Epigenetic suppression of creatine kinase B in adipocytes links endoplasmic reticulum stress to obesity-associated inflammation by Gianluca Renzi, Ivan Vlassakev, Mattias Hansen, Romane Higos, Simon Lecoutre, Merve Elmastas, Ondrej Hodek, Thomas Moritz, Lynn M. Alaeddine, Scott Frendo–Cumbo, Ingrid Dahlman, Alastair Kerr, Salwan Maqdasy, Niklas Mejhert, Mikael Rydén

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Exploring the ability of plasma pTau217, pTau181 and beta-amyloid in mirroring cerebrospinal fluid biomarker profile of Mild Cognitive Impairment by the fully automated Lumipulse®... by Marcella Catania, Claudia Battipaglia, Alberto Perego, Erika Salvi, Emanuela Maderna, Federico Angelo Cazzaniga, Paolo M. Rossini, Camillo Marra, Nicola Vanacore, Alberto Redolfi, Daniela Perani, Patrizia Spadin, Maria Cotelli, Stefano Cappa, Naike Caraglia, Pietro Tiraboschi, Fabrizio Tagliavini, Giuseppe Di Fede

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Detection of fusion events by RNA sequencing in FFPE versus freshly frozen colorectal cancer tissue samples by Maxim Sorokin, Maxim Sorokin, Maxim Sorokin, Maxim Sorokin, Vladimir Lyadov, Vladimir Lyadov, Vladimir Lyadov, Maria Suntsova, Marat Garipov, Anna Semenova, Natalia Popova, Egor Guguchkin, Rustam Heydarov, Marianna Zolotovskaia, Xiaowen Zhao, Qing Yan, Ye Wang, Evgeny Karpulevich, Anton Buzdin, Anton Buzdin, Anton Buzdin, Anton Buzdin

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Interrelationship between altered metabolites and the gut microbiota in people living with HIV with different immune responses to antiretroviral therapy by Xuebin Tian, Zhongyao Gao, Yiwen Xie, Xiangyun Lu, Yulong Zhao, Peng Yao, Mingqing Dong, Lifeng Yu, Nanping Wu

“…Conclusion: The multi-omics approach highlighted potential biomarkers for immune recovery in HIV, suggesting avenues for further research into treatment strategies.…”
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Effects of typical plant growth regulator chlormequat chloride on alkaloidal compounds in Corydalis yanhusuo and molecular mechanisms by Zixuan Du, Jiayin Cao, Jie Meng, Heng Zhou, Qing Hu, Ling Li, Yun Liao, Shui Miao, Wenting Li, Shen Ji, Tongshuai Wang

“…In conclusion, this study revealed a dose-dependent effect of chlormequat chloride on C. yanhusuo and its associated molecular mechanisms as determined by omics analysis.…”
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Novel predictive biomarkers for atonic postpartum hemorrhage as explored by proteomics and metabolomics by Jiangxue Qu, Hai Jiang, Huifeng Shi, Nana Huang, Jiawen Su, Yan Zhang, Lian Chen, Yangyu Zhao

“…In this study, we aimed to screen for potential predictive biomarkers for atonic PPH using combined omics approaches. Methods Collection of cervicovaginal fluid (CVF) samples from 27 women with atonic PPH and 32 women with normal delivery was performed for metabolomic (LC-MS/MS) and proteomic (LC-MS/MS) detection and subsequent confirmation experiments in this nested case-control study. …”
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An atlas of neuropathic pain-associated molecular pathological characteristics in the mouse spinal cord by Fu-Lu Dong, Lina Yu, Pei-Da Feng, Jin-Xuan Ren, Xue-Hui Bai, Jia-Qi Lin, De-Li Cao, Yu-Tao Deng, Yan Zhang, Hui-Hui Shen, Hao Gong, Wen-Xing Sun, Dong-Qiu Chi, Yixiao Mei, Longfei Ma, Ming-Zhe Yin, Meng-Na Li, Peng-Fei Zhang, Nan Hu, Bing-Lin Zhou, Ying Liu, Xuan-Jie Zheng, Yi-Fan Chen, Da Zhong, Yuan-Xiang Tao, Min Yan, Bao-Chun Jiang

“…In addition, for the first time, we systematically exhibit “cross-talk omics” between the DRG neurons and SC dorsal horn neurons and glial cells, indicating an altered communication profile under NP conditions. …”
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Pilot study of a ketogenic diet in bipolar disorder: a process evaluation by Benjamin P. Rigby, Nicole Needham, Helen Grossi, Ivana Kamenska, Iain H. Campbell, Ben Meadowcroft, Frances Creasy, Cheryl Fisher, Pankaj Bahuguna, John Norrie, Gerard Thompson, Melissa C. Gibbs, Maja Mitchell-Grigorjeva, Ailsa McLellan, Tessa Moses, Karl Burgess, Rachel Brown, Michael J. Thrippleton, Harry Campbell, Daniel J. Smith, Sharon A. Simpson

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Col1A1 as a new decoder of clinical features and immune microenvironment in ovarian cancer by Xiao Xiao, Fangyi Long, Shaolan Yu, Wengjuan Wu, Dayan Nie, Xiaoyan Ren, Wen Li, Xujuan Wang, Ling Yu, Pinghan Wang, Gang Wang

“…The TIMER and TISIDB databases to explore the potential relationship between COL1A1 expression and immune microenvironment in OC tissues. The LinkedOmics and INPUT2 databases were used to analyze differential gene expression in OC, This was followed by enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) annotations to identify and predict potential signaling pathways associated with COL1A1.ResultsOur study demonstrated that COL1A1 expression was significantly elevated in OC tissues compared to normal ovarian tissues. …”
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Multimodal data deep learning method for predicting symptomatic pneumonitis caused by lung cancer radiotherapy combined with immunotherapy by Mingyu Yang, Jianli Ma, Chengcheng Zhang, Liming Zhang, Jianyu Xu, Shilong Liu, Jian Li, Jiabin Han, Songliu Hu

“…This amalgamated model surpassed the performance of the radiomic feature model (AUC 0.811, 95% CI: 0.786-0.832, P value < 0.001), the clinical information model (AUC 0.711, 95% CI: 0.682-0.753, P value < 0.001), as well as the model that integrated omics attributes with clinical data (AUC 0.872, 95% CI: 0.845-0.896, P value < 0.001) utilizing deep neural networks (DNNs). …”
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Integrative transcriptomic and metabolomic reveals squalene alleviating the inflammatory response and enhancing immunity of hybrid grouper (♀ Epinephelus fuscoguttatus × ♂ E. lance... by Xiaobo Yan, Simiao Pan, Xiangxiang Suo, Weibin Huang, Tao Li, Shuang Zhang, Yuanzhi Yang, Beiping Tan, Xiaohui Dong

“…Therefore, the present study was designed to use corn oil as the main lipid source to create a model of inflammation or low immunity and investigate the regulatory effect of squalene on the immunity of grouper, and to perform hepatic transcriptomic and metabolomic assays of grouper using omics technology, with the aim of providing basic data for the study of the mechanism of squalene. …”
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The quality of Tibetan sheep meat from pastures was synergistically regulated by the rumen microbiota and related genes at different phenological stages by Xiaowei Chen, Yuzhu Sha, Xiu Liu, Yanyu He, Wenhao Li, Liangwei Yao, Jiqing Wang, Wenxin Yang, Qianling Chen, Min Gao, Wei Huang, Bin Ma, Bin Ma

“…In this study, RT-qPCR and 16S omics were employed to assess meat quality and intestinal microbiota. …”
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Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling by Walid Mottawea, Basit Yousuf, Salma Sultan, Tamer Ahmed, JuDong Yeo, Nico Hüttmann, Yingxi Li, Nour Elhouda Bouhlel, Hebatoallah Hassan, Xu Zhang, Zoran Minic, Riadh Hammami

“…First, we conducted a multi-omics profiling of MEVs’ contents from ex vivo and stool samples. …”
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DET induces apoptosis and suppresses tumor invasion in glioma cells via PI3K/AKT pathway by Rui Zhao, Mengran Wang, Zeyu Wu, Panpan Zhao, Huiling Dong, Yue Su, Chenghui Zhao, Min Qi, Shizhang Ling, Shizhang Ling, Xiaochun Jiang, Xiaochun Jiang

“…GBM-related targets were obtained through multi-omics approaches. A protein-protein interaction (PPI) network was constructed using Cytoscape and STRING, and target binding was evaluated through molecular docking. …”
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Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) by Lei Zhang, Wanting Zhang, Yingyin Cheng, Yutong Fang, Xin Guan, Ao Gong, Yanxin Jiang, You Duan, Lei Huang, Waqar Younas, Yaping Wang, Mijuan Shi, Xiao-Qin Xia

“…These findings not only provide new insights into the genome structure of the large-scale loach but also establish a crucial reference point for omics studies and serve as an essential genomic resource for breeding programs in this species.…”
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Mass cytometry: exploring the immune landscape of systemic autoimmune and inflammatory diseases in the past fourteen years by Aïcha Kante, Aïcha Kante, Mathieu F. Chevalier, Damien Sène, Damien Sène, Jeanne Chauffier, Jeanne Chauffier, Stéphane Mouly, Stéphane Mouly, Benjamin Glenn Chousterman, Benjamin Glenn Chousterman, Fériel Azibani, Benjamin Terrier, Benjamin Terrier, Théo Pezel, Théo Pezel, Cloé Comarmond, Cloé Comarmond

“…Future research designs could include mass cytometry findings in association to other -omics to stratify patients in adequate therapeutic arms and provide advancements in personalized therapies in the field of auto-immune and inflammatory diseases.…”
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Medium- to long-term health condition of patients post-COVID-19, exercise intolerance and potential mechanisms: A narrative review and perspective by Fabian Schwendinger, Denis Infanger, Debbie J Maurer, Thomas Radtke, Justin Carrard, Julia M Kröpfl, Aglaia Emmenegger, Henner Hanssen, Christoph Hauser, Udo Schwehr, Hans H Hirsch, Julijana Ivanisevic, Karoline Leuzinger, Aurélien E Martinez, Marc Maurer, Thomas Sigrist, Lukas Streese, Roland von Känel, Timo Hinrichs, Arno Schmidt-Trucksäss

“…Studies reporting blood biomarkers of disease-specific impairment and endothelial dysfunction yielded upregulated inflammation, hypercoagulability, organ and endothelial damage up to several months after infection. Omics’ scale lipid profiling studies provide preliminary evidence of alterations in several lipid subspecies, mostly during acute COVID-19, which might contribute to subsequent endothelial and cardiometabolic dysfunction. …”
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Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study by M. A. Kulyashov, R. Hamilton, Y. Afshin, S. K. Kolmykov, T. S. Sokolova, T. M. Khlebodarova, M. G. Kalyuzhnaya, I. R. Akberdin

“…The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20ZR, a prominent microbial chassis for methane capturing and valorization. …”
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Revealing the heterogeneity of treatment resistance in less‐defined subtype diffuse large B cell lymphoma patients by integrating programmed cell death patterns and liquid biopsy by Wei Hua, Jie Liu, Yue Li, Hua Yin, Hao‐Rui Shen, Jia‐Zhu Wu, Yi‐Lin Kong, Bi‐Hui Pan, Jun‐Heng Liang, Li Wang, Jian‐Yong Li, Rui Gao, Jin‐Hua Liang, Wei Xu

“…To identify robust prognostic biomarkers that can guide personalized management for less‐defined subtype DLBCL patients, we integrated multi‐omics data derived from 339 standard R‐CHOP‐treated patients diagnosed with less‐defined subtype DLBCL from three independent cohorts. …”
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scCamAge: A context-aware prediction engine for cellular age, aging-associated bioactivities, and morphometrics by Vishakha Gautam, Subhadeep Duari, Saveena Solanki, Mudit Gupta, Aayushi Mittal, Sakshi Arora, Anmol Aggarwal, Anmol Kumar Sharma, Sarthak Tyagi, Rathod Kunal Pankajbhai, Arushi Sharma, Sonam Chauhan, Shiva Satija, Suvendu Kumar, Sanjay Kumar Mohanty, Juhi Tayal, Nilesh Kumar Dixit, Debarka Sengupta, Anurag Mehta, Gaurav Ahuja

“…We present scCamAge, an advanced context-aware multimodal prediction engine that co-leverages image-based cellular spatiotemporal features at single-cell resolution alongside cellular morphometrics and aging-associated bioactivities such as genomic instability, mitochondrial dysfunction, vacuolar dynamics, reactive oxygen species levels, and epigenetic and proteasomal dysfunctions. scCamAge employed heterogeneous datasets comprising ∼1 million single yeast cells and was validated using pro-longevity drugs, genetic mutants, and stress-induced models. scCamAge also predicted a pro-longevity response in yeast cells under iterative thermal stress, confirmed using integrative omics analyses. Interestingly, scCamAge, trained solely on yeast images, without additional learning, surpasses generic models in predicting chemical and replication-induced senescence in human fibroblasts, indicating evolutionary conservation of aging-related morphometrics. …”
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