Standardization and validation of a novel reverse transcriptase polymerase chain reaction method for detecting virulent strains of the infectious bursal disease virus by Vladimir Longa-Bobadilla, Phillip Ormeño-Vásquez, Manuel Criollo-Orozco, Luis Tataje-Lavanda, Katherine Huamán-Gutierrez, Ángela Montalván, Mirko Zimic, Manolo Fernández-Sanchez, Manolo Fernández-Díaz

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PLGA-based biocompatible nanoparticles improved anti-breast tumor efficacy of 1,25(OH)2D3 through the SOCS3/STAT3/EMT signaling axis by JinJing Pan, Ping Wang, Linghong Xiong, Wenqing Yang, Jie Li, Kai Yang, Bingyan Li

“…It is noteworthy that PD significantly alleviates the adverse effects of increased serum calcium levels and weight loss in mice induced by 1,25(OH)2D3. Subsequently, bioinformatics analysis and western blot confirmed that PD showed a more pronounced upregulation of SOCS3 and a concurrent downregulation of JAK/STAT3 and PI3K/AKT signals compared to 1,25(OH)2D3 both in vivo and in vitro. …”
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EDF1 accelerates ganglioside GD3 accumulation to boost CD52-mediated CD8+ T cell dysfunction in neuroblastoma by Di Li, Meng Li, Zhenjian Zhuo, Huiqin Guo, Weixin Zhang, Yile Xu, Hai-Yun Wang, Jiabin Liu, Huimin Xia, Huiran Lin, Jue Tang, Jing He, Lei Miao

“…Methods We performed bulk-RNA sequencing and lipidomic analyses of children with mediastinal NB. Bioinformatics analysis and biological validation were applied to uncover the underlying mechanism. …”
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Derivation of allometric equations and carbon content estimation in mangrove forests of Malaysia by Waseem Razzaq Khan, Michele Giani, Stanislao Bevilacqua, Shoaib Ahmad Anees, Kaleem Mehmood, M. Nazre, Abdul Aziz Bin Abdul Haddy, Abang Norizan Bin Abang Median, Japanie Bin Bujang, Fatin-Norliyana Mohamad-Ismail, Johar Mohamed, Zaiton Samdin, Rambod Abiri, Tuan-Marina Tuan-Ibrahim, Lydia-Suzieana Mohammad, Hamid-Reza Naji, Seemab Akram, Hazandy Abdul-Hamid, Timothy Dube

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Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression by Alena Laschtowitz, Eric L. Lindberg, Anna-Maria Liebhoff, Laura Anne Liebig, Christian Casar, Silja Steinmann, Adrien Guillot, Jun Xu, Dorothee Schwinge, Michael Trauner, Ansgar Wilhelm Lohse, Stefan Bonn, Norbert Hübner, Christoph Schramm

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CTSG is a prognostic marker involved in immune infiltration and inhibits tumor progression though the MAPK signaling pathway in non-small cell lung cancer by Qian Dai, Xufeng Yao, Yanke Zhang, Qian Chai, Xueyi Feng, Hongbin Zhu, Lei Zhao

“…Transcriptome sequencing and subsequent bioinformatic analysis were performed to explore the signaling pathways regulated by CTSG. …”
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Molecular anti-tumorigenic mechanism of Radix Polygoni Multiflori-derived exosome-like nanoparticles by Mingqing Yang, Lining Xu, Weiyu Wang

“…RNA sequencing and qPCR experiments were performed, and the results of bioinformatic analyses revealed that RPM-ELNs could globally regulate expression levels of numerous genes associated with cancer and the cell cycle. …”
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Exploratory analysis of molecular traits of the mitochondrial DNA of leafcutting ants to infer taxonomic characters towards an integrative taxonomy by Perpetua Ndubuisi Onyinyechi, Natália Martins Travenzoli, Maykon Passos Cristiano, Danon Clemes Cardoso

“…., 2020, Atta Fabricius, 1804 and Acromyrmex Mayr, 1865 as models to evaluate a mitochondrial genome fragment regularly applied in phylogenetic and evolutionary studies. Bioinformatic analysis revealed shared structural evidence between species that can serve as diagnostic characters, distinguishing them from other species and supporting the classification of the three genera of leafcutting ants. …”
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The effects of the ketone body ?-hydroxybutyrate on the neuronal transcriptome by Zayn Cheema, Megan Chen, Dana Poon, Taara Reddy, John Vergis, Sinead O'Donovan

“…To assess the effect of BHB administration on the neuronal transcriptome, we reanalyzed a publicly available RNAseq dataset (GSE252513) using a bioinformatic “3-pod” approach. We conducted pathway analysis and identified leading edge genes using Gene Set Enrichment Analysis (GSEA) and conducted chemical perturbagen analysis using the iLINCS repository to identify drugs that are concordant and discordant with BHB administration. …”
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Landscape analysis of m6A modification reveals the dysfunction of bone metabolism in osteoporosis mice by Lifeng Zheng, Chao Lan, Xinyue Gao, An Zhu, Yaoqing Chen, Jinluan Lin, Sunjie Yan, Ximei Shen

“…This study aimed to explore the relationship between OP and RNA m6A methylation, investigating its underlying mechanisms through comprehensive bioinformatic analysis and experimental validation. The mRNA sequencing (mRNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) were performed on control mice as well as ovariectomized mice to discover differentially expressed genes (DEGs) and m6A regulators in OP. …”
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Characterization and phylogenetic analysis of the chloroplast genome of endangered Impatiens chishuiensis by LAN Wenxiang, MO Qing, HUANG Haiquan, HUANG Meijuan

“…[Methods] Based on the chloroplast genome sequence of I. chishuiensis, an endemic species in China, the assembly, annotation, gene characterization, sequence repetition and phylogenetic analysis of chloroplast genome were performed by bioinformatic softwares. [Results] (1) The chloroplast genome of I. chishuiensis has a typical tetrameric structure with a total GC content of 37% and a length of 152 892 bp. …”
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TMT-based quantitative proteomics reveals the genetic mechanisms of secondary hair follicle development in fine-wool sheep. by Li-Xia Qiu, Qian Yu, Hua-Qian Zhou, Wen-Hua Fan, Jing-Jing Zheng, Yong-Lin Yang, Wen-Zhe Zhang, Xin Cao, Hua Yang

“…We found that the density of secondary hair follicles and the secondary hair follicles/primary hair follicles ratio increased from 85 to 105 gestational days. Bioinformatic analysis identified 238, 35, and 348 differentially expressed proteins in the respective comparison periods. …”
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LAMB1 downregulation suppresses glioma progression by inhibiting aerobic glycolysis through regulation of the NF-κB/HK2 axis by Zhenxiang Zhao, Haiying Liu, Yingzi Liu, Junpeng Wen, Jiangwei Yuan

“…Western blotting was conducted to monitor the expression of HK1, HK2, PDHA, and PKM. Bioinformatic analysis was employed to investigate the downstream mechanism of LAMB1. …”
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DNA metabarcoding technology for the identification of the fecal microbiome in patients with chronic stress by Abraham Eudes Pérez Urruchi, Lucy Eliana Ramírez Elizalde, Flor de María Zapata Cornejo, María Luisa Matalinares Calvet, Miluska Vanessa Baylon Cuba, Fredy Fabian Dominguez

“…Next Generation Illumina genetic sequencing targeting the 16S rDNA gene was then performed, followed by bioinformatic analysis using QUIME II software. The results, at the psychological test level, 20 people with chronic stress were diagnosed, on the other hand, at the metabarcoding level, specifically at the Gender level, the Asteroleplasma bacteria present only in the 20 healthy patients was molecularly identified. …”
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Identification of mitochondrial carrier homolog 2 as an important therapeutic target of castration-resistant prostate cancer by Yankui Liu, Anjie Chen, Yufan Wu, Jiang Ni, Rong Wang, Yong Mao, Ning Sun, Yuanyuan Mi

“…Abstract We here investigate the expression of the mitochondrial carrier homolog 2 (MTCH2) and its potential function in castration-resistant prostate cancer (CRPC). Bioinformatic analyses reveal that MTCH2 overexpression is associated with critical clinical parameters of prostate cancer. …”
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Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames by Lei Chen, Xia Gao, Xiangshen Liu, Ye Zhu, Dong Wang

“…In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. …”
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Placental Vimentin Expression in Preeclampsia and Gestational Diabetes Mellitus by Fırat Asir, Suleyman Cemil Oglak, Tugcan Korak, Fatih Tas, Mehmet Yilmaz, Fikri Erdemci, Firat Sahin, Hayat Ayaz, Emine Zeynep Yilmaz, Gokhan Bolluk

“…Vimentin expression was generally recorded as negative in placental villi, fibrinoid substances, and connective tissue cells in the GDM group. Bioinformatic analysis showed that the AGE-RAGE signaling pathway and cancer-related pathways were mainly observed in Vimentin-associated pathways, which finally activate inflammatory pathways in both preeclampsia and GDM. …”
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Dataset for comparative analysis of precision metagenomics and traditional methods in urinary tract infection diagnosticsNCBI by Rob E. Carpenter, Sadia Almas, Vaibhav K. Tamrakar, Rahul Sharma

“…The dataset includes 47 urine samples, each analyzed by microbial culture, PCR, and precision metagenomics, followed by bioinformatic classification using the Explify® platform. precision metagenomics identified significantly more uropathogens (62 distinct organisms) compared to PCR (19 organisms) and microbial culture (13 organisms), with 98 % of samples testing positive for polymicrobial infections via precision metagenomics. …”
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CRIP1 inhibits cutaneous melanoma progression through TFAM-mediated mitochondrial biogenesis by Jianqiang Wu, Lixia Chen, Peijun Wen

“…However, the biological function and underlying mechanisms of CRIP1 in melanoma progression are largely unknown. Bioinformatic prediction of CRIP1 expression in melanoma and its association with clinical parameters and prognosis of patients. …”
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