843 Works

Circular RNA ZFR accelerates non-small cell lung cancer progression by acting as a miR-101-3p sponge to enhance CUL4B expression

Haifeng Zhang, Xiaolong Wang, Baoli Hu, Feng Zhang, Haitao Wei & Li Li
Non-small-cell lung carcinoma (NSCLC) is the most common type of lung cancer. Circular RNA ZFR (circZFR) is an identified circular RNA (circRNA) that is correlated with cancer progression. However, the role of circZFR in NSCLC remains unknown. In the present study, we aimed to investigate the function of circZFR in NSCLC and the underlying mechanism. The expression patterns of circZFR were determined using qRT-PCR in NSCLC samples and cell lines. The subcellular distribution of circZFR...

Circular RNA ZFR accelerates non-small cell lung cancer progression by acting as a miR-101-3p sponge to enhance CUL4B expression

Haifeng Zhang, Xiaolong Wang, Baoli Hu, Feng Zhang, Haitao Wei & Li Li
Non-small-cell lung carcinoma (NSCLC) is the most common type of lung cancer. Circular RNA ZFR (circZFR) is an identified circular RNA (circRNA) that is correlated with cancer progression. However, the role of circZFR in NSCLC remains unknown. In the present study, we aimed to investigate the function of circZFR in NSCLC and the underlying mechanism. The expression patterns of circZFR were determined using qRT-PCR in NSCLC samples and cell lines. The subcellular distribution of circZFR...

Identification of novel tetracycline resistance gene tet(X14) and its co-occurrence with tet(X2) in a tigecycline-resistant and colistin-resistant Empedobacter stercoris

Yingying Cheng, Yong Chen, Yang Liu, Yuqi Guo, Yanzi Zhou, Tingting Xiao, Shuntian Zhang, Hao Xu, Yunbo Chen, Tongling Shan, Yonghong Xiao & Kai Zhou
Tigecycline is one of the last-resort antibiotics to treat severe infections. Recently, tigecycline resistance has sporadically emerged with an increasing trend, and Tet(X) family represents a new resistance mechanism of tigecycline. In this study, a novel chromosome-encoded tigecycline resistance gene, tet(X14), was identified in a tigecycline-resistant and colistin-resistant Empedobacter stercoris strain ES183 recovered from a pig fecal sample in China. Tet(X14) shows 67.14-96.39% sequence identity to the other variants [Tet(X) to Tet(X13)]. Overexpression of Tet(X14)...

Additional file 4 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

Yongliang Li, Pai Qin, Aolong Sun, Wenjun Xiao, Fenglin Chen, Yang He, Keyao Yu, You Li, Meng Zhang & Xinhong Guo
Additional file 4: Table S1. Detailed information of all 138 TaRING zinc finger genes identified in tomato genome.

Additional file 5 of Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

Yongliang Li, Pai Qin, Aolong Sun, Wenjun Xiao, Fenglin Chen, Yang He, Keyao Yu, You Li, Meng Zhang & Xinhong Guo
Additional file 5: Table S2. One-to-one orthologous relationships among T.aestivum and T.aestivum, A.thaliana, A. tauschii, B. distachyon, H. vulgare, rice, S.italica and Zea mays, respectively.

Additional file 10 of Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings

Jia Li, Wei Xin, Weiping Wang, Shijiao Zhao, Lu Xu, Xingdong Jiang, Yuxuan Duan, Hongliang Zheng, Luomiao Yang, Hualong Liu, Yan Jia, Detang Zou & Jingguo Wang
Additional file 10: Table S9. Sequences of primers used in this study.

Additional file 1 of Surface fungal diversity and several mycotoxin-related genes’ expression profiles during the Lunar Palace 365 experiment

Jianlou Yang, Zikai Hao, Lantao Zhang, Yuming Fu & Hong Liu
Additional file 1: Supplementary Table S1. qPCR primer sequences, mycotoxin types, producers, and toxic effects in humans. Supplementary Table S2. ASV abundances and potential ecological functions (F01-F70). Supplementary Table S3. ISS dust, AIT, ILMAH, and LP1 surfaces merged fungal ASV table. Supplementary Table S4. Species abundance tables at the phylum level. Supplementary Table S5. Species abundance tables at the genus level. Supplementary Table S6. Trophic modes of the fungal microbiome in the different crew groups...

Additional file 3 of Genome-wide identification and characterization of lncRNAs in sunflower endosperm

Shuai Yu, Zhichao Zhang, Jing Li, Yanbin Zhu, Yanzhe Yin, Xiaoyu Zhang, Yuxin Dai, Ao Zhang, Cong Li, Yanshu Zhu, Jinjuan Fan, Yanye Ruan & Xiaomei Dong
Additional file 3: Table S3. GO Gene Ontology analysis of co-expressed protein-coding genes with all candidate lncRNAs.

Additional file 3 of Genetic diversity in the transmission-blocking vaccine candidate Plasmodium vivax gametocyte protein Pvs230 from the China–Myanmar border area and central Myanmar

Xin Zhao, Yubing Hu, Yan Zhao, Lin Wang, Zifang Wu, Myat Thu Soe, Myat Phone Kyaw, Liwang Cui, Xiaotong Zhu & Yaming Cao
Additional file 3: Table S3. Codon-based tests for selection on Pvs230 in China–Myanmar border and Myanmar isolates.

Effects of SLCO1B1 on elimination and toxicities of high-dose methotrexate in pediatric acute lymphoblastic leukemia - Supplementary Material

Fei-Fei Yang, Tian-Lin Xue, Chao Gao, Ying Wu, Wei Lin, Jun Li, Rui-Dong Zhang, Hu-Yong Zheng & Shu-Guang Liu
Supplementary Table S1. Treatment elements of consolidation therapy in CCLG-ALL-2018. Supplementary Table S2. Leucovorin rescue and MTX concentration

Comparative transcriptomic analysis reveal genes involved in the pathogenicity increase of Streptococcus suis epidemic strains

Jianping Wang, Pujun Liang, Hui Sun, Zongfu Wu, Marcelo Gottschalk, Kexin Qi & Han Zheng
Streptococcus suis epidemic strains were responsible for two outbreaks in China and possessed increased pathogenicity which was featured prominently by inducing an excessive inflammatory response at the early phase of infection. To discover the critical genes responsible for the pathogenicity increase of S. suis epidemic strains, the genome-wide transcriptional profiles of epidemic strain SC84 were investigated at the early phase of interaction with BV2 cells. The overall low expression levels of 89K pathogenicity island (PAI)...

Cancer-associated fibroblast-released extracellular vesicles carrying miR-199a-5p induces the progression of​ gastric cancer through regulation of FKBP5-mediated AKT1/mTORC1 signaling pathway

Yan Wang, Tao Li, Lei Yang, Xunlei Zhang, Xiaoli Wang, Xiaoqin Su, Congfei Ji & Zhenxin Wang
Accumulating evidence has unfolded the significance of extracellular vesicles (EVs) in diseases and cancers. Here, we attempted to discuss the role of cancer-associated fibroblasts (CAFs)-derived EVs containing miR-199a-5p in gastric tumorigenesis. Upregulated miR-199a-5p was first identified in cancer cells. Then, we selected CAFs for isolation of EVs which were co-cultured with AGS cells. We observed successful delivery of miR-199a-5p via CAF-derived EVs. Besides, miR-199a-5p promoted malignant properties of AGS cells. Moreover, miR-199a-5p downregulated FKBP5, leading...

Nonparametric prediction distribution from resolution-wise regression with heterogeneous data

Jialu Li, Wan Zhang, Peiyao Wang, Qizhai Li, Kai Zhang & Yufeng Liu
Modeling and inference for heterogeneous data have gained great interest recently due to rapid developments in personalized marketing. Most existing regression approaches are based on the conditional mean and may require additional cluster information to accommodate data heterogeneity. In this paper, we propose a novel nonparametric resolution-wise regression procedure to provide an estimated distribution of the response instead of one single value. We achieve this by decomposing the information of the response and the predictors...

RIOK3-Mediated Akt phosphorylation facilitates synergistic replication of Marek’s disease and reticuloendotheliosis viruses

Xusheng Du, Defang Zhou, Jing Zhou, Jingwen Xue & Ziqiang Cheng
Co-infection of Marek’s disease virus (MDV) and reticuloendotheliosis virus (REV) synergistically drives disease progression, yet little is known about the mechanism of the synergism. Here, we found that co-infection of REV and MDV increased their replication via the RIOK3-Akt pathway. Initially, we noticed that the viral titres of MDV and REV significantly increased in REV and MDV co-infected cells compared with single-infected cells. Furthermore, tandem mass tag peptide labelling coupled with LC/MS analysis showed that...

Additional file 4 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 4: Table S3.qPCR results of gDNA after DNase treatment. (recording data values of Additional file 1: Fig. S6B).

Additional file 5 of Rapid and sensitive single-cell RNA sequencing with SHERRY2

Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen & Yanyi Huang
Additional file 5: Table S4.Normalized abundance of marker genes in each GC cell type. (recording data values of Additional file 1: Fig. S7D).

Interstitial lung disease associated with anti-HER2 anti-body drug conjugates: results from clinical trials and the WHO's pharmacovigilance database

Zhuo Ma, Yi Zhang, Min Zhu, Lin Feng, Yuhui Zhang & Zhuoling An
Interstitial lung disease (ILD) events associated with anti-human epidermal growth factor receptor 2 (HER2) antibody-drug conjugates (ADCs) have aroused wide attention. In meta-analysis, we systematically reviewed literatures, and the outcomes were the proportion and risk of ILD related to anti-HER2 ADCs. A disproportionality analysis based on data from VigiBase was conducted to characterize the main features of anti-HER2 ADC-related ILD/pneumonitis. Two hundred and forty-five all-grade and 47 grade ≥ 3 ILD events with the proportion...

Interstitial lung disease associated with anti-HER2 anti-body drug conjugates: results from clinical trials and the WHO's pharmacovigilance database

Zhuo Ma, Yi Zhang, Min Zhu, Lin Feng, Yuhui Zhang & Zhuoling An
Interstitial lung disease (ILD) events associated with anti-human epidermal growth factor receptor 2 (HER2) antibody-drug conjugates (ADCs) have aroused wide attention. In meta-analysis, we systematically reviewed literatures, and the outcomes were the proportion and risk of ILD related to anti-HER2 ADCs. A disproportionality analysis based on data from VigiBase was conducted to characterize the main features of anti-HER2 ADC-related ILD/pneumonitis. Two hundred and forty-five all-grade and 47 grade ≥ 3 ILD events with the proportion...

From Black Box to Shining Spotlight: Using Random Forest Prediction Intervals to Illuminate the Impact of Assumptions in Linear Regression

Andrew J. Sage, Yang Liu & Joe Sato
We introduce a pair of Shiny web applications that allow users to visualize random forest prediction intervals alongside those produced by linear regression models. The apps are designed to help undergraduate students deepen their understanding of the role that assumptions play in statistical modeling by comparing and contrasting intervals produced by regression models with those produced by more flexible algorithmic techniques. We describe the mechanics of each approach, illustrate the features of the apps, provide...

Additional file 7 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Xueqian Jiang, Xijiang Yang, Fan Zhang, Tianhui Yang, Changfu Yang, Fei He, Ting Gao, Chuan Wang, Qingchuan Yang, Zhen Wang & Junmei Kang
Additional file 7: Table S5. The information of the seven candidates.

Additional file 8 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 8: Table S6. All genomic SNPs in gene body and 2 kb promoter of ELOVL gene family used for PCA analysis.

Data from \" Chemical Origin of Temperature-Dependent Phase Transition and Conductivity in Hydroxyapatite\"

Dingguo Xu & Jing Wang
This dataset contains data relates to the publication " Chemical Origin of Temperature-Dependent Phase Transition and Conductivity in Hydroxyapatite", by Wang et al., 2022. In this work, we use deep potential molecular dynamics simulation to study Temperature-Dependent Phase Transition and Conductivity in Hydroxyapatite. The deep neural network potential is trained on DFT calculations. This dataset contains the deep potential models and the DFT training data reported in the publication, the input files of vasp, lammps,...

Additional file 2 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 2. Table S2: Adjuvant treatment information.

Additional file 2 of Identification of molecular subtypes based on inflammatory response in lower-grade glioma

Wanzun Lin, Jing Gao, Haojiong Zhang, Li Chen, Xianxin Qiu, Qingting Huang, Jiyi Hu, Lin Kong & Jiade J. Lu
Additional file 2. Gene list of hallmark inflammatory response.

Flexible hyperspectral surface plasmon resonance microscopy

Ziwei Liu, Jingning Wu, Chen Cai, Bo Yang & Zhi-mei Qi
Dataset of the raw hyperspectral SPR datacube supporting the article titled 'Flexible Hyperspectral Surface Plasmon Resonance Microscopy'.

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Affiliations

  • Ministry of Education of the People's Republic of China
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  • Shanghai Jiao Tong University
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  • Zhejiang University
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  • Chinese Academy of Medical Sciences & Peking Union Medical College
    552
  • Capital Medical University
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