Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis by Hongbo Shi, Meitao Wu, Xiaoliang Wu, Zhuoxin Liu, Shuo Jiang, Gen Li, Yetong Yang, Yanghe Fu, Qiuping Wang, Guangde Zhang, Liang Cheng

“…In this study, we conducted an integrated multi-omics analysis to characterize the functional signatures of gut microbiome in AS. …”
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GTSE1-expressed osteoblastic cells facilitate formation of pro-metastatic tumor microenvironment in osteosarcoma by Linzhu Wang, Wenyue Li, Weihang Ji, Danyang Bing, Mingyue Liu, Kaidong Liu, Bo Chen, Zhangxiang Zhao, Yunyan Gu, Xuelian Li, Xiaoqiang E, Lei Yang

“…Augmentation of GTSE1 enhanced the abilities of cell migration and invasion, while silencing of GTSE1 impaired the abilities in human OB cell lines. …”
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Alternative mRNA splicing in anthracycline-induced cardiomyopathy – a COG-ALTE03N1 report by Purnima Singh, David K. Crossman, Changde Cheng, Patrick J. Trainor, Noha Sharafeldin, Xuexia Wang, Liting Zhou, Lindsey Hageman, Saro H. Armenian, Frank M. Balis, Douglas S. Hawkins, Frank G. Keller, Melissa M. Hudson, Joseph P. Neglia, Jill P. Ginsberg, Wendy Landier, Smita Bhatia

“…Event-level splicing tool, rMATS (replicate Multivariate Analysis of Transcript Splicing) was used for quantitative profiling of alternative splicing events. …”
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Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection by Xiaomeng Sun, Xiaomeng Sun, Ruiyu Zhang, Ruiyu Zhang, Zongping Wang, Zongping Wang, Haotian Zhang, Haotian Zhang, Hairun Wen, Hairun Wen, Junli Zhang, Naibin Yu, Naibin Yu, Zhe Wang, Zhe Wang, Huanhuan Tai, Huanhuan Tai, Qin Yang, Qin Yang

“…The URGs in Qgls8-R were significantly enriched in metabolic processes, phytohormone signaling, and response to biotic stress, while the URGs in Qgls8-S were mostly involved in plant growth and developmental processes. …”
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stGRL: spatial domain identification, denoising, and imputation algorithm for spatial transcriptome data based on multi-task graph contrastive representation learning by Xin Lu, Murong Zhou, Bo Gao, Fang Wang, Shuilin Jin, Qiaoming Liu, Guohua Wang

“…Abstract Background Spatial transcriptomics now enables sequencing while preserving the spatial location of cells. …”
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Transcriptome sequencing revealed that lymph node metastasis of papillary thyroid microcarcinoma is associated with high THBS4 expression and PDGFRA+ cancer-associated fibroblasts by LeYin Hu, Yi Lin, JingYu Zheng, Li Wan, Rui Zhao, Yi Ma, JianMin Li

“…Immunohistochemical analysis demonstrated increased THBS4(P < 0.01) and PDGFRA(P < 0.001) expression in LNM groups, while SMA staining showed no significant intergroup differences(P>0.05).ConclusionThis study’s findings indicate that THBS4 could be a potential biomarker for predicting the risk of lymph node metastasis in papillary thyroid microcarcinoma, thus potentially guiding more personalized surgical interventions. …”
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Transcriptomic Insights into Salt Stress Tolerance Mechanisms in <i>Melia azedarach</i>: 24-Epibrassinolide-Mediated Modulation of Auxin and ABA Signaling Pathways by Xiaoxian Li, Zin Myo Htet, Hong Chen, Jianbing Liu, Fangyuan Yu

“…This study investigates the molecular basis of salt stress responses in <i>Melia azedarach</i> L. and the modulating role of 24-epibrassinolide (EBR) through transcriptomic analysis. While salt stress significantly inhibited seedling growth, EBR application substantially mitigated these effects. …”
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Transcriptomics and non-targeted metabolomics provide mechanistic insights into the improvement of the growth performance and meat quality of lambs supplemented with fermented Lyci... by Jiale Liao, Wencan Ke, Bing Wang, Min Du, Qiang Lu, Yajun Zhang, Guijie Zhang

“…Post-mortem meat quality was also improved by FLBR, as evidenced by enhanced total antioxidant capacity, superoxide dismutase activity, pH, redness (a∗), tenderness and water holding capacity (P < 0.05 or P < 0.01), alongside a reduction in the malonaldehyde content (P < 0.001). Transcriptomic analysis identified 962 differentially expressed genes (DEGs, FLBR vs CON) and 782 DEGs (FLBR vs LBR) in LT, and 1313 DEGs (FLBR vs CON) and 1221 DEGs (FLBR vs LBR) in IMF. …”
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Potential effect of Wolbachia on virus restriction in the spider mite T. truncatus by Lucas Yago Melo Ferreira, João Pedro Nunes Santos, David Gabriel do Nascimento Souza, Lixsy Celeste Bernardez Orellana, Sabrina Ferreira de Santana, Anderson Gonçalves Sousa, Paula Luize Camargos Fonseca, Amanda Gabrielly Santana Silva, Vinicius Castro Santos, Isaque João da Silva de Faria, Roenick Proveti Olmo, Luis Gustavo Carvalho Pacheco, Marcio Gilberto Cardoso Costa, Carlos Priminho Pirovani, Anibal Ramadan Oliveira, Eric Roberto Guimarães Rocha Aguiar

“…However, the viral restriction phenotype vanishes in co-infected mites. Transcriptomics analysis of singly-infected mites revealed upregulation of piRNA and autophagy-related genes, while lipid metabolism processes-related genes were downregulated, indicating an endosymbiont-sharing mechanisms of viral interference. …”
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Peroxiredoxin 1-Toll-like receptor 4-p65 axis inhibits receptor activator of nuclear factor kappa-B ligand-mediated osteoclast differentiation by Jisu Park, Sanggil Kim, Hye-Yeon Jung, Eun Hwan Bae, Minhye Shin, Jae-Il Park, So-Young Choi, Sun-Ju Yi, Kyunghwan Kim

“…Utilizing pharmacological inhibitors, we reveal that PRDX1 inhibits osteoclastogenesis through both TLR4/TRIF and TLR4/MyD88 pathways. Transcriptome analysis revealed PRDX1-mediated alterations in gene expression, particularly upregulating serum amyloid A3 (Saa3) and aconitate decarboxylase 1 (Acod1). …”
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Single-nucleus transcriptomics reveals a distinct microglial state and increased MSR1-mediated phagocytosis as common features across dementia subtypes by Sook-Yoong Chia, Mengwei Li, Zhihong Li, Haitao Tu, Jolene Wei Ling Lee, Lifeng Qiu, Jingjing Ling, Richard Reynolds, Salvatore Albani, Eng-King Tan, Adeline Su Lyn Ng, Jinmiao Chen, Li Zeng

“…Abstract Background Alzheimer’s disease (AD), dementia with Lewy bodies (DLB), and Parkinson’s disease dementia (PDD) collectively represent the majority of dementia cases worldwide. While these subtypes share clinical, genetic, and pathological features, their transcriptomic similarities and differences remain poorly understood. …”
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Comparative Physiological and Transcriptomics Profiling Provides Integrated Insight into Melatonin Mediated Salt and Copper Stress Tolerance in <i>Selenicereus undatus</i> L. by Darya Khan, Xin Yang, Gong He, Raja Asad Ali Khan, Babar Usman, Liu Hui, Aamir Ali Khokhar, Qamar U Zaman, Hua-Feng Wang

“…Antioxidant activities were also modulated by stress. Transcriptomic analysis revealed 21 differentially expressed genes (DEGs) common across stress treatments and 13 DEGs specific to combined melatonin with stress treatments involved in stress signaling, secondary metabolite biosynthesis, and photosynthesis. …”
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Poneratoxin as a key tool for investigating the relationship between sodium channel hypersensitivity and impaired nerve cell function by Zirui Lü, Xiandong Dai, Jianjie Xu, Mu Zhu, Bo Chen, Yongbiao Guo, Zhenhua Gao, Fanhua Meng

“…In this study, for the first time, we conducted the evaluation of the excitotoxicity of PoTX and performed an in-depth analysis of transcriptomics and proteomics in vitro to elucidate its impact on the nervous system and underlying pharmacological mechanisms. …”
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Multi-omics characterization of diabetic nephropathy in the db/db mouse model of type 2 diabetes by Liping Wang, Ran Zhou, Guanghui Li, Xiaodan Zhang, Yan Li, Yinchen Shen, Junwei Fang

“…Orthogonal projection to latent structures-discriminant analysis (OPLS-DA) was applied to identify significant metabolic perturbations, while bidirectional O2PLS integration elucidated metabolic-transcriptomic correlations. …”
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Transcriptomic and Metabolomic Analyses Reveal the Attenuating Role of Cordycepin and <i>Cordyceps militaris</i> Extract on Acute Liver Injury Induced by LPS in Piglets by Ding Tan, Endian Li, Shijie Xiong, Yue Sun, Wenbo Cheng, Yong Su, Yang Lu

“…Compared with LPS, the transcriptomic analysis indicated that CPN supplementation significantly downregulated cell adhesion molecules, while CME supplementation significantly downregulated inflammatory mediator regulation of TRP channels, complement and coagulation cascades and cytokine-cytokine receptor interaction. …”
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Vitamin D exerts endogenous control over TH2 cell fate and immune plasticity by Vrushali D. Fangal, Ayşe Kılıç, Hooman Mirzakhani, Augusto A. Litonjua, Marie B. Demay, Bruce D. Levy, Scott T. Weiss

“…Summary: Circulating Vitamin D (Vit-D) has emerged as a potent immune modulator in asthma, yet its direct impact on TH2 cell regulation, the central effectors of allergic inflammation, remains unclear. Preliminary transcriptomic analysis of neonatal cord blood revealed that gestational Vit-D deficiency corresponds to elevated adaptive and innate immune responses, driven by TH2 immunity and antimicrobial responses related to asthma inflammation. …”
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Impact of dietary inclusion of bile acid and fat percent on growth, intestinal histomorphology, immune-physiological and transcriptomic responses of Nile tilapia (Oreochromis nilot... by Yi Yuan, Amira A. Omar, Wasseem Emam, Radi A. Mohamed

“…Fish-fed BA-supplemented diets had higher intestinal villus height, lysozyme activity, superoxide dismutase and catalase activities, and lower malonaldehyde concentration. Gene expression analysis revealed that BA supplementation upregulated (P &lt; 0.05) the expression of antioxidant-related genes (SOD, GPX, and CAT), growth-related genes (GHr1 and IGF1), and intestinal mucin gene (MUC2) while downregulating (P &lt; 0.05) the expression of fatty acid synthase (FAS) and pro-inflammatory genes (IL-1β and TNF-α). …”
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Characterizing tumor nicroenvironment features and identifying potential therapeutic targets in patients with diabetes mellitus and pancreatic cancer based on single-cell transcrip... by PENG Han, PAN Yuwei, WANG Xuesong

“…Method‍　‍By integrating single-cell transcriptome and bulk transcriptome data, bioinformatics analysis was conducted to compare the characteristics of tumor cells and tumor immune microenvironment between PDAC patients with DM (DM group) and those without DM (non-DM group). …”
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Transcriptome and Metabolome Analyses of <i>Taxus chinensis</i> var. <i>mairei</i> Tissues Provide New Insights into the Regulation of Paclitaxel Biosynthesis by Luyuan Jiang, Yanyan Li, Xiaoyang Jiang, Fenjuan Shao, Wenli Wu, Fan Xu, Iain Wilson, Angela Hoffman, Yanfang Yang, Deyou Qiu

“…In this study, we conducted integrated transcriptomic and metabolomic analyses of the root, leaf, shoot, bark, and wood of <i>Taxus chinensis</i> var. …”
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Gill transcriptome profiling reveals adaptation to brackish water in a selectively bred hybrid tilapia (Oreochromis niloticus x O. aureus) strain by Xiaofei Yu, July B. Ariñez, Priadi Setyawan, Zhitian Wu, Muhammad Hunaina Fariduddin Aththar, Mark Camara, Yang Fang, Martien A.M. Groenen, Hans Komen, John W.M. Bastiaansen, Hendrik-Jan Megens

“…Here, we investigated the salinity tolerance of this strain by performing a transcriptomic analysis using offsprings from the fifth generation of a breeding population. …”
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