Expression and delivery of HA1-M2e antigen using an innovative attenuated Salmonella–mediated delivery system confers promising protection against H9N2 avian influenza challenge by Ram Prasad Aganja, In-Shik Kim, Hyun-Jin Tae, John Hwa Lee

“…It demonstrated a safety profile with lower induction of inflammatory cytokines than the wild-type strain. Bioinformatics tools predicted that the HA1 and M2e sequences, which were designed as consensus sequences of South Korean strains (2000–2021), would have high antigenicity and favorable structures. …”
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circICMT upregulates and suppresses the malignant behavior of bladder cancer by Xin Luo, FangMei Xie, Guoqiang Qin, Ge Zou, Xu Lu, Chaofeng Zhang, Zeping Han, Ying Zhao, Xiaoyu Song, WenFeng Luo, Yongsheng Li, JinHua He, Jian Shen

“…Overexpression of circICMT can inhibit cell migration, proliferation and colony formation ability, while knockdown of circICMT promotes the malignant phenotype of bladder cancer cells. Bioinformatics predictions have found that circICMT can bind to a variety of miRNAs and RBPs and may form a complex regulatory network to regulate the progression of bladder cancer. …”
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Discovery of anti-Ebola virus multi-target inhibitors from traditional Chinese medicine database using molecular screening, biophysical investigation, and binding free energy calcu... by Abbas Khan, Abrar Mohammad Sayaf, Anwar Mohammad, Fahad M. Alshabrmi, Tarek Benameur, Dong-Qing Wei, Kar Kheng Yeoh, Abdelali Agouni

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Revealing the role of natural killer cells in ankylosing spondylitis: identifying diagnostic biomarkers and therapeutic targets by Yuling Chen, Yan Li, Yuan Xu, Qing Lv, Yuanchun Ye, Jieruo Gu

“…This study integrated bioinformatics methods with experimental validation to explore the role of natural killer (NK) cells in AS.Methods Two microarray datasets, GSE25101 and GSE73754, were selected, and the scRNA-seq data were obtained from GSE194315 and Liu’s research. …”
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First Indonesian Nasopharyngeal Cancer Whole Epigenome Sequencing Identify Tumour Suppressor CpG Methylation by Handoko, Adham M, Rachmadi L, Tobing DL, Asmarinah A, Fadilah F, Dai W, Lee AWM, Gondhowiardjo SA

“…Handoko,1– 3 Marlinda Adham,2,4 Lisnawati Rachmadi,2,5 Demak Lumban Tobing,6 Asmarinah,7 Fadilah,8 Wei Dai,9,10 Anne Wing Mui Lee,10 Soehartati A Gondhowiardjo2,3 1Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; 2Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; 3Department of Radiation Oncology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; 4Department of Otorhinolaryngology - Head and Neck Surgery, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; 5Department of Anatomical Pathology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; 6Department of Clinical Pathology, Dharmais Cancer Hospital, Jakarta, Indonesia; 7Medical Biology Department, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia; 8Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia-Bioinformatics Core Facilities, Indonesian Medical Education and Research Institute (IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; 9Department of Clinical Oncology, University of Hong Kong, Pokfulam, Hong Kong (SAR), People’s Republic of China; 10Clinical Oncology Center, University of Hong Kong – Shenzhen Hospital, Shenzhen, People’s Republic of ChinaCorrespondence: Soehartati A Gondhowiardjo; Handoko, Email handoko12@ui.ac.idIntroduction: Nasopharyngeal cancer (NPC) is a multifaceted disease characterized by genetic and epigenetic modifications. …”
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Exploring the Mechanism of Skeletal Muscle in a Tacrolimus-Induced Posttransplantation Diabetes Mellitus Model on Gene Expression Profiles by Chenlei Zheng, Cheng Wang, Tan Zhang, Ding Li, Xiao-feng Ni, Jian-Hu Lin, Linxiao Sun, Bicheng Chen

“…This study explored the molecular mechanism of muscle atrophy in a tacrolimus-induced PTDM model by bioinformatics analyses. We identified 275 DEGs and identified significant biomarkers for predicting the development and progression of tacrolimus-induced PTDM.…”
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Detection and characterization of bovine hepacivirus in cattle and sheep from Hulunbuir, northeastern China by Jingge Ma, Jingge Ma, Zhiwei Wei, Liang Li, Wei Wang, Ziyan Liu, Ziyan Liu, Ning Liu, Feng Wei, Xiangyu Zheng, Zedong Wang

“…BovHepV-positive samples were confirmed using semi-nested PCR with primers designed based on the obtained viral sequences. Comprehensive bioinformatics analyses were employed to assess sequence similarity, phylogenetic evolution, and recombination of the obtained viral strains.ResultsA total of 988 serum samples from sheep (520) and cattle (468) were collected from 12 administrative districts in Hulunbuir from June to August, 2022. …”
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The expression landscape and clinical significance of methyltransferase-like 17 in human cancer and hepatocellular carcinoma: a pan-cancer analysis using multiple databases by Yezhou Ding, Mingyang Feng, Wanqing Chi, Xiaoyin Wang, Baoyan An, Kehui Liu, Shike Lou, Xiaolin Wang, Hui Wang

“…First, we comprehensively analyzed RNA-seq data from the HPA database of 25 human tissues. An array of bioinformatics methods was employed to explore the potential oncogenic roles of METTL17, including analyzing its related prognosis, mutation, landscapes, tumor stemness index, immune cell infiltration, and other factors among different tumors. …”
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Co-occurrence of entomopathogenic nematodes and earthworms enhances enduring biocontrol activity and microbial diversity in a naturalized plant-soil system by Maryam Chelkha, Rubén Blanco-Pérez, David Labarga, María de Toro, Jorge Dueñas-Hernani, Kyle Wickings, Raquel Campos-Herrera

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CDK9 Expression Shows Role as a Potential Prognostic Biomarker in Breast Cancer Patients Who Fail to Achieve Pathologic Complete Response after Neoadjuvant Chemotherapy by Ashley J. Schlafstein, Allison E. Withers, Soumon Rudra, Diana Danelia, Jeffrey M. Switchenko, Donna Mister, Saul Harari, Hui Zhang, Waaqo Daddacha, Shahrzad Ehdaivand, Xiaoxian Li, Mylin A. Torres, David S. Yu

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Comprehensive analysis of full genome sequence and Bd-milRNA/target mRNAs to discover the mechanism of hypovirulence in Botryosphaeria dothidea strains on pear infection with BdCV1... by Wangcheng Hu, Hui Luo, Yuekun Yang, Qiong Wang, Ni Hong, Guoping Wang, Aiming Wang, Liping Wang

“…B. dothidea was predicted to express 3833 secreted proteins. In bioinformatics analysis, 351 CAZy members, 552 transporters, 128 kinases, and 1096 proteins associated with plant-host interaction (PHI) were identified. …”
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Effect of miR-144-3p-Targeted Regulation of PTEN on Proliferation, Apoptosis, and Osteogenic Differentiation of Bone Marrow Mesenchymal Stem Cells under Stretch by Shiyong Ling, Xi Luo, Bo Lv, Hua Wang, Mengzhi Xie, Kai Huang, Jingchuan Sun

“…Real-time quantitative reverse transcription PCR (qRT-PCR) was used to detect the expression of miR-144-3p and PTEN in the two groups of cells after osteogenic differentiation. Bioinformatics website and dual luciferase reporter were used to detect the relationship between miR-144-3p and PTEN. …”
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Genomic Characterization of Carbapenemase-Producing Enterobacteriaceae from Clinical and Epidemiological Human Samples by Alexander Tristancho-Baró, Laura Eva Franco-Fobe, Monica Pilar Ariza, Ana Milagro, Ana Isabel López-Calleja, Blanca Fortuño, Concepción López, Miriam Latorre-Millán, Laura Clusa, Rosa Martínez, Carmen Torres, Antonio Rezusta

“…De novo assembly was used to generate draft genomes in order to determine their complete taxonomic classification, resistome, plasmidome, sequence type (ST), core–genome multilocus sequence typing (cgMLST), and phylogenetic relationships using a suite of bioinformatics tools and in-house scripts. <b>Results</b>: Between 2021 and 2023, 0.4% out of 38,145 Enterobacteriaceae isolates were CPE. …”
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Downregulation of hnRNPA1 inhibits hepatocellular carcinoma cell progression by modulating alternative splicing of ZNF207 exon 9 by Qi Ouyang, Qi Ouyang, Wenhui He, Yiping Guo, Lin Li, Ying Mao, Xiang Li, Shuanglin Xiang, Xiang Hu, Jun He

“…We also explored the interaction between hnRNPA1 and ZNF207, as well as its splicing effects and downstream signaling pathways by RIP assay, bioinformatics, qPCR and Western blot.ResultshnRNPA1 was significantly upregulated in HCC tissues compared to normal tissues, correlating with poor patient survival. hnRNPA1 knockdown reduced Hep G2 cell proliferation and migration while increasing apoptosis. …”
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Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia by P. A. Dotsenko, K. A. Zolotareva, R. A. Ivanov, I. V. Chadaeva, N. L. Podkolodnyy, V. A. Ivanisenko, P. S. Demenkov, S. A. Lashin, M. P. Ponomarenko

“…In this work, we for the first time performed a comprehensive bioinformatics analysis of 568 human genes that, according to the NCBI Gene database as on September 15, 2024, were associated with pain generation, perception and anesthesia. …”
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The Effect of Diabetes-Associated Autoantigens on Cell Processes in Human PBMCs and Their Relevance to Autoimmune Diabetes Development by Jana Vcelakova, Radek Blatny, Zbynek Halbhuber, Michal Kolar, Ales Neuwirth, Lenka Petruzelkova, Tereza Ulmannova, Stanislava Kolouskova, Zdenek Sumnik, Pavlina Pithova, Maria Krivjanska, Dominik Filipp, Katerina Stechova

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Mechanism of Bone-metastatic LUAD Cells Promoting Angiogenesis 
Through HGF/YAP Signaling Pathway by Yan DENG, Rong QIU, Xingyu LIU, Yingyang SU, Yang XUE, Yuzhen DU

“…Results BM3-CM demonstrated a more pronounced impact on the proliferation, migration, and angiogenesis of HUVEC compared to A549-CM. Bioinformatics analysis, combined with in vitro experiment, demonstrated that the secretory protein HGF was significantly elevated in BM3 cells and BM3-CM (P<0.05). …”
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Dual disease co-expression analysis reveals potential roles of estrogen-related genes in postmenopausal osteoporosis and Parkinson’s disease by Dongdong Yu, Dongdong Yu, Jian Kang, Chengguo Ju, Qingyan Wang, Ye Qiao, Ye Qiao, Long Qiao, Long Qiao, Dongxiang Yang

“…Differentially expressed genes (DEGs) among PMO, PD, and ERGs were subjected to an array of bioinformatics analyses, including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses, in addition to protein-protein interaction (PPI) network analysis. …”
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The PHD transcription factor Cti6 is involved in the fungal colonization and aflatoxin B1 biological synthesis of Aspergillus flavus by Zhang Mengjuan, Lin Guanglan, Pan Xiaohua, Song Weitao, Tan Can, Chen Xuan, Yang Yanling, Zhuang Zhenhong

“…Crops models analysis showed that A. flavus Cti6 plays vital role in colonization and the production of AFB1 on the host grains mainly via PHD domain. Bioinformatics analysis showed Cti6 is conservative in Aspergillus spp., and mCherry mediated subcellular localization showed that most Cti6 accumulated in the nuclei, which reflected that Cti6 performed its important biological function in the nuclei in Aspergillus spp.. …”
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High trophic similarity between non-native common carp and gibel carp in Turkish freshwaters: Implications for management by Sadi Aksu, Özgür Emiroğlu, Paride Balzani, J. Robert Britton, Esengül Köse, Irmak Kurtul, Sercan Başkurt, Oğuzcan Mol, Emre Çınar, Phillip J. Haubrock, Pinar Oztopcu-Vatan, Ali Serhan Tarkan

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