Multi-omics and machine learning-driven CD8+ T cell heterogeneity score for head and neck squamous cell carcinoma by Di He, Zhan Yang, Tian Zhang, Yaxian Luo, Lianjie Peng, Jiatao Yan, Tao Qiu, Jingyu Zhang, Luying Qin, Zhichao Liu, Mouyuan Sun

“…Utilizing eight machine learning methods, we identified the key gene OLR1. Single-cell analysis of HNSCC tissues and peripheral blood, along with spatial transcriptome analysis, revealed that OLR1 predominantly functions in macrophages, modulating the immune microenvironment of HNSCC. …”
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Jasmonic acid improves cadmium tolerance in rice (Oryza sativa) by reducing the production of nitric oxide by Ji Bo Yang, Hao Yu Wang, Jing Huang, Chuan Jin Shan, Jing Yan, Chong Wei Zhong, Die Hu, Qiang Zhang, Ren Fang Shen, Xiao Fang Zhu, Da Li Zeng

“…JA mitigated Cd toxicity by decreasing Cd absorption in root cell wall and shoot, which was achieved by up-regulating the expression of the Cd-chelation and efflux-related genes such as OsHMA3, OsABCG36 and OsCAL1; down-regulating the transcript level of the Cd uptake and translocation-related genes, including OsHMA2, OsCCX2, OsNRAMP1/5, and OsZIP5/7. …”
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Physiological and multi-omics analysis revealed the mechanism of arbuscular mycorrhizal fungi to cadmium toxicity in green onion by Kunhao Xie, Yixuan Chen, Xiaoqin Wang, Xiaoya Zhou, Yizhe Cheng, Xianchang Yu, Jun Wang, Mintao Sun, Yansu Li, Chaoxing He

“…Transcriptomic and metabolomic correlation analyses revealed that differentially expressed genes and metabolites in AMF-inoculated green onion under Cd stress were predominantly enriched in the “phenylpropanoid biosynthesis” and “phenylalanine metabolism” pathways, upregulated the expression of the HCT, PRDX6, HPD, MIF, and HMA3 genes, and accumulation of the phenylalanine, L-tyrosine, and 1-O-sinapoyl-β-glucose metabolites. …”
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Tissue-friendly dentin treatments as a potential element in revascularization protocol (ex-vivo study) by Hala Fayek Khalil, Nadia Ezz El Din Metwalli, Sara Magdy, Mohamed Shamel

“…Osteogenic media also induced significant gene upregulation. Conclusions Dual Rinse HEDP and curcumin are tissue-friendly. …”
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Comparison of characteristics and immune responses between paired human nasal and bronchial epithelial organoids by Lu Zhu, Wenhao Yang, Jiaxin Luo, Danli Lu, Yanan Hu, Rui Zhang, Yan Li, Li Qiu, Zelian Chen, Lina Chen, Hanmin Liu

“…However, the similarities and differences in gene expression patterns and immune responses between these two sites have not been extensively studied. …”
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RTEL1 is upregulated in gastric cancer and promotes tumor growth by Chunyu Yang, Suzeng Wang, Ge Gao, Peiwen Xu, Mengyuan Qian, Yuan Yin, Surui Yao, Zhaohui Huang, Zehua Bian

“…Notably, CDC23 and TRIP13 are potential downstream target genes of RTEL1, which may mediate its tumor-promoting effects in GC. …”
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Synthetic wheat as a new source of flour quality under drought conditions: Associations with solvent retention capacity. by Niloofar Mokhtari, Mohammad Mahdi Majidi, Aghafakhr Mirlohi

“…Synthetic hexaploid lines are proposed as high-potential germplasm for improving bread wheat by introducing new genes (biotic and abiotic stresses) lost during common wheat evolution. …”
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PCSK9 affects vascular senescence through the SIRT1 pathway by Yuqin Wang, Shaoqing Cao, Zhangyu Wang, Chengsi Li, Jiangping Ye, Yehong Liu, Tianhui Jin, Yuting Zhou, Wentao Su, Gangjun Zong

“…PCSK9 overexpression accelerated cell senescence, activated a large number of oxidative stress pathways, and increased the expression of senescence-related genes (including P16, P21, and P53). In addition, inhibition of the sirtuin 1 (SIRT)1 oxidative stress pathway can attenuate the aging-promoting effects of PCSK9, which are elevated as a result of LPS induction.The SIRT1 activator was more efficient than LPS alone in inducing the expression of senescence-related genes. …”
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Whole genome sequencing in early onset advanced heart failure by Erik Linnér, Tomasz Czuba, Olof Gidlöf, Jakob Lundgren, Entela Bollano, Maria Hellberg, Selvi Celik, Neha Pimpalwar, Philipp Rentzsch, Molly Martorella, Anders Gummesson, Olle Melander, Sebastian Albinsson, Göran Dellgren, Jan Borén, Anders Jeppsson, R. Thomas Lumbers, Sonia Shah, Johan Nilsson, Pradeep Natarajan, Tuuli Lappalainen, Malin Levin, Hans Ehrencrona, J. Gustav Smith

“…We performed deep-coverage whole genome sequencing (WGS) in 102 Swedish HTx recipients. Gene lists were compiled through a systematic literature review. …”
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Maternal exposure to tris (2-butoxyethyl) phosphate induces F0 female reproductive toxicity and offspring developmental toxicity in zebrafish by Anqi Dong, Wenqian Lei, Weiqi Zhou, Wenwen Li, Jianghua Wang

“…The observed impacts on the F0 generation were linked to a marked decrease in 17β-estradiol concentrations and disruptions in the gene expression patterns along the hypothalamic-pituitary-gonadal-liver (HPGL) axis. …”
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Liver macrophage-derived exosomal miRNA-342-3p promotes liver fibrosis by inhibiting HPCAL1 in stellate cells by Wenshuai Li, Lirong Chen, Qi Zhou, Tiansheng Huang, Wanwei Zheng, Feifei Luo, Zhong Guang Luo, Jun Zhang, Jie Liu

“…The functions of miR-342-3p in exosomes were verified by qPCR and luciferase reporter gene experiments with HSCs. The function of the target gene Hippocalcin-like protein 1 (HPCAL1) in HSCs was verified by Western blotting, qPCR, cellular immunofluorescence and co-IP in vivo and in vitro. …”
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Effects of Hydrogen-rich Water on Cariogenic Bacteria by Zhibin Liu, Eungyung Kim, Su-Hyung Hong, Kirim Kim, Eun-Kyong Kim, Myoung-Ok Kim

“…The expression of genes encoding glucosyltransferases (gtfB, gtfC, and gtfI) and glucan-binding proteins (gbpC and dblB) were also decreased in the EHW group compared to the control. …”
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Small cell lung cancer with EML4-ALK fusion: report of a case responding to ALK TKI and literature review by Mingyue Wang, Hongzhi Liu, Ruixin Zhang, Runyu Li, Xiaoyu Qin, Fangling Ning, Lijun Tian

“…Abstract Purpose With the continuous development and progress of next-generation gene sequencing technology, many types of anaplastic lymphoma kinase (ALK) rearrangement have been discovered. …”
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Chromosomal genome assembly resolves drug resistance loci in the parasitic nematode Teladorsagia circumcincta. by Jennifer McIntyre, Alison Morrison, Kirsty Maitland, Duncan Berger, Daniel R G Price, Sam Dougan, Dionysis Grigoriadis, Alan Tracey, Nancy Holroyd, Katie Bull, Hannah Rose Vineer, Mike J Glover, Eric R Morgan, Alasdair J Nisbet, Tom N McNeilly, Yvonne Bartley, Neil Sargison, Dave Bartley, Matt Berriman, James A Cotton, Eileen Devaney, Roz Laing, Stephen R Doyle

“…The genome resource was further improved via annotation of 22,948 genes, with manual curation of over 3,200 of these, resulting in a robust and near complete resource (96.3% complete protein BUSCOs) to support basic and applied research on this important veterinary pathogen. …”
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LASSO–MOGAT: a multi-omics graph attention framework for cancer classification by Fadi Alharbi, Aleksandar Vakanski, Murtada K. Elbashir, Mohanad Mohammed

“…Combining gene expression data with other types of omics data has been reported by numerous works to improve cancer classification outcomes. …”
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Induction of systemic resistance through calcium signaling in Arabidopsis exposed to air plasma-generated dinitrogen pentoxide. by Shota Sasaki, Hiroto Iwamoto, Keisuke Takashima, Masatsugu Toyota, Atsushi Higashitani, Toshiro Kaneko

“…In addition, jasmonic acid (JA)-related gene expression was induced within 10 minutes, and a significant upregulation of the defense-related gene PDF1.2 was observed after 1 day of exposure to N2O5 gas. …”
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Impact of leachate from boiled-water-treated plastic products on male reproductive health: Insights from transcriptomic and metabolomic profiling by Xinghua Yu, Rui Yao, Ge Meng, Lingan Zeng, Leyi Zhou, Yingkang Shen, Amali Upekshika Wijayaraja, Reshmi Hareendra Kariyapperuma, Wentao Xu, Yuxiang Mei, Xinyan Gu, Wen-Long Lei, Pengfei Zhang, Fei Sun

“…Furthermore, transcriptomic and metabolomic profiling were employed to identify key genes and metabolites related to plastic exposure. …”
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High-efficiency biodegradation of crude oil and p-hydroxybenzoic acid by Acinetobacter haemolyticus JS-1: Integrated characterization and genomic analysis by Weiyi Tao, Jijie Lu, Junzhang Lin, Mingshan Ding, Weidong Wang, Shuang Li

“…These genes are likely contributed to its high degradation efficiency. …”
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Feature selection in single-cell RNA sequencing data: a comprehensive evaluation by Petros Paplomatas, Konstantinos Lazaros, Georgios N. Dimitrakopoulos, Aristidis Vrahatis

“…Unlike bulk RNA sequencing, scRNA-seq allows for examining gene expression at the individual cell level, revealing cellular heterogeneity and identifying rare cell types. …”
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Molecular pathways in reproductive cancers: a focus on prostate and ovarian cancer by Ayodeji Folorunsho Ajayi, Mega Obukohwo Oyovwi, Oyedayo Phillips Akano, Grace Bosede Akanbi, Florence Bukola Adisa

“…In prostate cancer, recurrent mutations in genes like AR, TP53, and PTEN drive tumor growth and progression. …”
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