Development of a machine learning-based predictive risk model combining fatty acid metabolism and ferroptosis for immunotherapy response and prognosis in prostate cancer by Zhenwei Wang, Zhihong Dai, Yuren Gao, Zhongxiang Zhao, Zhen Li, Liang Wang, Xiang Gao, Qiuqiu Qiu, Xiaofu Qiu, Zhiyu Liu

“…Functional enrichment analysis revealed distinct pathway activities, with high-risk patients showing enrichment in immune-related and proliferative pathways, while low-risk patients were enriched in metabolic pathways. …”
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Matrix Metalloproteinase-2 Knockout and Heterozygote Mice Are Protected from Hydronephrosis and Kidney Fibrosis after Unilateral Ureteral Obstruction. by Maria K Tveitarås, Trude Skogstrand, Sabine Leh, Frank Helle, Bjarne M Iversen, Christos Chatziantoniou, Rolf K Reed, Michael Hultström

“…Mmp2+/- OK and Mmp2+/- CL showed 0.43±0.09% and 0.22±0.06% (p<0.05) positivity, respectively. Transcriptomic analysis showed that 26 genes (out of 48 examined) were differentially expressed by ANOVA (p<0.05). 25 genes were upregulated in Mmp2+/+ OK compared to Mmp2+/+ CL: Adamts1, -2, Col1a1, -2, -3a1, -4a1, -5a1, -5a2, Dcn, Fbln1, -5, Fmod, Fn1, Itga2, Loxl1, Mgp, Mmp2, -3, Nid1, Pdgfb, Spp1, Tgfb1, Timp2, Trf, Vim. …”
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Sublethal THPS accelerates Pseudomonas-associated steel corrosion by stimulating biofilm development and microbial electron uptake by Xin Shi, Yimeng Zhang, Ruiyong Zhang, Chengpeng Li, Can Wang, Xiao Wang, Wolfgang Sand, Jizhou Duan

“…This study investigated the corrosion behavior of the biofilm-forming Pseudomonas stutzeri on X70 pipeline steel under sublethal concentrations of tetrakis(hydroxymethyl) phosphonium sulfate (THPS) using cell counting, weight loss measurements, surface characterization, and transcriptomic analysis. The results revealed that THPS accelerated the corrosion of X70 steel in the presence of P. stutzeri, compared to THPS-free conditions. …”
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Molecular mechanisms and therapeutic targets of acute exacerbations of chronic obstructive pulmonary disease with Pseudomonas aeruginosa infection by Zhiwei Lin, Shuang Liu, Ke Zhang, Tianyu Feng, Yewei Luo, Yu Liu, Baoqing Sun, Luqian Zhou

“…Methods We employed a multi-omics approach, integrating proteomic analyses of bronchoalveolar lavage fluid (BALF) and plasma with transcriptomic analysis of peripheral blood. A discovery cohort of 40 AECOPD with P. aeruginosa infection patients and 20 healthy controls was analyzed, followed by validation in an independent cohort of 20 patients and 10 controls. …”
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VIBE: an R-package for VIsualization of Bulk RNA Expression data for therapeutic targeting and disease stratification by Indu Khatri, Saskia D. van Asten, Leandro F. Moreno, Brandon W. Higgs, Christiaan Klijn, Christiaan Klijn, Francis Blokzijl, Iris C. R. M. Kolder

“…BackgroundDevelopment of cancer treatments such as antibody-based therapy relies on several factors across the drug-target axis, including the specificity of target expression and characterization of downstream signaling pathways. While existing tools for analyzing and visualizing transcriptomic data offer evaluation of individual gene-level expression, they lack a comprehensive assessment of pathway-guided analysis, relevant for single- and dual-targeting therapeutics. …”
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Temporal changes in the proanthocyanidins to anthocyanins ratio during dormancy associate with bloom time variations in peach by Protiva Rani Das, Md Tabibul Islam, Jianyang Liu, Zongrang Liu, Chris Dardick, Sherif M. Sherif

“…Late-bloom cultivars had higher PA levels during endodormancy, while early-bloom cultivars had higher ACN levels during ecodormancy. …”
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Epiplakin expression is lost in psoriatic skin lesions and is downregulated by IFN-γ in ex vivo skin cultures by Hannes Kühtreiber, Corinne Drexler, Corinne Drexler, Melanie Salek, Lisa Auer, Johannes Griss, Michael Mildner, Peter Fuchs, Peter Fuchs

“…We therefore used single-cell RNA sequencing (scRNAseq) analysis, immunofluorescence, and ex vivo cytokine treatment of human skin explants to investigate EPPK1 regulation in psoriasis. …”
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A noncarcinoma mouse cell line is nonsusceptible to Newcastle disease virus established by spontaneous immortalization by Hanlue Li, Zijie Zhou, Chuanyu Chang, Weiwei Shi, Yuzhen Li, Qiaolin Wei, Fanxing Meng, Jianxia Tian, Qiqi Hao, Jinming Liu, Haijin Liu, Zengqi Yang, Sa Xiao

“…Transcriptomic analysis revealed that the non-susceptibility of SLM-21 may be related to its broadly activated antiviral pathways and fine-tuned regulation of the cell cycle and DNA damage. …”
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Horizontal gene transfer-mediated enhancement of gut antifungal defense facilitates host plant adaptation in an invasive pest by Shouke Zhang, Xiayu Li, Zikun Li, Yuxin Zhang, Yiping Wang, Letian Xu

“…Single-cell transcriptomics and spatiotemporal profiling confirmed gut-specific expression, and phylogenetic analysis traced HcuChiA to a bacterial donor. …”
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<i>Colletotrichum gloeosporioides</i> Swiftly Manipulates the Transcriptional Regulation in <i>Citrus sinensis</i> During the Early Infection Stage by Siyu Zhang, Xinyou Wang, Wei Zeng, Leijian Zhong, Xiaoyong Yuan, Zhigang Ouyang, Ruimin Li

“…In this study, we analyzed the physiological and transcriptomic changes in <i>Citrus sinensis</i> at different stages of incubation with <i>C. gloeosporioides</i>. …”
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Dissecting the connection between volatile organic compounds and cardiovascular disease: immune cell-mediated mechanism by Qi Cao, Jiajing Liu, Daiyao Lu, Junhuai Song, Qiming Yu, Jinkun Wen, Bin Zheng

“…Transcriptomic analysis and pathway enrichment were conducted to identify biological pathways linked to VOC exposure and immune dysregulation. …”
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A novel pilus-associated gene cluster is implicated in Streptococcus agalactiae virulence by Wanyou Xu, Qiangsheng Lu, Meijuan Tian, Lvfeng Yuan, Yangming Song, Qiaoying Zeng, Jie Peng

“…Further transcriptomic analysis revealed that the Tnfsf15 gene plays a critical role in the regulation of A909 strain pathogenicity mediated by the BP, AP1, and SrtC gene clusters during host infection.…”
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Oral exposure to PET microplastics induces the pancreatic immune response and oxidative stress in immature pigs by Karol Mierzejewski, Aleksandra Kurzyńska, Monika Golubska, Ismena Gałęcka, Jarosław Całka, Iwona Bogacka

“…A low dose changed the expression of one gene, while a high dose affected the expression of 86 genes. …”
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CXCR4/CXCL12 axis promotes lymphatic metastasis in tongue squamous cell carcinoma via PI3K/AKT signaling pathway by Huiquan Lou, Yichao Xia, Shengjie Shao, Xiang Liu, Zengzheng Li, Hongbin Yu, Yongsheng Li

“…In vivo, CXCR4 overexpression accelerated tumor growth and lymphatic metastasis, while CXCR4 inhibition showed opposite effects. Transcriptomic analysis revealed comprehensive molecular alterations regulated by CXCR4/CXCL12 signaling. …”
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Hepatocyte FoxO1 depletion exacerbates hepatic inflammation in MASH by targeting cystathionine γ-lyase by Hui-Ting Chen, Chen Huang, Jia-Wei Chen, Si-Qi Yang, Jie-Min Cheng, Yong-Qiang Li, Han-Qing Chen, Yong-Jian Zhou

“…Using hepatocyte-specific FoxO1-knockout (KO) mice fed a methionine-choline-deficient diet and LPS-treated FoxO1-KO cells, we demonstrated that FoxO1 depletion exacerbates hepatic inflammation, ballooning degeneration, and upregulates TNF-α, CXCL8, and CXCL2 in vivo and in vitro. Transcriptomic analysis revealed that FoxO1 deficiency upregulated pro-inflammatory pathways while suppressing cysteine/methionine metabolism, with a notable reduction in cystathionine γ-lyase (CTH) expression. …”
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Integrative network pharmacology and multi-omics reveal anisodamine hydrobromide’s multi-target mechanisms in sepsis by Ying Chen, Danlei Weng, Wei Shi, Shuxing Wei, Wenqing Ji, Xiya Wang, Yali Xu, Xiaoman Wang, Xue Mei, Shubin Guo

“…Ani HBr inhibited ELANE-driven NET formation (HR = 1.176), associated with immunosuppression and endothelial damage, while enhancing CCL5-related cytotoxic T-cell recruitment (HR = 0.810). …”
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Advancements in multi-omics research to address challenges in Alzheimer’s disease: a systems biology approach utilizing molecular biomarkers and innovative strategies by Madison Cardillo, Madison Cardillo, Keyura Katam, Keyura Katam, Prashanth Suravajhala, Prashanth Suravajhala

“…By 2050, we may see over 115 million people diagnosed with this devastating condition. Unfortunately, while we currently lack effective cures, there are preventative measures that can slow disease progression in symptomatic patients. …”
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Lymphocyte Subpopulations in the Healthy Human Lacrimal Gland and Their Variations With Age and Sex, Systematic Review 1960–2023 by Claudia M. Trujillo‐Vargas, Luisa María Rendón‐Macías, Ronald Yamil Paredes Guerrero, Cinta S. dePaiva, Jaiberth Antonio Cardona‐Arias

“…The methodological quality was evaluated with the STROBE guidelines. A meta‐analysis of three selected articles dichotomizing lymphocytic infiltrates according to age group was also performed. …”
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ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data. by Brett A McKinney, Bill C White, Diane E Grill, Peter W Li, Richard B Kennedy, Gregory A Poland, Ann L Oberg

“…Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. …”
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MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication by Jonathan Cahn, Michael Regulski, Jason Lynn, Evan Ernst, Cristiane de Santis Alves, Srividya Ramakrishnan, Kapeel Chougule, Sharon Wei, Zhenyuan Lu, Xiaosa Xu, Umamaheswari Ramu, Jorg Drenkow, Cassidy Danyko, Melissa Kramer, Arun Seetharam, Matthew B. Hufford, W. Richard McCombie, Doreen Ware, David Jackson, Michael C. Schatz, Thomas R. Gingeras, Robert A. Martienssen

“…Transcriptomic analysis reveals that pollen grains share features with endosperm, and express dozens of “proto-miRNAs” potential vestiges of gene drive and hybrid incompatibility. …”
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