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Ahmed A, Ijaz M, Khan JA, Anjum AA. Biofilm forming multidrug resistant Staphylococcus aureus of dairy origin: molecular and evolutionary perspectives. IRANIAN JOURNAL OF VETERINARY RESEARCH 2023; 24:193-204. [PMID: 38269015 PMCID: PMC10804433 DOI: 10.22099/ijvr.2023.43941.6445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/16/2023] [Accepted: 02/26/2023] [Indexed: 01/26/2024]
Abstract
Background Biofilm production by Staphylococcus aureus is a prevailing cause of multidrug resistance. The evolutionary mechanisms of adaption with host and pathogenicity are poorly understood. Aims The present study aimed to investigate the biofilm-forming potential, associated multidrug resistance, and the evolutionary analysis of S. aureus isolated from bovine subclinical mastitis. Methods 122 S. aureus isolates were subjected to Congo red agar method (CRA), microtitre plate method (MTP), and PCR to check the biofilm-forming potential. The Kirby-Bauer disk diffusion method was used to evaluate the antibiotic resistance pattern. The icaA gene of isolates was subjected to molecular and evolutionary analysis using different bioinformatics tools. Results The results showed that 63.93% of S. aureus isolates carried the icaA gene and the detection rate of CRA was higher (36.07%) compared to the MTP test (24.59%). A total of 78.21% and 56.41% of biofilm-positive isolates were methicillin-resistant S. aureus (MRSA) and vancomycin-resistant S. aureus (VRSA), respectively. All S. aureus isolates (100%) showed multidrug resistance. The molecular analysis showed an evolutionary link between isolates and revealed a strong codon bias, three different recombination events, and positive selection in some residues of the semi-conserved segments of the icaA gene. Conclusion The study concluded that biofilm-positive isolates have a high tendency to exhibit methicillin, vancomycin, and multidrug resistance. The findings suggest that mutation and selection are the most likely causes of codon bias in the icaA gene sequences. The variations led by recombination events and positive selection are suggestive of bacterial strategy to combat antimicrobial effects and to escape the host's immune surveillance.
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Affiliation(s)
- A. Ahmed
- Ph.D. Student in Veterinary Medicine, Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - M. Ijaz
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - J. A. Khan
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - A. A. Anjum
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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2
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Digital Form for Assessing Dentists' Knowledge about Oral Care of People Living with HIV. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095055. [PMID: 35564449 PMCID: PMC9103845 DOI: 10.3390/ijerph19095055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/04/2022]
Abstract
Oral lesions are usually the first sign of HIV infection. The present study aimed to determine the level of the knowledge of dentists on the dental care needs of People Living with HIV (PLWH). This cross-sectional study was conducted between February and May 2021, in the Brazilian state of Pará, during which a total of 51 dentists received an anonymous digital form (Google® Forms Platform) composed of four blocks of discursive, dichotomous, and multiple-choice questions. The questions referred to various aspects of the dental care needs of PLWH, together with data on the professional activities of the dentists. After signing the term of informed consent, the dentists were divided into six subgroups according to the time (in years) since completing their bachelor’s degree in dentistry. The data were presented as descriptive statistics and percentages, and then analyzed using the Kappa test. Most (70.6%; 36 of 51) of the dentists were female, the mean age of the dentists was 32.5 years, and a majority (80.2%) were based in the city of Belem; the mean time since graduation was 8.5 years, with 22 (43.1%) having more than 5 years of professional experience, and 31 (60.8%) having graduated from a private dental college. Just over half (51%) of the 51 dentists had completed graduate courses, and the most common dental specialty was orthodontics (19.6%). Most (74.5%) of the dentists work in the private sector, 38 (74.5%) claimed to have already provided oral care to PLWH, and 43 (84.3%) had access to specialist content on the oral care needs of PLWH. In terms of the knowledge of the dentists with regard to the oral care needs of PLWH, four of the ten diagnostic questions obtained more inadequate answers than expected, whereas the final two questions (11–45.1% and 12–31.4%) demonstrated that many of the dentists adopt unnecessary modifications in their oral care protocol for PLWH, due to a fear of contamination. Overall, our results demonstrate a frequent lack of knowledge, especially with regard to the oral healthcare needs of PLWH, which may account for many of the stigmas that persist in the dental care of this vulnerable group.
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Artesi M, Hahaut V, Cole B, Lambrechts L, Ashrafi F, Marçais A, Hermine O, Griebel P, Arsic N, van der Meer F, Burny A, Bron D, Bianchi E, Delvenne P, Bours V, Charlier C, Georges M, Vandekerckhove L, Van den Broeke A, Durkin K. PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads. Genome Biol 2021; 22:97. [PMID: 33823910 PMCID: PMC8025556 DOI: 10.1186/s13059-021-02307-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
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Affiliation(s)
- Maria Artesi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
- Laboratory of Human Genetics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
| | - Vincent Hahaut
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, 9000 Ghent, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Fereshteh Ashrafi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ambroise Marçais
- Service d’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Olivier Hermine
- Service d’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3 Canada
| | - Natasa Arsic
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, S7N 5E3 Canada
| | - Frank van der Meer
- Faculty of Veterinary Medicine: Ecosystem and Public Health, Calgary, AB Canada
| | - Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Dominique Bron
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Elettra Bianchi
- Department of Pathology, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Department of Pathology, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Department of Human Genetics, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital and Ghent University, 9000 Ghent, Belgium
| | - Anne Van den Broeke
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
| | - Keith Durkin
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Avenue de l’Hôpital 11, 4000 Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, 1000 Brussels, Belgium
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Abstract
Therapeutic approaches towards a functional cure or eradication of HIV have gained renewed momentum upon encouraging data emerging from studies in SIV monkey models and recent results from human clinical studies. However, a multitude of questions remain to be addressed, including how to deal with the latent viral reservoir, how to boost the host immune response to the virus and what the hurdles are to reach relevant viral compartments in the body. Advances have been made especially with regard to identifying agents that can reactivate the latent virus in vivo and boost the cellular and humoral immunity, but it remains largely unclear whether any of these strategies can awaken a sufficiently large fraction of the viral reservoir and whether the boosted immunity can prevent rapid viral replication once antiretroviral treatments are stopped.
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Affiliation(s)
- Lucia Bailon
- Fundació Lluita contra la Sida, Infectious Disease Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Beatriz Mothe
- Fundació Lluita contra la Sida, Infectious Disease Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain
- Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), Vic, Spain
| | | | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain.
- Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), Vic, Spain.
- AELIX Therapeutics, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, Spain.
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Orlandi C, Canovari B, Bozzano F, Marras F, Pasquini Z, Barchiesi F, De Maria A, Magnani M, Casabianca A. A comparative analysis of unintegrated HIV-1 DNA measurement as a potential biomarker of the cellular reservoir in the blood of patients controlling and non-controlling viral replication. J Transl Med 2020; 18:204. [PMID: 32429953 PMCID: PMC7236182 DOI: 10.1186/s12967-020-02368-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The persistence of HIV-1 in reservoir cells is one of the major obstacles to eradicating the virus in infected individuals receiving combination antiretroviral therapy (ART). HIV-1 persists in infected cells as a stable integrated genome and more labile unintegrated DNA (uDNA), which includes linear, 1-LTR and 2-LTR circular DNA. 2-LTR circle DNA, although less abundant, is considered a surrogate marker of recent infection events and is currently used instead of the other unintegrated species as a diagnostic tool. This pilot study aimed to investigate how to best achieve the measurement of uDNA. METHODS A comparative analysis of two qPCR-based methods (U-assay and 2-LTR assay) was performed on the blood of 12 ART-naïve, 14 viremic and 29 aviremic On-ART patients and 20 untreated spontaneous controllers (HIC), sampled at a single time point. RESULTS The U-assay, which quantified all unintegrated DNA species, showed greater sensitivity than the 2-LTR assay (up to 75%, p < 0.0001), especially in viremic subjects, in whom other forms, in addition to 2-LTR circles, may also accumulate due to active viral replication. Indeed, in aviremic On-ART samples, the U-assay unexpectedly measured uDNA in a higher proportion of samples (76%, 22/29) than the 2-LTR assay (41%, 12/29), (p = 0.0164). A trend towards lower uDNA levels was observed in aviremic vs viremic On-ART patients, reaching significance when we combined aviremic On-ART and HIC (controllers) vs Off-ART and viremic On-ART subjects (non-controllers) (p = 0.0003), whereas 2-LTR circle levels remained constant (p ≥ 0.2174). These data were supported by the high correlation found between uDNA and total DNA (r = 0.69, p < 0.001). CONCLUSIONS The great advantage of the U-assay is that, unlike the 2-LTR assay, it allows the accurate evaluation of the totality of uDNA that can still be measured even during successful ART when plasma viremia is below the cut-off of common clinical tests (< 50 copies/mL) and 2-LTR circles are more likely to be under the quantification limit. UDNA measurement in blood cells may be used as a biomarker to reveal a so far hidden or underestimated viral reservoir. The potential clinical relevance of uDNA quantification may lead to improvements in diagnostic methods to support clinical strategies.
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Affiliation(s)
- Chiara Orlandi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Benedetta Canovari
- Malattie Infettive, Azienda Ospedaliera Ospedali Riuniti Marche Nord, Pesaro, Italy
| | | | - Francesco Marras
- Division of Infectious Diseases, Ospedale Policlinico S. Martino IRCCS, Genoa, Italy
| | - Zeno Pasquini
- Malattie Infettive, Azienda Ospedaliera Ospedali Riuniti Marche Nord, Pesaro, Italy
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, Ancona, Italy
| | - Francesco Barchiesi
- Malattie Infettive, Azienda Ospedaliera Ospedali Riuniti Marche Nord, Pesaro, Italy
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea De Maria
- Division of Infectious Diseases, Ospedale Policlinico S. Martino IRCCS, Genoa, Italy
- Department of Health Sciences, DISSAL, University of Genova, Genoa, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Anna Casabianca
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy.
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Salasc F, Gludish DW, Jarvis I, Boliar S, Wills MR, Russell DG, Lever AML, Mok HP. A novel, sensitive dual-indicator cell line for detection and quantification of inducible, replication-competent latent HIV-1 from reservoir cells. Sci Rep 2019; 9:19325. [PMID: 31852924 PMCID: PMC6920355 DOI: 10.1038/s41598-019-55596-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 11/15/2019] [Indexed: 11/28/2022] Open
Abstract
Understanding the mechanisms involved in HIV infection and latency, and development of a cure, rely on the availability of sensitive research tools such as indicator cells, which allow rigorous quantification of viral activity. Here we describe the construction and validation of a novel dual-indicator cell line, Sup-GGR, which offers two different readouts to quantify viral replication. A construct expressing both Gaussia luciferase and hrGFP in a Tat- and Rev-dependent manner was engineered into SupT1-CCR5 to create Sup-GGR cells. This cell line supports the replication of both X4 and R5-tropic HIV as efficiently as its parental cell line, SupT1-CCR5, and allows repeated sampling without the need to terminate the culture. Sup-GGR demonstrates comparable sensitivity and similar kinetics in virus outgrowth assays (VOA) to SupT1-CCR5 using clinical samples. However the Gaussia luciferase reporter is significantly less labor-intensive and allows earlier detection of reactivated latent viruses compared to the conventional HIV p24 ELISA assay. The Sup-GGR cell line constitutes a versatile new tool for HIV research and clinical trials.
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Affiliation(s)
- Fanny Salasc
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David W Gludish
- Cornell University College of Veterinary Medicine, New York, USA
| | - Isobel Jarvis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Saikat Boliar
- Cornell University College of Veterinary Medicine, New York, USA
| | - Mark R Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David G Russell
- Cornell University College of Veterinary Medicine, New York, USA.
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Yong Loo Lin School of Medicine National University of Singapore, Singapore, Singapore.
| | - Hoi-Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK.
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Abstract
HIV is one of the fastest evolving organisms known. It evolves about 1 million times faster than its host, humans. Because HIV establishes chronic infections, with continuous evolution, its divergence within a single infected human surpasses the divergence of the entire humanoid history. Yet, it is still the same virus, infecting the same cell types and using the same replication machinery year after year. Hence, one would think that most mutations that HIV accumulates are neutral. But the picture is more complicated than that. HIV evolution is also a clear example of strong positive selection, that is, mutants have a survival advantage. How do these facts come together?
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Affiliation(s)
- Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
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Saturnino C, Grande F, Aquaro S, Caruso A, Iacopetta D, Bonomo MG, Longo P, Schols D, Sinicropi MS. Chloro-1,4-dimethyl-9H-carbazole Derivatives Displaying Anti-HIV Activity. Molecules 2018; 23:E286. [PMID: 29385738 PMCID: PMC6017966 DOI: 10.3390/molecules23020286] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/18/2018] [Accepted: 01/27/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Despite the progress achieved by anti-retroviral drug research in the last decades, the discovery of novel compounds endowed with selective antiviral activity and reduced side effects is still a necessity. At present, the most urgent requirement includes the improvement of HIV (Human Immunodeficiency Virus) prevention and sexual transmission and the development of new drugs to treat the chronic lifelong infection. METHODS Six chloro-1,4-dimethyl-9H-carbazoles (2a,b-4a,b) have been prepared following opportunely modified known chemical procedures and tested in luciferase and Escherichia coli β-galactosidase expressing CD4⁺, CXCR4⁺, CCR5⁺ TZM-bl cells. RESULTS AND CONCLUSION a preliminary biological investigation on the synthesized small series of chloro-1,4-dimethyl-9H-carbazoles has been carried out. Among all tested compounds, a nitro-derivative (3b) showed the most interesting profile representing a suitable lead for the development of novel anti-HIV drugs.
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Affiliation(s)
- Carmela Saturnino
- Department of Science, University of Basilicata, 85100 Potenza, Italy.
| | - Fedora Grande
- Department of Pharmacy, Health & Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy.
| | - Stefano Aquaro
- Department of Pharmacy, Health & Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy.
| | - Anna Caruso
- Department of Pharmacy, Health & Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy.
| | - Domenico Iacopetta
- Department of Pharmacy, Health & Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy.
| | | | - Pasquale Longo
- Department of Chemistry and Biology, University of Salerno, 84084 Fisciano, Italy.
| | - Dominique Schols
- KU Leuven, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium.
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health & Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy.
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