mersenne Twister random sequence(MTRS). Under the condition of a symbol erasure channel, we identify that ANN can recognize both the PRBS generation and symbol mapping rules, by increasing the weights of NLE at specific positions, whereas the MTRS is currently safe owing to the limited input length of current ANN based NLE. Then, we design four channel models of fiber optical transmission to experimentally examine various impairments on the evolution of overfitting effect. When both the additive white Gaussian noise(AWGN) channel and the bandwidth limited channel are considered, the mitigation of overfitting becomes possible by the use of pruned PRBS(P-PRBS) training set with removing the generation and mapping rules determined input symbols. However, as for both the chromatic dispersion(CD) uncompensated channel and the CD managed channel, the overfitting effect becomes serious, because both CD and fiber nonlinearity induced inter-symbol interference(ISI) is beneficial for ANN to identify the PRBS symbol rules. Finally,possible solutions to mitigate the overfitting effect are summarized.

关键词： artificial neural network nonlinear equalizer pseudo-random binary sequence overfitting

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多导睡眠监测仪在精神分裂症患者中的应用及其对睡眠质量和结构的监测效果研究

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中国医学装备 2024年第3期21卷 97-101页

作者：张慧石林傅松年新疆医科大学第一附属医院心理医学三科乌鲁木齐830000

目的:探究与分析多导睡眠监测仪在精神分裂症患者中的应用及其对睡眠质量和结构的监测效果。方法:选取2021年3月至2023年5月新疆医科大学第一附属医院收治的90例精神分裂症患者作为观察组,同时选择80名健康志愿者作为健康对照组,所有受... 详细信息

目的:探究与分析多导睡眠监测仪在精神分裂症患者中的应用及其对睡眠质量和结构的监测效果。方法:选取2021年3月至2023年5月新疆医科大学第一附属医院收治的90例精神分裂症患者作为观察组,同时选择80名健康志愿者作为健康对照组,所有受试者均采用多导睡眠监测仪进行睡眠监测,对比两组匹兹堡睡眠质量指数(PSQI)评分、多导睡眠监测仪睡眠质量指标、睡眠结构指标、纺锤波指标;同时Pearson相关性分析探讨PSQI评分与睡眠参数的相关性。结果:健康对照组PSQI评分为(5.36±0.65)分,观察组PSQI评分为(14.24±3.58)分,观察组PSQI评分高于健康对照组,差异有统计学意义(t=23.115,P15.136、40.355、36.620、24.226,P0.05)。观察组治疗后与观察组治疗前相比睡眠总时间较长、睡眠潜伏期较短、REM期较长、觉醒次数较少,差异均有统计学意义(t=3.145、12.021、8.668、9.101,P14.781、15.899、9.901,P1%值较高、N2%值较高及N3%值较低,差异有统计学意义(t=10.163、9.483、10.065,P0.05)。观察组治疗后与治疗前相比N1%值较低、N2%值较低、N3%值较高(t=10.163、9.483、10.065,P1%值较高、N2%值较高、N3%值较低,差异均有统计学意义(t=7.628、4.210、7.153,P14、2.665、2.014,P1%、N2%呈现了明显的正相关性(r=-0.612、-0.269、-0.812、-0.778、-0.841;r=0.382、0.226、0.654、0.778,P<0.05)。结论:实施多导睡眠监测仪监测可观察到精神分裂症患者存在睡眠质量及结构异常的表现,且睡眠纺锤波的活性也呈现出了异常的表现,其指标与PSQI之间具有密切的关系。

关键词：多导睡眠监测仪精神分裂症睡眠质量睡眠结构睡眠纺锤波匹兹堡睡眠质量指数(PSQI)

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XRD and TEM analysis of the microstructure in the brazing joint of 3003 cladding aluminum alloy

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Journal of University of Science and Technology Beijing 2005年第6期12卷 531-534页

作者： Tao Feng songnian Lou Luhai Wu Yajiang Li School of Material Science and Engineering Shanghai Jiaotong University Shanghai 200030 China School of Material Science and Engineering. Shandong University Jinan 250061 China

The material used in this experiment was 3003 cladding aluminum alloy, the cladding metal was 4004 aluminum alloy. The aluminum plate was brazed by means of vacuum brazing. The microstructure in the brazing joint was studied by means of X-ray diffractometry （XRD） and transmission electron microscopy （TEM）. The test result indicates that the suitable brazing technique parameters are brazing temperature, 628℃; keeping time, 10 min; vacuum degree, 6.5×10^-4 Pa. XRD test indicates that there are new intermetallic compounds different from the base metal. TEM analysis indicates that Cu2Mg and CuaMn2Mg are formed in the brazing joint. The shape of Cu2Mg is irregular and the shape of Cu3Mn2Mg is circle, and there are tiny particles in it.

关键词： 3003 cladding aluminum alloy vacuum brazing microstructure joint

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RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 373-381页

作者： Wanfei Liu Shuangyang Wu Qiang Lin Shenghan Gao Feng Ding Xiaowei Zhang Hasan Awad Aljohi Jun Yu songnian hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Joint Center for Genomics Research(JCGR) King Abdulaziz City for Science and Technology and Chinese Academy of SciencesRiyadh 11442Saudi Arabia University of Chinese Academy of Sciences Beijing 100049China Grail Scientific Co.Ltd. Shenyang 110000China Shenzhen Institute of Geriatrics Shenzhen 518020China

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://***/projects/rgaat/and https://***/wushyer/RGAAT;2 at no cost.

关键词： Variant identification Genome assembly Genome annotation Genome comparison

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