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Balasundaram A, C Doss GP. Deciphering the Impact of Rare Missense Variants in EGFR-TKI-Resistant Non-Small-Cell Lung Cancer through Whole Exome Sequencing: A Computational Approach. ACS OMEGA 2024; 9:16288-16302. [PMID: 38617633 PMCID: PMC11007825 DOI: 10.1021/acsomega.3c10229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 04/16/2024]
Abstract
Targeted therapy revolutionizes the treatment of non-small-cell lung cancer (NSCLC), harboring molecular change. Epidermal growth factor receptor(EGFR) mutations play a crucial role in the development of NSCLC, serving as a pivotal factor in its pathogenesis. We elucidated the mechanisms of resistance and potential therapeutic strategies in NSCLC resistant to the EGFR-tyrosine kinase inhibitor (EGFR-TKI). This is achieved by identifying rare missense variants through whole exome sequencing (WES). The goal is to enhance our understanding, identify biomarkers, and lay the groundwork for targeted interventions, thereby offering hope for an improved NSCLC treatment landscape. We conducted WES analysis on 16 NSCLC samples with EGFR-TKI-resistant NSCLC obtained from SRA-NCBI (PRJEB50602) to reveal genomic profiles within the EGFR-TKI. Our findings showed that 48% of the variants were missense, and after filtering with the Ensembl variant effect predictor, 53 rare missense variants in 23 genes were identified as highly deleterious. Further examination using pathogenic tools like PredictSNP revealed 12 deleterious rare missense variants in 7 genes: ZNF717, PSPH, ESRRA, SEMA3G, PTPN7, CAVIN4, and MYBBP1A. Molecular dynamics simulation (MDS) suggested that the L385P variant alters the structural flexibility of ESRRA, potentially leading to unfolding of ERRα proteins. This could impact their function and alter ERRα expression. These insights from MDS enhance our understanding of the structural and dynamic consequences of the L385P ESRRA variant and provide valuable implications for subsequent therapeutic considerations and targeted interventions.
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Affiliation(s)
- Ambritha Balasundaram
- Laboratory of Integrative
Genomics, Department of Integrative Biology, School of BioSciences
and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Laboratory of Integrative
Genomics, Department of Integrative Biology, School of BioSciences
and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
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2
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Nakano H, Yoshida H, Yabe S, Fushimi E, Tanaka R, Yamasaki M, Nakagawa H. γ‐Oryzanol concentrations in various rice genotypes ripened under different air temperatures. Cereal Chem 2022. [DOI: 10.1002/cche.10597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroshi Nakano
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO)496 IzumiChikugoFukuoka833‐0041Japan
| | - Hiroe Yoshida
- Institute for Agro‐Environmental Sciences, National Agriculture and Food Research Organization (NARO)3‐1‐3 KannondaiTsukubaIbaraki305‐8604Japan
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO)360 Kusawa, AnochoTsuMie514‐2392Japan
| | - Shiori Yabe
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO)2‐1‐2 KannondaiTsukubaIbaraki305‐8518Japan
| | - Erina Fushimi
- Institute for Agro‐Environmental Sciences, National Agriculture and Food Research Organization (NARO)3‐1‐3 KannondaiTsukubaIbaraki305‐8604Japan
| | - Ryo Tanaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO)496 IzumiChikugoFukuoka833‐0041Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural ScienceKobe University1348 Uzurano‐choKasaiHyogo675‐2103Japan
- Graduate School of Science and TechnologyNiigata University8050 Ikarashi 2‐no‐cho, Nishi‐kuNiigata950‐2181Japan
| | - Hiroshi Nakagawa
- Institute for Agro‐Environmental Sciences, National Agriculture and Food Research Organization (NARO)3‐1‐3 KannondaiTsukubaIbaraki305‐8604Japan
- Core Technology Research Headquarters, National Agriculture and Food Research Organization (NARO)1‐31‐1 KannondaiTsukubaIbaraki305‐0856Japan
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3
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Identification of a novel anticancer mechanism of Paeoniae Radix extracts based on systematic transcriptome analysis. Biomed Pharmacother 2022; 148:112748. [PMID: 35219117 DOI: 10.1016/j.biopha.2022.112748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 11/21/2022] Open
Abstract
Paeoniae Radix (PR) has a great therapeutic value in many clinical applications; however, the presence of various bioactive compounds and its complicated effects on human health makes its precise mechanisms of action unclear. This study investigated the effects of PR at the molecular pathway level by profiling genome-wide gene expression changes following dose-dependent treatment of human lung cancer cells (A549) with PR water extract (WPR), PR ethanol extracts (EPR), as well as their individual components. We found that PR exerts anticancer effects in A549 cells by regulating numerous pathways. Specifically, EPR and two compounds, namely, hederagenin (HG) and oleanolic acid (OA), significantly downregulate the Aurora B pathway. Furthermore, we generated an integrated PR extracts-compounds-target genes network in the Aurora B pathway to understand their interactions. Our findings reinforce that inhibiting Aurora kinase activity is a therapeutic target for treating cancers, providing the potential for novel mechanisms of action for PR and its components against lung cancer.
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Rice Bran Stabilisation and Oil Extraction Using the Microwave-Assisted Method and Its Effects on GABA and Gamma-Oryzanol Compounds. Foods 2022; 11:foods11070912. [PMID: 35406999 PMCID: PMC8997534 DOI: 10.3390/foods11070912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Rice bran oil (RBO) is a valuable ingredient extracted from rice bran (RB), a side stream of polishing rice grain in the milling process. RBO is rich in bioactive ingredients with potential health benefits, such as gamma-oryzanol (GO) and gamma-aminobutyric acid (GABA). Despite its benefits, the quality of RBO depends on the degree of stabilisation of the RB, which is easily affected by lipase enzymes, and thus needs an effective treatment prior to RBO production. To assess the potential of the microwave-assisted method for RB stabilisation and RBO extraction, three Carolino rice varieties (Ariete, Teti, Luna) were tested. The effect of RB stabilisation was evaluated via acid value, water absorption, and GO and GABA levels. The RBO yield was optimised by solvent, temperature, and solvent-to-sample ratio, and the GO and fatty acid levels were determined. The RB stabilisation for the Luna variety did not affect the GO and GABA; for the Ariete and Teti varieties, the GO decreased by 34.4% and 24.2%, and the GABA increased by 26.5% and 47.0%, respectively. The GO levels in RBO samples were not affected by RB stabilisation. The RBO nutritional value was confirmed by the suitable ratio (>2) between polyunsaturated (PUFA) and saturated fatty acids (SFA), with the Teti variety presenting the highest ratio.
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Baek SJ, Hammock BD, Hwang IK, Li Q, Moustaid-Moussa N, Park Y, Safe S, Suh N, Yi SS, Zeldin DC, Zhong Q, Bradbury JA, Edin ML, Graves JP, Jung HY, Jung YH, Kim MB, Kim W, Lee J, Li H, Moon JS, Yoo ID, Yue Y, Lee JY, Han HJ. Natural Products in the Prevention of Metabolic Diseases: Lessons Learned from the 20th KAST Frontier Scientists Workshop. Nutrients 2021; 13:1881. [PMID: 34072678 PMCID: PMC8227583 DOI: 10.3390/nu13061881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 12/29/2022] Open
Abstract
The incidence of metabolic and chronic diseases including cancer, obesity, inflammation-related diseases sharply increased in the 21st century. Major underlying causes for these diseases are inflammation and oxidative stress. Accordingly, natural products and their bioactive components are obvious therapeutic agents for these diseases, given their antioxidant and anti-inflammatory properties. Research in this area has been significantly expanded to include chemical identification of these compounds using advanced analytical techniques, determining their mechanism of action, food fortification and supplement development, and enhancing their bioavailability and bioactivity using nanotechnology. These timely topics were discussed at the 20th Frontier Scientists Workshop sponsored by the Korean Academy of Science and Technology, held at the University of Hawaii at Manoa on 23 November 2019. Scientists from South Korea and the U.S. shared their recent research under the overarching theme of Bioactive Compounds, Nanoparticles, and Disease Prevention. This review summarizes presentations at the workshop to provide current knowledge of the role of natural products in the prevention and treatment of metabolic diseases.
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Affiliation(s)
- Seung J. Baek
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.J.B.); (I.-K.H.); (H.-Y.J.); (Y.-H.J.); (W.K.); (J.L.)
| | - Bruce D. Hammock
- Department of Entomology, University of California, Davis, CA 95616, USA;
| | - In-Koo Hwang
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.J.B.); (I.-K.H.); (H.-Y.J.); (Y.-H.J.); (W.K.); (J.L.)
| | - Qingxiao Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA;
| | - Naima Moustaid-Moussa
- Department of Nutritional Sciences & Obesity Research Institute, Texas Tech University, Lubbock, TX 79409, USA;
| | - Yeonhwa Park
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA; (Y.P.); (Y.Y.)
| | - Stephen Safe
- Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX 77843, USA;
| | - Nanjoo Suh
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA;
| | - Sun-Shin Yi
- Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea; (S.-S.Y.); (J.-S.M.); (I.-D.Y.)
| | - Darryl C. Zeldin
- National Institutes of Environmental Health, National Institutes of Health, Research Triangle Park, NC 27709, USA; (D.C.Z.); (J.A.B.); (M.L.E.); (J.P.G.); (H.L.)
| | - Qixin Zhong
- Department of Food Sciences, University of Tennessee, Knoxville, TN 37996, USA;
| | - Jennifer Alyce Bradbury
- National Institutes of Environmental Health, National Institutes of Health, Research Triangle Park, NC 27709, USA; (D.C.Z.); (J.A.B.); (M.L.E.); (J.P.G.); (H.L.)
| | - Matthew L. Edin
- National Institutes of Environmental Health, National Institutes of Health, Research Triangle Park, NC 27709, USA; (D.C.Z.); (J.A.B.); (M.L.E.); (J.P.G.); (H.L.)
| | - Joan P. Graves
- National Institutes of Environmental Health, National Institutes of Health, Research Triangle Park, NC 27709, USA; (D.C.Z.); (J.A.B.); (M.L.E.); (J.P.G.); (H.L.)
| | - Hyo-Young Jung
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.J.B.); (I.-K.H.); (H.-Y.J.); (Y.-H.J.); (W.K.); (J.L.)
| | - Young-Hyun Jung
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.J.B.); (I.-K.H.); (H.-Y.J.); (Y.-H.J.); (W.K.); (J.L.)
| | - Mi-Bo Kim
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA;
| | - Woosuk Kim
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.J.B.); (I.-K.H.); (H.-Y.J.); (Y.-H.J.); (W.K.); (J.L.)
| | - Jaehak Lee
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.J.B.); (I.-K.H.); (H.-Y.J.); (Y.-H.J.); (W.K.); (J.L.)
| | - Hong Li
- National Institutes of Environmental Health, National Institutes of Health, Research Triangle Park, NC 27709, USA; (D.C.Z.); (J.A.B.); (M.L.E.); (J.P.G.); (H.L.)
| | - Jong-Seok Moon
- Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea; (S.-S.Y.); (J.-S.M.); (I.-D.Y.)
| | - Ik-Dong Yoo
- Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea; (S.-S.Y.); (J.-S.M.); (I.-D.Y.)
| | - Yiren Yue
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA; (Y.P.); (Y.Y.)
| | - Ji-Young Lee
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA;
| | - Ho-Jae Han
- College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (S.J.B.); (I.-K.H.); (H.-Y.J.); (Y.-H.J.); (W.K.); (J.L.)
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Liu C, Xi X, Liu Y, Lu Y, Che F, Gu Y, Yu Y, Li H, Liu J, Wei Y. Isolation of Four Major Compounds of γ-Oryzanol from Rice Bran Oil by Ionic Liquids Modified High-Speed Countercurrent Chromatography and Antimicrobial Activity and Neuroprotective Effect of Cycloartenyl Ferulate In Vitro. Chromatographia 2021. [DOI: 10.1007/s10337-021-04044-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nakano H, Iwasawa N, Takai T, Arai‐Sanoh Y, Kondo M. Grain weight and the concentrations of phenylpropanoid glycosides and γ‐oryzanol in response to heat stress during ripening in rice. Cereal Chem 2021. [DOI: 10.1002/cche.10428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hiroshi Nakano
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
- Kyushu Okinawa Agricultural Research Center National Agriculture and Food Research Organization (NARO) Fukuoka Japan
| | - Norio Iwasawa
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
| | - Toshiyuki Takai
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
- Japan International Research Center for Agricultural Sciences (JIRCAS) Ibaraki Japan
| | - Yumiko Arai‐Sanoh
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
| | - Motohiko Kondo
- Institute of Crop Science National Agriculture and Food Research Organization (NARO) Ibaraki Japan
- Graduate School of Bioagricultural Sciences Nagoya University Furocho Japan
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Galetta D, Cortes-Dericks L. Promising Therapy in Lung Cancer: Spotlight on Aurora Kinases. Cancers (Basel) 2020; 12:cancers12113371. [PMID: 33202573 PMCID: PMC7697457 DOI: 10.3390/cancers12113371] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Lung cancer has remained one of the major causes of death worldwide. Thus, a more effective treatment approach is essential, such as the inhibition of specific cancer-promoting molecules. Aurora kinases regulate the process of mitosis—a process of cell division that is necessary for normal cell proliferation. Dysfunction of these kinases can contribute to cancer formation. In this review, we present studies indicating the implication of Aurora kinases in tumor formation, drug resistance, and disease prognosis. The effectivity of using Aurora kinase inhibitors in the pre-clinical and clinical investigations has proven their therapeutic potential in the setting of lung cancer. This work may provide further information to broaden the development of anticancer drugs and, thus, improve the conventional lung cancer management. Abstract Despite tremendous efforts to improve the treatment of lung cancer, prognosis still remains poor; hence, the search for efficacious therapeutic option remains a prime concern in lung cancer research. Cell cycle regulation including mitosis has emerged as an important target for cancer management. Novel pharmacological agents blocking the activities of regulatory molecules that control the functional aspects of mitosis such as Aurora kinases are now being investigated. The Aurora kinases, Aurora-A (AURKA), and Aurora B (AURKB) are overexpressed in many tumor entities such as lung cancer that correlate with poor survival, whereby their inhibition, in most cases, enhances the efficacy of chemo-and radiotherapies, indicating their implication in cancer therapy. The current knowledge on Aurora kinase inhibitors has increasingly shown high potential in ensuing targeted therapies in lung malignancies. In this review, we will briefly describe the biology of Aurora kinases, highlight their oncogenic roles in the pre-clinical and clinical studies in lung cancer and, finally, address the challenges and potentials of Aurora kinases to improve the therapy of this malignancy.
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Affiliation(s)
- Domenico Galetta
- Division of Thoracic Surgery, European Institute of Oncology, IRCCS, 20141 Milan, Italy
- Correspondence:
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Castanho A, Lageiro M, Calhelha RC, Ferreira ICFR, Sokovic M, Cunha LM, Brites C. Exploiting the bioactive properties of γ-oryzanol from bran of different exotic rice varieties. Food Funct 2019; 10:2382-2389. [PMID: 30950464 DOI: 10.1039/c8fo02596g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The rice industry is one of the most significant food industries since rice is a widely consumed cereal in the world. As a result of this substantial production, the rice industry has a significant amount of side streams, including bran, representing millions of tons of raw materials mainly designated to animal feed. Rice bran is a rich source of γ-oryzanol, a bioactive compound with substantial health benefits. In this perspective, different bran rice samples from distinct germplasm origins (Philippines, Italy and Portugal) were studied for their γ-oryzanol content by HPLC-PDA, cytotoxicity in four human tumour cell lines, hepatotoxicity in a normal cell line and for their antimicrobial effects on different bacterial and fungal strains. The Ballatinao sample presented the strongest activity against all the tumour cell lines, and was also the sample showing the highest amount of γ-oryzanol, suggesting its contribution to the exhibited cytotoxic properties. Regarding the antimicrobial activity, the tested samples were able to inhibit the majority of bacterial and fungal strains, with the Portuguese Ceres sample being the one presenting the highest bacterial inhibition and the Maluit and Dinorado samples, the highest fungal inhibition. Overall, the results show that rice bran extracts may be considered as potential candidates for antimicrobial agents when incorporated into food matrices.
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Affiliation(s)
- Ana Castanho
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Unidade de Tecnologia e Inovação (INIAV/UTI), Av. da República, Quinta do Marquês, 2784-505 Oeiras, Portugal.
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Definitive evidence of the presence of 24-methylenecycloartanyl ferulate and 24-methylenecycloartanyl caffeate in barley. Sci Rep 2019; 9:12572. [PMID: 31467350 PMCID: PMC6715696 DOI: 10.1038/s41598-019-48985-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
γ-Oryzanol (OZ), which has a lot of beneficial effects, is a mixture of ferulic acid esters of triterpene alcohols (i.e., triterpene alcohol type of OZ (TTA-OZ)) and ferulic acid esters of plant sterols (i.e., plant sterol type of OZ (PS-OZ)). Although it has been reported that OZ is found in several kinds of cereal typified by rice, TTA-OZ (e.g., 24-methylenecycloartanyl ferulate (24MCA-FA)) has been believed to be characteristic to rice and has not been found in other cereals. In this study, we isolated a compound considered as a TTA-OZ (i.e., 24MCA-FA) from barley and determined the chemical structure using by HPLC-UV-MS, high-resolution MS, and NMR. Based on these results, we proved for the first time that barley certainly contains 24MCA-FA (i.e., TTA-OZ). During the isolation and purification of 24MCA-FA from barley, we found the prospect that a compound with similar properties to OZ (compound-X) might exist. To confirm this finding, the compound-X was also isolated, determined the chemical structure, and identified as a caffeic acid ester of 24-methylenecycloartanol (24MCA-CA), which has rarely been reported before. We also quantified these compounds in various species of barley cultivars and found for the first time the existence of 24MCA-FA and 24MCA-CA in various barley. Through these findings, it opens the possibility to use barley as a new source of 24MCA-FA and 24MCA-CA.
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