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+
+
+
+ 20240830130631-bc15b8ade1b038ce870604ce0d8bd9bdbb2baa45
+ 20240830130631
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 08
+ 2024
+
+
+ 9
+
+ 100
+
+
+
+ exoTEDRF: An EXOplanet Transit and Eclipse Data
+Reduction Framework
+
+
+
+ Michael
+ Radica
+ https://orcid.org/0000-0002-3328-1203
+
+
+
+ 08
+ 30
+ 2024
+
+
+ 6898
+
+
+ 10.21105/joss.06898
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+
+
+
+ Software archive
+ 10.5281/zenodo.13370466
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/6898
+
+
+
+ 10.21105/joss.06898
+ https://joss.theoj.org/papers/10.21105/joss.06898
+
+
+ https://joss.theoj.org/papers/10.21105/joss.06898.pdf
+
+
+
+
+
+ JWST calibration pipeline
+ Bushouse
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+ 2022
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+Dencheva, N., Davies, J., Greenfield, P., Morrison, J., Hodge, P.,
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+Miller, T., Jedrzejewski, R., Hack, W., Davis, D., Crawford, S., Law,
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+Zenodo. https://doi.org/10.5281/zenodo.7437681
+
+
+ Eureka!: An End-to-End Pipeline for JWST
+Time-Series Observations
+ Bell
+ Journal of Open Source
+Software
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+ 7
+ 10.21105/joss.04503
+ 2022
+ Bell, T., Ahrer, E.-M., Brande, J.,
+Carter, A., Feinstein, A. D., Caloca, G., Mansfield, M., Zieba, S.,
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+Santos, L. A., Bean, J. L., Parmentier, V., Wong, I., Rauscher, E.,
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+
+
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+with JWST/NIRISS: Evidence for Strong Stellar Contamination in the
+Transmission Spectra
+ Lim
+ The Astrophysical Journal
+Letters
+ 1
+ 955
+ 10.3847/2041-8213/acf7c4
+ 2023
+ Lim, O., Benneke, B., Doyon, R.,
+MacDonald, R. J., Piaulet, C., Artigau, É., Coulombe, L.-P., Radica, M.,
+L’Heureux, A., Albert, L., Rackham, B. V., de Wit, J., Salhi, S., Roy,
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+Lafrenière, D., … Darveau-Bernier, A. (2023). Atmospheric Reconnaissance
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+Contamination in the Transmission Spectra. The Astrophysical Journal
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+https://doi.org/10.3847/2041-8213/acf7c4
+
+
+ The Near Infrared Imager and Slitless
+Spectrograph for the James Webb Space Telescope. III. Single Object
+Slitless Spectroscopy
+ Albert
+ Publications of the Astronomical Society of
+the Pacific
+ 1049
+ 135
+ 10.1088/1538-3873/acd7a3
+ 2023
+ Albert, L., Lafrenière, D., René,
+Doyon, Artigau, É., Volk, K., Goudfrooij, P., Martel, A. R., Radica, M.,
+Rowe, J., Espinoza, N., Roy, A., Filippazzo, J. C., Darveau-Bernier, A.,
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+ 2024
+ Radica, M., Coulombe, L.-P., Taylor,
+J., Albert, L., Allart, R., Benneke, B., Cowan, N. B., Dang, L.,
+Lafrenière, D., Thorngren, D., Artigau, É., Doyon, R., Flagg, L.,
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+the JWST NIRISS Transmission Spectrum of Hot Neptune LTT 9779b. The
+Astrophysical Journal Letters, 962(1), L20.
+https://doi.org/10.3847/2041-8213/ad20e4
+
+
+ Near-infrared transmission spectroscopy of
+HAT-P-18 b with NIRISS: Disentangling planetary and stellar features in
+the era of JWST
+ Fournier-Tondreau
+ Monthly Notices of the Royal Astronomical
+Society
+ 2
+ 528
+ 10.1093/mnras/stad3813
+ 2024
+ Fournier-Tondreau, M., MacDonald, R.
+J., Radica, M., Lafrenière, D., Welbanks, L., Piaulet, C., Coulombe,
+L.-P., Allart, R., Morel, K., Artigau, É., Albert, L., Lim, O., Doyon,
+R., Benneke, B., Rowe, J. F., Darveau-Bernier, A., Cowan, N. B., Lewis,
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+Astronomical Society, 528(2), 3354–3377.
+https://doi.org/10.1093/mnras/stad3813
+
+
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+Metal-rich Miscible Atmosphere on a Two-Earth-Radius
+Exoplanet
+ Benneke
+ arXiv e-prints
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+ 2024
+ Benneke, B., Roy, P.-A., Coulombe,
+L.-P., Radica, M., Piaulet, C., Ahrer, E.-M., Pierrehumbert, R.,
+Krissansen-Totton, J., Schlichting, H. E., Hu, R., Yang, J., Christie,
+D., Thorngren, D., Young, E. D., Pelletier, S., Knutson, H. A., Miguel,
+Y., Evans-Soma, T. M., Dorn, C., … Allart, R. (2024). JWST Reveals CH_4,
+CO_2, and H_2O in a Metal-rich Miscible Atmosphere on a Two-Earth-Radius
+Exoplanet. arXiv e-Prints, arXiv:2403.03325.
+https://doi.org/10.48550/arXiv.2403.03325
+
+
+ PACMAN: A pipeline to reduce and analyze
+Hubble Wide Field Camera 3 IR Grism data
+ Zieba
+ The Journal of Open Source
+Software
+ 80
+ 7
+ 10.21105/joss.04838
+ 2022
+ Zieba, S., & Kreidberg, L.
+(2022). PACMAN: A pipeline to reduce and analyze Hubble Wide Field
+Camera 3 IR Grism data. The Journal of Open Source Software, 7(80),
+4838. https://doi.org/10.21105/joss.04838
+
+
+ Tshirt
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+(2022). Tshirt. In GitHub repository. GitHub.
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+series
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+Software
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+ 6
+ 10.21105/joss.03285
+ 2021
+ Foreman-Mackey, D., Luger, R., Agol,
+E., Barclay, T., Bouma, L. G., Brandt, T. D., Czekala, I., David, T. J.,
+Dong, J., Gilbert, E. A., Gordon, T. A., Hedges, C., Hey, D. R., Morris,
+B. M., Price-Whelan, A. M., & Savel, A. B. (2021). exoplanet:
+Gradient-based probabilistic inference for exoplanet data & other
+astronomical time series. The Journal of Open Source Software, 6(62),
+3285. https://doi.org/10.21105/joss.03285
+
+
+ APPLESOSS: A Producer of ProfiLEs for SOSS.
+Application to the NIRISS SOSS Mode
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+ Publications of the Astronomical Society of
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+ 2022
+ Radica, M., Albert, L., Taylor, J.,
+Lafrenière, D., Coulombe, L.-P., Darveau-Bernier, A., Doyon, R., Cook,
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+ProfiLEs for SOSS. Application to the NIRISS SOSS Mode. Publications of
+the Astronomical Society of the Pacific, 134(1040), 104502.
+https://doi.org/10.1088/1538-3873/ac9430
+
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+Contamination. Application to the NIRISS SOSS Mode
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+ Transmission Spectroscopy of the Habitable
+Zone Exoplanet LHS 1140 b with JWST/NIRISS
+ Cadieux
+ The Astrophysical Journal
+Letters
+ 1
+ 970
+ 10.3847/2041-8213/ad5afa
+ 2024
+ Cadieux, C., Doyon, R., MacDonald, R.
+J., Turbet, M., Artigau, É., Lim, O., Radica, M., Fauchez, T. J., Salhi,
+S., Dang, L., Albert, L., Coulombe, L.-P., Cowan, N. B., Lafrenière, D.,
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+
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+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+6898
+10.21105/joss.06898
+
+exoTEDRF: An EXOplanet Transit and Eclipse Data Reduction
+Framework
+
+
+
+https://orcid.org/0000-0002-3328-1203
+
+Radica
+Michael
+
+
+
+
+
+Trottier Institute for Research on Exoplanets (iREx),
+Université de Montréal, Montréal, Canada
+
+
+
+
+5
+7
+2024
+
+9
+100
+6898
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+Python
+Astronomy
+JWST
+Exoplanets
+Teddy Bears
+
+
+
+
+
+ Summary
+
Since the start of science operations in July 2022, JWST has
+ delivered groundbreaking results on a regular basis. For spectroscopic
+ studies of exoplanet atmospheres the process of extracting robust and
+ reliable atmosphere spectra from the raw JWST observations is
+ critical. Especially as the field pushes to detect the signatures of
+ secondary atmospheres on rocky Earth-like planets it is imperative to
+ ensure that the spectral features that drive atmosphere inferences are
+ robust against the particular choices made during the data reduction
+ process.
+
Here, I present the community with exoTEDRF
+ (EXOplanet Transit and Eclipse Data Reduction Framework; formerly
+ known as supreme-SPOON), an end-to-end pipeline
+ for data reduction and light curve analysis of time series
+ observations (TSOs) of transiting exoplanets with JWST. The pipeline
+ is highly modular and designed to produce reliable spectra from raw
+ JWST exposures. exoTEDRF (pronounced
+ exo-tedorf) consists of four stages, each of which are further
+ subdivided into a series of steps. These steps can either be run
+ individually, for example in a Jupyter notebook, or via the command
+ line using the provided configuration files. The steps are highly
+ tunable, allowing full control over every parameter in the reduction.
+ Each step also produces diagnostic plots to allow the user to verify
+ their results at each intermediate stage, and compare outputs with
+ other pipelines if so desired. Finally,
+ exoTEDRF has also been designed to be run in
+ “batch” mode: simultaneously running multiple reductions, each
+ tweaking a subset of parameters, to understand any impacts on the
+ resulting atmosphere spectrum.
+
+
+ Overview of exoTEDRF Stages
+
Like similar pipelines (e.g. Eureka!,
+ Bell
+ et al., 2022; jwst,
+ Bushouse
+ et al., 2022), exoTEDRF is divided up
+ into four major stages which are summarized below:
+
+
+
Stage 1, Detector-level processing: Converts raw, 4D
+ (integrations, groups,
+
+ x-pixel,
+
+
+ y-pixel)
+ data frames to 3D (integrations,
+
+ x-pixel,
+
+
+ y-pixel)
+ slope images. Steps include superbias subtractions, correction of
+ 1/
+
+ f
+ noise, ramp fitting, etc.
+
+
+
Stage 2, Spectroscopic processing: Performs additional
+ calibrations to prepare slope images for spectral extraction.
+ Steps include, flat field correction, background subtraction,
+ etc.
+
+
+
Stage 3, Spectral extraction: Extract the 2D stellar spectra
+ from the 3D slope images.
+
+
+
Stage 4, Light curve fitting: An optional stage for the fitting
+ of extracted light curves.
+
+
+
In exoTEDRF, Stage 4 is an optional
+ installation which is currently built around the
+ exoUPRF library
+ (Radica,
+ 2024), and incorporates tools such as
+ ExoTiC-LD
+ (Grant
+ & Wakeford, 2022) for the estimation of stellar
+ limb-darkening parameters. In certain places (e.g., superbias
+ subtraction, flat field correction), exoTEDRF
+ simply provides a wrapper around the existing functionalities of the
+ jwst package maintained by the Space Telescope
+ Science Institute.
+
+
+ Statement of Need
+
Data analysis is a challenging process that is encountered by all
+ observational studies. Ensuring that the resulting atmosphere spectra
+ are robust against particular choices made in the reduction process is
+ critical, especially as we push to characterize the atmospheres of
+ small rocky planets. The modularity and tunability of
+ exoTEDRF make it easy to run multiple
+ reductions of a given dataset, and therefore robustly ascertain
+ whether the spectral features driving atmosphere inferences are
+ robust, or sensitive to the peculiarities of a given reduction.
+ Moreover, exoTEDRF has full support for TSOs
+ with NIRISS/SOSS
+ (Albert
+ et al., 2023), an observing mode which is underserved by the
+ current ecosystem of JWST reduction tools, including being the only
+ pipeline with the ability to run the ATOCA
+ extraction algorithm
+ (Darveau-Bernier
+ et al., 2022;
+ Radica
+ et al., 2022) to explicitly model the SOSS order overlap.
+
+
+ Documentation
+
Documentation for exoTEDRF, including
+ example notebooks, is available at
+ https://exotedrf.readthedocs.io/en/latest/.
+
+
+ Uses of exoTEDRF in Current Literature
+
exoTEDRF (particularly in its previous life
+ as supreme-SPOON) has been widely applied to
+ exoplanet TSOs. A list of current literature which has made use of
+ exoTEDRF includes: Feinstein et al.
+ (2023),
+ Coulombe et al.
+ (2023),
+ Radica et al.
+ (2023),
+ Albert et al.
+ (2023),
+ Lim et al.
+ (2023),
+ Radica et al.
+ (2024),
+ Fournier-Tondreau et al.
+ (2024),
+ Benneke et al.
+ (2024),
+ and Cadieux et al.
+ (2024).
+
+
+ Future Developments
+
The current release of exoTEDRF (v2.0.0)
+ currently supports the reduction of TSOs observed with JWST
+ NIRISS/SOSS as well as NIRSpec/BOTS. Support for observations MIRI/LRS
+ is in development and will be added in the coming months.
+ exoTEDRF has also been applied to exoplanet
+ observations from the Hubble Space Telescope using the UVIS mode
+ (Radica et al., 2024b, in prep). This functionality will also be made
+ available to the public.
+
Suggestions for additional features are always welcome!
+
+
+ Similar Tools
+
The following is a list of other open source pipelines tailored to
+ exoplanet observations with JWST, some of which general purpose, and
+ others which are more tailored to specific instruments:
+
+
+
General purpose: Eureka!
+ (Bell
+ et al., 2022), jwst
+ (Bushouse
+ et al., 2022), transitspectroscopy
+ (Nestor
+ Espinoza, 2022)
NIRSpec specific: ExoTiC-JEDI
+ (Alderson
+ et al., 2022)
+
+
+
Packages like exoplanet
+ (Foreman-Mackey
+ et al., 2021), Eureka!
+ (Bell
+ et al., 2022), and juliet
+ (Néstor
+ Espinoza et al., 2019) also enable similar light curve
+ fitting.
+
+
+ Acknowledgements
+
The foundations of exoTEDRF are built upon
+ many wonderful Python libraries, including
+ numpy
+ (Harris
+ et al., 2020), scipy
+ (Virtanen
+ et al., 2020), astropy
+ (Astropy
+ Collaboration et al., 2013,
+ 2018),
+ and matplotlib
+ (Hunter,
+ 2007).
+
MR acknowledges funding from the Natural Sciences and Engineering
+ Research Council of Canada, the Fonds de Recherche du Québec – Nature
+ et Technologies, and the Trottier Institute for Research on
+ Exoplanets. He would also like to thank the JWST Transiting Exoplanet
+ Community Early Release Science program for providing the forum where
+ much of the development of this pipeline occurred, and in particular,
+ Adina Feinstein, Louis-Philippe Coulombe, Néstor Espinoza, and Lili
+ Alderson for many helpful conversations.
+
+
+
+
+
+
+
+
+ BushouseHoward
+ EisenhamerJonathan
+ DenchevaNadia
+ DaviesJames
+ GreenfieldPerry
+ MorrisonJane
+ HodgePhil
+ SimonBernie
+ GrummDavid
+ DroettboomMichael
+ SlavichEdward
+ SoseyMegan
+ PaulyTyler
+ MillerTodd
+ JedrzejewskiRobert
+ HackWarren
+ DavisDavid
+ CrawfordSteven
+ LawDavid
+ GordonKarl
+ ReganMichael
+ CaraMihai
+ MacDonaldKen
+ BradleyLarry
+ ShanahanClare
+ JamiesonWilliam
+
+ JWST calibration pipeline
+ Zenodo; Zenodo
+ 202208
+ https://doi.org/10.5281/zenodo.7038885
+ 10.5281/zenodo.7038885
+
+
+
+
+
+ GrantDavid
+ WakefordHannah R.
+
+ Exo-TiC/ExoTiC-LD: ExoTiC-LD v3.0.0
+ Zenodo; Zenodo
+ 202212
+ https://doi.org/10.5281/zenodo.7437681
+ 10.5281/zenodo.7437681
+
+
+
+
+
+ BellTaylor
+ AhrerEva-Maria
+ BrandeJonathan
+ CarterAarynn
+ FeinsteinAdina D.
+ CalocaGiannina
+ MansfieldMegan
+ ZiebaSebastian
+ PiauletCaroline
+ BennekeBjörn
+ FilippazzoJoseph
+ MayErin
+ RoyPierre-Alexis
+ KreidbergLaura
+ StevensonKevin
+
+ Eureka!: An End-to-End Pipeline for JWST Time-Series Observations
+
+ 202211
+ 7
+ 79
+ 10.21105/joss.04503
+ 4503
+
+
+
+
+
+
+ EspinozaNéstor
+ KossakowskiDiana
+ BrahmRafael
+
+ juliet: a versatile modelling tool for transiting and non-transiting exoplanetary systems
+
+ 201912
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+ 2
+ https://arxiv.org/abs/1812.08549
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+
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+ FeinsteinAdina D.
+ RadicaMichael
+ WelbanksLuis
+ MurrayCatriona Anne
+ OhnoKazumasa
+ CoulombeLouis-Philippe
+ EspinozaNéstor
+ BeanJacob L.
+ TeskeJohanna K.
+ BennekeBjörn
+ LineMichael R.
+ RustamkulovZafar
+ SabaArianna
+ TsiarasAngelos
+ BarstowJoanna K.
+ FortneyJonathan J.
+ GaoPeter
+ KnutsonHeather A.
+ MacDonaldRyan J.
+ Mikal-EvansThomas
+ RackhamBenjamin V.
+ TaylorJake
+ ParmentierVivien
+ BatalhaNatalie M.
+ Berta-ThompsonZachory K.
+ CarterAarynn L.
+ ChangeatQuentin
+ dos SantosLeonardo A.
+ GibsonNeale P.
+ GoyalJayesh M.
+ KreidbergLaura
+ López-MoralesMercedes
+ LothringerJoshua D.
+ MiguelYamila
+ MolaverdikhaniKaran
+ MoranSarah E.
+ MorelloGiuseppe
+ MukherjeeSagnick
+ SingDavid K.
+ StevensonKevin B.
+ WakefordHannah R.
+ AhrerEva-Maria
+ AlamMunazza K.
+ AldersonLili
+ AllenNatalie H.
+ BatalhaNatasha E.
+ BellTaylor J.
+ BlecicJasmina
+ BrandeJonathan
+ CaceresClaudio
+ CasewellS. L.
+ ChubbKaty L.
+ CrossfieldIan J. M.
+ CrouzetNicolas
+ CubillosPatricio E.
+ DecinLeen
+ DésertJean-Michel
+ HarringtonJoseph
+ HengKevin
+ HenningThomas
+ IroNicolas
+ KemptonEliza M. -R.
+ KendrewSarah
+ KirkJames
+ KrickJessica
+ LagagePierre-Olivier
+ LendlMonika
+ ManciniLuigi
+ MansfieldMegan
+ MayE. M.
+ MayneN. J.
+ NikolovNikolay K.
+ PalleEnric
+ Petit dit de la RocheDominique J. M.
+ PiauletCaroline
+ PowellDiana
+ RedfieldSeth
+ RogersLaura K.
+ RomanMichael T.
+ RoyPierre-Alexis
+ NixonMatthew C.
+ SchlawinEverett
+ TanXianyu
+ TremblinP.
+ TurnerJake D.
+ VenotOlivia
+ WaalkesWilliam C.
+ WheatleyPeter J.
+ ZhangXi
+
+ Early Release Science of the exoplanet WASP-39b with JWST NIRISS
+
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+ BennekeBjörn
+ ChallenerRyan
+ PietteAnjali A. A.
+ WiserLindsey S.
+ MansfieldMegan
+ MacDonaldRyan J.
+ BeltzHayley
+ FeinsteinAdina D.
+ RadicaMichael
+ SavelArjun B.
+ Dos SantosLeonardo A.
+ BeanJacob L.
+ ParmentierVivien
+ WongIan
+ RauscherEmily
+ KomacekThaddeus D.
+ KemptonEliza M. -R.
+ TanXianyu
+ HammondMark
+ LewisNeil T.
+ LineMichael R.
+ LeeElspeth K. H.
+ ShivkumarHinna
+ CrossfieldIan J. M.
+ NixonMatthew C.
+ RackhamBenjamin V.
+ WakefordHannah R.
+ WelbanksLuis
+ ZhangXi
+ BatalhaNatalie M.
+ Berta-ThompsonZachory K.
+ ChangeatQuentin
+ DésertJean-Michel
+ EspinozaNéstor
+ GoyalJayesh M.
+ HarringtonJoseph
+ KnutsonHeather A.
+ KreidbergLaura
+ López-MoralesMercedes
+ ShporerAvi
+ SingDavid K.
+ StevensonKevin B.
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+ AhrerEva-Maria
+ AlamMunazza K.
+ BellTaylor J.
+ BlecicJasmina
+ CaceresClaudio
+ CarterAarynn L.
+ CasewellSarah L.
+ CrouzetNicolas
+ CubillosPatricio E.
+ DecinLeen
+ FortneyJonathan J.
+ GibsonNeale P.
+ HengKevin
+ HenningThomas
+ IroNicolas
+ KendrewSarah
+ LagagePierre-Olivier
+ LeconteJérémy
+ LendlMonika
+ LothringerJoshua D.
+ ManciniLuigi
+ Mikal-EvansThomas
+ MolaverdikhaniKaran
+ NikolovNikolay K.
+ OhnoKazumasa
+ PalleEnric
+ PiauletCaroline
+ RedfieldSeth
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+ TsaiShang-Min
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+ ArtigauÉtienne
+ CoulombeLouis-Philippe
+ RadicaMichael
+ L’HeureuxAlexandrine
+ AlbertLoı̈c
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+ de WitJulien
+ SalhiSalma
+ RoyPierre-Alexis
+ FlaggLaura
+ Fournier-TondreauMarylou
+ TaylorJake
+ CookNeil J.
+ LafrenièreDavid
+ CowanNicolas B.
+ KalteneggerLisa
+ RoweJason F.
+ EspinozaNéstor
+ DangLisa
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+ JohnstoneDoug
+ LineMichael R.
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+ MukherjeeSagnick
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