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Sarrazin-Gendron R, Ghasemloo Gheidari P, Butyaev A, Keding T, Cai E, Zheng J, Mutalova R, Mounthanyvong J, Zhu Y, Nazarova E, Drogaris C, Erhart K, Brouillette A, Richard G, Pitchford R, Caisse S, Blanchette M, McDonald D, Knight R, Szantner A, Waldispühl J. Improving microbial phylogeny with citizen science within a mass-market video game. Nat Biotechnol 2024:10.1038/s41587-024-02175-6. [PMID: 38622344 DOI: 10.1038/s41587-024-02175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/05/2024] [Indexed: 04/17/2024]
Abstract
Citizen science video games are designed primarily for users already inclined to contribute to science, which severely limits their accessibility for an estimated community of 3 billion gamers worldwide. We created Borderlands Science (BLS), a citizen science activity that is seamlessly integrated within a popular commercial video game played by tens of millions of gamers. This integration is facilitated by a novel game-first design of citizen science games, in which the game design aspect has the highest priority, and a suitable task is then mapped to the game design. BLS crowdsources a multiple alignment task of 1 million 16S ribosomal RNA sequences obtained from human microbiome studies. Since its initial release on 7 April 2020, over 4 million players have solved more than 135 million science puzzles, a task unsolvable by a single individual. Leveraging these results, we show that our multiple sequence alignment simultaneously improves microbial phylogeny estimations and UniFrac effect sizes compared to state-of-the-art computational methods. This achievement demonstrates that hyper-gamified scientific tasks attract massive crowds of contributors and offers invaluable resources to the scientific community.
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Affiliation(s)
| | | | | | - Timothy Keding
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Eddie Cai
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Jiayue Zheng
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Renata Mutalova
- School of Computer Science, McGill University, Montréal, QC, Canada
| | | | - Yuxue Zhu
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Elena Nazarova
- School of Computer Science, McGill University, Montréal, QC, Canada
| | | | - Kornél Erhart
- Massively Multiplayer Online Science, Gryon, Switzerland
| | | | | | | | | | | | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Attila Szantner
- School of Computer Science, McGill University, Montréal, QC, Canada
- Massively Multiplayer Online Science, Gryon, Switzerland
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montréal, QC, Canada.
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Drogaris C, Butyaev A, Nazarova E, Sarrazin-Gendron R, Patel H, Singh A, Kadota B, Waldispühl J. When online citizen science meets teaching: Storyfication of a science discovery game to teach, learn, and contribute to genomic research. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 52:145-155. [PMID: 37929794 DOI: 10.1002/bmb.21796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/22/2023] [Indexed: 11/07/2023]
Abstract
In the last decade, video games became a common vehicle for citizen science initiatives in life science, allowing participants to contribute to real scientific data analysis while learning about it. Since 2010, our scientific discovery game (SDG) Phylo enlists participants in comparative genomic data analysis. It is frequently used as a learning tool, but the activities were difficult to aggregate to build a coherent teaching activity. Here, we describe a strategy and series of recipes to facilitate the integration of SDGs in courses and implement this approach in Phylo. We developed new roles and functionalities enabling instructors to create assignments and monitor the progress of students. A story mode progressively introduces comparative genomics concepts, allowing users to learn and contribute to the analysis of real genomic sequences. Preliminary results from a user study suggest this framework may help to boost user motivation and clarify pedagogical objectives.
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Affiliation(s)
| | | | - Elena Nazarova
- School of Computer Science, McGill University, Montréal, QC, Canada
| | | | - Harsh Patel
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Akash Singh
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Brenden Kadota
- School of Computer Science, McGill University, Montréal, QC, Canada
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3
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Yallapragada VVB, Xu T, Walker SP, Tabirca S, Tangney M. Pepblock Builder VR - An Open-Source Tool for Gaming-Based Bio-Edutainment in Interactive Protein Design. Front Bioeng Biotechnol 2021; 9:674211. [PMID: 34055764 PMCID: PMC8160467 DOI: 10.3389/fbioe.2021.674211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
Proteins mediate and perform various fundamental functions of life. This versatility of protein function is an attribute of its 3D structure. In recent years, our understanding of protein 3D structure has been complemented with advances in computational and mathematical tools for protein modelling and protein design. 3D molecular visualisation is an essential part in every protein design and protein modelling workflow. Over the years, stand-alone and web-based molecular visualisation tools have been used to emulate three-dimensional view on computers. The advent of virtual reality provided the scope for immersive control of molecular visualisation. While these technologies have significantly improved our insights into protein modelling, designing new proteins with a defined function remains a complicated process. Current tools to design proteins lack user-interactivity and demand high computational skills. In this work, we present the Pepblock Builder VR, a gaming-based molecular visualisation tool for bio-edutainment and understanding protein design. Simulating the concepts of protein design and incorporating gaming principles into molecular visualisation promotes effective game-based learning. Unlike traditional sequence-based protein design and fragment-based stitching, the Pepblock Builder VR provides a building block style environment for complex structure building. This provides users a unique visual structure building experience. Furthermore, the inclusion of virtual reality to the Pepblock Builder VR brings immersive learning and provides users with "being there" experience in protein visualisation. The Pepblock Builder VR works both as a stand-alone and VR-based application, and with a gamified user interface, the Pepblock Builder VR aims to expand the horizons of scientific data generation to the masses.
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Affiliation(s)
- Venkata V. B. Yallapragada
- Cancer Research @ UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
| | - Tianshu Xu
- School of Computer Science and Information Technology, University College Cork, Cork, Ireland
| | - Sidney P. Walker
- Cancer Research @ UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
| | - Sabin Tabirca
- School of Computer Science and Information Technology, University College Cork, Cork, Ireland
- Department of Computer Science, Transylvania University of Braşov, Braşov, Romania
| | - Mark Tangney
- Cancer Research @ UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- iEd Hub, University College Cork, Cork, Ireland
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Das R, Keep B, Washington P, Riedel-Kruse IH. Scientific Discovery Games for Biomedical Research. Annu Rev Biomed Data Sci 2019; 2:253-279. [PMID: 34308269 DOI: 10.1146/annurev-biodatasci-072018-021139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Over the past decade, scientific discovery games (SDGs) have emerged as a viable approach for biomedical research, engaging hundreds of thousands of volunteer players and resulting in numerous scientific publications. After describing the origins of this novel research approach, we review the scientific output of SDGs across molecular modeling, sequence alignment, neuroscience, pathology, cellular biology, genomics, and human cognition. We find compelling results and technical innovations arising in problem-oriented games such as Foldit and Eterna and in data-oriented games such as EyeWire and Project Discovery. We discuss emergent properties of player communities shared across different projects, including the diversity of communities and the extraordinary contributions of some volunteers, such as paper writing. Finally, we highlight connections to artificial intelligence, biological cloud laboratories, new game genres, science education, and open science that may drive the next generation of SDGs.
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Affiliation(s)
- Rhiju Das
- Department of Biochemistry and Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Benjamin Keep
- Department of Learning Sciences, Stanford University, Stanford, California 94305, USA
| | - Peter Washington
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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Dsilva L, Mittal S, Koepnick B, Flatten J, Cooper S, Horowitz S. Creating custom Foldit puzzles for teaching biochemistry. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:133-139. [PMID: 30638297 PMCID: PMC6428574 DOI: 10.1002/bmb.21208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/27/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
The computer game Foldit is currently widely used as a biology and biochemistry teaching aid. Herein, we introduce a new feature of Foldit called "custom contests" that allows educators to create puzzles that fit their curriculum. The effectiveness of the custom contests is demonstrated by the use of five distinct custom contests in an upper-level biochemistry class. The new custom contest feature can be implemented in classes ranging from middle school to graduate school to enable educators to best complement their current curriculum. © 2019 International Union of Biochemistry and Molecular Biology, 47(2): 133-139, 2019.
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Affiliation(s)
- Lorna Dsilva
- College of Computer and Information Science, Northeastern University, Boston, MA 02115, USA
| | - Shubhi Mittal
- College of Computer and Information Science, Northeastern University, Boston, MA 02115, USA
| | - Brian Koepnick
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jeff Flatten
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Seth Cooper
- College of Computer and Information Science, Northeastern University, Boston, MA 02115, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA
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Abstract
Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make most effective use of our rapidly growing databases of whole genomes.
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Affiliation(s)
- Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.
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Baaden M, Delalande O, Ferey N, Pasquali S, Waldispühl J, Taly A. Ten simple rules to create a serious game, illustrated with examples from structural biology. PLoS Comput Biol 2018. [PMID: 29518072 PMCID: PMC5843163 DOI: 10.1371/journal.pcbi.1005955] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Marc Baaden
- Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Olivier Delalande
- Institut de Génétique et Développement de Rennes, Univ. Rennes 1, Rennes, France
| | | | - Samuela Pasquali
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des sciences pharmaceutiques et biologiques, Université Paris Descartes et Université Sorbonne Paris Cité, Paris, France
| | | | - Antoine Taly
- Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- * E-mail:
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Burnett S, Furlong M, Melvin PG, Singiser R. Games that Enlist Collective Intelligence to Solve Complex Scientific Problems. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2016; 17:133-136. [PMID: 27047610 PMCID: PMC4798797 DOI: 10.1128/jmbe.v17i1.983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
There is great value in employing the collective problem-solving power of large groups of people. Technological advances have allowed computer games to be utilized by a diverse population to solve problems. Science games are becoming more popular and cover various areas such as sequence alignments, DNA base-pairing, and protein and RNA folding. While these tools have been developed for the general population, they can also be used effectively in the classroom to teach students about various topics. Many games also employ a social component that entices students to continue playing and thereby to continue learning. The basic functions of game play and the potential of game play as a tool in the classroom are discussed in this article.
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Affiliation(s)
- Stephen Burnett
- Department of Biology, Clayton State University, Morrow, GA 30260
| | - Michelle Furlong
- Department of Biology, Clayton State University, Morrow, GA 30260
| | - Paul Guy Melvin
- Department of Biology, Clayton State University, Morrow, GA 30260
| | - Richard Singiser
- Department of Chemistry & Physics, Clayton State University, Morrow, GA 30260
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Van Vliet K, Moore C. Citizen Science Initiatives: Engaging the Public and Demystifying Science. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2016; 17:13-16. [PMID: 27047582 PMCID: PMC4798796 DOI: 10.1128/jmbe.v17i1.1019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The Internet and smart phone technologies have opened up new avenues for collaboration among scientists around the world. These technologies have also expanded citizen science opportunities and public participation in scientific research (PPSR). Here we discuss citizen science, what it is, who does it, and the variety of projects and methods used to increase scientific knowledge and scientific literacy. We describe a number of different types of citizen-science projects. These greatly increase the number of people involved, helping to speed the pace of data analysis and allowing science to advance more rapidly. As a result of the numerous advantages of citizen-science projects, these opportunities are likely to expand in the future and increase the rate of novel discoveries.
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Affiliation(s)
- Kim Van Vliet
- Corresponding author. Mailing address: St. Johns River State College, 5001 St. Johns Avenue, Palatka, Florida 32177. Phone: 352-281-4240. E-mail:
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Meignan D, Knust S, Frayret JM, Pesant G, Gaud N. A Review and Taxonomy of Interactive Optimization Methods in Operations Research. ACM T INTERACT INTEL 2015. [DOI: 10.1145/2808234] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This article presents a review and a classification of interactive optimization methods. These interactive methods are used for solving optimization problems. The interaction with an end user or decision maker aims at improving the efficiency of the optimization procedure, enriching the optimization model, or informing the user regarding the solutions proposed by the optimization system. First, we present the challenges of using optimization methods as a tool for supporting decision making, and we justify the integration of the user in the optimization process. This integration is generally achieved via a dynamic interaction between the user and the system. Next, the different classes of interactive optimization approaches are presented. This detailed review includes trial and error, interactive reoptimization, interactive multiobjective optimization, interactive evolutionary algorithms, human-guided search, and other approaches that are less well covered in the research literature. On the basis of this review, we propose a classification that aims to better describe and compare interaction mechanisms. This classification offers two complementary views on interactive optimization methods. The first perspective focuses on the user’s contribution to the optimization process, and the second concerns the components of interactive optimization systems. Finally, on the basis of this review and classification, we identify some open issues and potential perspectives for interactive optimization methods.
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Affiliation(s)
| | | | | | | | - Nicolas Gaud
- Université de Technologie de Belfort-Montéliard, Belfort, France
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Baynam G, Walters M, Claes P, Kung S, LeSouef P, Dawkins H, Bellgard M, Girdea M, Brudno M, Robinson P, Zankl A, Groza T, Gillett D, Goldblatt J. Phenotyping: targeting genotype's rich cousin for diagnosis. J Paediatr Child Health 2015; 51:381-6. [PMID: 25109851 DOI: 10.1111/jpc.12705] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 12/14/2022]
Abstract
There are many current and evolving tools to assist clinicians in their daily work of phenotyping. In medicine, the term 'phenotype' is usually taken to mean some deviation from normal morphology, physiology and behaviour. It is ascertained via history, examination and investigations, and a primary aim is diagnosis. Therefore, doctors are, by necessity, expert 'phenotypers'. There is an inherent and partially realised power in phenotypic information that when harnessed can improve patient care. Furthermore, phenotyping developments are increasingly important in an era of rapid advances in genomic technology. Fortunately, there is an expanding network of phenotyping tools that are poised for clinical translation. These tools will preferentially be implemented to mirror clinical workflows and to integrate with advances in genomic and information-sharing technologies. This will synergise with and augment the clinical acumen of medical practitioners. We outline key enablers of the ascertainment, integration and interrogation of clinical phenotype by using genetic diseases, particularly rare ones, as a theme. Successes from the test bed or rare diseases will support approaches to common disease.
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Affiliation(s)
- Gareth Baynam
- Genetic Services of Western Australia, Princess Margaret Hospital for Children, Perth, Western Australia, Australia; School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia; Office of Population Health Genomics, Department of Health, Government of Western Australia, Perth, Western Australia, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
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Sauermann H, Franzoni C. Crowd science user contribution patterns and their implications. Proc Natl Acad Sci U S A 2015; 112:679-84. [PMID: 25561529 PMCID: PMC4311847 DOI: 10.1073/pnas.1408907112] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Scientific research performed with the involvement of the broader public (the crowd) attracts increasing attention from scientists and policy makers. A key premise is that project organizers may be able to draw on underused human resources to advance research at relatively low cost. Despite a growing number of examples, systematic research on the effort contributions volunteers are willing to make to crowd science projects is lacking. Analyzing data on seven different projects, we quantify the financial value volunteers can bring by comparing their unpaid contributions with counterfactual costs in traditional or online labor markets. The volume of total contributions is substantial, although some projects are much more successful in attracting effort than others. Moreover, contributions received by projects are very uneven across time--a tendency toward declining activity is interrupted by spikes typically resulting from outreach efforts or media attention. Analyzing user-level data, we find that most contributors participate only once and with little effort, leaving a relatively small share of users who return responsible for most of the work. Although top contributor status is earned primarily through higher levels of effort, top contributors also tend to work faster. This speed advantage develops over multiple sessions, suggesting that it reflects learning rather than inherent differences in skills. Our findings inform recent discussions about potential benefits from crowd science, suggest that involving the crowd may be more effective for some kinds of projects than others, provide guidance for project managers, and raise important questions for future research.
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Affiliation(s)
- Henry Sauermann
- Georgia Institute of Technology, Scheller College of Business, Atlanta, GA 30308; and
| | - Chiara Franzoni
- Politecnico di Milano, School of Management, Milan 20133, Italy
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Soto W, Becerra D. A Multi-Objective Evolutionary Algorithm for Improving Multiple Sequence Alignments. ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2014. [DOI: 10.1007/978-3-319-12418-6_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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