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Chen L, Zhu S, Zhao L, Ye W. Identification of exosome-related gene features in psoriasis and construction of a diagnostic model via integrated bioinformatics analysis. Comput Methods Biomech Biomed Engin 2024:1-12. [PMID: 39358990 DOI: 10.1080/10255842.2024.2410224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 09/11/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND Psoriasis, a chronic inflammatory dermatosis, profoundly affects patients' well-being. Although exosomes are key in disease etiology, diagnostic potentials of associated genes are unclear. Our research targeted bioinformatics-based characterization of exosome-related genes and the development of a diagnostic model for psoriasis. METHODS Within GSE30999 dataset, an exosome-centric diagnostic model was formulated. Its diagnostic capability was appraised in GSE30999 and GSE14905 cohorts. Human keratinocytes (HaCaT) were used to construct psoriasis cell model. qRT-PCR was used to detect expression of diagnostic genes in the model. Construction of a protein-protein interaction network was undertaken, complemented by enrichment analyses. Comparative evaluation of immunological microenvironments between healthy controls and disease cohort was executed. Prospective miRNAs and transcription factors (TFs) were prognosticated using online prediction tools. RESULTS A distinctive diagnostic model with superior diagnostic performance, evidenced by an AUC value greater than 0.88, was unveiled. The model featured seven exosome-related biomarker genes (CCNA2, NDC80, CCNB1, CDCA8, KIF11, CENPF, and ASPM) interwoven in a complex network and chiefly linked in the regulation of Cell Cycle and Cellular Senescence. These genes were significantly overexpressed in psoriasis cell models. Immune infiltration analysis distinguished profound discrepancies (p < 0.05) in immunological microenvironment between disease and control groups with enrichment of T cells CD4 memory activated, Macrophages M1, and Neutrophils in the disease group. 11 miRNAs and 27 TFs were identified. CONCLUSION The study introduces a new and potent diagnostic model for psoriasis, with selection of credible exosome-associated biomarker genes. These discoveries aid in clinical diagnostics and research on exosome involvement in psoriasis.
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Affiliation(s)
- Lifen Chen
- Department of Clinical Laboratory, Lishui People's Hospital, Lishui City, Zhejiang Province, China
| | - Shuangmei Zhu
- Department of Radiation Oncology, Lishui People's Hospital, Lishui City, Zhejiang Province, China
| | - Lu Zhao
- Department of Ultrasound, Lishui People's Hospital, Lishui City, Zhejiang Province, China
| | - Wenxia Ye
- Department of Dermatology, Lishui People's Hospital, Lishui City, Zhejiang Province, China
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Xu S, Shi H, Liu Y, Lin J, Wu X, Lu R, Fan Y, Tan W. Identification of biomarkers associated with pathological tumor staging and their utility in the diagnosis and prognosis of prostate cancer. Lab Med 2024:lmae059. [PMID: 39141479 DOI: 10.1093/labmed/lmae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
OBJECTIVE Pathological tumor (pT) staging plays a crucial role in prostate cancer (PCa) diagnosis. This study aimed to identify pT stage-associated biomarkers and explored their utility in PCa prognosis. METHODS GSE69223 was used to identify potential targets differentially expressed between level 2 of pT staging (pT2) and level 3 of pT staging (pT3). Quantitative reverse transcriptase-polymerase chain reaction and immunohistochemistry were performed on tissues from patients with PCa to screen the pT stage-associated targets and to explore the prognostic value of these targets in PCa. RESULTS CENPI and SLC38A11 were most significantly upregulated, whereas ANO6 and KANK2 were mostly decreased in pT3 tumors compared with pT2 staging. ANO6 levels were negatively associated with preoperative prostate-specific antigen (PSA) levels, lymph node staging (N staging), Gleason score, and overall survival (OS); CENPI was positively associated with preoperative PSA levels, N staging, and OS, but was not associated with the Gleason score; SLC38A11 and KANK2 were not associated with OS. ANO6 and KANK2 were correlated with neutrophil markers, whereas CENPI was correlated with macrophage M2 types. CONCLUSION We identified 4 reliable PCa biomarkers associated with pT staging that would be valuable for diagnosing and determining PCa prognosis.
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Affiliation(s)
- Shiquan Xu
- Department of Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - He Shi
- Orthopedics and Sports Medicine Center, Qingdao Municipal Hospital, Qingdao, China
| | - Yiran Liu
- College of Traditional Chinese Medicine, Weifang Medical University, Weifang, China
| | - Jing Lin
- Department of Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xia Wu
- Department of Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Ruichun Lu
- Department of Cadre Healthcare/Geriatrics, Qingdao Municipal Hospital, Qingdao, China
| | - Yu Fan
- Department of Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Weiqiang Tan
- Department of Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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Cui Y, Jiang N. CDCA8 Facilitates Tumor Proliferation and Predicts a Poor Prognosis in Hepatocellular Carcinoma. Appl Biochem Biotechnol 2024; 196:1481-1492. [PMID: 37428386 DOI: 10.1007/s12010-023-04603-w] [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] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
CDCA8 expression is abnormally high in a variety of cancers and involved in the biological process of tumor malignancy. In this study, we discovered that the expression of CDCA8 was up-regulated in hepatocellular carcinoma cancer (HCC) tissues and high levels of CDCA8 are associated with larger tumor size, higher AFP (α-fetoprotein) levels, and unfavorable prognosis. Cell functional experiments revealed that CDCA8 silencing remarkably inhibited proliferation and promoted apoptosis in SNU-387 and Hep-3B cells. The results of flow cytometry showed that CDCA8 regulated CDK1 and cyclin B1 expression to arrest at the S phase, inhibited proliferation, and promoted apoptosis. In addition, in vivo studies have confirmed that silencing CDCA8 could regulate CDK1/cyclin B1 signaling axis to inhibit the growth of HCC xenograft tumor. Our study demonstrated CDCA8 acts an oncogene to facilitate cell proliferation of HCC via regulating cell cycle, indicating the promising application value of CDCA8 for HCC diagnosis and clinical treatment.
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Affiliation(s)
- Yunlong Cui
- Department of Hepatobiliary Surgery, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Ning Jiang
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Tianjin University of Sport, No.16 Donghai Road, West Tuanbo New Town, Jinghai District, Tianjin, China.
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Hu H, Umair M, Khan SA, Sani AI, Iqbal S, Khalid F, Sultan R, Abdel-Maksoud MA, Mubarak A, Dawoud TM, Malik A, Saleh IA, Al Amri AA, Algarzae NK, Kodous AS, Hameed Y. CDCA8, a mitosis-related gene, as a prospective pan-cancer biomarker: implications for survival prognosis and oncogenic immunology. Am J Transl Res 2024; 16:432-445. [PMID: 38463578 PMCID: PMC10918119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Human cell division cycle-associated protein 8 (CDCA8), a critical regulator of mitosis, has been identified as a prospective prognostic biomarker in several cancer types, including breast, colon, and lung cancers. This study analyzed the diagnostic/prognostic potential and clinical implications of CDCA8 across diverse cancers. METHODS Bioinformatics and molecular experiments. RESULTS Analyzing TCGA data via TIMER2 and GEPIA2 databases revealed significant up-regulation of CDCA8 in 23 cancer types compared to normal tissues. Prognostically, elevated CDCA8 expression correlated with poorer overall survival in KIRC, LUAD, and SKCM, emphasizing its potential as a prognostic marker. UALCAN analysis demonstrated CDCA8 up-regulation based on clinical variables, such as cancer stage, race, and gender, in these cancers. Epigenetic exploration indicated reduced CDCA8 promoter methylation levels in Kidney Renal Clear Cell Carcinoma (KIRC), Lung Adenocarcinoma (LUAD), and Skin Cutaneous Melanoma (SKCM) tissues compared to normal controls. Promoter methylation and mutational analyses showcased a hypomethylation and low mutation rate for CDCA8 in these cancers. Correlation analysis revealed positive associations between CDCA8 expression and infiltrating immune cells, particularly CD8+ and CD4+ T cells. Protein-protein interaction (PPI) network analysis unveiled key interacting proteins, while gene enrichment analysis highlighted their involvement in crucial cellular processes and pathways. Additionally, exploration of CDCA8-associated drugs through DrugBank presented potential therapeutic options for KIRC, LUAD, and SKCM. In vitro validation using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) confirmed elevated CDCA8 expression in LUAD cell lines (A549 and H1299) compared to control cell lines (Beas-2B and NL-20). CONCLUSION This study provides concise insights into CDCA8's multifaceted role in KIRC, LUAD, and SKCM, covering expression patterns, diagnostic and prognostic relevance, epigenetic regulation, mutational landscape, immune infiltration, and therapeutic implications.
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Affiliation(s)
- Hanjie Hu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Muhammad Umair
- Department of Physiology, Gomal Medical College, MTIDera Ismail Khan, Pakistan
| | - Sikandar Ali Khan
- Department of Biochemistry Khyber Girls Medical CollegePeshawar, Pakistan
| | - Aliya Irshad Sani
- Department of Biochemistry, Ziauddin Medical CollegeKarachi 74700, Pakistan
| | - Sahar Iqbal
- Department of Pathology, Azra Naheed Medical CollegeLahore 54000, Pakistan
| | - Fatima Khalid
- Department of Pathology, Al Aleem Medical CollegeLahore, Pakistan
| | - Rizwana Sultan
- Department of Pathology, Faculty of Veterinary and Animal Sciences, Cholistan University of Veterinary and Animal SciencesBahawalpur, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Turki M Dawoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud UniversitySaudi Arabia
| | | | - Abdul Aziz Al Amri
- Biochemistry Department, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Norah Khaled Algarzae
- Department of Physiology, College of Medicine, King Saud UniversityRiyadh 11149, Saudi Arabia
| | - Ahmad S Kodous
- Radiation Biology Department, National Center for Radiation Research & Technology (NCRRT), Egyptian Atomic-Energy Authority (EAEA)Egypt
- Department of Molecular Oncology, Cancer Institute (WIA)38, Sardar Patel Road, Chennai, P.O. Box 600036, Tamilnadu, India
| | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry Biotechnology and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
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Zhao J, Luo Z, Fu R, Zhou J, Chen S, Wang J, Chen D, Xie X. Disulfidptosis-related signatures for prognostic and immunotherapy reactivity evaluation in hepatocellular carcinoma. Eur J Med Res 2023; 28:571. [PMID: 38057871 PMCID: PMC10698993 DOI: 10.1186/s40001-023-01535-3] [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: 04/29/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common cancers in the world and a nonnegligible health concern on a worldwide scale. Disulfidptosis is a novel mode of cell death, which is mainly caused by the collapse of the actin skeleton. Although many studies have demonstrated that various types of cell death are associated with cancer treatment, the relationship between disulfidptosis and HCC has not been elucidated. METHODS Here, we mainly applied bioinformatics methods to construct a disulfidptosis related risk model in HCC patients. Specifically, transcriptome data and clinical information were downloaded from the Gene Expression Omnibus (GEO), International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) database. A total of 45 co-expressed genes were extracted between the disulfidptosis-related genes (DRGs) and the differential expression genes (DEGs) of liver hepatocellular carcinoma (LIHC) in the TCGA database. The LIHC cohort was divided into two subgroups with different prognosis by k-mean consensus clustering and functional enrichment analysis was performed. Subsequently, three hub genes (CDCA8, SPP2 and RDH16) were screened by Cox regression and LASSO regression analysis. In addition, a risk signature was constructed and the HCC cohort was divided into high risk score and low risk score subgroups to compare the prognosis, clinical features and immune landscape between the two subgroups. Finally, the prognostic model of independent risk factors was constructed and verified. CONCLUSIONS High DRGs-related risk score in HCC individuals predict poor prognosis and are associated with poor immunotherapy response, which indicates that risk score assessment model can be utilized to guide clinical treatment strategy.
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Affiliation(s)
- Jiajing Zhao
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Zeminshan Luo
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Ruizhi Fu
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Jinghong Zhou
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Shubiao Chen
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Jianjie Wang
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Dewang Chen
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China
| | - Xiaojun Xie
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, China.
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Gu P, Zhang M, Chen X, Du J, Chen L, He X, Li M. Prognostic value of cell division cycle-associated protein-3 in prostate cancer. Medicine (Baltimore) 2023; 102:e34655. [PMID: 37682152 PMCID: PMC10489371 DOI: 10.1097/md.0000000000034655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND The study was aimed to explore cell division cycle-associated protein-3 (CDCA3) expression and its correlation with clinicopathological characteristics, and identification of co-expressed genes of CDCA3 in prostate cancer (PCa). METHODS Data for CDCA3 mRNA expression in PCa were obtained from The Cancer Genome Atlas database. Furtherly, CDCA3 protein expression was examined by immunohistochemistry in 80 cases, including 20 normal prostate samples and 60 PCa samples. Then we used "survival" package to obtain the differentially expressed CDCA3 mRNA associated with prognosis of PCa patients. "pROC" package was used to analyze receiver operating characteristic of CDCA3. We used chi-square test, Kruskal-Wallis test and Wilcoxon rank sum test to identify clinicopathological parameters that correlated with CDCA3 expression. In order to determine the effects of CDCA3 expression and clinicopathological parameters on survival, univariate cox regression analysis was performed. Finally, the co-expressed genes of CDCA3 in PCa were explored by search tool for the retrieval of interacting genes, Kyoto encyclopedia of genes and genomes enrichment analysis and Spearman correlation analysis. RESULTS In this study, we found that CDCA3 expression was increased in PCa. PCa patients with higher CDCA3 expression had poor outcomes. In terms of receiver operating characteristic, CDCA3 had an area under the curve of 0.857. High CDCA3 expression was positively correlated with advanced T stage, N stage, Gleason score, and served as an independent predictor of progress free interval in PCa patients. Then 20 proteins closely related to CDCA3 were screened through STRING website. Functional enrichment analysis revealed that, Kyoto encyclopedia of genes and genomes pathway was mainly enriched in cell cycle, including 6 genes, BUB1, CCNA2, CDK1, CDC20, TTK, and CCNB2. CONCLUSION CDCA3 is significantly associated with the prognosis of PCa, which may be an indicator of the diagnosis and prognosis of PCa and a new therapeutic target.
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Affiliation(s)
- Peng Gu
- Department of Urology, Xishan People’s Hospital of Wuxi City, Wuxi, Jiangsu, China
| | - Minhao Zhang
- Department of Urology, Xishan People’s Hospital of Wuxi City, Wuxi, Jiangsu, China
| | - Xinhua Chen
- Department of Operating Room, Xishan People’s Hospital of Wuxi City, Wuxi, Jiangsu, China
| | - Jie Du
- Department of Urology, Xishan People’s Hospital of Wuxi City, Wuxi, Jiangsu, China
| | - Lu Chen
- Department of Pathology, Xishan People’s Hospital of Wuxi City, Wuxi, Jiangsu, China
| | - Xiaoliang He
- Department of Urology, Xishan People’s Hospital of Wuxi City, Wuxi, Jiangsu, China
| | - Meilin Li
- Department of Medicine, Wuxi No. 5 People’s Hospital, Wuxi, Jiangsu, China
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Feriz AM, Khosrojerdi A, Lotfollahi M, Shamsaki N, GhasemiGol M, HosseiniGol E, Fereidouni M, Rohban MH, Sebzari AR, Saghafi S, Leone P, Silvestris N, Safarpour H, Racanelli V. Single-cell RNA sequencing uncovers heterogeneous transcriptional signatures in tumor-infiltrated dendritic cells in prostate cancer. Heliyon 2023; 9:e15694. [PMID: 37144199 PMCID: PMC10151421 DOI: 10.1016/j.heliyon.2023.e15694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023] Open
Abstract
Prostate cancer (PCa) is one of the two solid malignancies in which a higher T cell infiltration in the tumor microenvironment (TME) corresponds with a worse prognosis for the tumor. The inability of T cells to eliminate tumor cells despite an increase in their number reinforces the possibility of impaired antigen presentation. In this study, we investigated the TME at single-cell resolution to understand the molecular function and communication of dendritic cells (DCs) (as professional antigen-presenting cells). According to our data, tumor cells stimulate the migration of immature DCs to the tumor site by inducing inflammatory chemokines. Many signaling pathways such as TNF-α/NF-κB, IL2/STAT5, and E2F up-regulated after DCs enter the tumor location. In addition, some molecules such as GPR34 and SLCO2B1 decreased on the surface of DCs. The analysis of molecular and signaling alterations in DCs revealed some suppression mechanisms of tumors, such as removing mature DCs, reducing the DC's survival, inducing anergy or exhaustion in the effector T cells, and enhancing the differentiation of T cells to Th2 and Tregs. In addition, we investigated the cellular and molecular communication between DCs and macrophages in the tumor site and found three molecular pairs including CCR5/CCL5, CD52/SIGLEC10, and HLA-DPB1/TNFSF13B. These molecular pairs are involved in the migration of immature DCs to the TME and disrupt the antigen-presenting function of DCs. Furthermore, we presented new therapeutic targets by the construction of a gene co-expression network. These data increase our knowledge of the heterogeneity and the role of DCs in PCa TME.
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Affiliation(s)
- Adib Miraki Feriz
- Birjand University of Medical Sciences (BUMS), Birjand, Iran
- Cellular and Molecular Research Center, BUMS, Birjand, Iran
| | | | - Mohammad Lotfollahi
- Computational Health Center, Helmholtz Munich, Germany
- Wellcome Sanger Institute, Cambridge, UK
| | - Neusha Shamsaki
- Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | - Mohammad GhasemiGol
- College of Engineering & Mines, University of North Dakota, North Dakota, USA
| | - Edris HosseiniGol
- Department of Computer Engineering, University of Birjand, Birjand, Iran
| | | | | | - Ahmad Reza Sebzari
- Radiation Oncology, Clinical Research Development Unit (CRDU), ValiAsr Hospital, BUMS, Birjand, Iran
| | - Samira Saghafi
- Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | - Patrizia Leone
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Bari, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology “G. Barresi”, University of Messina, Messina, Italy
| | - Hossein Safarpour
- Cellular and Molecular Research Center, BUMS, Birjand, Iran
- Corresponding author.
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Bari, Italy
- Corresponding author.
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