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Wang H, Xiong W, Laram Y, Hu L, Zhong W, Hu Y. Exploring the potential mechanism of Radix Bupleuri in the treatment of sepsis: a study based on network pharmacology and molecular docking. BMC Complement Med Ther 2024; 24:347. [PMID: 39354431 PMCID: PMC11446011 DOI: 10.1186/s12906-024-04637-5] [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: 02/28/2024] [Accepted: 09/09/2024] [Indexed: 10/03/2024] Open
Abstract
AIM To explore, using network pharmacology and RNA-seq technologies, potential active targets and mechanisms underpinning Radix Bupleuri's effectiveness during sepsis treatment. METHODS Following the Sepsis-3.0 criteria, the research cohort, comprising 23 sepsis patients and 10 healthy participants, was obtained from public databases. Peripheral blood samples were collected and subjected to RNA-seq analysis. Active ingredients and potential targets of Radix Bupleuri were identified using the Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine 2.0 (BATMAN-TCM 2.0) database and TCMSP database. Subsequently, protein-protein interaction (PPI) network construction, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted to explore cross-targets between disease and drugs. Survival analysis of key targets was performed using the GSE65682 dataset, and single-cell RNA-seq was employed for cellular localization analysis of key genes. Finally, molecular docking and Molecular dynamics simulation of the core target was conducted. RESULTS Differential expression analysis revealed 4253 genes associated with sepsis. Seventy-six active components and 1030 potential targets of Radix Bupleuri were identified. PPI, GO, and pathway enrichment analyses indicated involvement in the regulation of transmembrane transport, monatomic ion transport, and MAPK signaling. Survival curve analysis identified PIK3CD, ARRB2, SUCLG1, and SPI1 as key targets associated with lower mortality in the high expression group, while higher mortality was observed in the high PNP and FURIN expression groups. Single-cell RNA sequencing unveiled the cellular localization of PIK3CD, PNP, SPI1, and FURIN within macrophages, while ARRB2 and SUCLG1 exhibited localization in both macrophages and T-cells. Subsequent molecular docking and Molecular dynamics simulation indicated a potential binding interaction for Carvone-PIK3CD, Encecalin-ARRB2, Lauric Acid-SUCLG1, Pulegone-FURIN, Nootkatone-SPI1, and Saikogenin F-PNP. CONCLUSION Radix Bupleuri could modulate immune function by affecting PIK3CD, ARRB2, SUCLG1, FURIN, SPI1, and PNP, thereby potentially improving the prognosis of sepsis.
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Affiliation(s)
- Hao Wang
- Clinical Medical College, Southwest Medical University, Luzhou, People's Republic of China
| | - Wei Xiong
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Yongchu Laram
- Clinical Medical College, Southwest Medical University, Luzhou, People's Republic of China
| | - Li Hu
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Wu Zhong
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China.
| | - Yingchun Hu
- Department of Emergency Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China.
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Wang H, Laram Y, Hu L, Hu Y, Chen M. Exploring the potential mechanisms of Rehmannia glutinosa in treating sepsis based on network pharmacology. BMC Infect Dis 2024; 24:893. [PMID: 39217296 PMCID: PMC11366132 DOI: 10.1186/s12879-024-09796-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
The present study utilized network pharmacology to identify therapeutic targets and mechanisms of Rehmannia glutinosa in sepsis treatment. RNA-sequencing was conducted on peripheral blood samples collected from 23 sepsis patients and 10 healthy individuals. Subsequently, the RNA sequence data were analyzed for differential expression. Identification of active components and their putative targets was achieved through the HERB and SwissTarget Prediction databases, respectively. Functional enrichment analysis was performed using GO and KEGG pathways. Additionally, protein-protein interaction networks were constructed and survival analysis of key targets was conducted. Single-cell RNA sequencing provided cellular localization data, while molecular docking explored interactions with central targets. Results indicated significant involvement of identified targets in inflammation and Th17 cell differentiation. Survival analysis linked several targets with mortality rates, while molecular docking highlighted potential interactions between active components and specific targets, such as rehmaionoside a with ADAM17 and rehmapicrogenin with CD81. Molecular dynamics simulations confirmed the stability of these interactions, suggesting Rehmannia glutinosa's role in modulating immune functions in sepsis.
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Affiliation(s)
- Hao Wang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, People's Republic of China
| | - Yongchu Laram
- Department of Clinical Medicine, Southwest Medical University, Luzhou, People's Republic of China
| | - Li Hu
- Department of Emergency Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Yingchun Hu
- Department of Emergency Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China.
| | - Muhu Chen
- Department of Emergency Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China.
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Chen YJ, Li HF, Zhao FR, Yu M, Pan SY, Sun WZ, Yin YY, Zhu TT. Spermidine attenuates monocrotaline-induced pulmonary arterial hypertension in rats by inhibiting purine metabolism and polyamine synthesis-associated vascular remodeling. Int Immunopharmacol 2024; 132:111946. [PMID: 38552292 DOI: 10.1016/j.intimp.2024.111946] [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: 03/04/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024]
Abstract
Ensuring the homeostatic integrity of pulmonary artery endothelial cells (PAECs) is essential for combatting pulmonary arterial hypertension (PAH), as it equips the cells to withstand microenvironmental challenges. Spermidine (SPD), a potent facilitator of autophagy, has been identified as a significant contributor to PAECs function and survival. Despite SPD's observed benefits, a comprehensive understanding of its protective mechanisms has remained elusive. Through an integrated approach combining metabolomics and molecular biology, this study uncovers the molecular pathways employed by SPD in mitigating PAH induced by monocrotaline (MCT) in a Sprague-Dawley rat model. The study demonstrates that SPD administration (5 mg/kg/day) significantly corrects right ventricular impairment and pathological changes in pulmonary tissues following MCT exposure (60 mg/kg). Metabolomic profiling identified a purine metabolism disorder in MCT-treated rats, which SPD effectively normalized, conferring a protective effect against PAH progression. Subsequent in vitro analysis showed that SPD (0.8 mM) reduces oxidative stress and apoptosis in PAECs challenged with Dehydromonocrotaline (MCTP, 50 μM), likely by downregulating purine nucleoside phosphorylase (PNP) and modulating polyamine biosynthesis through alterations in S-adenosylmethionine decarboxylase (AMD1) expression and the subsequent production of decarboxylated S-adenosylmethionine (dcSAM). These findings advocate SPD's dual inhibitory effect on PNP and AMD1 as a novel strategy to conserve cellular ATP and alleviate oxidative injuries, thus providing a foundation for SPD's potential therapeutic application in PAH treatment.
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Affiliation(s)
- Yu-Jing Chen
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China
| | - Han-Fei Li
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China
| | - Fan-Rong Zhao
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China
| | - Miao Yu
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China
| | - Si-Yu Pan
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China
| | - Wen-Ze Sun
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China
| | - Yan-Yan Yin
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China
| | - Tian-Tian Zhu
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China; Department of Pharmacy, The first Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang 453003, China; Xinxiang Key Laboratory of Cascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, 453003, China.
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Skácel J, Djukic S, Baszczyňski O, Kalčic F, Bílek T, Chalupský K, Kozák J, Dvořáková A, Tloušt'ová E, Král'ová Z, Šmídková M, Voldřich J, Rumlová M, Pachl P, Brynda J, Vučková T, Fábry M, Snášel J, Pichová I, Řezáčová P, Mertlíková-Kaiserová H, Janeba Z. Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors. J Med Chem 2023; 66:6652-6681. [PMID: 37134237 DOI: 10.1021/acs.jmedchem.2c02097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Purine nucleoside phosphorylase (PNP) is a well-known molecular target with potential therapeutic applications in the treatment of T-cell malignancies and/or bacterial/parasitic infections. Here, we report the design, development of synthetic methodology, and biological evaluation of a series of 30 novel PNP inhibitors based on acyclic nucleoside phosphonates bearing a 9-deazahypoxanthine nucleobase. The strongest inhibitors exhibited IC50 values as low as 19 nM (human PNP) and 4 nM (Mycobacterium tuberculosis (Mt) PNP) and highly selective cytotoxicity toward various T-lymphoblastic cell lines with CC50 values as low as 9 nM. No cytotoxic effect was observed on other cancer cell lines (HeLa S3, HL60, HepG2) or primary PBMCs for up to 10 μM. We report the first example of the PNP inhibitor exhibiting over 60-fold selectivity for the pathogenic enzyme (MtPNP) over hPNP. The results are supported by a crystallographic study of eight enzyme-inhibitor complexes and by ADMET profiling in vitro and in vivo.
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Affiliation(s)
- Jan Skácel
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Stefan Djukic
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Faculty of Science, Charles University in Prague, Hlavova 2030/8, Prague 2 12843, Czech Republic
| | - Filip Kalčic
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Tadeáš Bílek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Karel Chalupský
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Jaroslav Kozák
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Alexandra Dvořáková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Eva Tloušt'ová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Zuzana Král'ová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Faculty of Science, Charles University in Prague, Hlavova 2030/8, Prague 2 12843, Czech Republic
| | - Markéta Šmídková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Jan Voldřich
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
| | - Michaela Rumlová
- University of Chemistry and Technology, Technická 5, Prague 16628, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Tereza Vučková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Milan Fábry
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Science, Vídeňská 1083, Prague 14220, Czech Republic
| | - Jan Snášel
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
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Tsui M, Biro J, Chan J, Min W, Dobbs K, Notarangelo LD, Grunebaum E. Purine nucleoside phosphorylase deficiency induces p53-mediated intrinsic apoptosis in human induced pluripotent stem cell-derived neurons. Sci Rep 2022; 12:9084. [PMID: 35641516 PMCID: PMC9156781 DOI: 10.1038/s41598-022-10935-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/15/2022] [Indexed: 01/04/2023] Open
Abstract
Purine nucleoside phosphorylase (PNP) is an important enzyme in the purine degradation and salvage pathway. PNP deficiency results in marked T lineage lymphopenia and severe immunodeficiency. Additionally, PNP-deficient patients and mice suffer from diverse non-infectious neurological abnormalities of unknown etiology. To further investigate the cause for these neurologic abnormalities, induced pluripotent stem cells (iPSC) from two PNP-deficient patients were differentiated into neurons. The iPSC-derived PNP-deficient neurons had significantly reduced soma and nuclei volumes. The PNP-deficient neurons demonstrated increased spontaneous and staurosporine-induced apoptosis, measured by cleaved caspase-3 expression, together with decreased mitochondrial membrane potential and increased cleaved caspase-9 expression, indicative of enhanced intrinsic apoptosis. Greater expression of tumor protein p53 was also observed in these neurons, and inhibition of p53 using pifithrin-α prevented the apoptosis. Importantly, treatment of the iPSC-derived PNP-deficient neurons with exogenous PNP enzyme alleviated the apoptosis. Inhibition of ribonucleotide reductase (RNR) in iPSC derived from PNP-proficient neurons with hydroxyurea or with nicotinamide and trichostatin A increased the intrinsic neuronal apoptosis, implicating RNR dysfunction as the potential mechanism for the damage caused by PNP deficiency. The findings presented here establish a potential mechanism for the neurological defects observed in PNP-deficient patients and reinforce the critical role that PNP has for neuronal viability.
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Affiliation(s)
- Michael Tsui
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON, Canada.,The Institute of Medical Sciences, The University to Toronto, Toronto, ON, Canada
| | - Jeremy Biro
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Jonathan Chan
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Weixian Min
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Eyal Grunebaum
- Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, ON, Canada. .,The Institute of Medical Sciences, The University to Toronto, Toronto, ON, Canada. .,Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G1X8, Canada.
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Mandal G, Biswas S, Anadon CM, Yu X, Gatenbee CD, Prabhakaran S, Payne KK, Chaurio RA, Martin A, Innamarato P, Moran C, Powers JJ, Harro CM, Mine JA, Sprenger KB, Rigolizzo KE, Wang X, Curiel TJ, Rodriguez PC, Anderson AR, Saglam O, Conejo-Garcia JR. IgA-dominated humoral immune responses govern patients' outcome in endometrial cancer. Cancer Res 2021; 82:859-871. [DOI: 10.1158/0008-5472.can-21-2376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
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Di Iorio P, Beggiato S, Ronci M, Nedel CB, Tasca CI, Zuccarini M. Unfolding New Roles for Guanine-Based Purines and Their Metabolizing Enzymes in Cancer and Aging Disorders. Front Pharmacol 2021; 12:653549. [PMID: 33935764 PMCID: PMC8085521 DOI: 10.3389/fphar.2021.653549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/12/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- P Di Iorio
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Chieti, Italy
| | - S Beggiato
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Chieti, Italy
| | - M Ronci
- Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Chieti, Italy.,Department of Pharmacy, University G. D'Annunzio Chieti, Chieti, Italy
| | - C B Nedel
- Laboratório de Biologia Celular de Gliomas, Programa de Pós-Graduação Em Biologia Celular e Do Desenvolvimento, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - C I Tasca
- Laboratório de Neuroquímica-4, Programa de Pós-Graduação Em Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - M Zuccarini
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Chieti, Italy
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