214 Works

Genome-wide analysis of the GRF gene family and their expression profiling in peach (Prunus persica)

Li Liu, Xiu-jie Li, Bo Li, Ming-yue Sun & Shao-xuan Li
Growth-regulating factors (GRFs) are plant-specific transcription factors with vital roles in multiple biological processes. Although GRFs have been identified in various plant species, a comprehensive analysis of GRF genes in peach (Prunus persica) has not yet been reported. In this study, 10 PpGRF genes distributed on 6 chromosomes were identified in peach genome and their properties were analyzed systematically. Expression pattern analysis suggested that most PpGRFs were preferentially expressed in young tissues. Multiple types of...

Subspace Estimation with Automatic Dimension and Variable Selection in Sufficient Dimension Reduction

Jing Zeng, Qing Mai & Xin Zhang
Sufficient dimension reduction (SDR) methods target finding lower-dimensional representations of a multivariate predictor to preserve all the information about the conditional distribution of the response given the predictor. The reduction is commonly achieved by projecting the predictor onto a low-dimensional subspace. The smallest such subspace is known as the Central Subspace (CS) and is the key parameter of interest for most SDR methods. In this article, we propose a unified and flexible framework for estimating...

Crop Yield Prediction Using Bayesian Spatially Varying Coefficient Models with Functional Predictors

Yeonjoo Park, Bo Li & Yehua Li
Reliable prediction for crop yield is crucial for economic planning, food security monitoring, and agricultural risk management. This study aims to develop a crop yield forecasting model at large spatial scales using meteorological variables closely related to crop growth. The influence of climate patterns on agricultural productivity can be spatially inhomogeneous due to local soil and environmental conditions. We propose a Bayesian spatially varying functional model (BSVFM) to predict county-level corn yield for five Midwestern...

UXT attenuates the CGAS-STING1 signaling by targeting STING1 for autophagic degradation

Mingyu Pan, Yue Yin, Tongyu Hu, Xinxia Wang, Tian Jia, Jing Sun, Quanyi Wang, Wei Meng, Juanjuan Zhu, Chunsun Dai, Haiyang Hu & Chen Wang
STING1 (stimulator of interferon response cGAMP interactor 1), the pivotal adaptor protein of CGAS (cyclic GMP-AMP synthase)-STING1 signaling, is critical for type I IFN production of innate immunity. However, excessive or prolonged activation of STING1 is associated with autoinflammatory and autoimmune diseases. Thus, preventing STING1 from over-activation is important to maintain immune homeostasis. Here, we reported that UXT (ubiquitously expressed prefoldin like chaperone), a small chaperone-like protein, was essential to prevent the excessive activation of...

Source Data for \"Chiral symmetry breaking and acoustic singularities in phase–locked dissipative microelectromechanics\"

Xin Zhou, Xingjing Ren, Xuezhong Wu, Hui Jing & Dingbang Xiao
This is a source data fileset for a work titled "Chiral symmetry breaking and acoustic singularities in phase–locked dissipative microelectromechanics".

Additional file 4 of STAT3/miR-130b-3p/MBNL1 feedback loop regulated by mTORC1 signaling promotes angiogenesis and tumor growth

Hongwu Li, Ping Liu, Dapeng Li, Zixi Wang, Zhao Ding, Meng Zhou, Xu Chen, Manli Miao, Junli Ding, Wei Lin, Yehai Liu & Xiaojun Zha
Additional file 4: Supplementary Table S8. List of the downregulated differentially expressed genes from RNA sequencing results in Tsc2-/- MEFs and Tsc2+/+ MEFs. All genes were identified with FDR-adjusted p-value<0.05 and absolute value of log2(FC)>1.

Additional file 3 of STAT3/miR-130b-3p/MBNL1 feedback loop regulated by mTORC1 signaling promotes angiogenesis and tumor growth

Hongwu Li, Ping Liu, Dapeng Li, Zixi Wang, Zhao Ding, Meng Zhou, Xu Chen, Manli Miao, Junli Ding, Wei Lin, Yehai Liu & Xiaojun Zha
Additional file 3: Supplementary Table S7. List of the predict target genes of miR-130b-3p from prediction softwares TargetScan, RNA22, PicTar, miRDB and miRWalk.

Additional file 2 of Mitochondrial phylogenomics of Acanthocephala: nucleotide alignments produce long-branch attraction artefacts

Jin-Wei Gao, Xi-Ping Yuan, Hao Wu, Chuan-Yu Xiang, Min Xie, Rui Song, Zhong-Yuan Chen, Yuan-An Wu & Dong-Sheng Ou
Additional file 2: Dataset S1. Comparative overall mitogenomic architecture features of the Acanthocephala. Dataset S2. Comparative features of individual genes in mitogenomes of the Acanthocephala.

Additional file 2 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Xiaozhen Liu, Qinmeng Liu, Sihuai Sun, Hengxi Sun, Yao Wang, Xihui Shen & Lei Zhang
Additional file 2: Table S2. The rumen microbiota and the presence of quorum sensing molecules.

Additional file 2 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Xiaozhen Liu, Qinmeng Liu, Sihuai Sun, Hengxi Sun, Yao Wang, Xihui Shen & Lei Zhang
Additional file 2: Table S2. The rumen microbiota and the presence of quorum sensing molecules.

Learning Coefficient Heterogeneity over Networks: A Distributed Spanning-Tree-Based Fused-Lasso Regression

Xin Zhang, Jia Liu & Zhengyuan Zhu
Identifying the latent cluster structure based on model heterogeneity is a fundamental but challenging task arises in many machine learning applications. In this paper, we study the clustered coefficient regression problem in the distributed network systems, where the data are locally collected and held by nodes. Our work aims to improve the regression estimation efficiency by aggregating the neighbors’ information while also identifying the cluster membership for nodes. To achieve efficient estimation and clustering, we...

Additional file 1 of Dissecting super-enhancer driven transcriptional dependencies reveals novel therapeutic strategies and targets for group 3 subtype medulloblastoma

Meng Li, Yujie Han, Chaochen Wang, Wenfeng Kang, Wenyan Jiang, Lei Zhang & Yujie Tang
Additional file 1: Supplementary Table S1

Additional file 4 of Dissecting super-enhancer driven transcriptional dependencies reveals novel therapeutic strategies and targets for group 3 subtype medulloblastoma

Meng Li, Yujie Han, Chaochen Wang, Wenfeng Kang, Wenyan Jiang, Lei Zhang & Yujie Tang
Additional file 4: Supplementary Table S4

VIBRATION CHARACTERISTICS, CHEMICAL BONDS AND WEAK INTERACTIONS OF 4- AND 5-HYDROXYSALICYLIC ACID INVESTIGATED BY TERAHERTZ SPECTROSCOPY AND DENSITY FUNCTIONAL THEORY

Yuan Tang, Zhi Li, Yan Guo, Xianhua Yin, Shan Tu & Dapeng Zhang
The terahertz (THz) absorption spectra of 4- and 5-hydroxysalicylic acid were measured by terahertz time-domain spectroscopy (THz-TDS) in the range of 0.4-2.8 THz. The unit cells of both were calculated by density functional theory (DFT), and the theoretical simulation and experimental data were basically in agreement. To further interpret the origin of the characteristic absorption peaks, vibration characteristics and interactions of the unit cell model were analyzed by using potential energy distribution (PED) and interaction...

Additional file 4 of Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

Fei Li, Ye Liu, Xiaohua Zhang, Lingzhi Liu, Yun Yan, Xin Ji, Fanshu Kong, Yafan Zhao, Junzhou Li, Ting Peng, Hongzheng Sun, Yanxiu Du & Quanzhi Zhao
Additional file 4. Table S4. Network statistics of differential metabolites and related genes.

miR-140-3p/usp36 axis mediates ubiquitination to regulate PKM2 and suppressed the malignant biological behavior of breast cancer through Warburg effect

Hao Wu, Yile Jiao, Chen Zhou, Xinyi Guo, Zhenru Wu & Qing Lv
Breast cancer is a phenomenon in which breast epithelial cells proliferate out of control under the action of various carcinogenic factors. However, the role of USP36 in breast cancer is unknown. We analyzed the expression of USP36 in breast cancer and its association with poor prognosis in breast cancer patients. The effect of USP36 on malignant biological behavior of breast cancer was verified by cell functional experiments. The upstream regulatory mechanism of USP36 was analyzed...

Additional file 9 of ELOVL gene family plays a virtual role in response to breeding selection and lipid deposition in different tissues in chicken (Gallus gallus)

Dandan Wang, Xinyan Li, Panpan Zhang, Yuzhu Cao, Ke Zhang, Panpan Qin, Yulong Guo, Zhuanjian Li, Yadong Tian, Xiangtao Kang, Xiaojun Liu & Hong Li
Additional file 9: Table S7. Gene specific primers used for qRT-PCR.

Data from Modelling cosmic radiation events in the tree-ring radiocarbon record

Qingyuan Zhang, Utkarsh Sharma, Jordan A. Dennis, Andrea Scifo, Margot Kuitems, Ulf Büntgen, Mathew J. Owens, Michael W. Dee & Benjamin J. S. Pope
Each posterior corner plot is available in full resolution as a .pdf, named DATE.pdf for each event date.

Additional file 1 of Transcriptome profiling of lung immune responses potentially related to acute respiratory distress syndrome in forest musk deer

Jie Tang, Lijuan Suo, Feiran Li, Kun Bian, Chao Yang & Yan Wang
Additional file 1.

Agricultural Crop- and Animal-specific Ammonia Emission Inventory

Yuyu Yang, Lei Liu, Pu Liu, Jia Ding, Hang Xu & Sheng Liu
All products (crop- and animal- specific NH3 emission inventories in the time span of 1961-2018) are provided in TIFF format at a spatial resolution of 0.5 degree by 0.5 degree (latitude by longitude) at figshare. The unit is kg N yr-1, stored in two folders (cropland and livestock).

Additional file 1 of Network meta-analysis on the effects of finerenone versus SGLT2 inhibitors and GLP-1 receptor agonists on cardiovascular and renal outcomes in patients with type 2 diabetes mellitus and chronic kidney disease

Yaofu Zhang, Li Jiang, Junheng Wang, Tongxin Wang, Chieh Chien, Weijun Huang, Xiaozhe Fu, Yonghua Xiao, Qiang Fu, Shidong Wang & Jinxi Zhao
Additional file 1. RoB-2 evaluation.

Additional file 2 of Network meta-analysis on the effects of finerenone versus SGLT2 inhibitors and GLP-1 receptor agonists on cardiovascular and renal outcomes in patients with type 2 diabetes mellitus and chronic kidney disease

Yaofu Zhang, Li Jiang, Junheng Wang, Tongxin Wang, Chieh Chien, Weijun Huang, Xiaozhe Fu, Yonghua Xiao, Qiang Fu, Shidong Wang & Jinxi Zhao
Additional file 2. Publication bias.

Additional file 8 of FMO3 deficiency of duck leads to decreased lipid deposition and increased antibacterial activity

Xingzheng Li, Jianlou Song, Xuefeng Shi, Mingyi Huang, Lei Liu, Guoqiang Yi, Ning Yang, Guiyun Xu & Jiangxia Zheng
Additional file 8: Table S1. FMO3 mRNA expression in the CL and TH groups.

Additional file 9 of FMO3 deficiency of duck leads to decreased lipid deposition and increased antibacterial activity

Xingzheng Li, Jianlou Song, Xuefeng Shi, Mingyi Huang, Lei Liu, Guoqiang Yi, Ning Yang, Guiyun Xu & Jiangxia Zheng
Additional file 9: Table S2. Differently expressed protein applying TMT10plex.

Additional file 5 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

Shi-Tao Jiang, Yao-Ge Liu, Lei Zhang, Xin-Ting Sang, Yi-Yao Xu & Xin Lu
Additional file 5: Table S4. Common differentially expressed genes of SS, NASH, and COVID-19 (n = 62).

Registration Year

  • 2022
    214

Resource Types

  • Dataset
    214

Affiliations

  • Third Affiliated Hospital of Harbin Medical University
    214
  • Sichuan University
    169
  • Shanghai Jiao Tong University
    166
  • Fudan University
    158
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    152
  • Huazhong University of Science and Technology
    120
  • Anhui Medical University
    113
  • Zhejiang University
    111
  • North West Agriculture and Forestry University
    109
  • Harbin Medical University
    105