Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery by Arda Halu, Sarvesh Chelvanambi, Julius L. Decano, Joan T. Matamalas, Mary Whelan, Takaharu Asano, Namitra Kalicharran, Sasha A. Singh, Joseph Loscalzo, Masanori Aikawa

“…We validate the drugs predicted in our proofs-of-concept using real-time polymerase chain reaction (qPCR) experiments. Results Cell type-specific gene-drug perturbation networks built using QUIZ-C are topologically distinct, reflecting the biological uniqueness of the cell lines in CMap, and are enriched in known drug targets. …”
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In Vitro Screening and Transfection Concentration Optimization of Cynomolgus Monkey IκBα-siRNA by Zhaoxing Ou, Rui Zeng, Yifan Lin, Si Zhang, Mohammad Alzogool, Peng Zeng, Yuqing Lan

“…The mRNA and protein levels of IκBα were examined by using real-time quantitative polymerase chain reaction (real-time PCR) and western blot to screen a pair of candidate valid sequences with the highest inhibitory rate. …”
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Tannin alleviated reproductive dysfunction in pregnant ewes infected with Haemonchus contortus by Xin Li, Xin Li, Hai Xiang, Hai Xiang, Rong Liang, Rong Liang, Xinyu Han, Xinyu Han, Rongzhen Zhong, Rongzhen Zhong, Hongyu Liu, Hongyu Liu, Yi Fang, Yi Fang

“…The mRNA levels of hypothalamic–pituitary–ovarian axis-related hormone receptors and placental tissue inflammation genes were detected by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Finally, fetal weights were measured, and fetal ovarian tissue samples were taken for transcriptomic analysis.ResultsThe results showed that tannins increased the levels of gonadotropin-releasing hormone (GnRH), follicle-stimulating hormone (FSH), luteinizing hormone (LH), estrogen (E2), progesterone (P4), human chorionic gonadotropin (hCG), red blood cell (RBC) counts, packed cell volume (PCV), and mRNA levels of gonadotropic axis receptors in pregnant ewes infected with H. contortus (p < 0.05). …”
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The Effect of Vascular Endothelial Growth Factor on Bone Marrow Mesenchymal Stem Cell Engraftment in Rat Fibrotic Liver upon Transplantation by Ke Yuan, Chunyou Lai, Lingling Wei, Tianhang Feng, Qinyan Yang, Tianying Zhang, Tao Lan, Yutong Yao, Guangming Xiang, Xiaolun Huang

“…Paraffin section staining, immunofluorescent staining, RT-qPCR (quantitative reverse transcription polymerase chain reaction), and Western blot were used to evaluate hepatic pathological changes and physiology function. …”
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4-Octyl itaconate inhibits synovitis in the mouse model of post-traumatic osteoarthritis and alleviates pain by Yu-Zhen Tang, Wan Chen, Bao-Yun Xu, Gang He, Xiu-Cheng Fan, Kang-Lai Tang

“…After 12 weeks of surgery, the efficacy of 4-OI treatment on PTOA in mice was evaluated using MRI, micro-CT, histological analysis, and quantitative real-time polymerase chain reaction. Finally, we utilized network pharmacology analysis to predict the mechanism of 4-OI in treating PTOA synovitis and conducted preliminary validation. …”
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Cooling and Sterile Inflammation in an Oxygen-Glucose-Deprivation/Reperfusion Injury Model in BV-2 Microglia by Jana Lücht, Nele Rolfs, Sylvia J. Wowro, Felix Berger, Katharina R. L. Schmitt, Giang Tong

“…Furthermore, inducible nitric oxide synthase (iNOS), ionized calcium-binding adaptor molecule 1 (Iba1), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), interleukin-1α (IL-1α), monocyte chemotactic protein 1 (MCP-1), transforming growth factor β (TGFβ), CIRBP, and RBM3 gene expressions were assessed via reverse transcription polymerase chain reaction, and TNF-α, IL-6, and IL-1β releases into the cultured supernatants were assessed via enzyme-linked immunosorbent assays (ELISA). …”
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Predicting hepatocellular carcinoma outcomes and immune therapy response with ATP-dependent chromatin remodeling-related genes, highlighting MORF4L1 as a promising target by Chao Xu, Litao Liang, Guoqing Liu, Yanzhi Feng, Bin Xu, Deming Zhu, Wenbo Jia, Jinyi Wang, Wenhu Zhao, Xiangyu Ling, Yongping Zhou, Wenzhou Ding, Lianbao Kong

“…Experimental validation was conducted using quantitative real-time Polymerase Chain Reaction (qRT-PCR), Western blotting, and functional assays in HCC cell lines and xenograft models. …”
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Study of the relationships of polymorphisms of the folate cycle genes with the levels of homocysteine and folic acid as risk factors of cardiovascular disorders in the post-covid p... by A.A. Shuprovych, O.V. Zinych, N.M. Kushnareva, K.P. Komisarenko

“…Polymorphisms of the genes: methylenetetrahydrofolate reductase (677C>T and 1298A>C), methionine synthase-reductase (66A>G) and methionine synthase (2756A>G) were determined by real time polymerase chain reaction. For each of the named polymorphisms, the examined patients were divided into 3 groups according to the nucleotide alleles in the corresponding position: 1) homozygous dominant, 2) heterozygous and 3) homozygous recessive. …”
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Quinazolinone Derivative MR2938 Protects DSS-Induced Barrier Dysfunction in Mice Through Regulating Gut Microbiota by Ling Lv, Mireguli Maimaitiming, Jichen Yang, Shuli Xia, Xin Li, Pingyuan Wang, Zhiqing Liu, Chang-Yun Wang

“…The inflammatory factor levels were performed by quantitative polymerase chain reaction (qPCR) and enzyme-linked immunosorbent assay (ELISA). …”
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Characterization and Study of Gene Expression Profiles of Human Periodontal Mesenchymal Stem Cells in Spheroid Cultures by Transcriptome Analysis by Takenori Suga, Michihiko Usui, Satoru Onizuka, Kotaro Sano, Tsuyoshi Sato, Kohji Nakazawa, Wataru Ariyoshi, Tatsuji Nishihara, Keisuke Nakashima

“…To confirm the results of the transcriptome analysis, we performed real-time polymerase chain reaction and western blotting analyses. Interestingly, we found that the mRNA and protein expressions of NR4A2 were strongly expressed in the spheroid-cultured hPDLMSCs. …”
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Relationship between mucin gene polymorphisms and different types of gallbladder stones by Gongqing Ren, Yongmao Fan, Ruizi Zhong, Gang Zou, Xiaojun Huang, Yue Zhang

“…We amplified SNP sites by polymerase chain reaction (PCR) using specific primer sets followed by DNA sequencing. …”
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Hu-lu-su-pian ameliorates hepatic steatosis by regulating CIDEA expression in AKT-driven MASLD mice by Rumeng Ren, Rumeng Ren, Qi Wang, Qi Wang, Dongjie Deng, Dongjie Deng, Aoao Guo, Aoao Guo, Xin Chen, Xin Chen, Yan Meng, Yan Meng, Ying Fang, Ying Fang, Guohua Zheng, Guohua Zheng, Zhong Xu, Zhong Xu, Man Li, Junjie Hu, Junjie Hu

“…Further examination of significant DEGs and proteins was performed using quantitative real-time polymerase chain reaction (RT-qPCR), Western blotting, and immunohistochemistry (IHC) techniques, respectively. …”
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JAK/STAT3 signaling promotes pain and depression-like behaviors in rats with bone cancer pain by regulating Th17 cell differentiation by Shuyan Wu, Jundan Jiang, Danfeng Wang, Daoyi Lin, Mingxue Lin, Pinzhong Chen, Jianghu Chen, Honghong Zhang, Ying Wang, Xiaohui Chen, Xiaochun Zheng

“…Changes in inflammatory factors and related protein expression levels in the amygdala were detected using western blotting, immunofluorescence, and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The effects of intra-amygdala injections of a lentivirus targeting retinoic acid-related orphan receptor γt (RORγt) (LV-shRORγt), nifuroxazide (a STAT3 antagonist), and colivelin (a STAT3 agonist) were evaluated. …”
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Identification and preliminary validation of biomarkers associated with mitochondrial and programmed cell death in pre-eclampsia by Rong Lin, Rong Lin, XiaoYing Weng, XiaoYing Weng, Liang Lin, Liang Lin, XuYang Hu, XuYang Hu, ZhiYan Liu, ZhiYan Liu, Jing Zheng, Jing Zheng, FenFang Shen, FenFang Shen, Rui Li, Rui Li

“…Clinical validation was conducted via real-time quantitative polymerase chain reaction (RT-qPCR), immunofluorescence, and Western blot.ResultsFour genes [solute carrier family 25 member 5 (SLC25A5), acyl-CoA synthetase family member 2 (ACSF2), mitochondrial fission factor (MFF), and phorbol-12-myristate-13-acetate–induced protein 1 (PMAIP1)] were identified as biomarkers distinguishing PE from normal controls. …”
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Qizhu Rougan Granules suppress liver fibrosis by inhibiting the expression of the P2Y14 receptor on hepatic stellate cells by Yujing Tao, Yujing Tao, Qun Niu, Qun Niu, Yuanqian Yao, Yuanqian Yao, Kaixin Wang, Kaixin Wang, Haijian Dong, Haijian Dong, Xin Zhao, Xin Zhao, Zijian Zeng, Zijian Zeng, Hui Li

“…Liver morphology and fibrosis were evaluated using hematoxylin-eosin (H&E) and Masson’s trichrome staining, while gene and protein expression levels were analyzed through quantitative reverse transcription polymerase chain reaction (RT-PCR) and western blot techniques.ResultsThe results showed that QZRG granules significantly reduced serum levels of AST, ALT, and ALP in CCl4-treated mice, alleviated liver damage, and reduced collagen accumulation. …”
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Network and systems biology approaches help investigate gene regulatory interactions between Salmonella disease and host in chickens: Model‐based in silico evidence combined with g... by Reza Tohidi, Hoda Javaheri Bargourooshi, Arash Javanmard

“…Next, we use five promising biomarkers for relative real‐time polymerase chain reaction (PCR) quantification: TLR4, IL8, NRAMP1, IFNγ and IgY genes in two case and control assays. …”
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NDM-1-Positive K. pneumoniae at a Teaching Hospital in Southwestern China: Clinical Characteristics, Antimicrobial Resistance, Molecular Characterization, Biofilm Assay, and Virule... by Kai Yang, Shumin Liu, Huanqin Li, Na Du, Jing Yao, Qiuyue He, Yan Du

“…Methods. The polymerase chain reaction (PCR) was used to screen isolated NDM-1-positive K. pneumoniae. …”
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Nucleotide variation in Foxp3 gene and prognosis of bladder cancer: a case-control study by Qin Li, Yan Zhang, Yan Zhang, Min Su, Yaping Song, Yanyun Wang, Bin Zhou, Lin Zhang

“…Two Foxp3 SNPs (rs3761548 C/A, rs5902434 del/ATT) were selected, and genotyping of the samples was performed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. …”
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Aspergillus fumigatus extract modulates human eosinophils via NOD2 and oxidative stress by Hisashi Sasaki, Jun Miyata, Yusuke Kawashima, Ryo Konno, Masaki Ishikawa, Yoshinori Hasegawa, Ryuta Onozato, Yo Otsu, Emiko Matsuyama, Keeya Sunata, Katsunori Masaki, Hiroki Kabata, Yoshifumi Kimizuka, Tomoe Abe, Shigeharu Ueki, Koichiro Asano, Akihiko Kawana, Koichi Fukunaga

“…The expression of specific factors was evaluated using quantitative real-time polymerase chain reaction and flow cytometry. Mechanistic analyses were performed using NOD2 inhibitor and N-acetyl-l-cysteine (NAC). …”
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Coinfection of severe acute respiratory syndrome coronavirus 2 and polyomavirus in a patient with coronavirus disease 2019 detected by enrichment next-generation sequencing: a case... by Gunadi, Esensi Tarian Geometri, Pramana Adhityo, Ali Zainal Abidin, Marcellus, Dyah Ayu Puspitarani, Fadila Dyah Trie Utami, Kristy Iskandar, Hendra Wibawa, Mohamad Saifudin Hakim

“…Her nasopharyngeal swab and real-time polymerase chain reaction were positive for the coronavirus disease 2019 nucleocapsid and open reading frame genes, with cycle threshold values of 32.33 and 33.74, respectively. …”
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