Oral Plaque from Type 2 Diabetic Patients Reduces the Clonogenic Capacity of Dental Pulp-Derived Mesenchymal Stem Cells by Antonella Bordin, Francesca Pagano, Eleonora Scaccia, Matteo Saccucci, Iole Vozza, Noemi Incerti, Antonella Polimeni, Elena Cavarretta, Isotta Chimenti, Elena De Falco

“…Cultures were also induced to differentiate towards the osteogenic lineage, and ALP and osteocalcin gene expression levels were evaluated by real-time qPCR. …”
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Role of Aging in Ulcerative Colitis Pathogenesis: A Focus on ETS1 as a Promising Biomarker by Ni M, Peng W, Wang X, Li J

“…In this study, we explored the role of aging-related genes (ARGs) in UC pathogenesis and diagnosis prediction.Methods: Gene expression data were obtained from four independent datasets (GSE75214, GSE87466, GSE94648, and GSE169568) in the GEO database, and ARGs were derived from multiple public databases. …”
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Exploring the anti-metastatic potential of sunitinib and novel analogs in colorectal cancer: insights into HIF-1α mediated metastasis by Fatemeh B. Rassouli, Maryam M. Matin, Maryam M. Matin, Farzin Hadizadeh, Farzin Hadizadeh, Masoud Nejabat, Hossein Allahverdizadeh, Hamidreza Jamali, Shahin Gharedaghi, Halimeh Hassanzadeh

“…For in vitro studies, analogs of sunitinib were synthesized, and cells were assessed for viability, migration, invasion, MMPs activity and gene expression in hypoxic condition.Results and DiscussionComputational analyses highlighted the importance of HIF-1α as a crucial mediator of metastasis in CRC. …”
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Sugemule-7 alleviates oxidative stress, neuroinflammation, and cell death, promoting synaptic plasticity recovery in mice with postpartum depression by Qiang Fu, Rui Qiu, Jiaquan Liang, Shuai Wu, Dezhi Huang, Yuxiang Qin, Qiaosheng Li, Xiaojie Shi, Xiyue Xiong, Zhongyong Jiang, Yuewen Chen, Yong Cheng

“…Transcriptomic sequencing of hippocampal and prefrontal cortex tissues supported our findings, revealing that differential gene expression is primarily involved in regulating synaptic plasticity. …”
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A model-based factorization method for scRNA data unveils bifurcating transcriptional modules underlying cell fate determination by Jun Ren, Ying Zhou, Yudi Hu, Jing Yang, Hongkun Fang, Xuejing Lyu, Jintao Guo, Xiaodong Shi, Qiyuan Li

“…Furthermore, MGPfactXMBD discovered evolutionary trajectories of tumor-associated CD8+ T cells and yielded new subtypes of CD8+ T cells with gene expression signatures significantly predictive of the responses to immune checkpoint inhibitor in independent cohorts. …”
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Antibacterial efficacy and antibiotic sensitivity augmentation potential of selected traditional medicinal plant extracts against Vibrio cholerae O1 E1 Tor Ogawa by Pruthviraj Chavan, Kamakshi Naik, Soumika Ghosal, Rajitha Charla, Rajalakshmi Patil, Jyoti N. Guruputranavar, Vishal S. Patil, Darasaguppe R. Harish, Subarna Roy

“…The hydroalcoholic extracts of PGAE, PGRPE, and CAE were tested for antibacterial activity against Vibrio cholerae by minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and virulence gene expression studies by reverse transcriptase-polymerase chain reaction (RT-PCR). …”
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Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma by Rui Mu, Yuehong Shen, Chuanbin Guo, Xinyun Zhang, Hongyu Yang, Huijun Yang

“…Finally, the hub gene’s differential mRNA expression levels were evaluated by means of the Gene Expression Profiling Interactive Analysis (GEPIA), and the Human Protein Atlas (HPA) was utilized for the validation of their translational levels. …”
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MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication by Jonathan Cahn, Michael Regulski, Jason Lynn, Evan Ernst, Cristiane de Santis Alves, Srividya Ramakrishnan, Kapeel Chougule, Sharon Wei, Zhenyuan Lu, Xiaosa Xu, Umamaheswari Ramu, Jorg Drenkow, Melissa Kramer, Arun Seetharam, Matthew B. Hufford, W. Richard McCombie, Doreen Ware, David Jackson, Michael C. Schatz, Thomas R. Gingeras, Robert A. Martienssen

“…Furthermore, the morphological traits selected during domestication are recapitulated, both in gene expression and within regulatory regions containing enhancer RNAs, while highlighting the conflict between enhancer activity and silencing of the neighboring transposable elements.…”
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Dufulin Impacts Plant Defense Against Tomato Yellow Leaf Curl Virus Infecting Tomato by Liping Huang, Yingying Tang, Shuaixin Wang, Jianbin Chen, Jiao Du, Shuo Yan, Deyong Zhang, Xiaobin Shi, Yong Liu, Fan Li

“…Plants treated with dufulin showed reduced symptomatology and lower viral titers compared to the controls. Analysis of gene expression revealed that <i>NPR1</i> was upregulated in the dufulin-treated plants, whereas <i>PI II</i> expression was consistently downregulated in the TYLCV-infected plants. …”
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Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer by Xiao K. Ran, Xiao F. Zhao, Zhen W. Wei, Hua Z. Pang, Yan F. Tang, Rong Liu, Tie X. Wu, Xu D. Liu

“…Following analysis of differential genes using bioinformatics, six candidate genes were screened out based on gene expression and cancer relevance. Experiments have verified that LAMA4[circle112550019-112550510] and KANK1[circle674459-674907] are real and expressed target genes, and their source genes are closely related to the survival time of patients with liver cancer.ConclusionOur research results revealed the main characteristics of eccDNAs in the blood of patients with HBV-related HCC and LC. …”
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Network pharmacology and experimental verification to investigate the mechanism of isoliquiritigenin for the treatment of Alzheimer’s disease by Waimao Gao, Guang Yang, Xinjuan Liu, Kaifan Hu, Jie Pan, Xingyu Wang, Yan Zhao, Ying Xu

“…Subsequently, the receiver operating characteristic (ROC) curve analysis and the assessment of hub gene expression levels between AD and healthy individuals were used to estimate a possible link between target genes in AD. …”
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Prognostic models of immune-related cell death and stress unveil mechanisms driving macrophage phenotypic evolution in colorectal cancer by Hao Liu, Chuhan Zhang, Sanfei Peng, Yuhan Yin, Yishi Xu, Sihan Wu, Liping Wang, Yang Fu

“…Furthermore, we performed enrichment analyses and deconvolution algorithms to elucidate the complex interactions between immune cell infiltration and the processes of PCD and stress within a substantial array of transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus data base (GEO) related to CRC. …”
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Profiling the Resident and Infiltrating Monocyte/Macrophages during Rejection following Kidney Transplantation by Jie Wang, Peiling Luo, Jingjie Zhao, Junhua Tan, Feifan Huang, Ruiying Ma, Peng Huang, Meiying Huang, Yuming Huang, Qiuju Wei, Liuzhi Wei, Zechen Wang, Lingzhang Meng

“…Furthermore, previously defined genes were mapped to all monocyte/macrophage types in the kidney and enriched the differential genes of the two main subpopulations using gene expression databases. Considering that various cases of rejection may be of the monocyte/macrophage type, the present data may serve as a reference for studies regarding immune tolerance following kidney transplantation.…”
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The expansion and loss of specific olfactory genes in relatives of parasitic lice, the stored-product psocids (Psocodea: Liposcelididae) by Jun Sun, Jian Wu, Sheng-Yuan Sun, Zhi-Dong Chen, Guy Smagghe, Jin-Jun Wang, Dan-Dan Wei

“…Simultaneously, analysis of gene expression profiles across different developmental stages revealed varying periods of peak expression for olfactory-related genes. …”
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AMPK regulates the maintenance and remodelling of the neuromuscular junction by Sean Y. Ng, Andrew I. Mikhail, Stephanie R. Mattina, Salah A. Mohammed, Shahzeb K. Khan, Eric M. Desjardins, Changhyun Lim, Stuart M. Phillips, Gregory R. Steinberg, Vladimir Ljubicic

“…Results: Our findings reveal an increased abundance of AMPK transcripts within the NMJ and an age-associated decline in AMPK activity and synapse-specific mitochondrial gene expression. Young mice null for skeletal muscle AMPK displayed a neuromuscular phenotype akin to aged animals. …”
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Aminoguanidine hemisulfate improves mitochondrial autophagy, oxidative stress, and muscle force in Duchenne muscular dystrophy via the AKT/FOXO1 pathway in mdx mice by Shiyue Sun, Tongtong Yu, Joo Young Huh, Yujie Cai, Somy Yoon, Hafiz Muhammad Ahmad Javaid

“…Methods Male wild-type (WT) and mdx mice were divided into three groups: WT, mdx, and AGH-treated mdx mice (40 mg/kg intraperitoneally for two weeks) at 6 weeks of age. Gene expression, western blotting, H&E staining, immunofluorescence, ROS assays, TUNEL apoptosis, glutathione activity, and muscle force measurements were performed. …”
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Heterochrony in orthodenticle expression is associated with ommatidial size variation between Drosophila species by Montserrat Torres-Oliva, Elisa Buchberger, Alexandra D. Buffry, Maike Kittelmann, Genoveva Guerrero, Lauren Sumner-Rooney, Pedro Gaspar, Georg C. Bullinger, Javier Figueras Jimenez, Fernando Casares, Saad Arif, Nico Posnien, Maria D. S. Nunes, Alistair P. McGregor, Isabel Almudi

“…Results Here, we used a combination of fine-scale mapping and gene expression analysis to further investigate positional candidate genes on the X chromosome. …”
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Tumor-Stroma Ratio is a Critical Indicator of Peritoneal Metastasis in Gastric Cancer by Zhong L, Huang H, Hou D, Zhou S, Lin Y, Yu Y, Yu J, Han F, Xie L

“…Additionally, the correlation between TSR and PM in GC was analyzed using Gene Expression Omnibus (GEO) datasets. To validate TSR’s clinical potential in diagnosing PM, 640 GC patients from two medical centers were enrolled. …”
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Analysis and Validation of Autophagy-Related Gene Biomarkers and Immune Cell Infiltration Characteristic in Bronchopulmonary Dysplasia by Integrating Bioinformatics and Machine Lea... by Xiao S, Ding Y, Du C, Lv Y, Yang S, Zheng Q, Wang Z, Zheng Q, Huang M, Xiao Q, Ren Z, Bi G, Yang J

“…We aim to screen and validate the signature genes of BPD by bioinformatics and in vivo experiment.Methods: GSE8586 was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the R program. …”
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Reestablishment of Redox Homeostasis in the Nociceptive Primary Afferent as a Mechanism of Antinociception Promoted by Mesenchymal Stem/Stromal Cells in Oxaliplatin-Induced Chronic... by Anna Lethicia L. Oliveira, Gisele G. L. Santos, Renan F. Espirito-Santo, Gessica Sabrina A. Silva, Afrânio F. Evangelista, Daniela N. Silva, Milena B. P. Soares, Cristiane Flora Villarreal

“…Four weeks later, mitochondrial morphology, gene expression profile, and oxidative stress markers in the sciatic nerve and dorsal root ganglia (DRG) were evaluated by transmission electron microscopy, RT-qPCR, and biochemical assays, respectively. …”
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