Nitroxoline evidence amoebicidal activity against Acanthamoeba castellanii through DNA damage and the stress response pathways by Lijun Chen, Wei Han, Wenwen Jing, Meng Feng, Qingtong Zhou, Xunjia Cheng

“…In this study, nitroxoline significantly reduced the viability of A. castellanii trophozoites in a dose- and time-dependent manner, inducing morphological changes and apoptosis. Transcriptomic analysis revealed substantial alterations in gene expression, including enrichment of metabolic pathways, DNA damage responses, and iron ion binding. …”
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Transcriptional Signatures of the Right Ventricle in End‐Stage Heart Failure by Jonah D. Garry, Giovanni E. Davogustto, Vineet Agrawal, Fei Ye, Kelsey Tomasek, Yan Ru Su, Tarek Absi, James D. West, Anna Hemnes, Evan L. Brittain

“…We compared gene expression between groups and performed pathway enrichment analysis. Pathways related to fatty acid metabolism and mitochondrial function were negatively enriched, while extracellular structure‐related pathways were positively enriched in stressed RVs (compensated and failing) compared to controls. …”
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The promising role of nanopore sequencing in cancer diagnostics and treatment by Xinming Su, Qingyuan Lin, Bin Liu, Chuntao Zhou, Liuyi Lu, Zihao Lin, Jiahua Si, Yuemin Ding, Shiwei Duan

“…In essence, this technology stands poised to unearth novel mechanisms underlying tumorigenesis while providing dependable support for the diagnosis and treatment of cancer.…”
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A pilot transcriptomic study of a novel multitargeted BRT regimen for anti–MDA5 antibody-positive dermatomyositis: improving survival over conventional therapy by Moe Tokunaga, Moe Tokunaga, Yu Nakai, Yoshiharu Sato, Mitori Hiratsuka, Yoshinori Matsumoto, Takeshi Nakatsue, Takako Saeki, Takatsune Umayahara, Jun Wada, Yoshinobu Koyama

“…Twelve-month survival was assessed. Transcriptome analysis was performed for six patients (BRT=3, TC=3), beginning with cluster analysis to evaluate whether changes in peripheral blood gene expression varied according to treatment or prognosis. …”
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Impact on the Leishmania mexicana transcriptome due to knockout of genes encoding orthologs of methyltransferases involved in m1A and m5C mRNA modifications by Angela Moreira Bezerra, Ariely Barbosa Leite, Christian Robson de Souza Reis, João Luiz de Lemos Padilha Pitta, Suellen Rodrigues Maran, Nilmar Silvio Moretti, Danielle Maria Nascimento Moura, Antonio Mauro Rezende

“…For the NSUN2 genes, enrichment analysis indicated impacts on biological processes mostly related to nucleotide metabolism and DNA binding. …”
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Comparison of the effects and mechanisms of Alismatis Rhizoma with and without salt processing in ameliorating edema due to kidney Yin deficiency based on UPLC-Q-TOF-MS and transcr... by Lin Yan, Zemin Ou, Yi Cheng, Yan Tong, Javed Iqbal, Jinyu Wang, Dewen Liu

“…This study employed ultra-performance liquid chromatography–quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and pattern analysis to compare the terpenoids between AR and SAR. …”
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Mesquite seed flour as a nutrient-rich alternative to fishmeal for common carp fingerlings (Cyprinus carpio): Environmental, growth performance, transcriptomic and intestinal micro... by María Fernanda Barragán-Longoria, Karla Jareth Pérez-Viveros, Arturo Cadena-Ramírez, Javier Castro-Rosas, José Roberto Villagómez-Ibarra, Jesus Hernandez-Perez, Silvia Hinojosa-Alvarez, Carlos Alberto Gómez-Aldapa, Rocio Alejandra Chavez-Santoscoy

“…Growth performance resulted similarly between MD and FM, with no significant differences in weight gain (379.40 ± 232.55 % for FM and 335.08 ± 219.69 % for MD). Transcriptomic analysis revealed differentially expressed genes involved in lipid metabolism, particularly fatty acid degradation and PPAR signaling pathways. …”
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Understanding the transition from embryogenesis to seed filling in Phaseolus vulgaris L. non-endospermic seeds by Cláudia Lopes, Pedro Fevereiro, Susana de Sousa Araújo, Susana de Sousa Araújo

“…MethodsTo accomplish this goal, we conducted a comprehensive analysis at 6, 10, 14, 18 and 20 DAA, integrating morphological, histological, and transcriptomic approaches. …”
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Insights into Lead Toxicity and Detoxification Mechanisms in the Silkworm, <i>Bombyx mori</i> by Dan-Dan Bian, Yan-Xia Shi, Kai-Wen Shi, Hui-Cong Du, Bo-Ping Tang, Qiu-Ning Liu

“…This study investigated the mechanisms of Pb toxicity and the associated detoxification and metabolic defense responses in silkworms, employing transcriptome sequencing, enzyme activity assays, and histopathological analysis. …”
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The potential of Trichoderma asperellum for degrading wheat straw and its key genes in lignocellulose degradation by Qijun Zhu, Weiwei Liu, Liye Song, Zhenzhen Guo, Zhiyao Bian, Yunsheng Han, Hongying Cai, Peilong Yang, Kun Meng

“…Enzymatic activity and structural analyses were performed to further confirm the lignocellulose-degrading ability of T. asperellum and to analyze the degradation mechanisms. Transcriptomic analysis revealed that, compared with the control group, the TN group had 4,548, 4,399, and 6,051 differentially expressed genes (DEGs) at 5, 10, and 30 days, respectively, mainly involved in cellulose and hemicellulose degradation, carbohydrate metabolism, carbohydrate transport, glycoside hydrolases, and polysaccharide binding. …”
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Spleen-based proteogenomics reveals that Escherichia coli infection induces activation of phagosome maturation pathway in chicken by Jiahui Shi, Songhao Jiang, Qiang Wang, Jilin Dong, Huiming Zhu, Peijia Wang, Shuhong Meng, Zhenpeng Zhang, Lei Chang, Guibin Wang, Xiaoqin Xu, Ping Xu, Yao Zhang

“…Various strategies were used for searching virulence factors, while little is known about the mechanism by which APEC survives in host or is eliminated by host. …”
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Integration of histopathology, transcriptomics and non-targeted metabolomics reveals toxic effects of thiamethoxam under acute stress in mirror carp (Cyprinus carpio var. Longke-11... by Dongchang Guo, Wenyang Song, Manhong Liu, Haixia Jiang, Xiaolong Wang, Zhiying Jia, Bin Xu

“…Transcriptomic analysis revealed that the number of differentially expressed genes (DEGs) increased with the concentration of THM. …”
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Impact of stocking density on oxidative stress, digestive enzyme activity, ATPase function, and transcriptomic changes in juvenile Crimson snapper (Lutjanus erythropterus) during l... by Jiaqi Su, Yu Guo, Jiayang Li, Karsoon Tan, Chuanxin Qin

“…In conclusion, 60 g/L is the optimum stocking density for L. erythropterus juveniles during road transport, while 80 g/L being a feasible but stressful alternative. …”
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Transcriptome and Physio-Biochemical Profiling Reveals Differentially Expressed Genes in Seedlings from Aerial and Subterranean Seeds Subjected to Drought Stress in <i>Amphicarpaea... by Jiancheng Kou, Yue Su, Tianyu Lei, Siqi Hou, Jiali Tian, Minglong Li, Shuzhen Zhang, Xiaodong Ding, Qiang Li, Jialei Xiao

“…To identify drought-associated genes and reveal the mechanisms underlying drought adaptability in AS and SS seedlings, we performed an RNA-seq-based transcriptomic analysis in AS and SS seedlings exposed to drought stress. …”
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Exploring the Therapeutic Potential of the DOT1L Inhibitor EPZ004777 Using Bioinformatics and Molecular Docking Approaches in Acute Myeloid Leukemia by Mehmet Kivrak, Ihsan Nalkiran, Hatice Sevim Nalkiran

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Differential effects of short-term and long-term ketogenic diet on gene expression in the aging mouse brain by Matthew S. Stratton, José Alberto López-Domínguez, Alessandro Canella, Jon J. Ramsey, Gino A. Cortopassi

“…Methods: We conducted transcriptome wide analysis on whole brain samples from 13-month-old mice, 13-month-old mice fed a ketogenic diet for 1 month, 26-month-old mice, and 26-month-old mice fed a ketogenic diet for 14 months. …”
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Identification and validation of biomarkers, construction of diagnostic models, and investigation of immunological infiltration characteristics for idiopathic frozen shoulder by Han-tao Jiang, Li-ping Shen, Meng-Qi Pang, Min-jiao Wu, Jiang Li, Wei-jie Gong, Gang Jin, Rang-teng Zhu

“…At the outset, we conducted differential expression analysis, weighted gene co-expression network analysis (WGCNA), and utilized the cytoHubba plugin, complemented by two machine learning algorithms, receiver operating characteristic (ROC) analysis, and expression level evaluation to identify biomarkers for FS. …”
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Dual roles of Anisakis pegreffii proteins in macrophage immune dynamics by Min-hao Zeng, Min-hao Zeng, Min-hao Zeng, Sarah Alsobaie, Xiao-xu Wang, Shan Li, Fahad M. Aldakheel, Mourad A. M. Aboul-Soud, Wei-bin Liu

“…Conversely, glycoproteins suppressed TNF-α transcription and reduced IL-4-induced Arg-1 expression, displaying immunosuppression. Transcriptomics analysis found that ABP enriched TNF and hematopoietic pathways, with IL6 and IL1β as key pro-inflammatory genes. …”
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Spatial distribution of maternal factors in pig mature oocytes by Fuquan Zhu, Meng Yang, Dayu Wang, Yuan Jiang, Chao Jia, Yanfeng Fu, Aochen Yu, Huijun Liu, Meixia Wang, Tingzhang Wang, Honglin Liu, Juan Li

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Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection by Agnieszka Kraft, Michaela B. Kirschner, Vanessa Orlowski, Manuel Ronner, Caroline Bodmer, Valentina Boeva, Isabelle Opitz, Mayura Meerang

“…In this study, we characterized the transcriptomic profile of EVs secreted by PM primary cells and explored their potential as a biomarker source for PM detection. …”
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