Single-cell and spatial analyses of the GDF family in tumors, with a focus on the prognostic and biological role of GDF15 in hepatocellular carcinoma by Xiaoqian Feng, Qian Huai, Fumin Zhang, Wenkang Yuan, Xingyu Li, Zhuo Yu, Hao Zhang, Yaoling Zhu, Xu Zhang, Baole Tao, Ying Dai, Yishan Du

“…Abstract Growth differentiation factors (GDFs) are a subfamily of the TGF-β superfamily whose expression increases in response to cellular stress and disease. Despite emerging cell- or animal-based evidence supporting an association between the GDF subfamily and cancer, systematic pan-cancer analyses of the GDF subfamily based on single-cell and spatial transcriptomes remains unavailable. …”
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Single-cell analysis reveals potential therapeutic markers of peripheral blood mononuclear cells from bladder cancer patients by Xingning Mao, Rirong Yang, Yunkun Yan, Yanyu Zeng, Mengying Bao, Rong Huang, Yan Dai, Qingyun Zhang, Yu Ye, Jiwen Cheng, Zengnan Mo, Haiying Zhang

“…Bladder cancer is the most prevalent malignancy of the urinary tract, with significant advancements in treatment achieved over recent decades. …”
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Carbamazepine-exposed earthworms are characterized by tissue-specific accumulation patterns and transcriptional profiles by Chubin Zhang, Filipe Cabreiro, Leon P. Barron, Stephen R. Stürzenbaum

“…Its mode of action is not species-specific and affects the nervous system of non-target organisms, including most likely the soil dwelling earthworms, which in turn has the potential to negatively impact soil quality. …”
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Comprehensive analysis of glycometabolism-related genes reveals PLOD2 as a prognostic biomarker and therapeutic target in gastric cancer by Wanchun Ye, Xiaolei Zhang, Zhongjie Tang, Yufeng Hu, Yuanliang Zheng, Yuping Yuan

“…Methods Transcriptomic and clinical data from GC patients were retrieved from TCGA and GEO databases. …”
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Combinatorial functionomics identifies HDAC6-dependent molecular vulnerability of radioresistant head and neck cancer by Sharon Pei Yi Chan, Celestia Pei Xuan Yeo, Boon Hao Hong, Evelyn Mui Cheng Tan, Chaw Yee Beh, Eugenia Li Ling Yeo, Dennis Jun Jie Poon, Pek Lim Chu, Khee Chee Soo, Melvin Lee Kiang Chua, Edward Kai-Hua Chow

“…Abstract Background Radiotherapy is the primary treatment modality for most head and neck cancers (HNCs). Despite the addition of chemotherapy to radiotherapy to enhance its tumoricidal effects, almost a third of HNC patients suffer from locoregional relapses. …”
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Localization is the key to action: regulatory peculiarities of lncRNAs by Joice de Faria Poloni, Fábio Henrique Schuster de Oliveira, Bruno César Feltes

“…To understand the transcriptomic profile of an individual cell in a multicellular organism, we must comprehend its surrounding environment and the cellular space where distinct molecular stimuli responses are located. …”
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Exploring salinity adaptation in teleost fish, focusing on omics perspectives on osmoregulation and gut microbiota by Evodia Moses Mkulo, Evodia Moses Mkulo, Evodia Moses Mkulo, Lukman Iddrisu, Mpwaga Alatwinusa Yohana, Anna Zheng, Anna Zheng, Anna Zheng, Jiahao Zhong, Jiahao Zhong, Jiahao Zhong, Minxuan Jin, Minxuan Jin, Minxuan Jin, Felix Danso, Linjuan Wang, Linjuan Wang, Linjuan Wang, Huijuan Zhang, Huijuan Zhang, Huijuan Zhang, Baogui Tang, Baogui Tang, Baogui Tang, Hui Zhou, Hui Zhou, Hui Zhou, Kwaku Amoah, Kwaku Amoah, Kwaku Amoah, Jiansheng Huang, Jiansheng Huang, Jiansheng Huang, Bei Wang, Bei Wang, Bei Wang, Zhongliang Wang, Zhongliang Wang, Zhongliang Wang, Zhongliang Wang

“…Transcriptomic analyses have identified key ion transport, osmoregulation, and stress response genes essential for adaptation, facilitating cellular adjustments and maintaining osmotic balance across habitats. …”
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Bioinformatics-based prognostic value and in vitro functional validation of PTK6 in cutaneous melanoma by Yanyan Niu, Yanyan Niu, Xiaoyu Liu, Aixiu Shi, Danli Tang, Xiaodong Yao, Yan Lu

“…The low-risk group was more sensitive to various chemotherapy drugs, and most immune checkpoint genes were negatively correlated with prognostic genes. …”
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STING regulates NETs formation by activating GSDMD in influenza viral pneumonia by Rongrong Huang, Rongrong Huang, Rongrong Huang, Ranran Chen, Ranran Chen, Ranran Chen, Lijuan Xing, Lijuan Xing, Lijuan Xing, Lianhao Wu, Lianhao Wu, Lianhao Wu, Wenwen Zhu, Junsong Jing, Junsong Jing, Junsong Jing, Ting Zhou, Yueguo Wu, Sheng Zhang, Zhenqiang You, Zhenqiang You, Zhenqiang You

“…BackgroundViral pneumonia is the most common and lethal pandemic disease, but there are no broad-spectrum antiviral drugs with high genetic barriers to resistance. …”
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Transitional CXCL14+ cancer‐associated fibroblasts enhance tumour metastasis and confer resistance to EGFR‐TKIs, revealing therapeutic vulnerability to filgotinib in lung adenocarc... by Weijiao Xu, Haitang Yang, Ke Xu, Anshun Zhu, Sean R. R. Hall, Yunxuan Jia, Baicheng Zhao, Enshuo Zhang, Gang Liu, Jianlin Xu, Thomas M. Marti, Ren‐Wang Peng, Patrick Dorn, Yongliang Niu, Xufeng Pan, Yajuan Zhang, Feng Yao

“…Methods We integrate multiple scRNA‐seq datasets to identify cell subclusters most relevant to tumor stage, patient survival, and EGFR–TKIs response. …”
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Integration of single-cell sequencing and mendelian randomization reveals novel causal pathways between monocytes and hepatocellular carcinoma by Jiang Yu, Jing Yu, Zhou Kang, Yong Peng

“…Abstract Background Hepatocellular carcinoma (HCC) represents one of the most prevalent malignant neoplasms worldwide, characterized by poor prognosis and low 5-year survival rates. …”
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Cellular and Molecular Atlas of Peripheral Blood Mononuclear Cells from a Pregnant Woman After Recovery from COVID-19 by Lili Du, Yingyu Liang, Xiaoyi Wang, Lijun Huang, Xingfei Pan, Jingsi Chen, Dunjin Chen, Dandan Shi

“…This study aimed to investigate the immune response of a pregnant woman who recovered from the coronavirus disease 2019 (COVID_RS) by using single-cell transcriptomic profiling of peripheral blood mononuclear cells (PBMCs) and to analyze the properties of different immune cell subsets. …”
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RNAi effector diversity in nematodes. by Johnathan J Dalzell, Paul McVeigh, Neil D Warnock, Makedonka Mitreva, David McK Bird, Pierre Abad, Colin C Fleming, Tim A Day, Angela Mousley, Nikki J Marks, Aaron G Maule

“…Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. …”
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Multi-omics investigation reveals unique markers in Klebsiella pneumoniae compared to closely related species by Lena-Sophie Swiatek, Kristin Surmann, Elias Eger, Justus U. Müller, Manuela Gesell Salazar, Stefan E. Heiden, Guido Werner, Nils-Olaf Hübner, Jürgen A. Bohnert, Karsten Becker, Uwe Völker, Michael Schwabe, Katharina Schaufler, Katharina Schaufler

“…Moreover, a large genomic dataset of over 6,000 publicly available genomes of KP, KV, and KQ was constructed for comparisons to other members of the KpSC.ResultsAmong eight clinical KP strains representing four different sequence types (STs), we identified 107 genes comprising the KP-specific core genome, while these genes were absent from two selected KV genomes. Transcriptome and proteome analyses in SHU revealed different regulatory patterns between KP and KV strains, with metabolic responses playing a pivotal role. …”
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Machine learning-driven multi-omics analysis identifies a prognostic gene signature associated with programmed cell death and metabolism in hepatocellular carcinoma by Xiang Li, Donghao Yin, Jiahao Geng, Yanyu Xu, Zijing Xu, Xuemeng Yang, Quanwei Li, Zimeng Shang, Zhiyun Yang, Zhong Xu, Jiabo Wang, Enxiang Zhang, Xinhua Song

“…Abstract Background Hepatocellular carcinoma (HCC) is the most prevalent primary liver malignancy, contributing significantly to global mortality due to limited therapeutic options. …”
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Bioenergetic programs of cancellous and cortical bone are distinct and differ with age and mechanical loading by Carolyn Chlebek, Tyler J. McNeill, Muyin Huang, Maia S. Raynor, Marjolein C. H. van der Meulen

“…To evaluate load-induced changes to bioenergetic activity in young and adult animals, we loaded the tibia of 10-wk and 26-wk female C57BL/6J mice and examined transcriptomic responses at the mid-diaphysis, and metaphyseal cortical shell and cancellous core. …”
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Quercetin, a Compound of the Total Flavonoids of Periploca forrestii Schltr., Ameliorates Rheumatoid Arthritis by Targeting TNF-α by Chen S, Xue W, Wu Z, Lu D, Zheng L, Zhou M, Li Y, Wang Y, Liu T

“…Chemical chromatography, thermal proteome profiling (TPP), molecular docking, surface plasmon resonance (SPR), cellular thermal shift assays (CETSA), drug affinity responsive target stability tests (DARTS), and transcriptomic analysis were used to study the potent molecules of TFPF and their protein targets and pathways. …”
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GM-CSF potentiates macrophages to retain an inflammatory feature from their circulating monocyte precursors in rheumatoid arthritis by Jianing Chen, Minghua Zhan, Yanling Zhao, Honglin Xu, Futai Feng, Zhou Bai, Ke Zhang, Lufan Fu, Fang Wang, Yongjing Cheng, Xuan Zhang, Yudong Liu

“…Strikingly, CCL22 was identified as the most upregulated chemokine in RA GM-DMs. Elevated synovial CCL22 expression strongly correlated with M1 macrophage infiltration and disease activity. …”
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Exogenous prostaglandin D2 as a modulator in bovine endometritis: implications for reducing antibiotic use in dairy cattle by Xiaolin Yang, Xiaolin Yang, Shuangyi Zhang, Shuangyi Zhang, Bo Liu, Bo Liu, Lili Guo, Lili Guo, Pengfei Gong, Pengfei Gong, Pengfei Gong, Jingze Wu, Jingze Wu, Yi Zhao, Yi Zhao, Wei Mao, Wei Mao, Jinshan Cao, Jinshan Cao

“…E. coli activates various molecular functions in bovine BMDMs, with the most closely related being the inflammatory response, in which Prostaglandin-Endoperoxide Synthase 2 (PTGS2) plays a crucial role. …”
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Genome-wide identification of the phosphofructokinase gene family in maize (Zea mays L.) and their expression levels under abiotic stress and phytohormones by Weichao Fu, Delong Fan, Shenkui Liu, Yuanyuan Bu

“…We identified the ZmPFK genes involved in stress and plant hormone response by combining promoter element analysis, transcriptome data, and RT-qPCR analysis. …”
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