[{"article_processing_charge":"Yes","APC_amount":"804 EUR","file_date_updated":"2025-01-09T12:16:53Z","has_accepted_license":"1","quality_controlled":"1","article_type":"original","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","corr_author":"1","type":"journal_article","doi":"10.1016/j.xpro.2024.103168","publication_status":"published","pmid":1,"publication_identifier":{"eissn":["2666-1667"]},"article_number":"103168","intvolume":"         5","OA_type":"gold","_id":"17232","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"3","year":"2024","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"external_id":{"pmid":["38968076"]},"publication":"STAR Protocols","file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2024_STARProtoc_Cheung2.pdf","file_id":"18810","creator":"dernst","file_size":6445556,"date_updated":"2025-01-09T12:16:53Z","checksum":"464f52ecc6ec92f509552823bb82bf79","success":1,"date_created":"2025-01-09T12:16:53Z","access_level":"open_access"}],"acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","scopus_import":"1","date_published":"2024-09-20T00:00:00Z","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-30T10:54:12Z","volume":5,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","ddc":["570"],"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1"}],"language":[{"iso":"eng"}],"department":[{"_id":"SiHi"},{"_id":"PreCl"}],"oa":1,"day":"20","date_created":"2024-07-14T22:01:10Z","citation":{"ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024)."},"publisher":"Elsevier","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian"},{"full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","first_name":"Peter"},{"last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}]},{"file":[{"checksum":"c8671c0ad483da6407cb16cc3fef1990","access_level":"open_access","success":1,"date_created":"2024-07-16T06:16:11Z","file_id":"17242","creator":"dernst","file_size":2896048,"date_updated":"2024-07-16T06:16:11Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_BioProtocol_Li.pdf"}],"publication":"Bio-protocol","external_id":{"pmid":["39007160"]},"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","date_published":"2024-07-05T00:00:00Z","scopus_import":"1","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING to E.M.B.).","oa_version":"Published Version","ddc":["570"],"title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","date_updated":"2025-03-06T10:28:18Z","volume":14,"citation":{"apa":"LI, Z., Huard, J., Bayer, E. M., &#38; Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-Protocol</i>. Bio-Protocol. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>","ieee":"Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” <i>Bio-protocol</i>, vol. 14, no. 13. Bio-Protocol, 2024.","mla":"LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>.","ista":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. 2024. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 14(13), e5029.","chicago":"LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>. Bio-Protocol, 2024. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>.","ama":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-protocol</i>. 2024;14(13). doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>","short":"Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024)."},"publisher":"Bio-Protocol","author":[{"first_name":"Ziqiang","last_name":"Li","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","full_name":"Li, Ziqiang"},{"first_name":"Jennifer","last_name":"Huard","full_name":"Huard, Jennifer"},{"full_name":"Bayer, Emmanuelle M.","first_name":"Emmanuelle M.","last_name":"Bayer"},{"full_name":"Wattelet-Boyer, Valérie","last_name":"Wattelet-Boyer","first_name":"Valérie"}],"date_created":"2024-07-14T22:01:11Z","day":"05","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"abstract":[{"lang":"eng","text":"CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene."}],"quality_controlled":"1","has_accepted_license":"1","file_date_updated":"2024-07-16T06:16:11Z","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.21769/BioProtoc.5029","article_type":"original","publication_status":"published","doi":"10.21769/BioProtoc.5029","type":"journal_article","issue":"13","license":"https://creativecommons.org/licenses/by/4.0/","_id":"17233","intvolume":"        14","article_number":"e5029","publication_identifier":{"eissn":["2331-8325"]},"pmid":1},{"publication_status":"published","doi":"10.3847/2041-8213/ad55f7","type":"journal_article","issue":"1","_id":"17234","article_number":"L13","intvolume":"       969","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"quality_controlled":"1","has_accepted_license":"1","file_date_updated":"2024-07-16T06:24:29Z","article_processing_charge":"Yes","isi":1,"DOAJ_listed":"1","fulldoi":"https://doi.org/10.3847/2041-8213/ad55f7","article_type":"original","oa_version":"Published Version","ddc":["520"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec","status":"public","volume":969,"date_updated":"2025-09-08T08:10:21Z","publisher":"IOP Publishing","citation":{"apa":"Wang, B., Leja, J., De Graaff, A., Brammer, G. B., Weibel, A., Van Dokkum, P., … Williams, C. C. (2024). RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>","ieee":"B. Wang <i>et al.</i>, “RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1. IOP Publishing, 2024.","ista":"Wang B, Leja J, De Graaff A, Brammer GB, Weibel A, Van Dokkum P, Baggen JFW, Suess KA, Greene JE, Bezanson R, Cleri NJ, Hirschmann M, Labbé I, Matthee JJ, Mcconachie I, Naidu RP, Nelson E, Oesch PA, Setton DJ, Williams CC. 2024. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 969(1), L13.","mla":"Wang, Bingjie, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1, L13, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>.","short":"B. Wang, J. Leja, A. De Graaff, G.B. Brammer, A. Weibel, P. Van Dokkum, J.F.W. Baggen, K.A. Suess, J.E. Greene, R. Bezanson, N.J. Cleri, M. Hirschmann, I. Labbé, J.J. Matthee, I. Mcconachie, R.P. Naidu, E. Nelson, P.A. Oesch, D.J. Setton, C.C. Williams, Astrophysical Journal Letters 969 (2024).","ama":"Wang B, Leja J, De Graaff A, et al. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. <i>Astrophysical Journal Letters</i>. 2024;969(1). doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>","chicago":"Wang, Bingjie, Joel Leja, Anna De Graaff, Gabriel B. Brammer, Andrea Weibel, Pieter Van Dokkum, Josephine F.W. Baggen, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” <i>Astrophysical Journal Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>."},"author":[{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"full_name":"De Graaff, Anna","first_name":"Anna","last_name":"De Graaff"},{"full_name":"Brammer, Gabriel B.","last_name":"Brammer","first_name":"Gabriel B."},{"full_name":"Weibel, Andrea","last_name":"Weibel","first_name":"Andrea"},{"first_name":"Pieter","last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter"},{"full_name":"Baggen, Josephine F.W.","last_name":"Baggen","first_name":"Josephine F.W."},{"first_name":"Katherine A.","last_name":"Suess","full_name":"Suess, Katherine A."},{"full_name":"Greene, Jenny E.","first_name":"Jenny E.","last_name":"Greene"},{"full_name":"Bezanson, Rachel","first_name":"Rachel","last_name":"Bezanson"},{"first_name":"Nikko J.","last_name":"Cleri","full_name":"Cleri, Nikko J."},{"first_name":"Michaela","last_name":"Hirschmann","full_name":"Hirschmann, Michaela"},{"first_name":"Ivo","last_name":"Labbé","full_name":"Labbé, Ivo"},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"},{"first_name":"Ian","last_name":"Mcconachie","full_name":"Mcconachie, Ian"},{"last_name":"Naidu","first_name":"Rohan P.","full_name":"Naidu, Rohan P."},{"full_name":"Nelson, Erica","first_name":"Erica","last_name":"Nelson"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"last_name":"Setton","first_name":"David J.","full_name":"Setton, David J."},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."}],"date_created":"2024-07-14T22:01:11Z","day":"01","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"JoMa"}],"abstract":[{"lang":"eng","text":"The identification of red, apparently massive galaxies at z > 7 in early James Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line compared to standard models of galaxy growth. A major uncertainty in the interpretation is whether the red colors are caused by evolved stellar populations, dust, or other effects such as emission lines or active galactic nuclei (AGNs). Here we show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4 μm and require formation histories extending hundreds of millions of years into the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies also show broad Balmer lines, with Hβ FWHM > 2500 km s−1, suggesting that dust-reddened AGNs contribute to, or even dominate, the spectral energy distributions of these galaxies at λrest ≳ 0.6 μm. All three galaxies have relatively narrow [O iii] lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically relaxed, inclined disks. Yet the inferred masses also remain highly uncertain. We model the high-quality spectra using Prospector to decompose the continuum into stellar and AGN components and explore limiting cases in stellar/AGN contribution. This produces a wide range of possible stellar masses, spanning M⋆ ∼ 109−1011M⊙. Nevertheless, all fits suggest a very early and rapid formation, most of which follow with a truncation in star formation. Potential origins and evolutionary tracks for these objects are discussed, from the cores of massive galaxies to low-mass galaxies with overmassive black holes. Intriguingly, we find all of these explanations to be incomplete; deeper and redder data are needed to understand the physics of these systems."}],"file":[{"file_size":3273303,"date_updated":"2024-07-16T06:24:29Z","creator":"dernst","file_id":"17243","file_name":"2024_AstrophysicalJourn_Wang.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2024-07-16T06:24:29Z","success":1,"access_level":"open_access","checksum":"bb1a6725586df12e745d091b5778bb2b"}],"publication":"Astrophysical Journal Letters","external_id":{"arxiv":["2405.01473"],"isi":["001257903200001"]},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","date_published":"2024-07-01T00:00:00Z","arxiv":1,"scopus_import":"1","acknowledgement":"We thank the anonymous referee for the helpful comments. B.W. and J.L. acknowledge support from JWST-GO04233.009-A. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project No. 562 (First Light at Cosmic Dawn: Exploiting the James Webb Space Telescope Revolution). This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The JWST data presented in this Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed can be accessed via doi:10.17909/3a4n-9p88. Computations for this research were performed on the Pennsylvania State University’s Institute for Computational and Data Sciences’ Roar supercomputer. This publication made use of the NASA Astrophysical Data System for bibliographic information. \r\nFacilities: HST (ACS, WFC3), JWST (NIRCam, NIRSpec). Software: Astropy (Astropy Collaboration et al. 2013, 2018, 2022), dynesty (Speagle 2020), EAzY (Brammer et al. 2008),\r\nemcee (Foreman-Mackey et al. 2013), Matplotlib (Hunter 2007), msaexp (Brammer 2023b), msafit (de Graaff et al. 2024a), NumPy (Harris et al. 2020), Prospector (Johnson et al. 2021), Python-FSPS (Johnson et al. 2023)."},{"oa":1,"abstract":[{"text":"We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors.","lang":"eng"}],"department":[{"_id":"AnHi"}],"language":[{"iso":"eng"}],"citation":{"apa":"Kohopää, K., Ronzani, A., Jabdaraghi, R. N., Bera, A., Ribeiro, M., Hazra, D., … Kemppinen, A. (2024). Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>","ieee":"K. Kohopää <i>et al.</i>, “Effect of ion irradiation on superconducting thin films,” <i>APL Materials</i>, vol. 12, no. 7. AIP Publishing, 2024.","ama":"Kohopää K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. 2024;12(7). doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>","short":"K. Kohopää, A. Ronzani, R.N. Jabdaraghi, A. Bera, M. Ribeiro, D. Hazra, J.L. Senior, M. Prunnila, J. Govenius, J.S. Lehtinen, A. Kemppinen, APL Materials 12 (2024).","chicago":"Kohopää, Katja, Alberto Ronzani, Robab Najafi Jabdaraghi, Arijit Bera, Mário Ribeiro, Dibyendu Hazra, Jorden L Senior, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>.","mla":"Kohopää, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>.","ista":"Kohopää K, Ronzani A, Jabdaraghi RN, Bera A, Ribeiro M, Hazra D, Senior JL, Prunnila M, Govenius J, Lehtinen JS, Kemppinen A. 2024. Effect of ion irradiation on superconducting thin films. APL Materials. 12(7), 071101."},"publisher":"AIP Publishing","author":[{"first_name":"Katja","last_name":"Kohopää","full_name":"Kohopää, Katja"},{"full_name":"Ronzani, Alberto","first_name":"Alberto","last_name":"Ronzani"},{"first_name":"Robab Najafi","last_name":"Jabdaraghi","full_name":"Jabdaraghi, Robab Najafi"},{"first_name":"Arijit","last_name":"Bera","full_name":"Bera, Arijit"},{"full_name":"Ribeiro, Mário","last_name":"Ribeiro","first_name":"Mário"},{"first_name":"Dibyendu","last_name":"Hazra","full_name":"Hazra, Dibyendu"},{"last_name":"Senior","first_name":"Jorden L","orcid":"0000-0002-0672-9295","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L"},{"full_name":"Prunnila, Mika","last_name":"Prunnila","first_name":"Mika"},{"first_name":"Joonas","last_name":"Govenius","full_name":"Govenius, Joonas"},{"first_name":"Janne S.","last_name":"Lehtinen","full_name":"Lehtinen, Janne S."},{"full_name":"Kemppinen, Antti","first_name":"Antti","last_name":"Kemppinen"}],"day":"01","date_created":"2024-07-14T22:01:11Z","title":"Effect of ion irradiation on superconducting thin films","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","date_updated":"2025-09-08T08:10:58Z","volume":12,"oa_version":"Published Version","ddc":["530"],"acknowledged_ssus":[{"_id":"EM-Fac"}],"scopus_import":"1","acknowledgement":"We thank J. A. Sauls for useful discussions. For funding of our research project, we acknowledge the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement Nos. 862660/Quantum e-leaps, 899558/aCryComm, 766853/EFINED, and ECSEL programme 101007322/MatQu. This project has also received funding from Business Finland through Quantum Technologies Industrial (QuTI) Project No. 128291 and from Research Council of Finland through Grant Nos. 310909, 350220 and Finnish Quantum Flagship project 359284. This work was performed as part of the Research Council of Finland Centres of Excellence program (Project Nos. 336817, 336819, 352934, and 352935). We also acknowledge funding from an internal strategic innovation project of VTT related to the development of quantum computing technologies. This research was supported by the Scientific Service Units of IST Austria through resources provided by Electron Microscopy Facility. J. Senior acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. Ronzani acknowledges funding from Research Council of Finland (Research Fellowship Project No. 356542).","month":"07","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","ec_funded":1,"file":[{"file_name":"2024_APLMaterial_Kohopaa.pdf","content_type":"application/pdf","relation":"main_file","file_size":9408198,"date_updated":"2024-07-16T06:30:30Z","file_id":"17244","creator":"dernst","success":1,"date_created":"2024-07-16T06:30:30Z","access_level":"open_access","checksum":"32a5cdf0ea9c937f806b6039f3219917"}],"publication":"APL Materials","external_id":{"isi":["001260942200003"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"publication_identifier":{"eissn":["2166-532X"]},"_id":"17235","issue":"7","intvolume":"        12","article_number":"071101","doi":"10.1063/5.0202851","type":"journal_article","publication_status":"published","article_type":"original","fulldoi":"https://doi.org/10.1063/5.0202851","isi":1,"article_processing_charge":"Yes","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2024-07-16T06:30:30Z"},{"quality_controlled":"1","has_accepted_license":"1","file_date_updated":"2024-07-16T06:38:08Z","article_processing_charge":"Yes (via OA deal)","isi":1,"corr_author":"1","fulldoi":"https://doi.org/10.1145/3626183.3659969","publication_status":"published","related_material":{"record":[{"status":"public","id":"21007","relation":"extended_version"}]},"doi":"10.1145/3626183.3659969","type":"conference","_id":"17236","OA_type":"hybrid","publication_identifier":{"isbn":["9798400704161"],"issn":["1548-6109"]},"publication":"Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2024_SPAA_Kolmogorov.pdf","creator":"dernst","file_id":"17245","date_updated":"2024-07-16T06:38:08Z","file_size":1116166,"checksum":"6ca18ac8508719dbd5d5735f4c991af2","access_level":"open_access","success":1,"date_created":"2024-07-16T06:38:08Z"}],"conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2024-06-17","end_date":"2024-06-21","location":"Nantes, France"},"external_id":{"isi":["001253331900044"],"arxiv":["2307.00115"]},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"403-414","month":"06","date_published":"2024-06-17T00:00:00Z","arxiv":1,"scopus_import":"1","oa_version":"Published Version","OA_place":"publisher","ddc":["510"],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut","date_updated":"2026-01-21T09:46:25Z","publisher":"Association for Computing Machinery","citation":{"ieee":"V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut,” in <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Nantes, France, 2024, pp. 403–414.","apa":"Kolmogorov, V. (2024). A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 403–414). Nantes, France: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>","ama":"Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In: <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2024:403-414. doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>","short":"V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–414.","chicago":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 403–14. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>.","mla":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2024, pp. 403–14, doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>.","ista":"Kolmogorov V. 2024. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 403–414."},"author":[{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-07-14T22:01:11Z","day":"17","oa":1,"department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain \"chaining\" algorithm that combines results of multiple calls to the maxflow algorithm.\r\nWe present an alternative approach that avoids solving the multicommodity flow problem and instead computes \"violating paths\". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors.\r\nWe also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.","lang":"eng"}]},{"citation":{"mla":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 605–15, doi:<a href=\"https://doi.org/10.1093/jeb/voae052\">10.1093/jeb/voae052</a>.","ista":"Barton NH. 2024. Limits to species’ range: The tension between local and global adaptation. Journal of Evolutionary Biology. 37(6), 605–615.","chicago":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae052\">https://doi.org/10.1093/jeb/voae052</a>.","ama":"Barton NH. Limits to species’ range: The tension between local and global adaptation. <i>Journal of Evolutionary Biology</i>. 2024;37(6):605-615. doi:<a href=\"https://doi.org/10.1093/jeb/voae052\">10.1093/jeb/voae052</a>","short":"N.H. Barton, Journal of Evolutionary Biology 37 (2024) 605–615.","apa":"Barton, N. H. (2024). Limits to species’ range: The tension between local and global adaptation. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae052\">https://doi.org/10.1093/jeb/voae052</a>","ieee":"N. H. Barton, “Limits to species’ range: The tension between local and global adaptation,” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6. Oxford University Press, pp. 605–615, 2024."},"publisher":"Oxford University Press","author":[{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"day":"01","date_created":"2024-07-14T22:01:12Z","oa":1,"abstract":[{"lang":"eng","text":"We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace."}],"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Limits to species' range: The tension between local and global adaptation","status":"public","date_updated":"2025-09-08T08:08:41Z","volume":37,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"605-615","acknowledgement":"This work was supported by a grant from the ERC, 101055327, “HaplotypeStructure”. I thank Himani Sachdeva, Michal Hledik, Jitka Polechova, and the reviewers for their helpful comments.","scopus_import":"1","month":"06","date_published":"2024-06-01T00:00:00Z","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2024_JourEvolutionaryBiology_Barton.pdf","creator":"dernst","file_id":"17241","date_updated":"2024-07-15T09:45:25Z","file_size":1194263,"checksum":"94e6b68bddf6cadcec29c7f41647359f","access_level":"open_access","success":1,"date_created":"2024-07-15T09:45:25Z"}],"publication":"Journal of Evolutionary Biology","external_id":{"isi":["001225323900001"],"pmid":["38683160"]},"project":[{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"year":"2024","_id":"17238","issue":"6","intvolume":"        37","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"pmid":1,"publication_status":"published","doi":"10.1093/jeb/voae052","type":"journal_article","corr_author":"1","isi":1,"article_type":"review","fulldoi":"https://doi.org/10.1093/jeb/voae052","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2024-07-15T09:45:25Z","article_processing_charge":"Yes (via OA deal)"},{"oa":1,"department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments."}],"author":[{"first_name":"Eléonore","last_name":"Vercruysse","full_name":"Vercruysse, Eléonore"},{"last_name":"Brückner","first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"last_name":"Gómez-González","first_name":"Manuel","full_name":"Gómez-González, Manuel"},{"first_name":"Alexandre","last_name":"Remson","full_name":"Remson, Alexandre"},{"full_name":"Luciano, Marine","first_name":"Marine","last_name":"Luciano"},{"full_name":"Kalukula, Yohalie","last_name":"Kalukula","first_name":"Yohalie"},{"full_name":"Rossetti, Leone","last_name":"Rossetti","first_name":"Leone"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Gabriele, Sylvain","last_name":"Gabriele","first_name":"Sylvain"}],"citation":{"apa":"Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M., Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous epithelial cell clusters. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>","ieee":"E. Vercruysse <i>et al.</i>, “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1492–1500, 2024.","mla":"Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>.","ista":"Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.","ama":"Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. <i>Nature Physics</i>. 2024;20:1492-1500. doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>","chicago":"Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>.","short":"E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y. Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20 (2024) 1492–1500."},"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.07.17.500364"}],"date_created":"2024-07-16T12:32:17Z","day":"01","status":"public","title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","volume":20,"date_updated":"2025-09-08T08:28:31Z","oa_version":"Preprint","OA_place":"repository","page":"1492-1500","date_published":"2024-09-01T00:00:00Z","month":"09","scopus_import":"1","acknowledgement":"M.L., E.V. and S.G. acknowledge funding from the European Regional Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS; Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23), the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen, ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow (Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively. E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund for Research Training in Industry and Agriculture (FRIA). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS foundation as a NOMIS fellow and by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen Center for Physics, which is supported by the National Science Foundation (Grant No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia (Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade and Business.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","ec_funded":1,"publication":"Nature Physics","external_id":{"isi":["001250246200004"]},"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"_id":"17269","OA_type":"green","intvolume":"        20","doi":"10.1038/s41567-024-02532-x","type":"journal_article","publication_status":"published","related_material":{"link":[{"url":"https://ista.ac.at/en/news/a-railroad-of-cells/","relation":"press_release","description":"News on ISTA website"}]},"fulldoi":"https://doi.org/10.1038/s41567-024-02532-x","article_type":"original","isi":1,"corr_author":"1","article_processing_charge":"No","quality_controlled":"1"},{"OA_type":"green","intvolume":"       287","article_number":"110562","issue":"8","_id":"17277","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"publication_status":"published","type":"journal_article","doi":"10.1016/j.jfa.2024.110562","isi":1,"corr_author":"1","fulldoi":"https://doi.org/10.1016/j.jfa.2024.110562","article_type":"original","quality_controlled":"1","article_processing_charge":"No","date_created":"2024-07-21T22:01:00Z","day":"15","author":[{"id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","full_name":"Brigati, Giovanni","last_name":"Brigati","first_name":"Giovanni"},{"full_name":"Dolbeault, Jean","last_name":"Dolbeault","first_name":"Jean"},{"first_name":"Nikita","last_name":"Simonov","full_name":"Simonov, Nikita"}],"publisher":"Elsevier","citation":{"ama":"Brigati G, Dolbeault J, Simonov N. Stability for the logarithmic Sobolev inequality. <i>Journal of Functional Analysis</i>. 2024;287(8). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">10.1016/j.jfa.2024.110562</a>","chicago":"Brigati, Giovanni, Jean Dolbeault, and Nikita Simonov. “Stability for the Logarithmic Sobolev Inequality.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">https://doi.org/10.1016/j.jfa.2024.110562</a>.","short":"G. Brigati, J. Dolbeault, N. Simonov, Journal of Functional Analysis 287 (2024).","mla":"Brigati, Giovanni, et al. “Stability for the Logarithmic Sobolev Inequality.” <i>Journal of Functional Analysis</i>, vol. 287, no. 8, 110562, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">10.1016/j.jfa.2024.110562</a>.","ista":"Brigati G, Dolbeault J, Simonov N. 2024. Stability for the logarithmic Sobolev inequality. Journal of Functional Analysis. 287(8), 110562.","apa":"Brigati, G., Dolbeault, J., &#38; Simonov, N. (2024). Stability for the logarithmic Sobolev inequality. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110562\">https://doi.org/10.1016/j.jfa.2024.110562</a>","ieee":"G. Brigati, J. Dolbeault, and N. Simonov, “Stability for the logarithmic Sobolev inequality,” <i>Journal of Functional Analysis</i>, vol. 287, no. 8. Elsevier, 2024."},"main_file_link":[{"url":"10.48550/arXiv.2303.12926","open_access":"1"}],"department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"This paper is devoted to stability results for the Gaussian logarithmic Sobolev inequality, with explicit stability constants.\r\n\r\n"}],"oa":1,"OA_place":"repository","oa_version":"Preprint","volume":287,"date_updated":"2025-09-08T08:25:34Z","title":"Stability for the logarithmic Sobolev inequality","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"date_published":"2024-10-15T00:00:00Z","month":"10","acknowledgement":"The authors thank Max Fathi and Pierre Cardaliaguet for fruitful discussions and Emanuel Indrei for stimulating interactions. They also thank an anonymous referee for useful comments and suggestions which have led to an improvement of the manuscript. They also want to express their gratitude to the managing editor, L. Gross, for his encouragements and questions. G.B. has been funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 754362. This work has been (partially) supported by the Project Conviviality ANR-23-CE40-0003 of the French National Research Agency.","scopus_import":"1","external_id":{"arxiv":["2303.12926"],"isi":["001271814000001"]},"publication":"Journal of Functional Analysis","year":"2024"},{"isi":1,"DOAJ_listed":"1","fulldoi":"https://doi.org/10.1126/sciadv.adk5462","article_type":"original","file_date_updated":"2024-07-22T06:29:27Z","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"Yes","OA_type":"gold","intvolume":"        10","article_number":"adk5462","issue":"28","_id":"17280","pmid":1,"publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","type":"journal_article","doi":"10.1126/sciadv.adk5462","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","date_published":"2024-07-12T00:00:00Z","acknowledgement":"Ajap1HA/HA and Ajap1W183C/+ mice were generated in collaboration with Pawel Pelczar at the center for transgenic models at the University of Basel, Switzerland. We thank the imaging core facility (IMCF, University of Basel) and in particular A. Ferrand for the technical assistance provided on the OMX 3D-SIM microscope.\r\nThis work was supported by a grant from the Swiss National Science Foundation (SNF) to B.B. (31003A-152970, 310030B-201291), an NIH grant to E.A. and E.H.S. (R01NS058721), DFG grants to B.F. (TRR 152 project ID 239283807, FA 332/15-1, 16-1), and grants to P.S. from AIMS-2-TRIALS, which are supported by the Innovative Medicines Initiatives from the European Commission joint undertaking under grant agreement No 777394.","scopus_import":"1","external_id":{"isi":["001280159000022"],"pmid":["38985877"]},"file":[{"creator":"dernst","file_id":"17287","file_size":7241489,"date_updated":"2024-07-22T06:29:27Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_ScienceAdv_Früh.pdf","checksum":"9cbc4501fcd4ba1c0811fd244031422b","access_level":"open_access","date_created":"2024-07-22T06:29:27Z","success":1}],"publication":"Science Advances","year":"2024","date_created":"2024-07-21T22:01:01Z","day":"12","citation":{"chicago":"Früh, Simon, Sami Boudkkazi, Peter Koppensteiner, Vita Sereikaite, Li Yuan Chen, Diego Fernandez-Fernandez, Pascal D. Rem, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>.","ama":"Früh S, Boudkkazi S, Koppensteiner P, et al. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. 2024;10(28). doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>","short":"S. Früh, S. Boudkkazi, P. Koppensteiner, V. Sereikaite, L.Y. Chen, D. Fernandez-Fernandez, P.D. Rem, D. Ulrich, J. Schwenk, Z. Chen, E.L. Monnier, T. Fritzius, S.M. Innocenti, V. Besseyrias, L. Trovò, M. Stawarski, E. Argilli, E.H. Sherr, B. Van Bon, E.J. Kamsteeg, M. Iascone, A. Pilotta, M.R. Cutrì, M.S. Azamian, A. Hernández-García, S.R. Lalani, J.A. Rosenfeld, X. Zhao, T.P. Vogel, H. Ona, D.A. Scott, P. Scheiffele, K. Strømgaard, M. Tafti, M. Gassmann, B. Fakler, R. Shigemoto, B. Bettler, Science Advances 10 (2024).","ista":"Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez D, Rem PD, Ulrich D, Schwenk J, Chen Z, Monnier EL, Fritzius T, Innocenti SM, Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, Van Bon B, Kamsteeg EJ, Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann M, Fakler B, Shigemoto R, Bettler B. 2024. Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. Science Advances. 10(28), adk5462.","mla":"Früh, Simon, et al. “Monoallelic de Novo AJAP1 Loss-of- Function Variants Disrupt Trans-Synaptic Control of Neurotransmitter Release.” <i>Science Advances</i>, vol. 10, no. 28, adk5462, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk5462\">10.1126/sciadv.adk5462</a>.","ieee":"S. Früh <i>et al.</i>, “Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release,” <i>Science Advances</i>, vol. 10, no. 28. American Association for the Advancement of Science, 2024.","apa":"Früh, S., Boudkkazi, S., Koppensteiner, P., Sereikaite, V., Chen, L. Y., Fernandez-Fernandez, D., … Bettler, B. (2024). Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk5462\">https://doi.org/10.1126/sciadv.adk5462</a>"},"publisher":"American Association for the Advancement of Science","author":[{"first_name":"Simon","last_name":"Früh","full_name":"Früh, Simon"},{"full_name":"Boudkkazi, Sami","last_name":"Boudkkazi","first_name":"Sami"},{"full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter"},{"full_name":"Sereikaite, Vita","first_name":"Vita","last_name":"Sereikaite"},{"full_name":"Chen, Li Yuan","first_name":"Li Yuan","last_name":"Chen"},{"last_name":"Fernandez-Fernandez","first_name":"Diego","full_name":"Fernandez-Fernandez, Diego"},{"first_name":"Pascal D.","last_name":"Rem","full_name":"Rem, Pascal D."},{"last_name":"Ulrich","first_name":"Daniel","full_name":"Ulrich, Daniel"},{"first_name":"Jochen","last_name":"Schwenk","full_name":"Schwenk, Jochen"},{"full_name":"Chen, Ziyang","first_name":"Ziyang","last_name":"Chen"},{"first_name":"Elodie Le","last_name":"Monnier","full_name":"Monnier, Elodie Le"},{"full_name":"Fritzius, Thorsten","last_name":"Fritzius","first_name":"Thorsten"},{"last_name":"Innocenti","first_name":"Sabrina M.","full_name":"Innocenti, Sabrina M."},{"last_name":"Besseyrias","first_name":"Valérie","full_name":"Besseyrias, Valérie"},{"last_name":"Trovò","first_name":"Luca","full_name":"Trovò, Luca"},{"first_name":"Michal","last_name":"Stawarski","full_name":"Stawarski, Michal"},{"full_name":"Argilli, Emanuela","last_name":"Argilli","first_name":"Emanuela"},{"full_name":"Sherr, Elliott H.","first_name":"Elliott H.","last_name":"Sherr"},{"full_name":"Van Bon, Bregje","last_name":"Van Bon","first_name":"Bregje"},{"last_name":"Kamsteeg","first_name":"Erik Jan","full_name":"Kamsteeg, Erik Jan"},{"full_name":"Iascone, Maria","last_name":"Iascone","first_name":"Maria"},{"full_name":"Pilotta, Alba","last_name":"Pilotta","first_name":"Alba"},{"full_name":"Cutrì, Maria R.","first_name":"Maria R.","last_name":"Cutrì"},{"last_name":"Azamian","first_name":"Mahshid S.","full_name":"Azamian, Mahshid S."},{"first_name":"Andrés","last_name":"Hernández-García","full_name":"Hernández-García, Andrés"},{"first_name":"Seema R.","last_name":"Lalani","full_name":"Lalani, Seema R."},{"full_name":"Rosenfeld, Jill A.","first_name":"Jill A.","last_name":"Rosenfeld"},{"first_name":"Xiaonan","last_name":"Zhao","full_name":"Zhao, Xiaonan"},{"full_name":"Vogel, Tiphanie P.","last_name":"Vogel","first_name":"Tiphanie P."},{"full_name":"Ona, Herda","last_name":"Ona","first_name":"Herda"},{"first_name":"Daryl A.","last_name":"Scott","full_name":"Scott, Daryl A."},{"full_name":"Scheiffele, Peter","last_name":"Scheiffele","first_name":"Peter"},{"full_name":"Strømgaard, Kristian","first_name":"Kristian","last_name":"Strømgaard"},{"first_name":"Mehdi","last_name":"Tafti","full_name":"Tafti, Mehdi"},{"last_name":"Gassmann","first_name":"Martin","full_name":"Gassmann, Martin"},{"last_name":"Fakler","first_name":"Bernd","full_name":"Fakler, Bernd"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Bettler, Bernhard","last_name":"Bettler","first_name":"Bernhard"}],"language":[{"iso":"eng"}],"department":[{"_id":"RySh"},{"_id":"PreCl"}],"abstract":[{"text":"Adherens junction–associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in Ajap1−/− and Ajap1W183C/+ mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function AJAP1 variants.","lang":"eng"}],"oa":1,"ddc":["570"],"OA_place":"publisher","oa_version":"Published Version","volume":10,"date_updated":"2025-09-08T08:15:54Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release"},{"corr_author":"1","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1093/imrn/rnae062","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2024-07-22T06:40:19Z","article_processing_charge":"Yes (via OA deal)","_id":"17281","issue":"13","intvolume":"      2024","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"publication_status":"published","doi":"10.1093/imrn/rnae062","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"10189-10218","scopus_import":"1","acknowledgement":"This work was supported by the National Science Foundation [Grant No. DMS-2143142 to S.O.]; and the European Research Council [Grant No. 101020331].The third author acknowledges the support of the University of Colorado Boulder, where a portion of this work was completed. The authors thank Martin Auer, Vadim Gorin, Brian Hall, and Noah Williams for comments, corrections, and references. The authors also wish to thank the anonymous referees for useful feedback and corrections.","month":"07","date_published":"2024-07-01T00:00:00Z","publication":"International Mathematics Research Notices","file":[{"date_updated":"2024-07-22T06:40:19Z","file_size":1233508,"creator":"dernst","file_id":"17288","file_name":"2024_IMRN_Campbell.pdf","content_type":"application/pdf","relation":"main_file","success":1,"date_created":"2024-07-22T06:40:19Z","access_level":"open_access","checksum":"f36a7dbf53f23d5833db711052e69b49"}],"external_id":{"isi":["001198019500001"]},"year":"2024","publisher":"Oxford University Press","citation":{"ama":"Campbell AJ, O’Rourke S, Renfrew DT. The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation. <i>International Mathematics Research Notices</i>. 2024;2024(13):10189-10218. doi:<a href=\"https://doi.org/10.1093/imrn/rnae062\">10.1093/imrn/rnae062</a>","short":"A.J. Campbell, S. O’Rourke, D.T. Renfrew, International Mathematics Research Notices 2024 (2024) 10189–10218.","chicago":"Campbell, Andrew J, Sean O’Rourke, and David T Renfrew. “The Fractional Free Convolution of R-Diagonal Elements and Random Polynomials under Repeated Differentiation.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/imrn/rnae062\">https://doi.org/10.1093/imrn/rnae062</a>.","mla":"Campbell, Andrew J., et al. “The Fractional Free Convolution of R-Diagonal Elements and Random Polynomials under Repeated Differentiation.” <i>International Mathematics Research Notices</i>, vol. 2024, no. 13, Oxford University Press, 2024, pp. 10189–218, doi:<a href=\"https://doi.org/10.1093/imrn/rnae062\">10.1093/imrn/rnae062</a>.","ista":"Campbell AJ, O’Rourke S, Renfrew DT. 2024. The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation. International Mathematics Research Notices. 2024(13), 10189–10218.","ieee":"A. J. Campbell, S. O’Rourke, and D. T. Renfrew, “The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation,” <i>International Mathematics Research Notices</i>, vol. 2024, no. 13. Oxford University Press, pp. 10189–10218, 2024.","apa":"Campbell, A. J., O’Rourke, S., &#38; Renfrew, D. T. (2024). The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnae062\">https://doi.org/10.1093/imrn/rnae062</a>"},"author":[{"id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","full_name":"Campbell, Andrew J","last_name":"Campbell","first_name":"Andrew J"},{"full_name":"O'Rourke, Sean","last_name":"O'Rourke","first_name":"Sean"},{"first_name":"David T","last_name":"Renfrew","full_name":"Renfrew, David T","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3493-121X"}],"day":"01","date_created":"2024-07-21T22:01:01Z","oa":1,"abstract":[{"text":"We extend the free convolution of Brown measures of R-diagonal elements introduced by Kösters and Tikhomirov [ 28] to fractional powers. We then show how this fractional free convolution arises naturally when studying the roots of random polynomials with independent coefficients under repeated differentiation. When the proportion of derivatives to the degree approaches one, we establish central limit theorem-type behavior and discuss stable distributions.","lang":"eng"}],"department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["510"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","title":"The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation","volume":2024,"date_updated":"2025-09-08T08:16:32Z"},{"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"external_id":{"isi":["001258097800003"],"arxiv":["2209.11149"],"pmid":["38947856"]},"publication":"Calculus of Variations and Partial Differential Equations","file":[{"checksum":"a0cf0e0ba2157aabb287cb597be17dac","date_created":"2024-07-22T07:05:32Z","success":1,"access_level":"open_access","creator":"dernst","file_id":"17289","file_size":416622,"date_updated":"2024-07-22T07:05:32Z","content_type":"application/pdf","relation":"main_file","file_name":"2024_CalculusVariations_Brooks.pdf"}],"ec_funded":1,"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).J. M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117), and by the Austrian Science Fund (FWF), Project SFB F65. We thank the anonymous referee for valuable comments on the paper.","month":"07","date_published":"2024-07-01T00:00:00Z","arxiv":1,"ddc":["510"],"oa_version":"Published Version","volume":63,"date_updated":"2025-09-08T08:24:51Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Characterisation of gradient flows for a given functional","status":"public","day":"01","date_created":"2024-07-21T22:01:01Z","author":[{"last_name":"Brooks","first_name":"Morris","full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas"}],"citation":{"apa":"Brooks, M., &#38; Maas, J. (2024). Characterisation of gradient flows for a given functional. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-024-02755-z\">https://doi.org/10.1007/s00526-024-02755-z</a>","ieee":"M. Brooks and J. Maas, “Characterisation of gradient flows for a given functional,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 63, no. 6. Springer Nature, 2024.","ista":"Brooks M, Maas J. 2024. Characterisation of gradient flows for a given functional. Calculus of Variations and Partial Differential Equations. 63(6), 153.","mla":"Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a given Functional.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 63, no. 6, 153, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00526-024-02755-z\">10.1007/s00526-024-02755-z</a>.","chicago":"Brooks, Morris, and Jan Maas. “Characterisation of Gradient Flows for a given Functional.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00526-024-02755-z\">https://doi.org/10.1007/s00526-024-02755-z</a>.","ama":"Brooks M, Maas J. Characterisation of gradient flows for a given functional. <i>Calculus of Variations and Partial Differential Equations</i>. 2024;63(6). doi:<a href=\"https://doi.org/10.1007/s00526-024-02755-z\">10.1007/s00526-024-02755-z</a>","short":"M. Brooks, J. Maas, Calculus of Variations and Partial Differential Equations 63 (2024)."},"publisher":"Springer Nature","abstract":[{"text":"Let  X  be a vector field and  Y  be a co-vector field on a smooth manifold  M. Does there exist a smooth Riemannian metric  gαβ  on  M  such that  Yβ=gαβXα ? The main result of this note gives necessary and sufficient conditions for this to be true. As an application of this result we show that a finite-dimensional ergodic Lindblad equation admits a gradient flow structure for the von Neumann relative entropy if and only if the condition of BKM-detailed balance holds.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"oa":1,"file_date_updated":"2024-07-22T07:05:32Z","has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","corr_author":"1","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1007/s00526-024-02755-z","publication_status":"published","type":"journal_article","doi":"10.1007/s00526-024-02755-z","article_number":"153","intvolume":"        63","_id":"17282","issue":"6","pmid":1,"publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]}},{"corr_author":"1","fulldoi":"https://doi.org/10.1145/3656462","article_type":"original","quality_controlled":"1","has_accepted_license":"1","file_date_updated":"2024-07-22T07:17:14Z","article_processing_charge":"Yes (via OA deal)","_id":"17283","OA_type":"hybrid","article_number":"232","intvolume":"         8","publication_identifier":{"eissn":["2475-1421"]},"publication_status":"published","doi":"10.1145/3656462","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"month":"06","date_published":"2024-06-20T00:00:00Z","scopus_import":"1","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant. Petr Novotný\r\nis supported by the Czech Science Foundation grant no. GA23-06963S.\r\n","publication":"Proceedings of the ACM on Programming Languages","file":[{"checksum":"8cbf220f284a4a87d093db5320c5afdd","access_level":"open_access","success":1,"date_created":"2024-07-22T07:17:14Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_ACMProgLang_Chatterjee.pdf","creator":"dernst","file_id":"17290","date_updated":"2024-07-22T07:17:14Z","file_size":355421}],"external_id":{"arxiv":["2404.03430"]},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"year":"2024","ec_funded":1,"publisher":"Association for Computing Machinery","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Kafshdar Goharshadi","first_name":"Ehsan","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","orcid":"0000-0002-8595-0587","full_name":"Kafshdar Goharshadi, Ehsan"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr","first_name":"Petr","last_name":"Novotný"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde"}],"citation":{"ista":"Chatterjee K, Goharshady E, Novotný P, Zikelic D. 2024. Equivalence and similarity refutation for probabilistic programs. Proceedings of the ACM on Programming Languages. 8, 232.","mla":"Chatterjee, Krishnendu, et al. “Equivalence and Similarity Refutation for Probabilistic Programs.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 8, 232, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3656462\">10.1145/3656462</a>.","short":"K. Chatterjee, E. Goharshady, P. Novotný, D. Zikelic, Proceedings of the ACM on Programming Languages 8 (2024).","ama":"Chatterjee K, Goharshady E, Novotný P, Zikelic D. Equivalence and similarity refutation for probabilistic programs. <i>Proceedings of the ACM on Programming Languages</i>. 2024;8. doi:<a href=\"https://doi.org/10.1145/3656462\">10.1145/3656462</a>","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Petr Novotný, and Dorde Zikelic. “Equivalence and Similarity Refutation for Probabilistic Programs.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3656462\">https://doi.org/10.1145/3656462</a>.","ieee":"K. Chatterjee, E. Goharshady, P. Novotný, and D. Zikelic, “Equivalence and similarity refutation for probabilistic programs,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 8. Association for Computing Machinery, 2024.","apa":"Chatterjee, K., Goharshady, E., Novotný, P., &#38; Zikelic, D. (2024). Equivalence and similarity refutation for probabilistic programs. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3656462\">https://doi.org/10.1145/3656462</a>"},"date_created":"2024-07-21T22:01:01Z","day":"20","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"abstract":[{"text":"We consider the problems of statically refuting equivalence and similarity of output distributions defined by a pair of probabilistic programs. Equivalence and similarity are two fundamental relational properties of probabilistic programs that are essential for their correctness both in implementation and in compilation. In this work, we present a new method for static equivalence and similarity refutation. Our method refutes equivalence and similarity by computing a function over program outputs whose expected value with respect to the output distributions of two programs is different. The function is computed simultaneously with an upper expectation supermartingale and a lower expectation submartingale for the two programs, which we show to together provide a formal certificate for refuting equivalence and similarity. To the best of our knowledge, our method is the first approach to relational program analysis to offer the combination of the following desirable features: (1) it is fully automated, (2) it is applicable to infinite-state probabilistic programs, and (3) it provides formal guarantees on the correctness of its results. We implement a prototype of our method and our experiments demonstrate the effectiveness of our method to refute equivalence and similarity for a number of examples collected from the literature.","lang":"eng"}],"oa_version":"Published Version","OA_place":"publisher","ddc":["000"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Equivalence and similarity refutation for probabilistic programs","status":"public","volume":8,"date_updated":"2025-04-14T07:52:47Z"},{"type":"journal_article","doi":"10.1038/s41586-024-07671-y","related_material":{"link":[{"url":"https://github.com/heiniglab/gaertner_megakaryocytes","relation":"software"}]},"publication_status":"published","pmid":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"intvolume":"       631","_id":"17284","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-07-22T06:16:11Z","has_accepted_license":"1","quality_controlled":"1","article_type":"original","fulldoi":"https://doi.org/10.1038/s41586-024-07671-y","corr_author":"1","isi":1,"volume":631,"date_updated":"2025-09-08T08:14:25Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis","ddc":["570"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Platelet homeostasis is essential for vascular integrity and immune defence1,2. Although the process of platelet formation by fragmenting megakaryocytes (MKs; thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of MKs by their progenitor cells (megakaryopoiesis) remains unclear3,4. Here we use intravital imaging to track the cellular dynamics of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver IFNα to the MK niche triggering local on-demand proliferation and maturation of MK progenitors. This pDC-dependent feedback loop is crucial for MK and platelet homeostasis at steady state and under stress. pDCs are best known for their ability to function as vigilant detectors of viral infection5. We show that virus-induced activation of pDCs interferes with their function as homeostatic sensors of megakaryopoiesis. Consequently, activation of pDCs by SARS-CoV-2 leads to excessive megakaryopoiesis. Together, we identify a pDC-dependent homeostatic circuit that involves innate immune sensing and demand-adapted release of inflammatory mediators to maintain homeostasis of the megakaryocytic lineage."}],"department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"day":"18","date_created":"2024-07-21T22:01:02Z","publisher":"Springer Nature","author":[{"last_name":"Gärtner","first_name":"Florian R","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"},{"full_name":"Ishikawa-Ankerhold, Hellen","first_name":"Hellen","last_name":"Ishikawa-Ankerhold"},{"last_name":"Stutte","first_name":"Susanne","full_name":"Stutte, Susanne"},{"last_name":"Fu","first_name":"Wenwen","full_name":"Fu, Wenwen"},{"full_name":"Weitz, Jutta","first_name":"Jutta","last_name":"Weitz"},{"last_name":"Dueck","first_name":"Anne","full_name":"Dueck, Anne"},{"full_name":"Nelakuditi, Bhavishya","first_name":"Bhavishya","last_name":"Nelakuditi"},{"full_name":"Fumagalli, Valeria","first_name":"Valeria","last_name":"Fumagalli"},{"last_name":"Van Den Heuvel","first_name":"Dominic","full_name":"Van Den Heuvel, Dominic"},{"last_name":"Belz","first_name":"Larissa","full_name":"Belz, Larissa"},{"last_name":"Sobirova","first_name":"Gulnoza","full_name":"Sobirova, Gulnoza"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"full_name":"Titova, Anna","last_name":"Titova","first_name":"Anna"},{"first_name":"Alejandro Martinez","last_name":"Navarro","full_name":"Navarro, Alejandro Martinez"},{"full_name":"Pekayvaz, Kami","first_name":"Kami","last_name":"Pekayvaz"},{"last_name":"Lorenz","first_name":"Michael","full_name":"Lorenz, Michael"},{"first_name":"Louisa","last_name":"Von Baumgarten","full_name":"Von Baumgarten, Louisa"},{"last_name":"Kranich","first_name":"Jan","full_name":"Kranich, Jan"},{"first_name":"Tobias","last_name":"Straub","full_name":"Straub, Tobias"},{"full_name":"Popper, Bastian","last_name":"Popper","first_name":"Bastian"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden"},{"last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"first_name":"Chenglong","last_name":"Guo","full_name":"Guo, Chenglong"},{"full_name":"Piontek, Guido","last_name":"Piontek","first_name":"Guido"},{"last_name":"Von Stillfried","first_name":"Saskia","full_name":"Von Stillfried, Saskia"},{"full_name":"Boor, Peter","first_name":"Peter","last_name":"Boor"},{"last_name":"Colonna","first_name":"Marco","full_name":"Colonna, Marco"},{"full_name":"Clauß, Sebastian","last_name":"Clauß","first_name":"Sebastian"},{"first_name":"Christian","last_name":"Schulz","full_name":"Schulz, Christian"},{"last_name":"Brocker","first_name":"Thomas","full_name":"Brocker, Thomas"},{"full_name":"Walzog, Barbara","first_name":"Barbara","last_name":"Walzog"},{"last_name":"Scheiermann","first_name":"Christoph","full_name":"Scheiermann, Christoph"},{"first_name":"William C.","last_name":"Aird","full_name":"Aird, William C."},{"last_name":"Nerlov","first_name":"Claus","full_name":"Nerlov, Claus"},{"full_name":"Stark, Konstantin","first_name":"Konstantin","last_name":"Stark"},{"first_name":"Tobias","last_name":"Petzold","full_name":"Petzold, Tobias"},{"full_name":"Engelhardt, Stefan","first_name":"Stefan","last_name":"Engelhardt"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Rudelius, Martina","last_name":"Rudelius","first_name":"Martina"},{"full_name":"Oostendorp, Robert A.J.","first_name":"Robert A.J.","last_name":"Oostendorp"},{"last_name":"Iannacone","first_name":"Matteo","full_name":"Iannacone, Matteo"},{"full_name":"Heinig, Matthias","last_name":"Heinig","first_name":"Matthias"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"}],"citation":{"apa":"Gärtner, F. R., Ishikawa-Ankerhold, H., Stutte, S., Fu, W., Weitz, J., Dueck, A., … Massberg, S. (2024). Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07671-y\">https://doi.org/10.1038/s41586-024-07671-y</a>","ieee":"F. R. Gärtner <i>et al.</i>, “Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis,” <i>Nature</i>, vol. 631. Springer Nature, pp. 645–653, 2024.","short":"F.R. Gärtner, H. Ishikawa-Ankerhold, S. Stutte, W. Fu, J. Weitz, A. Dueck, B. Nelakuditi, V. Fumagalli, D. Van Den Heuvel, L. Belz, G. Sobirova, Z. Zhang, A. Titova, A.M. Navarro, K. Pekayvaz, M. Lorenz, L. Von Baumgarten, J. Kranich, T. Straub, B. Popper, V. Zheden, W. Kaufmann, C. Guo, G. Piontek, S. Von Stillfried, P. Boor, M. Colonna, S. Clauß, C. Schulz, T. Brocker, B. Walzog, C. Scheiermann, W.C. Aird, C. Nerlov, K. Stark, T. Petzold, S. Engelhardt, M.K. Sixt, R. Hauschild, M. Rudelius, R.A.J. Oostendorp, M. Iannacone, M. Heinig, S. Massberg, Nature 631 (2024) 645–653.","chicago":"Gärtner, Florian R, Hellen Ishikawa-Ankerhold, Susanne Stutte, Wenwen Fu, Jutta Weitz, Anne Dueck, Bhavishya Nelakuditi, et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07671-y\">https://doi.org/10.1038/s41586-024-07671-y</a>.","ama":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, et al. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. <i>Nature</i>. 2024;631:645-653. doi:<a href=\"https://doi.org/10.1038/s41586-024-07671-y\">10.1038/s41586-024-07671-y</a>","ista":"Gärtner FR, Ishikawa-Ankerhold H, Stutte S, Fu W, Weitz J, Dueck A, Nelakuditi B, Fumagalli V, Van Den Heuvel D, Belz L, Sobirova G, Zhang Z, Titova A, Navarro AM, Pekayvaz K, Lorenz M, Von Baumgarten L, Kranich J, Straub T, Popper B, Zheden V, Kaufmann W, Guo C, Piontek G, Von Stillfried S, Boor P, Colonna M, Clauß S, Schulz C, Brocker T, Walzog B, Scheiermann C, Aird WC, Nerlov C, Stark K, Petzold T, Engelhardt S, Sixt MK, Hauschild R, Rudelius M, Oostendorp RAJ, Iannacone M, Heinig M, Massberg S. 2024. Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis. Nature. 631, 645–653.","mla":"Gärtner, Florian R., et al. “Plasmacytoid Dendritic Cells Control Homeostasis of Megakaryopoiesis.” <i>Nature</i>, vol. 631, Springer Nature, 2024, pp. 645–53, doi:<a href=\"https://doi.org/10.1038/s41586-024-07671-y\">10.1038/s41586-024-07671-y</a>."},"ec_funded":1,"year":"2024","external_id":{"pmid":["38987596"],"isi":["001281636500020"]},"project":[{"call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"publication":"Nature","file":[{"checksum":"aa004afc72d2489f0fb0fcbc9919fbbd","access_level":"open_access","date_created":"2024-07-22T06:16:11Z","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"2024_Nature_Gaertner.pdf","creator":"dernst","file_id":"17286","date_updated":"2024-07-22T06:16:11Z","file_size":15704819}],"scopus_import":"1","acknowledgement":"We thank S. Helmer, N. Blount, E. Raatz and Z. Sisic for technical assistance. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) SFB 1123 (S.M. project B06); SFB 914 (S.M. projects B02 and Z01, H.I.-A. project Z01, S.S. project A06, K.S. project B02, C. Schulz project A10, B.W. project A02, C. Scheiermann project B09); SFB 1054 (T.B. project B03); FOR2033 (F.G., R.A.J.O., S.M.); Individual research grant project ID: 514478744 (F.G.); Heisenberg Programme project ID: 514477451 (F.G.); the DZHK (German Center for Cardiovascular Research) (MHA 1.4VD (S.M.), Postdoc Start-up Grant, 81×3600213 (F.G.)); and LMUexcellence NFF (F.G.). W.F. received funding from China Scholarship Council (CSC, no. 201306270012). P.B. is supported by the German Research Foundation (DFG, project IDs 322900939, 432698239 and 445703531), European Research Council (ERC Consolidator grant no. 101001791) and the Federal Ministry of Education and Research (BMBF, STOP-FSGS-01GM2202C and NATON within the framework of the Network of University Medicine, no. 01KX2121). S.v.S. is supported by the START-Program of the Faculty of Medicine of the RWTH Aachen University (AZ 125/17). A.D. and S.E. are supported by the German Research Foundation (SFB TRR 267); S.E. by the BMBF in the framework of the Cluster4future program (CNATM—Cluster for Nucleic Acid Therapeutics Munich). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 833440 to S.M.). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687. The project is funded by the European Union (ERC, MEKanics, 101078110). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","month":"07","date_published":"2024-07-18T00:00:00Z","page":"645-653","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"2251-2266","date_published":"2024-10-01T00:00:00Z","month":"10","acknowledgement":"We thank Prof. Kang Chong from Institute of Botany, the Chinese Academy of Science for valuable comments, Dr. Haoran Li for the help with western blot of H3K36me3 in Tasdg8-cr lines. This research was supported by National Natural Science Foundation (31970529), Beijing Natural Science Foundation Outstanding Youth Project (JQ23026), National Key Research and Development Program of China (2021YFD1201500), and the Major Basic Research Program of Shandong Natural Science Foundation (ZR2019ZD15).","scopus_import":"1","publication":"Science China Life Sciences","external_id":{"pmid":["38987431"],"isi":["001268807700002"]},"year":"2024","publisher":"Springer Nature","author":[{"last_name":"Liu","first_name":"Xuemei","full_name":"Liu, Xuemei"},{"first_name":"Min","last_name":"Deng","full_name":"Deng, Min"},{"last_name":"Shi","first_name":"Bingxin","full_name":"Shi, Bingxin"},{"full_name":"Zhu, Kehui","last_name":"Zhu","first_name":"Kehui"},{"full_name":"Chen, Jinchao","first_name":"Jinchao","last_name":"Chen"},{"last_name":"Xu","first_name":"Shujuan","full_name":"Xu, Shujuan","id":"9724dd9d-f591-11ee-bd51-e97ed0652286"},{"last_name":"Bie","first_name":"Xiaomin","full_name":"Bie, Xiaomin"},{"full_name":"Zhang, Xiansheng","last_name":"Zhang","first_name":"Xiansheng"},{"full_name":"Lin, Xuelei","first_name":"Xuelei","last_name":"Lin"},{"first_name":"Jun","last_name":"Xiao","full_name":"Xiao, Jun"}],"citation":{"chicago":"Liu, Xuemei, Min Deng, Bingxin Shi, Kehui Zhu, Jinchao Chen, Shujuan Xu, Xiaomin Bie, Xiansheng Zhang, Xuelei Lin, and Jun Xiao. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.” <i>Science China Life Sciences</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s11427-024-2664-0\">https://doi.org/10.1007/s11427-024-2664-0</a>.","ama":"Liu X, Deng M, Shi B, et al. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. <i>Science China Life Sciences</i>. 2024;67:2251-2266. doi:<a href=\"https://doi.org/10.1007/s11427-024-2664-0\">10.1007/s11427-024-2664-0</a>","short":"X. Liu, M. Deng, B. Shi, K. Zhu, J. Chen, S. Xu, X. Bie, X. Zhang, X. Lin, J. Xiao, Science China Life Sciences 67 (2024) 2251–2266.","mla":"Liu, Xuemei, et al. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.” <i>Science China Life Sciences</i>, vol. 67, Springer Nature, 2024, pp. 2251–66, doi:<a href=\"https://doi.org/10.1007/s11427-024-2664-0\">10.1007/s11427-024-2664-0</a>.","ista":"Liu X, Deng M, Shi B, Zhu K, Chen J, Xu S, Bie X, Zhang X, Lin X, Xiao J. 2024. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. Science China Life Sciences. 67, 2251–2266.","apa":"Liu, X., Deng, M., Shi, B., Zhu, K., Chen, J., Xu, S., … Xiao, J. (2024). Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat. <i>Science China Life Sciences</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11427-024-2664-0\">https://doi.org/10.1007/s11427-024-2664-0</a>","ieee":"X. Liu <i>et al.</i>, “Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat,” <i>Science China Life Sciences</i>, vol. 67. Springer Nature, pp. 2251–2266, 2024."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.12.19.572364"}],"date_created":"2024-07-21T22:01:02Z","day":"01","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"abstract":[{"text":"Winter plants rely on vernalization, a crucial process for adapting to cold conditions and ensuring successful reproduction. However, understanding the role of histone modifications in guiding the vernalization process in winter wheat remains limited. In this study, we investigated the transcriptome and chromatin dynamics in the shoot apex throughout the life cycle of winter wheat in the field. Two core histone modifications, H3K27me3 and H3K36me3, exhibited opposite patterns on the key vernalization gene VERNALIZATION1 (VRN1), correlating with its induction during cold exposure. Moreover, the H3K36me3 level remained high at VRN1 after cold exposure, which may maintain its active state. Mutations in FERTILIZATION-INDEPENDENT ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS (TaSDG8/TaEFS), components of the writer complex for H3K27me3 and H3K36me3, respectively, affected flowering time. Intriguingly, VRN1 lost its high expression after the cold exposure memory in the absence of H3K36me3. During embryo development, VRN1 was silenced with the removal of active histone modifications in both winter and spring wheat, with selective restoration of H3K27me3 in winter wheat. The mutant of Tafie-cr-87, a component of H3K27me3 “writer” complex, did not influence the silence of VRN1 during embryo development, but rather attenuated the cold exposure requirement of winter wheat. Integrating gene expression with H3K27me3 and H3K36me3 patterns identified potential regulators of flowering. This study unveils distinct roles of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and resetting in winter wheat.","lang":"eng"}],"oa_version":"Preprint","OA_place":"repository","title":"Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat","status":"public","date_updated":"2025-09-08T08:15:08Z","volume":67,"isi":1,"fulldoi":"https://doi.org/10.1007/s11427-024-2664-0","article_type":"original","quality_controlled":"1","article_processing_charge":"No","_id":"17285","OA_type":"green","intvolume":"        67","publication_identifier":{"issn":["1674-7305"],"eissn":["1869-1889"]},"pmid":1,"publication_status":"published","doi":"10.1007/s11427-024-2664-0","type":"journal_article"},{"fulldoi":"https://doi.org/10.1016/j.jmr.2024.107708","article_type":"original","isi":1,"corr_author":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-07-23T06:23:51Z","quality_controlled":"1","has_accepted_license":"1","pmid":1,"publication_identifier":{"issn":["1090-7807"]},"OA_type":"hybrid","article_number":"107708","intvolume":"       364","_id":"17291","type":"journal_article","doi":"10.1016/j.jmr.2024.107708","related_material":{"record":[{"relation":"research_data","status":"public","id":"17042"}]},"publication_status":"published","date_published":"2024-07-01T00:00:00Z","month":"07","scopus_import":"1","acknowledgement":"This research was supported by the French Agence Nationale de la Recherche (\r\nANR-16-CE11-0030-12, TransPepNMR). This work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI, France (ANR-10-INBS-0005-02\r\n) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche), CBH-EUR-GS (ANR-17-EURE-0003). Financial support from the IR INFRANALYTICS FR2054 for conducting the research and intramural funding by the Institute of Science and Technology Austria (ISTA) are gratefully acknowledged.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","external_id":{"pmid":["38901173"],"isi":["001259302800001"]},"publication":"Journal of Magnetic Resonance","file":[{"date_updated":"2024-07-23T06:23:51Z","file_size":2236665,"file_id":"17316","creator":"dernst","file_name":"2024_JourMagneticResonance_Vallet.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2024-07-23T06:23:51Z","success":1,"access_level":"open_access","checksum":"4b59f4f0c287ecbafd808da1212ced38"}],"language":[{"iso":"eng"}],"department":[{"_id":"PaSc"}],"abstract":[{"text":"Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13Csingle bond13C and heteronuclear 1Hsingle bond15N, 1Hsingle bond13C and 15Nsingle bond13C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3–4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples.","lang":"eng"}],"oa":1,"date_created":"2024-07-22T07:44:10Z","day":"01","citation":{"short":"A. Vallet, I. Ayala, B. Perrone, A. Hassan, J.-P. Simorre, C. Bougault, P. Schanda, Journal of Magnetic Resonance 364 (2024).","chicago":"Vallet, Alicia, Isabel Ayala, Barbara Perrone, Alia Hassan, Jean-Pierre Simorre, Catherine Bougault, and Paul Schanda. “MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jmr.2024.107708\">https://doi.org/10.1016/j.jmr.2024.107708</a>.","ama":"Vallet A, Ayala I, Perrone B, et al. MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. <i>Journal of Magnetic Resonance</i>. 2024;364. doi:<a href=\"https://doi.org/10.1016/j.jmr.2024.107708\">10.1016/j.jmr.2024.107708</a>","ista":"Vallet A, Ayala I, Perrone B, Hassan A, Simorre J-P, Bougault C, Schanda P. 2024. MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. Journal of Magnetic Resonance. 364, 107708.","mla":"Vallet, Alicia, et al. “MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.” <i>Journal of Magnetic Resonance</i>, vol. 364, 107708, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jmr.2024.107708\">10.1016/j.jmr.2024.107708</a>.","ieee":"A. Vallet <i>et al.</i>, “MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments,” <i>Journal of Magnetic Resonance</i>, vol. 364. Elsevier, 2024.","apa":"Vallet, A., Ayala, I., Perrone, B., Hassan, A., Simorre, J.-P., Bougault, C., &#38; Schanda, P. (2024). MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2024.107708\">https://doi.org/10.1016/j.jmr.2024.107708</a>"},"author":[{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"first_name":"Barbara","last_name":"Perrone","full_name":"Perrone, Barbara"},{"last_name":"Hassan","first_name":"Alia","full_name":"Hassan, Alia"},{"last_name":"Simorre","first_name":"Jean-Pierre","full_name":"Simorre, Jean-Pierre"},{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"}],"publisher":"Elsevier","volume":364,"date_updated":"2025-09-09T12:01:41Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","title":"MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments","OA_place":"publisher","ddc":["570"],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-07-19T00:00:00Z","month":"07","acknowledgement":"We acknowledge the Mountain Research Initiative (MRI) for sponsoring the workshop ‘Cryosphere-groundwater Interactions: A Missing Link in Mountain Water Research’ via their funding from the Swiss Academy of Sciences (SCNAT) under project no. FNW0004 004-2019-00. M.v.T. was supported by a Walter Benjamin fellowship from the German Research Foundation (DFG) under project no. 510684314. C.A.-W. was supported by the Banting Postdoctoral Fellowships programme, administered by the government of Canada. G.C. acknowledges the support of the DFG research unit (FOR2793/2) investigating the ‘Sensitivity of High Alpine Geosystems to Climate Change since 1850’ (SEHAG) under grant CH981/3-2. F.D. acknowledges funding from the Dirección de Fomento de la Investigación at PUCP. I.d.G. acknowledges funding from the European Research Council (ERC) under grant agreement GROW-101041110. V.Y. was supported by Nazarbayev University under CRP research grant no. 021220CRP2122. We thank D. Masovic of VAW, ETH Zurich, for drawing Fig. 1.","scopus_import":"1","page":"624-637","external_id":{"isi":["001390137500016"]},"publication":"Nature Water","year":"2024","date_created":"2024-07-22T09:46:52Z","day":"19","citation":{"apa":"van Tiel, M., Aubry-Wake, C., Somers, L., Andermann, C., Avanzi, F., Baraer, M., … Yapiyev, V. (2024). Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. <i>Nature Water</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44221-024-00277-8\">https://doi.org/10.1038/s44221-024-00277-8</a>","ieee":"M. van Tiel <i>et al.</i>, “Cryosphere–groundwater connectivity is a missing link in the mountain water cycle,” <i>Nature Water</i>, vol. 2. Springer Nature, pp. 624–637, 2024.","ista":"van Tiel M, Aubry-Wake C, Somers L, Andermann C, Avanzi F, Baraer M, Chiogna G, Daigre C, Das S, Drenkhan F, Farinotti D, Fyffe CL, de Graaf I, Hanus S, Immerzeel W, Koch F, McKenzie JM, Müller T, Popp AL, Saidaliyeva Z, Schaefli B, Schilling OS, Teagai K, Thornton JM, Yapiyev V. 2024. Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. Nature Water. 2, 624–637.","mla":"van Tiel, Marit, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link in the Mountain Water Cycle.” <i>Nature Water</i>, vol. 2, Springer Nature, 2024, pp. 624–37, doi:<a href=\"https://doi.org/10.1038/s44221-024-00277-8\">10.1038/s44221-024-00277-8</a>.","short":"M. van Tiel, C. Aubry-Wake, L. Somers, C. Andermann, F. Avanzi, M. Baraer, G. Chiogna, C. Daigre, S. Das, F. Drenkhan, D. Farinotti, C.L. Fyffe, I. de Graaf, S. Hanus, W. Immerzeel, F. Koch, J.M. McKenzie, T. Müller, A.L. Popp, Z. Saidaliyeva, B. Schaefli, O.S. Schilling, K. Teagai, J.M. Thornton, V. Yapiyev, Nature Water 2 (2024) 624–637.","ama":"van Tiel M, Aubry-Wake C, Somers L, et al. Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. <i>Nature Water</i>. 2024;2:624-637. doi:<a href=\"https://doi.org/10.1038/s44221-024-00277-8\">10.1038/s44221-024-00277-8</a>","chicago":"Tiel, Marit van, Caroline Aubry-Wake, Lauren Somers, Christoff Andermann, Francesco Avanzi, Michel Baraer, Gabriele Chiogna, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link in the Mountain Water Cycle.” <i>Nature Water</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s44221-024-00277-8\">https://doi.org/10.1038/s44221-024-00277-8</a>."},"author":[{"full_name":"van Tiel, Marit","first_name":"Marit","last_name":"van Tiel"},{"full_name":"Aubry-Wake, Caroline","first_name":"Caroline","last_name":"Aubry-Wake"},{"full_name":"Somers, Lauren","last_name":"Somers","first_name":"Lauren"},{"first_name":"Christoff","last_name":"Andermann","full_name":"Andermann, Christoff"},{"full_name":"Avanzi, Francesco","last_name":"Avanzi","first_name":"Francesco"},{"full_name":"Baraer, Michel","last_name":"Baraer","first_name":"Michel"},{"last_name":"Chiogna","first_name":"Gabriele","full_name":"Chiogna, Gabriele"},{"full_name":"Daigre, Clémence","first_name":"Clémence","last_name":"Daigre"},{"first_name":"Soumik","last_name":"Das","full_name":"Das, Soumik"},{"first_name":"Fabian","last_name":"Drenkhan","full_name":"Drenkhan, Fabian"},{"last_name":"Farinotti","first_name":"Daniel","full_name":"Farinotti, Daniel"},{"first_name":"Catriona Louise","last_name":"Fyffe","full_name":"Fyffe, Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228"},{"first_name":"Inge","last_name":"de Graaf","full_name":"de Graaf, Inge"},{"first_name":"Sarah","last_name":"Hanus","full_name":"Hanus, Sarah"},{"last_name":"Immerzeel","first_name":"Walter","full_name":"Immerzeel, Walter"},{"full_name":"Koch, Franziska","last_name":"Koch","first_name":"Franziska"},{"full_name":"McKenzie, Jeffrey M.","first_name":"Jeffrey M.","last_name":"McKenzie"},{"full_name":"Müller, Tom","last_name":"Müller","first_name":"Tom"},{"last_name":"Popp","first_name":"Andrea L.","full_name":"Popp, Andrea L."},{"first_name":"Zarina","last_name":"Saidaliyeva","full_name":"Saidaliyeva, Zarina"},{"full_name":"Schaefli, Bettina","last_name":"Schaefli","first_name":"Bettina"},{"full_name":"Schilling, Oliver S.","last_name":"Schilling","first_name":"Oliver S."},{"full_name":"Teagai, Kapiolani","last_name":"Teagai","first_name":"Kapiolani"},{"first_name":"James M.","last_name":"Thornton","full_name":"Thornton, James M."},{"full_name":"Yapiyev, Vadim","first_name":"Vadim","last_name":"Yapiyev"}],"publisher":"Springer Nature","main_file_link":[{"url":"https://insu.hal.science/insu-04674297","open_access":"1"}],"department":[{"_id":"FrPe"}],"language":[{"iso":"eng"}],"abstract":[{"text":"The mountain cryosphere and groundwater play pivotal roles in shaping the hydrological cycle, yet their connectivity remains incompletely understood. Current knowledge on meltwater recharge and consequent groundwater discharge processes is better developed for snow–groundwater connectivity than for glacier–groundwater connectivity. Estimates of meltwater recharge vary considerably, which is probably a function of not only inherent catchment characteristics but also of the different spatio-temporal scales involved and the uncertainties in the methods used. This hinders a comprehensive understanding of the mountain water cycle. As glaciers retreat, permafrost thaws and snowpack diminishes, the relative importance of mountain groundwater is expected to increase. However, shifting and declining recharge from the cryosphere may decrease absolute groundwater amounts and fluxes with as-yet unknown effects on catchment-scale hydrological processes. We therefore stress the need to better quantify mountain cryosphere–groundwater connectivity to predict climate change impacts on mountain water supply and to support sustainable water resource management of downstream socio-ecological systems.","lang":"eng"}],"oa":1,"OA_place":"repository","oa_version":"Submitted Version","volume":2,"date_updated":"2025-12-02T13:42:28Z","title":"Cryosphere–groundwater connectivity is a missing link in the mountain water cycle","status":"public","isi":1,"fulldoi":"https://doi.org/10.1038/s44221-024-00277-8","article_type":"original","quality_controlled":"1","article_processing_charge":"No","OA_type":"green","intvolume":"         2","_id":"17302","publication_identifier":{"issn":["2731-6084"]},"publication_status":"published","type":"journal_article","doi":"10.1038/s44221-024-00277-8"},{"year":"2024","file":[{"checksum":"e0505553b3cee624fa865f0cc5a99ecc","access_level":"open_access","success":1,"date_created":"2024-07-29T10:56:01Z","creator":"dernst","file_id":"17339","file_size":1276645,"date_updated":"2024-07-29T10:56:01Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_AnnualReviewBiophys_Lo.pdf"}],"publication":"Annual Review of Biophysics","external_id":{"isi":["001278237500021"],"pmid":["38382113"]},"project":[{"name":"Bacterial cytoplasm glass transition: passive physiological switch or active survival strategy","grant_number":"ALTF 44-2021","_id":"eb872896-77a9-11ec-83b8-f59a38ec17f8"}],"page":"487-510","date_published":"2024-07-01T00:00:00Z","month":"07","acknowledgement":"We would like to thank all members of the Pilizota lab, as well as Calin Guet, Orkun Soyer, Munehiro Asally, Peter Swain, and in particular Matt Scott and Ariel Amir, for their support, comments, and useful discussions. T.P. and W.-C.L. were supported by the Leverhulme Trust, grant RPG-2019-187, and T.P. is supported by EPSRC Fellowship EP/V03264X/1. E.K. was supported by a European Molecular Biology Organization Long-Term Postdoctoral Fellowship, ALTF 44-2021.","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Bacterial Electrophysiology","status":"public","date_updated":"2025-09-08T08:34:43Z","volume":53,"oa_version":"Published Version","ddc":["570"],"oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"abstract":[{"text":"Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.","lang":"eng"}],"citation":{"apa":"Lo, W. C., Krasnopeeva, E., &#38; Pilizota, T. (2024). Bacterial Electrophysiology. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">https://doi.org/10.1146/annurev-biophys-030822-032215</a>","ieee":"W. C. Lo, E. Krasnopeeva, and T. Pilizota, “Bacterial Electrophysiology,” <i>Annual Review of Biophysics</i>, vol. 53. Annual Reviews, pp. 487–510, 2024.","chicago":"Lo, Wei Chang, Ekaterina Krasnopeeva, and Teuta Pilizota. “Bacterial Electrophysiology.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2024. <a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">https://doi.org/10.1146/annurev-biophys-030822-032215</a>.","short":"W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024) 487–510.","ama":"Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. <i>Annual Review of Biophysics</i>. 2024;53:487-510. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">10.1146/annurev-biophys-030822-032215</a>","ista":"Lo WC, Krasnopeeva E, Pilizota T. 2024. Bacterial Electrophysiology. Annual Review of Biophysics. 53, 487–510.","mla":"Lo, Wei Chang, et al. “Bacterial Electrophysiology.” <i>Annual Review of Biophysics</i>, vol. 53, Annual Reviews, 2024, pp. 487–510, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">10.1146/annurev-biophys-030822-032215</a>."},"publisher":"Annual Reviews","author":[{"full_name":"Lo, Wei Chang","last_name":"Lo","first_name":"Wei Chang"},{"last_name":"Krasnopeeva","first_name":"Ekaterina","full_name":"Krasnopeeva, Ekaterina","id":"1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A"},{"full_name":"Pilizota, Teuta","first_name":"Teuta","last_name":"Pilizota"}],"date_created":"2024-07-28T22:01:09Z","day":"01","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","has_accepted_license":"1","file_date_updated":"2024-07-29T10:56:01Z","fulldoi":"https://doi.org/10.1146/annurev-biophys-030822-032215","article_type":"original","isi":1,"doi":"10.1146/annurev-biophys-030822-032215","type":"journal_article","publication_status":"published","publication_identifier":{"issn":["1936-122X"],"eissn":["1936-1238"]},"pmid":1,"_id":"17325","intvolume":"        53"},{"publication_status":"published","doi":"10.3847/1538-4357/ad4708","type":"journal_article","_id":"17326","issue":"1","article_number":"42","intvolume":"       970","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2024-07-29T11:02:48Z","article_processing_charge":"Yes","DOAJ_listed":"1","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.3847/1538-4357/ad4708","oa_version":"Published Version","ddc":["520"],"title":"Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","date_updated":"2025-09-08T08:42:20Z","volume":970,"author":[{"last_name":"Bhattacharya","first_name":"Shatanik","full_name":"Bhattacharya, Shatanik"},{"last_name":"Das","first_name":"Srijan B","full_name":"Das, Srijan B","id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","orcid":"0000-0003-0896-7972"},{"orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","first_name":"Lisa Annabelle"},{"full_name":"Panda, Subrata","first_name":"Subrata","last_name":"Panda"},{"full_name":"Hanasoge, Shravan M.","last_name":"Hanasoge","first_name":"Shravan M."}],"citation":{"ista":"Bhattacharya S, Das SB, Bugnet LA, Panda S, Hanasoge SM. 2024. Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars. Astrophysical Journal. 970(1), 42.","mla":"Bhattacharya, Shatanik, et al. “Detectability of Axisymmetric Magnetic Fields from the Core to the Surface of Oscillating Post-Main-Sequence Stars.” <i>Astrophysical Journal</i>, vol. 970, no. 1, 42, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/1538-4357/ad4708\">10.3847/1538-4357/ad4708</a>.","chicago":"Bhattacharya, Shatanik, Srijan B Das, Lisa Annabelle Bugnet, Subrata Panda, and Shravan M. Hanasoge. “Detectability of Axisymmetric Magnetic Fields from the Core to the Surface of Oscillating Post-Main-Sequence Stars.” <i>Astrophysical Journal</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/1538-4357/ad4708\">https://doi.org/10.3847/1538-4357/ad4708</a>.","short":"S. Bhattacharya, S.B. Das, L.A. Bugnet, S. Panda, S.M. Hanasoge, Astrophysical Journal 970 (2024).","ama":"Bhattacharya S, Das SB, Bugnet LA, Panda S, Hanasoge SM. Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars. <i>Astrophysical Journal</i>. 2024;970(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/ad4708\">10.3847/1538-4357/ad4708</a>","ieee":"S. Bhattacharya, S. B. Das, L. A. Bugnet, S. Panda, and S. M. Hanasoge, “Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars,” <i>Astrophysical Journal</i>, vol. 970, no. 1. IOP Publishing, 2024.","apa":"Bhattacharya, S., Das, S. B., Bugnet, L. A., Panda, S., &#38; Hanasoge, S. M. (2024). Detectability of axisymmetric magnetic fields from the core to the surface of oscillating post-main-sequence stars. <i>Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ad4708\">https://doi.org/10.3847/1538-4357/ad4708</a>"},"publisher":"IOP Publishing","day":"15","date_created":"2024-07-28T22:01:09Z","oa":1,"abstract":[{"lang":"eng","text":"Magnetic fields in the stellar interiors are key candidates to explain observed core rotation rates inside solar-like stars along their evolution. Recently, asteroseismic estimates of radial magnetic field amplitudes near the hydrogen-burning shell (H-shell) inside about 24 red giants (RGs) have been obtained by measuring frequency splittings from their power spectra. Using general Lorentz-stress (magnetic) kernels, we investigated the potential for detectability of near-surface magnetism in a 1.3 M⊙ star of supersolar metallicity as it evolves from a mid subgiant to a late subgiant into an RG. Based on these sensitivity kernels, we decompose an RG into three zones—deep core, H-shell, and near-surface. The subgiants instead required decomposition into an inner core, an outer core, and a near-surface layer. Additionally, we find that for a low-frequency g-dominated dipolar mode in the presence of a typical stable magnetic field, ∼25% of the frequency shift comes from the H-shell and the remaining from deeper layers. The ratio of the subsurface tangential field to the radial field in the H-burning shell decides if subsurface fields may be potentially detectable. For p-dominated dipole modes close to vmax, this ratio is around two orders of magnitude smaller in subgiant phases than the corresponding RG. Further, with the availability of magnetic kernels, we propose lower limits of field strengths in crucial layers in our stellar model during its evolutionary phases. The theoretical prescription outlined here provides the first formal way to devise inverse problems for stellar magnetism and can be seamlessly employed for slow rotators."}],"department":[{"_id":"LiBu"}],"language":[{"iso":"eng"}],"file":[{"success":1,"date_created":"2024-07-29T11:02:48Z","access_level":"open_access","checksum":"acb42a87deecbc9228fbbe6a48a37ec6","file_name":"2024_AstrophysicalJourn_Bhattacharya.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2024-07-29T11:02:48Z","file_size":3912290,"creator":"dernst","file_id":"17340"}],"publication":"Astrophysical Journal","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"external_id":{"isi":["001270972500001"],"arxiv":["2404.17167"]},"year":"2024","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. S.\r\nB.D. acknowledges Prof. Jeroen Tromp at Princeton University for supporting a part of this work. S.M.H., S.B., and S.P. acknowledge support from the Department of Atomic Energy,\r\nGovernment of India, under Project Identification No. RTI 4002. The authors would like to thank the reviewer(s) and data editor for their constructive comments and suggestions. The\r\ngeneration of the stellar models was done using the Modules for Experiments in Stellar Astrophysics (MESA Paxton et al. 2011, 2013, 2015, 2018, 2019; we have used MESA version\r\nr22.05.1 for RG and r23.05.1 for SG models, MESA-SDK version x86_64-linux-22.6.1). The eigenfrequencies and eigenfunctions for this model were calculated using the GYRE\r\n(Townsend & Teitler 2013) code. The code to calculate the kernels and the splittings has been written completely in Python 3.8.16.","month":"07","date_published":"2024-07-15T00:00:00Z","arxiv":1},{"publication_identifier":{"isbn":["9783959773232"],"issn":["1868-8969"]},"_id":"17327","intvolume":"       299","article_number":"2","doi":"10.4230/LIPIcs.FSCD.2024.2","type":"conference","publication_status":"published","alternative_title":["LIPIcs"],"fulldoi":"https://doi.org/10.4230/LIPIcs.FSCD.2024.2","corr_author":"1","isi":1,"article_processing_charge":"Yes","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2024-07-29T11:15:59Z","oa":1,"abstract":[{"lang":"eng","text":"Sequential decision-making in probabilistic environments is a fundamental problem with many applications in AI and economics. In this paper, we present an algorithm for synthesizing sequential decision-making agents that optimize statistical properties such as maximum and average response times. In the general setting of sequential decision-making, the environment is modeled as a random process that generates inputs. The agent responds to each input, aiming to maximize rewards and minimize costs within a specified time horizon. The corresponding synthesis problem is known to be PSPACE-hard. We consider the special case where the input distribution, reward, and cost depend on input-output statistics specified by counter automata. For such problems, this paper presents the first PTIME synthesis algorithms. We introduce the notion of statistical abstraction, which clusters statistically indistinguishable input-output sequences into equivalence classes. This abstraction allows for a dynamic programming algorithm whose complexity grows polynomially with the considered horizon, making the statistical case exponentially more efficient than the general case. We evaluate our algorithm on three different application scenarios of a client-server protocol, where multiple clients compete via bidding to gain access to the service offered by the server. The synthesized policies optimize profit while guaranteeing that none of the server’s clients is disproportionately starved of the service."}],"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"ista":"Cano F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. 2024. Abstraction-based decision making for statistical properties. 9th International Conference on Formal Structures for Computation and Deduction. FSCD: Conference on Formal Structures for Computation and Deduction, LIPIcs, vol. 299, 2.","mla":"Cano, Filip, et al. “Abstraction-Based Decision Making for Statistical Properties.” <i>9th International Conference on Formal Structures for Computation and Deduction</i>, vol. 299, 2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSCD.2024.2\">10.4230/LIPIcs.FSCD.2024.2</a>.","ama":"Cano F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. Abstraction-based decision making for statistical properties. In: <i>9th International Conference on Formal Structures for Computation and Deduction</i>. Vol 299. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSCD.2024.2\">10.4230/LIPIcs.FSCD.2024.2</a>","chicago":"Cano, Filip, Thomas A Henzinger, Bettina Könighofer, Konstantin Kueffner, and Kaushik Mallik. “Abstraction-Based Decision Making for Statistical Properties.” In <i>9th International Conference on Formal Structures for Computation and Deduction</i>, Vol. 299. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.FSCD.2024.2\">https://doi.org/10.4230/LIPIcs.FSCD.2024.2</a>.","short":"F. Cano, T.A. Henzinger, B. Könighofer, K. Kueffner, K. Mallik, in:, 9th International Conference on Formal Structures for Computation and Deduction, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","apa":"Cano, F., Henzinger, T. A., Könighofer, B., Kueffner, K., &#38; Mallik, K. (2024). Abstraction-based decision making for statistical properties. In <i>9th International Conference on Formal Structures for Computation and Deduction</i> (Vol. 299). Tallinn, Estonia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSCD.2024.2\">https://doi.org/10.4230/LIPIcs.FSCD.2024.2</a>","ieee":"F. Cano, T. A. Henzinger, B. Könighofer, K. Kueffner, and K. Mallik, “Abstraction-based decision making for statistical properties,” in <i>9th International Conference on Formal Structures for Computation and Deduction</i>, Tallinn, Estonia, 2024, vol. 299."},"author":[{"full_name":"Cano, Filip","first_name":"Filip","last_name":"Cano"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Könighofer, Bettina","last_name":"Könighofer","first_name":"Bettina"},{"orcid":"0000-0001-8974-2542","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","full_name":"Kueffner, Konstantin","first_name":"Konstantin","last_name":"Kueffner"},{"full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","last_name":"Mallik"}],"day":"01","date_created":"2024-07-28T22:01:09Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Abstraction-based decision making for statistical properties","status":"public","date_updated":"2025-12-02T13:43:50Z","volume":299,"oa_version":"Published Version","ddc":["000"],"scopus_import":"1","acknowledgement":"This work is partly supported by the European Research Council under Grant No.: ERC2020-AdG 101020093. It is also partially supported by the State Government of Styria, Austria –\r\nDepartment Zukunftsfonds Steiermark.","date_published":"2024-07-01T00:00:00Z","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2024_LIPICs_Cano.pdf","file_id":"17341","creator":"dernst","file_size":1391381,"date_updated":"2024-07-29T11:15:59Z","checksum":"cc6bb89be0eaa404a6ce019392cd293e","success":1,"date_created":"2024-07-29T11:15:59Z","access_level":"open_access"}],"publication":"9th International Conference on Formal Structures for Computation and Deduction","external_id":{"isi":["001587746100002"]},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"conference":{"start_date":"2024-07-10","name":"FSCD: Conference on Formal Structures for Computation and Deduction","end_date":"2024-07-13","location":"Tallinn, Estonia"}},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2024-07-29T07:37:31Z","fulldoi":"https://doi.org/10.1145/3662158.3662768","corr_author":"1","doi":"10.1145/3662158.3662768","type":"conference","publication_status":"published","publication_identifier":{"isbn":["9798400706684"]},"_id":"17329","year":"2024","ec_funded":1,"file":[{"checksum":"65a40437f83373fa79dd999d5287509e","access_level":"open_access","date_created":"2024-07-29T07:37:31Z","success":1,"creator":"dernst","file_id":"17335","file_size":750908,"date_updated":"2024-07-29T07:37:31Z","relation":"main_file","content_type":"application/pdf","file_name":"2024_ACMPODC_Alistarh.pdf"}],"publication":"Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"conference":{"location":"Nantes, France","name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2024-06-17","end_date":"2024-06-21"},"page":"40-49","acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) grant. We thank James Aspnes and Thomas Sauerwald for several helpful discussions on Ehrenfest random walks.","scopus_import":"1","date_published":"2024-06-17T00:00:00Z","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","title":"Game dynamics and equilibrium computation in the population protocol model","date_updated":"2025-04-14T07:52:47Z","oa_version":"Published Version","ddc":["000"],"oa":1,"abstract":[{"text":"We initiate the study of game dynamics in the population protocol model: n agents each maintain a current local strategy and interact in pairs uniformly at random. Upon each interaction, the agents play a two-person game and receive a payoff from an underlying utility function, and they can subsequently update their strategies according to a fixed local algorithm. In this setting, we ask how the distribution over agent strategies evolves over a sequence of interactions, and we introduce a new distributional equilibrium concept to quantify the quality of such distributions. As an initial example, we study a class of repeated prisoner's dilemma games, and we consider a family of simple local update algorithms that yield non-trivial dynamics over the distribution of agent strategies. We show that these dynamics are related to a new class of high-dimensional Ehrenfest random walks, and we derive exact characterizations of their stationary distributions, bounds on their mixing times, and prove their convergence to approximate distributional equilibria. Our results highlight trade-offs between the local state space of each agent, and the convergence rate and approximation factor of the underlying dynamics. Our approach opens the door towards the further characterization of equilibrium computation for other classes of games and dynamics in the population setting.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"DaAl"},{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","citation":{"ama":"Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. Game dynamics and equilibrium computation in the population protocol model. In: <i>Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2024:40-49. doi:<a href=\"https://doi.org/10.1145/3662158.3662768\">10.1145/3662158.3662768</a>","chicago":"Alistarh, Dan-Adrian, Krishnendu Chatterjee, Mehrdad Karrabi, and John M Lazarsfeld. “Game Dynamics and Equilibrium Computation in the Population Protocol Model.” In <i>Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing</i>, 40–49. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3662158.3662768\">https://doi.org/10.1145/3662158.3662768</a>.","short":"D.-A. Alistarh, K. Chatterjee, M. Karrabi, J.M. Lazarsfeld, in:, Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2024, pp. 40–49.","ista":"Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. 2024. Game dynamics and equilibrium computation in the population protocol model. Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 40–49.","mla":"Alistarh, Dan-Adrian, et al. “Game Dynamics and Equilibrium Computation in the Population Protocol Model.” <i>Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2024, pp. 40–49, doi:<a href=\"https://doi.org/10.1145/3662158.3662768\">10.1145/3662158.3662768</a>.","ieee":"D.-A. Alistarh, K. Chatterjee, M. Karrabi, and J. M. Lazarsfeld, “Game dynamics and equilibrium computation in the population protocol model,” in <i>Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing</i>, Nantes, France, 2024, pp. 40–49.","apa":"Alistarh, D.-A., Chatterjee, K., Karrabi, M., &#38; Lazarsfeld, J. M. (2024). Game dynamics and equilibrium computation in the population protocol model. In <i>Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing</i> (pp. 40–49). Nantes, France: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3662158.3662768\">https://doi.org/10.1145/3662158.3662768</a>"},"author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"67638922-f394-11eb-9cf6-f20423e08757","full_name":"Karrabi, Mehrdad","first_name":"Mehrdad","last_name":"Karrabi"},{"full_name":"Lazarsfeld, John M","id":"17ce3656-183e-11ef-84c3-8932383e1b23","first_name":"John M","last_name":"Lazarsfeld"}],"day":"17","date_created":"2024-07-28T22:01:10Z"}]