[{"article_type":"original","external_id":{"arxiv":["2202.10026"]},"status":"public","oa":1,"acknowledgement":"We thank the referee for her/his positive and constructive report, which has allowed us to improve the quality of our article. H.D. and S.M. acknowledge support from the CNES PLATO grant at CEA/DAp. T.V.R. gratefully acknowledges support from the Research Foundation Flanders (FWO) under grant agreement No. 12ZB620N and V414021N. This research was supported in part by the National Science Foundation under Grant No. NSF PHY-1748958. C.A. is supported by the KU Leuven Research Council (grant C16/18/005: PARADISE) as well as from the BELgian federal Science Policy Office (BELSPO) through a PLATO PRODEX grant.","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"citation":{"ama":"Dhouib H, Mathis S, Bugnet LA, Van Reeth T, Aerts C. Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field. <i>Astronomy &#38; Astrophysics</i>. 2022;661. doi:<a href=\"https://doi.org/10.1051/0004-6361/202142956\">10.1051/0004-6361/202142956</a>","short":"H. Dhouib, S. Mathis, L.A. Bugnet, T. Van Reeth, C. Aerts, Astronomy &#38; Astrophysics 661 (2022).","ista":"Dhouib H, Mathis S, Bugnet LA, Van Reeth T, Aerts C. 2022. Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field. Astronomy &#38; Astrophysics. 661, A133.","mla":"Dhouib, H., et al. “Detecting Deep Axisymmetric Toroidal Magnetic Fields in Stars: The Traditional Approximation of Rotation for Differentially Rotating Deep Spherical Shells with a General Azimuthal Magnetic Field.” <i>Astronomy &#38; Astrophysics</i>, vol. 661, A133, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202142956\">10.1051/0004-6361/202142956</a>.","ieee":"H. Dhouib, S. Mathis, L. A. Bugnet, T. Van Reeth, and C. Aerts, “Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field,” <i>Astronomy &#38; Astrophysics</i>, vol. 661. EDP Sciences, 2022.","chicago":"Dhouib, H., S. Mathis, Lisa Annabelle Bugnet, T. Van Reeth, and C. Aerts. “Detecting Deep Axisymmetric Toroidal Magnetic Fields in Stars: The Traditional Approximation of Rotation for Differentially Rotating Deep Spherical Shells with a General Azimuthal Magnetic Field.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202142956\">https://doi.org/10.1051/0004-6361/202142956</a>.","apa":"Dhouib, H., Mathis, S., Bugnet, L. A., Van Reeth, T., &#38; Aerts, C. (2022). Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202142956\">https://doi.org/10.1051/0004-6361/202142956</a>"},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":661,"year":"2022","_id":"11621","arxiv":1,"extern":"1","abstract":[{"text":"Context. Asteroseismology has revealed small core-to-surface rotation contrasts in stars in the whole Hertzsprung–Russell diagram. This is the signature of strong transport of angular momentum (AM) in stellar interiors. One of the plausible candidates to efficiently carry AM is magnetic fields with various topologies that could be present in stellar radiative zones. Among them, strong axisymmetric azimuthal (toroidal) magnetic fields have received a lot of interest. Indeed, if they are subject to the so-called Tayler instability, the accompanying triggered Maxwell stresses can transport AM efficiently. In addition, the electromotive force induced by the fluctuations of magnetic and velocity fields could potentially sustain a dynamo action that leads to the regeneration of the initial strong axisymmetric azimuthal magnetic field.\r\n\r\nAims. The key question we aim to answer is whether we can detect signatures of these deep strong azimuthal magnetic fields. The only way to answer this question is asteroseismology, and the best laboratories of study are intermediate-mass and massive stars with external radiative envelopes. Most of these are rapid rotators during their main sequence. Therefore, we have to study stellar pulsations propagating in stably stratified, rotating, and potentially strongly magnetised radiative zones, namely magneto-gravito-inertial (MGI) waves.\r\n\r\nMethods. We generalise the traditional approximation of rotation (TAR) by simultaneously taking general axisymmetric differential rotation and azimuthal magnetic fields into account. Both the Coriolis acceleration and the Lorentz force are therefore treated in a non-perturbative way. Using this new formalism, we derive the asymptotic properties of MGI waves and their period spacings.\r\n\r\nResults. We find that toroidal magnetic fields induce a shift in the period spacings of gravity (g) and Rossby (r) modes. An equatorial azimuthal magnetic field with an amplitude of the order of 105 G leads to signatures that are detectable in period spacings for high-radial-order g and r modes in γ Doradus (γ Dor) and slowly pulsating B (SPB) stars. More complex hemispheric configurations are more difficult to observe, particularly when they are localised out of the propagation region of MGI modes, which can be localised in an equatorial belt.\r\n\r\nConclusions. The magnetic TAR, which takes into account toroidal magnetic fields in a non-perturbative way, is derived. This new formalism allows us to assess the effects of the magnetic field in γ Dor and SPB stars on g and r modes. We find that these effects should be detectable for equatorial fields thanks to modern space photometry using observations from Kepler, TESS CVZ, and PLATO.","lang":"eng"}],"publisher":"EDP Sciences","title":"Detecting deep axisymmetric toroidal magnetic fields in stars: The traditional approximation of rotation for differentially rotating deep spherical shells with a general azimuthal magnetic field","publication":"Astronomy & Astrophysics","oa_version":"Preprint","date_created":"2022-07-19T08:04:15Z","day":"19","language":[{"iso":"eng"}],"month":"05","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2202.10026"}],"intvolume":"       661","date_updated":"2022-08-22T07:58:54Z","doi":"10.1051/0004-6361/202142956","article_processing_charge":"No","date_published":"2022-05-19T00:00:00Z","author":[{"last_name":"Dhouib","first_name":"H.","full_name":"Dhouib, H."},{"first_name":"S.","last_name":"Mathis","full_name":"Mathis, S."},{"first_name":"Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"first_name":"T.","last_name":"Van Reeth","full_name":"Van Reeth, T."},{"last_name":"Aerts","first_name":"C.","full_name":"Aerts, C."}],"quality_controlled":"1","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","magnetohydrodynamics (MHD) / waves / stars","rotation / stars: magnetic field / stars","oscillations / methods"],"article_number":"A133"},{"abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","oa_version":"Published Version","date_created":"2022-07-20T11:21:53Z","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"citation":{"apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>"},"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"248","has_accepted_license":"1","year":"2022","_id":"11626","supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Shani, Eilon","first_name":"Eilon","last_name":"Shani"}],"date_updated":"2024-10-29T10:22:45Z","doi":"10.15479/at:ista:11626","related_material":{"record":[{"id":"9287","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7142"},{"relation":"part_of_dissertation","status":"public","id":"7465"},{"id":"8138","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"status":"public","relation":"part_of_dissertation","id":"8931"},{"relation":"part_of_dissertation","status":"public","id":"10411"}]},"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","author":[{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","first_name":"Michelle C"}],"date_published":"2022-07-20T00:00:00Z","degree_awarded":"PhD","file_date_updated":"2022-07-25T11:48:45Z","day":"20","ddc":["575"],"language":[{"iso":"eng"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"07","publication_status":"published","file":[{"date_created":"2022-07-25T09:08:47Z","content_type":"application/pdf","access_level":"open_access","creator":"mgallei","relation":"main_file","file_name":"Thesis_Gallei.pdf","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","file_size":9730864,"file_id":"11645","date_updated":"2022-07-25T09:08:47Z"},{"access_level":"closed","creator":"mgallei","relation":"source_file","date_created":"2022-07-25T09:09:09Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"11646","date_updated":"2022-07-25T09:39:58Z","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","file_name":"Thesis_Gallei_source.docx","file_size":19560720},{"file_size":24542837,"checksum":"3994f7f20058941b5bb8a16886b21e71","file_name":"Thesis_Gallei_to_print.pdf","date_updated":"2022-07-25T09:39:58Z","file_id":"11647","content_type":"application/pdf","date_created":"2022-07-25T09:09:32Z","description":"This is the print version of the thesis including the full appendix","relation":"source_file","access_level":"closed","creator":"mgallei"},{"file_name":"Thesis_Gallei_Appendix.pdf","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","file_size":15435966,"file_id":"11650","date_updated":"2022-07-25T11:48:45Z","date_created":"2022-07-25T11:48:45Z","content_type":"application/pdf","creator":"mgallei","access_level":"open_access","relation":"main_file"}]},{"abstract":[{"text":"In [3], Poonen and Slavov recently developed a novel approach to Bertini irreducibility theorems over an arbitrary field, based on random hyperplane slicing. In this paper, we extend their work by proving an analogous bound for the dimension of the exceptional locus in the setting of linear subspaces of higher codimensions.","lang":"eng"}],"arxiv":1,"date_created":"2022-07-24T22:01:41Z","oa_version":"Published Version","publication":"Finite Fields and their Applications","department":[{"_id":"TiBr"}],"title":"The Bertini irreducibility theorem for higher codimensional slices","publisher":"Elsevier","citation":{"short":"P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).","mla":"Kmentt, Philip, and Alec L. Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>, vol. 83, no. 10, 102085, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>.","ista":"Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional slices. Finite Fields and their Applications. 83(10), 102085.","ama":"Kmentt P, Shute AL. The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and their Applications</i>. 2022;83(10). doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>","apa":"Kmentt, P., &#38; Shute, A. L. (2022). The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>","ieee":"P. Kmentt and A. L. Shute, “The Bertini irreducibility theorem for higher codimensional slices,” <i>Finite Fields and their Applications</i>, vol. 83, no. 10. Elsevier, 2022.","chicago":"Kmentt, Philip, and Alec L Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>."},"publication_identifier":{"issn":["10715797"],"eissn":["10902465"]},"oa":1,"status":"public","issue":"10","article_type":"original","external_id":{"arxiv":["2111.06697"],"isi":["000835490600001"]},"_id":"11636","has_accepted_license":"1","year":"2022","volume":83,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","scopus_import":"1","quality_controlled":"1","date_published":"2022-10-01T00:00:00Z","author":[{"last_name":"Kmentt","first_name":"Philip","id":"c90670c9-0bf0-11ed-86f5-ed522ece2fac","full_name":"Kmentt, Philip"},{"orcid":"0000-0002-1812-2810","last_name":"Shute","first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","full_name":"Shute, Alec L"}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.ffa.2022.102085","date_updated":"2023-08-03T12:12:57Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-02-02T07:56:34Z","article_number":"102085","month":"10","isi":1,"language":[{"iso":"eng"}],"ddc":["510"],"day":"01","intvolume":"        83","file":[{"file_size":247615,"file_name":"2022_FiniteFields_Kmentt.pdf","checksum":"3ca88decb1011180dc6de7e0862153e1","date_updated":"2023-02-02T07:56:34Z","file_id":"12475","content_type":"application/pdf","success":1,"date_created":"2023-02-02T07:56:34Z","relation":"main_file","creator":"dernst","access_level":"open_access"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e3001684","file_date_updated":"2022-07-25T07:38:49Z","quality_controlled":"1","scopus_import":"1","doi":"10.1371/journal.pbio.3001684","date_updated":"2023-08-03T12:11:44Z","article_processing_charge":"No","date_published":"2022-06-21T00:00:00Z","author":[{"last_name":"Zhao","first_name":"Lina","full_name":"Zhao, Lina"},{"first_name":"Lorenz A.","last_name":"Fenk","full_name":"Fenk, Lorenz A."},{"last_name":"Nilsson","first_name":"Lars","full_name":"Nilsson, Lars"},{"full_name":"Amin-Wetzel, Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","first_name":"Niko Paresh","last_name":"Amin-Wetzel"},{"last_name":"Ramirez","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425","full_name":"Ramirez, Nelson"},{"last_name":"De Bono","orcid":"0000-0001-8347-0443","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario"},{"full_name":"Chen, Changchun","last_name":"Chen","first_name":"Changchun"}],"publication_status":"published","file":[{"date_created":"2022-07-25T07:38:49Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"df4902f854ad76769d3203bfdc69f16c","file_name":"2022_PLoSBiology_Zhao.pdf","file_size":3721585,"date_updated":"2022-07-25T07:38:49Z","file_id":"11643"}],"intvolume":"        20","language":[{"iso":"eng"}],"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z"}],"month":"06","isi":1,"day":"21","ddc":["570"],"pmid":1,"oa_version":"Published Version","date_created":"2022-07-24T22:01:42Z","publisher":"Public Library of Science","department":[{"_id":"MaDe"}],"title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","publication":"PLoS Biology","abstract":[{"lang":"eng","text":"The ability to detect and respond to acute oxygen (O2) shortages is indispensable to aerobic life. The molecular mechanisms and circuits underlying this capacity are poorly understood. Here, we characterize the behavioral responses of feeding Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of turning maneuvers followed by a persistent switch to rapid forward movement as animals seek to avoid and escape hypoxia. While the behavioral responses to 1% O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome function inhibits escape from 1% O2 due to increased cGMP signaling. A primary source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP) receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+ decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial complex I (MCIII), which lead to persistently high reactive oxygen species (ROS), abrogate acute hypoxia responses. In particular, repressing the expression of isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1% O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia responses. Our results implicate ROS and precise regulation of intracellular cGMP in the modulation of acute responses to hypoxia by C. elegans."}],"year":"2022","has_accepted_license":"1","_id":"11637","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":20,"publication_identifier":{"eissn":["1545-7885"]},"citation":{"chicago":"Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>.","ieee":"L. Zhao <i>et al.</i>, “ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans,” <i>PLoS Biology</i>, vol. 20, no. 6. Public Library of Science, 2022.","apa":"Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono, M., &#38; Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>","ama":"Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. 2022;20(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>","short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","mla":"Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>, vol. 20, no. 6, e3001684, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>.","ista":"Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C. 2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 20(6), e3001684."},"article_type":"original","external_id":{"pmid":["35727855"],"isi":["000828679600001"]},"issue":"6","status":"public","acknowledgement":" This work was funded by H2020 European Research Council (ERC Advanced grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0) to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","oa":1},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":4,"has_accepted_license":"1","year":"2022","_id":"11638","external_id":{"arxiv":["2106.02349"]},"article_type":"original","issue":"2","acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","status":"public","oa":1,"publication_identifier":{"issn":["2643-1564"]},"citation":{"apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>"},"funded_apc":"1","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"title":"Inferring couplings in networks across order-disorder phase transitions","publication":"Physical Review Research","oa_version":"Published Version","date_created":"2022-07-24T22:01:42Z","arxiv":1,"abstract":[{"text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data.","lang":"eng"}],"publication_status":"published","file":[{"date_updated":"2022-07-25T07:47:23Z","file_id":"11644","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","file_size":1379683,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2022-07-25T07:47:23Z","success":1,"content_type":"application/pdf"}],"intvolume":"         4","day":"24","ddc":["530"],"language":[{"iso":"eng"}],"month":"06","article_number":"023240","file_date_updated":"2022-07-25T07:47:23Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2022-07-25T07:52:35Z","doi":"10.1103/PhysRevResearch.4.023240","article_processing_charge":"No","author":[{"full_name":"Ngampruetikorn, Vudtiwat","first_name":"Vudtiwat","last_name":"Ngampruetikorn"},{"full_name":"Sachdeva, Vedant","first_name":"Vedant","last_name":"Sachdeva"},{"full_name":"Torrence, Johanna","first_name":"Johanna","last_name":"Torrence"},{"first_name":"Jan","last_name":"Humplik","full_name":"Humplik, Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwab","first_name":"David J.","full_name":"Schwab, David J."},{"full_name":"Palmer, Stephanie E.","last_name":"Palmer","first_name":"Stephanie E."}],"date_published":"2022-06-24T00:00:00Z","quality_controlled":"1","scopus_import":"1"},{"_id":"11639","year":"2022","page":"7753-7786","volume":68,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Zhang, Y., &#38; Vatedka, S. (2022). List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>","ieee":"Y. Zhang and S. Vatedka, “List decoding random Euclidean codes and Infinite constellations,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12. IEEE, pp. 7753–7786, 2022.","chicago":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.","mla":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12, IEEE, 2022, pp. 7753–86, doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>.","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","ama":"Zhang Y, Vatedka S. List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. 2022;68(12):7753-7786. doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>"},"publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"acknowledgement":"This work was done when Shashank Vatedka was at the Chinese University of Hong Kong, where he was supported in part by CUHK Direct Grants 4055039 and 4055077. He would like to acknowledge funding from a seed grant offered by IIT Hyderabad and the Start-up Research Grant (SRG/2020/000910) from the Science and Engineering Board, India. Yihan Zhang has received funding from the European Union’s Horizon 2020 research and innovation programme\r\nunder grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","status":"public","oa":1,"article_type":"original","external_id":{"arxiv":["1901.03790"],"isi":["000891796100007"]},"issue":"12","oa_version":"Preprint","date_created":"2022-07-24T22:01:42Z","title":"List decoding random Euclidean codes and Infinite constellations","department":[{"_id":"MaMo"}],"publication":"IEEE Transactions on Information Theory","publisher":"IEEE","abstract":[{"text":"We study the list decodability of different ensembles of codes over the real alphabet under the assumption of an omniscient adversary. It is a well-known result that when the source and the adversary have power constraints P and N respectively, the list decoding capacity is equal to 1/2logP/N. Random spherical codes achieve constant list sizes, and the goal of the present paper is to obtain a better understanding of the smallest achievable list size as a function of the gap to capacity. We show a reduction from arbitrary codes to spherical codes, and derive a lower bound on the list size of typical random spherical codes. We also give an upper bound on the list size achievable using nested Construction-A lattices and infinite Construction-A lattices. We then define and study a class of infinite constellations that generalize Construction-A lattices and prove upper and lower bounds for the same. Other goodness properties such as packing goodness and AWGN goodness of infinite constellations are proved along the way. Finally, we consider random lattices sampled from the Haar distribution and show that if a certain conjecture that originates in analytic number theory is true, then the list size grows as a polynomial function of the gap-to-capacity.","lang":"eng"}],"arxiv":1,"intvolume":"        68","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1901.03790","open_access":"1"}],"publication_status":"published","language":[{"iso":"eng"}],"isi":1,"month":"12","day":"01","scopus_import":"1","quality_controlled":"1","date_published":"2022-12-01T00:00:00Z","author":[{"last_name":"Zhang","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan"},{"full_name":"Vatedka, Shashank","last_name":"Vatedka","first_name":"Shashank"}],"date_updated":"2023-08-03T12:12:19Z","doi":"10.1109/TIT.2022.3189542","article_processing_charge":"No"},{"publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2023-02-02T08:11:23Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":6431779,"file_name":"2022_MolecularEcologyRes_Szep.pdf","checksum":"3102e203e77b884bffffdbe8e548da88","date_updated":"2023-02-02T08:11:23Z","file_id":"12477"}],"intvolume":"        22","license":"https://creativecommons.org/licenses/by-nc/4.0/","language":[{"iso":"eng"}],"project":[{"_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172","name":"Rate of Adaptation in Changing Environment","call_identifier":"H2020"}],"isi":1,"month":"11","day":"01","ddc":["570"],"tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file_date_updated":"2023-02-02T08:11:23Z","quality_controlled":"1","scopus_import":"1","doi":"10.1111/1755-0998.13676","date_updated":"2023-08-03T12:11:01Z","article_processing_charge":"Yes (via OA deal)","date_published":"2022-11-01T00:00:00Z","author":[{"last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"},{"orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"},{"first_name":"Katalin","last_name":"Csilléry","full_name":"Csilléry, Katalin"}],"year":"2022","has_accepted_license":"1","_id":"11640","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"2941-2955","volume":22,"publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"citation":{"ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” <i>Molecular Ecology Resources</i>, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>.","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>","ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955. doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955.","mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955."},"external_id":{"isi":["000825873600001"]},"article_type":"original","issue":"8","acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich.","oa":1,"status":"public","oa_version":"Published Version","date_created":"2022-07-24T22:01:43Z","ec_funded":1,"publisher":"Wiley","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","department":[{"_id":"NiBa"}],"publication":"Molecular Ecology Resources","abstract":[{"text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.","lang":"eng"}]},{"oa":1,"status":"public","acknowledgement":"Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266 to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows (20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer project and also would like to thank Hideki Shigematsu for critical reading of the manuscript. And we are indebted to the two anonymous reviewers who helped us to improve our manuscript.","article_type":"original","external_id":{"isi":["000837950900001"],"pmid":["35861182"]},"issue":"5","citation":{"ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. 2022;71(5):249-261. doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>","mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>.","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","ieee":"C. Gerle <i>et al.</i>, “Structures of multisubunit membrane complexes with the CRYO ARM 200,” <i>Microscopy</i>, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022.","chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>.","apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>"},"publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"page":"249-261","volume":71,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11648","year":"2022","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Progress in structural membrane biology has been significantly accelerated by the ongoing 'Resolution Revolution' in cryo electron microscopy (cryo-EM). In particular, structure determination by single particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella enterica."}],"department":[{"_id":"LeSa"}],"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","publication":"Microscopy","publisher":"Oxford University Press","oa_version":"Published Version","date_created":"2022-07-25T10:04:58Z","pmid":1,"day":"01","ddc":["570"],"language":[{"iso":"eng"}],"month":"10","isi":1,"intvolume":"        71","publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2023-02-03T08:34:48Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":7812696,"file_name":"2022_Microscopy_Gerle.pdf","checksum":"23b51c163636bf9313f7f0818312e67e","file_id":"12498","date_updated":"2023-02-03T08:34:48Z"}],"date_published":"2022-10-01T00:00:00Z","author":[{"last_name":"Gerle","first_name":"Christoph","full_name":"Gerle, Christoph"},{"last_name":"Kishikawa","first_name":"Jun-ichi","full_name":"Kishikawa, Jun-ichi"},{"full_name":"Yamaguchi, Tomoko","last_name":"Yamaguchi","first_name":"Tomoko"},{"first_name":"Atsuko","last_name":"Nakanishi","full_name":"Nakanishi, Atsuko"},{"first_name":"Mehmet Orkun","orcid":"0000-0002-3219-2022","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"full_name":"Makino, Fumiaki","first_name":"Fumiaki","last_name":"Makino"},{"first_name":"Tomoko","last_name":"Miyata","full_name":"Miyata, Tomoko"},{"full_name":"Kawamoto, Akihiro","last_name":"Kawamoto","first_name":"Akihiro"},{"first_name":"Ken","last_name":"Yokoyama","full_name":"Yokoyama, Ken"},{"full_name":"Namba, Keiichi","last_name":"Namba","first_name":"Keiichi"},{"last_name":"Kurisu","first_name":"Genji","full_name":"Kurisu, Genji"},{"full_name":"Kato, Takayuki","first_name":"Takayuki","last_name":"Kato"}],"date_updated":"2023-08-03T12:13:37Z","doi":"10.1093/jmicro/dfac037","article_processing_charge":"No","scopus_import":"1","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"quality_controlled":"1","file_date_updated":"2023-02-03T08:34:48Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","contributor":[{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","first_name":"Vincent K"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","first_name":"Andrea"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sax","first_name":"Luca"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"first_name":"Francisco","last_name":"Hontoria "},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"_id":"11653","year":"2022","file":[{"file_size":2209382998,"checksum":"5f1d7c6d7ab5375ed2564521432bed0c","file_name":"Data.zip","date_updated":"2022-08-08T22:30:04Z","file_id":"11655","embargo":"2022-08-07","content_type":"application/x-zip-compressed","date_created":"2022-07-26T12:37:52Z","relation":"main_file","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","access_level":"open_access","creator":"melkrewi","title":"Supplementary Datasets"}],"has_accepted_license":"1","oa":1,"status":"public","ddc":["570"],"day":"05","citation":{"ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","short":"M.N. Elkrewi, (2022).","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>."},"month":"08","file_date_updated":"2022-08-08T22:30:04Z","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","date_created":"2022-07-26T11:01:47Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2022-08-05T00:00:00Z","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","first_name":"Marwan N"}],"article_processing_charge":"No","date_updated":"2024-02-21T12:35:53Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12248"}]},"doi":"10.15479/AT:ISTA:11653","abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}]},{"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"language":[{"iso":"eng"}],"month":"07","day":"27","ddc":["510"],"publication_status":"submitted","file":[{"content_type":"application/pdf","date_created":"2022-07-27T09:25:53Z","relation":"main_file","creator":"scultrer","access_level":"open_access","file_size":639266,"file_name":"D-S-E.pdf","checksum":"b2f511e8b1cae5f1892b0cdec341acac","date_updated":"2022-07-27T09:25:53Z","file_id":"11659"}],"quality_controlled":"1","date_updated":"2022-07-28T07:57:48Z","article_processing_charge":"No","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","first_name":"Ranita"},{"full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832"},{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","last_name":"Saghafian"}],"date_published":"2022-07-27T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-07-27T09:25:53Z","citation":{"ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>.","mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>, Schloss Dagstuhl - Leibniz Zentrum für Informatik.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik, n.d.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik."},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","status":"public","oa":1,"year":"2022","has_accepted_license":"1","_id":"11658","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"date_created":"2022-07-27T09:27:34Z","publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","publication":"Leibniz International Proceedings on Mathematics"},{"publication_status":"submitted","file":[{"content_type":"application/pdf","date_created":"2022-07-27T09:30:30Z","relation":"main_file","access_level":"open_access","creator":"scultrer","file_size":564836,"file_name":"window 1.pdf","checksum":"95903f9d1649e8e437a967b6f2f64730","date_updated":"2022-07-27T09:30:30Z","file_id":"11661"}],"day":"25","ddc":["510"],"project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00342"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"month":"07","file_date_updated":"2022-07-27T09:30:30Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas"},{"orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Saghafian, Morteza","first_name":"Morteza","last_name":"Saghafian"}],"date_published":"2022-07-25T00:00:00Z","alternative_title":["LIPIcs"],"date_updated":"2022-07-28T08:05:34Z","article_processing_charge":"No","quality_controlled":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11660","year":"2022","has_accepted_license":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. ","oa":1,"status":"public","citation":{"ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>.","mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs."},"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","publication":"LIPIcs","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa_version":"Submitted Version","ec_funded":1,"date_created":"2022-07-27T09:31:15Z","abstract":[{"lang":"eng","text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. "}]},{"title":"Constant-time Dynamic (Δ +1)-Coloring","publication":"ACM Transactions on Algorithms","publisher":"Association for Computing Machinery (ACM)","oa_version":"None","date_created":"2022-07-27T10:58:53Z","abstract":[{"text":"We give a fully dynamic (Las-Vegas style) algorithm with constant expected amortized time per update that maintains a proper (Δ +1)-vertex coloring of a graph with maximum degree at most Δ. This improves upon the previous O(log Δ)-time algorithm by Bhattacharya et al. (SODA 2018). Our algorithm uses an approach based on assigning random ranks to vertices and does not need to maintain a hierarchical graph decomposition. We show that our result does not only have optimal running time but is also optimal in the sense that already deciding whether a Δ-coloring exists in a dynamically changing graph with maximum degree at most Δ takes Ω (log n) time per operation.","lang":"eng"}],"extern":"1","volume":18,"type":"journal_article","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11662","year":"2022","status":"public","acknowledgement":"We want to thank an anonymous referee who pointed out a mistake in our conference paper as well as suggesting a fix using an approach in References.","article_type":"original","issue":"2","citation":{"ista":"Henzinger MH, Peng P. 2022. Constant-time Dynamic (Δ +1)-Coloring. ACM Transactions on Algorithms. 18(2), 16.","mla":"Henzinger, Monika H., and Pan Peng. “Constant-Time Dynamic (Δ +1)-Coloring.” <i>ACM Transactions on Algorithms</i>, vol. 18, no. 2, 16, Association for Computing Machinery (ACM), 2022, doi:<a href=\"https://doi.org/10.1145/3501403\">10.1145/3501403</a>.","short":"M.H. Henzinger, P. Peng, ACM Transactions on Algorithms 18 (2022).","ama":"Henzinger MH, Peng P. Constant-time Dynamic (Δ +1)-Coloring. <i>ACM Transactions on Algorithms</i>. 2022;18(2). doi:<a href=\"https://doi.org/10.1145/3501403\">10.1145/3501403</a>","apa":"Henzinger, M. H., &#38; Peng, P. (2022). Constant-time Dynamic (Δ +1)-Coloring. <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery (ACM). <a href=\"https://doi.org/10.1145/3501403\">https://doi.org/10.1145/3501403</a>","ieee":"M. H. Henzinger and P. Peng, “Constant-time Dynamic (Δ +1)-Coloring,” <i>ACM Transactions on Algorithms</i>, vol. 18, no. 2. Association for Computing Machinery (ACM), 2022.","chicago":"Henzinger, Monika H, and Pan Peng. “Constant-Time Dynamic (Δ +1)-Coloring.” <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery (ACM), 2022. <a href=\"https://doi.org/10.1145/3501403\">https://doi.org/10.1145/3501403</a>."},"publication_identifier":{"eissn":["1549-6333"],"issn":["1549-6325"]},"article_number":"16","author":[{"first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Peng, Pan","last_name":"Peng","first_name":"Pan"}],"date_published":"2022-03-04T00:00:00Z","doi":"10.1145/3501403","date_updated":"2022-07-27T11:08:13Z","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","intvolume":"        18","publication_status":"published","day":"04","language":[{"iso":"eng"}],"month":"03"},{"article_processing_charge":"No","related_material":{"record":[{"id":"10604","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-08-02T13:50:08Z","doi":"10.25338/B81931","date_published":"2022-01-06T00:00:00Z","author":[{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"keyword":["Biological sciences"],"abstract":[{"lang":"eng","text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes."}],"publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","date_created":"2022-07-29T06:45:41Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","ddc":["570"],"day":"06","oa":1,"status":"public","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","month":"01","citation":{"chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>.","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","apa":"Turelli, M., &#38; Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>","ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, <a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","mla":"Turelli, Michael, and Nicholas H. Barton. <i>Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","short":"M. Turelli, N.H. Barton, (2022)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","license":"https://creativecommons.org/publicdomain/zero/1.0/","year":"2022","_id":"11686","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}]},{"month":"05","citation":{"ama":"Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>","mla":"Parvizian, Mahsa, et al. <i>Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.”</i> Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","ista":"Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","short":"M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022).","ieee":"M. Parvizian <i>et al.</i>, “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022.","chicago":"Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>.","apa":"Parvizian, M., Duran Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van den Eynden, D., … De Roo, J. (2022). Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>"},"ddc":["540"],"day":"12","status":"public","oa":1,"year":"2022","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6542908"}],"_id":"11695","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","abstract":[{"text":"Data underlying the figures in the publication \"The chemistry of Cu3N and Cu3PdN nanocrystals\" ","lang":"eng"}],"article_processing_charge":"No","doi":"10.5281/ZENODO.6542908","related_material":{"record":[{"id":"11451","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-08-03T07:19:12Z","author":[{"full_name":"Parvizian, Mahsa","first_name":"Mahsa","last_name":"Parvizian"},{"full_name":"Duran Balsa, Alejandra","last_name":"Duran Balsa","first_name":"Alejandra"},{"first_name":"Rohan","last_name":"Pokratath","full_name":"Pokratath, Rohan"},{"first_name":"Curran","last_name":"Kalha","full_name":"Kalha, Curran"},{"last_name":"Lee","first_name":"Seungho","full_name":"Lee, Seungho"},{"first_name":"Dietger","last_name":"Van den Eynden","full_name":"Van den Eynden, Dietger"},{"first_name":"Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Regoutz","first_name":"Anna","full_name":"Regoutz, Anna"},{"last_name":"De Roo","first_name":"Jonathan","full_name":"De Roo, Jonathan"}],"date_published":"2022-05-12T00:00:00Z","date_created":"2022-07-29T09:31:13Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Zenodo","department":[{"_id":"MaIb"}],"title":"Data for \"The chemistry of Cu3N and Cu3PdN nanocrystals\""},{"day":"01","isi":1,"month":"10","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.05677"}],"intvolume":"        17","publication_status":"published","date_published":"2022-10-01T00:00:00Z","author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"last_name":"Forkert","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","full_name":"Forkert, Dominik L"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan"},{"full_name":"Mugnolo, Delio","last_name":"Mugnolo","first_name":"Delio"}],"article_processing_charge":"No","date_updated":"2023-08-03T12:25:49Z","doi":"10.3934/nhm.2022023","scopus_import":"1","quality_controlled":"1","acknowledgement":"ME acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG), Grant SFB 1283/2 2021 – 317210226. DF and JM were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117). JM also acknowledges support by the Austrian Science Fund (FWF), Project SFB F65. The work of DM was partially supported by the Deutsche Forschungsgemeinschaft\r\n(DFG), Grant 397230547. This article is based upon work from COST Action\r\n18232 MAT-DYN-NET, supported by COST (European Cooperation in Science\r\nand Technology), www.cost.eu. We wish to thank Martin Burger and Jan-Frederik\r\nPietschmann for useful discussions. We are grateful to the anonymous referees for\r\ntheir careful reading and useful suggestions.","status":"public","oa":1,"issue":"5","article_type":"original","external_id":{"isi":["000812422100001"],"arxiv":["2105.05677"]},"citation":{"chicago":"Erbar, Matthias, Dominik L Forkert, Jan Maas, and Delio Mugnolo. “Gradient Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric Graph.” <i>Networks and Heterogeneous Media</i>. American Institute of Mathematical Sciences, 2022. <a href=\"https://doi.org/10.3934/nhm.2022023\">https://doi.org/10.3934/nhm.2022023</a>.","ieee":"M. Erbar, D. L. Forkert, J. Maas, and D. Mugnolo, “Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph,” <i>Networks and Heterogeneous Media</i>, vol. 17, no. 5. American Institute of Mathematical Sciences, pp. 687–717, 2022.","apa":"Erbar, M., Forkert, D. L., Maas, J., &#38; Mugnolo, D. (2022). Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. <i>Networks and Heterogeneous Media</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/nhm.2022023\">https://doi.org/10.3934/nhm.2022023</a>","ama":"Erbar M, Forkert DL, Maas J, Mugnolo D. Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. <i>Networks and Heterogeneous Media</i>. 2022;17(5):687-717. doi:<a href=\"https://doi.org/10.3934/nhm.2022023\">10.3934/nhm.2022023</a>","short":"M. Erbar, D.L. Forkert, J. Maas, D. Mugnolo, Networks and Heterogeneous Media 17 (2022) 687–717.","ista":"Erbar M, Forkert DL, Maas J, Mugnolo D. 2022. Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. Networks and Heterogeneous Media. 17(5), 687–717.","mla":"Erbar, Matthias, et al. “Gradient Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric Graph.” <i>Networks and Heterogeneous Media</i>, vol. 17, no. 5, American Institute of Mathematical Sciences, 2022, pp. 687–717, doi:<a href=\"https://doi.org/10.3934/nhm.2022023\">10.3934/nhm.2022023</a>."},"publication_identifier":{"issn":["1556-1801"],"eissn":["1556-181X"]},"volume":17,"page":"687-717","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"11700","year":"2022","arxiv":1,"abstract":[{"lang":"eng","text":"This paper contains two contributions in the study of optimal transport on metric graphs. Firstly, we prove a Benamou–Brenier formula for the Wasserstein distance, which establishes the equivalence of static and dynamical optimal transport. Secondly, in the spirit of Jordan–Kinderlehrer–Otto, we show that McKean–Vlasov equations can be formulated as gradient flow of the free energy in the Wasserstein space of probability measures. The proofs of these results are based on careful regularisation arguments to circumvent some of the difficulties arising in metric graphs, namely, branching of geodesics and the failure of semi-convexity of entropy functionals in the Wasserstein space."}],"publication":"Networks and Heterogeneous Media","title":"Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph","department":[{"_id":"JaMa"}],"publisher":"American Institute of Mathematical Sciences","date_created":"2022-07-31T22:01:46Z","ec_funded":1,"oa_version":"Preprint"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"file_date_updated":"2022-08-01T10:39:36Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","doi":"10.1088/1361-6544/abd613","date_updated":"2023-08-03T12:25:08Z","author":[{"first_name":"Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti","full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"date_published":"2022-08-04T00:00:00Z","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2022-08-01T10:39:36Z","success":1,"date_updated":"2022-08-01T10:39:36Z","file_id":"11715","file_size":2122096,"checksum":"997a4bff2dfbee3321d081328c2f1e1a","file_name":"2022_Nonlinearity_Agresti.pdf"}],"publication_status":"published","intvolume":"        35","license":"https://creativecommons.org/licenses/by/3.0/","month":"08","isi":1,"language":[{"iso":"eng"}],"ddc":["510"],"day":"04","date_created":"2022-07-31T22:01:47Z","oa_version":"Published Version","publisher":"IOP Publishing","publication":"Nonlinearity","department":[{"_id":"JuFi"}],"title":"Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence","abstract":[{"lang":"eng","text":"In this paper we develop a new approach to nonlinear stochastic partial differential equations with Gaussian noise. Our aim is to provide an abstract framework which is applicable to a large class of SPDEs and includes many important cases of nonlinear parabolic problems which are of quasi- or semilinear type. This first part is on local existence and well-posedness. A second part in preparation is on blow-up criteria and regularization. Our theory is formulated in an Lp-setting, and because of this we can deal with nonlinearities in a very efficient way. Applications to several concrete problems and their quasilinear variants are given. This includes Burgers' equation, the Allen–Cahn equation, the Cahn–Hilliard equation, reaction–diffusion equations, and the porous media equation. The interplay of the nonlinearities and the critical spaces of initial data leads to new results and insights for these SPDEs. The proofs are based on recent developments in maximal regularity theory for the linearized problem for deterministic and stochastic evolution equations. In particular, our theory can be seen as a stochastic version of the theory of critical spaces due to Prüss–Simonett–Wilke (2018). Sharp weighted time-regularity allow us to deal with rough initial values and obtain instantaneous regularization results. The abstract well-posedness results are obtained by a combination of several sophisticated splitting and truncation arguments."}],"arxiv":1,"has_accepted_license":"1","year":"2022","_id":"11701","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":35,"page":"4100-4210","publication_identifier":{"eissn":["1361-6544"],"issn":["0951-7715"]},"citation":{"ama":"Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. <i>Nonlinearity</i>. 2022;35(8):4100-4210. doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>","mla":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>, vol. 35, no. 8, IOP Publishing, 2022, pp. 4100–210, doi:<a href=\"https://doi.org/10.1088/1361-6544/abd613\">10.1088/1361-6544/abd613</a>.","ista":"Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. Nonlinearity. 35(8), 4100–4210.","short":"A. Agresti, M. Veraar, Nonlinearity 35 (2022) 4100–4210.","ieee":"A. Agresti and M. Veraar, “Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence,” <i>Nonlinearity</i>, vol. 35, no. 8. IOP Publishing, pp. 4100–4210, 2022.","chicago":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part I. Stochastic Maximal Regularity and Local Existence.” <i>Nonlinearity</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-6544/abd613\">https://doi.org/10.1088/1361-6544/abd613</a>.","apa":"Agresti, A., &#38; Veraar, M. (2022). Nonlinear parabolic stochastic evolution equations in critical spaces Part I. Stochastic maximal regularity and local existence. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6544/abd613\">https://doi.org/10.1088/1361-6544/abd613</a>"},"issue":"8","external_id":{"arxiv":["2001.00512"],"isi":["000826695900001"]},"article_type":"original","oa":1,"status":"public","acknowledgement":"The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO)."},{"quality_controlled":"1","scopus_import":"1","date_updated":"2022-08-01T11:00:25Z","doi":"10.1073/pnas.2122147119","article_processing_charge":"No","date_published":"2022-07-18T00:00:00Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e2122147119","file_date_updated":"2022-08-01T10:58:28Z","language":[{"iso":"eng"}],"month":"07","day":"18","ddc":["570"],"pmid":1,"publication_status":"published","file":[{"date_created":"2022-08-01T10:58:28Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"06c866196a8957f0c37b8a121771c885","file_name":"2022_PNAS_Barton.pdf","file_size":848511,"date_updated":"2022-08-01T10:58:28Z","file_id":"11716"}],"intvolume":"       119","abstract":[{"text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.","lang":"eng"}],"oa_version":"Published Version","date_created":"2022-07-31T22:01:47Z","publisher":"Proceedings of the National Academy of Sciences","title":"The \"New Synthesis\"","department":[{"_id":"NiBa"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"mla":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30, e2122147119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>.","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ama":"Barton NH. The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(30). doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>","apa":"Barton, N. H. (2022). The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","ieee":"N. H. Barton, “The ‘New Synthesis,’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30. Proceedings of the National Academy of Sciences, 2022."},"external_id":{"pmid":["35858408"]},"article_type":"original","issue":"30","oa":1,"status":"public","acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","year":"2022","has_accepted_license":"1","_id":"11702","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":119},{"file":[{"checksum":"aa4c137f82635e700856c359dccfaa0a","file_name":"2022_PLoSGenetics_Toups.pdf","file_size":1620272,"date_updated":"2022-08-01T07:49:25Z","file_id":"11708","date_created":"2022-08-01T07:49:25Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"publication_status":"published","intvolume":"        18","isi":1,"month":"07","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"day":"06","pmid":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e1010226","file_date_updated":"2022-08-01T07:49:25Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","doi":"10.1371/journal.pgen.1010226","date_updated":"2023-08-03T12:17:12Z","date_published":"2022-07-06T00:00:00Z","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"},{"full_name":"Pannell, John R.","last_name":"Pannell","first_name":"John R."}],"year":"2022","has_accepted_license":"1","_id":"11703","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":18,"publication_identifier":{"eissn":["1553-7404"]},"citation":{"chicago":"Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>.","ieee":"M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis,” <i>PLoS Genetics</i>, vol. 18, no. 7. Public Library of Science, 2022.","apa":"Toups, M. A., Vicoso, B., &#38; Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>","ama":"Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. 2022;18(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>","ista":"Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226.","mla":"Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>.","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022)."},"issue":"7","article_type":"original","external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"oa":1,"acknowledgement":"JRP was supported by the Swiss National Science Foundation (https://www.snf.ch/en), Sinergia grant 26073998. BV was supported by the European Research Council (https://erc.europa.eu/) under the European Union’s Horizon 2020 research and innovation program, grant number 715257. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nPlants were grown in Lausanne by Aline Revel, and RNA extraction and library preparation were performed by Dessislava Savova Bianchi. All sequencing and the IsoSeq3 analysis were carried out by Center for Integrative Genomics at the University of Lausanne. All other computational analyses were performed on the server at IST Austria.","status":"public","date_created":"2022-07-31T22:01:48Z","ec_funded":1,"oa_version":"Published Version","publisher":"Public Library of Science","publication":"PLoS Genetics","department":[{"_id":"BeVi"}],"title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","abstract":[{"text":"Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.","lang":"eng"}]},{"day":"18","ddc":["510"],"language":[{"iso":"eng"}],"isi":1,"month":"07","intvolume":"        17","publication_status":"published","file":[{"date_created":"2022-08-01T08:02:38Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"1ddd9b91e6dec31ab0e7a8433ca2d452","file_name":"2022_PLoSONE_Budanur.pdf","file_size":1421256,"file_id":"11712","date_updated":"2022-08-01T08:02:38Z"}],"author":[{"orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"date_published":"2022-07-18T00:00:00Z","date_updated":"2023-08-03T12:24:22Z","doi":"10.1371/journal.pone.0269975","related_material":{"record":[{"status":"public","relation":"research_data","id":"11711"}]},"article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","file_date_updated":"2022-08-01T08:02:38Z","article_number":"e0269975","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"status":"public","external_id":{"isi":["000911392100055"]},"article_type":"original","issue":"7","citation":{"ama":"Budanur NB, Hof B. An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. 2022;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>","mla":"Budanur, Nazmi B., and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>, vol. 17, no. 7, e0269975, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pone.0269975\">10.1371/journal.pone.0269975</a>.","short":"N.B. Budanur, B. Hof, PLoS ONE 17 (2022).","ista":"Budanur NB, Hof B. 2022. An autonomous compartmental model for accelerating epidemics. PLoS ONE. 17(7), e0269975.","ieee":"N. B. Budanur and B. Hof, “An autonomous compartmental model for accelerating epidemics,” <i>PLoS ONE</i>, vol. 17, no. 7. Public Library of Science, 2022.","chicago":"Budanur, Nazmi B, and Björn Hof. “An Autonomous Compartmental Model for Accelerating Epidemics.” <i>PLoS ONE</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>.","apa":"Budanur, N. B., &#38; Hof, B. (2022). An autonomous compartmental model for accelerating epidemics. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0269975\">https://doi.org/10.1371/journal.pone.0269975</a>"},"publication_identifier":{"eissn":["1932-6203"]},"volume":17,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11704","year":"2022","has_accepted_license":"1","abstract":[{"lang":"eng","text":"In Fall 2020, several European countries reported rapid increases in COVID-19 cases along with growing estimates of the effective reproduction rates. Such an acceleration in epidemic spread is usually attributed to time-dependent effects, e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc. In this case however the acceleration occurred when counter measures such as testing and contact tracing exceeded their capacity limit. Considering Austria as an example, here we show that this dynamics can be captured by a time-independent, i.e. autonomous, compartmental model that incorporates these capacity limits. In this model, the epidemic acceleration coincides with the exhaustion of mitigation efforts, resulting in an increasing fraction of undetected cases that drive the effective reproduction rate progressively higher. We demonstrate that standard models which does not include this effect necessarily result in a systematic underestimation of the effective reproduction rate."}],"department":[{"_id":"BjHo"}],"title":"An autonomous compartmental model for accelerating epidemics","publication":"PLoS ONE","publisher":"Public Library of Science","oa_version":"Published Version","date_created":"2022-07-31T22:01:48Z"},{"article_number":"e202207002","file_date_updated":"2023-02-02T08:01:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-03T12:23:52Z","doi":"10.1002/anie.202207002","article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0002-9515-4277","last_name":"Chang","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng"},{"full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","last_name":"Liu","orcid":"0000-0001-7313-6740"},{"last_name":"Lee","orcid":"0000-0002-6962-8598","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"last_name":"Spadaro","first_name":"Maria","full_name":"Spadaro, Maria"},{"full_name":"Koskela, Kristopher M.","last_name":"Koskela","first_name":"Kristopher M."},{"last_name":"Kleinhanns","first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","last_name":"Costanzo","orcid":"0000-0001-9732-3815","first_name":"Tommaso"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Brutchey, Richard L.","first_name":"Richard L.","last_name":"Brutchey"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria"}],"date_published":"2022-08-26T00:00:00Z","quality_controlled":"1","scopus_import":"1","publication_status":"published","file":[{"checksum":"ad601f2b9e26e46ab4785162be58b5ed","file_name":"2022_AngewandteChemieInternat_Chang.pdf","file_size":4072650,"file_id":"12476","date_updated":"2023-02-02T08:01:00Z","date_created":"2023-02-02T08:01:00Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"intvolume":"        61","day":"26","ddc":["540"],"project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"08","isi":1,"publisher":"Wiley","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","publication":"Angewandte Chemie - International Edition","oa_version":"Published Version","date_created":"2022-07-31T22:01:48Z","ec_funded":1,"abstract":[{"text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe.","lang":"eng"}],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":61,"year":"2022","has_accepted_license":"1","_id":"11705","external_id":{"isi":["000828274200001"]},"article_type":"original","issue":"35","oa":1,"status":"public","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"citation":{"ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. 2022;61(35). doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002.","short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35, e202207002, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207002\">10.1002/anie.202207002</a>.","ieee":"C. Chang <i>et al.</i>, “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 35. Wiley, 2022.","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>.","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207002\">https://doi.org/10.1002/anie.202207002</a>"}}]