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Merzah M, Póliska S, Balogh L, Sándor J, Szász I, Natae S, Fiatal S. A Transcriptomic Analysis of Smoking-Induced Gene Expression Alterations in Coronary Artery Disease Patients. Int J Mol Sci 2023; 24:13920. [PMID: 37762221 PMCID: PMC10530857 DOI: 10.3390/ijms241813920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/21/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Smoking is a well established risk factor for coronary artery disease (CAD). Despite this, there have been no previous studies investigating the effects of smoking on blood gene expression in CAD patients. This single-centre cross-sectional study was designed with clearly defined inclusion criteria to address this gap. We conducted a high-throughput approach using next generation sequencing analysis with a single-end sequencing protocol and a read length of 75-cycles. Sixty-one patients with a median age of 67 years (range: 28-88 years) were recruited, and only 44 subjects were included for further analyses. Our investigation revealed 120 differentially expressed genes (DEGs) between smokers and nonsmokers, with a fold change (FC) of ≥1.5 and a p-value < 0.05. Among these DEGs, 15 were upregulated and 105 were downregulated. Notably, when applying a more stringent adjusted FC ≥ 2.0, 31 DEGs (5 upregulated, annotated to immune response pathways, and 26 downregulated, involving oxygen and haem binding or activity, with FDR ≤ 0.03) remained statistically significant at an alpha level of <0.05. Our results illuminate the molecular mechanisms underlying CAD, fortifying existing epidemiological evidence. Of particular interest is the unexplored overexpression of RCAN3, TRAV4, and JCHAIN genes, which may hold promising implications for the involvement of these genes in CAD among smokers.
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Affiliation(s)
- Mohammed Merzah
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (M.M.); (J.S.); (S.N.)
| | - Szilárd Póliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - László Balogh
- Cardiology and Cardiac Surgery Clinic, University of Debrecen, H-4032 Debrecen, Hungary
| | - János Sándor
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (M.M.); (J.S.); (S.N.)
- ELKH-DE Public Health Research Group, Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - István Szász
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (M.M.); (J.S.); (S.N.)
- ELKH-DE Public Health Research Group, Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Shewaye Natae
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (M.M.); (J.S.); (S.N.)
| | - Szilvia Fiatal
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (M.M.); (J.S.); (S.N.)
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Wang M, Wu Y, Li X, Dai M, Li S. IGJ suppresses breast cancer growth and metastasis by inhibiting EMT via the NF‑κB signaling pathway. Int J Oncol 2023; 63:105. [PMID: 37539706 PMCID: PMC10552693 DOI: 10.3892/ijo.2023.5553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Breast cancer metastasis is the primary cause of mortality of patients with breast cancer. The present study aimed to explore the role and underlying mechanisms of IGJ in the invasion and metastasis of breast cancer. The Cancer Genome Atlas database was utilized to analyze the differential gene expression profiles in patients with breast cancer with or without metastasis; the target gene, joining chain of multimeric IgA and IgM (JCHAIN, also known as IGJ, as referred to herein), with significant expression and with prognostic value was screened. The expression levels of IGJ in human breast cancer paired tissues and cell lines were detected using reverse transcription‑quantitative PCR and western blot analysis. IGJ differential expression was detected in paired human breast cancer tissues using immunohistochemistry. The role of IGJ in breast cancer was verified using CCK‑8, invasion and migration assays, and scratch tests in vivo and in vitro. Further exploration of the role and mechanism of IGJ in breast cancer was conducted through Gene Set Enrichment Analysis, Kyoto Encyclopedia of Genes and Genomes analysis, western blot analysis and immunofluorescence experiments. Through the analysis of gene expression profiles, it was found that IGJ was poorly expressed in patients with breast cancer with metastasis compared to patients with non‑metastatic breast cancer. The overexpression of IGJ was associated with an improved distant metastasis‑free survival and overall survival (OS). COX multivariate regression analysis demonstrated that IGJ was an independent prognostic factor for the OS and relapse‑free survival of patients with breast cancer. In comparison to healthy breast cancer adjacent tissues and cell lines, IGJ was poorly expressed in breast cancer tissues and cell lines (P<0.05). Further analyses indicated that the overexpression of IGJ suppressed the proliferation, invasion and metastasis of breast cancer cells in vivo and in vitro by inhibiting the occurrence of epithelial‑to‑mesenchymal transition (EMT) and suppressing the nuclear translocation of p65. Finally, rescue experiments indicated that IGJ restricted the proliferation and metastasis of breast cancer cells by regulating the NF‑κB signaling pathway. On the whole, the present study demonstrates that IGJ suppresses the invasion and metastasis of breast cancer by inhibiting both the occurrence of EMT and the NF‑κB signaling pathway. These findings may provide novel biomarkers and potential therapeutic targets for the treatment of metastatic breast cancer.
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Affiliation(s)
- Mengxue Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016
| | - Yushen Wu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016
| | - Xunjia Li
- Department of Nephrology, Chongqing Traditional Chinese Medicine Hospital, Chongqing 400013
| | - Meng Dai
- Department of Geriatric Oncology, Department of Palliative care, Chongqing University Cancer Hospital, Chongqing 400030, P.R. China
| | - Shengwei Li
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010
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Graves OK, Kim W, Özcan M, Ashraf S, Turkez H, Yuan M, Zhang C, Mardinoglu A, Li X. Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma. Biomed Pharmacother 2023; 161:114486. [PMID: 36906970 DOI: 10.1016/j.biopha.2023.114486] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the one of the most common subtypes in lung cancer. Although various targeted therapies have been used in the clinical practice, the 5-year overall survival rate of patients is still low. Thus, it is urgent to identify new therapeutic targets and develop new drugs for the treatment of the LUAD patients. METHODS Survival analysis was used to identify the prognostic genes. Gene co-expression network analysis was used to identify the hub genes driving the tumor development. A profile-based drug repositioning approach was used to repurpose the potentially useful drugs for targeting the hub genes. MTT and LDH assay were used to measure the cell viability and drug cytotoxicity, respectively. Western blot was used to detect the expression of the proteins. FINDINGS We identified 341 consistent prognostic genes from two independent LUAD cohorts, whose high expression was associated with poor survival outcomes of patients. Among them, eight genes were identified as hub genes due to their high centrality in the key functional modules in the gene-co-expression network analysis and these genes were associated with the various hallmarks of cancer (e.g., DNA replication and cell cycle). We performed drug repositioning analysis for three of the eight genes (CDCA8, MCM6, and TTK) based on our drug repositioning approach. Finally, we repurposed five drugs for inhibiting the protein expression level of each target gene and validated the drug efficacy by performing in vitro experiments. INTERPRETATION We found the consensus targetable genes for the treatment of LUAD patients with different races and geographic characteristics. We also proved the feasibility of our drug repositioning approach for the development of new drugs for disease treatment.
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Affiliation(s)
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Mehmet Özcan
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Sajda Ashraf
- Trustlife Labs, Drug Research & Development Center, 34774 Istanbul, Turkey.
| | - Hasan Turkez
- Trustlife Labs, Drug Research & Development Center, 34774 Istanbul, Turkey.
| | - Meng Yuan
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden.
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden; Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK.
| | - Xiangyu Li
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm SE-17165, Sweden; Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA 92101, USA; Guangzhou Laboratory, Guangzhou 510005, China.
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Feng X, Zhang T, Chou J, Liu L, Miller LD, Sullivan CA, Browne JD. Comprehensive gene cluster analysis of head and neck squamous cell carcinoma TCGA RNA-seq data defines B cell immunity-related genes as a robust survival predictor. Head Neck 2022; 44:443-452. [PMID: 34841601 PMCID: PMC8766919 DOI: 10.1002/hed.26944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The authors aimed to define novel gene expression signatures that are associated with patients' survival with head and neck squamous cell carcinoma (HNSCC). METHODS TCGA RNA-seq data were used for gene expression clusters extraction from 499 tumor samples by the "EPIG" method. Tumor samples were then partitioned into lower and higher than median level groups for survival relevant analysis by Kaplan-Meier estimator. RESULTS We found that two gene clusters (_1, _2) are favorably, while two (_3, _4) are unfavorably, associated with patients' survival with HNSCC. Notably, most genes on the top lists of cluster_2 are associated with B cells. A gene expression signature with combined genes from cluster_2 and _4 was further determined to be associated with HNSCC survival rate. CONCLUSION Our work strongly supported a favorable role of B cells in patients' survival with HNSCC and identified a novel coexpressed gene signature as prognostic biomarker for patients' survival with HNSCC estimation.
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Affiliation(s)
- Xin Feng
- Departments of Otolaryngology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tan Zhang
- Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jeff Chou
- Center for Cancer Genomics and Precision Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Liang Liu
- Center for Cancer Genomics and Precision Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Lance D. Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Christopher A. Sullivan
- Departments of Otolaryngology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - James D. Browne
- Departments of Otolaryngology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Kim H, Yu SJ, Yeo I, Cho YY, Lee DH, Cho Y, Cho EJ, Lee JH, Kim YJ, Lee S, Jun J, Park T, Yoon JH, Kim Y. Prediction of Response to Sorafenib in Hepatocellular Carcinoma: A Putative Marker Panel by Multiple Reaction Monitoring-Mass Spectrometry (MRM-MS). Mol Cell Proteomics 2017; 16:1312-1323. [PMID: 28550167 DOI: 10.1074/mcp.m116.066704] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/10/2017] [Indexed: 12/11/2022] Open
Abstract
Sorafenib is the only standard treatment for unresectable hepatocellular carcinoma (HCC), but it provides modest survival benefits over placebo, necessitating predictive biomarkers of the response to sorafenib. Serum samples were obtained from 115 consecutive patients with HCC before sorafenib treatment and analyzed by multiple reaction monitoring-mass spectrometry (MRM-MS) and ELISA to quantify candidate biomarkers. We verified a triple-marker panel to be predictive of the response to sorafenib by MRM-MS, comprising CD5 antigen-like (CD5L), immunoglobulin J (IGJ), and galectin-3-binding protein (LGALS3BP), in HCC patients. This panel was a significant predictor (AUROC > 0.950) of the response to sorafenib treatment, having the best cut-off value (0.4) by multivariate analysis. In the training set, patients who exceeded this cut-off value had significantly better overall survival (median, 21.4 months) than those with lower values (median, 8.6 months; p = 0.001). Further, a value that was lower than this cutoff was an independent predictor of poor overall survival [hazard ratio (HR), 2.728; 95% confidence interval (CI), 1.312-5.672; p = 0.007] and remained an independent predictive factor of rapid progression (HR, 2.631; 95% CI, 1.448-4.780; p = 0.002). When applied to the independent validation set, levels of the cut-off value for triple-marker panel maintained their prognostic value for poor clinical outcomes. On the contrast, the triple-marker panel was not a prognostic factor for patients who were treated with transarterial chemoembolization (TACE). The discriminatory signature of a triple-marker panel provides new insights into targeted proteomic biomarkers for individualized sorafenib therapy.
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Affiliation(s)
- Hyunsoo Kim
- From the ‡Department of Biomedical Engineering.,§Institute of Medical and Biological Engineering, Medical Research Center, and
| | - Su Jong Yu
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Injun Yeo
- From the ‡Department of Biomedical Engineering
| | - Young Youn Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Dong Hyeon Lee
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Yuri Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Eun Ju Cho
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Jeong-Hoon Lee
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | - Yoon Jun Kim
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea
| | | | - Jongsoo Jun
- **Department of Statistics, Seoul National University, Daehak-dong, Seoul 151-742 Korea
| | - Taesung Park
- ‖Interdisciplinary program in Bioinformatics and.,**Department of Statistics, Seoul National University, Daehak-dong, Seoul 151-742 Korea
| | - Jung-Hwan Yoon
- ¶Department of Internal Medicine and Liver Research Institute, Yongon-Dong, Seoul 110-799 Korea;
| | - Youngsoo Kim
- From the ‡Department of Biomedical Engineering; .,§Institute of Medical and Biological Engineering, Medical Research Center, and
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Petrušić V, Živković I, Stojanović M, Stojićević I, Marinković E, Dimitrijević L. Hexameric immunoglobulin M in humans: desired or unwanted? Med Hypotheses 2011; 77:959-61. [PMID: 21903335 DOI: 10.1016/j.mehy.2011.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 08/12/2011] [Indexed: 01/04/2023]
Abstract
Immunoglobulin M (IgM) is the first antibody produced upon infection, and is often suggested as the first line of defense of human immune system. In addition to being present on the surface of naïve B cells as a monomeric molecule, IgM is always secreted as a polymer. The most abundant IgM polymer in humans is pentamer, composed of five monomeric units, joined together by so-called joining or J chain. On the other hand, it is well known that hexameric IgM can be also found in human sera. Its presence is often related to different dissorders (Waldenström's macroglobulinemia, cold agglutinin, and recurrent urinary bacterial infections), although it is believed that small amounts of hexamer are present in normal human sera as well. Unlike pentamer, IgM hexamer contains six monomeric blocks and completely lacks J chain. Although it has been decades since its discovery, the precise function of IgM hexamer is still unknown. Since it was documented that hexamer is very potent in activating complement, it is suggested that its production in humans must be under strict control, and that it is produced in special conditions, when strong activation of complement is absolutely needed. However, the question is whether hexameric IgM is really a secret weapon or just an undesirable molecule in humans. According to structural and known functional characteristics of both pentamers and hexamers of IgM, it can be concluded that hexamers are, in addition to being maybe too reactive to be around, probably not that efficient in protecting us from bacterial and viral infections.
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Affiliation(s)
- Vladimir Petrušić
- Institute of Virology, Vaccines and Sera - Torlak, Vojvode Stepe 458, 11221 Belgrade, Serbia.
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Antipova NV, Snezhkov EV, Zavalova LL, Shakhparonov MI. [An immunological study of secreted human polymeric immunoglobulins' J-peptide tissue specificity]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 36:774-8. [PMID: 21317943 DOI: 10.1134/s1068162010060063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Contents of J-peptide of secreted human polymeric immunoglobulins may vary considerably with different pathologies, reflecting the state of the adaptive immune system. In this work assessed the content of J-peptide in various tissues of healthy people to use as a baseline for studies related to the change in the content of J-peptide in pathologies.
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Petrušić V, Stojanović M, Zivković I, Inić-Kanada A, Dimitrijević L. Changes in composition of IgM polymers in patients suffering from recurrent urinary bacterial infections after bacterial immunization treatment. Immunol Invest 2010; 39:781-95. [PMID: 20718658 DOI: 10.3109/08820139.2010.497831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
IgM is the first antibody produced during the immune response to infection or immunization, and it can be secreted as pentamer (containing a small polypeptide, termed as J chain) or hexamer (lacking J chain). In this paper we have analyzed structural characteristics (by electrophoresis and immunoblot) and anti-bacterial specificity (by enzyme-linked immunosorbent assay) of IgM antibodies purified from female patients suffering from recurrent bacterial infections of lower urinary tract and therapeutically immunized with the mixture of heat-inactivated uropathogenic bacteria. We report on changes in the composition of IgM polymers in tested patients. The immunization induced the raise of the levels of hexamers in patients that did not respond to immunization (non-responders), while the IgM polymers remained on the pentameric level in immunization dependent responders. We propose that the composition of IgM polymers could influence the immunization outcome and should be taken in count regarding the treatment of recurrent bacterial infections.
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Affiliation(s)
- Vladimir Petrušić
- Institute of Virology, Vaccines and Sera - Torlak, Department of Research and Development, Belgrade, Serbia.
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Mingaleeva RN, Chernov IP, Kopantzev EP, Zavalova LL, Sass AV, Sverdlov ED. Comparative analysis of herpes simplex virus thymidine kinase gene expression potentiation via HIV-1 Tat-TAR system and cancer-specific promoters in P53(+) and P53(-) cells. Mol Biol 2010. [DOI: 10.1134/s0026893310030131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Vayshlya NA, Zinovyeva MV, Sass AV, Kopantzev EP, Vinogradova TV, Sverdlov ED. Increased expression of BIRC5 in non-small cell lung cancer and esophageal squamous cell carcinoma does not correlate with the expression of its inhibitors SMAC/DIABLO and PML. Mol Biol 2008. [DOI: 10.1134/s0026893308040146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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