ATP6AP1 drives pyroptosis-mediated immune evasion in hepatocellular carcinoma: a machine learning-guided therapeutic target by Lei Tang, Xiyue Wang, Zhengzheng Xia, Jiayu Yan, Shanshan Lin

“…Pyroptosis is a form of cell death with complex dual functions in tumor immunity. However, the precise regulatory mechanisms and interactions between pyroptosis and immune evasion in HCC remain poorly understood. …”
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Unraveling the oxidative stress landscape in diabetic foot ulcers: insights from bulk RNA and single-cell RNA sequencing data by Jialiang Lin, Linjuan Huang, Weiming Li, Haijun Xiao, Mingmang Pan

“…Results Bulk RNA-seq analysis identified 63 oxidative stress-related genes of DFU (DORGs), and the top 59 genes were screened out for key nodes with close functional associations. Functional enrichment analysis showed significant involvement in oxidative stress response. …”
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The UFMylation pathway is impaired in Alzheimer’s disease by Tingxiang Yan, Michael G. Heckman, Emily C. Craver, Chia-Chen Liu, Bailey D. Rawlinson, Xue Wang, Melissa E. Murray, Dennis W. Dickson, Nilufer Ertekin-Taner, Zhenkun Lou, Guojun Bu, Wolfdieter Springer, Fabienne C. Fiesel

“…We further studied associations of the UFMylation cascade with cellular stress pathways using Spearman correlations with bulk RNAseq expression data and functionally validated these interactions using gene-edited neurons that were generated by CRISPR-Cas9. …”
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Comparative transcriptome analysis reveals key genes and signaling pathways mediated by salicylic acid in potato by Aie Chen, Beini Zhang, Huijie Wang, Jiangqing Wang, Ji Wei, Yuxin Jia, Hongyang Wang

“…While its signaling roles have been extensively characterized in model species, the molecular mechanisms and SA-responsive genes in potato remain largely uncharacterized. …”
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The Significance and Diagnostic Potential of CEA and FIB in Colorectal Cancer by Lin Zhu, Jie Feng, Xu Zhang, Xuemei Wei, Cuiling Ming, Yanhong Gao

“…Gene Ontology functional analysis in CRC showed that FGA and related genes were enriched in biological processes including biosynthesis of ribonucleoprotein complex and non‐coding ribonucleic acid metabolic process; in cellular components, they were primarily enriched in pre‐ribosomes; and in molecular functions, they were mainly enriched in binding of unfolded protein. …”
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Comprehensive bioinformatics analysis of EXOSC family genes in head and neck squamous cell carcinoma by Xuezhong Zhang, Mengmeng Zhao, Tingting Chu, Jiasha Wei, Qingmei Jia

“…Gene co-expression and enrichment analyses were used to elucidate potential molecular functions, and a protein–protein interaction (PPI) network was constructed via GeneMANIA. …”
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FCGBP promotes ovarian cancer progression via activation of IL-6/JAK-STAT signaling pathway by Zhiqin Fu, Kelie Chen, Fang Zheng, Wangang Gong, Ding Chao, Chao Lu

“…This study aimed to investigate the clinical relevance, functional role, and underlying mechanisms of FCGBP in ovarian cancer progression. …”
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Neighborhood Resources and Health Outcomes Among Stroke Survivors in a Population‐Based Cohort by Leanna M. Delhey, Xu Shi, Lewis B. Morgenstern, Devin L. Brown, Melinda A. Smith, Erin C. Case, Mellanie V. Springer, Lynda D. Lisabeth

“…We fit multivariable Cox regression and mixed linear models. We considered interactions with stroke severity, ethnicity, and sex. …”
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Application of GUHA data mining method in cohort data to explore paths associated with premature death: a 29-year follow-up study by Lily Nosraty, Esko Turunen, Saila Kyrönlahti, Clas-Håkan Nygård, Prakash KC, Subas Neupane

“…This highlights the complexity of premature mortality and the need for comprehensive models considering multiple interacting factors.…”
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TRIP13-induced NUSAP1 upregulation promotes CcRCC progression through EMT and PI3K/AKT/mTOR pathway by Xiaolong Chen, Qing Wang, Zhiqiang Zhu, Zheng Peng, Kunyuan Huang, Guanyun Deng, Kehua Jiang, Kun Chen, Fa Sun

“…In vivo tumorigenic potential was assessed through a nude mouse xenograft model. Protein expression and interactions were analyzed by western blotting, co-immunoprecipitation, and RT-qPCR. …”
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An Integrated Approach Utilizing Single-Cell and Bulk RNA-Sequencing for the Identification of a Mitophagy-Associated Genes Signature: Implications for Prognostication and Therapeu... by Yuke Zhang, Li Ding, Zhijin Zhang, Liliang Shen, Yadong Guo, Wentao Zhang, Yang Yu, Zhuoran Gu, Ji Liu, Aimaitiaji Kadier, Jiang Geng, Shiyu Mao, Xudong Yao

“…Furthermore, the cellular functions of the genes of interest were verified in vitro. …”
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PD-L1 pfeRNAs as blood-based predictors of treatment response of unresectable malignant pleural mesothelioma patients administered Durvalumab with cisplatin and pemetrexed as first... by Andrei Gurau, Suguru Yamauchi, Kaitlyn Ecoff, Kristen P. Rodgers, James R. Eshleman, Charles Conover Talbot Jr, Peng Huang, Joshua Choi, Patrick M. Forde, Valsamo Anagnostou, Malcolm Brock, Yuping Mei

“…However, the limited patient response to Durva-CP needs predictors to select optimal candidates and monitor the developed resistance. Protein functional effector sncRNA (pfeRNA) reveals a fundamental mechanism underlying the regulation of protein activity. …”
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Using computational pharmacology and experimental verification to decode mechanism of Qing-Wei-San in treating periodontitis by Yanhong Liu, Wenqi Li, Jingxiao Chen, Yi Li, Jieqi Cai, Yongxi Luo, Jiahao Lin, Lu Chen, Aiping Lu, Daogang Guan, Huiyong Xu

“…Subsequently, approximate equivalent component group (AECG) capable of mediating these active proteins was screened based on a cumulative contribution rate model. The systems pharmacology results indicate that the targets of the AECG derived from the optimized CES effectively cover both drug targets and pathogenic genes at the functional level. …”
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A Study on the Possibility of Molecular Communication between Honey Bees and Sunflower through the Interspecies Transfer of Small RNAs by Leila Gharehdaghi, Gholamhosein Tahmasbi, Taher Harkinezhad

“…In other words, miRNAs can be transferred not only between cells and tissues within an organism but also across different species while maintaining their regulatory functions. Given the vital role of honeybees in plant pollination, this insect may serve as a more suitable model for studying these interactions. …”
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Target oxidative stress-induced disulfidptosis: novel therapeutic avenues in Parkinson’s disease by Junshi Zhang, Tingting Liu, Haojie Wu, Jianshe Wei, Qiumin Qu

“…LASSO regression was applied for feature selection, with subsequent experimental validation in MPTP-induced PD mouse models. Single-cell transcriptomic profiling and molecular docking studies were performed to map target gene expression and assess drug-target interactions. …”
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An FPGA-Based SiNW-FET Biosensing System for Real-Time Viral Detection: Hardware Amplification and 1D CNN for Adaptive Noise Reduction by Ahmed Hadded, Mossaad Ben Ayed, Shaya A. Alshaya

“…The SiNW-FET biosensor, functionalized with antibodies specific to viral antigens, detects impedance shifts caused by antibody–antigen interactions, providing a highly sensitive platform for viral detection. …”
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Immune Regulation and Disulfidptosis in Atherosclerosis Influence Disease Progression and Therapy by Wei Lu, Zhidong Zhang, Gang Qiao, Gangqiang Zou, Guangfeng Li

“…A diagnostic risk score model was developed and rigorously tested through Receiver Operating Characteristic analysis. …”
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Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion by Hong Li, Hong Li, Yixin Zhou, Wenya Xue, Pan Yin, Luyu Liu, Shaobo Wu, Yahao Zhao, Qi An, Yang Sun

“…Dgat2 was significantly elevated in ischemia-reperfusion mouse models, confirmed by RT-PCR and Western blot. Functional enrichment indicated that Dgat2 may be involved in biological oxidation and lipid metabolism. …”
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Bioinformatics-driven exploration of key genes and mechanisms underlying oxidative stress in traumatic brain injury by Bin Ren, Jifang Liang, Leifang Yang, Xiaocong Wei, Min Guo, Hong Li

“…Differential expression analysis and machine learning models were executed to select key genes, which were further validated using receiver operating characteristic (ROC) curves. …”
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Enhanced adsorption of phenol using EDTA-4Na- and KOH-modified almond shell biochar by Yanqin Chen, Donghui Wang, Xueli Wang, Jing Wu, Shifang Song

“…The adsorption of phenol by A-BC is a spontaneous exothermic process involving both physical adsorption and chemical adsorption (including hydrogen bonding and π-π interactions). The pseudo-second-order kinetic model adequately describes the adsorption process, which consists of liquid film diffusion, surface adsorption, and intraparticle diffusion stages. …”
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