Comparative transcriptomic rhythms in the mouse and human prefrontal cortex by Jennifer N. Burns, Jennifer N. Burns, Aaron K. Jenkins, Xiangning Xue, Kaitlyn A. Petersen, Kaitlyn A. Petersen, Kyle D. Ketchesin, Kyle D. Ketchesin, Megan S. Perez, Megan S. Perez, Chelsea A. Vadnie, Madeline R. Scott, Madeline R. Scott, Marianne L. Seney, Marianne L. Seney, George C. Tseng, Colleen A. McClung, Colleen A. McClung

“…Moreover, emerging evidence suggests that circadian rhythms in gene expression are present across the brain, including in the PFC, and that these rhythms are altered in disease. …”
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Ethanol extract of Polygonatum cyrtonema Hua mitigates non-alcoholic steatohepatitis in mice by Dongliang Chen, Yue Shen, Yue Shen, Fang Huang, Bo Huang, Shangfu Xu, Shangfu Xu, Lisheng Li, Lisheng Li, Jie Liu, Zheng Li, Xia Li

“…RNAseq identified unique gene expression profiles in response to high-fat diet (HFD) compared to the PCE treatments. …”
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Ferroptosis-related genes participate in the microglia-induced neuroinflammation of spinal cord injury via NF-κB signaling: evidence from integrated single-cell and spatial transcr... by Siqiao Wang, Li Yang, Zhourui Wu, Chen Li, Shaoke Wang, Zhihui Xiao, Bei Ma, Rongrong Zhu, Liming Cheng

“…Methods Micro-array datasets (GSE45006, GSE69334), RNA sequencing (RNA-seq) dataset (GSE151371), spatial transcriptome datasets (GSE214349, GSE184369), and single cell RNA sequencing (scRNA-seq) datasets (GSE162610, GSE226286) were available from the Gene Expression Omnibus (GEO) database. Through weighted gene co-expression network analysis and differential expression analysis in GSE45006, we identified differentially expressed time- and immune-related genes (DETIRGs) associated with chronic SCI and differentially expressed ferroptosis- and immune-related genes (DEFIRGs), which were validated in GSE151371. …”
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Cisplatin resistance alters ovarian cancer spheroid formation and impacts peritoneal invasion by Lydia C. Powell, Marcos Quintela, David W. James, Emenike Onyido, David Howard, Kadie Edwards, Jordan L. Turney, Charlotte R. Morgan, Jenny Worthington, Nicole Williams, Alexander Dulebo, Heiko Haschke, Deyarina Gonzalez, R. Steven Conlan, Lewis W. Francis

“…CR SKOV3 spheroids (IC50: 25.5 µM) had a significantly greater area and perimeter and were less spherical, with a reduced Young’s modulus, (p < 0.01) compared to parental (P) SKOV3 spheroids (IC50: 5.4 µM). Gene expression arrays revealed upregulation of genes associated with cell adhesion, extracellular matrix (ECM) and epithelial-to-mesenchymal transition (EMT) in CR spheroids, while immunofluorescence assays demonstrated increased protein expression of PAI-1 (p < 0.05; implicated in cell adhesion) and reduced protein expression of Tenascin-C (p < 0.01; implicated in elasticity) in CR spheroids compared to P spheroids. …”
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Uridine-cytidine kinase 2 is correlated with immune, DNA damage repair and promotion of cancer stemness in pan-cancer by Jinlong Tian, Yanlei Li, Yu Tong, Yuan Zhang, Tingxiao Zhao, Yao Kang, Qing Bi

“…Furthermore, single-cell datasets, acquired from the Gene Expression Omnibus (GEO) database, were used to validate the relationship between UCK2 and immune cells. …”
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Identification of key miRNAs and target genes in extracellular vesicles derived from low-intensity pulsed ultrasound-treated stem cells by Xin Yin, Xin Yin, Jialian Yi, Fugang Mao, Qisheng Tang, Xinyu Zhang, Xiaoyu Yang, Hongqing Xie, Linping Wang, Shuifen Sun, Xin Yu, Xin Yu, Jie Liu, Lihong Jiang, Lihong Jiang

“…Specifically, it sought to identify key miRNAs and their target mRNAs associated with enhanced therapeutic efficacy in LIPUS-treated stem cell-derived EVs.MethodsUtilizing miRNA deep-sequencing data from the Gene Expression Omnibus database, differential gene analysis was performed. …”
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Carboxylesterase 4A Inhibits the Malignant Biological Behavior of Nasopharyngeal Carcinoma via the PI3K/AKT Pathway by Qiaoli Chen MS, Quanxiang Hao MBBS, Yanping Yang MBBS, Limei Li PhD, Danping Li MS, Ran Zhao MS, Wanqi Wei MBBS, Lixian Deng MBBS, Jiaming Su MBBS, Ziyuan Liang MBBS, Shiyue Tang MS, Yaomin Lu MBBS, Yushan Liang PhD, Zhe Zhang PhD, Xiaoying Zhou PhD, Xue Xiao PhD, Ping Li PhD, Yi Huang PhD, Weilin Zhao PhD

“…Method A standardized mean difference (SMD) analysis was used to analyze the dysregulation of CES4A based on the gene expression omnibus (GEO) database. qRT-PCR and immunohistochemical staining (IHC) were used to identify the mRNA and protein levels of CES4A in NPC cell lines and tissues, respectively. …”
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Genome-wide transcriptome analysis and drug target discovery reveal key genes and pathways in thyroid cancer metastasis by Minjing Zou, Amal Qattan, Monther Al-Alwan, Hazem Ghebeh, Naif Binjumah, Latifa Al-Haj, Khalid S. A. Khabar, Abdulmohsen Altaweel, Falah Almohanna, Abdullah M. Assiri, Abdelilah Aboussekhra, Ali S. Alzahrani, Ali S. Alzahrani, Yufei Shi

“…MethodsWe performed genome-wide transcriptome analysis comparing gene expression profile of metastatic thyroid cancer cells (Met) with primary tumor cells established from transgenic mouse models of papillary thyroid cancer (PTC), follicular thyroid cancer (FTC), poorly differentiated thyroid cancer (PDTC), and anaplastic thyroid cancer (ATC).ResultsGenes involved in tumor microenvironment (TME), inflammation, and immune escape were significantly overexpressed in Met cells. …”
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Chemokine associations with blood cerebrospinal fluid (CSF) barrier permeability and delirium by Paul Denver, Lucas Tortorelli, Karen Hov, Jens Petter Berg, Lasse M. Giil, Arshed Nazmi, Ana Lopez-Rodriguez, Daire Healy, Carol Murray, Robyn Barry, Leiv Otto Watne, Colm Cunningham

“…Modelling acute systemic inflammation, we used bacterial LPS (250 μg/kg) or sterile laparotomy surgery in mice to demonstrate de novo synthesis of chemokines at the choroid plexus (CP) and microvasculature. Gene expression data showed CP-enriched expression of Il1b, Tnfa, Cxcl1 and Ccl3 in both models and immunohistochemistry showed cytokine and chemokine synthesis in CP stromal (IL-1β, CCL2/MCP1) or epithelial cells (CXCL10/IP-10) cells and at the microvasculature. …”
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Effects of organic acid blends on the growth performance, intestinal morphology, microbiota, and serum lipid parameters of broiler chickens by Swapnali Waghmare, Mahesh Gupta, K.B. Bahiram, J.P. Korde, Rekha Bhat, Yashwant Datar, Pushpendra Rajora, M.M. Kadam, Megha Kaore, N.V. Kurkure

“…Compared with the control (T1), the combination of Acidapure powder and liquid (T4) increased the gene expression of the tight junction proteins Claudin-1 and Zona Occludense 1 (ZO-1). …”
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The multi-omics signatures of telomere length in childhood by Congrong Wang, Dries S. Martens, Mariona Bustamante, Rossella Alfano, Michelle Plusquin, Lea Maitre, John Wright, Rosemary R. C. McEachan, Johanna Lepeule, Remy Slama, Marina Vafeiadi, Leda Chatzi, Regina Grazuleviciene, Kristine B. Gutzkow, Hector Keun, Eva Borràs, Eduard Sabidó, Angel Carracedo, Georgia Escarami, Augusto Anguita-Ruiz, Dolors Pelegrí-Sisó, Juan R. Gonzalez, Martine Vrijheid, Tim S. Nawrot

“…Blood DNA methylation, gene expression, miRNA expression, plasma proteins and serum and urinary metabolites were measured through microarrays or (semi-) targeted assays. …”
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Characterizing tumor biology and immune microenvironment in high-grade serous ovarian cancer via single-cell RNA sequencing: insights for targeted and personalized immunotherapy st... by Fu Zhao, Fu Zhao, Xiaojing Jiang, Yumeng Li, Tianjiao Huang, Zhikai Xiahou, Wenyang Nie, Qian Li

“…Utilizing single-cell RNA sequencing (scRNA-seq), the study systematically examines tumor heterogeneity and immune microenvironment, focusing on biomarkers influencing drug response and immune activity, aiming to enhance patient outcomes and quality of life.MethodsscRNA-seq data was obtained from the GEO database in this study. Differential gene expression was analyzed using gene ontology and gene set enrichment methods. …”
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Construction of complex three-dimensional vascularized liver tissue model in vitro based on a biphasic cell-laden embedding medium by Weikang Lv, Haoran Yu, Abdellah Aazmi, Tuya Naren, Wanli Cheng, Mengfei Yu, Zhen Wang, Xiaobin Xu, Huayong Yang, Liang Ma

“…Transcriptome sequencing revealed that liver tissues with higher vascular density exhibited upregulated gene expression in metabolic and angiogenesis-related pathways. …”
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A bibliometric analysis of the top 100 most cited articles on corticospinal tract regeneration from 2004 to 2024 by Saijilafu, Saijilafu, Ling-Chen Ye, Huanyi Li, Haokun Li, Xinyi Lin, Kehui Hu, Zekai Huang, Chimedragchaa Chimedtseren, Linjun Fang, Saijilahu, Ren-Jie Xu

“…A thorough keyword analysis revealed pivotal themes in the field, encompassing the optic nerve, gene expression, CST integrity and regeneration, diffusion tensor imaging, myelin-associated glycoproteins, inhibitors of neurite outgrowth, and methods of electrical and intracortical microstimulation.ConclusionThis investigation provides a bibliometric analysis of CST regeneration, underscoring the significant contribution of the United States to this field. …”
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Myeloid-derived suppressor cells exhibit distinct characteristics in bone marrow and blood of individuals with diffuse large B-cell lymphoma by Paris Efstratiou, Athina Damianaki, Aglaia Kavidopoulou, Polymnia Ioannidou, Effrosyni Markaki, Ioannis Moysis Skianis, Electra Tsagliotis, Vasilia Kaliafentaki, Angelos Mattheakakis, Maria Ximeri, Eleftherios Manouras, Matthieu Lavigne, Panayotis Verginis, Panayotis Verginis, Panayotis Verginis, Christina Kalpadakis

“…Despite that MDSC frequencies did not demonstrate any significant correlation with disease characteristics and outcome, our findings propose that gene expression profiling should be evaluated for their potential prognostic impact. …”
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Dual-release hydrocortisone treatment improves serum and peripheral blood mononuclear cell inflammatory and immune profiles in patients with autoimmune primary adrenal insufficienc... by Laura Tomasello, Antonina Coppola, Giuseppe Pizzolanti, Giuseppe Pizzolanti, Carla Giordano, Giorgio Arnaldi, Valentina Guarnotta

“…Secondary outcomes included the evaluation of the CD4+CD25+Foxp3+ Treg population and the gene expression levels of IL-6, IL-17A, cyclooxygenase (COX)-2, heat shock proteins (HSP)-70, indoleamine-2,3-dioxygenase (IDO), programmed death-ligand 1 (PD-L1), inducible nitric oxide synthase (iNOS), and thioredoxin (TXN)-1.MethodsWe prospectively included 15 patients with PAI on conventional glucocorticoid (GC) replacement therapy, 15 switched to dual-release hydrocortisone (DR-HC), and 20 healthy controls. …”
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α-Methyl-Tryptophan Inhibits SLC6A14 Expression and Exhibits Immunomodulatory Effects in Crohn’s Disease by Su Y, Li J, Chen Y, Bao J, Lei Z, Ma M, Zhang W, Liu Q, Xu B, Hu T, Hu Y

“…Traditional diagnostic and therapeutic methods have limitations, necessitating the exploration of more effective strategies.Methods: In this study, we employed the Gene Expression Omnibus database to identify genes that are differentially expressed in CD. …”
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Deciphering the role of epigenetics in plant pathogen resistance: Strategies for sustainable sugarcane management by Faisal Mehdi, Yuanli Wu, Shuzhen Zhang, Yimei Gan, Zhengying Cao, Shuting Jiang, Limei Zan, Benpeng Yang

“…Under normal conditions, plants adjust their gene expression in response to pathogenic threats. Specific transcription factors are activated by external stimuli, which then enhance the expression of defense-related genes. …”
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Identification of ALEKSIN as a novel multi-IRF inhibitor of IRF- and STAT-mediated transcription in vascular inflammation and atherosclerosis by Aleksandra Antonczyk, Katarzyna Kluzek, Natalia Herbich, Mahdi Eskandarian Boroujeni, Bart Krist, Dorota Wronka, Anna Karlik, Lukasz Przybyl, Adam Plewinski, Joanna Wesoly, Hans A. R. Bluyssen

“…Based on their promoting role in atherosclerosis, we hypothesized that the inhibition of pro-inflammatory target gene expression through multi-IRF inhibitors may be a promising strategy to treat CVDs. …”
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The miR-1269a/PCDHGA9/CXCR4/β-catenin pathway promotes colorectal cancer invasion and metastasis by Haitao Mei, Qingshan Luo, Junyong Weng, Jialing Hao, Jinfeng Cai, Runkai Zhou, Ce Bian, Yingzi Ye, Shengzheng Luo, Yugang Wen

“…Methods PCDHGA9 expression was detected using quantitative real-time quantitative polymerase chain reaction (RT-qPCR) in 63 pairs of colorectal cancer tissues. Differential gene expression from high-throughput sequencing was analyzed using ingenuity pathway analysis (IPA) to explore the biological functions of PCDHGA9 and its potential regulated genes. …”
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