[{"citation":{"ista":"Kusakabe H, Verhamme A, Blaizot J, Garel T, Wisotzki L, Leclercq F, Bacon R, Schaye J, Gallego SG, Kerutt J, Matthee JJ, Maseda M, Nanayakkara T, Pelló R, Richard J, Tresse L, Urrutia T, Vitte E. 2022. The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. Astronomy &#38; Astrophysics. 660, A44.","chicago":"Kusakabe, Haruka, Anne Verhamme, Jérémy Blaizot, Thibault Garel, Lutz Wisotzki, Floriane Leclercq, Roland Bacon, et al. “The MUSE EXtremely Deep Field: Individual Detections of Ly<i>α</i> Haloes around Rest-Frame UV-Selected Galaxies at <i>z</i> ≃ 2.9–4.4.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202142302\">https://doi.org/10.1051/0004-6361/202142302</a>.","mla":"Kusakabe, Haruka, et al. “The MUSE EXtremely Deep Field: Individual Detections of Ly<i>α</i> Haloes around Rest-Frame UV-Selected Galaxies at <i>z</i> ≃ 2.9–4.4.” <i>Astronomy &#38; Astrophysics</i>, vol. 660, A44, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202142302\">10.1051/0004-6361/202142302</a>.","apa":"Kusakabe, H., Verhamme, A., Blaizot, J., Garel, T., Wisotzki, L., Leclercq, F., … Vitte, E. (2022). The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202142302\">https://doi.org/10.1051/0004-6361/202142302</a>","ama":"Kusakabe H, Verhamme A, Blaizot J, et al. The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. <i>Astronomy &#38; Astrophysics</i>. 2022;660. doi:<a href=\"https://doi.org/10.1051/0004-6361/202142302\">10.1051/0004-6361/202142302</a>","short":"H. Kusakabe, A. Verhamme, J. Blaizot, T. Garel, L. Wisotzki, F. Leclercq, R. Bacon, J. Schaye, S.G. Gallego, J. Kerutt, J.J. Matthee, M. Maseda, T. Nanayakkara, R. Pelló, J. Richard, L. Tresse, T. Urrutia, E. Vitte, Astronomy &#38; Astrophysics 660 (2022).","ieee":"H. Kusakabe <i>et al.</i>, “The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4,” <i>Astronomy &#38; Astrophysics</i>, vol. 660. EDP Sciences, 2022."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"article_number":"A44","arxiv":1,"month":"04","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication_status":"published","intvolume":"       660","abstract":[{"lang":"eng","text":"Hydrogen Lyα haloes (LAHs) are commonly used as a tracer of the circumgalactic medium (CGM) at high redshifts. In this work, we aim to explore the existence of Lyα haloes around individual UV-selected galaxies, rather than around Lyα emitters (LAEs), at high redshifts. Our sample was continuum-selected with F775W ≤ 27.5, and spectroscopic redshifts were assigned or constrained for all the sources thanks to the deepest (100- to 140-h) existing Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) data with adaptive optics. The final sample includes 21 galaxies that are purely F775W-magnitude selected within the redshift range z ≈ 2.9 − 4.4 and within a UV magnitude range −20 ≤ M1500 ≤ −18, thus avoiding any bias toward LAEs. We tested whether galaxy’s Lyα emission is significantly more extended than the MUSE PSF-convolved continuum component. We find 17 LAHs and four non-LAHs. We report the first individual detections of extended Lyα emission around non-LAEs. The Lyα halo fraction is thus as high as 81.0−11.2+10.3%, which is close to that for LAEs at z = 3 − 6 in the literature. This implies that UV-selected galaxies generally have a large amount of hydrogen in their CGM. We derived the mean surface brightness (SB) profile for our LAHs with cosmic dimming corrections and find that Lyα emission extends to 5.4 arcsec (≃40 physical kpc at the midpoint redshift z = 3.6) above the typical 1σ SB limit. The incidence rate of surrounding gas detected in Lyα per one-dimensional line of sight per unit redshift, dn/dz, is estimated to be 0.76−0.09+0.09 for galaxies with M1500 ≤ −18 mag at z ≃ 3.7. Assuming that Lyα emission and absorption arise in the same gas, this suggests, based on abundance matching, that LAHs trace the same gas as damped Lyα systems (DLAs) and sub-DLAs."}],"volume":660,"date_created":"2022-07-05T14:27:26Z","article_type":"original","scopus_import":"1","day":"07","author":[{"first_name":"Haruka","full_name":"Kusakabe, Haruka","last_name":"Kusakabe"},{"first_name":"Anne","full_name":"Verhamme, Anne","last_name":"Verhamme"},{"full_name":"Blaizot, Jérémy","last_name":"Blaizot","first_name":"Jérémy"},{"last_name":"Garel","full_name":"Garel, Thibault","first_name":"Thibault"},{"first_name":"Lutz","last_name":"Wisotzki","full_name":"Wisotzki, Lutz"},{"first_name":"Floriane","full_name":"Leclercq, Floriane","last_name":"Leclercq"},{"last_name":"Bacon","full_name":"Bacon, Roland","first_name":"Roland"},{"last_name":"Schaye","full_name":"Schaye, Joop","first_name":"Joop"},{"last_name":"Gallego","full_name":"Gallego, Sofia G.","first_name":"Sofia G."},{"full_name":"Kerutt, Josephine","last_name":"Kerutt","first_name":"Josephine"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X"},{"first_name":"Michael","full_name":"Maseda, Michael","last_name":"Maseda"},{"last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya","first_name":"Themiya"},{"last_name":"Pelló","full_name":"Pelló, Roser","first_name":"Roser"},{"last_name":"Richard","full_name":"Richard, Johan","first_name":"Johan"},{"full_name":"Tresse, Laurence","last_name":"Tresse","first_name":"Laurence"},{"last_name":"Urrutia","full_name":"Urrutia, Tanya","first_name":"Tanya"},{"full_name":"Vitte, Eloïse","last_name":"Vitte","first_name":"Eloïse"}],"title":"The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4","oa_version":"Published Version","date_published":"2022-04-07T00:00:00Z","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions. We would like to express our gratitude to Edmund Christian Herenz, Leindert Boogard, Miroslava Dessauges, Moupiya Maji, Valentin Mauerhofer, Charlotte Paola Simmonds Wagemann, Masami Ouchi, Kazuhiro Shimasaku, Akio Inoue, and Rieko Momose for giving insightful comments and suggestions. H.K. is grateful to Liam McCarney for useful suggestions on English writing through the UniGE’s Tandems linguistiques. H.K. acknowledges support from Swiss Government Excellence Scholarships and Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship. H.K., F.L., and A.V. are supported by the SNF grant PP00P2 176808. A.V. and T.G. are supported by the ERC Starting Grant 757258“TRIPLE”. This work was supported by the Programme National Cosmology et Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, co-funded by CEA and CNES. This work is based on observations taken by VLT, which is operated by European Southern Observatory. This research made use of Astropy, which is a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018), and other software and packages: MARZ, MPDAF (Piqueras et al. 2019), PHOTUTILS, Numpy (Harris et al. 2020), Scipy (Virtanen et al. 2020), and matplotlib (Hunter 2007).","status":"public","publication":"Astronomy & Astrophysics","extern":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations"],"year":"2022","external_id":{"arxiv":["2201.07257"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2201.07257"}],"quality_controlled":"1","_id":"11488","date_updated":"2022-07-19T09:33:24Z","type":"journal_article","article_processing_charge":"No","doi":"10.1051/0004-6361/202142302","publisher":"EDP Sciences"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        23","abstract":[{"text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["1422-0067"]},"file_date_updated":"2022-07-06T07:36:59Z","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","oa_version":"Published Version","author":[{"first_name":"V","full_name":"Bilanovičová, V","last_name":"Bilanovičová"},{"full_name":"Rýdza, N","last_name":"Rýdza","first_name":"N"},{"first_name":"L","last_name":"Koczka","full_name":"Koczka, L"},{"first_name":"M","last_name":"Hess","full_name":"Hess, M"},{"first_name":"E","full_name":"Feraru, E","last_name":"Feraru"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"T","last_name":"Nodzyński","full_name":"Nodzyński, T"}],"day":"06","article_type":"original","date_created":"2022-07-05T15:14:34Z","volume":23,"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"11","citation":{"mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>"},"month":"06","file":[{"relation":"main_file","checksum":"e997a57a928ec9d51fad8ce824a05935","file_name":"2022_IntJMolSci_Bilanovicova.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"11492","file_size":2324542,"date_created":"2022-07-06T07:36:59Z","date_updated":"2022-07-06T07:36:59Z","creator":"cchlebak"}],"department":[{"_id":"JiFr"}],"ddc":["570"],"page":"6352","quality_controlled":"1","publisher":"MDPI","doi":"10.3390/ijms23116352","article_processing_charge":"Yes","type":"journal_article","date_updated":"2023-08-09T10:13:57Z","_id":"11489","project":[{"call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"publication":"International Journal of Molecular Sciences","status":"public","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","date_published":"2022-06-06T00:00:00Z","pmid":1,"external_id":{"isi":["000808733300001"],"pmid":["35683031"]},"year":"2022","isi":1},{"year":"2022","external_id":{"arxiv":["2111.14855"]},"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / techniques: spectroscopic / galaxies: stellar content / galaxies: formation"],"status":"public","publication":"Astronomy & Astrophysics","extern":"1","date_published":"2022-03-30T00:00:00Z","acknowledgement":"We thank the referee for thoughtful and constructive comments that have improved the quality of this manuscript. Based on observations collected at the European Southern Observatory under ESO programme 1101.A-0127. This work made use of v2.2.1 of the Binary Population and Spectral Synthesis (BPASS) models as described in Eldridge et al. (2017) and Stanway & Eldridge (2018). A.F. acknowledges the support from grant PRIN MIUR2017-20173ML3WW_001. T.N. acknowledges support from Australian Research Council Laureate Fellowship FL180100060.","article_processing_charge":"No","doi":"10.1051/0004-6361/202142187","publisher":"EDP Sciences","_id":"11490","date_updated":"2022-07-19T09:33:46Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.14855"}],"quality_controlled":"1","arxiv":1,"month":"03","article_number":"A10","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Matthee JJ, Feltre A, Maseda M, et al. Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field. <i>Astronomy &#38; Astrophysics</i>. 2022;660. doi:<a href=\"https://doi.org/10.1051/0004-6361/202142187\">10.1051/0004-6361/202142187</a>","short":"J.J. Matthee, A. Feltre, M. Maseda, T. Nanayakkara, L. Boogaard, R. Bacon, A. Verhamme, F. Leclercq, H. Kusakabe, T. Urrutia, L. Wisotzki, Astronomy &#38; Astrophysics 660 (2022).","ieee":"J. J. Matthee <i>et al.</i>, “Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field,” <i>Astronomy &#38; Astrophysics</i>, vol. 660. EDP Sciences, 2022.","ista":"Matthee JJ, Feltre A, Maseda M, Nanayakkara T, Boogaard L, Bacon R, Verhamme A, Leclercq F, Kusakabe H, Urrutia T, Wisotzki L. 2022. Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field. Astronomy &#38; Astrophysics. 660, A10.","chicago":"Matthee, Jorryt J, Anna Feltre, Michael Maseda, Themiya Nanayakkara, Leindert Boogaard, Roland Bacon, Anne Verhamme, et al. “Deciphering Stellar Metallicities in the Early Universe: Case Study of a Young Galaxy at z = 4.77 in the MUSE EXtremely Deep Field.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202142187\">https://doi.org/10.1051/0004-6361/202142187</a>.","mla":"Matthee, Jorryt J., et al. “Deciphering Stellar Metallicities in the Early Universe: Case Study of a Young Galaxy at z = 4.77 in the MUSE EXtremely Deep Field.” <i>Astronomy &#38; Astrophysics</i>, vol. 660, A10, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202142187\">10.1051/0004-6361/202142187</a>.","apa":"Matthee, J. J., Feltre, A., Maseda, M., Nanayakkara, T., Boogaard, L., Bacon, R., … Wisotzki, L. (2022). Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202142187\">https://doi.org/10.1051/0004-6361/202142187</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","scopus_import":"1","author":[{"first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee"},{"full_name":"Feltre, Anna","last_name":"Feltre","first_name":"Anna"},{"last_name":"Maseda","full_name":"Maseda, Michael","first_name":"Michael"},{"first_name":"Themiya","last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya"},{"last_name":"Boogaard","full_name":"Boogaard, Leindert","first_name":"Leindert"},{"full_name":"Bacon, Roland","last_name":"Bacon","first_name":"Roland"},{"full_name":"Verhamme, Anne","last_name":"Verhamme","first_name":"Anne"},{"full_name":"Leclercq, Floriane","last_name":"Leclercq","first_name":"Floriane"},{"last_name":"Kusakabe","full_name":"Kusakabe, Haruka","first_name":"Haruka"},{"first_name":"Tanya","full_name":"Urrutia, Tanya","last_name":"Urrutia"},{"first_name":"Lutz","last_name":"Wisotzki","full_name":"Wisotzki, Lutz"}],"title":"Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field","oa_version":"Published Version","volume":660,"date_created":"2022-07-05T15:25:35Z","article_type":"original","intvolume":"       660","abstract":[{"lang":"eng","text":"Directly characterising the first generations of stars in distant galaxies is a key quest of observational cosmology. We present a case study of ID53 at z = 4.77, the UV-brightest (but L⋆) star-forming galaxy at z > 3 in the MUSE eXtremely Deep Field with a mass of ≈109 M⊙. In addition to very strong Lyman-α (Lyα) emission, we clearly detect the (stellar) continuum and an N V P Cygni feature, interstellar absorption, fine-structure emission and nebular C IV emission lines in the 140 h spectrum. Continuum emission from two spatially resolved components in Hubble Space Telescope data are blended in the MUSE data, but we show that the nebular C IV emission originates from a subcomponent of the galaxy. The UV spectrum can be fit with recent BPASS stellar population models combined with single-burst or continuous star formation histories (SFHs), a standard initial mass function, and an attenuation law. Models with a young age and low metallicity (log10(age/yr) = 6.5–7.6 and [Z/H] = −2.15 to −1.15) are preferred, but the details depend on the assumed SFH. The intrinsic Hα luminosity of the best-fit models is an order of magnitude higher than the Hα luminosity inferred from Spitzer/IRAC data, which either suggests a high escape fraction of ionising photons, a high relative attenuation of nebular to stellar dust, or a complex SFH. The metallicity appears lower than the metallicity in more massive galaxies at z = 3 − 5, consistent with the scenario according to which younger galaxies have lower metallicities. This chemical immaturity likely facilitates Lyα escape, explaining why the Lyα equivalent width is anti-correlated with stellar metallicity. Finally, we stress that uncertainties in SFHs impose a challenge for future inferences of the stellar metallicity of young galaxies. This highlights the need for joint (spatially resolved) analyses of stellar spectra and photo-ionisation models."}],"publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]}},{"external_id":{"arxiv":["2202.06642"]},"year":"2022","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations"],"status":"public","extern":"1","publication":"Astronomy & Astrophysics","acknowledgement":"We thank the referee for thoughtful and constructive comments that have improved the quality of this manuscript. Based on observations collected at the European Southern Observatory under ESO programme 1101.A-0127. This work made use of v2.2.1 of the Binary Population and Spectral Synthesis (BPASS) models as described in Eldridge et al. (2017) and Stanway & Eldridge (2018). A.F. acknowledges the support from grant PRIN MIUR2017-20173ML3WW_001. T.N. acknowledges support from Australian Research Council Laureate Fellowship FL180100060.","date_published":"2022-03-25T00:00:00Z","publisher":"EDP Sciences","doi":"10.1051/0004-6361/202141900","article_processing_charge":"No","type":"journal_article","date_updated":"2022-07-19T09:47:16Z","_id":"11497","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2202.06642"}],"month":"03","arxiv":1,"article_number":"183","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Kerutt J, Wisotzki L, Verhamme A, et al. Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep. <i>Astronomy &#38; Astrophysics</i>. 2022;659. doi:<a href=\"https://doi.org/10.1051/0004-6361/202141900\">10.1051/0004-6361/202141900</a>","short":"J. Kerutt, L. Wisotzki, A. Verhamme, K.B. Schmidt, F. Leclercq, E.C. Herenz, T. Urrutia, T. Garel, T. Hashimoto, M. Maseda, J.J. Matthee, H. Kusakabe, J. Schaye, J. Richard, B. Guiderdoni, V. Mauerhofer, T. Nanayakkara, E. Vitte, Astronomy &#38; Astrophysics 659 (2022).","ieee":"J. Kerutt <i>et al.</i>, “Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep,” <i>Astronomy &#38; Astrophysics</i>, vol. 659. EDP Sciences, 2022.","ista":"Kerutt J, Wisotzki L, Verhamme A, Schmidt KB, Leclercq F, Herenz EC, Urrutia T, Garel T, Hashimoto T, Maseda M, Matthee JJ, Kusakabe H, Schaye J, Richard J, Guiderdoni B, Mauerhofer V, Nanayakkara T, Vitte E. 2022. Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep. Astronomy &#38; Astrophysics. 659, 183.","chicago":"Kerutt, J., L. Wisotzki, A. Verhamme, K. B. Schmidt, F. Leclercq, E. C. Herenz, T. Urrutia, et al. “Equivalent Widths of Lyman α Emitters in MUSE-Wide and MUSE-Deep.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202141900\">https://doi.org/10.1051/0004-6361/202141900</a>.","mla":"Kerutt, J., et al. “Equivalent Widths of Lyman α Emitters in MUSE-Wide and MUSE-Deep.” <i>Astronomy &#38; Astrophysics</i>, vol. 659, 183, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202141900\">10.1051/0004-6361/202141900</a>.","apa":"Kerutt, J., Wisotzki, L., Verhamme, A., Schmidt, K. B., Leclercq, F., Herenz, E. C., … Vitte, E. (2022). Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202141900\">https://doi.org/10.1051/0004-6361/202141900</a>"},"oa_version":"Published Version","title":"Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep","author":[{"first_name":"J.","full_name":"Kerutt, J.","last_name":"Kerutt"},{"first_name":"L.","last_name":"Wisotzki","full_name":"Wisotzki, L."},{"first_name":"A.","last_name":"Verhamme","full_name":"Verhamme, A."},{"full_name":"Schmidt, K. B.","last_name":"Schmidt","first_name":"K. B."},{"first_name":"F.","last_name":"Leclercq","full_name":"Leclercq, F."},{"last_name":"Herenz","full_name":"Herenz, E. C.","first_name":"E. C."},{"last_name":"Urrutia","full_name":"Urrutia, T.","first_name":"T."},{"first_name":"T.","last_name":"Garel","full_name":"Garel, T."},{"first_name":"T.","last_name":"Hashimoto","full_name":"Hashimoto, T."},{"full_name":"Maseda, M.","last_name":"Maseda","first_name":"M."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"first_name":"H.","full_name":"Kusakabe, H.","last_name":"Kusakabe"},{"first_name":"J.","last_name":"Schaye","full_name":"Schaye, J."},{"first_name":"J.","last_name":"Richard","full_name":"Richard, J."},{"last_name":"Guiderdoni","full_name":"Guiderdoni, B.","first_name":"B."},{"first_name":"V.","full_name":"Mauerhofer, V.","last_name":"Mauerhofer"},{"full_name":"Nanayakkara, T.","last_name":"Nanayakkara","first_name":"T."},{"first_name":"E.","last_name":"Vitte","full_name":"Vitte, E."}],"day":"25","scopus_import":"1","article_type":"original","date_created":"2022-07-06T08:17:27Z","volume":659,"intvolume":"       659","abstract":[{"text":"Context. The hydrogen Lyman α line is often the only measurable feature in optical spectra of high-redshift galaxies. Its shape and strength are influenced by radiative transfer processes and the properties of the underlying stellar population. High equivalent widths of several hundred Å are especially hard to explain by models and could point towards unusual stellar populations, for example with low metallicities, young stellar ages, and a top-heavy initial mass function. Other aspects influencing equivalent widths are the morphology of the galaxy and its gas properties.\r\nAims. The aim of this study is to better understand the connection between the Lyman α rest-frame equivalent width (EW0) and spectral properties as well as ultraviolet (UV) continuum morphology by obtaining reliable EW0 histograms for a statistical sample of galaxies and by assessing the fraction of objects with large equivalent widths.\r\nMethods. We used integral field spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE) combined with broad-band data from the Hubble Space Telescope (HST) to measure EW0. We analysed the emission lines of 1920 Lyman α emitters (LAEs) detected in the full MUSE-Wide (one hour exposure time) and MUSE-Deep (ten hour exposure time) surveys and found UV continuum counterparts in archival HST data. We fitted the UV continuum photometric images using the Galfit software to gain morphological information on the rest-UV emission and fitted the spectra obtained from MUSE to determine the double peak fraction, asymmetry, full-width at half maximum, and flux of the Lyman α line.\r\nResults. The two surveys show different histograms of Lyman α EW0. In MUSE-Wide, 20% of objects have EW0 > 240 Å, while this fraction is only 11% in MUSE-Deep and ≈16% for the full sample. This includes objects without HST continuum counterparts (one-third of our sample), for which we give lower limits for EW0. The object with the highest securely measured EW0 has EW0 = 589 ± 193 Å (the highest lower limit being EW0 = 4464 Å). We investigate the connection between EW0 and Lyman α spectral or UV continuum morphological properties.\r\nConclusions. The survey depth has to be taken into account when studying EW0 distributions. We find that in general, high EW0 objects can have a wide range of spectral and UV morphological properties, which might reflect that the underlying causes for high EW0 values are equally varied.","lang":"eng"}],"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"year":"2022","external_id":{"arxiv":["2108.03850"]},"acknowledgement":"We thank the referee for the valuable comments. We are also grateful to Koh Takahashi, Nozomu Tominaga, Chiaki Kobayashi, Yutaka Hirai, and Daichi Kashino for having useful discussions. This paper includes data gathered with the 10 m Keck Telescope located at W. M. Keck Observatory, Hawaii. We thank the staff of Keck Observatory for their help with the observations. The Hyper Suprime-Cam (HSC) collaboration includes the astronomical communities of Japan and Taiwan, and Princeton University. The HSC instrumentation and software were developed by the National Astronomical Observatory of Japan (NAOJ), the Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), the University of Tokyo, the High Energy Accelerator Research Organization (KEK), the Academia Sinica Institute for Astronomy and Astrophysics in Taiwan (ASIAA), and Princeton University. Based on data collected at the Subaru Telescope and retrieved from the HSC data archive system, which is operated by the Subaru Telescope and Astronomy Data Center at NAOJ. This work was supported by the joint research program of the Institute for Cosmic Ray Research (ICRR), University of Tokyo. The Cosmic Dawn Center is funded by the Danish National Research Foundation under grant No. 140. S.F. acknowledges support from the European Research Council (ERC) Consolidator Grant funding scheme (project ConTExt, grant No. 648179). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 847523 “INTERACTIONS.” This work is supported by World Premier International Research Center Initiative (WPI Initiative), MEXT, Japan, as well as the KAKENHI Grant-in-Aid for Scientific Research (A; 15H02064, 17H01110, 17H01114, 20H00180, and 21H04467) through the Japan Society for the Promotion of Science (JSPS). This work has been supported in part by JSPS KAKENHI grant Nos. JP17K05382, JP20K04024, and JP21H04499 (K.N.). Yuki Isobe, Kimihiko Nakajima, Yuichi Harikane, Takashi Kojima, and Masato Onodera are supported by JSPS KAKENHI grant Nos. 21J20785, 20K22373,19J01222, 18J12840, and 17K14257, respectively.","date_published":"2022-01-31T00:00:00Z","publication":"The Astrophysical Journal","status":"public","extern":"1","_id":"11509","date_updated":"2022-07-21T05:51:25Z","type":"journal_article","article_processing_charge":"No","doi":"10.3847/1538-4357/ac3509","publisher":"IOP Publishing","main_file_link":[{"url":"https://arxiv.org/abs/2108.03850","open_access":"1"}],"quality_controlled":"1","article_number":"111","month":"01","arxiv":1,"citation":{"chicago":"Isobe, Yuki, Masami Ouchi, Akihiro Suzuki, Takashi J. Moriya, Kimihiko Nakajima, Ken’ichi Nomoto, Michael Rauch, et al. “EMPRESS. IV. Extremely Metal-Poor Galaxies Including Very Low-Mass Primordial Systems with M∗= 10<sup>4</sup>-10<sup>5</sup>⊙ and 2%–3% (O/H): High (Fe/O) Suggestive of Metal Enrichment by Hypernovae/Pair-Instability Supernovae.” <i>The Astrophysical Journal</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.3847/1538-4357/ac3509\">https://doi.org/10.3847/1538-4357/ac3509</a>.","ista":"Isobe Y, Ouchi M, Suzuki A, Moriya TJ, Nakajima K, Nomoto K, Rauch M, Harikane Y, Kojima T, Ono Y, Fujimoto S, Inoue AK, Kim JH, Komiyama Y, Kusakabe H, Lee C-H, Maseda M, Matthee JJ, Michel-Dansac L, Nagao T, Nanayakkara T, Nishigaki M, Onodera M, Sugahara Y, Xu Y. 2022. EMPRESS. IV. Extremely metal-poor galaxies including very low-mass primordial systems with M∗= 10<sup>4</sup>-10<sup>5</sup>⊙ and 2%–3% (O/H): High (Fe/O) suggestive of metal enrichment by hypernovae/pair-instability supernovae. The Astrophysical Journal. 925(2), 111.","apa":"Isobe, Y., Ouchi, M., Suzuki, A., Moriya, T. J., Nakajima, K., Nomoto, K., … Xu, Y. (2022). EMPRESS. IV. Extremely metal-poor galaxies including very low-mass primordial systems with M∗= 10<sup>4</sup>-10<sup>5</sup>⊙ and 2%–3% (O/H): High (Fe/O) suggestive of metal enrichment by hypernovae/pair-instability supernovae. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ac3509\">https://doi.org/10.3847/1538-4357/ac3509</a>","mla":"Isobe, Yuki, et al. “EMPRESS. IV. Extremely Metal-Poor Galaxies Including Very Low-Mass Primordial Systems with M∗= 10<sup>4</sup>-10<sup>5</sup>⊙ and 2%–3% (O/H): High (Fe/O) Suggestive of Metal Enrichment by Hypernovae/Pair-Instability Supernovae.” <i>The Astrophysical Journal</i>, vol. 925, no. 2, 111, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.3847/1538-4357/ac3509\">10.3847/1538-4357/ac3509</a>.","ama":"Isobe Y, Ouchi M, Suzuki A, et al. EMPRESS. IV. Extremely metal-poor galaxies including very low-mass primordial systems with M∗= 10<sup>4</sup>-10<sup>5</sup>⊙ and 2%–3% (O/H): High (Fe/O) suggestive of metal enrichment by hypernovae/pair-instability supernovae. <i>The Astrophysical Journal</i>. 2022;925(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ac3509\">10.3847/1538-4357/ac3509</a>","ieee":"Y. Isobe <i>et al.</i>, “EMPRESS. IV. Extremely metal-poor galaxies including very low-mass primordial systems with M∗= 10<sup>4</sup>-10<sup>5</sup>⊙ and 2%–3% (O/H): High (Fe/O) suggestive of metal enrichment by hypernovae/pair-instability supernovae,” <i>The Astrophysical Journal</i>, vol. 925, no. 2. IOP Publishing, 2022.","short":"Y. Isobe, M. Ouchi, A. Suzuki, T.J. Moriya, K. Nakajima, K. Nomoto, M. Rauch, Y. Harikane, T. Kojima, Y. Ono, S. Fujimoto, A.K. Inoue, J.H. Kim, Y. Komiyama, H. Kusakabe, C.-H. Lee, M. Maseda, J.J. Matthee, L. Michel-Dansac, T. Nagao, T. Nanayakkara, M. Nishigaki, M. Onodera, Y. Sugahara, Y. Xu, The Astrophysical Journal 925 (2022)."},"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":925,"date_created":"2022-07-06T12:01:48Z","article_type":"original","day":"31","scopus_import":"1","author":[{"full_name":"Isobe, Yuki","last_name":"Isobe","first_name":"Yuki"},{"first_name":"Masami","full_name":"Ouchi, Masami","last_name":"Ouchi"},{"first_name":"Akihiro","full_name":"Suzuki, Akihiro","last_name":"Suzuki"},{"first_name":"Takashi J.","full_name":"Moriya, Takashi J.","last_name":"Moriya"},{"first_name":"Kimihiko","last_name":"Nakajima","full_name":"Nakajima, Kimihiko"},{"last_name":"Nomoto","full_name":"Nomoto, Ken’ichi","first_name":"Ken’ichi"},{"first_name":"Michael","full_name":"Rauch, Michael","last_name":"Rauch"},{"first_name":"Yuichi","last_name":"Harikane","full_name":"Harikane, Yuichi"},{"last_name":"Kojima","full_name":"Kojima, Takashi","first_name":"Takashi"},{"full_name":"Ono, Yoshiaki","last_name":"Ono","first_name":"Yoshiaki"},{"full_name":"Fujimoto, Seiji","last_name":"Fujimoto","first_name":"Seiji"},{"first_name":"Akio K.","full_name":"Inoue, Akio K.","last_name":"Inoue"},{"first_name":"Ji Hoon","last_name":"Kim","full_name":"Kim, Ji Hoon"},{"first_name":"Yutaka","last_name":"Komiyama","full_name":"Komiyama, Yutaka"},{"last_name":"Kusakabe","full_name":"Kusakabe, Haruka","first_name":"Haruka"},{"first_name":"Chien-Hsiu","last_name":"Lee","full_name":"Lee, Chien-Hsiu"},{"last_name":"Maseda","full_name":"Maseda, Michael","first_name":"Michael"},{"orcid":"0000-0003-2871-127X","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee"},{"full_name":"Michel-Dansac, Leo","last_name":"Michel-Dansac","first_name":"Leo"},{"full_name":"Nagao, Tohru","last_name":"Nagao","first_name":"Tohru"},{"first_name":"Themiya","last_name":"Nanayakkara","full_name":"Nanayakkara, Themiya"},{"first_name":"Moka","last_name":"Nishigaki","full_name":"Nishigaki, Moka"},{"first_name":"Masato","last_name":"Onodera","full_name":"Onodera, Masato"},{"full_name":"Sugahara, Yuma","last_name":"Sugahara","first_name":"Yuma"},{"full_name":"Xu, Yi","last_name":"Xu","first_name":"Yi"}],"title":"EMPRESS. IV. Extremely metal-poor galaxies including very low-mass primordial systems with M∗= 10⁴-10⁵⊙ and 2%–3% (O/H): High (Fe/O) suggestive of metal enrichment by hypernovae/pair-instability supernovae","oa_version":"Published Version","publication_status":"published","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"abstract":[{"lang":"eng","text":"We present Keck/LRIS follow-up spectroscopy for 13 photometric candidates of extremely metal-poor galaxies (EMPGs) selected by a machine-learning technique applied to the deep (∼26 AB mag) optical and wide-area (∼500 deg2) Subaru imaging data in the EMPRESS survey. Nine out of the 13 candidates are EMPGs with an oxygen abundance (O/H) less than ∼10% solar value (O/H)⊙, and four sources are contaminants of moderately metal-rich galaxies or no emission-line objects. Notably, two out of the nine EMPGs have extremely low stellar masses and oxygen abundances of 5 × 10⁴x–7 × -10⁵ M⊙ and 2%–3% (O/H)⊙, respectively. With a sample of five EMPGs with (Fe/O) measurements, two (three) of which are taken from this study (the literature), we confirm that two EMPGs with the lowest (O/H) ratios of ∼2% (O/H)⊙ show high (Fe/O) ratios of ∼0.1, close to the solar abundance ratio. Comparing galaxy chemical enrichment models, we find that the two EMPGs cannot be explained by a scenario of metal-poor gas accretion/episodic star formation history due to their low (N/O) ratios. We conclude that the two EMPGs can be reproduced by the inclusion of bright hypernovae and/or hypothetical pair-instability supernovae (SNe) preferentially produced in a metal-poor environment. This conclusion implies that primordial galaxies at z ∼ 10 could have a high abundance of Fe that did not originate from Type Ia SNe with delays and that Fe may not serve as a cosmic clock for primordial galaxies."}],"intvolume":"       925"},{"date_published":"2022-02-17T00:00:00Z","acknowledgement":"We thank the reviewer for several valuable comments that improved the clarity of the manuscript. P.F.W. acknowledges the support of the fellowship by the East Asian Core Observatories Association. This work is based on observations made with ESO VLT Telescopes at the La Silla Paranal Observatory under programmes ID 194-A.2005 and 1100.A-0949 (The LEGA-C Public Spectroscopy Survey). This project has received funding from the European Research Council (ERC) under the European Union—Horizon 2020 research and innovation program (grant agreement No. 683184).","extern":"1","status":"public","publication":"The Astrophysical Journal","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"year":"2022","external_id":{"arxiv":["2112.08372"]},"main_file_link":[{"url":"https://arxiv.org/abs/2112.08372","open_access":"1"}],"quality_controlled":"1","_id":"11510","date_updated":"2022-07-19T09:37:42Z","type":"journal_article","article_processing_charge":"No","doi":"10.3847/1538-4357/ac4419","publisher":"IOP Publishing","citation":{"ista":"Sobral D, van der Wel A, Bezanson R, Bell E, Muzzin A, D’Eugenio F, Darvish B, Gallazzi A, Wu P-F, Maseda M, Matthee JJ, Paulino-Afonso A, Straatman C, van Dokkum PG. 2022. The LEGA-C of nature and nurture in stellar populations at z ∼ 0.6–1.0: Dn4000 and Hδ reveal different assembly histories for quiescent galaxies in different environments. The Astrophysical Journal. 926(2), 117.","chicago":"Sobral, David, Arjen van der Wel, Rachel Bezanson, Eric Bell, Adam Muzzin, Francesco D’Eugenio, Behnam Darvish, et al. “The LEGA-C of Nature and Nurture in Stellar Populations at z ∼ 0.6–1.0: Dn4000 and Hδ Reveal Different Assembly Histories for Quiescent Galaxies in Different Environments.” <i>The Astrophysical Journal</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.3847/1538-4357/ac4419\">https://doi.org/10.3847/1538-4357/ac4419</a>.","apa":"Sobral, D., van der Wel, A., Bezanson, R., Bell, E., Muzzin, A., D’Eugenio, F., … van Dokkum, P. G. (2022). The LEGA-C of nature and nurture in stellar populations at z ∼ 0.6–1.0: Dn4000 and Hδ reveal different assembly histories for quiescent galaxies in different environments. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ac4419\">https://doi.org/10.3847/1538-4357/ac4419</a>","mla":"Sobral, David, et al. “The LEGA-C of Nature and Nurture in Stellar Populations at z ∼ 0.6–1.0: Dn4000 and Hδ Reveal Different Assembly Histories for Quiescent Galaxies in Different Environments.” <i>The Astrophysical Journal</i>, vol. 926, no. 2, 117, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.3847/1538-4357/ac4419\">10.3847/1538-4357/ac4419</a>.","ama":"Sobral D, van der Wel A, Bezanson R, et al. The LEGA-C of nature and nurture in stellar populations at z ∼ 0.6–1.0: Dn4000 and Hδ reveal different assembly histories for quiescent galaxies in different environments. <i>The Astrophysical Journal</i>. 2022;926(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ac4419\">10.3847/1538-4357/ac4419</a>","ieee":"D. Sobral <i>et al.</i>, “The LEGA-C of nature and nurture in stellar populations at z ∼ 0.6–1.0: Dn4000 and Hδ reveal different assembly histories for quiescent galaxies in different environments,” <i>The Astrophysical Journal</i>, vol. 926, no. 2. IOP Publishing, 2022.","short":"D. Sobral, A. van der Wel, R. Bezanson, E. Bell, A. Muzzin, F. D’Eugenio, B. Darvish, A. Gallazzi, P.-F. Wu, M. Maseda, J.J. Matthee, A. Paulino-Afonso, C. Straatman, P.G. van Dokkum, The Astrophysical Journal 926 (2022)."},"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"article_number":"117","arxiv":1,"month":"02","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"publication_status":"published","intvolume":"       926","abstract":[{"text":"Galaxy evolution is driven by a variety of physical processes that are predicted to proceed at different rates for different dark matter haloes and environments across cosmic times. A record of this evolution is preserved in galaxy stellar populations, which we can access using absorption-line spectroscopy. Here we explore the large LEGA-C survey (DR3) to investigate the role of the environment and stellar mass on stellar populations at z ∼ 0.6–1 in the COSMOS field. Leveraging the statistical power and depth of LEGA-C, we reveal significant gradients in Dn4000 and Hδ equivalent widths (EWs) distributions over the stellar mass versus environment 2D spaces for the massive galaxy population (M > 1010 M⊙) at z ∼ 0.6–1.0. Dn4000 and Hδ EWs primarily depend on stellar mass, but they also depend on environment at fixed stellar mass. By splitting the sample into centrals and satellites, and in terms of star-forming galaxies and quiescent galaxies, we reveal that the significant environmental trends of Dn4000 and Hδ EW, when controlling for stellar mass, are driven by quiescent galaxies. Regardless of being centrals or satellites, star-forming galaxies reveal Dn4000 and Hδ EWs, which depend strongly on their stellar mass and are completely independent of the environment at 0.6 < z < 1.0. The environmental trends seen for satellite galaxies are fully driven by the trends that hold only for quiescent galaxies, combined with the strong environmental dependency of the quiescent fraction at fixed stellar mass. Our results are consistent with recent predictions from simulations that point toward massive galaxies forming first in overdensities or the most compact dark matter haloes.","lang":"eng"}],"volume":926,"date_created":"2022-07-06T12:38:42Z","article_type":"original","day":"17","scopus_import":"1","author":[{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"first_name":"Arjen","full_name":"van der Wel, Arjen","last_name":"van der Wel"},{"first_name":"Rachel","full_name":"Bezanson, Rachel","last_name":"Bezanson"},{"last_name":"Bell","full_name":"Bell, Eric","first_name":"Eric"},{"first_name":"Adam","full_name":"Muzzin, Adam","last_name":"Muzzin"},{"full_name":"D’Eugenio, Francesco","last_name":"D’Eugenio","first_name":"Francesco"},{"first_name":"Behnam","full_name":"Darvish, Behnam","last_name":"Darvish"},{"last_name":"Gallazzi","full_name":"Gallazzi, Anna","first_name":"Anna"},{"full_name":"Wu, Po-Feng","last_name":"Wu","first_name":"Po-Feng"},{"first_name":"Michael","full_name":"Maseda, Michael","last_name":"Maseda"},{"orcid":"0000-0003-2871-127X","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee"},{"first_name":"Ana","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana"},{"last_name":"Straatman","full_name":"Straatman, Caroline","first_name":"Caroline"},{"full_name":"van Dokkum, Pieter G.","last_name":"van Dokkum","first_name":"Pieter G."}],"oa_version":"Published Version","title":"The LEGA-C of nature and nurture in stellar populations at z ∼ 0.6–1.0: Dn4000 and Hδ reveal different assembly histories for quiescent galaxies in different environments"},{"publisher":"IOP Publishing","doi":"10.3847/1538-4357/ac350b","article_processing_charge":"No","type":"journal_article","date_updated":"2022-07-19T09:38:03Z","_id":"11511","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04561"}],"external_id":{"arxiv":["2102.04561"]},"year":"2022","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","publication":"The Astrophysical Journal","extern":"1","date_published":"2022-01-13T00:00:00Z","acknowledgement":"We thank our anonymous referee for the constructive feedback. We extend our gratitude to Maarten Baes, Simon Lilly, Rafael Ottersberg, Gabriele Pezzulli, Alvio Renzini, and Andrea Weibel for insightful discussions. A.G. gratefully acknowledges financial support from the Fund for Scientific Research Flanders (FWO-Vlaanderen, project G.0G04.16N). This work used the DiRAC Data Centric system at Durham University, operated by the ICC on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, and STFC DiRAC Operations grant ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure.\r\n\r\nWe have benefited from the data analysis tool Topcat (Taylor 2013) and the programming language Python, including the numpy (van der Walt et al. 2011), matplotlib (Hunter 2007), and scipy (Virtanen et al. 2020) packages.","oa_version":"Published Version","title":"On the variation in stellar α-enhancements of star-forming galaxies in the EAGLE simulation","author":[{"last_name":"Gebek","full_name":"Gebek, Andrea","first_name":"Andrea"},{"orcid":"0000-0003-2871-127X","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee"}],"scopus_import":"1","day":"13","article_type":"original","date_created":"2022-07-06T12:48:32Z","volume":924,"abstract":[{"text":"The ratio of α-elements to iron in galaxies holds valuable information about the star formation history (SFH) since their enrichment occurs on different timescales. The fossil record of stars in galaxies has mostly been excavated for passive galaxies, since the light of star-forming galaxies is dominated by young stars, which have much weaker atmospheric absorption features. Here we use the largest reference cosmological simulation of the EAGLE project to investigate the origin of variations in stellar α-enhancement among star-forming galaxies at z = 0, and their impact on integrated spectra. The definition of α-enhancement in a composite stellar population is ambiguous. We elucidate two definitions—termed “mean” and “galactic” α-enhancement—in more detail. While a star-forming galaxy has a high “mean” α-enhancement when its stars formed rapidly, a galaxy with a large “galactic” α-enhancement generally had a delayed SFH. We find that absorption-line strengths of Mg and Fe correlate with variations in α-enhancement. These correlations are strongest for the “galactic” α-enhancement. However, we show that these are mostly caused by other effects that are cross-correlated with α-enhancement, such as variations in the light-weighted age. This severely complicates the retrieval of α-enhancements in star-forming galaxies. The ambiguity is not severe for passive galaxies, and we confirm that spectral variations in these galaxies are caused by measurable variations in α-enhancements. We suggest that this more complex coupling between α-enhancement and SFHs can guide the interpretation of new observations of star-forming galaxies.","lang":"eng"}],"intvolume":"       924","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"publication_status":"published","month":"01","arxiv":1,"article_number":"73","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","citation":{"chicago":"Gebek, Andrea, and Jorryt J Matthee. “On the Variation in Stellar α-Enhancements of Star-Forming Galaxies in the EAGLE Simulation.” <i>The Astrophysical Journal</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.3847/1538-4357/ac350b\">https://doi.org/10.3847/1538-4357/ac350b</a>.","ista":"Gebek A, Matthee JJ. 2022. On the variation in stellar α-enhancements of star-forming galaxies in the EAGLE simulation. The Astrophysical Journal. 924(2), 73.","apa":"Gebek, A., &#38; Matthee, J. J. (2022). On the variation in stellar α-enhancements of star-forming galaxies in the EAGLE simulation. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ac350b\">https://doi.org/10.3847/1538-4357/ac350b</a>","mla":"Gebek, Andrea, and Jorryt J. Matthee. “On the Variation in Stellar α-Enhancements of Star-Forming Galaxies in the EAGLE Simulation.” <i>The Astrophysical Journal</i>, vol. 924, no. 2, 73, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.3847/1538-4357/ac350b\">10.3847/1538-4357/ac350b</a>.","ama":"Gebek A, Matthee JJ. On the variation in stellar α-enhancements of star-forming galaxies in the EAGLE simulation. <i>The Astrophysical Journal</i>. 2022;924(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ac350b\">10.3847/1538-4357/ac350b</a>","ieee":"A. Gebek and J. J. Matthee, “On the variation in stellar α-enhancements of star-forming galaxies in the EAGLE simulation,” <i>The Astrophysical Journal</i>, vol. 924, no. 2. IOP Publishing, 2022.","short":"A. Gebek, J.J. Matthee, The Astrophysical Journal 924 (2022)."}},{"volume":512,"date_created":"2022-07-07T09:21:30Z","article_type":"original","scopus_import":"1","day":"01","author":[{"last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"last_name":"Pezzulli","full_name":"Pezzulli, Gabriele","first_name":"Gabriele"},{"first_name":"Max","full_name":"Gronke, Max","last_name":"Gronke"},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"full_name":"Hayes, Matthew","last_name":"Hayes","first_name":"Matthew"},{"first_name":"Dawn","full_name":"Erb, Dawn","last_name":"Erb"},{"first_name":"Daniel","full_name":"Schaerer, Daniel","last_name":"Schaerer"},{"full_name":"Amorín, Ricardo","last_name":"Amorín","first_name":"Ricardo"},{"full_name":"Tacchella, Sandro","last_name":"Tacchella","first_name":"Sandro"},{"first_name":"Ana Paulino-Afonso","full_name":"Ana Paulino-Afonso, Ana Paulino-Afonso","last_name":"Ana Paulino-Afonso"},{"first_name":"Mario","last_name":"Llerena","full_name":"Llerena, Mario"},{"last_name":"Calhau","full_name":"Calhau, João","first_name":"João"},{"full_name":"Röttgering, Huub","last_name":"Röttgering","first_name":"Huub"}],"oa_version":"Preprint","title":"(Re)Solving reionization with Lyα: How bright Lyα emitters account for the z ≈ 2 − 8 cosmic ionizing background","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","abstract":[{"text":"The cosmic ionizing emissivity from star-forming galaxies has long been anchored to UV luminosity functions. Here, we introduce an emissivity framework based on Lyα emitters (LAEs), which naturally hones in on the subset of galaxies responsible for the ionizing background due to the intimate connection between production and escape of Lyα and LyC photons. Using constraints on the escape fractions of bright LAEs (LLyα > 0.2L*) at z ≈ 2 obtained from resolved Lyα profiles, and arguing for their redshift-invariance, we show that: (i) quasars and LAEs together reproduce the relatively flat emissivity at z ≈ 2–6, which is non-trivial given the strong evolution in both the star formation density and quasar number density at these epochs and (ii) LAEs produce late and rapid reionization between z ≈ 6−9 under plausible assumptions. Within this framework, the >10 × rise in the UV population-averaged fesc between z ≈ 3–7 naturally arises due to the same phenomena that drive the growing LAE fraction with redshift. Generally, a LAE dominated emissivity yields a peak in the distribution of the ionizing budget with UV luminosity as reported in latest simulations. Using our adopted parameters (⁠fesc=50 per cent⁠, ξion = 1025.9 Hz erg−1 for half the bright LAEs), a highly ionizing minority of galaxies with MUV < −17 accounts for the entire ionizing budget from star-forming galaxies. Rapid flashes of LyC from such rare galaxies produce a ‘disco’ ionizing background. We conclude proposing tests to further develop our suggested Lyα-anchored formalism.","lang":"eng"}],"intvolume":"       512","arxiv":1,"month":"06","citation":{"chicago":"Matthee, Jorryt J, Rohan P. Naidu, Gabriele Pezzulli, Max Gronke, David Sobral, Pascal A. Oesch, Matthew Hayes, et al. “(Re)Solving Reionization with Lyα: How Bright Lyα Emitters Account for the z ≈ 2 − 8 Cosmic Ionizing Background.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/mnras/stac801\">https://doi.org/10.1093/mnras/stac801</a>.","ista":"Matthee JJ, Naidu RP, Pezzulli G, Gronke M, Sobral D, Oesch PA, Hayes M, Erb D, Schaerer D, Amorín R, Tacchella S, Ana Paulino-Afonso AP-A, Llerena M, Calhau J, Röttgering H. 2022. (Re)Solving reionization with Lyα: How bright Lyα emitters account for the z ≈ 2 − 8 cosmic ionizing background. Monthly Notices of the Royal Astronomical Society. 512(4), 5960–5977.","apa":"Matthee, J. J., Naidu, R. P., Pezzulli, G., Gronke, M., Sobral, D., Oesch, P. A., … Röttgering, H. (2022). (Re)Solving reionization with Lyα: How bright Lyα emitters account for the z ≈ 2 − 8 cosmic ionizing background. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stac801\">https://doi.org/10.1093/mnras/stac801</a>","mla":"Matthee, Jorryt J., et al. “(Re)Solving Reionization with Lyα: How Bright Lyα Emitters Account for the z ≈ 2 − 8 Cosmic Ionizing Background.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 512, no. 4, Oxford University Press, 2022, pp. 5960–77, doi:<a href=\"https://doi.org/10.1093/mnras/stac801\">10.1093/mnras/stac801</a>.","ama":"Matthee JJ, Naidu RP, Pezzulli G, et al. (Re)Solving reionization with Lyα: How bright Lyα emitters account for the z ≈ 2 − 8 cosmic ionizing background. <i>Monthly Notices of the Royal Astronomical Society</i>. 2022;512(4):5960-5977. doi:<a href=\"https://doi.org/10.1093/mnras/stac801\">10.1093/mnras/stac801</a>","ieee":"J. J. Matthee <i>et al.</i>, “(Re)Solving reionization with Lyα: How bright Lyα emitters account for the z ≈ 2 − 8 cosmic ionizing background,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 512, no. 4. Oxford University Press, pp. 5960–5977, 2022.","short":"J.J. Matthee, R.P. Naidu, G. Pezzulli, M. Gronke, D. Sobral, P.A. Oesch, M. Hayes, D. Erb, D. Schaerer, R. Amorín, S. Tacchella, A.P.-A. Ana Paulino-Afonso, M. Llerena, J. Calhau, H. Röttgering, Monthly Notices of the Royal Astronomical Society 512 (2022) 5960–5977."},"issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"_id":"11521","date_updated":"2022-08-18T10:42:47Z","type":"journal_article","article_processing_charge":"No","doi":"10.1093/mnras/stac801","publisher":"Oxford University Press","main_file_link":[{"url":"https://arxiv.org/abs/2110.11967","open_access":"1"}],"quality_controlled":"1","page":"5960-5977","keyword":["galaxies: high-redshift","intergalactic medium","cosmology: observations","dark ages","reionization","first stars","ultraviolet: galaxies"],"year":"2022","external_id":{"arxiv":["2110.11967"]},"date_published":"2022-06-01T00:00:00Z","acknowledgement":"We thank an anonymous referee for an encouraging and constructive report that helped improving the quality of this work. We acknowledge illuminating conversations with Xiaohan Wu, Chris Cain, Anna-Christina Eilers, Simon Lilly and Ruari Mackenzie. RPN gratefully acknowledges an Ashford Fellowship granted by Harvard University. MG was supported by NASA through the NASA Hubble Fellowship grant HST-HF2-51409. PO acknowledges support from the Swiss National Science Foundation through the SNSF Professorship grant 190079. GP acknowledges support from the Netherlands Research School for Astronomy (NOVA). MH is fellow of the Knut and Alice Wallenberg Foundation. DE is supported by the US National Science Foundation (NSF) through Astronomy & Astrophysics grant AST-1909198. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant No. 140. RA acknowledges support from Fondecyt Regular Grant 1202007. ST is supported by the 2021 Research Fund 1.210134.01 of UNIST (Ulsan National Institute of Science & Technology). MLl acknowledges support from the ANID/Scholarship Program/Doctorado Nacional/2019-21191036. JC acknowledges support from the Spanish Ministry of Science and Innovation, project PID2019-107408GB-C43 (ESTALLIDOS) and from Gobierno de Canarias through EU FEDER funding, project PID2020010050.","status":"public","extern":"1","publication":"Monthly Notices of the Royal Astronomical Society"},{"doi":"10.15479/AT:ISTA:11542","author":[{"first_name":"Rouven","orcid":"0000-0001-5297-733X","full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz"}],"contributor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","contributor_type":"contact_person"}],"article_processing_charge":"No","title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","oa_version":"None","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T12:34:51Z","_id":"11542","type":"research_data","date_created":"2022-07-08T11:03:02Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-07-08T10:56:52Z","year":"2022","related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1","relation":"contains"}],"record":[{"status":"public","relation":"used_in_publication","id":"11995"}]},"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"file":[{"creator":"rschulz","date_updated":"2022-07-08T10:56:52Z","file_size":135784571,"date_created":"2022-07-08T10:56:52Z","file_id":"11543","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access","file_name":"Source Data.xlsx","success":1,"checksum":"71e8186583f3adbb6c69a88ac9e6e49b","relation":"main_file"}],"oa":1,"status":"public","citation":{"chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","short":"R. Schulz, (2022)."},"date_published":"2022-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"ieee":"A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker modules and Verma modules,” <i>Journal of Algebra</i>, vol. 609, no. 11. Elsevier, pp. 145–179, 2022.","short":"A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.","ama":"Brown A, Romanov A. Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. 2022;609(11):145-179. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>","apa":"Brown, A., &#38; Romanov, A. (2022). Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>","mla":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>, vol. 609, no. 11, Elsevier, 2022, pp. 145–79, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>.","ista":"Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker modules and Verma modules. Journal of Algebra. 609(11), 145–179.","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>."},"issue":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"file":[{"file_id":"12473","date_created":"2023-02-02T07:32:48Z","file_size":582962,"creator":"dernst","date_updated":"2023-02-02T07:32:48Z","relation":"main_file","checksum":"82abaee3d7837f703e499a9ecbb25b7c","file_name":"2022_JournalAlgebra_Brown.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"month":"11","file_date_updated":"2023-02-02T07:32:48Z","publication_status":"published","publication_identifier":{"issn":["0021-8693"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       609","abstract":[{"lang":"eng","text":"We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings.\r\nWe show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category\r\nN have the structure of highest weight categories and we establish a BGG reciprocity theorem for N ."}],"volume":609,"date_created":"2022-07-08T11:40:07Z","article_type":"original","day":"01","scopus_import":"1","author":[{"last_name":"Brown","full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam"},{"last_name":"Romanov","full_name":"Romanov, Anna","first_name":"Anna"}],"oa_version":"Published Version","title":"Contravariant pairings between standard Whittaker modules and Verma modules","ec_funded":1,"acknowledgement":"We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting discussions. The first author acknowledges the support of the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The second author is supported by the National Science Foundation Award No. 1803059 and the Australian Research Council grant DP170101579.","date_published":"2022-11-01T00:00:00Z","status":"public","publication":"Journal of Algebra","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"keyword":["Algebra and Number Theory"],"isi":1,"year":"2022","external_id":{"isi":["000861841100004"]},"quality_controlled":"1","page":"145-179","ddc":["510"],"_id":"11545","date_updated":"2023-08-03T11:56:30Z","type":"journal_article","article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.jalgebra.2022.06.017","publisher":"Elsevier"},{"type":"journal_article","date_updated":"2023-08-03T11:55:42Z","_id":"11546","publisher":"Royal Society of London","doi":"10.1098/rstb.2021.0203","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","ddc":["570"],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"external_id":{"isi":["000812317300005"]},"isi":1,"year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","date_published":"2022-08-01T00:00:00Z","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"status":"public","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","article_type":"original","date_created":"2022-07-08T11:41:56Z","volume":377,"oa_version":"Published Version","title":"Inversions and parallel evolution","author":[{"first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"scopus_import":"1","day":"01","publication_status":"published","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"file_date_updated":"2023-02-02T08:20:29Z","intvolume":"       377","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"has_accepted_license":"1","article_number":"20210203","file":[{"checksum":"49f69428f3dcf5ce3ff281f7d199e9df","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","success":1,"file_id":"12479","date_updated":"2023-02-02T08:20:29Z","creator":"dernst","file_size":920304,"date_created":"2023-02-02T08:20:29Z"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"month":"08","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1856","citation":{"ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>."},"language":[{"iso":"eng"}],"oa":1},{"date_created":"2022-07-10T22:01:52Z","volume":5,"title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","oa_version":"Published Version","author":[{"first_name":"David","full_name":"Molina-Granada, David","last_name":"Molina-Granada"},{"first_name":"Emiliano","full_name":"González-Vioque, Emiliano","last_name":"González-Vioque"},{"first_name":"Marris G.","full_name":"Dibley, Marris G.","last_name":"Dibley"},{"first_name":"Raquel","full_name":"Cabrera-Pérez, Raquel","last_name":"Cabrera-Pérez"},{"full_name":"Vallbona-Garcia, Antoni","last_name":"Vallbona-Garcia","first_name":"Antoni"},{"full_name":"Torres-Torronteras, Javier","last_name":"Torres-Torronteras","first_name":"Javier"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989"},{"first_name":"Michael T.","full_name":"Ryan, Michael T.","last_name":"Ryan"},{"last_name":"Cámara","full_name":"Cámara, Yolanda","first_name":"Yolanda"},{"full_name":"Martí, Ramon","last_name":"Martí","first_name":"Ramon"}],"day":"23","scopus_import":"1","publication_status":"published","publication_identifier":{"eissn":["23993642"]},"file_date_updated":"2022-07-13T07:44:58Z","intvolume":"         5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.","lang":"eng"}],"has_accepted_license":"1","article_number":"620","file":[{"file_size":2335369,"date_created":"2022-07-13T07:44:58Z","date_updated":"2022-07-13T07:44:58Z","creator":"kschuh","file_id":"11571","file_name":"2022_communicationsbiology_Molina-Granada.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"965f88bbcef3fd0c3e121340555c4467"}],"department":[{"_id":"LeSa"}],"month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","citation":{"short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022).","ieee":"D. Molina-Granada <i>et al.</i>, “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” <i>Communications Biology</i>, vol. 5, no. 1. Springer Nature, 2022.","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. 2022;5(1). doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>","mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>, vol. 5, no. 1, 620, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>.","apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>","chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>.","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620."},"language":[{"iso":"eng"}],"oa":1,"type":"journal_article","date_updated":"2023-08-03T11:51:58Z","_id":"11551","publisher":"Springer Nature","doi":"10.1038/s42003-022-03568-6","article_processing_charge":"No","quality_controlled":"1","ddc":["570"],"external_id":{"pmid":[" 35739187"],"isi":["000815098500002"]},"year":"2022","isi":1,"date_published":"2022-06-23T00:00:00Z","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","pmid":1,"publication":"Communications Biology","status":"public"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"24","citation":{"ieee":"J. Qiang <i>et al.</i>, “Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets,” <i>Physical Review Letters</i>, vol. 128, no. 24. American Physical Society, 2022.","short":"J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun, W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt, I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022).","ama":"Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. 2022;128(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>","apa":"Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>","mla":"Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>, vol. 128, no. 24, 243201, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>.","ista":"Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W, Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I, Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201.","chicago":"Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>."},"month":"06","arxiv":1,"article_number":"243201","department":[{"_id":"MiLe"}],"intvolume":"       128","abstract":[{"text":"Rotational dynamics of D2 molecules inside helium nanodroplets is induced by a moderately intense femtosecond pump pulse and measured as a function of time by recording the yield of HeD+ ions, created through strong-field dissociative ionization with a delayed femtosecond probe pulse. The yield oscillates with a period of 185 fs, reflecting field-free rotational wave packet dynamics, and the oscillation persists for more than 500 periods. Within the experimental uncertainty, the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier analysis, is the same as Bgas for an isolated D2 molecule. Our observations show that the D2 molecules inside helium nanodroplets essentially rotate as free D2 molecules.","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"oa_version":"Submitted Version","title":"Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets","author":[{"full_name":"Qiang, Junjie","last_name":"Qiang","first_name":"Junjie"},{"first_name":"Lianrong","last_name":"Zhou","full_name":"Zhou, Lianrong"},{"last_name":"Lu","full_name":"Lu, Peifen","first_name":"Peifen"},{"first_name":"Kang","last_name":"Lin","full_name":"Lin, Kang"},{"first_name":"Yongzhe","full_name":"Ma, Yongzhe","last_name":"Ma"},{"last_name":"Pan","full_name":"Pan, Shengzhe","first_name":"Shengzhe"},{"first_name":"Chenxu","full_name":"Lu, Chenxu","last_name":"Lu"},{"first_name":"Wenyu","full_name":"Jiang, Wenyu","last_name":"Jiang"},{"first_name":"Fenghao","last_name":"Sun","full_name":"Sun, Fenghao"},{"last_name":"Zhang","full_name":"Zhang, Wenbin","first_name":"Wenbin"},{"first_name":"Hui","full_name":"Li, Hui","last_name":"Li"},{"first_name":"Xiaochun","full_name":"Gong, Xiaochun","last_name":"Gong"},{"first_name":"Ilya Sh","last_name":"Averbukh","full_name":"Averbukh, Ilya Sh"},{"first_name":"Yehiam","full_name":"Prior, Yehiam","last_name":"Prior"},{"first_name":"Constant A.","full_name":"Schouder, Constant A.","last_name":"Schouder"},{"first_name":"Henrik","last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik"},{"full_name":"Cherepanov, Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","first_name":"Igor"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"full_name":"Jäger, Wolfgang","last_name":"Jäger","first_name":"Wolfgang"},{"full_name":"Wu, Jian","last_name":"Wu","first_name":"Jian"}],"scopus_import":"1","day":"16","date_created":"2022-07-10T22:01:52Z","volume":128,"project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"status":"public","publication":"Physical Review Letters","date_published":"2022-06-16T00:00:00Z","ec_funded":1,"external_id":{"arxiv":["2201.09281"],"isi":["000820659700002"]},"year":"2022","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.09281"}],"publisher":"American Physical Society","doi":"10.1103/PhysRevLett.128.243201","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-03T11:54:14Z","_id":"11552"},{"oa_version":"None","title":"The dynamics of complex box mappings","author":[{"first_name":"Trevor","full_name":"Clark, Trevor","last_name":"Clark"},{"orcid":"0000-0002-9156-8616","first_name":"Kostiantyn","last_name":"Drach","full_name":"Drach, Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115"},{"first_name":"Oleg","last_name":"Kozlovski","full_name":"Kozlovski, Oleg"},{"full_name":"Strien, Sebastian Van","last_name":"Strien","first_name":"Sebastian Van"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2022-07-10T22:01:53Z","volume":8,"intvolume":"         8","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:\r\n• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.\r\n• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:\r\n  • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;\r\n  • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n   • the QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.\r\n• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:\r\n   • puzzle pieces shrink to points,\r\n   • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings\r\nare the analogues of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points."}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"eissn":["2199-6806"],"issn":["2199-6792"]},"file_date_updated":"2022-07-12T10:04:55Z","month":"06","file":[{"date_updated":"2022-07-12T10:04:55Z","creator":"kschuh","file_size":2509915,"date_created":"2022-07-12T10:04:55Z","file_id":"11559","content_type":"application/pdf","access_level":"open_access","file_name":"2022_ArnoldMathematicalJournal_Clark.pdf","success":1,"checksum":"16e7c659dee9073c6c8aeb87316ef201","relation":"main_file"}],"department":[{"_id":"VaKa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","citation":{"ista":"Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box mappings. Arnold Mathematical Journal. 8(2), 319–410.","chicago":"Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>.","apa":"Clark, T., Drach, K., Kozlovski, O., &#38; Strien, S. V. (2022). The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>","mla":"Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>.","ama":"Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. 2022;8(2):319-410. doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>","ieee":"T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex box mappings,” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2. Springer Nature, pp. 319–410, 2022.","short":"T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal 8 (2022) 319–410."},"publisher":"Springer Nature","doi":"10.1007/s40598-022-00200-7","article_processing_charge":"No","type":"journal_article","date_updated":"2023-02-16T10:02:12Z","_id":"11553","ddc":["500"],"page":"319-410","quality_controlled":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00209-y"},{"url":"https://doi.org/10.1007/s40598-022-00218-x","relation":"erratum"}]},"year":"2022","project":[{"name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707","call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"publication":"Arnold Mathematical Journal","status":"public","date_published":"2022-06-01T00:00:00Z","acknowledgement":"We would also like to thank Dzmitry Dudko and Dierk Schleicher for many stimulating discussions and encouragement during our work on this project, and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are grateful to Leon Staresinic who carefully read the revised version of the manuscript and provided many helpful suggestions.","ec_funded":1},{"publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.jcp.2022.111439","type":"journal_article","_id":"11556","date_updated":"2023-08-03T11:55:06Z","ddc":["518"],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"external_id":{"isi":["000917225500013"],"arxiv":["2103.09481"]},"year":"2022","isi":1,"keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"status":"public","publication":"Journal of Computational Physics","date_published":"2022-10-15T00:00:00Z","acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","oa_version":"Preprint","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","day":"15","author":[{"last_name":"Kalinov","full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","orcid":"0000-0003-2189-3904","first_name":"Aleksei"},{"first_name":"A.I.","last_name":"Osinskiy","full_name":"Osinskiy, A.I."},{"first_name":"S.A.","full_name":"Matveev, S.A.","last_name":"Matveev"},{"last_name":"Otieno","full_name":"Otieno, W.","first_name":"W."},{"first_name":"N.V.","full_name":"Brilliantov, N.V.","last_name":"Brilliantov"}],"date_created":"2022-07-11T12:19:59Z","article_type":"original","volume":467,"abstract":[{"lang":"eng","text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise."}],"intvolume":"       467","publication_identifier":{"issn":["0021-9991"]},"publication_status":"published","arxiv":1,"month":"10","article_number":"111439","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439."}},{"external_id":{"isi":["000821915500002"]},"year":"2022","isi":1,"date_published":"2022-07-07T00:00:00Z","acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","publication":"Genome Biology","status":"public","type":"journal_article","_id":"11587","date_updated":"2023-08-03T12:04:18Z","publisher":"BioMed Central","article_processing_charge":"No","doi":"10.1186/s13059-022-02711-0","quality_controlled":"1","ddc":["570"],"file":[{"relation":"main_file","checksum":"2c30ef84151d257a6b835b4e069b70ac","success":1,"file_name":"2022_GenomeBiology_Zhang.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"11597","file_size":3146207,"date_created":"2022-07-18T08:15:24Z","date_updated":"2022-07-18T08:15:24Z","creator":"dernst"}],"article_number":"149","department":[{"_id":"FyKo"}],"month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022.","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>","mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>.","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.","chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2022-07-17T22:01:53Z","article_type":"original","volume":23,"oa_version":"Published Version","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","scopus_import":"1","day":"07","author":[{"first_name":"Runxuan","last_name":"Zhang","full_name":"Zhang, Runxuan"},{"last_name":"Kuo","full_name":"Kuo, Richard","first_name":"Richard"},{"first_name":"Max","full_name":"Coulter, Max","last_name":"Coulter"},{"last_name":"Calixto","full_name":"Calixto, Cristiane P.G.","first_name":"Cristiane P.G."},{"first_name":"Juan Carlos","last_name":"Entizne","full_name":"Entizne, Juan Carlos"},{"first_name":"Wenbin","full_name":"Guo, Wenbin","last_name":"Guo"},{"last_name":"Marquez","full_name":"Marquez, Yamile","first_name":"Yamile"},{"last_name":"Milne","full_name":"Milne, Linda","first_name":"Linda"},{"first_name":"Stefan","orcid":"0000-0003-3413-1343","full_name":"Riegler, Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler"},{"full_name":"Matsui, Akihiro","last_name":"Matsui","first_name":"Akihiro"},{"last_name":"Tanaka","full_name":"Tanaka, Maho","first_name":"Maho"},{"first_name":"Sarah","last_name":"Harvey","full_name":"Harvey, Sarah"},{"first_name":"Yubang","last_name":"Gao","full_name":"Gao, Yubang"},{"first_name":"Theresa","full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh"},{"full_name":"Paniagua, Alejandro","last_name":"Paniagua","first_name":"Alejandro"},{"full_name":"Crespi, Martin","last_name":"Crespi","first_name":"Martin"},{"last_name":"Denby","full_name":"Denby, Katherine","first_name":"Katherine"},{"last_name":"Hur","full_name":"Hur, Asa Ben","first_name":"Asa Ben"},{"first_name":"Enamul","last_name":"Huq","full_name":"Huq, Enamul"},{"first_name":"Michael","last_name":"Jantsch","full_name":"Jantsch, Michael"},{"full_name":"Jarmolowski, Artur","last_name":"Jarmolowski","first_name":"Artur"},{"first_name":"Tino","last_name":"Koester","full_name":"Koester, Tino"},{"full_name":"Laubinger, Sascha","last_name":"Laubinger","first_name":"Sascha"},{"first_name":"Qingshun Quinn","last_name":"Li","full_name":"Li, Qingshun Quinn"},{"first_name":"Lianfeng","last_name":"Gu","full_name":"Gu, Lianfeng"},{"last_name":"Seki","full_name":"Seki, Motoaki","first_name":"Motoaki"},{"first_name":"Dorothee","last_name":"Staiger","full_name":"Staiger, Dorothee"},{"first_name":"Ramanjulu","full_name":"Sunkar, Ramanjulu","last_name":"Sunkar"},{"first_name":"Zofia","full_name":"Szweykowska-Kulinska, Zofia","last_name":"Szweykowska-Kulinska"},{"first_name":"Shih Long","full_name":"Tu, Shih Long","last_name":"Tu"},{"last_name":"Wachter","full_name":"Wachter, Andreas","first_name":"Andreas"},{"first_name":"Robbie","last_name":"Waugh","full_name":"Waugh, Robbie"},{"last_name":"Xiong","full_name":"Xiong, Liming","first_name":"Liming"},{"full_name":"Zhang, Xiao Ning","last_name":"Zhang","first_name":"Xiao Ning"},{"full_name":"Conesa, Ana","last_name":"Conesa","first_name":"Ana"},{"first_name":"Anireddy S.N.","full_name":"Reddy, Anireddy S.N.","last_name":"Reddy"},{"last_name":"Barta","full_name":"Barta, Andrea","first_name":"Andrea"},{"first_name":"Maria","full_name":"Kalyna, Maria","last_name":"Kalyna"},{"first_name":"John W.S.","full_name":"Brown, John W.S.","last_name":"Brown"}],"file_date_updated":"2022-07-18T08:15:24Z","publication_status":"published","publication_identifier":{"eissn":["1474-760X"]},"intvolume":"        23","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species."}],"has_accepted_license":"1"},{"doi":"10.3324/haematol.2021.278896","article_processing_charge":"No","publisher":"Ferrata Storti Foundation","date_updated":"2023-08-03T12:01:01Z","_id":"11588","type":"journal_article","page":"1669-1680","ddc":["570"],"quality_controlled":"1","isi":1,"year":"2022","external_id":{"isi":["000823746100018"]},"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Haematologica","ec_funded":1,"acknowledgement":"This study was supported by the Deutsche Forschungsgemeinschaft (DFG) SFB 914 ( to SM [B02 and Z01]), the DFG SFB 1123 (to SM [B06]), the DFG FOR 2033 (to SM), the German\r\nCenter for Cardiovascular Research (DZHK) (Clinician Scientist Programme), MHA 1.4VD (to SM), Postdoc Start-up Grant, 81X3600213 (to FG), 81X3600222 (to LN), the FP7 program\r\n(project 260309, PRESTIGE [to SM]). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 83344, ERC-2018-ADG “IMMUNOTHROMBOSIS” [to SM] and the Marie Skłodowska Curie Individual Fellowship (EU project 747687, LamelliActin [to FG]). ","date_published":"2022-07-01T00:00:00Z","author":[{"last_name":"Nicolai","full_name":"Nicolai, Leo","first_name":"Leo"},{"first_name":"Rainer","full_name":"Kaiser, Rainer","last_name":"Kaiser"},{"last_name":"Escaig","full_name":"Escaig, Raphael","first_name":"Raphael"},{"first_name":"Marie Louise","full_name":"Hoffknecht, Marie Louise","last_name":"Hoffknecht"},{"first_name":"Afra","full_name":"Anjum, Afra","last_name":"Anjum"},{"first_name":"Alexander","last_name":"Leunig","full_name":"Leunig, Alexander"},{"first_name":"Joachim","full_name":"Pircher, Joachim","last_name":"Pircher"},{"first_name":"Andreas","last_name":"Ehrlich","full_name":"Ehrlich, Andreas"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"first_name":"Hellen","full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold"},{"full_name":"Aird, William C.","last_name":"Aird","first_name":"William C."},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"},{"last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","first_name":"Florian R"}],"scopus_import":"1","day":"01","oa_version":"Published Version","title":"Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo","volume":107,"article_type":"original","date_created":"2022-07-17T22:01:54Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","intvolume":"       107","abstract":[{"lang":"eng","text":"Visualizing cell behavior and effector function on a single cell level has been crucial for understanding key aspects of mammalian biology. Due to their small size, large number and rapid recruitment into thrombi, there is a lack of data on fate and behavior of individual platelets in thrombosis and hemostasis. Here we report the use of platelet lineage restricted multi-color reporter mouse strains to delineate platelet function on a single cell level. We show that genetic labeling allows for single platelet and megakaryocyte (MK) tracking and morphological analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven Confetti expression, we provide insights into temporal gene expression patterns as well as spatial clustering of MK in the bone marrow. In the vasculature, shape analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia formation with no evidence of lamellipodia formation. Single cell tracking in complex thrombi reveals prominent myosin-dependent motility of platelets and highlights thrombus formation as a highly dynamic process amenable to modification and intervention of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry, as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions of multicolor reporter mice compared to wild-type controls. In conclusion, platelet lineage multicolor reporter mice prove useful in furthering our understanding of platelet and MK biology on a single cell level."}],"publication_status":"published","publication_identifier":{"issn":["0390-6078"],"eissn":["1592-8721"]},"file_date_updated":"2022-07-18T07:51:55Z","month":"07","department":[{"_id":"MiSi"}],"file":[{"success":1,"file_name":"2022_Haematologica_Nicolai.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"9b47830945f3c30428fe9cfee2dc4a8a","file_size":1722094,"date_created":"2022-07-18T07:51:55Z","date_updated":"2022-07-18T07:51:55Z","creator":"dernst","file_id":"11595"}],"oa":1,"language":[{"iso":"eng"}],"issue":"7","citation":{"apa":"Nicolai, L., Kaiser, R., Escaig, R., Hoffknecht, M. L., Anjum, A., Leunig, A., … Gärtner, F. R. (2022). Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. Ferrata Storti Foundation. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>","mla":"Nicolai, Leo, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>, vol. 107, no. 7, Ferrata Storti Foundation, 2022, pp. 1669–80, doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>.","chicago":"Nicolai, Leo, Rainer Kaiser, Raphael Escaig, Marie Louise Hoffknecht, Afra Anjum, Alexander Leunig, Joachim Pircher, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>. Ferrata Storti Foundation, 2022. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>.","ista":"Nicolai L, Kaiser R, Escaig R, Hoffknecht ML, Anjum A, Leunig A, Pircher J, Ehrlich A, Lorenz M, Ishikawa-Ankerhold H, Aird WC, Massberg S, Gärtner FR. 2022. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica. 107(7), 1669–1680.","ieee":"L. Nicolai <i>et al.</i>, “Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo,” <i>Haematologica</i>, vol. 107, no. 7. Ferrata Storti Foundation, pp. 1669–1680, 2022.","short":"L. Nicolai, R. Kaiser, R. Escaig, M.L. Hoffknecht, A. Anjum, A. Leunig, J. Pircher, A. Ehrlich, M. Lorenz, H. Ishikawa-Ankerhold, W.C. Aird, S. Massberg, F.R. Gärtner, Haematologica 107 (2022) 1669–1680.","ama":"Nicolai L, Kaiser R, Escaig R, et al. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. 2022;107(7):1669-1680. doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_published":"2022-06-16T00:00:00Z","acknowledgement":"RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript.","pmid":1,"publication":"Frontiers in Plant Science","status":"public","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.3389/fpls.2022.1100792"}]},"external_id":{"isi":["000819250500001"],"pmid":["35783951"]},"isi":1,"year":"2022","quality_controlled":"1","ddc":["580"],"type":"journal_article","_id":"11589","date_updated":"2023-08-03T12:01:47Z","publisher":"Frontiers","article_processing_charge":"No","doi":"10.3389/fpls.2022.862398","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","ieee":"R. Wang <i>et al.</i>, “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” <i>Frontiers in Plant Science</i>, vol. 13. Frontiers, 2022.","chicago":"Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>.","ista":"Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.","mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>, vol. 13, 862398, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>.","apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>"},"language":[{"iso":"eng"}],"oa":1,"file":[{"checksum":"95313515637c0f84de591d204375d764","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_FrontiersPlantScience_Wang.pdf","file_id":"11596","creator":"dernst","date_updated":"2022-07-18T08:05:15Z","date_created":"2022-07-18T08:05:15Z","file_size":5040638}],"article_number":"862398","department":[{"_id":"JiFr"}],"month":"06","file_date_updated":"2022-07-18T08:05:15Z","publication_status":"published","publication_identifier":{"eissn":["1664-462X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.","lang":"eng"}],"intvolume":"        13","has_accepted_license":"1","date_created":"2022-07-17T22:01:54Z","article_type":"original","volume":13,"oa_version":"Published Version","title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","day":"16","scopus_import":"1","author":[{"first_name":"Ren","last_name":"Wang","full_name":"Wang, Ren"},{"first_name":"Ellie","full_name":"Himschoot, Ellie","last_name":"Himschoot"},{"first_name":"Jian","full_name":"Chen, Jian","last_name":"Chen"},{"full_name":"Boudsocq, Marie","last_name":"Boudsocq","first_name":"Marie"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}]},{"day":"01","scopus_import":"1","author":[{"full_name":"Brauneis, Fabian","last_name":"Brauneis","first_name":"Fabian"},{"full_name":"Backert, Timothy G.","last_name":"Backert","first_name":"Timothy G."},{"first_name":"Simeon I.","last_name":"Mistakidis","full_name":"Mistakidis, Simeon I."},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Hans Werner","full_name":"Hammer, Hans Werner","last_name":"Hammer"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"}],"title":"Artificial atoms from cold bosons in one dimension","oa_version":"Published Version","volume":24,"date_created":"2022-07-17T22:01:55Z","article_type":"original","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        24","abstract":[{"lang":"eng","text":"We investigate the ground-state properties of weakly repulsive one-dimensional bosons in the presence of an attractive zero-range impurity potential. First, we derive mean-field solutions to the problem on a finite ring for the two asymptotic cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering state. Moreover, we derive the critical line that separates these regimes in the parameter space. In the thermodynamic limit, this critical line determines the maximum number of bosons that can be bound by the impurity potential, forming an artificial atom. Second, we validate the mean-field results using the flow equation approach and the multi-layer multi-configuration time-dependent Hartree method for atomic mixtures. While beyond-mean-field effects destroy long-range order in the Bose gas, the critical boson number is unaffected. Our findings are important for understanding such artificial atoms in low-density Bose gases with static and mobile impurities."}],"file_date_updated":"2022-07-18T06:33:13Z","publication_status":"published","publication_identifier":{"issn":["1367-2630"]},"month":"06","department":[{"_id":"MiLe"}],"article_number":"063036","file":[{"relation":"main_file","checksum":"dc67b60f2e50e9ef2bd820ca0d7333d2","file_name":"2022_NewJournalPhysics_Brauneis.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"11594","file_size":3415721,"date_created":"2022-07-18T06:33:13Z","date_updated":"2022-07-18T06:33:13Z","creator":"dernst"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"apa":"Brauneis, F., Backert, T. G., Mistakidis, S. I., Lemeshko, M., Hammer, H. W., &#38; Volosniev, A. (2022). Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>","mla":"Brauneis, Fabian, et al. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>, vol. 24, no. 6, 063036, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>.","ista":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. 2022. Artificial atoms from cold bosons in one dimension. New Journal of Physics. 24(6), 063036.","chicago":"Brauneis, Fabian, Timothy G. Backert, Simeon I. Mistakidis, Mikhail Lemeshko, Hans Werner Hammer, and Artem Volosniev. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>.","ieee":"F. Brauneis, T. G. Backert, S. I. Mistakidis, M. Lemeshko, H. W. Hammer, and A. Volosniev, “Artificial atoms from cold bosons in one dimension,” <i>New Journal of Physics</i>, vol. 24, no. 6. IOP Publishing, 2022.","short":"F. Brauneis, T.G. Backert, S.I. Mistakidis, M. Lemeshko, H.W. Hammer, A. Volosniev, New Journal of Physics 24 (2022).","ama":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. 2022;24(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>"},"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","doi":"10.1088/1367-2630/ac78d8","publisher":"IOP Publishing","_id":"11590","date_updated":"2023-08-03T11:57:41Z","type":"journal_article","ddc":["530"],"quality_controlled":"1","year":"2022","isi":1,"external_id":{"isi":["000818530000001"]},"status":"public","publication":"New Journal of Physics","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"ec_funded":1,"acknowledgement":"This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (FB, H-WH, AGV) and European Union's Horizon 2020 research and innovation programme under the Marie Skĺodowska-Curie Grant Agreement No. 754411 (AGV). ML acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). SIM acknowledges support from the NSF through a grant for ITAMP at Harvard University.","date_published":"2022-06-01T00:00:00Z"},{"arxiv":1,"month":"06","department":[{"_id":"JoFi"}],"article_number":"062454","oa":1,"language":[{"iso":"eng"}],"citation":{"ieee":"J. Agustí, Y. Minoguchi, J. M. Fink, and P. Rabl, “Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","short":"J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).","ama":"Agustí J, Minoguchi Y, Fink JM, Rabl P. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>","apa":"Agustí, J., Minoguchi, Y., Fink, J. M., &#38; Rabl, P. (2022). Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>","mla":"Agustí, J., et al. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>, vol. 105, no. 6, 062454, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>.","ista":"Agustí J, Minoguchi Y, Fink JM, Rabl P. 2022. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. Physical Review A. 105(6), 062454.","chicago":"Agustí, J., Y. Minoguchi, Johannes M Fink, and P. Rabl. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>."},"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","day":"29","author":[{"first_name":"J.","full_name":"Agustí, J.","last_name":"Agustí"},{"full_name":"Minoguchi, Y.","last_name":"Minoguchi","first_name":"Y."},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"first_name":"P.","last_name":"Rabl","full_name":"Rabl, P."}],"title":"Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams","oa_version":"Preprint","volume":105,"date_created":"2022-07-17T22:01:55Z","article_type":"original","abstract":[{"text":"We investigate the deterministic generation and distribution of entanglement in large quantum networks by driving distant qubits with the output fields of a nondegenerate parametric amplifier. In this setting, the amplifier produces a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated reservoir for the qubits and relaxes them into a highly entangled steady state. Here we are interested in the maximal amount of entanglement and the optimal entanglement generation rates that can be achieved with this scheme under realistic conditions taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation delays into account. By combining exact numerical simulations of the full network with approximate analytic results, we predict the optimal working point for the amplifier and the corresponding qubit-qubit entanglement under various conditions. Our findings show that this passive conversion of Gaussian into discrete-variable entanglement offers a robust and experimentally very attractive approach for operating large optical, microwave, or hybrid quantum networks, for which efficient parametric amplifiers are currently developed.","lang":"eng"}],"intvolume":"       105","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"publication_status":"published","isi":1,"year":"2022","external_id":{"arxiv":["2204.02993"],"isi":["000824330200003"]},"publication":"Physical Review A","status":"public","project":[{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"}],"ec_funded":1,"date_published":"2022-06-29T00:00:00Z","acknowledgement":"We thank T. Mavrogordatos and D. Zhu for initial contribution on the presented topic and K. Fedorov for stimulating discussions on entangled microwave beams. This work was supported by the Austrian Science Fund (FWF) through Grant No. P32299 (PHONED) and the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 899354 (SuperQuLAN). Most of the computational results presented were obtained using the CLIP cluster [65].","article_processing_charge":"No","doi":"10.1103/PhysRevA.105.062454","publisher":"American Physical Society","_id":"11591","date_updated":"2023-08-03T11:58:16Z","type":"journal_article","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2204.02993","open_access":"1"}],"quality_controlled":"1"}]