Unsupervised evaluation of pre-trained DNA language model embeddings by Raghav Awasthi, Gayan Samuditha Mend Mend Arachchige, Xiaofeng Zhu

“…However, they have struggled with tasks such as learning individual-level personal transcriptome variation, highlighting the need for robust evaluation approaches. …”
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Molecular Adjuvant Potential of <i>GCSF</i> and <i>MCSF</i> in Starry Flounder Challenged with <i>Streptococcus parauberis</i> by Min-Young Sohn, Gyoungsik Kang, Kyung-Ho Kim, Ha-Jeong Son, Chan-Il Park

“…The <i>GCSF</i> gene (594 bp, 198 aa) features a conserved IL-6 domain, while the <i>MCSF</i> gene (621 bp, 207 aa) contains a predicted transmembrane region. …”
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SPAG6 Promotes Multiple Myeloma Through Activation of the MAPK/ERK Signaling Pathway by Junnan Li, Xinyu Yan, Li Ding, Jiaxiu Yin, Ping Li, Lin Liu

“…In vitro, SPAG6 overexpression promoted cell proliferation, migration, and the resistance to apoptosis in MM cells, while down - expression had contrary effects. Mechanistic studies revealed that SPAG6 directly interacts with dual-specificity phosphatase 1 (DUSP1). …”
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Brain Specific RagA Overexpression Triggers Depressive‐Like Behaviors in Mice via Activating ADORA2A Signaling Pathway by Jia Zhao, Yilu Sun, Yibin Feng, Jianhui Rong

“…RNA‐seq profiling of the prefrontal cortex (PFC) transcriptome highlights adenosine A2a receptor (ADORA2A) as a key differentially expressed gene (DEG). …”
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Identification and Analysis of Stress-Associated Protein (SAP) Transcription Factor Family Members in <i>Pinus massoniana</i> by Yulu Zhao, Xingyue Ren, Jingjing Zhang, Wenya Yu, Qiong Yu, Kongshu Ji

“…For example, <i>PmSAP8</i> and <i>PmSAP12</i> responded strongly to ABA, MeJA, and H₂O₂ treatments, while <i>PmSAP3</i> and <i>PmSAP5</i> showed significant upregulation under ETH and NaCl stress. …”
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NKX3-2 Induces Ovarian Cancer Cell Migration by HDAC6-Mediated Repositioning of Lysosomes and Inhibition of Autophagy by Alessandra Ferraresi, Ian Ghezzi, Amreen Salwa, Andrea Esposito, Danny N. Dhanasekaran, Ciro Isidoro

“…In ovarian cancer cells, lysophosphatidic acid (LPA) modulates the transcriptome profile and promotes cell invasiveness by the downregulation of autophagy. …”
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Potential Targets Related to Skin Aging: Based on eQTL and GWAS Datasets by Shi H, Cao X

“…Then, enrichment analysis results showed there were 60 GO terms may involved in the process of SG, like fatty-acyl-CoA metabolic process, while KEGG enrichment pathways identified mainly involved in mechanisms related to fatty acid metabolism, energy generation, and inflammation regulation. …”
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FgUbiH Is Essential for Vegetative Development, Energy Metabolism, and Antioxidant Activity in <i>Fusarium graminearum</i> by Jinwen Ge, Huanchen Zhai, Lei Tang, Shuaibing Zhang, Yangyong Lv, Pingan Ma, Shan Wei, Yu Zhou, Xiaofu Wu, Yang Lei, Fengguang Zhao, Yuansen Hu

“…Coenzyme Q (CoQ) is ubiquitously produced across organisms and functions as a hydrogen carrier in energy metabolism. While UbiH in <i>Escherichia coli</i> serves as a hydroxylase in CoQ biosynthesis, its role in phytopathogenic fungi is not well understood. …”
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<i>Saussurea involucrata CML6</i> Enhances Freezing Tolerance by Activating Antioxidant Defense and the CBF-COR Pathway in Plants by Mengjuan Hou, Hui Kong, Jin Li, Wenwen Xia, Jianbo Zhu

“…<i>SiCML6</i> enhances freezing tolerance by mitigating oxidative damage through boosted T-AOC and osmoprotectant accumulation while activating the CBF-COR signaling pathway. This gene is a novel target for improving crop cold resistance.…”
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Human lung organoids reveal conserved CYP1A1 and metallothionein activation in response to particulate matter exposure by Seri Choi, Seung-Yeon Kim, Ji Won Baek, Won Keun Oh, Kee K. Kim, Eun-Mi Kim

“…ERM exposure dose-dependently upregulated CYP1A1 expression and enzymatic activity while enhancing reactive oxygen species production. …”
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Analysis of Alternative Splicing Events and Identification of Key Genes in <i>Brassica napus</i> Leaves Infected by <i>Leptosphaeria biglobosa</i> by Xinning Ma, Lin Yuan, Jiuru Huangfu, Mengjiao Yan, Chen Guo, Lili Zhao, Hongxia Sun, Xiaoqing Jia, Ziqin Li, Haiyan Huangfu

“…Intron retention (RI) was the most common AS event, accounting for approximately 55% of all events, while alternative 5′ splice site events were least common, comprising only 2%. …”
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The intersection between circulatory microRNAs and biomarkers of neurodegeneration by Amber Yaqub, Rima Mustafa, M. Arfan Ikram, Mohsen Ghanbari

“…Plasma levels of 591 well-expressed circulatory miRNAs were measured by the HTG EdgeSeq Whole Transcriptome Assay, while t-tau, NfL, Aβ-40 and Aβ-42 were analysed using the Simoa NF-light® and N3PA assays. …”
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Role and mechanism of tigecycline in delaying the resistance of Klebsiella pneumoniae to polymyxin B by inhibiting cpxR by ZHANG Huanhuan, ZHANG Huanhuan, FENG Wei, HUA Shangjun

“…Transcriptomic and proteomic analyses indicated that in strain 686K·R, the expression levels of the PhoP/Q two-component system, lipopolysaccharide (LPS) modification enzymes, and efflux pump systems were significantly up-regulated (|Log2FC|≥2, P<0.0001), while TGC co-administration markedly inhibited these expression changes. …”
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Molecular turn in Yersinia pestis pathogenesis: implications of the gppA frameshift for bacterial survival in human macrophage by Hongyan Chen, Shiyang Cao, Yazhou Zhou, Tong Wang, Yang Jiao, Yafang Tan, Yarong Wu, Yifan Ren, Yajun Song, Jing-Ren Zhang, Zongmin Du, Ruifu Yang

“…Yersinia pestis, the etiological agent of the devastating plague, has caused three pandemics in human history. While known for its fatality, it has long been intriguing that biovar microtus strains are highly attenuated to humans. …”
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Genetic and therapeutic heterogeneity shape the baseline and longitudinal immune ecosystem of ovarian clear cell carcinoma by Min Yu, Fei Xu, Xiaohua Wu, Jiajia Li, Xiaojun Chen, Lihua Chen, Jiaxin Chen, Mengdong Ni, Siyu Xia, Jiana Li, Chaohua Liu

“…Background Ovarian clear cell carcinoma (OCCC) is a rare and chemo-resistant subtype of ovarian cancer. While immunotherapy has demonstrated effectiveness in some OCCC cases, the mechanisms for heterogeneous immunoreactivity and potential combinatory strategies remain unclear.Methods Tumor samples from 13 patients with OCCC underwent single-cell mRNA-seq and TCR-seq to generate 1 40 683 cells transcriptome, while additionally 31 formalin-fixed paraffin-embedded samples were used for immunohistochemistry. …”
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Pericytes Promote More Vascularization than Stromal Cells via an Interleukin‐6‐Dependent Mechanism in Microfluidic Chips by Julian Gonzalez‐Rubio, Hannah Kubiza, Yong Xu, Hiltrud Koenigs‐Werner, Mona Sophie Schmitz, Michaela Schedel, Christian Apel, Stefan Jockenhoevel, Christian G. Cornelissen, Anja Lena Thiebes

“…Pericytes can wrap around endothelial vessels acting as mural cells, while stromal cells remain separated. Whole‐transcriptome sequencing confirms an upregulation of pro‐vascularization genes in endothelial cell‐pericyte co‐cultures, while metabolism increases and inflammation decreases in stromal cell co‐cultures. …”
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Pilot Study on the Profiling and Functional Analysis of mRNA, miRNA, and lncRNA in the Skeletal Muscle of Mongolian Horses, Xilingol Horses, and Grassland-Thoroughbreds by Wenqi Ding, Wendian Gong, Tugeqin Bou, Lin Shi, Yanan Lin, Huize Wu, Manglai Dugarjaviin, Dongyi Bai

“…Whole-transcriptome analysis identified 105 differentially expressed genes (DEGs) in the CY vs. …”
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Effect of ketamine and esketamine on RNA expression and its relevance for depression: A systematic review by Claudia Pisanu, Rosana Carvalho Silva, Mattia Meattini, Massimo Gennarelli, Bernhard T. Baune, Alessio Squassina, Alessandra Minelli

“…Twelve studies met inclusion criteria, only one of which explored the effect of esketamine, while all others focused on racemic ketamine. Five studies examined peripheral blood gene expression in patients with TRD, while seven assessed mRNA changes in vitro using human-derived cells. …”
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<i>Polygonatum sibiricum</i> Polysaccharides Alleviate LPS-Induced Liver Injury in Chicks by Suppressing Inflammation and Oxidative Stress Through the PPAR Signaling Pathway by Yang Li, Jian Li, Xiaowang Liu, Zhili Cheng, Nana Gao, Jungang Kang, Xiaodan Wang

“…During this period, the LPS and PSP groups were intraperitoneally injected with 1500 μg/kg LPS on days 14, 16, 18, and 20, while the CON group received normal saline. On day 21, organs were collected for analysis. …”
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Gestational high-sucrose diet mediated vascular hyper-contractility in mesenteric arteries from offspring by Xinying Liu, Meng Liu, Chunxia Wang, Liting Duan, Qinggui Ren, Shuli Jiang, Jing Han, Hongwei Fu, Xiao Sun, Dongmei Man, Xueqin Feng

“…N(G)-Nitro-l-arginine methyl ester (L-NAME) increased PE-mediated vascular tension in CON group, while no effect in HS group, suggesting that endothelial nitric oxide (NO) system dysfunction in MAs exposed to prenatal HS. …”
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