Exploring the Mechanisms of Zhenbao Pills in the Treatment of Stroke through Network Pharmacology Combined with Mendelian Randomization by Yanhong Liu, Yunqi Hua, Xiaoe Jia

“…Furthermore, molecular docking and Gene Expression Omnibus (GEO) datasets were used for preliminary confirmation. …”
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Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in color... by Xiaoyu Qin, Wenjuan Xu, Jinxiu Wu, Ming Li

“…We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Cancer Genome Atlas (TCGA) colorectal cancer samples to uncover NK cell-related genes. …”
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Characterization of Escherichia coli outer membrane vesicles and the impact of pathogenic ones on NLR signaling pathways by Roghayeh Mohammadzadeh, Ava Behrouzi, Farzam Vaziri, Seyed Davar Siadat

“…Besides, it was revealed that OMVs can regulate gene expression. …”
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RETRACTED: Palmitic Acid Impedes Extravillous Trophoblast Activity by Increasing MRP1 Expression and Function by Yunali Ashar, Qiuxu Teng, John N. D. Wurpel, Zhe-Sheng Chen, Sandra E. Reznik

“…Palmitic acid increased <i>ABCC1</i> gene expression and MRP1 protein expression in both cell lines. …”
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Identification of the immune infiltration and biomarkers in ulcerative colitis based on liquid–liquid phase separation-related genes by Zhixing Hong, Shilin Fang, Haihang Nie, Jingkai Zhou, Yuntian Hong, Lan Liu, Qiu Zhao

“…External cohort and UC cell model validation indicated the similar immune infiltration levels, gene expression and cytokine expression patterns. We determined the seven high accuracy diagnostic genes of UC patients and provide a new perspective on immunoregulation in UC pathogenesis. …”
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Reduction of nutrients concentration in culture medium has no effect on bovine embryo production, pregnancy and birth rates by Ligiane de Oliveira Leme, Mauricio Machaim Franco, Otávio Augusto de Faria, Alexandre Rodrigues Caetano, Juliana Gonçalves de Souza, Luciano de Rezende Carvalheira, Emivaldo de Siqueira Filho, Margot Alves Nunes Dode

“…First, embryos produced under these three treatments were evaluated for production, quality, lipid content, gene expression, and methylation patterns. The results indicated that all parameters analyzed were similar across all treatments (P > 0.05), suggesting that reducing media components does not affect embryo development and quality. …”
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XGBoost-enhanced ensemble model using discriminative hybrid features for the prediction of sumoylation sites by Salman Khan, Sumaiya Noor, Tahir Javed, Afshan Naseem, Fahad Aslam, Salman A. AlQahtani, Nijad Ahmad

“…Abstract Posttranslational modifications (PTMs) are essential for regulating protein localization and stability, significantly affecting gene expression, biological functions, and genome replication. …”
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Inference of a three-gene network underpinning epidermal stem cell development in Caenorhabditis elegans by Alicja Brożek, Arianna Ceccarelli, Andreas Christ Sølvsten Jørgensen, Mark Hintze, Vahid Shahrezaei, Michalis Barkoulas

“…Our findings reveal TF regulatory relationships in seam cells and demonstrate a flexible mathematical framework for inferring gene regulatory networks from gene expression data.…”
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5-Aminolevulinic acid activates the MdWRKY71-MdMADS1 module to enhance anthocyanin biosynthesis in apple by Liuzi Zhang, Huihui Tao, Jianting Zhang, Yuyan An, Liangju Wang

“…In this study, we firstly demonstrated that ALA upregulates gene expression of the transcription factor MdMADS1, which in turn directly binds to and activates transcription of the key anthocyanin biosynthetic genes, MdCHS and MdUFGT. …”
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Exosome-like nanovesicles derived from kale juice enhance collagen production by downregulating Smad7 in human skin fibroblasts by Peihan Hsu, Yuriko Kamijyo, Emiri Koike, Saki Ichikawa, Yifeng Zheng, Tomohiro Ohno, Shigeru Katayama, Shigeru Katayama

“…Plant-derived exosome-like nanovesicles (ELNs) are critical mediators of cross-kingdom communication, modulating gene expression in animal cells despite their plant origin. …”
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Effects of high-intensity interval training on physical performance, systolic blood pressure, oxidative stress and inflammatory markers in skeletal muscle of spontaneously hyperten... by Thaynara Zanoni D'Almeida, Mariana Janini Gomes, Leticia Estevam Engel, Ines Cristina Giometti, Natalia Zamberlan Ferreira, Rafael Stuani, Camila Renata Corrêa, Robson Chacon Castoldi, Sarah Gomes Nunes, Andreo Fernando Aguiar, Anthony César Castilho, Marina Politi Okoshi, Francis Lopes Pacagnelli

“…The following variables were measured in the tibialis anterior (TA) muscle: gene expression of the NADPH oxidase complex (NOX2, NOX4, p22phox, p47phox) and the NF-kB pathway (NF-kB and Ik-B), lipid peroxidation (malonaldehyde; MDA), protein carbonylation, hydrophilic antioxidant capacity (HAC) and pro-inflammatory cytokines (IL-6 and TNF-α).…”
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Using DIMet for Differential Analysis of Labeled Metabolomics Data: A Step-by-step Guide Showcasing the Glioblastoma Metabolism by Johanna Galvis, Joris Guyon, Thomas Daubon, Macha Nikolski

“…Integrating metabolomics data with gene expression profiles further enriches the analysis, as we demonstrated in our prior study on glioblastoma metabolic symbiosis. …”
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Neutrophil Extracellular Traps Contribute to the Disease Severity of Dengue Virus Infection by Cucunawangsih Cucunawangsih, Ratna Sari Wijaya, Nata Pratama Hardjo Lugito, Ivet Suriapranata

“…Results: Based on the transcriptomic analysis, the whole blood gene expression functional in neutrophil activities and NETs formation was upregulated with dengue disease severity. …”
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Glymphatic dysfunction and neurodegeneration in ALS: Longitudinal insights from rNLS8 TDP-43 mice by Akram Zamani, Adam K. Walker, David K. Wright

“…Motor function, advanced MRI biomarkers of neurodegeneration, and cortical glymphatic pathway gene expression were assessed together with dynamic contrast-enhanced MRI (DCE-MRI) assessment of glymphatic function at 0-, 3-, 7-, and 21-days after removing mice from Dox feed to initiate cytoplasmic human TDP-43 expression. …”
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Circadian rhythm related genes signature in glioma for drug resistance prediction: a comprehensive analysis integrating transcriptomics and machine learning by Junbo Liao, Yingxing Duan, Xiangwang Xu, Yaxue Liu, Chaohong Zhan, Gelei Xiao

“…The studies of immune cell infiltration, genetic variations, differential gene expression pattern, and single cell analysis were performed for exploring the mechanisms of chemotherapy resistance in glioma. …”
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Multiomics-based assessment of the impact of airflow on diverse plant callus cultures by June-Sik Kim, Muneo Sato, Mikiko Kojima, Muchamad Imam Asrori, Yukiko Uehara-Yamaguchi, Yumiko Takebayashi, Thi Nhung Do, Thi Yen Do, Kieu Oanh Nguyen Thi, Hitoshi Sakakibara, Keiichi Mochida, Shinjiro Ogita, Masami Yokota Hirai

“…For each sample, gene expression was profiled with high-throughput RNA sequencing, 442 metabolites were measured using liquid chromatography (LC) with triple-quadrupole mass spectrometry (LC–QqQMS), and 31 phytohormones were quantified using ultra-performance LC coupled with a tandem quadrupole mass spectrometer equipped with an electrospray interface (UPLC-ESI-qMS/MS) and ultra-high-performance LC–orbitrap MS (UHPLC-Orbitrap MS). …”
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Modeling and designing enhancers by introducing and harnessing transcription factor binding units by Jiaqi Li, Pengcheng Zhang, Xi Xi, Liyang Liu, Lei Wei, Xiaowo Wang

“…Abstract Enhancers serve as pivotal regulators of gene expression throughout various biological processes by interacting with transcription factors (TFs). …”
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Inhibition of STING-mediated type I IFN signaling by African swine fever virus DP71L by Lakmal Ranathunga, Sachini Abesinghe, Ji-Won Cha, Niranjan Dodantenna, Kiramage Chathuranga, Asela Weerawardhana, D. K. Haluwana, Nuwan Gamage, Jong-Soo Lee

“…Consistently, knockdown of DP71L enhanced antiviral gene expression in ASFV-infected cells. Taken together, these results highlight the important role of DP71L with respect to inhibition of interferon responses and provide guidance for a better understanding of ASFV pathogenesis and the development of live attenuated ASFV vaccines.…”
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KLF5 promotes esophageal squamous cell carcinoma radioresistance by targeting the Keap1-Nrf2 pathway by Yang Wang, Yue-ying Yang, Abulajiang Kamili, Dilimulati Aishanjiang, Yi Liu

“…The purpose of this article is to study the mechanism of KLF5's effect on ESCC radiosensitivity. Methods WGCNA gene expression profiling identified core genes associated with ESCC radiosensitivity. …”
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Sargassum fusiforme and its fucoidan alleviates high-fat diet induced obesity associated with the improvement of the gut microbiota profile by Xiaoyu Ling, Zhengyang Li, Ning Su, Lingqing Kong, Shiwei Han, Dafeng Song

“…This study investigates the mechanisms by exploring changes in gut microbiota composition, gene expression, and metabolites in mice fed a high-fat diet after intervention with Sargassum fusiforme (SF) and Sargassum fusiforme fucoidan (SFF) through integration of 16S rRNA sequencing, transcriptomics, and non-targeted metabolomics. …”
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