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    Comparative Transcriptomic Analyses of Peripheral Blood Mononuclear Cells of COVID-19 Patients without Pneumonia and with Severe Pneumonia in the First Year of Follow-Up
    (Mdpi, 2024) Kayalar, Ozgecan; Cetinkaya, Pelin Duru; Eldem, Vahap; Baris, Serap Argun; Kokturk, Nurdan; Kuralay, Selim Can; Rajabi, Hadi
    The multisystemic effects of COVID-19 may continue for a longer time period following the acute phase, depending on the severity of the disease. However, long-term systemic transcriptomic changes associated with COVID-19 disease and the impact of disease severity are not fully understood. We aimed to investigate the impact of COVID-19 and its severity on transcriptomic alterations in peripheral blood mononuclear cells (PBMCs) following 1 year of the disease. PBMCs were isolated from the peripheral blood of healthy control donors who did not have COVID-19 (C; n = 13), from COVID-19 patients without pneumonia (NP; n = 11), and from COVID-19 patients with severe pneumonia (SP; n = 10) after 1-year of follow-up. Following RNA isolation from PBMCs, high-quality RNAs were sequenced after creating a library. Differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElncRNAs) were identified using Benjamini-Hochberg correction and they were analysed for hierarchical clustering and principal component analysis (PCA). Intergroup comparisons (C vs. NP, C vs. SP, and NP vs. SP) of DEGs and DElncRNAs were performed and hub genes were determined. Functional enrichment analyses of DEGs and DElncRNAs were made using Metascape (v3.5.20240101) and the first version of NCPATH. The RNA sequencing analysis revealed 4843 DEGs and 1056 DElncRNAs in C vs. NP, 1651 DEGs and 577 DElncRNAs in C vs. SP, and 954 DEGs and 148 DElncRNAs in NP vs. SP, with 291 DEGs and 70 DElncRNAs shared across all groups, respectively. We identified 14 hub genes from 291 DEGs, with functional enrichment analysis showing upregulated DEGs mainly linked to inflammation and osteoclast differentiation and downregulated DEGs to viral infections and immune responses. The analysis showed that 291 common and 14 hub genes were associated with pneumonia and that these genes could be regulated by the transcription factors JUN and NF kappa B1 carrying the NF kappa B binding site. We also revealed unique immune cell signatures across DEG categories indicating that the upregulated DEGs were associated with neutrophils and monocytes, while downregulated DEGs were associated with CD4 memory effector T cells. The comparative transcriptomic analysis of NP and SP groups with 52 gene signatures suggestive of IPF risk showed a lower risk of IPF in the SP group than the NP patients. Our findings suggest that COVID-19 may cause long term pathologies by modulating the expression of various DEGs, DeLncRNAs, and hub genes at the cellular level.
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    Evaluation of Patients with COVID-19 Followed Up in Intensive Care Units in the Second Year of the Pandemic: A Multicenter Point Prevalence Study (vol 25, pg 11, 2024)
    (Aves, 2024) Balbay, Ege Gulec; Kayalar, Ozgecan; Balbay, Oner; Dikensoy, Oner; Arbak, Peri; Bayram, Hasan
    [No abstract available]
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    Impact of Earthquakes on Lung Health
    (Aves, 2024) Balbay, Ege Gulec; Kayalar, Ozgecan; Balbay, Oner; Dikensoy, Oner; Arbak, Peri; Bayram, Hasan
    Earthquakes are catastrophic natural disasters that cause extensive damage to infrastructure and disrupt the lives of millions worldwide. Beyond the immediate physical and psychological damage caused by earthquakes, these events can significantly impact respiratory health. The inhalation of dust, smoke, particulates, toxic gases, and asbestos exposure can lead to various respiratory health pathologies. These include respiratory infections, exacerbations of pre-existing respiratory diseases, chest traumas, and pulmonary and venous thromboembolism. Longitudinal studies are necessary to assess the long-term respiratory health effects in affected populations. By addressing these knowledge gaps, future mitigation strategies and preparedness measures can be developed to minimize the respiratory health impacts of earthquakes and improve the well-being of affected communities. Robust building infrastructure and comprehensive earthquake preparedness are emerging as the most important determinants for not only mitigating building collapse but also significantly reducing the potential health impacts that follow. This comprehensive review aims to provide a systematic overview of the lung health impacts of earthquakes. It highlights the need for further research to identify specific pollutants, air contaminants, and environmental factors contributing to respiratory health issues following earthquakes.