Elucidating the Differential Mechanisms of Jingui Shenqi Pill and Mingmu Dihuang Pill in the Treatment of Diabetic Nephropathy Based on Yin-Yang Theory by Bi S, Xu Z, Yuan A, Wang Z, Liu Y, Yu B, Tian J, Liu C, Qiao L, Wang Z, Zhang Y

“…In vitro, JGSQ alleviated fibrosis and enhanced adhesion via FN and E-cad, while MMDH reduced interstitial fibrosis via FN and VIM. …”
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TMF Attenuates Cognitive Impairment and Neuroinflammation by Inhibiting the MAPK/NF-κB Pathway in Alzheimer’s Disease: A Multi-Omics Analysis by Yonglin Liu, Xi Xu, Xiaoming Wu, Guodong Yang, Jiaxin Luo, Xinli Liang, Jie Chen, Yiguang Li

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The intensity of the transcriptional response varies across infection with distinct viral strains in an insect host by Allyson M. Ray, Anja Tehel, Jason L. Rasgon, Robert J. Paxton, Christina M. Grozinger

“…Deformed wing virus (DWV) is one of the most damaging viruses of honey bees (Apis mellifera) across the globe, with variant DWV-B currently expanding at the expense of variant DWV-A. While previous research has characterized general host transcriptomic responses to viral exposure, host responses to different DWV strains have not been fully explored. …”
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The Response Characteristics of One <i>Saccharomyces cerevisiae</i> Strain Under Continuous Passage in Artificial Culture Medium by Tengyu Ma, Hongguang Zhu, Jiajia Yin, Yu Tian, Wenjing Yan, Haixin Sun

“…It thrived in a pH range of 4–5.5 and efficiently utilized various carbon and nitrogen sources; (2) After serial subculturing, the strain’s ethanol production capacity and fermentation rate partially declined and then stabilized, while maintaining strong tolerance to high ethanol concentrations and hyperosmotic stress; (3) Transcriptomic analysis revealed significant differential expression of genes related to lipid metabolism, amino acid metabolism, and other pathways under high-glucose stress following continuous subculturing. …”
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Integrated Multi-Omics Analysis of the Developmental Stages of <i>Antheraea pernyi</i> Pupae: Dynamic Changes in Metabolite Profiles and Gene Expression by Shuhui Ma, Yongxin Sun, Yajie Li, Xuejun Li, Zhixin Wen, Rui Mi, Nan Meng, Xingfan Du

“…This study integrated non-targeted metabolomics and transcriptomics to investigate dynamic changes in <i>Antheraea pernyi</i> pupae across five developmental stages. …”
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Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes by Mengshi Zhang, Changyi Zhang, Anayancy Ramos, Rachel J. Whitaker, Marvin Whiteley

“…This cross-domain framework enables more accurate functional inference in microbiomes without requiring organism-specific proteomic data, offering a powerful new tool for microbial ecology, systems biology, and functional genomics.IMPORTANCEDeciphering the biology of natural microbial communities is limited by the lack of functional data. While transcriptomics enables gene expression profiling, mRNA levels often fail to predict protein abundance, the primary indicator of microbial function. …”
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Shared transcriptional regulators and network rewiring identify therapeutic targets linking type 2 diabetes mellitus and hypertension by Claudia Desireé Norzagaray-Valenzuela, Claudia Desireé Norzagaray-Valenzuela, Marco Antonio Valdez-Flores, Josue Camberos-Barraza, Josue Camberos-Barraza, Alberto Kousuke De la Herrán-Arita, Juan Fidel Osuna-Ramos, Javier Magaña-Gómez, Carla Angulo-Rojo, Alma Marlene Guadrón-Llanos, Katia Aviña-Padilla, Loranda Calderón-Zamora

“…Protein interaction networks revealed key hub genes such as GNB1, JAK1, and RPS3 as T2DM-specific hubs, while MAPK1, BUB1B, and RPS6 were central in HTN. …”
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The impact of Sarcocystis infection on lamb flavor metabolites and its underlying molecular mechanisms by Kang Zhang, Huan Teng, Huan Teng, Li Zhu, Bin Ni, Lai Jiewei, Li Shanshan, Zhao Yunong, Xiao Guo, DanQu Lamu

“…Phenolic and acidic metabolites were markedly upregulated, intensifying bitterness and sourness, while ketone and lactone metabolites were downregulated, reducing fatty and creamy aromas. …”
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Integrative profiling of lung cancer biomarkers EGFR, ALK, KRAS, and PD-1 with emphasis on nanomaterials-assisted immunomodulation and targeted therapy by Li Peng, Hongmei Li, Wencai Yan, Yingjie Liu, Haihao Zhu, Yingcai Hong

“…Docking results showed strong EGFR–Gefitinib affinity (−5.94 kcal/mol, Kd 4.38 × 10-5 M), while KRAS inhibitors Adagrasib and Sotorasib demonstrated moderate binding (−3.94 and −3.72 kcal/mol, respectively). …”
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Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility by Jing Yang, Lingtao Yang, Ying Zhou, Fengyang Cao, Hongkun Fang, Huan Ma, Jun Ren, Chunyu Huang, Lianghui Diao, Qiyuan Li, Qionghua Chen

“…Abstract Background Recurrent implantation failure (RIF) remains a significant barrier in assisted reproductive technology (ART), where multiple transfers of high-quality embryos fail to achieve pregnancy. While embryo-related factors have been extensively investigated, the contribution of endometrial dysfunction to RIF remains poorly characterized. …”
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Hepatocellular carcinoma hosts cholinergic neural cells and tumoral hepatocytes harboring targetable muscarinic receptors by Charlotte A. Hernandez, Claire Verzeroli, Armando Andres Roca Suarez, Abud-José Farca-Luna, Laurie Tonon, Roger Esteban-Fabró, Roser Pinyol, Marie-Laure Plissonnier, Ievgeniia Chicherova, Anaëlle Dubois, Pascale Bellaud, Marine Seffals, Bruno Turlin, Alain Fautrel, Gabriel Ichim, Michel Rivoire, Guillaume Passot, Zuzana Macek-Jilkova, Thomas Decaens, Alain Viari, Barbara Testoni, Sandra Rebouissou, Josep M. Llovet, Fabien Zoulim, Romain Parent

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A single-cell landscape of the regenerating spinal cord of zebrafish by Lei Yao, Xinyi Cai, Saishuai Yang, Yixing Song, Lingyan Xing, Guicai Li, Zhiming Cui, Jiajia Chen

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MOGAN for LUAD Subtype Classification by Integrating Three Omics Data Types by Haibin He, Longxing Wang, Mingyue Ma

“…Methods In this study, we used the Generative Adversarial Network (GAN) to mine transcriptomic, proteomic, and epigenomic information and generate an integrated data set. …”
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GePIF4 Increases the Multi-Flower/Capsule-Bearing Traits and Gastrodin Biosynthesis in <i>Gastrodia elata</i> by Yue Xu, Zhiqing Wu, Yugang Gao, Pu Zang, Xinyu Yang, Yan Zhao, Qun Liu

“…Sexual reproduction is a primary method to address this degeneration, while the number of flowers and capsules is directly related to sexual reproduction. …”
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Natural killer cell subpopulations in the peripheral blood of single ventricle/hypoplastic left heart syndrome patients via single-cell RNA sequencing by Hui-Qi Qu, Kushagra Goel, Kayleigh Ostberg, Diana J. Slater, Fengxiang Wang, James Snyder, Cuiping Hou, Garnet Eister, John J. Connolly, Michael March, Joseph T. Glessner, Joseph T. Glessner, Joseph T. Glessner, Charlly Kao, Hakon Hakonarson, Hakon Hakonarson, Hakon Hakonarson, Hakon Hakonarson, Hakon Hakonarson

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Organic Acids Metabolic Response and Transcription Factor Expression Changes of Highland Barley Seedlings Under Na₂SeO₃ Treatment by Xiaozhuo Wu, Huichun Xie, Jianxia Ma, Guigong Geng, Xiaoli Yang, Feng Qiao

“…With Na₂SeO₃ concentration increased, the pigment content, O₂⁻ production rate, and soluble protein content in highland barley seedlings decreased, while the contents of soluble sugar, MDA, and H₂O₂ increased. …”
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Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs by Frank Wessely, Martin Bartl, Reinhard Guthke, Pu Li, Stefan Schuster, Christoph Kaleta

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ASXL1 truncating variants in BOS and myeloid leukemia drive shared disruption of Wnt-signaling pathways but have differential isoform usage of RUNX3 by Isabella Lin, Zain Awamleh, Mili Sinvhal, Andrew Wan, Leroy Bondhus, Angela Wei, Bianca E. Russell, Rosanna Weksberg, Valerie A. Arboleda

“…Notably, our data revealed significant de-repression of posterior homeobox A (HOXA) genes and upregulation of Wnt-signaling and hematopoietic regulator HOXB4. While we discovered many shared epigenetic and transcriptomic features, we also identified differential splice isoforms in RUNX3 where the long isoform, p46, is preferentially expressed in BOS, while the shorter p44 isoform is expressed in AML-ASXL1. …”
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Single‐cell polyadenylation site mapping reveals 3′ isoform choice variability by Lars Velten, Simon Anders, Aleksandra Pekowska, Aino I Järvelin, Wolfgang Huber, Vicent Pelechano, Lars M Steinmetz

“…Here, we perform genome‐wide quantification of polyadenylation site usage in single mouse embryonic and neural stem cells using a novel single‐cell transcriptomic method, BATSeq. By applying BATBayes, a statistical framework for analyzing single‐cell isoform data, we find that while the developmental state of the cell globally determines isoform usage, single cells from the same state differ in the choice of isoforms. …”
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mNSF: multi-sample non-negative spatial factorization by Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O’Brien, Loyal A. Goff, Kasper D. Hansen

“…Through simulations and real data analysis, we demonstrate mNSF’s efficacy in identifying true factors, shared anatomical regions, and region-specific biological functions. mNSF’s performance is comparable to alignment-based methods when alignment is feasible, while enabling analysis in scenarios where spatial alignment is unfeasible. mNSF shows promise as a robust method for analyzing spatially resolved transcriptomics data across multiple samples.…”
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