[{"file_date_updated":"2024-07-16T06:16:11Z","publication":"Bio-protocol","scopus_import":"1","author":[{"full_name":"Li, Ziqiang","last_name":"Li","first_name":"Ziqiang","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3"},{"first_name":"Jennifer","last_name":"Huard","full_name":"Huard, Jennifer"},{"first_name":"Emmanuelle M.","full_name":"Bayer, Emmanuelle M.","last_name":"Bayer"},{"first_name":"Valérie","last_name":"Wattelet-Boyer","full_name":"Wattelet-Boyer, Valérie"}],"intvolume":"        14","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.).","file":[{"date_updated":"2024-07-16T06:16:11Z","content_type":"application/pdf","checksum":"c8671c0ad483da6407cb16cc3fef1990","file_size":2896048,"file_id":"17242","date_created":"2024-07-16T06:16:11Z","creator":"dernst","file_name":"2024_BioProtocol_Li.pdf","relation":"main_file","access_level":"open_access","success":1}],"pmid":1,"publication_identifier":{"eissn":["2331-8325"]},"oa":1,"publication_status":"published","department":[{"_id":"MiSi"}],"external_id":{"pmid":["39007160"]},"date_created":"2024-07-14T22:01:11Z","language":[{"iso":"eng"}],"volume":14,"quality_controlled":"1","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."}],"license":"https://creativecommons.org/licenses/by/4.0/","article_number":"e5029","has_accepted_license":"1","date_published":"2024-07-05T00:00:00Z","oa_version":"Published Version","year":"2024","date_updated":"2025-03-06T10:28:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","publisher":"Bio-Protocol","day":"05","issue":"13","ddc":["570"],"doi":"10.21769/BioProtoc.5029","article_type":"original","_id":"17233","title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis","month":"07","article_processing_charge":"Yes","citation":{"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>.","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>","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>","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>.","short":"Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024)."}},{"volume":969,"quality_controlled":"1","article_number":"L13","abstract":[{"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.","lang":"eng"}],"publication_status":"published","date_created":"2024-07-14T22:01:11Z","department":[{"_id":"JoMa"}],"external_id":{"arxiv":["2405.01473"],"isi":["001257903200001"]},"language":[{"iso":"eng"}],"DOAJ_listed":"1","file":[{"file_size":3273303,"date_created":"2024-07-16T06:24:29Z","file_id":"17243","file_name":"2024_AstrophysicalJourn_Wang.pdf","creator":"dernst","date_updated":"2024-07-16T06:24:29Z","checksum":"bb1a6725586df12e745d091b5778bb2b","content_type":"application/pdf","success":1,"relation":"main_file","access_level":"open_access"}],"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).","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"oa":1,"file_date_updated":"2024-07-16T06:24:29Z","publication":"Astrophysical Journal Letters","author":[{"last_name":"Wang","full_name":"Wang, Bingjie","first_name":"Bingjie"},{"first_name":"Joel","last_name":"Leja","full_name":"Leja, Joel"},{"first_name":"Anna","full_name":"De Graaff, Anna","last_name":"De Graaff"},{"last_name":"Brammer","full_name":"Brammer, Gabriel B.","first_name":"Gabriel B."},{"first_name":"Andrea","last_name":"Weibel","full_name":"Weibel, Andrea"},{"full_name":"Van Dokkum, Pieter","last_name":"Van Dokkum","first_name":"Pieter"},{"first_name":"Josephine F.W.","last_name":"Baggen","full_name":"Baggen, Josephine F.W."},{"first_name":"Katherine A.","full_name":"Suess, Katherine A.","last_name":"Suess"},{"first_name":"Jenny E.","last_name":"Greene","full_name":"Greene, Jenny E."},{"full_name":"Bezanson, Rachel","last_name":"Bezanson","first_name":"Rachel"},{"full_name":"Cleri, Nikko J.","last_name":"Cleri","first_name":"Nikko J."},{"first_name":"Michaela","last_name":"Hirschmann","full_name":"Hirschmann, Michaela"},{"last_name":"Labbé","full_name":"Labbé, Ivo","first_name":"Ivo"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"last_name":"Mcconachie","full_name":"Mcconachie, Ian","first_name":"Ian"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"last_name":"Nelson","full_name":"Nelson, Erica","first_name":"Erica"},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"full_name":"Setton, David J.","last_name":"Setton","first_name":"David J."},{"first_name":"Christina C.","full_name":"Williams, Christina C.","last_name":"Williams"}],"scopus_import":"1","isi":1,"intvolume":"       969","_id":"17234","month":"07","title":"RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec","article_processing_charge":"Yes","citation":{"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.","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).","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>.","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>.","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.","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>","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>"},"ddc":["520"],"arxiv":1,"article_type":"original","doi":"10.3847/2041-8213/ad55f7","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"1","type":"journal_article","publisher":"IOP Publishing","day":"01","date_published":"2024-07-01T00:00:00Z","has_accepted_license":"1","date_updated":"2025-09-08T08:10:21Z","year":"2024","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"file":[{"file_id":"17244","date_created":"2024-07-16T06:30:30Z","file_name":"2024_APLMaterial_Kohopaa.pdf","creator":"dernst","file_size":9408198,"content_type":"application/pdf","checksum":"32a5cdf0ea9c937f806b6039f3219917","date_updated":"2024-07-16T06:30:30Z","success":1,"relation":"main_file","access_level":"open_access"}],"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).","publication_identifier":{"eissn":["2166-532X"]},"oa":1,"file_date_updated":"2024-07-16T06:30:30Z","publication":"APL Materials","scopus_import":"1","author":[{"first_name":"Katja","full_name":"Kohopää, Katja","last_name":"Kohopää"},{"first_name":"Alberto","full_name":"Ronzani, Alberto","last_name":"Ronzani"},{"last_name":"Jabdaraghi","full_name":"Jabdaraghi, Robab Najafi","first_name":"Robab Najafi"},{"first_name":"Arijit","full_name":"Bera, Arijit","last_name":"Bera"},{"first_name":"Mário","full_name":"Ribeiro, Mário","last_name":"Ribeiro"},{"full_name":"Hazra, Dibyendu","last_name":"Hazra","first_name":"Dibyendu"},{"full_name":"Senior, Jorden L","last_name":"Senior","first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","orcid":"0000-0002-0672-9295"},{"last_name":"Prunnila","full_name":"Prunnila, Mika","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."},{"first_name":"Antti","full_name":"Kemppinen, Antti","last_name":"Kemppinen"}],"isi":1,"intvolume":"        12","ec_funded":1,"volume":12,"quality_controlled":"1","article_number":"071101","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"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_status":"published","date_created":"2024-07-14T22:01:11Z","department":[{"_id":"AnHi"}],"external_id":{"isi":["001260942200003"]},"language":[{"iso":"eng"}],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"7","publisher":"AIP Publishing","day":"01","type":"journal_article","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_published":"2024-07-01T00:00:00Z","has_accepted_license":"1","date_updated":"2025-09-08T08:10:58Z","oa_version":"Published Version","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17235","month":"07","title":"Effect of ion irradiation on superconducting thin films","article_processing_charge":"Yes","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>","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>","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.","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>.","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).","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."},"ddc":["530"],"article_type":"original","doi":"10.1063/5.0202851"},{"abstract":[{"lang":"eng","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."}],"quality_controlled":"1","external_id":{"isi":["001253331900044"],"arxiv":["2307.00115"]},"department":[{"_id":"VlKo"}],"date_created":"2024-07-14T22:01:11Z","language":[{"iso":"eng"}],"corr_author":"1","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","success":1,"checksum":"6ca18ac8508719dbd5d5735f4c991af2","content_type":"application/pdf","date_updated":"2024-07-16T06:38:08Z","file_id":"17245","date_created":"2024-07-16T06:38:08Z","creator":"dernst","file_name":"2024_SPAA_Kolmogorov.pdf","file_size":1116166}],"oa":1,"publication_identifier":{"isbn":["9798400704161"],"issn":["1548-6109"]},"file_date_updated":"2024-07-16T06:38:08Z","scopus_import":"1","publication":"Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures","author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"article_processing_charge":"Yes (via OA deal)","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2024-06-17","location":"Nantes, France","end_date":"2024-06-21"},"citation":{"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>.","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.","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>","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>","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.","short":"V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–414.","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>."},"related_material":{"record":[{"status":"public","relation":"extended_version","id":"21007"}]},"_id":"17236","title":"A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut","month":"06","OA_place":"publisher","doi":"10.1145/3626183.3659969","OA_type":"hybrid","arxiv":1,"ddc":["510"],"type":"conference","day":"17","publisher":"Association for Computing Machinery","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"403-414","has_accepted_license":"1","date_published":"2024-06-17T00:00:00Z","year":"2024","oa_version":"Published Version","date_updated":"2026-01-21T09:46:25Z"},{"article_processing_charge":"No","citation":{"short":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal of Evolutionary Biology 37 (2024) 677–692.","mla":"Reynes, Lauric, et al. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:<a href=\"https://doi.org/10.1093/jeb/voae048\">10.1093/jeb/voae048</a>.","ieee":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, and M. Valero, “Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations,” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6. Oxford University Press, pp. 677–692, 2024.","ama":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. <i>Journal of Evolutionary Biology</i>. 2024;37(6):677-692. doi:<a href=\"https://doi.org/10.1093/jeb/voae048\">10.1093/jeb/voae048</a>","apa":"Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., &#38; Valero, M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae048\">https://doi.org/10.1093/jeb/voae048</a>","chicago":"Reynes, Lauric, Louise Fouqueau, Didier Aurelle, Stephane Mauger, Christophe Destombe, and Myriam Valero. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae048\">https://doi.org/10.1093/jeb/voae048</a>.","ista":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. 2024. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. Journal of Evolutionary Biology. 37(6), 677–692."},"_id":"17237","title":"Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations","month":"06","doi":"10.1093/jeb/voae048","article_type":"original","arxiv":1,"publisher":"Oxford University Press","day":"01","type":"journal_article","issue":"6","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"677-692","date_published":"2024-06-01T00:00:00Z","oa_version":"Preprint","year":"2024","date_updated":"2025-06-04T07:23:23Z","abstract":[{"text":"The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.","lang":"eng"}],"volume":37,"quality_controlled":"1","external_id":{"arxiv":["2404.14003"],"pmid":["38629140"]},"department":[{"_id":"NiBa"}],"date_created":"2024-07-14T22:01:12Z","language":[{"iso":"eng"}],"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2404.14003","open_access":"1"}],"acknowledgement":"This work was funded by the EU project MARFOR Biodiversa/004/2015. L.F. was additionally funded by the Region Bretagne (ARED 2017 REEALG) and the NOMIS Foundation. The project leading to this publication has received funding from the EC2CO (CNRS) fund and from the European FEDER Fund under project 1166-39417.\r\nThis work is especially dedicated to the memory of Gernot Glöckner who contributed to the sequencing of Laminaria digitata genome and passed away in very recent time. The authors thank the ABiMS platform of the Roscoff biological station (http://abims.sb-roscoff.fr) for providing the HPC resources that contributed to the search results reported in this document. We also acknowledge the staff of the “Cluster de calcul intensif HPC” Platform of the OSU Institut Pythéas (Aix-Marseille Université, INSU-CNRS) for providing the computing facilities.","pmid":1,"oa":1,"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"scopus_import":"1","author":[{"last_name":"Reynes","full_name":"Reynes, Lauric","first_name":"Lauric"},{"orcid":"0000-0003-0371-9339","last_name":"Fouqueau","full_name":"Fouqueau, Louise","first_name":"Louise","id":"1676e173-8143-11ed-8927-fe165216a93f"},{"first_name":"Didier","full_name":"Aurelle, Didier","last_name":"Aurelle"},{"full_name":"Mauger, Stephane","last_name":"Mauger","first_name":"Stephane"},{"first_name":"Christophe","full_name":"Destombe, Christophe","last_name":"Destombe"},{"full_name":"Valero, Myriam","last_name":"Valero","first_name":"Myriam"}],"publication":"Journal of Evolutionary Biology","intvolume":"        37"},{"file":[{"success":1,"relation":"main_file","access_level":"open_access","date_created":"2024-07-15T09:45:25Z","file_id":"17241","file_name":"2024_JourEvolutionaryBiology_Barton.pdf","creator":"dernst","file_size":1194263,"content_type":"application/pdf","checksum":"94e6b68bddf6cadcec29c7f41647359f","date_updated":"2024-07-15T09:45:25Z"}],"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.","pmid":1,"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"oa":1,"publication":"Journal of Evolutionary Biology","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"file_date_updated":"2024-07-15T09:45:25Z","scopus_import":"1","isi":1,"intvolume":"        37","abstract":[{"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.","lang":"eng"}],"volume":37,"quality_controlled":"1","department":[{"_id":"NiBa"}],"external_id":{"isi":["001225323900001"],"pmid":["38683160"]},"date_created":"2024-07-14T22:01:12Z","language":[{"iso":"eng"}],"corr_author":"1","publication_status":"published","type":"journal_article","publisher":"Oxford University Press","day":"01","issue":"6","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"605-615","date_published":"2024-06-01T00:00:00Z","has_accepted_license":"1","project":[{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"year":"2024","oa_version":"Published Version","date_updated":"2025-09-08T08:08:41Z","article_processing_charge":"Yes (via OA deal)","citation":{"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.","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>.","short":"N.H. Barton, Journal of Evolutionary Biology 37 (2024) 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>.","ista":"Barton NH. 2024. Limits to species’ range: The tension between local and global adaptation. Journal of Evolutionary Biology. 37(6), 605–615.","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>","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>"},"_id":"17238","title":"Limits to species' range: The tension between local and global adaptation","month":"06","doi":"10.1093/jeb/voae052","article_type":"review","ddc":["570"]},{"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"28","publisher":"American Chemical Society","day":"16","type":"journal_article","project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"date_published":"2024-07-16T00:00:00Z","has_accepted_license":"1","date_updated":"2025-12-16T09:01:10Z","year":"2024","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"18485-18492","_id":"17239","month":"07","title":"In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures","article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. 2024. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 18(28), 18485–18492.","chicago":"Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Šarić, and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>.","apa":"Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., &#38; Garcia, R. (2024). In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>","ama":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. 2024;18(28):18485-18492. doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>","ieee":"C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Šarić, and R. Garcia, “In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,” <i>ACS Nano</i>, vol. 18, no. 28. American Chemical Society, pp. 18485–18492, 2024.","short":"C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano 18 (2024) 18485–18492.","mla":"Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>, vol. 18, no. 28, American Chemical Society, 2024, pp. 18485–92, doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>."},"ddc":["540"],"article_type":"original","OA_type":"hybrid","OA_place":"publisher","doi":"10.1021/acsnano.4c03839","pmid":1,"acknowledgement":"We are grateful to Nancy Forde (Simon Fraser University) for her motivating comments. Financial support from the Ministerio de Ciencia, Innovación y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged. A.Š. and K.K. acknowledge support from the Royal Society University Research Fellowship and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant No. 585 80296).","file":[{"content_type":"application/pdf","checksum":"b7e9ce718e92f568bcb3810e8e28e458","date_updated":"2025-01-09T12:06:48Z","creator":"dernst","file_name":"2024_ACSNano_GarciaSacristan.pdf","file_id":"18808","date_created":"2025-01-09T12:06:48Z","file_size":10036838,"access_level":"open_access","relation":"main_file","success":1}],"oa":1,"publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"publication":"ACS Nano","file_date_updated":"2025-01-09T12:06:48Z","scopus_import":"1","author":[{"first_name":"Clara","full_name":"Garcia-Sacristan, Clara","last_name":"Garcia-Sacristan"},{"first_name":"Victor G.","full_name":"Gisbert, Victor G.","last_name":"Gisbert"},{"full_name":"Klein, Kevin","last_name":"Klein","first_name":"Kevin","id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Garcia, Ricardo","last_name":"Garcia","first_name":"Ricardo"}],"intvolume":"        18","isi":1,"ec_funded":1,"volume":18,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes."}],"publication_status":"published","date_created":"2024-07-14T22:01:12Z","department":[{"_id":"AnSa"}],"external_id":{"isi":["001263155500001"],"pmid":["38958189"]},"language":[{"iso":"eng"}]},{"citation":{"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>.","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>","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>.","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."},"related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/a-railroad-of-cells/","relation":"press_release"}]},"article_processing_charge":"No","title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","month":"09","_id":"17269","doi":"10.1038/s41567-024-02532-x","OA_place":"repository","article_type":"original","OA_type":"green","type":"journal_article","publisher":"Springer Nature","day":"01","status":"public","page":"1492-1500","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","oa_version":"Preprint","date_updated":"2025-09-08T08:28:31Z","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"date_published":"2024-09-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","volume":20,"language":[{"iso":"eng"}],"corr_author":"1","external_id":{"isi":["001250246200004"]},"department":[{"_id":"EdHa"}],"date_created":"2024-07-16T12:32:17Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/2022.07.17.500364","open_access":"1"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"oa":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.","ec_funded":1,"isi":1,"intvolume":"        20","publication":"Nature Physics","scopus_import":"1","author":[{"full_name":"Vercruysse, Eléonore","last_name":"Vercruysse","first_name":"Eléonore"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"last_name":"Gómez-González","full_name":"Gómez-González, Manuel","first_name":"Manuel"},{"first_name":"Alexandre","last_name":"Remson","full_name":"Remson, Alexandre"},{"first_name":"Marine","full_name":"Luciano, Marine","last_name":"Luciano"},{"first_name":"Yohalie","full_name":"Kalukula, Yohalie","last_name":"Kalukula"},{"first_name":"Leone","last_name":"Rossetti","full_name":"Rossetti, Leone"},{"last_name":"Trepat","full_name":"Trepat, Xavier","first_name":"Xavier"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Gabriele","full_name":"Gabriele, Sylvain","first_name":"Sylvain"}]},{"status":"public","type":"journal_article","day":"15","publisher":"Elsevier","issue":"8","date_published":"2024-10-15T00:00:00Z","oa_version":"Preprint","year":"2024","date_updated":"2025-09-08T08:25:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17277","title":"Stability for the logarithmic Sobolev inequality","month":"10","article_processing_charge":"No","citation":{"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>.","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.","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>","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>","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>.","ista":"Brigati G, Dolbeault J, Simonov N. 2024. Stability for the logarithmic Sobolev inequality. Journal of Functional Analysis. 287(8), 110562."},"arxiv":1,"OA_place":"repository","doi":"10.1016/j.jfa.2024.110562","OA_type":"green","article_type":"original","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.","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"oa":1,"main_file_link":[{"url":"10.48550/arXiv.2303.12926","open_access":"1"}],"scopus_import":"1","author":[{"first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","full_name":"Brigati, Giovanni","last_name":"Brigati"},{"first_name":"Jean","last_name":"Dolbeault","full_name":"Dolbeault, Jean"},{"full_name":"Simonov, Nikita","last_name":"Simonov","first_name":"Nikita"}],"publication":"Journal of Functional Analysis","isi":1,"intvolume":"       287","volume":287,"quality_controlled":"1","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"}],"article_number":"110562","publication_status":"published","department":[{"_id":"JaMa"}],"external_id":{"isi":["001271814000001"],"arxiv":["2303.12926"]},"date_created":"2024-07-21T22:01:00Z","corr_author":"1","language":[{"iso":"eng"}]},{"abstract":[{"text":"An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult due to the complexities and convergence problems of Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes, or lack thereof, in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes and reveal that they tend to form when the mixture components have similar boiling points and strong interactions.","lang":"eng"}],"article_number":"034111","quality_controlled":"1","volume":161,"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001281819100016"],"arxiv":["2405.02216"],"pmid":["39007379"]},"department":[{"_id":"BiCh"},{"_id":"GradSch"}],"date_created":"2024-07-21T22:01:00Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.02216"}],"oa":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"acknowledgement":"B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No. EP/P020259/1).","pmid":1,"intvolume":"       161","isi":1,"publication":"Journal of Chemical Physics","scopus_import":"1","author":[{"first_name":"Xiaoyu","id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","last_name":"Wang","full_name":"Wang, Xiaoyu"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632"}],"citation":{"ama":"Wang X, Cheng B. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. <i>Journal of Chemical Physics</i>. 2024;161(3). doi:<a href=\"https://doi.org/10.1063/5.0217232\">10.1063/5.0217232</a>","apa":"Wang, X., &#38; Cheng, B. (2024). Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0217232\">https://doi.org/10.1063/5.0217232</a>","chicago":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0217232\">https://doi.org/10.1063/5.0217232</a>.","ista":"Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 161(3), 034111.","mla":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal of Chemical Physics</i>, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0217232\">10.1063/5.0217232</a>.","short":"X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).","ieee":"X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures,” <i>Journal of Chemical Physics</i>, vol. 161, no. 3. AIP Publishing, 2024."},"related_material":{"link":[{"relation":"software","url":"https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0"}]},"article_processing_charge":"No","title":"Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures","month":"07","_id":"17278","doi":"10.1063/5.0217232","article_type":"original","arxiv":1,"publisher":"AIP Publishing","type":"journal_article","day":"14","issue":"3","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","oa_version":"Preprint","date_updated":"2025-09-08T08:26:09Z","date_published":"2024-07-14T00:00:00Z"},{"_id":"17279","title":"Rescuing T cells from stiff tumors","month":"07","article_processing_charge":"No","citation":{"ista":"Avellaneda Sarrió M, Sixt MK. 2024. Rescuing T cells from stiff tumors. Cell Chemical Biology. 31(7), 1242–1243.","chicago":"Avellaneda Sarrió, Mario, and Michael K Sixt. “Rescuing T Cells from Stiff Tumors.” <i>Cell Chemical Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">https://doi.org/10.1016/j.chembiol.2024.06.011</a>.","apa":"Avellaneda Sarrió, M., &#38; Sixt, M. K. (2024). Rescuing T cells from stiff tumors. <i>Cell Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">https://doi.org/10.1016/j.chembiol.2024.06.011</a>","ama":"Avellaneda Sarrió M, Sixt MK. Rescuing T cells from stiff tumors. <i>Cell Chemical Biology</i>. 2024;31(7):1242-1243. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">10.1016/j.chembiol.2024.06.011</a>","ieee":"M. Avellaneda Sarrió and M. K. Sixt, “Rescuing T cells from stiff tumors,” <i>Cell Chemical Biology</i>, vol. 31, no. 7. Elsevier, pp. 1242–1243, 2024.","mla":"Avellaneda Sarrió, Mario, and Michael K. Sixt. “Rescuing T Cells from Stiff Tumors.” <i>Cell Chemical Biology</i>, vol. 31, no. 7, Elsevier, 2024, pp. 1242–43, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2024.06.011\">10.1016/j.chembiol.2024.06.011</a>.","short":"M. Avellaneda Sarrió, M.K. Sixt, Cell Chemical Biology 31 (2024) 1242–1243."},"doi":"10.1016/j.chembiol.2024.06.011","article_type":"review","status":"public","type":"journal_article","day":"18","publisher":"Elsevier","issue":"7","date_published":"2024-07-18T00:00:00Z","oa_version":"None","year":"2024","date_updated":"2025-09-08T08:27:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"1242-1243","volume":31,"quality_controlled":"1","abstract":[{"text":"In a recent issue of Cell, Zhang et al.1 demonstrate that mechanical features of a solid tumor can drive T cells into dysfunctionality and identify pathways that revert this “exhausted” state.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001275725000001"],"pmid":["39029454"]},"department":[{"_id":"MiSi"}],"date_created":"2024-07-21T22:01:00Z","corr_author":"1","language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"eissn":["2451-9448"],"issn":["2451-9456"]},"scopus_import":"1","author":[{"orcid":"0000-0001-6406-524X","last_name":"Avellaneda Sarrió","full_name":"Avellaneda Sarrió, Mario","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","first_name":"Mario"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"}],"publication":"Cell Chemical Biology","isi":1,"intvolume":"        31"},{"article_processing_charge":"Yes","citation":{"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>","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>","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>.","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>.","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).","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."},"_id":"17280","title":"Monoallelic de novo AJAP1 loss-of- function variants disrupt trans-synaptic control of neurotransmitter release","month":"07","doi":"10.1126/sciadv.adk5462","OA_place":"publisher","OA_type":"gold","article_type":"original","ddc":["570"],"publisher":"American Association for the Advancement of Science","type":"journal_article","day":"12","issue":"28","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-12T00:00:00Z","has_accepted_license":"1","year":"2024","oa_version":"Published Version","date_updated":"2025-09-08T08:15:54Z","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"}],"article_number":"adk5462","volume":10,"quality_controlled":"1","department":[{"_id":"RySh"},{"_id":"PreCl"}],"external_id":{"isi":["001280159000022"],"pmid":["38985877"]},"date_created":"2024-07-21T22:01:01Z","language":[{"iso":"eng"}],"publication_status":"published","DOAJ_listed":"1","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.","file":[{"date_updated":"2024-07-22T06:29:27Z","checksum":"9cbc4501fcd4ba1c0811fd244031422b","content_type":"application/pdf","file_size":7241489,"creator":"dernst","file_name":"2024_ScienceAdv_Früh.pdf","file_id":"17287","date_created":"2024-07-22T06:29:27Z","access_level":"open_access","relation":"main_file","success":1}],"pmid":1,"publication_identifier":{"eissn":["2375-2548"]},"oa":1,"publication":"Science Advances","scopus_import":"1","file_date_updated":"2024-07-22T06:29:27Z","author":[{"full_name":"Früh, Simon","last_name":"Früh","first_name":"Simon"},{"full_name":"Boudkkazi, Sami","last_name":"Boudkkazi","first_name":"Sami"},{"orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"full_name":"Sereikaite, Vita","last_name":"Sereikaite","first_name":"Vita"},{"full_name":"Chen, Li Yuan","last_name":"Chen","first_name":"Li Yuan"},{"first_name":"Diego","full_name":"Fernandez-Fernandez, Diego","last_name":"Fernandez-Fernandez"},{"first_name":"Pascal D.","last_name":"Rem","full_name":"Rem, Pascal D."},{"last_name":"Ulrich","full_name":"Ulrich, Daniel","first_name":"Daniel"},{"last_name":"Schwenk","full_name":"Schwenk, Jochen","first_name":"Jochen"},{"first_name":"Ziyang","full_name":"Chen, Ziyang","last_name":"Chen"},{"first_name":"Elodie Le","full_name":"Monnier, Elodie Le","last_name":"Monnier"},{"first_name":"Thorsten","full_name":"Fritzius, Thorsten","last_name":"Fritzius"},{"full_name":"Innocenti, Sabrina M.","last_name":"Innocenti","first_name":"Sabrina M."},{"first_name":"Valérie","last_name":"Besseyrias","full_name":"Besseyrias, Valérie"},{"last_name":"Trovò","full_name":"Trovò, Luca","first_name":"Luca"},{"last_name":"Stawarski","full_name":"Stawarski, Michal","first_name":"Michal"},{"full_name":"Argilli, Emanuela","last_name":"Argilli","first_name":"Emanuela"},{"first_name":"Elliott H.","last_name":"Sherr","full_name":"Sherr, Elliott H."},{"first_name":"Bregje","full_name":"Van Bon, Bregje","last_name":"Van Bon"},{"first_name":"Erik Jan","full_name":"Kamsteeg, Erik Jan","last_name":"Kamsteeg"},{"full_name":"Iascone, Maria","last_name":"Iascone","first_name":"Maria"},{"full_name":"Pilotta, Alba","last_name":"Pilotta","first_name":"Alba"},{"first_name":"Maria R.","last_name":"Cutrì","full_name":"Cutrì, Maria R."},{"first_name":"Mahshid S.","last_name":"Azamian","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."},{"first_name":"Jill A.","last_name":"Rosenfeld","full_name":"Rosenfeld, Jill A."},{"full_name":"Zhao, Xiaonan","last_name":"Zhao","first_name":"Xiaonan"},{"first_name":"Tiphanie P.","last_name":"Vogel","full_name":"Vogel, Tiphanie P."},{"first_name":"Herda","full_name":"Ona, Herda","last_name":"Ona"},{"first_name":"Daryl A.","full_name":"Scott, Daryl A.","last_name":"Scott"},{"first_name":"Peter","last_name":"Scheiffele","full_name":"Scheiffele, Peter"},{"full_name":"Strømgaard, Kristian","last_name":"Strømgaard","first_name":"Kristian"},{"first_name":"Mehdi","full_name":"Tafti, Mehdi","last_name":"Tafti"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"full_name":"Fakler, Bernd","last_name":"Fakler","first_name":"Bernd"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Bernhard","full_name":"Bettler, Bernhard","last_name":"Bettler"}],"intvolume":"        10","isi":1},{"intvolume":"      2024","isi":1,"publication":"International Mathematics Research Notices","file_date_updated":"2024-07-22T06:40:19Z","scopus_import":"1","author":[{"last_name":"Campbell","full_name":"Campbell, Andrew J","id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","first_name":"Andrew J"},{"first_name":"Sean","last_name":"O'Rourke","full_name":"O'Rourke, Sean"},{"last_name":"Renfrew","full_name":"Renfrew, David T","first_name":"David T","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3493-121X"}],"publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"oa":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.","file":[{"date_updated":"2024-07-22T06:40:19Z","checksum":"f36a7dbf53f23d5833db711052e69b49","content_type":"application/pdf","file_size":1233508,"creator":"dernst","file_name":"2024_IMRN_Campbell.pdf","file_id":"17288","date_created":"2024-07-22T06:40:19Z","access_level":"open_access","relation":"main_file","success":1}],"publication_status":"published","corr_author":"1","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"external_id":{"isi":["001198019500001"]},"date_created":"2024-07-21T22:01:01Z","quality_controlled":"1","volume":2024,"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"}],"year":"2024","oa_version":"Published Version","date_updated":"2025-09-08T08:16:32Z","date_published":"2024-07-01T00:00:00Z","has_accepted_license":"1","page":"10189-10218","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","type":"journal_article","day":"01","publisher":"Oxford University Press","issue":"13","ddc":["510"],"doi":"10.1093/imrn/rnae062","article_type":"original","title":"The fractional free convolution of R-diagonal elements and random polynomials under repeated differentiation","month":"07","_id":"17281","citation":{"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>.","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.","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>","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>","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.","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>.","short":"A.J. Campbell, S. O’Rourke, D.T. Renfrew, International Mathematics Research Notices 2024 (2024) 10189–10218."},"article_processing_charge":"Yes (via OA deal)"},{"arxiv":1,"ddc":["510"],"doi":"10.1007/s00526-024-02755-z","article_type":"original","title":"Characterisation of gradient flows for a given functional","month":"07","_id":"17282","citation":{"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>","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>","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>.","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>.","short":"M. Brooks, J. Maas, Calculus of Variations and Partial Differential Equations 63 (2024).","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."},"article_processing_charge":"Yes (via OA deal)","year":"2024","oa_version":"Published Version","date_updated":"2025-09-08T08:24:51Z","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"has_accepted_license":"1","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","day":"01","type":"journal_article","publisher":"Springer Nature","issue":"6","publication_status":"published","corr_author":"1","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"external_id":{"arxiv":["2209.11149"],"pmid":["38947856"],"isi":["001258097800003"]},"date_created":"2024-07-21T22:01:01Z","quality_controlled":"1","volume":63,"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"}],"article_number":"153","ec_funded":1,"intvolume":"        63","isi":1,"scopus_import":"1","author":[{"orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris","last_name":"Brooks","first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"last_name":"Maas","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338"}],"file_date_updated":"2024-07-22T07:05:32Z","publication":"Calculus of Variations and Partial Differential Equations","oa":1,"publication_identifier":{"eissn":["1432-0835"],"issn":["0944-2669"]},"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.","file":[{"date_created":"2024-07-22T07:05:32Z","file_id":"17289","file_name":"2024_CalculusVariations_Brooks.pdf","creator":"dernst","file_size":416622,"content_type":"application/pdf","checksum":"a0cf0e0ba2157aabb287cb597be17dac","date_updated":"2024-07-22T07:05:32Z","success":1,"relation":"main_file","access_level":"open_access"}],"pmid":1},{"volume":8,"quality_controlled":"1","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"}],"article_number":"232","publication_status":"published","external_id":{"arxiv":["2404.03430"]},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_created":"2024-07-21T22:01:01Z","corr_author":"1","language":[{"iso":"eng"}],"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","file":[{"file_size":355421,"file_name":"2024_ACMProgLang_Chatterjee.pdf","creator":"dernst","date_created":"2024-07-22T07:17:14Z","file_id":"17290","date_updated":"2024-07-22T07:17:14Z","checksum":"8cbf220f284a4a87d093db5320c5afdd","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file"}],"oa":1,"publication_identifier":{"eissn":["2475-1421"]},"scopus_import":"1","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"orcid":"0000-0002-8595-0587","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","first_name":"Ehsan","last_name":"Kafshdar Goharshadi","full_name":"Kafshdar Goharshadi, Ehsan"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","full_name":"Novotný, Petr"},{"orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"publication":"Proceedings of the ACM on Programming Languages","file_date_updated":"2024-07-22T07:17:14Z","ec_funded":1,"intvolume":"         8","_id":"17283","title":"Equivalence and similarity refutation for probabilistic programs","month":"06","article_processing_charge":"Yes (via OA deal)","citation":{"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>","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>","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>.","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).","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."},"arxiv":1,"ddc":["000"],"doi":"10.1145/3656462","OA_place":"publisher","article_type":"original","OA_type":"hybrid","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Association for Computing Machinery","day":"20","type":"journal_article","has_accepted_license":"1","date_published":"2024-06-20T00:00:00Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"oa_version":"Published Version","year":"2024","date_updated":"2025-04-14T07:52:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":631,"quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","date_created":"2024-07-21T22:01:02Z","department":[{"_id":"EM-Fac"},{"_id":"MiSi"},{"_id":"Bio"}],"external_id":{"isi":["001281636500020"],"pmid":["38987596"]},"corr_author":"1","language":[{"iso":"eng"}],"pmid":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.","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_name":"2024_Nature_Gaertner.pdf","creator":"dernst","file_id":"17286","date_created":"2024-07-22T06:16:11Z","file_size":15704819,"checksum":"aa004afc72d2489f0fb0fcbc9919fbbd","content_type":"application/pdf","date_updated":"2024-07-22T06:16:11Z"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"oa":1,"scopus_import":"1","author":[{"orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","last_name":"Gärtner","full_name":"Gärtner, Florian R"},{"first_name":"Hellen","full_name":"Ishikawa-Ankerhold, Hellen","last_name":"Ishikawa-Ankerhold"},{"first_name":"Susanne","last_name":"Stutte","full_name":"Stutte, Susanne"},{"full_name":"Fu, Wenwen","last_name":"Fu","first_name":"Wenwen"},{"first_name":"Jutta","full_name":"Weitz, Jutta","last_name":"Weitz"},{"last_name":"Dueck","full_name":"Dueck, Anne","first_name":"Anne"},{"full_name":"Nelakuditi, Bhavishya","last_name":"Nelakuditi","first_name":"Bhavishya"},{"first_name":"Valeria","full_name":"Fumagalli, Valeria","last_name":"Fumagalli"},{"full_name":"Van Den Heuvel, Dominic","last_name":"Van Den Heuvel","first_name":"Dominic"},{"full_name":"Belz, Larissa","last_name":"Belz","first_name":"Larissa"},{"first_name":"Gulnoza","last_name":"Sobirova","full_name":"Sobirova, Gulnoza"},{"first_name":"Zhe","full_name":"Zhang, Zhe","last_name":"Zhang"},{"first_name":"Anna","last_name":"Titova","full_name":"Titova, Anna"},{"full_name":"Navarro, Alejandro Martinez","last_name":"Navarro","first_name":"Alejandro Martinez"},{"first_name":"Kami","last_name":"Pekayvaz","full_name":"Pekayvaz, Kami"},{"last_name":"Lorenz","full_name":"Lorenz, Michael","first_name":"Michael"},{"last_name":"Von Baumgarten","full_name":"Von Baumgarten, Louisa","first_name":"Louisa"},{"first_name":"Jan","last_name":"Kranich","full_name":"Kranich, Jan"},{"first_name":"Tobias","last_name":"Straub","full_name":"Straub, Tobias"},{"first_name":"Bastian","last_name":"Popper","full_name":"Popper, Bastian"},{"orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Chenglong","last_name":"Guo","full_name":"Guo, Chenglong"},{"first_name":"Guido","last_name":"Piontek","full_name":"Piontek, Guido"},{"full_name":"Von Stillfried, Saskia","last_name":"Von Stillfried","first_name":"Saskia"},{"first_name":"Peter","last_name":"Boor","full_name":"Boor, Peter"},{"first_name":"Marco","last_name":"Colonna","full_name":"Colonna, Marco"},{"first_name":"Sebastian","full_name":"Clauß, Sebastian","last_name":"Clauß"},{"full_name":"Schulz, Christian","last_name":"Schulz","first_name":"Christian"},{"last_name":"Brocker","full_name":"Brocker, Thomas","first_name":"Thomas"},{"first_name":"Barbara","last_name":"Walzog","full_name":"Walzog, Barbara"},{"full_name":"Scheiermann, Christoph","last_name":"Scheiermann","first_name":"Christoph"},{"first_name":"William C.","last_name":"Aird","full_name":"Aird, William C."},{"last_name":"Nerlov","full_name":"Nerlov, Claus","first_name":"Claus"},{"last_name":"Stark","full_name":"Stark, Konstantin","first_name":"Konstantin"},{"first_name":"Tobias","full_name":"Petzold, Tobias","last_name":"Petzold"},{"full_name":"Engelhardt, Stefan","last_name":"Engelhardt","first_name":"Stefan"},{"last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"first_name":"Martina","last_name":"Rudelius","full_name":"Rudelius, Martina"},{"full_name":"Oostendorp, Robert A.J.","last_name":"Oostendorp","first_name":"Robert A.J."},{"last_name":"Iannacone","full_name":"Iannacone, Matteo","first_name":"Matteo"},{"first_name":"Matthias","full_name":"Heinig, Matthias","last_name":"Heinig"},{"first_name":"Steffen","full_name":"Massberg, Steffen","last_name":"Massberg"}],"publication":"Nature","file_date_updated":"2024-07-22T06:16:11Z","isi":1,"intvolume":"       631","ec_funded":1,"_id":"17284","month":"07","title":"Plasmacytoid dendritic cells control homeostasis of megakaryopoiesis","article_processing_charge":"Yes (in subscription journal)","related_material":{"link":[{"url":"https://github.com/heiniglab/gaertner_megakaryocytes","relation":"software"}]},"citation":{"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.","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>.","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>.","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.","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>","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>"},"ddc":["570"],"article_type":"original","doi":"10.1038/s41586-024-07671-y","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","day":"18","publisher":"Springer Nature","has_accepted_license":"1","project":[{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"date_published":"2024-07-18T00:00:00Z","date_updated":"2025-09-08T08:14:25Z","year":"2024","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"645-653"},{"page":"2251-2266","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","oa_version":"Preprint","date_updated":"2025-09-08T08:15:08Z","date_published":"2024-10-01T00:00:00Z","day":"01","publisher":"Springer Nature","type":"journal_article","status":"public","doi":"10.1007/s11427-024-2664-0","OA_place":"repository","OA_type":"green","article_type":"original","citation":{"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>","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>","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>.","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.","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>.","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.","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."},"article_processing_charge":"No","title":"Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat","month":"10","_id":"17285","intvolume":"        67","isi":1,"author":[{"first_name":"Xuemei","full_name":"Liu, Xuemei","last_name":"Liu"},{"first_name":"Min","full_name":"Deng, Min","last_name":"Deng"},{"first_name":"Bingxin","last_name":"Shi","full_name":"Shi, Bingxin"},{"last_name":"Zhu","full_name":"Zhu, Kehui","first_name":"Kehui"},{"first_name":"Jinchao","full_name":"Chen, Jinchao","last_name":"Chen"},{"first_name":"Shujuan","id":"9724dd9d-f591-11ee-bd51-e97ed0652286","full_name":"Xu, Shujuan","last_name":"Xu"},{"full_name":"Bie, Xiaomin","last_name":"Bie","first_name":"Xiaomin"},{"last_name":"Zhang","full_name":"Zhang, Xiansheng","first_name":"Xiansheng"},{"last_name":"Lin","full_name":"Lin, Xuelei","first_name":"Xuelei"},{"first_name":"Jun","full_name":"Xiao, Jun","last_name":"Xiao"}],"publication":"Science China Life Sciences","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/2023.12.19.572364","open_access":"1"}],"publication_identifier":{"eissn":["1869-1889"],"issn":["1674-7305"]},"oa":1,"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).","pmid":1,"language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"external_id":{"isi":["001268807700002"],"pmid":["38987431"]},"date_created":"2024-07-21T22:01:02Z","publication_status":"published","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","volume":67},{"language":[{"iso":"eng"}],"corr_author":"1","date_created":"2024-07-22T07:44:10Z","external_id":{"pmid":["38901173"],"isi":["001259302800001"]},"department":[{"_id":"PaSc"}],"publication_status":"published","article_number":"107708","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","volume":364,"isi":1,"intvolume":"       364","publication":"Journal of Magnetic Resonance","author":[{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"last_name":"Perrone","full_name":"Perrone, Barbara","first_name":"Barbara"},{"first_name":"Alia","full_name":"Hassan, Alia","last_name":"Hassan"},{"full_name":"Simorre, Jean-Pierre","last_name":"Simorre","first_name":"Jean-Pierre"},{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"scopus_import":"1","file_date_updated":"2024-07-23T06:23:51Z","publication_identifier":{"issn":["1090-7807"]},"oa":1,"pmid":1,"file":[{"date_updated":"2024-07-23T06:23:51Z","checksum":"4b59f4f0c287ecbafd808da1212ced38","content_type":"application/pdf","file_size":2236665,"creator":"dernst","file_name":"2024_JourMagneticResonance_Vallet.pdf","file_id":"17316","date_created":"2024-07-23T06:23:51Z","access_level":"open_access","relation":"main_file","success":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.","OA_type":"hybrid","article_type":"original","OA_place":"publisher","doi":"10.1016/j.jmr.2024.107708","ddc":["570"],"related_material":{"record":[{"status":"public","relation":"research_data","id":"17042"}]},"citation":{"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.","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>.","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>","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>","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.","short":"A. Vallet, I. Ayala, B. Perrone, A. Hassan, J.-P. Simorre, C. Bougault, P. Schanda, Journal of Magnetic Resonance 364 (2024).","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>."},"article_processing_charge":"Yes (via OA deal)","month":"07","title":"MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments","_id":"17291","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-09T12:01:41Z","year":"2024","oa_version":"Published Version","date_published":"2024-07-01T00:00:00Z","has_accepted_license":"1","day":"01","publisher":"Elsevier","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public"},{"abstract":[{"text":"The Gibbons-Hawking ansatz provides a large family of circle-invariant hyperkähler 4-manifolds, and thus Calabi-Yau 2-folds. In this setting, we prove versions of the Thomas conjecture on existence of special Lagrangian representatives of Hamiltonian isotopy classes of Lagrangians, and the Thomas-Yau conjecture on longtime existence of the Lagrangian mean curvature ow. We also make observations concerning closed geodesics, curve shortening flow and minimal surfaces.","lang":"eng"}],"quality_controlled":"1","volume":126,"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001271790200007"],"arxiv":["2002.10391"]},"department":[{"_id":"TaHa"}],"date_created":"2024-07-22T07:45:31Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2002.10391","open_access":"1"}],"publication_identifier":{"issn":["0022-040X"]},"oa":1,"intvolume":"       126","isi":1,"scopus_import":"1","publication":"Journal of Differential Geometry","author":[{"first_name":"Jason D.","last_name":"Lotay","full_name":"Lotay, Jason D."},{"last_name":"Oliveira","full_name":"Oliveira, Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","first_name":"Goncalo"}],"citation":{"apa":"Lotay, J. D., &#38; Oliveira, G. (2024). Special Lagrangians, Lagrangian mean curvature flow and the Gibbons-Hawking ansatz. <i>Journal of Differential Geometry</i>. International Press. <a href=\"https://doi.org/10.4310/jdg/1717348872\">https://doi.org/10.4310/jdg/1717348872</a>","ama":"Lotay JD, Oliveira G. Special Lagrangians, Lagrangian mean curvature flow and the Gibbons-Hawking ansatz. <i>Journal of Differential Geometry</i>. 2024;126(3):1121-1184. doi:<a href=\"https://doi.org/10.4310/jdg/1717348872\">10.4310/jdg/1717348872</a>","ista":"Lotay JD, Oliveira G. 2024. Special Lagrangians, Lagrangian mean curvature flow and the Gibbons-Hawking ansatz. Journal of Differential Geometry. 126(3), 1121–1184.","chicago":"Lotay, Jason D., and Goncalo Oliveira. “Special Lagrangians, Lagrangian Mean Curvature Flow and the Gibbons-Hawking Ansatz.” <i>Journal of Differential Geometry</i>. International Press, 2024. <a href=\"https://doi.org/10.4310/jdg/1717348872\">https://doi.org/10.4310/jdg/1717348872</a>.","short":"J.D. Lotay, G. Oliveira, Journal of Differential Geometry 126 (2024) 1121–1184.","mla":"Lotay, Jason D., and Goncalo Oliveira. “Special Lagrangians, Lagrangian Mean Curvature Flow and the Gibbons-Hawking Ansatz.” <i>Journal of Differential Geometry</i>, vol. 126, no. 3, International Press, 2024, pp. 1121–84, doi:<a href=\"https://doi.org/10.4310/jdg/1717348872\">10.4310/jdg/1717348872</a>.","ieee":"J. D. Lotay and G. Oliveira, “Special Lagrangians, Lagrangian mean curvature flow and the Gibbons-Hawking ansatz,” <i>Journal of Differential Geometry</i>, vol. 126, no. 3. International Press, pp. 1121–1184, 2024."},"article_processing_charge":"No","title":"Special Lagrangians, Lagrangian mean curvature flow and the Gibbons-Hawking ansatz","month":"03","_id":"17292","OA_place":"repository","doi":"10.4310/jdg/1717348872","article_type":"original","OA_type":"green","arxiv":1,"day":"01","publisher":"International Press","type":"journal_article","issue":"3","status":"public","page":"1121-1184","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","oa_version":"Preprint","date_updated":"2025-09-08T08:27:51Z","date_published":"2024-03-01T00:00:00Z"},{"status":"public","publisher":"Springer Nature","type":"journal_article","day":"19","oa_version":"Submitted Version","year":"2024","date_updated":"2025-12-02T13:42:28Z","date_published":"2024-07-19T00:00:00Z","page":"624-637","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cryosphere–groundwater connectivity is a missing link in the mountain water cycle","month":"07","_id":"17302","citation":{"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.","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.","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>.","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.","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>","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>"},"article_processing_charge":"No","doi":"10.1038/s44221-024-00277-8","OA_place":"repository","article_type":"original","OA_type":"green","publication_identifier":{"issn":["2731-6084"]},"oa":1,"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.","main_file_link":[{"open_access":"1","url":"https://insu.hal.science/insu-04674297"}],"isi":1,"intvolume":"         2","scopus_import":"1","publication":"Nature Water","author":[{"first_name":"Marit","last_name":"van Tiel","full_name":"van Tiel, Marit"},{"first_name":"Caroline","last_name":"Aubry-Wake","full_name":"Aubry-Wake, Caroline"},{"first_name":"Lauren","full_name":"Somers, Lauren","last_name":"Somers"},{"full_name":"Andermann, Christoff","last_name":"Andermann","first_name":"Christoff"},{"last_name":"Avanzi","full_name":"Avanzi, Francesco","first_name":"Francesco"},{"full_name":"Baraer, Michel","last_name":"Baraer","first_name":"Michel"},{"first_name":"Gabriele","last_name":"Chiogna","full_name":"Chiogna, Gabriele"},{"last_name":"Daigre","full_name":"Daigre, Clémence","first_name":"Clémence"},{"first_name":"Soumik","last_name":"Das","full_name":"Das, Soumik"},{"first_name":"Fabian","last_name":"Drenkhan","full_name":"Drenkhan, Fabian"},{"first_name":"Daniel","last_name":"Farinotti","full_name":"Farinotti, Daniel"},{"full_name":"Fyffe, Catriona Louise","last_name":"Fyffe","id":"001b0422-8d15-11ed-bc51-cab6c037a228","first_name":"Catriona Louise"},{"last_name":"de Graaf","full_name":"de Graaf, Inge","first_name":"Inge"},{"full_name":"Hanus, Sarah","last_name":"Hanus","first_name":"Sarah"},{"full_name":"Immerzeel, Walter","last_name":"Immerzeel","first_name":"Walter"},{"last_name":"Koch","full_name":"Koch, Franziska","first_name":"Franziska"},{"full_name":"McKenzie, Jeffrey M.","last_name":"McKenzie","first_name":"Jeffrey M."},{"first_name":"Tom","last_name":"Müller","full_name":"Müller, Tom"},{"last_name":"Popp","full_name":"Popp, Andrea L.","first_name":"Andrea L."},{"last_name":"Saidaliyeva","full_name":"Saidaliyeva, Zarina","first_name":"Zarina"},{"last_name":"Schaefli","full_name":"Schaefli, Bettina","first_name":"Bettina"},{"first_name":"Oliver S.","last_name":"Schilling","full_name":"Schilling, Oliver S."},{"last_name":"Teagai","full_name":"Teagai, Kapiolani","first_name":"Kapiolani"},{"last_name":"Thornton","full_name":"Thornton, James M.","first_name":"James M."},{"last_name":"Yapiyev","full_name":"Yapiyev, Vadim","first_name":"Vadim"}],"quality_controlled":"1","volume":2,"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"}],"publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"FrPe"}],"external_id":{"isi":["001390137500016"]},"date_created":"2024-07-22T09:46:52Z"}]