NALCN expression is down-regulated and associated with immune infiltration in gastric cancer by Xuewei Li, Xuewei Li, Na Wu, Chen Wang, Beibei Pei, Xiaoyan Ma, Jun Xie, Jun Xie, Wenhui Yang

“…Data obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were utilized to investigate the correlation between NALCN expression and immune cell infiltration in GC. …”
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Multiomic characterization, immunological and prognostic potential of SMAD3 in pan-cancer and validation in LIHC by Tao Zhou, Dan Dan Zhang, Jiejing jin, Jinyang Xie, Jianhua Yu, Chao Zhu, Rong Wan

“…We extensively harnessed data from authoritative sources, including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), cBioPortal, Human Protein Atlas (HPA), UALCAN, and various other databases. …”
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Analysis of mRNA Pentatricopeptide Repeat Domain 1 as a prospective oncogene in clear cell renal cell carcinoma that accelerates tumor cells proliferation and invasion via the Akt/... by Zhongbao Zhou, Yulong Li, Yumeng Chai, Yong Zhang, Pu Yan

“…Abstract Background Although pentatricopeptide repeat domain 1 (PTCD1) has been found to modulate mitochondrial metabolic and oxidative phosphorylation, its contribution in the growth of clear cell renal cell carcinoma (ccRCC) remains unknown. Methods The Cancer Genome Atlas (TCGA) dataset was utilized to examine the transcriptional alterations, patient characteristics, clinical outcomes, as well as pathway activation of PTCD1. …”
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RNA m6A involves in regulation of oxidative stress and apoptosis may via NF-kB pathway in cadmium-induced lung cells by Nan Zhang, Jie Yang, Yuan Zhao, Wenhong Li, Bo Zhao, Rongxian Li, Zuoshun He, Shiyan Gu

“…Proteomic assay revealed that in passage 40 cells, 350 proteins showed differentially expressed in comparison to control, and these proteins were primarily enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of “pathways in cancer” and “Chemical carcinoma-reactive oxygen species”. …”
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Identification of biomarkers for the diagnosis of type 2 diabetes mellitus with metabolic associated fatty liver disease by bioinformatics analysis and experimental validation by Guiling Wu, Guiling Wu, Sihui Wu, Sihui Wu, Tian Xiong, Tian Xiong, Tian Xiong, You Yao, You Yao, Yu Qiu, Yu Qiu, Yu Qiu, Liheng Meng, Cuihong Chen, Xi Yang, Xi Yang, Xi Yang, Xinghuan Liang, Yingfen Qin

“…We utilised protein–protein interactions (PPIs), Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes to identify T2DM-associated MAFLD genes and potential mechanisms. …”
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High-throughput methylation sequencing reveals novel biomarkers for the early detection of renal cell carcinoma by Wenhao Guo, Weiwu Chen, Jie Zhang, Mingzhe Li, Hongyuan Huang, Qian Wang, Xiaoyi Fei, Jian Huang, Tongning Zheng, Haobo Fan, Yunfei Wang, Hongcang Gu, Guoqing Ding, Yicheng Chen

“…Using a training set from The Cancer Genome Atlas (TCGA) dataset of 443 early-stage RCC tumors and matched normal tissues, we applied LASSO regression and identified 23 methylation signatures. …”
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Plasmodium falciparum transcription factor AP2-06B is mutated at high frequency in Southeast Asia but does not associate with drug resistance by Qiyang Shi, Changhong Wang, Wenluan Yang, Xiaoqin Ma, Jianxia Tang, Jiayao Zhang, Guoding Zhu, Yinlong Wang, Yaobao Liu, Xiaoqin He

“…To determine whether AP2-06B can alter the expression of pfk13 and pfcrt, as well as cause artemisinin and quinoline resistance in Plasmodium, we generated both a K3124R mutation and conditional knockdown of AP2-06B in Pf3D7 using CRISPR/Cas9-mediated genome editing.ResultsChIP-Seq analysis showed that AP2-06B can bind to the loci of the Plasmodium genes pfk13 and pfcrt. …”
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Association between chronic obstructive pulmonary disease and osteoporosis: Mendelian randomization combined with bibliometric analysis by Fangjun Yang, Huaming Wang, Miaomiao Liu, Shengtai Pei, Xiaoming Qiu

“…These BMD measurements were derived primarily from a genome-wide association study (GWAS) and summary statistics from the International Genetic Factors Consortium for Osteoporosis (GEFOS). …”
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Identification of potential druggable targets for endometriosis through Mendelian randomization analysis by Peng Chen, Xin Wei, Xiao-Ke Li, Yi-Hang Zhou, Yi-Hang Zhou, Qi-Fang Liu, Ling Ou-Yang

“…This study aimed to identify both cerebrospinal fluid (CSF) and plasma protein markers as promising therapeutic targets for EM.MethodsWe utilized Mendelian randomization (MR) analysis to explore potential disease-causing proteins, utilizing genetic datasets from genome-wide association studies (GWAS) and protein quantitative trait loci (pQTL) analyses. …”
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EHMT2‐mediated R‐loop formation promotes the malignant progression of prostate cancer via activating Aurora B by Yuyang Zhang, Mingqin Su, Yiming Chen, Li Cui, Wei Xia, Renfang Xu, Dong Xue, Xiansheng Zhang, Xingliang Feng

“…Methods Bioinformatic analyses were conducted to identify genes overexpressed in PCa tissues using The Cancer Genome Atlas (TCGA) and GEO datasets. Western blotting and immunohistochemistry assays were applied to determine the expression levels of euchromatic histone lysine methyltransferase 2 (EHMT2), pT232‐Aurora B and Cullin 3 (CUL3). …”
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circASAP1 induces renal clear cell carcinoma ferroptosis by binding to HNRNPC and thereby regulating GPX4 by Yunfei Wang, Taowei Yang, Qihao Li, Zhousan Zheng, Lican Liao, Junjie Cen, Wei Chen, Junhang Luo, Yi Xu, Mi Zhou, Jiaxing Zhang

“…Proteins altered by circASAP1 were enriched in the ferroptosis pathway on the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Conclusions The relationship between circRNA and the ASAP1/HNRNPC/GPX4 axis was demonstrated by experimental data, which was further confirmed by rescue experiments. circASAP1 influenced tumor growth and ferroptosis in animal experiments and predicted the prognosis of patients with ccRCC. …”
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Interaction study of the effects of environmental exposure and gene polymorphisms of inflammatory and immune-active factors on chronic obstructive pulmonary disease by Rui Wang, Yuanyuan Li, Yuting Jiang, Xiaona Liu, Hongqi Feng, Zhe Jiao, Bingyun Li, Chang Liu, Yuncheng Shen, Fang Chu, Chenpeng Zhu, Dianjun Sun, Wei Zhang

“…Single nucleotide polymorphism (SNP) in the human genome may influence the risk of developing COPD and the response to treatment. …”
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Construction of the bromodomain-containing protein-associated prognostic model in triple-negative breast cancer by Wei Chen, Yushuai Yu, Chenxi Wang, Zirong Jiang, Xiewei Huang, Yidan Lin, Hongjing Han, Qing Wang, Hui Zhang

“…Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) network analysis were conducted to investigate active pathways and molecular interactions. …”
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Assessment of Antibiotic Resistance Among Isolates of <i>Klebsiella</i> spp. and <i>Raoultella</i> spp. in Wildlife and Their Environment from Portugal: A Positive Epidemiologic Ou... by Carolina Sabença, Rani de la Rivière, Paulo Barros, João Alexandre Cabral, Roberto Sargo, Luís Sousa, Maria de Lurdes Enes Dapkevicius, Filipe Silva, Filipa Lopes, Ana Carolina Abrantes, Madalena Vieira-Pinto, Manuela Caniça, Gilberto Igrejas, Carmen Torres, Patrícia Poeta

“…Extended-spectrum β-lactamase (ESBL) production was tested by the double-disc synergy test, and one ESBL-producing <i>K. pneumoniae</i> isolate was screened by PCR and whole-genome sequencing. Biofilm production was analyzed using the microtiter plate method. …”
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An exceptionally rare case of a diffuse midline glioma with concomitant H3.1 K27M and G34R mutations in the HIST1H3C (H3C3) gene by Zita Reisz, Rita Pereira, Smitha Nevis, Alan Mackay, Leena Bhaw, Yura Grabovska, Ross Laxton, Valeria Molinari, Anna Burford, Barnaby Clark, Cristina Bleil, Bassel Zebian, Erika Pace, Annette Weiser, Fernando Carceller, Lynley Marshall, Andrew King, Istvan Bodi, Safa Al-Sarraj, Chris Jones, Matthew Clarke

“…Further molecular studies (whole exome, whole genome sequencing) revealed concurrent H3.1 K27M and G34R mutations (clonal, in the same reads) of H3C3, FGF11 and PIK3CA somatic variants, and a pathogenic germline NBN variant. …”
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Association between sex steroid hormones and α-klotho: Results from the NHANES 2013-2016 and Mendelian randomization study by Andong Guo, Pengcheng Chen, Jishuang Cao, Chenrui Wu, Sentai Ding

“…Then, utilizing summary data from genome-wide association studies (GWAS), a bidirectional two-sample Mendelian randomization (MR) was conducted to assess the causal relationship between sex steroid hormones and α-Klotho. …”
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Differential impact of TIM-3 ligands on NK cell function by Xin Zhang, Lazar Vujanovic, Riyue Bao, Robert L Ferris, Tullia C Bruno, Aditi Kulkarni, Hridesh Banerjee, Housaiyin Li, Juncheng Wang, Lawrence P Kane, Pragati Upadhyay, Jennifer L Anderson, Onyedikachi Victor Onyekachi, Lidia M R B Arantes

“…In vitro killing, proliferation and cytokine production assays were implemented to evaluate whether the four TIM-3 ligands differentially modulate TIM-3+ NK cell functions, and whether disruption of TIM-3/ligand interaction can enhance NK cell-mediated antitumor effector mechanisms. Finally, The Cancer Genome Atlas survival analysis and digital spatial profiling were employed to study the potential impact of etiology-associated differences on patients with HNSCC outcomes.Results We demonstrate that TIM-3 is highly prevalent on circulating and tumor-infiltrating NK cells. …”
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Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance by Qiwen Tian, Hailv Ye, Xuan Zhou, Junyi Wang, Lifang Zhang, Wenxuan Sun, Chenxin Duan, Minyu Fan, Wei Zhou, Chuyun Bi, Qiong Ye, Aloysius Wong

“…Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.IMPORTANCEProbiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. …”
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Glioma Image-Level and Slide-Level Gene Predictor (GLISP) for Molecular Diagnosis and Predicting Genetic Events of Adult Diffuse Glioma by Minh-Khang Le, Masataka Kawai, Kenta Masui, Takashi Komori, Takakazu Kawamata, Yoshihiro Muragaki, Tomohiro Inoue, Ippei Tahara, Kazunari Kasai, Tetsuo Kondo

“…In this study, the Cancer Genome Atlas whole-slide images (WSIs) were used to train the model. …”
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Genetic Biomarkers and Circulating White Blood Cells in Osteoarthritis: A Bioinformatics and Mendelian Randomization Analysis by Yimin Pan, Xiaoshun Sun, Jun Tan, Chao Deng, Changwu Wu, Georg Osterhoff, Nikolas Schopow

“…Data sources encompassed the largest genome-wide analysis for OA and a comprehensive GWAS summary for circulating WBC counts. …”
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