Publications
Preprints
2025
2024
2023
2022
2021
2020 and older
Preprints
A collaboration between immune cells and the choroid plexus epithelium in brain inflammation
Xu, H., Lotfy, P., Gelb, S., Pragana, A., Hehnly, C., Shipley, FB., Zawadzki, ME., Cui, J., Deng, L., Taylor, M., Webb, M., Lidov, HGW., Andermann, ML., Chiu, IM., Ordovas-Montanes, J., Lehtinen, MK.
bioRxiv
Enhanced production of eicosanoids in plasma and activation of DNA damage pathways in PBMCs are correlated with the severity of ancestral COVID-19 infection
Tomalka, JA., Owings, A., Galeas-Pena, M., Ziegler, CGK., Robinson, TO., Wichman, TG., Laird, H., Williams, HB., Dhaliwal, NS., Everman, S., Zafar, Y., Shalek, AK., Horwitz, BH., Ordovas-Montanes, J., Glover, SC., Gibert, Y.
medRxiv
Severe COVID-19 is associated with fungal colonization of the nasopharynx and potent induction of IL-17 responses in the nasal epithelium
Ziegler, CGK., Owings, AH., Miao, VN., Navia, AW., Tang, Y., Bromley, JD., Lotfy, P., Sloan, M., Laird, H., Williams, HB., George, M., Drake, RS., Pride, Y., Abraham, GE., Senitko, M., Robinson, TO., Lionakis, MS., Shalek, AK., Ordovas-Montanes, J., Horwitz, BH., Glover, SC.
medRxiv
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
Cao, Y.*, Guo, Z.*, Vangala, P., Donnard, E., Liu, P., McDonel, P., Ordovas-Montanes, J., Shalek, A.K., Finberg, R.W., Wang, J.P., Garber, M.
* Co-main authors
bioRxiv
2025
Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2
Walsh, J. ML., Miao, VN., Owings, AH., Tang, Y., Bromley, JD., Kazer, SW., ... & Ordovas-Montanes, J.
Nature Immunology
2024
Primary nasal viral infection rewires the tissue-scale memory response
Kazer, SW., Match, CM., Langan, EM., Messou, MA., LaSalle, TJ., O'Leary, E., Marbourg, J., Naughton, K., von Andrian, UH., Ordovas-Montanes, J.
Immunity
An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection
Ziegler, CGK., Owings, AH., Galeas-Pena, M., Kazer, SW., Miao, VN., Navia, AW., Tang, Y., Bromley, JD., Lotfy, P., Sloan, M., Laird, H., Williams, HB., George, M., Drake, RS., Pride, Y., Abraham, GE III., Senitko, M., Robinson, TO., Diamond, G., Lionakis, MS., Shalek, AK., Ordovas-Montanes, J., Horwitz, BH., Glover, SC.
Microbiology Spectrum
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2023
A Roadmap for the Human Gut Cell Atlas
Zilbauer, M., James, KR., Kaur, M., Pott, S., Li, Z., Burger, A., Thiagarajah, JR., Burclaff, J., Jahnsen, FL., Perrone, F., Ross, AD., Matteoli, G., Stakenborg, N., Sujino, T., Moor, A., Bartolome-Casado, R., Bækkevold, ES., Zhou, R., Xie, B., Lau, KS., Din, S., Magness, ST., Yao, Q., Beyaz, S., Arends, M., Denadai-Souza, A., Coburn, LA., Gaublomme, JT., Baldock, R., Papatheodorou, I., Ordovas-Montanes, J., Boeckxstaens, G., Hupalowska, A., Teichmann, SA., Regev, A., Xavier, RJ., Simmons, A., Snyder, MP., Wilson, KT., Gut Cell Atlas Consortium, Human Cell Atlas Gut Biological Network Consortium.
Natural Reviews Gastroenterology & Hepatology
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Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing
Dudchenko, O., Ordovas-Montanes, J., Bingle, CD.
Biochemical Journal
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Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases
Weeks, EM., Ulirsch, JC., Cheng, NY., Trippe, BL., Fine, RS., Miao, J., Patwardhan, TA., Kanai, M., Nasser, J., Fulco, CP., Tashman, KC., Aguet, F., Li, T., Ordovas-Montanes, J., Smillie, CS., Biton, M., Shalek, AK., Ananthakrishnan, AN., Xavier, RJ., Regev, A., Gupta, RM., Lage, K., Ardlie, KG., Hirschhorn, JN., Lander, ES., Engreitz, JM., Finucane, HK.
Nature Genetics
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2022
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation
Kummerlowe, C., Mwakamui, S., Hughes, TK., Mulugeta, N., Mudenda, V., Besa, E., Zyambo, K., Shay, JES., Fleming, I., Vukovic, M., Doran, BA., Aicher, TP., Wadsworth, MH 2nd, Bramante, JT., Uchida, AM., Fardoos, R., Asowata, OE., Herbert, N., Yilmaz, ÖH., Kløverpris, HN., Garber, JJ., Ordovas-Montanes, J., Gartner, ZJ., Wallach, T., Shalek, AK., Kelly, P.
Science Translational Medicine
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Robust differentiation of human enteroendocrine cells from intestinal stem cells
Zeve, D., Stas, E., de Sousa Casal, J., Mannam, P., Qi, W., Yin, X., Dubois, S., Shah, MS., Syverson, EP., Hafner, S., Karp, JM., Carlone, DL, Ordovas-Montanes, J., Breault, DT.
Nature Communications
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Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation
Mead, BE., Hattori, K., Levy, L., Imada, S., Goto, N., Vukovic, M., Sze, D., Kummerlowe, C., Matute, JD., Duan, J, Langer, R., Blumberg, RS., Ordovas-Montanes, J., Yilmaz, OH., Karp, JM., Shalek, AK.
Nature Biomedical Engineering
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Rapid and sustained effect of dupilumab on clinical and mechanistic outcomes in aspirin-exacerbated respiratory disease
Buchheit, KM., Soahil, A., Hacker, J., Maurer, R., Gakpo, D., Bensko, JC., Taliaferro, F., Ordovas-Montanes, J., Laidlaw, TM.
Journal of Allergy and Clinical Immunology
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2021
Cyclin D3 drives intertial cell cycling in dark zone germinal center B cells
Pae, J., Ersching, J., Castro, TBR, Schips, M., Mesin, L., Allon, SJ., Ordovas-Montanes, J., Mlynarczyk, C., Melnick, A., Efeyan, A., Shalek, AK., Meyer-Hermann, M., Victora, G.
Journal of Experimental Medicine
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Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip
Bein, A.*, Kim, S.*, Goyal, G.*, Cao, W.*, Fadel, C.*, Naziripour, A., Sharma, S., Swenor, B., LoGrande, N., Nurani, A., Miao, V. N., Navia, A. W., Ziegler, C., Ordovas-Montanes, J., Prabhala, P., Kim, MS., Prantil-Baun, R., Rodas, M., Jiang, A., O'Sullivan, L., Tillya, G., Shalek, AK., Ingber, DE.
* Co-main authors
Cell
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Spatiotemporal single-cell profiling reveals that invasive and tissue-resident memory donor CD8+ T cells drive gastrointestinal acute graft-versus-host disease
Tkachev, V.#, Kaminski. J., Potter, EL., Furlan, SN., Yu, A., Hunt, DJ., McGuckin, C., Zheng, H., Colonna, L., Gerdemann, U., Carlson, J., Hoffman, M., Olvera, J., English, C., Baldessari, A., Panoskaltsis-Mortari, A., Watkins, B., Qayed, M., Suessmuth, Y., Betz, K., Bratrude, B., Langston, A., Horan, JT., Ordovas-Montanes, J., Shalek, AK., Blazar, BR., Roederer, M., Kean, LS.#
# Co-corresponding authors
Science Translational Medicine
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Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation
Dwyer, DF.*, Ordovas-Montanes, J.*, Allon, SJ., Buchheit, KM., Vukovic, M., Derakhshan, T., Feng, C., Lai, J., Hughes, TK., Nyquist, SK., Giannetti, MP., Berger, B., Bhattacharyya, N., Roditi, RE., Katz, HR., Nawijn, MC., Berg, M., Van Den Berge, M., Laidlaw, TM., Shalek, AK.#, Barrett, NA.#, Boyce, JA.#
* Co-main authors, # Co-corresponding authors
Science Immunology
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Mepolizumab targets multiple immune cells in aspirin-exacerbated respiratory disease
Buchheit, KM., Lewis, E., Gakpo, D., Hacker, J., Sohail, A., Taliaferro, F., Giron, EB., Asare, C., Vukovic, M., Bensko, JC., Dwyer, DF., Shalek, AK., Ordovas-Montanes, J., Laidlaw, TM.
Journal of Allergy and Clinical Immunology
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Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Ziegler, CGK.*, Miao, VN.*, Owings, AH.*, Navia, AW.*, Tang, Y.*, Bromley, JD., Lotfy, P., Sloan, M., Laird, H., Williams, HB., George, M., Drake, RS., Christian, T., Parker, A., Sindel, CS., Burger, MW., Pride, Y., Hasan, M., Abraham III, GE., Senitko, M., Robinson, TO., Shalek, A.K.#, Glover, SC.#, Horwitz, BH.#, Ordovas-Montanes, J.#
* Co-main authors, # Co-corresponding authors
Cell
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Prior upregulation of interferon pathways in the
nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children
Costa-Martins, AG., Mane, K., Lindsey, BB., Ogava, RL., Castro, Í., Jagne, YJ., Sallah, HJ., Armitage, EP., Jarju, S., Ahadzie, B., Ellis-Watson, R., Tregoning, JS., Bingle, CD., Bogaert, D., Clarke, E., Ordovas-Montanes, J., Jeffries, D., Kampmann, B., Nakaya, HI., de Silva, TI.
Cell Reports Medicine
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Desmosterol suppresses macrophage inflammasome
activation and protects against vascular
inflammation and atherosclerosis
Zhang, X., McDonald, JG., Aryal, B., Canfran‐Duque, A., Goldberg, EL., Araldi, E., Ding, W., Fan, Y., Thompson, BM., Singh, AK. Li, Q.,Tellides, G., Ordovas-Montanes, J., Garcia Milian, R., Deep Dixit, V., Ikonen, E., Suarez, Y., Fernandez-Hernando, C.
Proceedings of the National Academy of Sciences
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Variants in STXBP3 are Associated with Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation
Ouahed, J.*, Kelsen, JR.*, Spessott, WA., Kooshesh, K., Sanmillan, ML., Dawany, N., Sullivan, KE., Hamilton, KE., Slowik, V., Nejentsev, S., Neves, JF., Flores, H., Chung, WK., Wilson, A., Anyane-Yeboa, K., Wou, K., Jain, P., Field, M., Tollefson, S., Dent, MH., Li, D., Naito, T., McGovern, DPB., Kwong, AC., Taliaferro, F., Ordovas-Montanes, J., Horwitz, BH., Kotlarz, D., Klein, C., Evans, J., Dorsey, J., Warner, N., Elkadri, A., Muise, AM., Goldsmith, J., Thompson, B., Engelhardt, KR., Cant, AJ., Hambleton, S., Barclay, A., Toth-Petroczy, A., Vuzman, D., Carmichael, N., Bodea, C., Cassa, CA., Devoto, M., Maas, RL., Behrens, EM., Giraudo, CG., Snapper, SB.
* Co-main authors
Journal of Crohn's and Colitis
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2020
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
Hughes, TK.*, Wadsworth, MH.*, Gierahn, TM.*, Do, T., Weiss, D., Andrade P.R., Ma, F., de Andrade Silva, BJ., Shao, S., Tsoi, LC., Ordovas-Montanes, J., Gudjonsson, JE., Modlin, RL., Love, JC.^#, Shalek, AK.^#
* Co-main authors, ^ Co-senior authors, # Co-corresponding authors
bioRxiv
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Immunity
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Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
Mitsialis V., Wall S., Liu P., Ordovas-Montanes, J., Parmet, T., Vukovic, M., Spencer, D., Field, M., McCourt, C., Tthaker, J., Bousvaros, A., BCH IBD Center, BWH Crohn’s and Colitis Center, Shalek. A., Kean, L., Horwitz, B., Goldsmith, J., Tseng, G., Snapper, S.B.^#, Konnikova, L^#.
^ Co-senior authors, # Co-corresponding authors
Gastroenterology
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SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
Ziegler, C.G.K.*, Allon, S.J.*, Nyquist, S.K.*, Mbano, I.M.*, Miao, V.N., Tzouanas, C.N., Cao, Y., Yousif, A.S., Bals, J., Hauser, B.M., Feldman, J., Muus, C., Wadsworth II, M.H., Kazer, S.W., Hughes, T.K., Doran, B., Gatter, G.J., Vukovic, M., Taliaferro, F., Mead, B.E., Guo, Z., Wang, J.P., Gras, D., Plaisant, M., Ansari, M., Angelidis, I., Adler, H., Sucre, J.M.S., Taylor, C.J., Lin, B., Waghray, A., Mitsialis, V., Dwyer, D.F., Buchheit, K.M., Boyce, J.A., Barrett, N.A., Laidlaw, T.M., Carroll, S.L., Colonna, L., Tkachev, V., Peterson, C.W., Yu, A., Zheng, H.B., Gideon, H.P., Winchell, C.G., Lin, P.L., Bingle, C.D., Snapper, S.B., Kropski, J.A., Theis, F.J., Schiller, H.B., Zaragosi, L.-E., Barbry, P., Leslie, A., Kiem, H.-P., Flynn, J.L., Fortune, S.M., Berger, B., Finberg, R.W., Kean, L.S., Garber, M., Schmidt, A.G., Lingwood, D., Shalek, A.K.#, Ordovas-Montanes, J.#, HCA Lung Biological Network
* Co-main authors, # Co-corresponding authors
Cell
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Distribution and Storage of Inflammatory Memory in Barrier Tissue
Ordovas-Montanes, J., Beyaz, S., Rakoff-Nahoum S., Shalek, A.K.
Nature Reviews Immunology
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Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Kazer, SW., Aicher, TP., Muema, DM., Carroll, SL., Ordovas-Montanes, J., Miao, VN., Tu, AA., Ziegler, CGK., Nyquist, SK., Wong, EB., Ismail, N., Moodly, A., Berger, B., Love, JC., Dong, K., Leslie, A., Ndhlovu, ZM., Ndung’u T., Walker, BD., Shalek, AK.
bioRxiv
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Nature Medicine
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IL-5Rα marks nasal polyp IgG4- and IgE-expressing cells in aspirin-exacerbated respiratory disease
Buchheit, KM., Dwyer, DF., Ordovas-Montanes, J., Katz, H., Lewis, E., Vukovic, M., Lai, J., Bankova, L., Bhattacharyya, N., Shalek, AK., Barrett, NA., Boyce, JA., Laidlaw, TM.
bioRxiv
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Journal of Allergy and Clinical Immunology
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2019
Intra- and inter-cellular rewiring of the human colon during ulcerative colitis
Smillie, CS.*, Biton, M.*, Ordovas-Montanes, J.*, Sullivan, K., Burgin, G., Graham, DB., Herbst, RH., Rogel, N., Slyper, M., Waldman, J., Sud, M., Andrews, EA., Haber, AL., Vickovic, S., Dionne, D., Nguyen, LT., Villani, AC., Hofree, M., Creasey, EA., Huang, H., Rozenblatt-Rosen, O., Garber, JJ., Khalili, H., Desch, AN., Daly, MJ., Ananthakrishnan, AN.#, Shalek, AK.#, Xavier, RJ.#, Regev, A.#.
* Co-main authors, # Co-corresponding authors
bioRxiv
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Cell
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Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration.
Pepe-Mooney, BJ.*, Dill, MT.*, Alemany, A., Ordovas-Montanes, J., Matsushita, Y., Rao, A., Sen, A., Miyazaki, M, Anakk, S., Dawson, PA., Ono, N., Shalek, AK., van Oudenaarden, A., Camargo, FD.#
* Co-main authors, # Corresponding author
Cell Stem Cell
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2018
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
Biton, M.*, Haber, AL.*, Beyaz, S., Rogel, N., Smillie, C., Sh*ekhar, K., Chen, Z., Wu, C., Ordovas-Montanes, J., Alvarez, D., Herbst, RH., Tirosh, I., Burgin, G., Dionne, D., Zhang, M., Rozenblatt-Rosen, O., Shi, HN., Kuchroo, V., Yilmaz, O., Regev, A.^, Xavier, RJ.*#
* Co-main authors, ^ Senior author, # Corresponding author
bioRxiv
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Cell
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Allergic inflammatory memory in human respiratory epithelial progenitor cells
Ordovas-Montanes, J.*, Dwyer, DF.*, Nyquist, SK., Buchheit, KM., Vukovic, M., Deb, C., Wadsworth, MH., Hughes, TK., Kazer, SW., Yoshimoto, E., Bhattacharyya, N., Cahill, KN., Katz, HR., Laidlaw, TM., Boyce, JA., Barrett, NA#. Shalek, AK#.
* Co-main authors, # Co-corresponding authors
bioRxiv
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Nature
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Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Mead, BE.*#, Ordovas-Montanes, J.*, Braun, AP., Levy, L., Szucs, MJ, MacMullan, M., Ammendolia, D., Zheng, Y., Bhargava, P., Yin, X., Hughes, TK., Wadsworth III, MH., Ahmad, R., Rakoff-Nahoum, S., Carr, S., Langer, R., Collins JJ., Shalek, AK., Karp, JM.#
* Co-main authors, # Co-corresponding authors
BMC Biology
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A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
Martin-Gayo, E., Cole, M., Kolb, KE., Ouyang, Z., Cronin, J., Kazer, SW., Ordovas-Montanes, J., Lichterfeld, M., Walker, BD., Yosef, N.#, Shalek, AK.#, Yu, XG.#
# Co-corresponding authors
Genome Biology
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2017
Novel in vitro booster vaccination to rapidly generate antigen-specific fully human monoclonal antibodies from healthy individuals
Nandin, IS.*, Fong, C.*, Deantonio, C., Torreno-Pina, JA., Pecetta, S., Maldonado, P., Gasparrini, F., Ordovas-Montanes, J., Kazer, SW., Kjaer, S., Borley, DW., Nair, U., Coleman, JA., Lingwood, D., Shalek, AK., Meffre, E., Poignard, P., Burton, DR., Batista, FD.#
* Co-main authors, # Corresponding author
Journal of Experimental Medicine
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2016
The Whiteboard Revolution: Illuminating Science Communication in the Digital Age
Mar, FA., Ordovas-Montanes, J., Oksenberg, N., Olson, AM.
Trends in Immunology
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2015
The regulation of immunological processes by peripheral neurons in homeostasis and disease
Ordovas-Montanes, J., Rakoff-Nahoum, S., Huang, S., Riol-Blanco, L., Barreiro, O., von Andrian, UH.
Trends in Immunology
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2014
2012
Impaired intrinsic immunity to HSV-1 in human iPSC-derived TLR3-deficient CNS cells
Lafaille, FG., Pessach, IM., Zhang, SY., Ciancanelli, M., Herman, M., Mostoslavsky, G., Ordovas-Montanes, J., Jouanguy, E., Plancoulaine, S., Tu, E., Elkabetz, Y., Schlaeger, TM., Daley, GQ., Tardieu, M., Abel, L., Casanova, JL., Studer, L., Notarangelo, LD.
Nature
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2011