Sequencing Analysis of Invasive Carbapenem-Resistant <i>Klebsiella pneumoniae</i> Isolates Secondary to Gastrointestinal Colonization by Gaetano Maugeri, Maddalena Calvo, Dafne Bongiorno, Dalida Bivona, Giuseppe Migliorisi, Grete Francesca Privitera, Guido Scalia, Stefania Stefani

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Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data by Caitlin Guccione, Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio Gonzalez, Gregory D. Sepich-Poore, Kyuto Sonehara, Mohsen Zakeri, Yang Chen, Amanda Hazel Dilmore, Neil Damle, Sergio E. Baranzini, George Hightower, Teruaki Nakatsuji, Richard L. Gallo, Ben Langmead, Yukinori Okada, Kit Curtius, Rob Knight

“…We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. …”
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Citrus aurantium L. extract alleviate depression by inhibiting gut microbiota-mediated inflammation in mice by Tao Li, Guirong Zeng, Lingfeng Zhu, Yanyang Wu, Qun Zhang, Fuhua Fu, Donglin Su, Gaoyang Li, Qili Li, Yang Shan

“…Meanwhile, FEMC reduced the abundance of the Prevotellaceae_Ga6A1_group, [Ruminococcus]_torques_group, which have been reported to be closely related to inflammation. Bioinformatics analysis revealed that mitogen-activated protein kinase (MAPK) signaling pathway and lipopolysaccharide biosynthesis were involved in the anti-inflammatory effect of FEMC in the CUMS animal model. …”
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A Missense Mutation in OPA1 Causes Dominant Optic Atrophy in a Chinese Family by Shaoyi Mei, Xiaosheng Huang, Lin Cheng, Shiming Peng, Tianhui Zhu, Liang Chen, Yan Wang, Jun Zhao

“…The disease-causing mutation was identified by bioinformatics analysis and confirmed by segregation analysis. …”
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Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users by Vilde Kaldhusdal, Mathias Franzen Boger, Annelie Tjernlund, Adam D. Burgener, Frideborg Bradley, Julie Lajoie, Kenneth Omollo, Joshua Kimani, Keith Fowke, Paulo Czarnewski, Kristina Broliden

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Successful Traceability of Wildlife Samples Contributes to Wildlife Conservation: A Case Study of Tracing the Snub-Nosed Monkey (<i>Rhinopithecus</i> spp.) by Xibo Wang, Ying Shen, Yang Teng, Ruifeng Wu, Shuhao Liu, Jilai Zhao, Can Hu, Ming Li, Huijuan Pan, Jiwei Qi

“…To address these limitations, we developed a bioinformatics-based pipeline for the rapid identification of traceable nuclear genome loci. …”
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A novel de novo GABRA2 gene missense variant causing developmental epileptic encephalopathy in a Chinese patient by Li Yang, Xingyu Wan, Ran Hua, Junhong Jiang, Baotian Wang, Rui Tao, De Wu

“…Methods Genetic diagnosis was performed using trio‐whole exome sequencing, followed by bioinformatics predictions of pathogenicity. Structural modeling assessed the potential impact of the variant. …”
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Novel Compound Heterozygous BBS2 and Homozygous MKKS Variants Detected in Chinese Families with Bardet–Biedl Syndrome by Li Huang, Limei Sun, Zhirong Wang, Songshan Li, Chonglin Chen, Xiaoling Luo, Xiaoyan Ding

“…Whole exome sequencing was performed in the two families, followed by a multistep bioinformatics analysis. Sanger sequencing was used to verify the variants and to perform a segregation analysis. …”
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Multi-omics analysis reveals novel causal pathways in psoriasis pathogenesis by Hua Guo, Jinyang Gao, Liping Gong, Yanqing Wang

“…Publicly available datasets were utilized, including psoriasis GWAS data from the European Molecular Biology Laboratory–European Bioinformatics Institute and the UK Biobank. Heterogeneity in dependent instruments (HEIDI) test and colocalization analyses were performed to identify shared causal variants, and multi-omics integration was employed to construct potential regulatory pathways. …”
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Gene Expression Signatures of Peripheral Blood Mononuclear Cells during the Early Post-Transplant Period in Patients Developing Cardiac Allograft Vasculopathy by Khurram Shahzad, Martin Cadeiras, Sarfaraz Memon, Barry Zeeberg, Tod Klingler, Anshu Sinha, Esteban G. Tabak, Sreevalsa Unniachan, Mario C. Deng

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The MIR181A2HG/miR‐5680/VCAN‐CD44 Axis Regulates Gastric Cancer Lymph Node Metastasis by Promoting M2 Macrophage Polarization by Weijie Zang, Yongpu Yang, Junjie Chen, Qinsheng Mao, Wanjiang Xue, Yilin Hu

“…Methods The expression of MIR181A2HG in GC was identified through bioinformatics screening analysis and qRT‐PCR validation. …”
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The key role of the NUDT3 gene in lung adenocarcinoma progression and its association with the manganese ion metabolism family by Deyong Ge, Xinyu Xu, Liyi Fang, Huihui Tao

“…GAPDH was used as the reference gene for normalization, and the relative expression levels of NUDT3 in these cell lines were analyzed to confirm bioinformatics findings. Results NUDT3 was found to be significantly upregulated in lung adenocarcinoma and highly correlated with tumor mutation burden (TMB) and mutation enrichment (MEs). …”
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EZH2 Mediates miR-146a-5p/HIF-1α to Alleviate Inflammation and Glycolysis after Acute Spinal Cord Injury by Shuangfei Ni, Bo Yang, Lei Xia, Huafeng Zhang

“…ChIP verified the enrichment of H3K27me3 in the miR-146a-5p promoter region. Bioinformatics predicted the binding sites of HIF-1α and miR-146a-5p, and dual-luciferase reporter assay verified the binding of HIF-1α and miR-146a-5p. …”
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Proteomic Identification and Functional Analysis of Babesia microti Reveals Heparin-Binding Proteins by Yu Chun Cai, Bin Xu, Yan Hong Chu, Ying Fang Yu, Jia Hui Sun, Zi Ran Mo, Han Yin Yang, Shu Ning Yan, Mu Xin Chen, Jia Xu Chen

“…This study aims to use proteomics to identify Babesia microti proteins with high binding affinity to heparin. Bioinformatics was utilized to analyze the subcellular localization and biological functions of these proteins. …”
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Scrutinizing the evidence of anthracene toxicity on adrenergic receptor beta-2 and its bioremediation by fungal manganese peroxidase via in silico approaches by Muhammad Naveed, Khadija Khatoon, Tariq Aziz, Rida Naveed, Muhammad Nouman Majeed, Maida Salah Ud Din, Tayyab Javed, Ayaz Ali Khan, Abdullah F. Alasmari

“…This study aims to alleviate the adverse environmental effects of anthracene through fungal degradation, focusing on bioremediation approaches using bioinformatics. Toxicity prediction using Pro-Tox 3.0 identified anthracene as a compound of toxicity class 4 with a LD50 of 316 mg/kg. …”
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Impact of phytoconstituents on oral health practices: a post COVID-19 observation by Harsh Kumar, Reena Singh, Daljeet Singh Dhanjal, Chirag Chopra, Natália Cruz-Martins, Gheyath K. Nasrallah, Amin F. Majdalawieh, Sivakumar Manickam, Shahida Anusha Siddiqui, Dinesh Kumar, Indu Sharma, Varun Sharma

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Integrated Analysis and Validation of Ferroptosis-Related Genes Associated with Ischemia/Reperfusion Injury in Lung Transplantation by Li Q, Yin J, Lin Q, He J, Shi X, Nie H

“…This study aims to explore the role of ferroptosis in lung transplantation-related ischemia/reperfusion injury and to identify its potential molecular mechanisms through bioinformatics analysis.Methods: Transcriptome data from lung transplant patients were obtained from the Gene Expression Omnibus (GEO) database. …”
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PLCG2 and IFNAR1: The Potential Biomarkers Mediated by Immune Infiltration and Osteoclast Differentiation of Ankylosing Spondylitis in the Peripheral Blood by Bo Han, Qiaobo Xie, Weishi Liang, Peng Yin, Xianjun Qu, Yong Hai

“…We performed bioinformatics analysis using R software to validate different expression levels. …”
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SIGLEC11 promotes M2 macrophage polarization through AKT–mTOR signaling and facilitates the progression of gastric cancer by Chen Li, Yang Lu, Yihao Liu, Minmin Shi, Zhenggang Zhu, Jingxin Yin, Qimeng Shi, Da Fu, Zhenqiang Wang

“…This study aimed to elucidate the prognostic relevance of SIGLEC11 expression and its role in the immune microenvironment in patients with GC.Methods SIGLEC11 expression profile was analyzed using bioinformatics, immunohistochemistry, and immunofluorescence staining. …”
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Atrial Arrhythmias in Patients with Severe COVID-19 by Kai-Yue Han, Qi Qiao, Ye-Qian Zhu, Xin-Guang Chen, Xing-Xing Kang, Gao-Feng Zhang, Xun-Chao Cai, Yong Du, Jing Jin, Ruo-Min Di, Chen-Xi Yang, Feng-Xiang Zhang, Ying-Jia Xu

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