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1. Incidence of COVID-19 mRNA vaccine symptomatic breakthrough infections during Omicron circulation in adults with or without infection prior to vaccination

Author

Durier, Christine, Ninove, Laetitia, van der Werf, Sylvie, Lefebvre, Maeva, Desaint, Corinne, Bauer, Rebecca, Attia, Mikael, Lecompte, Anne-Sophie, Lachatre, Marie, Maakaroun-Vermesse, Zoha, Nicolas, Jean-François, Verdon, Renaud, Kiladjian, Jean-Jacques, Loubet, Paul, Schmidt-Mutter, Catherine, Corbin, Violaine, Ansart, Séverine, Melica, Giovanna, Resch, Martine, Netzer, Emmanuelle, Kherabi, Yousra, Tardieu, Raphaëlle, Lelièvre, Jean-Daniel, Tartour, Eric, Meyer, Laurence, de Lamballerie, Xavier, and Launay, Odile

Published
2024
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2. Neutralising antibody responses to SARS-CoV-2 omicron among elderly nursing home residents following a booster dose of BNT162b2 vaccine: A community-based, prospective, longitudinal cohort study

Author

Bruel, Timothée, Pinaud, Laurie, Tondeur, Laura, Planas, Delphine, Staropoli, Isabelle, Porrot, Françoise, Guivel-Benhassine, Florence, Attia, Mikaël, Pelleau, Stéphane, Woudenberg, Tom, Duru, Cécile, Koffi, Aymar Davy, Castelain, Sandrine, Fernandes-Pellerin, Sandrine, Jolly, Nathalie, De Facci, Louise Perrin, Roux, Emmanuel, Ungeheuer, Marie-Noëlle, Van Der Werf, Sylvie, White, Michael, Schwartz, Olivier, and Fontanet, Arnaud

Published
2022
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3. SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

Author

Temmam, Sarah, Montagutelli, Xavier, Herate, Cécile, Donati, Flora, Regnault, Béatrice, Attia, Mikael, Baquero Salazar, Eduard, Chretien, Delphine, Conquet, Laurine, Jouvion, Grégory, Pipoli Da Fonseca, Juliana, Cokelaer, Thomas, Amara, Faustine, Relouzat, Francis, Naninck, Thibaut, Lemaitre, Julien, Derreudre‐Bosquet, Nathalie, Pascal, Quentin, Bonomi, Massimiliano, Bigot, Thomas, Munier, Sandie, Rey, Felix A, Le Grand, Roger, van der Werf, Sylvie, and Eloit, Marc

Published
2023
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4. Humoral immunity to SARS-CoV-2 and seasonal coronaviruses in children and adults in north-eastern France

Author

Woudenberg, Tom, Pelleau, Stéphane, Anna, François, Attia, Mikael, Donnadieu, Françoise, Gravet, Alain, Lohmann, Caroline, Seraphin, Hélène, Guiheneuf, Raphaël, Delamare, Catherine, Stefic, Karl, Marlet, Julien, Brochot, Etienne, Castelain, Sandrine, Augereau, Olivier, Sibilia, Jean, Dubos, François, Meddour, Damia, Guen, Christèle Gras-Le, Coste-Burel, Marianne, Imbert-Marcille, Berthe-Marie, Chauvire-Drouard, Anne, Schweitzer, Cyril, Gatin, Amélie, Lomazzi, Sandra, Joulié, Aline, HAAS, Hervé, Cantais, Aymeric, Bertholon, Frederique, Chinazzo-Vigouroux, Marie-France, Abdallah, Mohamed SI, Arowas, Laurence, Charneau, Pierre, Hoen, Bruno, Demeret, Caroline, Werf, Sylvie Van Der, Fontanet, Arnaud, and White, Michael

Published
2021
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6. Application of Machine Learning Prediction of Individual SARS-CoV-2 Vaccination and Infection Status to the French Serosurveillance Survey From March 2020 to 2022: Cross-Sectional Study

Author

Bougeard, Stéphanie, primary, Huneau-Salaun, Adeline, additional, Attia, Mikael, additional, Richard, Jean-Baptiste, additional, Demeret, Caroline, additional, Platon, Johnny, additional, Allain, Virginie, additional, Le Vu, Stéphane, additional, Goyard, Sophie, additional, Gillon, Véronique, additional, Bernard-Stoecklin, Sibylle, additional, Crescenzo-Chaigne, Bernadette, additional, Jones, Gabrielle, additional, Rose, Nicolas, additional, van der Werf, Sylvie, additional, Lantz, Olivier, additional, Rose, Thierry, additional, and Noël, Harold, additional

Published
2023
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7. Acute tubulointerstitial nephritis with or without uveitis: a novel form of post-acute COVID-19 syndrome in children

Author

Avramescu, Marina, primary, Isnard, Pierre, additional, Temmam, Sarah, additional, Chevalier, Agnès, additional, Bastard, Paul, additional, Attia, Mikael, additional, Berthaud, Romain, additional, Fila, Marc, additional, Dossier, Claire, additional, Hogan, Julien, additional, Ulinski, Tim, additional, Leguevaques, Damia, additional, Louillet, Férielle, additional, Casado, Edouard Martinez, additional, Halimi, Jean-Michel, additional, Cloarec, Sylvie, additional, Zaloszyc, Ariane, additional, Faudeux, Camille, additional, Rousset-Rouvière, Caroline, additional, Clavé, Stéphanie, additional, Harambat, Jérôme, additional, Rollot, Edouard, additional, Simon, Thomas, additional, Nallet-Amate, Megan, additional, Ranchin, Bruno, additional, Bacchetta, Justine, additional, Porcheret, Florence, additional, Bernard, Josselin, additional, Ryckewaert, Amélie, additional, Jamet, Anne, additional, Fourgeaud, Jacques, additional, Da Rocha, Nicolas, additional, Pérot, Philippe, additional, Kuperwasser, Nicolas, additional, Bouazza, Naïm, additional, Rabant, Marion, additional, Duong Van Huyen, Jean-Paul, additional, Robert, Matthieu P., additional, Zuber, Julien, additional, Casanova, Jean-Laurent, additional, Eloit, Marc, additional, Sermet-Gaudelus, Isabelle, additional, and Boyer, Olivia, additional

Published
2023
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8. Application of Machine Learning Prediction of Individual SARS-CoV-2 Vaccination and Infection Status to the French Serosurveillance Survey From March 2020 to 2022: Cross-Sectional Study (Preprint)

Author

Bougeard, Stéphanie, primary, Huneau-Salaun, Adeline, additional, Attia, Mikael, additional, Richard, Jean-Baptiste, additional, Demeret, Caroline, additional, Platon, Johnny, additional, Allain, Virginie, additional, Le Vu, Stéphane, additional, Goyard, Sophie, additional, Gillon, Véronique, additional, Bernard-Stoecklin, Sibylle, additional, Crescenzo-Chaigne, Bernadette, additional, Jones, Gabrielle, additional, Rose, Nicolas, additional, van der Werf, Sylvie, additional, Lantz, Olivier, additional, Rose, Thierry, additional, and Noël, Harold, additional

Published
2023
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9. High-risk exposure without personal protective equipment and infection with SARS-CoV-2 in-hospital workers - The CoV-CONTACT cohort

Author

Duval, Xavier, Burdet, Charles, Lina, Bruno, Tubiana, Sarah, Van Der Werf, Sylvie, Abad, Fanny, Abry, Dominique, Alavoine, Loubna, Allain, Jean-Sébastien, Amiel-Taieb, Karline, Audoin, Pierre, Augustin, Shana, Ayala, Sandrine, Bansard, Hélène, Bertholon, Fréderique, Boissel, Nolwenn, Botelho-Nevers, Elisabeth, Bouiller, Kévin, Bourgeon, Marilou, Boutrou, Mathilde, Brick, Lysiane, Bruneau, Léa, Caumes, Eric, Chabouis, Agnès, Chan Thien, Eric, Chirouze, Catherine, Coignard, Bruno, Costa, Yolande, Costenoble, Virginie, Cour, Sylvie, Cracowski, Claire, Cracowski Jean, Luc, Deplanque, Dominique, Dequand, Stéphane, Desille-Dugast, Mireille, Desmarets, Maxime, Detoc, Maelle, Dewitte, Marie, Djossou, Felix, Ecobichon, Jean-Luc, Elrezzi, Elise, Faurous, William, Fortuna, Viviane, Fouchard, Julie, Gantier, Emilie, Gautier, Céline, Gerardin, Patrick, Gerset, Sandrine, Gilbert, Marie, Gissot, Valérie, Guillemin, Francis, Hartard, Cédric, Hazevis, Béatrice, Hocquet, Didier, Hodaj, Enkelejda, Ilic-Habensus, Emila, A, Jeudy, Jeulin, Helene, Kane, Maty, Kasprzyk, Emmanuelle, Kikoine, John, Laine, Fabrice, Laviolle, Bruno, Lebeaux, David, Leclercq, Anne, Ledru, Eric, Lefevre, Benjamin, Legoas, Carole, Legrand, Amélie, Legrand, Karine, Lehacaut, Jonathan, Lehur, Claire, Lemouche, Dalila, Lepiller, Quentin, Lepuil, Sévérine, Letienne, Estelle, Lucarelli, Aude, Lucet, Jean-Christophe, Madeline, Isabelle, Maillot, Adrien, Malapate, Catherine, Malvy, Denis, Mandic, Milica, Marty-Quinternet, Solène, Meghadecha, Mohamed, Mergeay-Fabre, Mayka, Mespoulhe, Pauline, Meunier, Alexandre, Migaud, Maria-Claire, Motiejunaite, Justina, Nathalie, Gay, Nguyen, Duc, Oubbea, Soumaya, Pagadoy, Maïder, Paris, Adeline, Paris, Christophe, Payet, Christine, Peiffer-Smadja, Nathan, Perez, Lucas, Perreau, Pauline, Pierrez, Nathalie, Pistone, Thierry, Postolache, Andreea, Rasoamanana, Patrick, Reminiac, Cécile, Rexah, Jade, Roche-Gouanvic, Elise, Rousseau, Alexandra, Schoemaecker, Betty, Simon, Sandrine, Soler, Catherine, Somers, Stéphanie, Sow, Khaly, Tardy, Bernard, Terzian, Zaven, Thy, Michael, Tournier, Anne, Tyrode, Sandrine, Vauchy, Charline, Verdon, Renaud, Vernet, Pauline, Vignali, Valérie, Waucquier, Nawal, Do Thi Thu, Huong, Laouénan, Cédric, Mentre, France, Pauline, Manchon, Dechanet, Aline, Letrou, Sophie, Quintin, Caroline, Frezouls, Wahiba, Le Hingrat, Quentin, Houhou, Nadhira, Damond, Florence, Descamps, Dianes, Charpentier, Charlotte, Visseaux, Benoit, Vabret, Astrid, Bouscambert, Maud, Behillil, Sylvie, Gaillanne, Laurence, Benmalek, Nabil, Attia, Mikael, Barbet, Marion, Demeret, Caroline, Rose, Thierry, Petres, Stéphane, Escriou, Nicolas, Goyard, Sophie, Kafif, Ouifiya, Piquard, Valentine, Mailles, Alexandra, Simondon, Anne, Dreyere, Marion, Morel, Bruno, Vesval, Thiphaine, Amat, Karine, Ammour, Douae, Aqourras, Khadija, Couffin-Cadiergues, Sandrine, Delmas, Christelle, Desan, Vristi, Jean, Michel Doute, Esperou, Hélène, Hendou, Samia, Kouakam, Christelle, Le Meut, Guillaume, Lemestre, Soizic, Leturque, Nicolas, Marcoul, Emmanuelle, Nguefang, Solange, Roufai, Layidé, Abel, Laurent, Caillat-Zucman, Sophie, Manchon, Pauline, Blanquart, François, Guedj, Jérémie, Yazdanpanah, Yazdan, Attia, Mikaël, Bielicki, Julia Anna, Bruijning-Verhagen, Patricia, Goossens, Herman, Descamps, Diane, and van der Werf, Sylvie

Published
2021
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10. Structural organization of the inactive X chromosome in the mouse

Author

Giorgetti, Luca, Lajoie, Bryan R., Carter, Ava C., Attia, Mikael, Zhan, Ye, Xu, Jin, Chen, Chong Jian, Kaplan, Noam, Chang, Howard Y., Heard, Edith, and Dekker, Job

Subjects
Observations, Physiological aspects, Methods, Chromosomes -- Physiological aspects, RNA sequencing -- Methods, Gene expression -- Observations
Abstract

To investigate the structure of the Xi chromosome, we performed allele-specific Hi-C in a clonal neural progenitor cell (NPC) line that was derived from highly polymorphic F1 mouse embryonic stem [...], X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region (1,2), although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts (3). A role for Xist in organizing the inactive X (Xi) chromosome has been proposed (4-6). Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite (7-10). However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions, remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes in different neural progenitor clones are associated with the presence of different TAD-like structures after XCI. These findings suggest a key role for transcription and CTCF in the formation of TADs in the context of the Xi chromosome in neural progenitors.

Published
2016

13. Humoral Immunity to SARS-CoV-2 and Inferred Protection from Infection in a French Longitudinal Community Cohort

Author

Woudenberg, Tom, primary, Pinaud, Laurie, additional, Garcia, Laura, additional, Tondeur, Laura, additional, Pelleau, Stephane, additional, de Thoisy, Alix, additional, Donnadieu, Francoise, additional, Backovic, Marija, additional, Attia, Mikael, additional, Hoze, Nathanael, additional, Duru, Cecile, additional, Koffi, Aymar Davy, additional, Castelain, Sandrine, additional, Ungeheuer, Marie-Noelle, additional, Fernandes Pellerin, Sandrine, additional, Planas, Delphine, additional, Bruel, Timothee, additional, CAUCHEMEZ, SIMON, additional, Schwarz, Olivier, additional, Fontanet, Arnaud, additional, and White, Michael, additional

Published
2022
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14. Molecular coupling of Tsix regulation and pluripotency

Author

Navarro, Pablo, Oldfield, Andrew, Legoupi, Julie, Festuccia, Nicola, Dubois, Agnes, Attia, Mikael, Schoorlemmer, Jon, Rougeulle, Claire, Chambers, Ian, and Avner, Philip

Subjects
Embryonic stem cells, X chromosome inactivation, Chromatin, DNA binding proteins
Abstract

X-inactivation reprogramming in female mice is a model for the epigenetic processes underlying the acquisition of pluripotency (1). The inactivation of the paternal X chromosome that characterizes the earliest cleavage-stages [...], The reprogramming of X-chromosome inactivation during the acquisition of pluripotency in vivo and in vitro (1) is accompanied by the repression of Xist (2), the trigger of X-inactivation (3), and the upregulation of its antisense counterpart Tsix (4). We have shown that key factors supporting pluripotency--Nanog, Oct4 and Sox2--bind within Xist intron 1 in undifferentiated embryonic stem cells (ESC) to repress Xist transcription (5). However, the relationship between transcription factors of the pluripotency network and Tsix regulation has remained unclear (5,6). Here we show that Tsix upregulation in embryonic stem cells depends on the recruitment of the pluripotent marker Rex1, and of the reprogramming-associated factors Klf4 and c-Myc, by the DXPas34 minisatellite associated with the Tsix promoter. Upon deletion of DXPas34, binding of the three factors is abrogated and the transcriptional machinery is no longer efficiently recruited to the Tsixpromoter. Additional analyses including knockdown experiments further demonstrate that Rex1 is critically important for efficient transcription elongation of Tsix. Hence, distinct embryonic-stem-cell-specific complexes couple X-inactivation reprogramming and pluripotency, with Nanog, Oct4 and Sox2 repressing Xist to facilitate the reactivation of the inactive X, and Klf4, c-Myc and Rexl activating Tsix to remodel Xist chromatin (7-10) and ensure random X-inactivation upon differentiation (1). The holistic pattern of Xist/Tsix regulation by pluripotent factors that we have identified suggests a general direct governance of complex epigenetic processes by the machinery dedicated to pluripotency.

Published
2010
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15. High-risk exposure without personal protective equipment and infection with SARS-CoV-2 in-hospital workers - The CoV-CONTACT cohort

Author

Tubiana, Sarah, primary, Burdet, Charles, additional, Houhou, Nadhira, additional, Thy, Michael, additional, Manchon, Pauline, additional, Blanquart, François, additional, Charpentier, Charlotte, additional, Guedj, Jérémie, additional, Alavoine, Loubna, additional, Behillil, Sylvie, additional, Leclercq, Anne, additional, Lucet, Jean-Christophe, additional, Yazdanpanah, Yazdan, additional, Attia, Mikaël, additional, Demeret, Caroline, additional, Rose, Thierry, additional, Bielicki, Julia Anna, additional, Bruijning-Verhagen, Patricia, additional, Goossens, Herman, additional, Descamps, Diane, additional, van der Werf, Sylvie, additional, Lina, Bruno, additional, Duval, Xavier, additional, Tubiana, Sarah, additional, Van Der Werf, Sylvie, additional, Abad, Fanny, additional, Abry, Dominique, additional, Allain, Jean-Sébastien, additional, Amiel-Taieb, Karline, additional, Audoin, Pierre, additional, Augustin, Shana, additional, Ayala, Sandrine, additional, Bansard, Hélène, additional, Bertholon, Fréderique, additional, Boissel, Nolwenn, additional, Botelho-Nevers, Elisabeth, additional, Bouiller, Kévin, additional, Bourgeon, Marilou, additional, Boutrou, Mathilde, additional, Brick, Lysiane, additional, Bruneau, Léa, additional, Caumes, Eric, additional, Chabouis, Agnès, additional, Chan Thien, Eric, additional, Chirouze, Catherine, additional, Coignard, Bruno, additional, Costa, Yolande, additional, Costenoble, Virginie, additional, Cour, Sylvie, additional, Cracowski, Claire, additional, Cracowski Jean, Luc, additional, Deplanque, Dominique, additional, Dequand, Stéphane, additional, Desille-Dugast, Mireille, additional, Desmarets, Maxime, additional, Detoc, Maelle, additional, Dewitte, Marie, additional, Djossou, Felix, additional, Ecobichon, Jean-Luc, additional, Elrezzi, Elise, additional, Faurous, William, additional, Fortuna, Viviane, additional, Fouchard, Julie, additional, Gantier, Emilie, additional, Gautier, Céline, additional, Gerardin, Patrick, additional, Gerset, Sandrine, additional, Gilbert, Marie, additional, Gissot, Valérie, additional, Guillemin, Francis, additional, Hartard, Cédric, additional, Hazevis, Béatrice, additional, Hocquet, Didier, additional, Hodaj, Enkelejda, additional, Ilic-Habensus, Emila, additional, A, Jeudy, additional, Jeulin, Helene, additional, Kane, Maty, additional, Kasprzyk, Emmanuelle, additional, Kikoine, John, additional, Laine, Fabrice, additional, Laviolle, Bruno, additional, Lebeaux, David, additional, Ledru, Eric, additional, Lefevre, Benjamin, additional, Legoas, Carole, additional, Legrand, Amélie, additional, Legrand, Karine, additional, Lehacaut, Jonathan, additional, Lehur, Claire, additional, Lemouche, Dalila, additional, Lepiller, Quentin, additional, Lepuil, Sévérine, additional, Letienne, Estelle, additional, Lucarelli, Aude, additional, Madeline, Isabelle, additional, Maillot, Adrien, additional, Malapate, Catherine, additional, Malvy, Denis, additional, Mandic, Milica, additional, Marty-Quinternet, Solène, additional, Meghadecha, Mohamed, additional, Mergeay-Fabre, Mayka, additional, Mespoulhe, Pauline, additional, Meunier, Alexandre, additional, Migaud, Maria-Claire, additional, Motiejunaite, Justina, additional, Nathalie, Gay, additional, Nguyen, Duc, additional, Oubbea, Soumaya, additional, Pagadoy, Maïder, additional, Paris, Adeline, additional, Paris, Christophe, additional, Payet, Christine, additional, Peiffer-Smadja, Nathan, additional, Perez, Lucas, additional, Perreau, Pauline, additional, Pierrez, Nathalie, additional, Pistone, Thierry, additional, Postolache, Andreea, additional, Rasoamanana, Patrick, additional, Reminiac, Cécile, additional, Rexah, Jade, additional, Roche-Gouanvic, Elise, additional, Rousseau, Alexandra, additional, Schoemaecker, Betty, additional, Simon, Sandrine, additional, Soler, Catherine, additional, Somers, Stéphanie, additional, Sow, Khaly, additional, Tardy, Bernard, additional, Terzian, Zaven, additional, Tournier, Anne, additional, Tyrode, Sandrine, additional, Vauchy, Charline, additional, Verdon, Renaud, additional, Vernet, Pauline, additional, Vignali, Valérie, additional, Waucquier, Nawal, additional, Do Thi Thu, Huong, additional, Laouénan, Cédric, additional, Mentre, France, additional, Pauline, Manchon, additional, Dechanet, Aline, additional, Letrou, Sophie, additional, Quintin, Caroline, additional, Frezouls, Wahiba, additional, Le Hingrat, Quentin, additional, Damond, Florence, additional, Descamps, Dianes, additional, Visseaux, Benoit, additional, Vabret, Astrid, additional, Bouscambert, Maud, additional, Gaillanne, Laurence, additional, Benmalek, Nabil, additional, Attia, Mikael, additional, Barbet, Marion, additional, Petres, Stéphane, additional, Escriou, Nicolas, additional, Goyard, Sophie, additional, Kafif, Ouifiya, additional, Piquard, Valentine, additional, Mailles, Alexandra, additional, Simondon, Anne, additional, Dreyere, Marion, additional, Morel, Bruno, additional, Vesval, Thiphaine, additional, Amat, Karine, additional, Ammour, Douae, additional, Aqourras, Khadija, additional, Couffin-Cadiergues, Sandrine, additional, Delmas, Christelle, additional, Desan, Vristi, additional, Jean, Michel Doute, additional, Esperou, Hélène, additional, Hendou, Samia, additional, Kouakam, Christelle, additional, Le Meut, Guillaume, additional, Lemestre, Soizic, additional, Leturque, Nicolas, additional, Marcoul, Emmanuelle, additional, Nguefang, Solange, additional, Roufai, Layidé, additional, Abel, Laurent, additional, and Caillat-Zucman, Sophie, additional

Published
2021
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