The acquisition of additional control over quorum sensing regulation reduces the variability of final cell density in Burkholderia by Marco Fondi, Christopher Riccardi, Francesca Di Patti, Francesca Vaccaro, Francesca Coscione, Alessio Mengoni, Elena Perrin

“…However, the selective advantages provided by these alternative configurations on QS-related phenotypes is poorly predictable only based on their underlying network structure. …”
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Sex differences in autism spectrum disorder using class imbalance adjusted functional connectivity by Jong Young Namgung, Jongmin Mun, Yeongjun Park, Jaeoh Kim, Bo-yong Park

“…The sex-related differences in the gradients were highly associated with higher-order cognitive control processes. Transcriptomic association analysis provided potential biological underpinnings, specifying gene enrichment in the cortex, thalamus, and striatum during development. …”
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Multiomics integration and machine learning reveal prognostic programmed cell death signatures in gastric cancer by Zihao Bai, Hao Wang, Jingru Han, Jia An, Zhaocong Yang, Xuming Mo

“…The relationship between GMPS and immune therapy response, alongside gastric cancer’s microenvironmental features, provides insights for personalized treatment.…”
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The distinctive signature of regulatory CD4 T cells committed in the human thymus by Alexandre A. S. F. Raposo, Susana Paço, Miguel Ângelo-Dias, Pedro Rosmaninho, Afonso R. M. Almeida, Afonso R. M. Almeida, Ana E. Sousa, Ana E. Sousa

“…We established the human tTreg Expression Signature by comparing genome-wide transcriptomic profiles between tTregs and their conventional counterparts (tTconvs). …”
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Development and pan-cancer validation of an epigenetics-based random survival forest model for prognosis prediction and drug response in OS by Chaoyi Yin, Kede Chi, Zhiqing Chen, Shabin Zhuang, Yongsheng Ye, Binshan Zhang, Cailiang Cai

“…BackgroundOsteosarcoma (OS) exhibits significant epigenetic heterogeneity, yet its systematic characterization and clinical implications remain largely unexplored.MethodsWe analyzed single-cell transcriptomes of five primary OS samples, identifying cell type-specific epigenetic features and their evolutionary trajectories. …”
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A Comparison of Computational Approaches for Intron Retention Detection by Jiantao Zheng, Cuixiang Lin, Zhenpeng Wu, Hong-Dong Li

“…This systematic analysis provides helpful guidance for interrogating transcriptomic data from the point of view of IR.…”
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A novel antidepressant mechanism of baicalin: enhancing KIF5A-mediated axoplasmic transport and vesicular trafficking in glutamatergic neurons by Shuaifei Lu, Shuaifei Lu, Jiduo Shen, Jiduo Shen, Xiaohui Jin, Xiaohui Jin, Changjing Zhang, Changjing Zhang, Baoying Wang, Baoying Wang, Xianghua Liu, Xianghua Liu, Ming Bai, Ming Bai, Erping Xu, Erping Xu, Xiangli Yan, Xiangli Yan, Yucheng Li, Yucheng Li

“…Hippocampal neuronal pathology was examined using transmission electron microscopy (TEM), Nissl, and Golgi staining. Transcriptomic analysis was conducted to explore the molecular mechanisms of baicalin. …”
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Identification and validation of shared biomarkers and drug repurposing in psoriasis and Crohn’s disease: integrating bioinformatics, machine learning, and experimental approaches... by Xiaolong Li, Xiaolong Li, Hui Cao, Mutian Niu, Mutian Niu, Qingbo Liu, Bin Liang, Junfeng Hou, Junfeng Hou, Jian Tu, Jian Tu, Jintao Gao, Jintao Gao

“…Immune infiltration analysis underscored the involvement of hub genes in immune regulation, while single-cell transcriptomic analysis revealed the cellular localization of these hub genes. …”
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GDF15 is associated with hepatocellular senescence and correlates with mortality in patients with alcohol-associated hepatitis by Teresa Rubio-Tomás, David Martí-Aguado, Delia Blaya, Silvia Ariño, Beatriz Aguilar-Bravo, Raquel A. Martínez García de la Torre, Marc Miravet-Marti, Raquel Ferrer-Lorente, Laura Zanatto, Zengqing Xu, Laura Garcia-Tercero, Carlos Mateos-Sánchez, Juan José Lozano, Isabella Dotti, Johanne Poisson, Marion Tanguy, Azucena Salas, Pierre-Emmanuel Rautou, Ramon Bataller, Pau Sancho-Bru

“…Methods: Senescence was evaluated in transcriptomic data from patients at different ALD stages: advanced fibrosis (n = 10), cirrhosis (n = 10), and AH (n = 29). …”
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Pharmacological effects and mechanisms of Xuanfei Baidu Decoction in the treatment of viral pneumonia by Jingsheng Zhang, Bo Pang, Qiyue Sun, Jing Sun, Shan Cao, Yingli Xu, Yu Zhang, Xinqi Deng, Shanshan Guo, Lei Bao, Zihan Geng, Shuran Li, Ronghua Zhao, Daohan Wang, Xiaolan Cui, Bin Qu, Yu Wang

“…Proteomics and single-cell transcriptomic analyses were conducted to explore the potential mechanisms underlying XFBD’s pharmacological effects. …”
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Genome-wide identification and functional characterization of the LBD transcription factor gene family in Zanthoxylum armatum DC. reveal its potential role in leaf variation by Yifei Deng, Chong Sun, Xueqian Fu, Yuan Guo, Yongxing Zhu, Chongyu Liu, Ruxin Xu, Han Liu, Qiang Li, Ning Tang, Mi Kuang, Wenying Yang, Xia Liu, Zexiong Chen

“…Our findings will not only enhance our understanding of the genetic mechanisms underlying the adaptive variation in Z. armatum but also provide valuable resources for the genetic improvement of this plant.…”
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NAC transcription factors are key regulators of Brassinolide-Enhanced drought tolerance in Camellia oil tree by Kaizheng Lu, Yiyang Gu, YiXin Du, Yaxuan Yao, Xiaofeng Tan, Lichao Wu, Junqin Zhou, Jun Yuan

“…Leaf anatomical observation, hormone quantification, and transcriptomic profiling were performed on leaf samples collected at days 2, 4, and 6 following treatments. …”
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WDR36 Regulates Trophectoderm Differentiation During Human Preimplantation Embryonic Development Through Glycolytic Metabolism by Shiyu An, Shuyue Hou, Feifei Xu, Huanyu Yan, Wenyi Zhang, Jinfeng Xiang, Haoran Chen, Hanwen Zhang, Lingling Dong, Xiaobin Sun, Ran Huo, Yun Chen, Xi Wang, Yang Yang

“…Taken together, the study has established a mechanistic connection between WDR36, glucose metabolism, and cell fate determination during early embryonic lineage commitment, which may provide potential insights into novel therapeutic targets for early adverse pregnancy interventions.…”
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SMAD3 and HIF-1α orchestrate metabolic transition to aerobic glycolysis as a critical prerequisite for spontaneous reprogramming of spermatogonial stem cells by Yihui Cai, Jian Wen, Hongyang Liu, Rui Wei, Xiaoxiao Li, Yao Dong, Keren Cheng, Kang Zou

“…Here we employed a multi-omics approach, integrating transcriptomics, metabolomics, and DNA methylation analyses to focus on the interplay between exogenous growth factors, metabolic pathways, and signaling cascades, particularly the role of SMAD3 in these networks. …”
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Intranasally administrated fusion-inhibitory lipopeptides block SARS-CoV-2 infection in mice and enable long-term protective immunity by Said Mougari, Valérie Favède, Camilla Predella, Olivier Reynard, Stephanie Durand, Magalie Mazelier, Edoardo Pizzioli, Didier Decimo, Francesca T. Bovier, Lauren M. Lapsley, Candace Castagna, Nicole A. P. Lieberman, Guillaume Noel, Cyrille Mathieu, Bernard Malissen, Thomas Briese, Alexander L. Greninger, Christopher A. Alabi, N. Valerio Dorrello, Stéphane Marot, Anne-Geneviève Marcelin, Ana Zarubica, Anne Moscona, Matteo Porotto, Branka Horvat

“…Intranasal administration in mice allows the maintenance of homeostatic transcriptomic immune profile in lungs, prevents body-weight loss, decreases viral load and shedding, and protects mice from death caused by SARS-CoV-2 variants. …”
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Astrocytic BDNF Modulates Sensitivity to Stress-Induced Anxiety-Like Behaviors by Wei-Peng Li, Gui-Yu Liu, Shi-Yun Wang, Jiao Hu, Wen-Juan Ji, Jun-Ming Zhu, Qing-Yu Chang, Tian-Yi Li, Guo-Rong Wei, Jian-Qing Shang, Hong-Zhan Li, Fu-Hua Peng, Yun-Yan Zhao, Xiao-Hong Su, Wei Xie

“…Our study provides critical mechanistic insights into astrocytic regulation of anxiety sensitivity and highlights astrocytic BDNF as a promising therapeutic target for stress-related anxiety disorders.…”
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Cadmium exposure promotes inflammation through the PPAR signaling pathway in the small intestine and colon of Hu sheep by Huimin Zhang, Shuo Yan, Ruilin Du, Yue Xue, Wenna Yao, Teligun, Yulong Zhao, Yongfa Li, Hanggai Bao, Shuo Cao, Xihe Li, Siqin Bao, Yongli Song

“…We revealed for the first time the mechanism of intestinal injury in Hu sheeps under cadmium environmental exposure and provided new prevention and treatment methods of intestinal diseases under the environmental exposure to trace metals.…”
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The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality by David A. Salamanca-Díaz, Helen R. Horkan, Helena García-Castro, Elena Emili, Miguel Salinas-Saavedra, Alberto Pérez-Posada, Maria Eleonora Rossi, Marta Álvarez-Presas, Rowan Mac Gabhann, Paula Hillenbrand, Febrimarsa, Camille Curantz, Paris K. Weavers, Yasmine Lund-Ricard, Tassilo Förg, Manuel H. Michaca, Steven M. Sanders, Nathan J. Kenny, Jordi Paps, Uri Frank, Jordi Solana

“…In summary, the Hydractinia cell atlas provides insights into the cellular and molecular mechanisms underpinning coloniality.…”
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Synphilin-1 regulates mechanotransduction in rigidity sensing through interaction with zyxin by Seok Gi Kim, Jinyan Li, Ji Su Hwang, Muhammad Anwar Ul Hassan, Ye Eun Sim, Ju Yeon Lee, Jung-Soon Mo, Myeong Ok Kim, Gwang Lee, Sungsu Park

“…Molecular changes are analyzed using RNA sequencing-based transcriptomic and liquid chromatography-tandem mass spectrometry-based proteomic analyses. …”
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Mature tertiary lymphoid structures evoke intra-tumoral T and B cell responses via progenitor exhausted CD4+ T cells in head and neck cancer by Hao Li, Meng-Jie Zhang, Boxin Zhang, Wen-Ping Lin, Shu-Jin Li, Dian Xiong, Qing Wang, Wen-Da Wang, Qi-Chao Yang, Cong-Fa Huang, Wei-Wei Deng, Zhi-Jun Sun

“…Furthermore, patients with mTLS manifest improved overall survival and response to ICB compared to those with non-mTLS. Overall, our study provides insights into mechanisms underlying mTLS-mediated intra-tumoral immunity events against cancer.…”
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