Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions. by Karen Campos-León, Jack Ferguson, Thomas Günther, C David Wood, Steven W Wingett, Selin Pekel, Christy S Varghese, Leanne S Jones, Joanne D Stockton, Csilla Várnai, Michelle J West, Andrew Beggs, Adam Grundhoff, Boris Noyvert, Sally Roberts, Joanna L Parish

“…The virus-induced changes to the host cell's transcriptome are thought to contribute to carcinogenesis. Here, we show by RNA-sequencing that oncogenic HPV18 episome replication in primary human foreskin keratinocytes (HFKs) drives host transcriptional changes that are consistent between multiple HFK donors. …”
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Computational Study Protocol: Leveraging Synthetic Data to Validate a Benchmark Study for Differential Abundance Tests for 16S Microbiome Sequencing Data [version 2; peer review: 2... by Clemens Kreutz, Eva Kohnert

“…Building on Nearing et al.’s study (1), who assessed 14 differential abundance tests using 38 experimental 16S rRNA datasets in a case-control design, we are generating synthetic datasets that mimic the experimental data to verify their findings. …”
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NT5E (CD73) as a prognostic biomarker and therapeutic target associated with immune infiltration in lung adenocarcinoma by Leyan Chen, Tuoya Qi, Bishu Zhang, Xuelong Wang, Mingfeng Zheng

“…We found that NT5E was significantly overexpressed at both the mRNA and protein levels in LUAD tissues. Elevated NT5E expression was significantly linked to multiple clinicopathological factors, including metastasis and pathological stage, and served as a strong predictor of poor prognosis in LUAD patients. …”
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Pediatric pancreatic acinar cell carcinoma with a non-canonical BRAF-KMT2C fusion and a classic SND1-BRAF fusion: a case report and literature review by Yaqin Wang, Jiasi Zhang, Dimin Nie, Ai Zhang, Qun Hu, Aiguo Liu

“…Comprehensive genomic profiling by next-generation sequencing identified a non-canonical BRAF fusion with KMT2C at the DNA level and a classic SND1-BRAF fusion at the RNA level. The patient underwent surgical resection through a Whipple operation followed by six cycles of mFOLIRINOX chemotherapy and radiation therapy, achieving a favorable outcome up to now. …”
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Astrocytic Acid-Sensing Ion Channel 1a Contributes to the Development of Epileptic Cognitive Impairment by Wen Li, Huimin Zhou, Xiaona Li, Gengyao Hu, Dong Wei

“…Status epilepticus (SE) in C57/BL6 mice was induced using lithium–pilocarpine; the impact of ASIC1a on astrocytes was assessed using rAAV–ASIC1a–NC and rAAV–ASIC1a–shRNA, injected in the CA3 region of mice. Behavioral assessments were conducted using the Morris water maze (MWM). …”
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Characterization of Interleukin-15-Transpresenting Dendritic Cells for Clinical Use by J. M. J. Van den Bergh, E. L. J. M. Smits, M. Versteven, H. De Reu, Z. N. Berneman, V. F. I. Van Tendeloo, E. Lion

“…In this study, we demonstrate that upon electroporation with both IL-15 and IL-15Rα-encoding messenger RNA, mature DC become highly positive for surface IL-15, without influencing the expression of prototypic mature DC markers and with preservation of their cytokine-producing capacity and their migratory profile. …”
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Crosstalk between non-coding RNAs and programmed cell death in colorectal cancer: implications for targeted therapy by Seyed Reza Taha, Mehdi Karimi, Bahar Mahdavi, Milad Yousefi Tehrani, Ali Bemani, Shahriar Kabirian, Javad Mohammadi, Sina Jabbari, Meysam Hushmand, Alireza Mokhtar, Mohammad Hossein Pourhanifeh

“…The targeted modulation of ncRNA-PCD interactions presents promising avenues for personalized cancer treatment, which may improve patient outcomes by enhancing therapeutic effectiveness and reducing resistance.…”
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Characterization of Vaccine-Enhanced Humoral Immune Responses Against Emergent SARS-CoV-2 Variants in a Convalescent Cohort by Jared Sheehan, Amber J. Trauth, Michael E. Hagensee, Alistair J. Ramsay

“…Our primary goal was to characterize hybrid antibody (Ab) responses in a patient cohort infected with ancestral Wuhan-Hu-1 virus and vaccinated between 6 and 10 months later with the Wuhan-Hu-1–based BNT162b2 mRNA vaccine. We were particularly interested in determining the efficacy of neutralizing Ab responses against subsequently emergent SARS-CoV-2 variants. …”
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Silica Nanoparticles Loaded With Selenium Quantum Dots Reduce Myocardial Ischemia-Reperfusion Injury by Alleviating Ferroptosis and Mitochondrial Dysfunction by Li T, Yang B, Liu X, Shi D, Wang Z, Chen Y, Shen C

“…Taixi Li,1,* Boshen Yang,1,* Xijian Liu,2 Dongmei Shi,1 Zhixiang Wang,1 Yizhi Chen,1 Chengxing Shen1 1Department of Cardiology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China; 2School of Chemistry and Chemical Engineering, Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Shanghai Engineering Technology Research Center for Pharmaceutical Intelligent Equipment, Shanghai University of Engineering Science, Shanghai, 201620, People’s Republic of China*These authors contributed equally to this workCorrespondence: Chengxing Shen, Department of Cardiology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China, Email shencx@sjtu.edu.cnPurpose: Myocardial ischemia-reperfusion (IR) injury, a significant challenge in cardiovascular treatment, is primarily driven by ferroptosis and mitochondrial dysfunction. …”
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A Novel Pathogenic Splicing Mutation of OFD1 is Responsible for a Boy with Joubert Syndrome Exhibiting Orofaciodigital Spectrum Anomalies, Polydactyly and Retinitis Pigmentosa by Chen L, Zhao MF, Deng HW, Liao M, Fan LL, Zhong QB, Wang J, Li K, Wu ZH, Yin JY

“…Whole exome sequencing and Sanger sequencing revealed a splicing mutation (NM_003611.2, c.2387+1G>A) in the OFD1 gene of the patient and his mother. mRNA sequencing further confirmed this mutation. …”
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OPTIMIZATION OF CONCENTRATION AND SOAKING TIME OF HARRIS HEMATOXYLIN IN DNA BAND EXAMINATION USING ELECTROPHORESIS by Siti Nuristiqomah Fajri, Asep Iin Nur Indra, Fusvita Merdekawati, Acep Tantan H.

“…The amplified DNA I6S rRNA gene from Escherichia coli (584 bp), which had undergone electrophoresis, was stained using harris hematoxylin dye at 0.01%; 0.02%; 0.03%; 0.04%; and 0.05% concentrations and immersion times soaking times of 10, 15, 20, and 30 minutes variations. …”
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Antimicrobial Resistance of Escherichia coli Isolated from Ground Beef in Huasca de Ocampo, Hidalgo, Mexico by A. P. Cordero-López, V. Vega-Sánchez, V. M. Martínez-Juárez, J. I. Olave-Leyva, F. R. Gómez-De Anda, N. E. Reyes-Rodríguez

“…The isolated strains were identified by traditional means and molecular by the 16S rRNA gene, the antibiotic sensitivity profile was identified by the Kirby-Bauer method and genotypic identification was performed for the type 1 integrase gene. …”
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The Expression and Clinical Significance of Different Forms of Mer Receptor Tyrosine Kinase in Systemic Lupus Erythematosus by Huaqun Zhu, Xiaolin Sun, Lei Zhu, Fanlei Hu, Lianjie Shi, Zhanguo Li, Yin Su

“…Real-time quantitative PCR was applied to evaluate the mRNA levels of MerTK and ADAM17. Results. Both mMer expression on CD14+ monocytes/macrophages and sMer levels in plasma significantly increased in SLE patients compared to healthy subjects. …”
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Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer by Noah Sasa, Toshihiro Kishikawa, Masashi Mori, Rie Ito, Yumie Mizoro, Masami Suzuki, Hirotaka Eguchi, Hidenori Tanaka, Takahito Fukusumi, Motoyuki Suzuki, Yukinori Takenaka, Keisuke Nimura, Yukinori Okada, Hidenori Inohara

“…Heterozygous loss of ataxia-telangiectasia mutated (ATM) was observed in 67% of tumors, with its downregulation confirmed by single-cell RNA sequencing and immunohistochemistry, suggesting ATM haploinsufficiency contributes to carcinogenesis. …”
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Actinidia deliciosa as a complemental therapy against nephropathy and oxidative stress in diabetic rats by Ali Y. Naoom, Wenyi Kang, Nora F. Ghanem, Mohamed M. Abdel-Daim, Fatma M. El-Demerdash

“…Furthermore, histological, immunohistochemical alpha-smooth muscle actin immunoreactivity (α-SMA-ir) and histochemical (collagen, total protein, DNA, and RNA) alterations were observed in rat kidneys. Moreover, STZ produced upregulation of inflammatory associated genes (tumor necrosis factor-alpha; TNF-α and transforming growth factor β1; TGF-β1) and triggered apoptosis by upregulating apoptotic related gene [Bcl2-associated X protein (Bax)] and downregulating anti-apoptotic related gene B-cell lymphoma-2 (Bcl-2) based on real-time PCR data. …”
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Molecular Mechanism During Mycelium Subculture Degeneration of <i>Volvariella volvacea</i> by Lidan Feng, Lujuan Wang, Yuanxi Lei, Jie Li, Fengyun Zhao

“…Thus, five generations of subcultured strains (M1–M5) were obtained after 20 months of mycelial subculturing, their production traits were determined, and transcriptomic analysis was performed using RNA-seq; the differentially expressed genes were verified via RT-qPCR. …”
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Engineering a phi15-based expression system for stringent gene expression in Pseudomonas putida by Eveline-Marie Lammens, Daniel C. Volke, Alison Kerremans, Yannick Aerts, Maarten Boon, Pablo I. Nikel, Rob Lavigne

“…Abstract The T7 phage RNA polymerase (RNAP) is a widely used expression platform, but its implementation in non-model microbial hosts poses significant challenges due to cytotoxicity. …”
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Comparative transcriptomic and phenotypic analysis of monoclonal and polyclonal Populus deltoides genotypes by Macy Gosselaar, Macy Gosselaar, Mark A. Arick, Chuan-Yu Hsu, Heidi Renninger, Courtney M. Siegert, Waqar Shafqat, Daniel G. Peterson, Austin Himes

“…Phenotypic results showed that polyclonal plots exhibited higher leaf area index (LAI; p &lt; 0.01, 2.96 ± 0.057 m2) and total biomass (p &lt; 0.01, 2.74 ± 0.06) compared to monoclonal plots, indicating superior productivity. RNA sequencing revealed upregulation of key genes such as exocyst subunit exo70 family protein H7 (EXO70H7), NDH-dependent cyclic electron flow 5 (NDF5), and expansin-like A3 (EXLA3). …”
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Bivalirudin exerts antiviral activity against respiratory syncytial virus-induced lung infections in neonatal mice by Zhuang Shihao, Tang Qiuyu, Chen Ping, Wang Chengyi, Liu Guanghua

“…Furthermore, RSV-infected mice demonstrated altered clotting parameters such as D-dimer, soluble thrombomodulin, and increased inflammatory cytokines IL-5, 6, IFN-γ, IL-13, and CXCL1. Additionally, the mRNA expression analysis displayed increased levels of IL-33, TLR3, and TLR7 genes in RSV-infected lung tissue. …”
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Liposomal Formulations: A Recent Update by Surendra S. Agrawal, Vrinda Baliga, Vaishali Y. Londhe

“…Advanced drug delivery technologies like magnetic targeting and ultrasound. Pro Drug, RNA Liposomes approach may improve liposomal medication administration. …”
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