Multi-omics reveals the mechanism of quality discrepancy between Gayal (Bos frontalis) and yellow cattle beef by Lin Han, Runqi Fu, Chunjia Jin, Huan Gao, Binlong Fu, Qian Li, Ye Yu, Min Qi, Jiawei Zhang, Shengyong Mao, Jing Leng

“…Conclusions These findings provide actionable insights into the genetic and microbial factors underlying beef quality, offering a foundation for enhancing local cattle resources, optimizing breeding programs, and advancing the production of premium beef to meet both market and dietary needs.…”
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α-Lipoic acid mitigates age-related macular degeneration via ferroptosis: integrative multi-omics and network pharmacology by Yaqiong Zhang, Yaqiong Zhang, Yuanyuan Chen, Chenglin Sun, Fang Li, Yin Shen, Yin Shen

“…BackgroundAge-related macular degeneration (AMD) is a leading cause of irreversible vision loss among the elderly. α-Lipoic acid (ALA), a naturally occurring antioxidant and iron-chelator, has shown potential in modulating ferroptosis, but its mechanism in AMD remains unclear.MethodsNetwork pharmacology, transcriptomic profiling, and machine learning were used to identify potential molecular targets of ALA in AMD. …”
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Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers by Jingni He, Devika Ganesamoorthy, Jessie J.-Y. Chang, Jianshu Zhang, Sharon L. Trevor, Kristen S. Gibbons, Stephen J. McPherson, Jessica C. Kling, Luregn J. Schlapbach, Antje Blumenthal, Lachlan J. M. Coin, RAPIDS Study Group

“…Abstract Background RNA sequencing of whole blood has been increasingly employed to find transcriptomic signatures of disease states. These studies traditionally utilize short-read sequencing of cDNA, missing important aspects of RNA expression such as differential isoform abundance and poly(A) tail length variation. …”
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Maternal exposure to polystyrene nanoplastics induces sex-specific cardiotoxicity in offspring mice by Xiuli Chen, Shenzhen Huang, Li Wang, Kan Liu, Haiying Wu

“…Heart tissues were collected and weighed, and the transcriptomes of the offspring hearts were sequenced and analyzed using high-throughput RNA sequencing. …”
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Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms by Hanqi Li, Jiayi Zhang, Yu Shi, Huanhuan Wang, Ruida Yang, Shaobo Wu, Yue Li, Xue Yang, Qingguang Liu, Liankang Sun

“…Investigating matrix stiffness-related signatures provides crucial insights into HCC prognosis and therapeutic response. …”
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Mechanism of mTOR/RILP-regulated autophagic flux in increased susceptibility to myocardial ischemia-reperfusion in diabetic mice by Jiyao Zhao, Wei Shi, Yan Zheng, Junjie Wang, Muzhao Yuan, Yultuz Anwar, Yuxuan He, Haiping Ma, Jianjiang Wu

“…A comprehensive understanding of the intrinsic mechanisms underlying this phenomenon is therefore of paramount importance.PurposesThe objective of this study is to investigate the potential mechanism of action between impaired autophagic flux and increased vulnerability in diabetic myocardium. This will provide a foundation for the clinical search for effective preventive and curative measures.MethodsThe transcriptomic alterations in autophagy-related genes following myocardial exposure to I/RI were analyzed by single-cell sequencing. …”
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A Halophilic Bacterium for Bioremediation of Saline–Alkali Land: The Triadic and Synergetic Response Mechanism of <i>Oceanobacillus picturae</i> DY09 to Salt Stress by Tianying Nie, Liuqing Wang, Yilan Liu, Siqi Fu, Jiahui Wang, Kunpeng Cui, Lu Wang

“…In this study, a trinity salt-tolerance-integrated strategy of “dynamic perception–hierarchical response–system synergy” of halophilic bacteria was initially proposed, which provided a research idea for exploring the salt–alkali-tolerant mechanism of halophilic bacteria and a theoretical basis for the further development and application of this strain.…”
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Investigating the action model of the resistance enhancement induced by bacterial volatile organic compounds against Botrytis cinerea in tomato fruit by Jianhua Chen, Kexin Cao, Kexin Cao, Xuan Lu, Ding Huang, Ruhong Ming, Rumei Lu, Rongshao Huang, Liangbo Li

“…This study provides new insights into the mechanisms by which VOCs fumigation manages postharvest grey mould in tomatoes.…”
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Age, sex, and cell type-resolved hypothalamic gene expression across the pubertal transition in mice by Dustin J. Sokolowski, Huayun Hou, Kyoko E. Yuki, Anna Roy, Cadia Chan, Wendy Choi, Mariela Faykoo-Martinez, Matt Hudson, Christina Corre, Liis Uusküla-Reimand, Anna Goldenberg, Mark R. Palmert, Michael D. Wilson

“…Conclusion Together, by incorporating multiple biological timepoints and using sex as a variable, we identified gene and cell-type changes that may participate in orchestrating the pubertal transition and provided a resource for future studies of postnatal hypothalamic gene regulation.…”
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The Role of Oxytocin Neurons in the Paraventricular Nucleus in Chronic-Sleep-Deprivation-Mediated Abnormal Cardiovascular Responses by Yifei Zhang, Yuxin Wang, Zhendong Xu, Xiangjie Kong, Hairong Wang, Zhibing Lu, Ming Chen, Linlin Bi

“…In this study, using an automated sleep deprivation system, mice were given chronic sleep deprivation (cSD) for 7 days, 6 h per day. cSD induced blood transcriptomic alterations accompanied by lower heart rate, higher blood pressure, and elevated cardiac autophagy/apoptosis. …”
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Foliar Fe2O3 nanoparticles enhance cadmium tolerance in Amaranthus hypochondriacus by modulating cell wall immobilization and antioxidant defenses by Yanfeng Hu, Jia You, Yue Xiang, Runze Tian, Jianli Wang, Zhongbao Shen, Yansheng Li

“…This work highlights the potential of Fe-NPs for Cd remediation in A. hypochondriacus, and provides the first evidence that Fe-NPs enhance Cd tolerance, at least partially, through WAKL-mediated Cd immobilization in the cell wall.…”
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<i>Cladophialophora guangxiense</i> sp. nov., a New Species of Dark Septate Endophyte, Mitigates Tomato Bacterial Wilt and Growth Promotion Activities by Xihong Wei, Yanyan Long, Yanlu Chen, Stanley Nyenje Mataka, Xue Jiang, Yi Zhou, Zhengxiang Sun, Ling Xie

“…It colonized tomato seedling roots, enhancing the activity of antioxidant and defensive enzyme systems. Transcriptomic and qPCR approaches were used to study the induction response of the strain HX2 infection by comparing the gene expression profiles. …”
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Artificial intelligence-driven genotype–epigenotype–phenotype approaches to resolve challenges in syndrome diagnosticsResearch in context by Christopher C.Y. Mak, Hannah Klinkhammer, Sanaa Choufani, Nikola Reko, Angela K. Christman, Elise Pisan, Martin M.C. Chui, Mianne Lee, Fiona Leduc, Jennifer C. Dempsey, Pedro A. Sanchez-Lara, Hannah M. Bombei, John A. Bernat, Laurence Faivre, Frederic Tran Mau-Them, Irene Valenzuela Palafoll, Natalie Canham, Ajoy Sarkar, Yuri A. Zarate, Bert Callewaert, Ewelina Bukowska-Olech, Aleksander Jamsheer, Andreas Zankl, Marjolaine Willems, Laura Duncan, Bertrand Isidor, Benjamin Cogne, Odile Boute, Clémence Vanlerberghe, Alice Goldenberg, Elliot Stolerman, Karen J. Low, Vianney Gilard, Jeanne Amiel, Angela E. Lin, Christopher T. Gordon, Dan Doherty, Peter M. Krawitz, Rosanna Weksberg, Tzung-Chien Hsieh, Brian H.Y. Chung

“…Funding: The specific funding of this article is provided in the acknowledgements section.…”
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Inhibition of Interleukin-33 to Reduce Glomerular Endothelial Inflammation in Diabetic Kidney Disease by Alexis Hofherr, Elena Liarte Marin, Barbara Musial, Asha Seth, Tim Slidel, James Conway, David Baker, Pernille B.L. Hansen, Benjamin Challis, Stefano Bartesaghi, Maria Bhat, Roberto Pecoits-Filho, Xiao Tu, Viknesh Selvarajah, Kevin Woollard, Hiddo J.L. Heerspink

“…The findings from the FRONTIER-1 study will provide valuable insights into the therapeutic potential of IL-33 inhibition in DKD.…”
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Cellular imbalance in proximal and distal lung of CFTR −/− sheep in utero and at birth by Shih-Hsing Leir, Svyatoslav Tkachenko, Alekh Paranjapye, Arnaud J. Van Wettere, Jenny L. Kerschner, Iuri Viotti Perisse, Cheyenne M. Marriott, Tayler Patrick, Ying Liu, Kenneth L. White, Irina A. Polejaeva, Ann Harris

“…Methods Here we used the sheep model of CF (CFTR −/− ) and age-matched wild-type (WT) sheep of the same breed to investigate the single cell transcriptomes of proximal and distal lung tissue at 80 days and 120 days of gestation and at term (147 days). …”
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Genome-wide association study identifies candidate SNP markers and genes associated with low nitrogen tolerance in Brassica napus by Jingdong Chen, Jingdong Chen, Lingli Xie, Xianfei Hou, Rui Yang, Jin Liu, Xigang Dai, Tianyuan Xue, Shuai Yin, Benbo Xu, Xuekun Zhang, Changli Zeng, Jinsong Xu

“…These findings broaden our understanding of the genetic mechanisms underlying LN tolerance and provide promising targets for breeding B. napus varieties with improved nitrogen use efficiency.…”
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Glutamate transporter SLC1A6 promotes resistance to immunotherapy in cancer by Chenchen Li, Yi Lin, Haoran Zheng, Hengda Zeng, Longhao Xu, Daqin Wu, Jianwen Lao, Peicong Cai, Shuai Liang, Chunhui Wang, Tianxin Lin, Wenlong Zhong

“…Targeting SLC1A6 may provide a promising therapeutic strategy for improving responses to neoadjuvant immunotherapy and advancing combination treatment approaches.…”
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Integrative analyses of single‐cell and bulk RNA sequencing reveal tumour microenvironment features associated with neoadjuvant immunochemotherapy response in oesophageal squamous... by Xianxian Wu, Xiaoxing Ye, Wei Ji, Xiangyang Yu, Ahuan Xie, Zichang Xiang, Zhilin Sui, Jiquan Tang, Zhentao Yu

“…Conclusions This study has unveiled a potential regulatory network among immune cells, stromal cells and malignant epithelial cells under different pathological response conditions and provides a valuable resource for discovering novel targeted therapies for ESCC.…”
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Advancements in biomarkers and machine learning for predicting of bronchopulmonary dysplasia and neonatal respiratory distress syndrome in preterm infants by Hanieh Talebi, Seyed Alireza Dastgheib, Maryam Vafapour, Reza Bahrami, Mohammad Golshan-Tafti, Mahsa Danaei, Sepideh Azizi, Amirhossein Shahbazi, Melina Pourkazemi, Maryam Yeganegi, Amirmasoud Shiri, Ali Masoudi, Heewa Rashnavadi, Hossein Neamatzadeh

“…Research into endoplasmic reticulum stress-related genes, differentially expressed genes, and ferroptosis-related genes provides valuable insights into BPD's pathophysiology. …”
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Enhancing Monacolin K and GABA Biosynthesis in <i>Monascus pilosus</i> via <i>GAD</i> Overexpression: Multi-Omics Elucidation of Regulatory Mechanisms by Wenlan Mo, Yiyang Cai, Simei Huang, Lishi Xiao, Yanfang Ye, Bin Yang, Chan Zhang, Zhiwei Huang

“…Based on previous transcriptomic analyses conducted in our laboratory, a significant positive correlation was identified between the expression level of the <i>GAD</i> gene and MK production in <i>M. pilosus</i>. …”
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