Drug Efficacy Recommendation System of Glioblastoma (GBM) Using Deep Learning by Sajid Naveed, Mujtaba Husnain, Ali Samad, Amna Ikram, Hina Afreen, Ghulam Gilanie, Najah Alsubaie

“…Each cell line provides gene expression values, which are further normalized through Z-transformation for each gene. …”
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Construction of a circRNA-miRNA-mRNA Regulatory Network for Coronary Artery Disease by Bioinformatics Analysis by Zebo Zhang, Haiyan Qian, Li Wang, Zhenbo Tao, Keai Cheng, Kaiyue Wang, Yanqing Xie, Lina Zhang

“…In this study, we aim to construct a circRNA-related competing endogenous RNA (ceRNA) network in CAD. Methods. The gene expression profiles of CAD were obtained from Gene Expression Omnibus datasets. …”
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Investigating the Pulmonary Host Response of <i>Acinetobacter baumannii</i> Infection-Associated Pneumonia by Metagenomic Next-Generation Sequencing by Mu-Jung Chou, Chih-Hung Cheng, Hui-Ching Wang, Ming-Ju Tsai, Chau-Chyun Sheu, Wei-An Chang

“…<b>Conclusions:</b> mNGS provides information not only on pathogen gene expression but also on host gene expression. In this study, we found that pneumonia with <i>A. baumannii</i> carrying the NDM resistance gene triggers stronger immune responses in the lung, while pneumonia with <i>A. baumannii</i> lacking antimicrobial resistance genes is more linked to iron-related pathways.…”
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Calcium hydroxide nanoparticles induce cell death, genomic instability, oxidative stress and apoptotic gene dysregulation on human HepG2 cells by Hanan R. H. Mohamed, Esraa H. Ibrahim, Shahd E. E. Shaheen, Nesma O. E. Hussein, Ayman Diab, Gehan Safwat

“…Treatment with the IC50 concentration of Ca(OH)2NPs selectively induced significant DNA damage, excessive ROS generation, and marked dysregulation of apoptotic (p53 and Bax) and anti-apoptotic (Bcl-2) gene expression in HepG2 cells, triggering apoptosis. …”
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Modulating the anti-inflammatory and barrier protective effects on intestinal epithelial cells utilizing an aqueous Aspalathus linearis extract in vitro by Shana De Bruyn-Orr, Stefan Abel, Mariam Rado, Mariska Lilly

“…Cell viability, protein and gene expression of pro-inflammatory cytokines were investigated to determine the anti-inflammatory effect of both extracts. …”
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Effects of ursolic acid on growth performance, serum biochemistry, antioxidant capacity, and intestinal health of broilers by X.W. Zhang, X. Li, Y. Yin, M. Wang, Y.F. Wang, J.Y. Chen, Y.R. Zhao

“…Additionally, interleukin 10 gene expression in jejunal mucosa was higher (P < 0.05). …”
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Dissecting Causal Relationships Between Antihypertensive Drug, Gut Microbiota, and Type 2 Diabetes Mellitus and Its Complications: A Mendelian Randomization Study by He Zheng, Shiping Wu, Wenbin Wang, Weida Qiu, Yingqing Feng

“…Similarly, a 1‐SD decrease of SLC12A2 (genetically a proxy for diuretics, for example, Torasemide) gene expression was correlated with a reduced risk of T2DM (OR, 0.88; 95% CI, 0.83–0.92). …”
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The Link between Type III Reg and STAT3-Associated Cytokines in Inflamed Colonic Tissues by Xin Xu, Hirokazu Fukui, Ying Ran, Xuan Wang, Yoshihito Inoue, Nobuhiko Ebisudani, Heihachiro Nishimura, Toshihiko Tomita, Tadayuki Oshima, Jiro Watari, Hiroshi Kiyama, Hiroto Miwa

“…In the present study, we investigated the profile of Reg family gene expression in a colitis model and focused on the regulation of Reg IIIβ and IIIγ, which are overexpressed in inflamed colonic mucosa. …”
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Composition analysis and mechanism of Guizhi Fuling capsule in anti-cisplatin-resistant ovarian cancer by Lei Dou, Yan Yan, Enting Lu, Fangmei Li, Dongli Tian, Lei Deng, Xue Zhang, Rongjin Zhang, Yin Li, Yi Zhang, Ye Sun

“…Methods: First, differences in cisplatin resistance, PA2G4 gene expression, migration, and invasion in A2780 cells and A2780/DDP cells were analyzed by qRT-PCR, scratch assay, transwell, immunofluorescence, and western blotting. …”
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Identification of EGR1 as a Key Diagnostic Biomarker in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) Through Machine Learning and Immune Analysis by Wu X, Pan T, Fang Z, Hui T, Yu X, Liu C, Guo Z, Liu C

“…Finally, the expression of the key genes was further validated using the palmitic acid-induced AML-12 cell line and the MCD mouse model.Results: In this study, through differential gene expression (DEGs) analysis and machine learning techniques, we successfully identified 10 hub genes. …”
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Tanshinone I Ameliorates Psoriasis-Like Dermatitis by Suppressing Inflammation and Regulating Keratinocyte Differentiation by Wang Q, Luo X, Su Y, Jin Y, Kuang Q, Li S, Shen W, Zhu Y

“…In TNF-α-stimulated HaCaT cells, Tan-I induced G1-phase cell cycle arrest, reduced apoptosis, and suppressed inflammatory gene expression. RNA-seq further showed that Tan-I normalized cell cycle signaling and apoptosis pathways disrupted by TNF-α. …”
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Expression Analysis of Nitrogen Metabolism-Related Genes Reveals Differences in Adaptation to Low-Nitrogen Stress between Two Different Barley Cultivars at Seedling Stage by Zhiwei Chen, Chenghong Liu, Yifei Wang, Ting He, Runhong Gao, Hongwei Xu, Guimei Guo, Yingbo Li, Longhua Zhou, Ruiju Lu, Jianhua Huang

“…In the present study, two barley cultivars, BI-04 (tolerant to low nitrogen) and BI-45 (sensitive to low nitrogen), were used for gene expression analysis under low-nitrogen stress, including 10 genes related to primary nitrogen metabolism. …”
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DOCK4 Is a Platinum-Chemosensitive and Prognostic-Related Biomarker in Ovarian Cancer by Qianqian Zhao, Jie Zhong, Ping Lu, Xiao Feng, Ying Han, Chenqi Ling, Wenke Guo, Weijin Zhou, Fudong Yu

“…The present study is aimed at optimizing candidate genes by integrating platinum-chemotherapy expression data and PPAR family genes with their targets. The gene expression profiles were obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. …”
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Molecular Characterization of the Onset and Progression of Colitis in Inoculated Interleukin-10 Gene-Deficient Mice: A Role for PPARα by Bianca Knoch, Matthew P. G. Barnett, Janine Cooney, Warren C. McNabb, Diane Barraclough, William Laing, Shuotun Zhu, Zaneta A. Park, Paul MacLean, Scott O. Knowles, Nicole C. Roy

“…Gene expression changes in 12-week-old Il10-/- mice were related to PPARα signaling likely to control colitis, but how PPARα activation might regulate intestinal IL10 production remains to be determined.…”
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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking by Daniel P. Neumann, Katherine A. Pillman, B. Kate Dredge, Andrew G. Bert, Caroline A. Phillips, Rachael Lumb, Yesha Ramani, Cameron P. Bracken, Brett G. Hollier, Luke A. Selth, Traude H. Beilharz, Gregory J. Goodall, Philip A. Gregory

“…Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. …”
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Immune and genomic biomarkers of immunotherapy response in cancer of unknown primary by Madhu Singh, Linda Mileshkin, Penelope Schofield, Bo Gao, Gary Richardson, Andrew Pattison, Rodney J Hicks, Niko Thio, Mark Warren, Colin Wood, Stephen B Fox, Anna DeFazio, Andrew Fellowes, Christopher Steer, David Bowtell, Nicholas Wilcken, Tharani Sivakumaran, Atara Posner, Dariush Etemadmoghadam, Krista Fisher, Samantha Webb, Christos S Karapetis, Ian M Collins, Narayan Karanth, Owen W J Prall, Richard William Tothill

“…Immune and stromal-related gene expression was explored by NanoString, including genes associated with immunotherapy response (IR) in other solid malignancies. …”
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DI-GEP: A New Lifetime Extending Algorithm for Target Tracking in Wireless Sensor Networks by Shucheng Dai, Chuan Li, Chun Chen

“…In this paper, a new energy-efficient method based on Distributed Incremental Gene Expression Programming (DI-GEP) is proposed to collaboratively mine moving patterns of moving targets in order to turn on/off some sensor nodes at certain time to save energy further. …”
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Structures and mechanisms of the RNA m⁶A writer by Deng Ting, Ma Jinbiao

“…N⁶-methyladenosine (m⁶A) is the most prevalent epigenetic modification found in eukaryotic mRNAs and plays a crucial role in regulating gene expression by influencing numerous aspects of mRNA metabolism. …”
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Anatomy Ontology Matching Using Markov Logic Networks by Chunhua Li, Pengpeng Zhao, Jian Wu, Zhiming Cui

“…The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. …”
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Long Noncoding RNAs in Metabolic Syndrome Related Disorders by Magdalena Losko, Jerzy Kotlinowski, Jolanta Jura

“…Noncoding genes (noncoding RNA, sequences, and pseudogenes) comprise 67% of all genes and they are represented by housekeeping noncoding RNAs (transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA)) that are engaged in basic cellular processes and by regulatory noncoding RNA (short and long noncoding RNA (ncRNA)) that are important for gene expression/transcript stability. In this review, we summarize data concerning the significance of long noncoding RNAs (lncRNAs) in metabolic syndrome related disorders, focusing on adipose tissue and pancreatic islands.…”
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