Preserved egg white alleviates DSS-induced colitis in mice through the reduction of oxidative stress, modulation of infl ammatory cytokines, NF-κB, MAPK and gut microbiota composit... by Lingyu Li, Ning Qiu, Yaqi Meng, Chenyan Wang, Yoshinori Mine, Russell Keast, Vincent Guyonnet

“…The results showed that treatment with PEW in mice with DSS-induced colitis for 14 days effectively improved the clinical signs, inhibited the secretion and gene expression of pro-inflammatory cytokines, and reduced myeloperoxidase (MPO) activity and oxidative stress levels. …”
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Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates by Yuchen Wang, Zhidong Zhang, Suhua Chen, Yangping Wu, Qiujie Li, Yi Cao, Yu Zhang, Aihua Chen

“…MicroRNAs (miRNAs) are a class of non-coding RNAs that modulate gene expression at the post-transcriptional level. Characterized by their dynamic expression patterns, miRNAs play a crucial role in regulating a multitude of biological processes, including metabolism and autophagy. …”
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Improving doublet cell removal efficiency through multiple algorithm runs by Yong She, Chaoye Wang, Qi Zhao

“…Finally, compared to running the algorithm once, we found that the MRDR strategy was more beneficial for differential gene expression analysis and cell trajectory inference when using default analysis parameters. …”
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Characterization of Human Mesenchymal Stem Cells Isolated from the Testis by Letizia De Chiara, Elvira Smeralda Famulari, Sharmila Fagoonee, Saskia K. M. van Daalen, Stefano Buttiglieri, Alberto Revelli, Emanuela Tolosano, Lorenzo Silengo, Ans M. M. van Pelt, Fiorella Altruda

“…Spontaneously arising pluripotent stem cells can be obtained in culture from murine spermatogonial stem cells (SSCs), while the pluripotency of the human counterpart remains a matter of debate. Recent gene expression profiling studies have demonstrated that embryonic stem cell- (ESC-) like cells obtained from the human testis are indeed closer to mesenchymal stem cells (MSCs) than to pluripotent stem cells. …”
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Involvement of the TGF-β pathway in epithelialmesenchymal transition promoted by the pulmonary microenvironment in Mycoplasma pneumoniae pneumonia by Fan Lu, Wang Huixia, Xu Nuo, Guo Yun, Li Ling

“…Among these, the TGF-β pathway exhibited the most pronounced changes in gene expression. Further analysis confirmed that BALF from these patients induced EMT in human bronchial epithelial cells and mouse lung tissues and that TGF-β receptor kinase inhibitor (TRKI) effectively reversed this process. …”
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Endometrial Cancer and Hypermethylation: Regulation of DNA and MicroRNA by Epigenetics by Kouji Banno, Iori Kisu, Megumi Yanokura, Kenta Masuda, Yusuke Kobayashi, Arisa Ueki, Kosuke Tsuji, Wataru Yamagami, Hiroyuki Nomura, Nobuyuki Susumu, Daisuke Aoki

“…Silencing of genes such as APC and CHFR, Sprouty 2, RASSF1A, GPR54, CDH1, and RSK4 by DNA hypermethylation, onset of Lynch syndrome due to hereditary epimutation of hMLH1 and hMSH2 mismatch repair genes, and regulation of gene expression by microRNAs may also underlie the carcinogenic mechanisms of endometrial cancer. …”
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Enhanced bioaccumulation and toxicity of Fenpropathrin by polystyrene nano(micro)plastics in the model insect, silkworm (Bombyx mori) by Abrar Muhammad, Zhaoyi Qian, Yu Li, Xiaoyu Lei, Junaid Iqbal, Xiaoqiang Shen, Jintao He, Nan Zhang, Chao Sun, Yongqi Shao

“…Additionally, the pollutants caused physical and oxidative damage to the midgut and altered gene expression related to juvenile hormone (JH) and silk protein synthesis. …”
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The Different Effects of IFN-β and IFN-γ on the Tumor-Suppressive Activity of Human Amniotic Fluid-Derived Mesenchymal Stem Cells by Jingchun Du, Anqi Liu, Rui Zhu, Chengbo Zhou, Heng Su, Guie Xie, Yingshan Deng, Xia Xu

“…The different target gene expression profiles of AFMSCs regulated by IFN-β and IFN-γ determined the different antitumor effects of IFN-β- and IFN-γ-primed AFMSCs on tumor cells. …”
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Prognostic model and immune-infiltrating cell landscape based on differentially expressed autophagy-related genes in TP53-mutated multiple myeloma by Yan-Hua Zheng, Hong-Yuan Shen, Xiang Chen, Juan Feng, Guang-Xun Gao

“…Material and methods Information about MM patients with TP53 mutations was downloaded from the Gene Expression Omnibus (GEO) database. Cox proportional hazard regression was employed to determine the independent prognostic ARG and construct a risk signature. …”
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EZH2 inhibition induces pyroptosis via RHA-mediated S100A9 overexpression in myelodysplastic syndromes by Qi Zhang, Yingwan Luo, Li Ye, Yuxia Wang, Lu Wang, Wenli Yang, Wei Lang, Shuanghong Zhu, Lingxu Jiang, Weimei Jin, Chen Mei, Xinping Zhou, Yanling Ren, Liya Ma, Gaixiang Xu, Bowatte Gedara Lakmal Vimukthi Bandara Bowattage, Hongyan Tong, Jie Sun

“…Enhancer of zeste homolog 2 (EZH2) is an important regulator in gene expression through methyltransferase-dependent or methyltransferase-independent mechanisms. …”
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Identification of critical biomarkers and immune landscape patterns in glioma based on multi-database by Hanzhang Yuan, Jingsheng Cheng, Jun Xia, Zeng Yang, Lixin Xu

“…Patients and methods Differentially expressed genes (DEGs) of glioma were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The potential biomarkers were identified using weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression. …”
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IL-13 Augments Histone Demethylase JMJD2B/KDM4B Expression Levels, Activity, and Nuclear Translocation in Airway Fibroblasts in Asthma by Khuloud Bajbouj, Mahmood Y. Hachim, Rakhee K. Ramakrishnan, Huwaida Fazel, Jumana Mustafa, Shahed Alzaghari, Mahmoud Eladl, Jasmin Shafarin, Ronald Olivenstein, Qutayba Hamid

“…Publicly available transcriptomic datasets from Gene Expression Omnibus (GEO) were used to identify differentially expressed genes on an epigenetic level upon IL-13 exposure in lung fibroblasts. …”
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Genomic and algorithm-based predictive risk assessment models for benzene exposure by Minyun Jiang, Minyun Jiang, Na Cai, Na Cai, Juan Hu, Lei Han, Lei Han, Fanwei Xu, Baoli Zhu, Baoli Zhu, Baoli Zhu, Baoli Zhu, Boshen Wang

“…AimIn this research, we leveraged bioinformatics and machine learning to pinpoint key risk genes associated with occupational benzene exposure and to construct genomic and algorithm-based predictive risk assessment models.Subject and methodsWe sourced GSE9569 and GSE21862 microarray data from the Gene Expression Omnibus. Utilizing R software, we performed an initial screen for differentially expressed genes (DEGs), which was followed by the enrichment analyses to elucidate the affected functions and pathways. …”
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High-Throughput Analysis of the T Cell Receptor Beta Chain Repertoire in PBMCs from Chronic Hepatitis B Patients with HBeAg Seroconversion by Yachao Qu, Yong Huang, Di Liu, Yinuo Huang, Zhiyi Zhang, Zhiqiang Mi, Xiaoping An, Yigang Tong, Jun Lu

“…These results illustrate the presence of biased TCRVβ and Jβ gene expression in the chronic hepatitis B patients. TRBVβ12-4, Vβ28, Jβ2-1, V7-2-01-J2-1, V12-4-J1-1, and V28-1-J1-5 may be associated with the development and treatment of CHB.…”
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Preventive Effect of Salicylate and Pyridoxamine on Diabetic Nephropathy by Tarek Kamal Abouzed, Seiichi Munesue, Ai Harashima, Yusuke Masuo, Yukio Kato, Khaled Khailo, Hiroshi Yamamoto, Yasuhiko Yamamoto

“…Attenuation of macrophage infiltration into the kidneys and upregulation of antiglycating enzyme glyoxalase 1 gene expression were found only in the salicylate treatment group. …”
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Characterization of the Cannabis sativa glandular trichome epigenome by Lee J. Conneely, Bhavna Hurgobin, Sophia Ng, Muluneh Tamiru-Oli, Mathew G. Lewsey

“…Corresponding transcriptomic (RNA-seq) datasets were integrated, and tissue-specific analyses conducted to relate chromatin states to glandular trichome specific gene expression. Results The promoters of cannabinoid and terpenoid biosynthetic genes, specialised metabolite transporter genes, defence related genes, and starch and sucrose metabolism were enriched specifically in trichomes for histone marks H3K4me3 and H3K56ac, consistent with active transcription. …”
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Transcriptome Analysis and Phytohormone Profile Reveal Core Phytohormone Regulating Parthenocarpy in Fingered Citron by Qianbin Chen, Jinjian Xu, Xinjian Zou, Yanjun Zhang, Xiaoxian Zhu, Kewei Zhang, Wenrong Chen, Fanglei Liao, Weidong Guo

“…Virus-induced gene silencing (VIGS) experiments demonstrated that silencing <i>CmsABI5</i> led to decreased ABA levels, while auxin levels remained unchanged, resulting in disrupted parthenocarpy and increased ethylene levels, indicating a secondary hormonal response. Additionally, gene expression changes associated with failed parthenocarpy showed down-regulation of SAUR50 and up-regulation of <i>PP2C 56</i>, linking these changes to ABA signaling. …”
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Long Noncoding RNA HCG9 Promotes Osteosarcoma Progression through RAD51 by Acting as a ceRNA of miR-34b-3p by Lu Wang, ShuangQing Li, Lin Qi, Lin Ling

“…The candidate lncRNA was further verified by qRT-PCR, and the association of gene expression with clinicopathological features was evaluated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. …”
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Using RNA-Seq to Explore the Repair Mechanism of the Three Methods and Three-Acupoint Technique on DRGs in Sciatic Nerve Injured Rats by Tao-tao Lv, Yan-jun Mo, Tian-yuan Yu, Shuai Shao, Meng-qian Lu, Yu-ting Luo, Yi Shen, Yu-mo Zhang, Wong Steven

“…To study the effects of the three methods and three-acupoint technique on DRG gene expression in SNI model rats and to elucidate the molecular mechanism of the three methods and three-acupoint technique on promoting recovery in peripheral nerve injury. …”
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Regulation of NK cell development, maturation, and antitumor responses by the nuclear receptor NR2F6 by Johannes Woelk, Florian Hornsteiner, Stephanie Aschauer-Wallner, Patrizia Stoitzner, Gottfried Baier, Natascha Hermann-Kleiter

“…Subsequent transcriptome analysis reveals significant changes in gene expression profiles of NK cells from IL-15 complex treated Nr2f6-deficient mice, with notable alterations in essential NK genes such as Klrg1, Prdm1, Stat5a, Zeb2, and Prf1. …”
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